From a2629daa3f2c59be2b1c4fc1b9122ca75150e37b Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Sat, 19 Mar 2022 17:09:42 -0700
Subject: [PATCH 001/148] Init

---
 .../expectation_maximization.py               | 357 ++++++++++++++++++
 tests/test_expectation_maximization.py        |   9 +
 2 files changed, 366 insertions(+)
 create mode 100644 iterative_refinement/expectation_maximization.py
 create mode 100644 tests/test_expectation_maximization.py

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
new file mode 100644
index 0000000..4f1164a
--- /dev/null
+++ b/iterative_refinement/expectation_maximization.py
@@ -0,0 +1,357 @@
+"""
+References
+1. Nelson, P. C. (2019). Chapter 12 : Single Particle Reconstruction in Cryo-electron Microscopy. 
+        In Physical Models of Living Systems (pp. 305–325).
+        https://repository.upenn.edu/cgi/viewcontent.cgi?article=1665&context=physics_papers
+2. Scheres, S. H. W. (2012). RELION: Implementation of a Bayesian approach to cryo-EM structure determination. 
+        Journal of Structural Biology, 180(3), 519–530. 
+        http://doi.org/10.1016/j.jsb.2012.09.006
+3. Sigworth, F. J., Doerschuk, P. C., Carazo, J.-M., & Scheres, S. H. W. (2010). 
+        An Introduction to Maximum-Likelihood Methods in Cryo-EM. 
+        In Methods in Enzymology (1st ed., Vol. 482, pp. 263–294). Elsevier Inc. 
+        http://doi.org/10.1016/S0076-6879(10)82011-7
+
+Note that functions are defined in place for readability. code should be filled out and refactored for performance
+"""
+
+import numpy as np
+from compSPI.transforms import do_fft, do_ifft # currently only 2D ffts in compSPI.transforms. can use torch.fft for 3d fft and convert back to numpy array
+
+
+def do_iterative_refinement(map_3d_init, particles, ctf_info):
+    """
+    Performs interative refimenent in a Bayesean expectation maximization setting,
+    i.e. maximum a posteriori estimation.
+
+    Input
+    _________
+    map_3d_init
+        initial estimate
+        input map
+        shape (n_pix,n_pix,n_pix)
+    particles
+        particles to be reconstructed
+        shape (n_pix,n_pix)
+
+    
+    Returns
+    _________
+    
+    map_3d_final  
+        shape (n_pix,n_pix,n_pix)
+
+    map_3d_r_final
+        final updated map
+        shape (n_pix,n_pix,n_pix)
+    half_map_3d_r_1
+        half map 1
+    half_map_3d_r_2
+        half map 2
+    fsc_1d
+        final 1d fsc
+        shape (n_pix//2,)
+    
+    """
+
+    # split particles up into two half sets for statistical validation
+
+    def do_split(arr):
+        idx_half = arr.shape[0] // 2
+        arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
+        assert arr_1.shape[0] == arr_2.shape[0]
+        return parr_1, arr_2
+
+    particles_1, particles_2 = do_split(particles)
+
+    def do_build_ctf(ctf_params):
+        """
+        Build 2D array of ctf from ctf params
+
+        Input
+        ___
+        Params of ctfs (defocus, etc)
+            Suggest list of dicts, one for each particle.
+
+        Returns
+        ___
+        ctfs
+            type np.ndarray
+            shape (n_ctfs,n_pix,n_pix)
+
+        """
+        n_ctfs = len(ctf_params)
+        # TODO: see simSPI.transfer
+        # https://github.com/compSPI/simSPI/blob/master/simSPI/transfer.py#L57
+        ctfs = np.ones((n_ctfs,n_pix,n_pix))
+
+        return ctfs
+
+    ctfs = do_build_ctf(ctf_info)
+    ctfs_1, ctfs_2 = do_split(ctfs)
+
+    # work in Fourier space. so particles can stay in Fourier space the whole time. 
+    # they are experimental measurements and are fixed in the algorithm
+    particles_f_1 = do_fft(particles_1)
+    particles_f_2 = do_fft(particles_2)
+
+    n_pix = map_3d_init.shape[0] 
+        # suggest 32 or 64 to start with. real data will be more like 128 or 256.
+        # can have issues with ctf at small pixels and need to zero pad to avoid artefacts 
+            # artefacts from ctf not going to zero at edges, and sinusoidal ctf rippling too fast
+            # can zero pad when do Fourier convolution (fft is on zero paded and larger sized array) 
+
+    max_n_iters = 7 # in practice programs using 3-10 iterations.
+
+    half_map_3d_r_1,half_map_3d_r_2 = map_3d_init, map_3d_init.copy() 
+        # should diverge because different particles averaging in
+
+    for iteration in range(max_n_iters):
+
+        half_map_3d_f_1 = do_fft(half_map_3d_r_1,d=3)
+        half_map_3d_f_2 = do_fft(half_map_3d_r_2,d=3)
+
+
+        # align particles to 3D volume
+            # decide on granularity of rotations
+            # i.e. how finely the rotational SO(3) space is sampled in a grid search. 
+            # smarter method is branch and bound... 
+                # perhaps can make grid up front of slices, and then only compute norms on finer grid later. so re-use slices
+
+
+            # def do_adaptive_grid_search(particle, map_3d):
+            #   # a la branch and bound
+            #   # not sure exactly how you decide how finely gridded to make it. 
+            #   # perhaps heuristics based on how well the signal agrees in half_map_1, half_map_2 (Fourier frequency)
+                
+
+        def grid_SO3_uniform(n_rotations):
+            """
+            uniformly grid (not sample) SO(3)
+            can use some intermediate encoding of SO(3) like quaternions, axis angle, Euler
+            final output 3x3 rotations
+        
+            """
+            # TODO: sample over the sphere at given granularity. 
+                # easy: draw uniform samples of rotations on sphere. lots of code for this all over the internet. quick solution in geomstats
+                # harder: draw samples around some rotation using ProjectedNormal distribution (ask Geoff)
+                # unknown difficulty: make a regular grid of SO(3) at given granularity. Khanh says non-trivial.
+            rots = np.ones((n_rotations,3,3))
+            return rots
+
+        n_rotations = 1000
+        rots = grid_SO3(n_rotations)
+
+        def do_xy0_plane(n_pix):
+            """
+            generate xy0 plane
+            xy values are over the xy plane
+            all z values are 0
+            see how meshgrid and generate coordinates functions used in https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L96
+            
+            """
+
+            ### methgrid
+            xy0_plane = np.ones(n_pix**2,3)
+            return xy0
+
+        xy0_plane = do_xy0_plane(n_pix):
+
+
+        def do_slices(map_3d_f,rots):
+            """
+            generates slice coordinates by rotating xy0 plane 
+            interpolate values from map_3d_f onto 3D coordinates
+            see how scipy map_values used to interpolate in https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L111
+
+            Returns
+            ___
+            slices
+                slice of map_3d_f
+                by Fourier slice theorem corresponds to Fourier transform of projection of rotated map_3d_f
+
+            """
+            n_rotations = rots.shape[0]
+            ### TODO: map_values interpolation
+            xyz_rotated = np.ones_like(xy0_plane)
+            slices = np.random.normal(size=n_rotations*n_pix**2).reshape(n_rotations,n_pix,n_pix)
+            return slices, xyz_rotated
+
+        slices_1, xyz_rotated = do_slices(half_map_3d_1_f,rots) # Here rots are the same for the half maps, but could be different in general
+        slices_2, xyz_rotated = do_slices(half_map_3d_2_f,rots)
+
+
+        def do_conv_ctf(projection_f, ctf):
+            """
+            Apply CTF to projection
+            """
+
+            # TODO: vectorize and have shape match
+            projection_f_conv_ctf = ctf*projection_f
+            return 
+
+
+
+        def do_bayesean_weights(particle, slices):
+            """
+            compute bayesean weights of particle to slice
+            under gaussian white noise model
+
+            Input
+            ____
+            slices
+                shape (n_slices, n_pix,n_pix)
+                dtype complex32 or complex64
+
+            Returns
+            ___
+            bayesean_weights
+                shape (n_slices,)
+                dtyle float32 or float64
+            
+            """
+            n_slices = slices.shape[0]
+            particle_l2 = np.linalg.norm(particle, ord='fro')**2
+            slices_l2 = np.linalg.norm(slices,axis=(1,2),ord='fro')**2 # TODO: check right axis. should n_slices l2 norms, one for each slice
+                # can precompute slices_l2 and keep for all particles if slices the same for different particles
+
+            corr = np.zeros(slices)
+            a_slice_corr = particle.dot(slices) # |particle|^2 - particle.dot(a_slice) + |a_slice|^2
+            ### see Sigrowth et al and Nelson for how to get bayes factors
+            bayes_factors = np.random.normal(n_slices) # TODO: replace placeholder with right shape
+            return bayes_factors
+
+
+
+        # initialize
+        map_3d_f_updated_1 = np.zeros_like(half_map_3d_f_1) # complex
+        map_3d_f_updated_2 = np.zeros_like(half_map_3d_f_2) # complex
+        counts_3d_updated_1 = np.zeros_like(half_map_3d_r_1) # float/real
+        counts_3d_updated_2 = np.zeros_like(half_map_3d_r_2) # float/real
+
+        for particle_idx in range(particles_1_f.shape[0]):
+            ctf_1 = ctfs_1[particle_idx]
+            ctf_2 = ctfs_2[particle_idx]
+            particle_f_1 = particles_f_1[particle_idx]
+            particle_f_2 = particles_f_2[particle_idx]
+
+            def do_wiener_filter(projection, ctf, small_number):
+                wfilter = ctf/(ctf*ctf+small_number)
+                projection_wfilter_f = projection*w_filter
+                return projection_wfilter_f
+
+
+            particle_f_deconv_1 = do_wiener_filter(particles_f_1, ctf_1)
+            particle_f_deconv_1 = do_wiener_filter(particles_f_1, ctf_1)
+
+            slices_conv_ctfs_1 = do_conv_ctf(slices_1, ctf_1) # all slices get convolved with the ctf for the particle
+            slices_conv_ctfs_2 = do_conv_ctf(slices_2, ctf_2)
+
+            bayes_factors_1 = do_bayesean_weights(particles_1_f[particle_idx], slices_conv_ctfs_1)
+            bayes_factors_2 = do_bayesean_weights(particles_2_f[particle_idx], slices_conv_ctfs_2)
+
+            def do_insert_slice(slice_real,xyz,n_pix):
+                """
+                Update map_3d_f_updated with values from slice. Requires interpolation of off grid 
+                see "Insert Fourier slices" in https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/fourier_slice_2D_3D_with_trilinear.ipynb
+                    # TODO: vectorize so can take in many slices; 
+                    # i.e. do the compoutation in a vetorized way and return inserted_slices_3d, counts_3d of shape (n_slice,n_pix,n_pix,n_pix)
+
+                Input
+                ___
+
+                slice
+                    type array of shape (n_pix,n_pix)
+                    dtype float32 or float64. real since imaginary and real part done separately
+                xyz
+                    type array of shape (n_pix**2,3)
+                volume_3d_shape: float n_pix
+
+
+
+
+                Return
+                ___
+                inserted_slice_3d
+                count_3d
+
+                """
+
+                volume_3d = np.zeros((n_pix,n_pix,n_pix))
+                # TODO: write insertion code. use linear interpolation (order of interpolation kernel) so not expensive. 
+                # nearest neightbors cheaper, but we can afford to do better than that
+
+                return inserted_slice_3d, count_3d
+
+
+            for one_slice_idx in range(bayes_factors_1.shape[0]):
+                xyz = xyz_rotated[one_slice_idx]               
+                inserted_slice_3d_r, count_3d_r = do_insert_slice(particle_f_deconv_1.real,xyz,volume_3d) # if this can be vectorized, can avoid loop over slices
+                inserted_slice_3d_i, count_3d_i = do_insert_slice(particle_f_deconv_1.imag,xyz,volume_3d) # if this can be vectorized, can avoid loop over slices
+                map_3d_f_updated_1 += inserted_slice_3d_r + 1j*inserted_slice_3d_i
+                counts_3d_updated_1 += count_3d_r + count_3d_i
+            
+            for one_slice_idx in range(bayes_factors_2.shape[0]):
+                xyz = xyz_rotated[one_slice_idx]               
+                inserted_slice_3d_r, count_3d_r = do_insert_slice(particle_f_deconv_2.real,xyz,volume_3d) # if this can be vectorized, can avoid loop over slices
+                inserted_slice_3d_i, count_3d_i = do_insert_slice(particle_f_deconv_2.imag,xyz,volume_3d) # if this can be vectorized, can avoid loop over slices
+                map_3d_f_updated_2 += inserted_slice_3d_r + 1j*inserted_slice_3d_i
+                counts_3d_updated_2 += count_3d_r + count_3d_i
+
+
+        # apply noise model
+        # half_map_1, half_map_2 come from doing the above independently
+        # filter by noise estimate (e.g. multiply both half maps by FSC)
+
+        def do_fsc(map_3d_f_1,map_3d_f_2):
+            """
+            Estimate noise from half maps
+                for now do noise estimate as FSC between half maps
+    
+            """
+            # TODO: write fast vectorized fsc from code snippets in 
+                # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/fsc.ipynb
+                # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/mFSC.ipynb
+                # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/guinier_fsc_sharpen.ipynb
+            n_pix = map_3d_f_1.shape[0]
+            fsc_1d = np.ones(n_pix//2) 
+            return noise_estimate
+
+
+        fsc_1d = do_estimate_noise(map_3d_f_updated_1,map_3d_f_updated_2)
+
+        def do_expand_1d_3d(arr_1d):
+            n_pix = arr_1d.shape[0]*2
+            arr_3d = np.ones((n_pix,n_pix,n_pix)) 
+            # TODO: arr_1d fsc_1d to 3d (spherical shells)
+            return arr_3d
+
+        fsc_3d = do_expand_1d_3d(fsc_1d)
+        
+        # multiplicative filter on maps with fsc
+        # The FSC is 1D, one number per spherical shells
+        # it can be expanded back to a multiplicative filter of the same shape as the maps
+        map_3d_f_filtered_1 = map_3d_f_updated_1*fsc_3d
+        map_3d_f_filtered_2 = map_3d_f_updated_2*fsc_3d
+
+        # update iteration
+        half_map_3d_f_1 = map_3d_f_filtered_1
+        half_map_3d_f_2 = map_3d_f_filtered_2
+
+    # final map
+    fsc_1d = do_estimate_noise(half_map_3d_f_1,half_map_3d_f_2)
+    fsc_3d = do_expand_1d_3d(fsc_1d)
+    map_3d_f_final = (half_map_3d_f_1 + half_map_3d_f_2 / 2)*fsc_3d
+    map_3d_r_final = do_ifft(map_3d_f_final)
+    half_map_3d_r_1 = do_ifft(half_map_3d_f_1)
+    half_map_3d_r_2 = do_ifft(half_map_3d_f_2)
+
+    return map_3d_r_final, half_map_3d_r_1, half_map_3d_r_2, fsc_1d
+
+
+
+
+
+        
+
+
+
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
new file mode 100644
index 0000000..6ce316a
--- /dev/null
+++ b/tests/test_expectation_maximization.py
@@ -0,0 +1,9 @@
+def test_do_iterative_refinement():
+	n_pix = 64 
+	map_3d_init = np.random.normal(size=n_pix**3).reshape(n_pix,n_pix,n_pix)
+	particles = np.random.normal(size=n_pix**2).reshape(n_pix,n_pix)
+	map_3d_r_final, half_map_3d_r_1, half_map_3d_r_2, fsc_1d = iterative_refinement(map_3d_init, particles)
+	assert map_3d_r_final.shape == (n_pix,n_pix,n_pix)
+	assert fsc_1d.dtype = np.float32
+	assert half_map_3d_r_1.dtype = np.float32
+	assert half_map_3d_r_2.dtype = np.float32
\ No newline at end of file

From ccc4359697dde3aa62b5865646b26c9975fb12f4 Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Sun, 20 Mar 2022 14:42:45 -0700
Subject: [PATCH 002/148] precommit yaml

---
 iterative_refinement/expectation_maximization.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 4f1164a..486c125 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -11,7 +11,7 @@
         In Methods in Enzymology (1st ed., Vol. 482, pp. 263–294). Elsevier Inc. 
         http://doi.org/10.1016/S0076-6879(10)82011-7
 
-Note that functions are defined in place for readability. code should be filled out and refactored for performance
+Iterative refinement in Bayesian expection maximization setting.
 """
 
 import numpy as np
@@ -20,11 +20,11 @@
 
 def do_iterative_refinement(map_3d_init, particles, ctf_info):
     """
-    Performs interative refimenent in a Bayesean expectation maximization setting,
+    Performs interative refimenent in a Bayesian expectation maximization setting,
     i.e. maximum a posteriori estimation.
 
     Input
-    _________
+    -----
     map_3d_init
         initial estimate
         input map
@@ -35,7 +35,7 @@ def do_iterative_refinement(map_3d_init, particles, ctf_info):
 
     
     Returns
-    _________
+    -------
     
     map_3d_final  
         shape (n_pix,n_pix,n_pix)

From 186fddc7176b37db0aa4fbf6710086dff1b6fd63 Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Sun, 20 Mar 2022 14:42:56 -0700
Subject: [PATCH 003/148] remove ref

---
 iterative_refinement/expectation_maximization.py | 15 ++-------------
 1 file changed, 2 insertions(+), 13 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 486c125..8f54012 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -1,21 +1,10 @@
 """
-References
-1. Nelson, P. C. (2019). Chapter 12 : Single Particle Reconstruction in Cryo-electron Microscopy. 
-        In Physical Models of Living Systems (pp. 305–325).
-        https://repository.upenn.edu/cgi/viewcontent.cgi?article=1665&context=physics_papers
-2. Scheres, S. H. W. (2012). RELION: Implementation of a Bayesian approach to cryo-EM structure determination. 
-        Journal of Structural Biology, 180(3), 519–530. 
-        http://doi.org/10.1016/j.jsb.2012.09.006
-3. Sigworth, F. J., Doerschuk, P. C., Carazo, J.-M., & Scheres, S. H. W. (2010). 
-        An Introduction to Maximum-Likelihood Methods in Cryo-EM. 
-        In Methods in Enzymology (1st ed., Vol. 482, pp. 263–294). Elsevier Inc. 
-        http://doi.org/10.1016/S0076-6879(10)82011-7
-
 Iterative refinement in Bayesian expection maximization setting.
 """
 
 import numpy as np
-from compSPI.transforms import do_fft, do_ifft # currently only 2D ffts in compSPI.transforms. can use torch.fft for 3d fft and convert back to numpy array
+from compSPI.transforms import do_fft, do_ifft
+# currently only 2D ffts in compSPI.transforms. can use torch.fft for 3d fft and convert back to numpy array
 
 
 def do_iterative_refinement(map_3d_init, particles, ctf_info):

From 62b9f42613ebbc4783d6d7cadd5f83a9f673ab2d Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Sun, 20 Mar 2022 21:43:52 +0000
Subject: [PATCH 004/148] Format code with black and isort

---
 iterative_refinement/expectation_maximization.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 8f54012..826a0ef 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -4,6 +4,7 @@
 
 import numpy as np
 from compSPI.transforms import do_fft, do_ifft
+
 # currently only 2D ffts in compSPI.transforms. can use torch.fft for 3d fft and convert back to numpy array
 
 

From ee5adab3702379f2a073bad87b20b5f261c44b42 Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Sun, 20 Mar 2022 16:34:21 -0700
Subject: [PATCH 005/148] Docstrings, precommit broken?

---
 .../expectation_maximization.py               | 502 ++++++++++--------
 tests/test_expectation_maximization.py        |   2 +-
 2 files changed, 288 insertions(+), 216 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 826a0ef..5380c3e 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -1,347 +1,419 @@
 """
-Iterative refinement in Bayesian expection maximization setting.
+Iterative refinement in Bayesian expection maximization setting
+for reconstruction of particles.
 """
 
 import numpy as np
 from compSPI.transforms import do_fft, do_ifft
 
-# currently only 2D ffts in compSPI.transforms. can use torch.fft for 3d fft and convert back to numpy array
-
 
 def do_iterative_refinement(map_3d_init, particles, ctf_info):
     """
-    Performs interative refimenent in a Bayesian expectation maximization setting,
-    i.e. maximum a posteriori estimation.
-
-    Input
-    -----
-    map_3d_init
-        initial estimate
-        input map
-        shape (n_pix,n_pix,n_pix)
-    particles
-        particles to be reconstructed
-        shape (n_pix,n_pix)
-
-    
+    Performs interative refimenent in a Bayesian expectation
+    maximization setting, i.e. maximum a posteriori estimation.
+
+    Parameters
+    ----------
+    map_3d_init : arr
+        Initial particle map.
+        Shape (n_pix,n_pix,n_pix)
+    particles : arr
+        Particles to be reconstructed.
+        Shape (n_pix,n_pix)
+
     Returns
     -------
-    
-    map_3d_final  
-        shape (n_pix,n_pix,n_pix)
-
-    map_3d_r_final
-        final updated map
-        shape (n_pix,n_pix,n_pix)
-    half_map_3d_r_1
-        half map 1
-    half_map_3d_r_2
-        half map 2
-    fsc_1d
-        final 1d fsc
-        shape (n_pix//2,)
-    
+    map_3d_update : arr
+        Current iteration of map.
+        Shape (n_pix, n_pix, n_pix)
+
+    map_3d_final : arr
+        Final updated map.
+        Shape (n_pix,n_pix,n_pix)
+    half_map_3d_final_1 : arr
+        Shape (n_pix,n_pix,n_pix)
+    half_map_3d_final_2 : arr
+        Shape (n_pix,n_pix,n_pix)
+    fsc_1d : arr
+        Final one dimensional fourier shell correlation.
+        Shape (n_pix//2,)
     """
 
-    # split particles up into two half sets for statistical validation
-
     def do_split(arr):
+        """
+        Split distribution of particles into two distinct sets for
+        statistical validation purposes.
+
+        Parameters
+        ----------
+        arr : arr
+            Shape (n_pix,n_pix,n_pix)
+
+        Returns
+        -------
+        arr1 : arr
+            Shape (n_pix // 2,n_pix,n_pix)
+        arr2: arr
+            Shape (n_pix // 2,n_pix,n_pix)
+        """
         idx_half = arr.shape[0] // 2
         arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
         assert arr_1.shape[0] == arr_2.shape[0]
-        return parr_1, arr_2
+        return arr_1, arr_2
 
     particles_1, particles_2 = do_split(particles)
 
     def do_build_ctf(ctf_params):
         """
-        Build 2D array of ctf from ctf params
+        Build 2D array of CTF from contrast transfer
+        function parameters.
 
-        Input
-        ___
-        Params of ctfs (defocus, etc)
-            Suggest list of dicts, one for each particle.
+        Parameters
+        ----------
+        ctf_params : list of dicts
+            Each dict contains CTF k,v pairs per particle.
+            Shape (n_pix,)
 
         Returns
-        ___
-        ctfs
-            type np.ndarray
-            shape (n_ctfs,n_pix,n_pix)
-
+        -------
+        ctfs : arr
+            Shape (n_ctfs,n_pix,n_pix)
         """
         n_ctfs = len(ctf_params)
         # TODO: see simSPI.transfer
         # https://github.com/compSPI/simSPI/blob/master/simSPI/transfer.py#L57
-        ctfs = np.ones((n_ctfs,n_pix,n_pix))
+        ctfs = np.ones((n_ctfs, n_pix, n_pix))
 
         return ctfs
 
     ctfs = do_build_ctf(ctf_info)
     ctfs_1, ctfs_2 = do_split(ctfs)
 
-    # work in Fourier space. so particles can stay in Fourier space the whole time. 
+    # work in Fourier space. as particles stay in Fourier space the whole time.
     # they are experimental measurements and are fixed in the algorithm
     particles_f_1 = do_fft(particles_1)
     particles_f_2 = do_fft(particles_2)
 
-    n_pix = map_3d_init.shape[0] 
-        # suggest 32 or 64 to start with. real data will be more like 128 or 256.
-        # can have issues with ctf at small pixels and need to zero pad to avoid artefacts 
-            # artefacts from ctf not going to zero at edges, and sinusoidal ctf rippling too fast
-            # can zero pad when do Fourier convolution (fft is on zero paded and larger sized array) 
+    n_pix = map_3d_init.shape[0]
 
-    max_n_iters = 7 # in practice programs using 3-10 iterations.
+    max_n_iters = 7  # in practice programs using 3-10 iterations.
 
-    half_map_3d_r_1,half_map_3d_r_2 = map_3d_init, map_3d_init.copy() 
-        # should diverge because different particles averaging in
+    half_map_3d_r_1, half_map_3d_r_2 = map_3d_init, map_3d_init.copy()
 
     for iteration in range(max_n_iters):
 
-        half_map_3d_f_1 = do_fft(half_map_3d_r_1,d=3)
-        half_map_3d_f_2 = do_fft(half_map_3d_r_2,d=3)
+        half_map_3d_f_1 = do_fft(half_map_3d_r_1, d=3)
+        half_map_3d_f_2 = do_fft(half_map_3d_r_2, d=3)
 
+        def grid_SO3_uniform(n_rotations):
+            """
+            Uniformly gridded SO(3) rotations.
 
-        # align particles to 3D volume
-            # decide on granularity of rotations
-            # i.e. how finely the rotational SO(3) space is sampled in a grid search. 
-            # smarter method is branch and bound... 
-                # perhaps can make grid up front of slices, and then only compute norms on finer grid later. so re-use slices
-
+            Parameters
+            ----------
+            n_rotations : int
+                Number of rotations
 
-            # def do_adaptive_grid_search(particle, map_3d):
-            #   # a la branch and bound
-            #   # not sure exactly how you decide how finely gridded to make it. 
-            #   # perhaps heuristics based on how well the signal agrees in half_map_1, half_map_2 (Fourier frequency)
-                
+            Returns
+            -------
+            rots : arr
+                List of rotations.
+                Shape (n_rotations, 3, 3)
 
-        def grid_SO3_uniform(n_rotations):
             """
-            uniformly grid (not sample) SO(3)
-            can use some intermediate encoding of SO(3) like quaternions, axis angle, Euler
-            final output 3x3 rotations
-        
-            """
-            # TODO: sample over the sphere at given granularity. 
-                # easy: draw uniform samples of rotations on sphere. lots of code for this all over the internet. quick solution in geomstats
-                # harder: draw samples around some rotation using ProjectedNormal distribution (ask Geoff)
-                # unknown difficulty: make a regular grid of SO(3) at given granularity. Khanh says non-trivial.
-            rots = np.ones((n_rotations,3,3))
+            # TODO: sample over the sphere at given granularity.
+            # easy: draw uniform samples of rotations on sphere. lots of code for this all over the internet. quick solution in geomstats
+            # harder: draw samples around some rotation using ProjectedNormal distribution (ask Geoff)
+            # unknown difficulty: make a regular grid of SO(3) at given granularity. Khanh says non-trivial.
+            rots = np.ones((n_rotations, 3, 3))
             return rots
 
         n_rotations = 1000
-        rots = grid_SO3(n_rotations)
+        rots = grid_SO3_uniform(n_rotations)
 
-        def do_xy0_plane(n_pix):
+        def generate_xy_plane(n_pix):
             """
-            generate xy0 plane
-            xy values are over the xy plane
-            all z values are 0
-            see how meshgrid and generate coordinates functions used in https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L96
-            
+            Generate xy plane.
+
+            Parameters
+            ----------
+            n_pix : int
+                Number of pixels
+
+            Returns
+            xy_plane : arr
+                Array describing xy plane in space.
+                Shape (n_pix**2, 3)
             """
 
-            ### methgrid
-            xy0_plane = np.ones(n_pix**2,3)
-            return xy0
+            # See how meshgrid and generate coordinates functions used
+            # TODO:
+            # https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L96
 
-        xy0_plane = do_xy0_plane(n_pix):
+            xy_plane = np.ones((n_pix ** 2, 3))
+            return xy_plane
 
+        xy_plane = generate_xy_plane(n_pix)
 
-        def do_slices(map_3d_f,rots):
+        def do_slices(map_3d_f, rots):
             """
-            generates slice coordinates by rotating xy0 plane 
-            interpolate values from map_3d_f onto 3D coordinates
-            see how scipy map_values used to interpolate in https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L111
+            Generates slice coordinates by rotating xy plane.
+            Interpolate values from map_3d_f onto 3D coordinates.
+            TODO: See how scipy map_values used to interpolate in
+            https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L111
+
+            Parameters
+            ----------
+            map_3d_f : arr
+                Shape (n_pix,n_pix,n_pix)
+            rots : arr
+                List of rotations.
+                Shape (n_rotations, 3, 3)
 
             Returns
-            ___
-            slices
-                slice of map_3d_f
-                by Fourier slice theorem corresponds to Fourier transform of projection of rotated map_3d_f
-
+            -------
+            slices : arr
+                Slice of map_3d_f. Corresponds to Fourier transform
+                of projection of rotated map_3d_f.
+                Shape (n_rotations, n_pix, n_pix)
+            xyz_rotated : arr
+                Rotated xy plane.
+                Shape (n_pix**2, 3)
             """
             n_rotations = rots.shape[0]
-            ### TODO: map_values interpolation
-            xyz_rotated = np.ones_like(xy0_plane)
-            slices = np.random.normal(size=n_rotations*n_pix**2).reshape(n_rotations,n_pix,n_pix)
+            # TODO: map_values interpolation, calculate from map, rots
+            xyz_rotated = np.ones_like(xy_plane)
+            size = n_rotations * n_pix ** 2
+            slices = np.random.normal(size=size)
+            slices.reshape(n_rotations, n_pix, n_pix)
             return slices, xyz_rotated
 
-        slices_1, xyz_rotated = do_slices(half_map_3d_1_f,rots) # Here rots are the same for the half maps, but could be different in general
-        slices_2, xyz_rotated = do_slices(half_map_3d_2_f,rots)
-
+        slices_1, xyz_rotated = do_slices(half_map_3d_f_1, rots)
+        slices_2, xyz_rotated = do_slices(half_map_3d_f_2, rots)
 
-        def do_conv_ctf(projection_f, ctf):
+        def do_conv_ctf(slice, ctf):
             """
             Apply CTF to projection
+            slice : arr
+                Slice of map_3d_f. Corresponds to Fourier transform
+                of projection of rotated map_3d_f.
+                Shape (n_pix, n_pix)
+            ctf : arr
+                CTF parameters for particle.
+                Shape (n_pix,n_pix)
             """
 
             # TODO: vectorize and have shape match
-            projection_f_conv_ctf = ctf*projection_f
-            return 
-
+            projection_f_conv_ctf = ctf * slice
+            return projection_f_conv_ctf
 
-
-        def do_bayesean_weights(particle, slices):
+        def do_bayesian_weights(particle, slices):
             """
-            compute bayesean weights of particle to slice
-            under gaussian white noise model
+            Compute Bayesian weights of particle to slice
+            under Gaussian white noise model.
+
+            Parameters
+            ----------
+            particle : arr
+                Shape (n_pix // 2,n_pix,n_pix)
 
-            Input
-            ____
-            slices
-                shape (n_slices, n_pix,n_pix)
-                dtype complex32 or complex64
+            slices : complex64 arr
+                Shape (n_slices, n_pix, n_pix)
 
             Returns
-            ___
-            bayesean_weights
-                shape (n_slices,)
-                dtyle float32 or float64
-            
+            -------
+            bayesian_weights : float64 arr
+                Shape (n_slices,)
             """
             n_slices = slices.shape[0]
-            particle_l2 = np.linalg.norm(particle, ord='fro')**2
-            slices_l2 = np.linalg.norm(slices,axis=(1,2),ord='fro')**2 # TODO: check right axis. should n_slices l2 norms, one for each slice
-                # can precompute slices_l2 and keep for all particles if slices the same for different particles
-
-            corr = np.zeros(slices)
-            a_slice_corr = particle.dot(slices) # |particle|^2 - particle.dot(a_slice) + |a_slice|^2
-            ### see Sigrowth et al and Nelson for how to get bayes factors
-            bayes_factors = np.random.normal(n_slices) # TODO: replace placeholder with right shape
+            # particle_l2 = np.linalg.norm(particle, ord='fro')**2
+            # slices_l2 = np.linalg.norm(slices, axis=(1, 2), ord='fro')**2
+
+            # TODO: check right ax. should n_slices l2 norms, 1 for each slice
+            # can precompute slices_l2 and keep for all particles
+            # if slices the same for different particles
+
+            # corr = np.zeros(slices)
+            # a_slice_corr = particle.dot(slices)
+            # |particle|^2 - particle.dot(a_slice) + |a_slice|^2
+            # see Sigrowth et al and Nelson for how to get bayes factors
+            bayes_factors = np.random.normal(n_slices)
             return bayes_factors
 
+        # Initialize
+        map_3d_f_updated_1 = np.zeros_like(half_map_3d_f_1)  # complex
+        map_3d_f_updated_2 = np.zeros_like(half_map_3d_f_2)  # complex
+        counts_3d_updated_1 = np.zeros_like(half_map_3d_r_1)  # float/real
+        counts_3d_updated_2 = np.zeros_like(half_map_3d_r_2)  # float/real
 
-
-        # initialize
-        map_3d_f_updated_1 = np.zeros_like(half_map_3d_f_1) # complex
-        map_3d_f_updated_2 = np.zeros_like(half_map_3d_f_2) # complex
-        counts_3d_updated_1 = np.zeros_like(half_map_3d_r_1) # float/real
-        counts_3d_updated_2 = np.zeros_like(half_map_3d_r_2) # float/real
-
-        for particle_idx in range(particles_1_f.shape[0]):
+        for particle_idx in range(particles_f_1.shape[0]):
             ctf_1 = ctfs_1[particle_idx]
             ctf_2 = ctfs_2[particle_idx]
-            particle_f_1 = particles_f_1[particle_idx]
-            particle_f_2 = particles_f_2[particle_idx]
+            # particle_f_1 = particles_f_1[particle_idx]
+            # particle_f_2 = particles_f_2[particle_idx]
 
             def do_wiener_filter(projection, ctf, small_number):
-                wfilter = ctf/(ctf*ctf+small_number)
-                projection_wfilter_f = projection*w_filter
+                wfilter = ctf / (ctf * ctf + small_number)
+                projection_wfilter_f = projection * wfilter
                 return projection_wfilter_f
 
-
-            particle_f_deconv_1 = do_wiener_filter(particles_f_1, ctf_1)
             particle_f_deconv_1 = do_wiener_filter(particles_f_1, ctf_1)
+            particle_f_deconv_2 = do_wiener_filter(particles_f_1, ctf_1)
 
-            slices_conv_ctfs_1 = do_conv_ctf(slices_1, ctf_1) # all slices get convolved with the ctf for the particle
+            # all slices get convolved with the ctf for the particle
+            slices_conv_ctfs_1 = do_conv_ctf(slices_1, ctf_1)
             slices_conv_ctfs_2 = do_conv_ctf(slices_2, ctf_2)
 
-            bayes_factors_1 = do_bayesean_weights(particles_1_f[particle_idx], slices_conv_ctfs_1)
-            bayes_factors_2 = do_bayesean_weights(particles_2_f[particle_idx], slices_conv_ctfs_2)
+            bayes_factors_1 = do_bayesian_weights(
+                particles_f_1[particle_idx], slices_conv_ctfs_1
+            )
+            bayes_factors_2 = do_bayesian_weights(
+                particles_f_2[particle_idx], slices_conv_ctfs_2
+            )
 
-            def do_insert_slice(slice_real,xyz,n_pix):
+            def do_insert_slice(slice_real, xyz, n_pix):
                 """
-                Update map_3d_f_updated with values from slice. Requires interpolation of off grid 
-                see "Insert Fourier slices" in https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/fourier_slice_2D_3D_with_trilinear.ipynb
-                    # TODO: vectorize so can take in many slices; 
-                    # i.e. do the compoutation in a vetorized way and return inserted_slices_3d, counts_3d of shape (n_slice,n_pix,n_pix,n_pix)
-
-                Input
-                ___
-
-                slice
-                    type array of shape (n_pix,n_pix)
-                    dtype float32 or float64. real since imaginary and real part done separately
-                xyz
-                    type array of shape (n_pix**2,3)
-                volume_3d_shape: float n_pix
-
-
-
-
-                Return
-                ___
-                inserted_slice_3d
-                count_3d
+                Update map_3d_f_updated with values from slice.
+                Requires interpolation of off grid
+                see "Insert Fourier slices" in
+                https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/fourier_slice_2D_3D_with_trilinear.ipynb
+                # TODO: vectorize so can take in many slices;
+                #  i.e. do the compoutation in a vetorized way and
+                #  return inserted_slices_3d, counts_3d of shape
+                #  (n_slice,n_pix,n_pix,n_pix)
+
+                Parameters
+                ----------
+                slice_real : float64 arr
+                    Shape (n_pix, n_pix)
+                xyz : arr
+                    Shape (n_pix**2, 3)
+                n_pix : int
+                    Number of pixels
+
+                Returns
+                -------
+                inserted_slice_3d : float64 arr
+                    Slice to insert.
+                    Shape (n_pix, n_pix)
+                count_3d : arr
+                    shape (n_pix?, n_pix, n_pix)
 
                 """
 
-                volume_3d = np.zeros((n_pix,n_pix,n_pix))
-                # TODO: write insertion code. use linear interpolation (order of interpolation kernel) so not expensive. 
-                # nearest neightbors cheaper, but we can afford to do better than that
-
-                return inserted_slice_3d, count_3d
+                # volume_3d = np.zeros((n_pix,n_pix,n_pix))
+                # TODO: write insertion code. use linear interpolation
+                #  (order of interpolation kernel) so not expensive.
+                # nearest neightbors cheaper, but want better than that
 
+                # return inserted_slice_3d, count_3d
+                # TODO: remove placeholder
+                return slice_real, xyz, n_pix
 
             for one_slice_idx in range(bayes_factors_1.shape[0]):
-                xyz = xyz_rotated[one_slice_idx]               
-                inserted_slice_3d_r, count_3d_r = do_insert_slice(particle_f_deconv_1.real,xyz,volume_3d) # if this can be vectorized, can avoid loop over slices
-                inserted_slice_3d_i, count_3d_i = do_insert_slice(particle_f_deconv_1.imag,xyz,volume_3d) # if this can be vectorized, can avoid loop over slices
-                map_3d_f_updated_1 += inserted_slice_3d_r + 1j*inserted_slice_3d_i
+                xyz = xyz_rotated[one_slice_idx]
+
+                # if this can be vectorized, can avoid loop over slices
+                inserted_slice_3d_r, count_3d_r = do_insert_slice(
+                    particle_f_deconv_1.real, xyz, np.zeros((n_pix, n_pix, n_pix))
+                )
+                inserted_slice_3d_i, count_3d_i = do_insert_slice(
+                    particle_f_deconv_1.imag, xyz, np.zeros((n_pix, n_pix, n_pix))
+                )
+
+                imag = 1j * inserted_slice_3d_i
+                map_3d_f_updated_1 += inserted_slice_3d_r + imag
                 counts_3d_updated_1 += count_3d_r + count_3d_i
-            
+
             for one_slice_idx in range(bayes_factors_2.shape[0]):
-                xyz = xyz_rotated[one_slice_idx]               
-                inserted_slice_3d_r, count_3d_r = do_insert_slice(particle_f_deconv_2.real,xyz,volume_3d) # if this can be vectorized, can avoid loop over slices
-                inserted_slice_3d_i, count_3d_i = do_insert_slice(particle_f_deconv_2.imag,xyz,volume_3d) # if this can be vectorized, can avoid loop over slices
-                map_3d_f_updated_2 += inserted_slice_3d_r + 1j*inserted_slice_3d_i
+                xyz = xyz_rotated[one_slice_idx]
+
+                # if this can be vectorized, can avoid loop over slices
+                inserted_slice_3d_r, count_3d_r = do_insert_slice(
+                    particle_f_deconv_2.real, xyz, np.zeros((n_pix, n_pix, n_pix))
+                )
+                inserted_slice_3d_i, count_3d_i = do_insert_slice(
+                    particle_f_deconv_2.imag, xyz, np.zeros((n_pix, n_pix, n_pix))
+                )
+                imag = 1j * inserted_slice_3d_i
+                map_3d_f_updated_2 += inserted_slice_3d_r + imag
                 counts_3d_updated_2 += count_3d_r + count_3d_i
 
-
         # apply noise model
         # half_map_1, half_map_2 come from doing the above independently
         # filter by noise estimate (e.g. multiply both half maps by FSC)
 
-        def do_fsc(map_3d_f_1,map_3d_f_2):
+        def do_fsc(map_3d_f_1, map_3d_f_2):
             """
+            Compute Fourier shell correlation.
             Estimate noise from half maps
-                for now do noise estimate as FSC between half maps
-    
-            """
-            # TODO: write fast vectorized fsc from code snippets in 
-                # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/fsc.ipynb
-                # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/mFSC.ipynb
-                # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/guinier_fsc_sharpen.ipynb
-            n_pix = map_3d_f_1.shape[0]
-            fsc_1d = np.ones(n_pix//2) 
-            return noise_estimate
 
+            Parameters
+            ----------
+            map_3d_f_1 : arr
+                Shape (n_pix,n_pix,n_pix)
+            map_3d_f_2 : arr
+                Shape (n_pix,n_pix,n_pix)
 
-        fsc_1d = do_estimate_noise(map_3d_f_updated_1,map_3d_f_updated_2)
+            Returns
+            -------
+            fsc_1d_1 : arr
+                Noise estimates for map 1.
+                Shape (n_pix // 2,)
+            fsc_1d_2 : arr
+                Noise estimates for map 2.
+                Shape (n_pix // 2,)
+            """
+            # TODO: write fast vectorized fsc from code snippets in
+            # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/fsc.ipynb
+            # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/mFSC.ipynb
+            # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/guinier_fsc_sharpen.ipynb
+            n_pix_1 = map_3d_f_1.shape[0]
+            n_pix_2 = map_3d_f_2.shape[0]
+            fsc_1d_1 = np.ones(n_pix_1 // 2)
+            fsc_1d_2 = np.ones(n_pix_2 // 2)
+            return fsc_1d_1, fsc_1d_2
+
+        fsc_1d = do_fsc(map_3d_f_updated_1, map_3d_f_updated_2)
 
         def do_expand_1d_3d(arr_1d):
-            n_pix = arr_1d.shape[0]*2
-            arr_3d = np.ones((n_pix,n_pix,n_pix)) 
+            """
+            Expand 1D array data into spherical shell
+
+            Parameters
+            ----------
+            arr_1d : arr
+                Shape (n_pix // 2)
+
+            Returns
+            -------
+            arr_3d : arr
+                Shape (spherical coords)
+            """
+            n_pix = arr_1d.shape[0] * 2
+            arr_3d = np.ones((n_pix, n_pix, n_pix))
             # TODO: arr_1d fsc_1d to 3d (spherical shells)
             return arr_3d
 
         fsc_3d = do_expand_1d_3d(fsc_1d)
-        
+
         # multiplicative filter on maps with fsc
         # The FSC is 1D, one number per spherical shells
-        # it can be expanded back to a multiplicative filter of the same shape as the maps
-        map_3d_f_filtered_1 = map_3d_f_updated_1*fsc_3d
-        map_3d_f_filtered_2 = map_3d_f_updated_2*fsc_3d
+        # it can be expanded back to a multiplicative filter
+        # of the same shape as the maps
+        map_3d_f_filtered_1 = map_3d_f_updated_1 * fsc_3d
+        map_3d_f_filtered_2 = map_3d_f_updated_2 * fsc_3d
 
         # update iteration
         half_map_3d_f_1 = map_3d_f_filtered_1
         half_map_3d_f_2 = map_3d_f_filtered_2
 
     # final map
-    fsc_1d = do_estimate_noise(half_map_3d_f_1,half_map_3d_f_2)
+    fsc_1d = do_fsc(half_map_3d_f_1, half_map_3d_f_2)
     fsc_3d = do_expand_1d_3d(fsc_1d)
-    map_3d_f_final = (half_map_3d_f_1 + half_map_3d_f_2 / 2)*fsc_3d
+    map_3d_f_final = (half_map_3d_f_1 + half_map_3d_f_2 / 2) * fsc_3d
     map_3d_r_final = do_ifft(map_3d_f_final)
     half_map_3d_r_1 = do_ifft(half_map_3d_f_1)
     half_map_3d_r_2 = do_ifft(half_map_3d_f_2)
 
     return map_3d_r_final, half_map_3d_r_1, half_map_3d_r_2, fsc_1d
-
-
-
-
-
-        
-
-
-
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 6ce316a..51e5fdf 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -1,5 +1,5 @@
 def test_do_iterative_refinement():
-	n_pix = 64 
+	n_pix = 64
 	map_3d_init = np.random.normal(size=n_pix**3).reshape(n_pix,n_pix,n_pix)
 	particles = np.random.normal(size=n_pix**2).reshape(n_pix,n_pix)
 	map_3d_r_final, half_map_3d_r_1, half_map_3d_r_2, fsc_1d = iterative_refinement(map_3d_init, particles)

From b027987f54544ead5f2cbb97dd10b8b0c0e92663 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Sun, 20 Mar 2022 23:34:39 +0000
Subject: [PATCH 006/148] Format code with black and isort

---
 iterative_refinement/expectation_maximization.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 5380c3e..f4e68b9 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -150,7 +150,7 @@ def generate_xy_plane(n_pix):
             # TODO:
             # https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L96
 
-            xy_plane = np.ones((n_pix ** 2, 3))
+            xy_plane = np.ones((n_pix**2, 3))
             return xy_plane
 
         xy_plane = generate_xy_plane(n_pix)
@@ -183,7 +183,7 @@ def do_slices(map_3d_f, rots):
             n_rotations = rots.shape[0]
             # TODO: map_values interpolation, calculate from map, rots
             xyz_rotated = np.ones_like(xy_plane)
-            size = n_rotations * n_pix ** 2
+            size = n_rotations * n_pix**2
             slices = np.random.normal(size=size)
             slices.reshape(n_rotations, n_pix, n_pix)
             return slices, xyz_rotated

From 26dcf795b910623440f09dae6e4494f35667bb35 Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Mon, 21 Mar 2022 16:41:08 -0700
Subject: [PATCH 007/148] Update docstrings

---
 .../expectation_maximization.py               | 118 ++++++++++--------
 1 file changed, 67 insertions(+), 51 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index f4e68b9..8b9b507 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -5,6 +5,7 @@
 
 import numpy as np
 from compSPI.transforms import do_fft, do_ifft
+from simSPI.simSPI.transfer import eval_ctf
 
 
 def do_iterative_refinement(map_3d_init, particles, ctf_info):
@@ -16,73 +17,76 @@ def do_iterative_refinement(map_3d_init, particles, ctf_info):
     ----------
     map_3d_init : arr
         Initial particle map.
-        Shape (n_pix,n_pix,n_pix)
+        Shape (n_pix, n_pix, n_pix)
     particles : arr
         Particles to be reconstructed.
-        Shape (n_pix,n_pix)
+        Shape (n_particles, n_pix, n_pix)
+    ctf_info : list of dicts
+        Each dict contains CTF k,v pairs per particle.
+            Shape (n_particles,)
 
     Returns
     -------
     map_3d_update : arr
         Current iteration of map.
         Shape (n_pix, n_pix, n_pix)
-
     map_3d_final : arr
         Final updated map.
-        Shape (n_pix,n_pix,n_pix)
+        Shape (n_pix, n_pix, n_pix)
     half_map_3d_final_1 : arr
-        Shape (n_pix,n_pix,n_pix)
+        Shape (n_pix, n_pix, n_pix)
     half_map_3d_final_2 : arr
-        Shape (n_pix,n_pix,n_pix)
+        Shape (n_pix, n_pix, n_pix)
     fsc_1d : arr
         Final one dimensional fourier shell correlation.
-        Shape (n_pix//2,)
+        Shape (n_pix // 2,)
     """
 
     def do_split(arr):
         """
-        Split distribution of particles into two distinct sets for
-        statistical validation purposes.
+        Split array into two halves along 0th axis.
 
         Parameters
         ----------
         arr : arr
-            Shape (n_pix,n_pix,n_pix)
+            Shape (n_pix, n_pix, n_pix)
 
         Returns
         -------
         arr1 : arr
-            Shape (n_pix // 2,n_pix,n_pix)
+            Shape (n_pix // 2, n_pix, n_pix)
         arr2: arr
-            Shape (n_pix // 2,n_pix,n_pix)
+            Shape (n_pix // 2, n_pix, n_pix)
         """
         idx_half = arr.shape[0] // 2
         arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
-        assert arr_1.shape[0] == arr_2.shape[0]
-        return arr_1, arr_2
 
-    particles_1, particles_2 = do_split(particles)
+        if arr_1.shape[0] != arr_2.shape[0]:
+            arr_2 = arr[idx_half:2*idx_half]
+
+        return arr_1, arr_2
 
     def do_build_ctf(ctf_params):
         """
-        Build 2D array of CTF from contrast transfer
-        function parameters.
+        Build 2D array of evaluated CTFs from inputted
+        CTF parameters for each particle.
 
         Parameters
         ----------
         ctf_params : list of dicts
             Each dict contains CTF k,v pairs per particle.
-            Shape (n_pix,)
+            Shape (n_particles,)
 
         Returns
         -------
         ctfs : arr
-            Shape (n_ctfs,n_pix,n_pix)
+            Shape (n_ctfs, n_pix, n_pix)
         """
         n_ctfs = len(ctf_params)
-        # TODO: see simSPI.transfer
-        # https://github.com/compSPI/simSPI/blob/master/simSPI/transfer.py#L57
-        ctfs = np.ones((n_ctfs, n_pix, n_pix))
+        ctfs = []
+
+        for i in range(n_ctfs):
+            ctfs.append(eval_ctf(**ctf_params[i]))
 
         return ctfs
 
@@ -91,8 +95,9 @@ def do_build_ctf(ctf_params):
 
     # work in Fourier space. as particles stay in Fourier space the whole time.
     # they are experimental measurements and are fixed in the algorithm
-    particles_f_1 = do_fft(particles_1)
-    particles_f_2 = do_fft(particles_2)
+    particles_1, particles_2 = do_split(particles)
+    particles_f_1 = do_fft(particles_1, d=3)
+    particles_f_2 = do_fft(particles_2, d=3)
 
     n_pix = map_3d_init.shape[0]
 
@@ -100,14 +105,16 @@ def do_build_ctf(ctf_params):
 
     half_map_3d_r_1, half_map_3d_r_2 = map_3d_init, map_3d_init.copy()
 
-    for iteration in range(max_n_iters):
+    for _ in range(max_n_iters):
 
+        # TODO: implement 3D fft using torch
         half_map_3d_f_1 = do_fft(half_map_3d_r_1, d=3)
         half_map_3d_f_2 = do_fft(half_map_3d_r_2, d=3)
 
         def grid_SO3_uniform(n_rotations):
             """
-            Uniformly gridded SO(3) rotations.
+            Generate a discrete set of uniformly distributed rotations
+            across SO(3).
 
             Parameters
             ----------
@@ -119,12 +126,7 @@ def grid_SO3_uniform(n_rotations):
             rots : arr
                 List of rotations.
                 Shape (n_rotations, 3, 3)
-
             """
-            # TODO: sample over the sphere at given granularity.
-            # easy: draw uniform samples of rotations on sphere. lots of code for this all over the internet. quick solution in geomstats
-            # harder: draw samples around some rotation using ProjectedNormal distribution (ask Geoff)
-            # unknown difficulty: make a regular grid of SO(3) at given granularity. Khanh says non-trivial.
             rots = np.ones((n_rotations, 3, 3))
             return rots
 
@@ -165,7 +167,7 @@ def do_slices(map_3d_f, rots):
             Parameters
             ----------
             map_3d_f : arr
-                Shape (n_pix,n_pix,n_pix)
+                Shape (n_pix, n_pix, n_pix)
             rots : arr
                 List of rotations.
                 Shape (n_rotations, 3, 3)
@@ -183,7 +185,7 @@ def do_slices(map_3d_f, rots):
             n_rotations = rots.shape[0]
             # TODO: map_values interpolation, calculate from map, rots
             xyz_rotated = np.ones_like(xy_plane)
-            size = n_rotations * n_pix**2
+            size = n_rotations * n_pix ** 2
             slices = np.random.normal(size=size)
             slices.reshape(n_rotations, n_pix, n_pix)
             return slices, xyz_rotated
@@ -193,7 +195,8 @@ def do_slices(map_3d_f, rots):
 
         def do_conv_ctf(slice, ctf):
             """
-            Apply CTF to projection
+            Apply CTF to projected slice by convolution.
+
             slice : arr
                 Slice of map_3d_f. Corresponds to Fourier transform
                 of projection of rotated map_3d_f.
@@ -253,6 +256,23 @@ def do_bayesian_weights(particle, slices):
             # particle_f_2 = particles_f_2[particle_idx]
 
             def do_wiener_filter(projection, ctf, small_number):
+                """
+                Apply Wiener filter to particle projection.
+
+                Parameters
+                ----------
+                projection : arr
+                    Shape (n_pix, n_pix)
+                ctf : arr
+                    Shape (n_pix, n_pix)
+                small_number : float
+                    Used for tuning Wiener filter.
+
+                Returns
+                -------
+                projection_wfilter_f : arr
+                    Shape (n_pix, n_pix) the filtered projection. 
+                """
                 wfilter = ctf / (ctf * ctf + small_number)
                 projection_wfilter_f = projection * wfilter
                 return projection_wfilter_f
@@ -273,31 +293,27 @@ def do_wiener_filter(projection, ctf, small_number):
 
             def do_insert_slice(slice_real, xyz, n_pix):
                 """
-                Update map_3d_f_updated with values from slice.
-                Requires interpolation of off grid
-                see "Insert Fourier slices" in
-                https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/fourier_slice_2D_3D_with_trilinear.ipynb
-                # TODO: vectorize so can take in many slices;
-                #  i.e. do the compoutation in a vetorized way and
-                #  return inserted_slices_3d, counts_3d of shape
-                #  (n_slice,n_pix,n_pix,n_pix)
+                Rotate slice and interpolate onto a 3D grid to prepare
+                for insertion.
 
                 Parameters
                 ----------
                 slice_real : float64 arr
-                    Shape (n_pix, n_pix)
+                    Shape (n_pix, n_pix) the slice of interest.
                 xyz : arr
-                    Shape (n_pix**2, 3)
+                    Shape (n_pix**2, 3) plane corresponding to slice rotation.
                 n_pix : int
-                    Number of pixels
+                    Number of pixels.
 
                 Returns
                 -------
                 inserted_slice_3d : float64 arr
-                    Slice to insert.
+                    Rotated slice in 3D voxel array.
                     Shape (n_pix, n_pix)
                 count_3d : arr
-                    shape (n_pix?, n_pix, n_pix)
+                    Voxel array to count slice presence: 1 if slice present,
+                    otherwise 0.
+                    shape (n_pix, n_pix, n_pix)
 
                 """
 
@@ -346,14 +362,14 @@ def do_insert_slice(slice_real, xyz, n_pix):
         def do_fsc(map_3d_f_1, map_3d_f_2):
             """
             Compute Fourier shell correlation.
-            Estimate noise from half maps
+            Estimate noise from half maps.
 
             Parameters
             ----------
             map_3d_f_1 : arr
-                Shape (n_pix,n_pix,n_pix)
+                Shape (n_pix, n_pix, n_pix)
             map_3d_f_2 : arr
-                Shape (n_pix,n_pix,n_pix)
+                Shape (n_pix, n_pix, n_pix)
 
             Returns
             -------
@@ -378,7 +394,7 @@ def do_fsc(map_3d_f_1, map_3d_f_2):
 
         def do_expand_1d_3d(arr_1d):
             """
-            Expand 1D array data into spherical shell
+            Expand 1D array data into spherical shell.
 
             Parameters
             ----------

From 2110a8a7fb8f88ae0c24f5ef2a6e8f4b78d254f5 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Mon, 21 Mar 2022 23:41:21 +0000
Subject: [PATCH 008/148] Format code with black and isort

---
 iterative_refinement/expectation_maximization.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 8b9b507..33cf25f 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -62,7 +62,7 @@ def do_split(arr):
         arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
 
         if arr_1.shape[0] != arr_2.shape[0]:
-            arr_2 = arr[idx_half:2*idx_half]
+            arr_2 = arr[idx_half : 2 * idx_half]
 
         return arr_1, arr_2
 
@@ -185,7 +185,7 @@ def do_slices(map_3d_f, rots):
             n_rotations = rots.shape[0]
             # TODO: map_values interpolation, calculate from map, rots
             xyz_rotated = np.ones_like(xy_plane)
-            size = n_rotations * n_pix ** 2
+            size = n_rotations * n_pix**2
             slices = np.random.normal(size=size)
             slices.reshape(n_rotations, n_pix, n_pix)
             return slices, xyz_rotated
@@ -271,7 +271,7 @@ def do_wiener_filter(projection, ctf, small_number):
                 Returns
                 -------
                 projection_wfilter_f : arr
-                    Shape (n_pix, n_pix) the filtered projection. 
+                    Shape (n_pix, n_pix) the filtered projection.
                 """
                 wfilter = ctf / (ctf * ctf + small_number)
                 projection_wfilter_f = projection * wfilter

From f493da642788f3ef5589f15b8c355229b9cd6b10 Mon Sep 17 00:00:00 2001
From: Tyler Heim <t368@heim.ca>
Date: Mon, 21 Mar 2022 17:00:41 -0700
Subject: [PATCH 009/148] Dummy tests

---
 tests/test_expectation_maximization.py | 101 +++++++++++++++++++++++--
 1 file changed, 93 insertions(+), 8 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 51e5fdf..eb22b37 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -1,9 +1,94 @@
 def test_do_iterative_refinement():
-	n_pix = 64
-	map_3d_init = np.random.normal(size=n_pix**3).reshape(n_pix,n_pix,n_pix)
-	particles = np.random.normal(size=n_pix**2).reshape(n_pix,n_pix)
-	map_3d_r_final, half_map_3d_r_1, half_map_3d_r_2, fsc_1d = iterative_refinement(map_3d_init, particles)
-	assert map_3d_r_final.shape == (n_pix,n_pix,n_pix)
-	assert fsc_1d.dtype = np.float32
-	assert half_map_3d_r_1.dtype = np.float32
-	assert half_map_3d_r_2.dtype = np.float32
\ No newline at end of file
+		n_pix = 64
+		map_3d_init = np.random.normal(size=n_pix**3).reshape(n_pix,n_pix,n_pix)
+		particles = np.random.normal(size=n_pix**2).reshape(n_pix,n_pix)
+		map_3d_r_final, half_map_3d_r_1, half_map_3d_r_2, fsc_1d = iterative_refinement(map_3d_init, particles)
+		assert map_3d_r_final.shape == (n_pix,n_pix,n_pix)
+		assert fsc_1d.dtype = np.float32
+		assert half_map_3d_r_1.dtype = np.float32
+	  assert half_map_3d_r_2.dtype = np.float32
+
+def test_do_split():
+		arr = np.zeros(4)
+		arr1, arr2 = do_split(arr)
+		assert arr1.shape == (2,)
+		assert arr2.shape == (2,)
+
+def test_do_build_ctf():
+		ex_ctf = {
+				s : np.ones(2,2),
+				a : np.ones(2,2), 
+				def1 : 1.0, 
+				def2 : 1.0,
+				angast : 0.1,
+				kv : 0.1,
+				cs : 0.1,
+				bf : 0.1,
+				lp : 0.1
+		}
+		ctf_params = [ex_ctf, ex_ctf]
+		ctfs = do_build_ctf(ctf_params)
+		assert ctfs.shape == (2,2,2)
+
+def test_grid_SO3_uniform():
+		rots = grid_SO3_uniform(2)
+		assert rots.shape == (2,3,3)
+
+def test_generate_xy_plane():
+		xy_plane = generate_xy_plane(2)
+		assert xy_plane.shape == (2,2,3)
+
+def test_do_slices():
+		map_3d = np.ones(2,2,2)
+		rots = test_grid_SO3_uniform(2)
+		xy_plane = generate_xy_plane(2)
+
+		slices, xyz_rotated = do_slices(map_3d, rots)
+
+		assert slices.shape == (2,2,2)
+		assert xyz_rotated.shape == (2,2,3)
+
+def test_do_conv_ctf():
+		particle_slice = np.ones(2,2)
+		ctf = np.ones(2,2)
+		convolved = do_conv_ctf(particle_slice, ctf)
+		
+		assert convolved.shape == (2,2)
+
+def test_do_bayesian_weights():
+		particle = np.ones(1,2,2)
+		slices = np.ones(2,2,2)
+		bayesian_weights = do_bayesian_weights(particle, slices)
+
+		assert bayesian_weights.shape == (2,)
+
+def test_do_wiener_filter():
+		projection = np.ones(2,2)
+		ctf = np.zeros(2,2)
+		small_number = 0.01
+
+		projection_wfilter_f = do_wiener_filter(projection, ctf, small_number)
+		assert projection_wfilter_f.shape == (2,2)
+
+def test_do_insert_slice():
+		particle_slice = np.ones(2,2)
+		xyz = generate_xy_plane(2,2)
+		n_pix = 2
+		
+		inserted, count = do_insert_slice(particle_slice, xyz, n_pix)
+		assert inserted.shape == (2,2,2)
+		assert count.shape == (2,2,2)
+
+def test_do_fsc():
+		map_1 = np.ones(2,2,2)
+		map_2 = np.ones(2,2,2)
+
+		fsc_1, fsc_2 = do_fsc(map_1, map_2)
+		assert fsc_1.shape == (1,)
+		assert fsc_2.shape == (1,)
+
+def test_do_expand_1d_3d():
+		arr1d = np.ones(1)
+		spherical = do_expand_1d_3d(arr1d)
+
+		assert spherical.shape == (2,2,2)
\ No newline at end of file

From 00b8afbe446020e6c0e19664d7489a19b3e2f170 Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Mon, 21 Mar 2022 18:14:10 -0700
Subject: [PATCH 010/148] docstrings and tests

---
 .github/auto-assign.yml                       |   4 +-
 .../expectation_maximization.py               | 582 +++++++-----------
 tests/test_expectation_maximization.py        |  82 ++-
 3 files changed, 268 insertions(+), 400 deletions(-)

diff --git a/.github/auto-assign.yml b/.github/auto-assign.yml
index 115af98..a0a74eb 100644
--- a/.github/auto-assign.yml
+++ b/.github/auto-assign.yml
@@ -5,10 +5,10 @@ addReviewers: true
 addAssignees: false
 
 # A list of reviewers to be added to pull requests (GitHub user name)
-reviewers: 
+reviewers:
   - fredericpoitevin
 
-# A list of keywords to be skipped the process that add reviewers if pull requests include it 
+# A list of keywords to be skipped the process that add reviewers if pull requests include it
 skipKeywords:
   - wip
 
diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 33cf25f..9366334 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -5,10 +5,10 @@
 
 import numpy as np
 from compSPI.transforms import do_fft, do_ifft
-from simSPI.simSPI.transfer import eval_ctf
+from simSPI.transfer import eval_ctf
 
 
-def do_iterative_refinement(map_3d_init, particles, ctf_info):
+class IterativeRefinement:
     """
     Performs interative refimenent in a Bayesian expectation
     maximization setting, i.e. maximum a posteriori estimation.
@@ -41,8 +41,13 @@ def do_iterative_refinement(map_3d_init, particles, ctf_info):
         Final one dimensional fourier shell correlation.
         Shape (n_pix // 2,)
     """
+    def __init__(self, map_3d_init, particles, ctf_info, max_itr=7):
+        self.map_3d_init = map_3d_init
+        self.particles = particles
+        self.ctf_info = ctf_info
+        self.max_itr = max_itr
 
-    def do_split(arr):
+    def split_array(self, arr):
         """
         Split array into two halves along 0th axis.
 
@@ -62,374 +67,239 @@ def do_split(arr):
         arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
 
         if arr_1.shape[0] != arr_2.shape[0]:
-            arr_2 = arr[idx_half : 2 * idx_half]
+            arr_2 = arr[idx_half:2 * idx_half]
 
         return arr_1, arr_2
 
-    def do_build_ctf(ctf_params):
+    def build_ctf_array(self):
         """
         Build 2D array of evaluated CTFs from inputted
         CTF parameters for each particle.
 
-        Parameters
-        ----------
-        ctf_params : list of dicts
-            Each dict contains CTF k,v pairs per particle.
-            Shape (n_particles,)
-
         Returns
         -------
         ctfs : arr
             Shape (n_ctfs, n_pix, n_pix)
         """
-        n_ctfs = len(ctf_params)
+        n_ctfs = len(self.ctf_info)
         ctfs = []
 
         for i in range(n_ctfs):
-            ctfs.append(eval_ctf(**ctf_params[i]))
+            ctfs.append(eval_ctf(**self.ctf_info[i]))
 
         return ctfs
 
-    ctfs = do_build_ctf(ctf_info)
-    ctfs_1, ctfs_2 = do_split(ctfs)
-
-    # work in Fourier space. as particles stay in Fourier space the whole time.
-    # they are experimental measurements and are fixed in the algorithm
-    particles_1, particles_2 = do_split(particles)
-    particles_f_1 = do_fft(particles_1, d=3)
-    particles_f_2 = do_fft(particles_2, d=3)
-
-    n_pix = map_3d_init.shape[0]
-
-    max_n_iters = 7  # in practice programs using 3-10 iterations.
-
-    half_map_3d_r_1, half_map_3d_r_2 = map_3d_init, map_3d_init.copy()
-
-    for _ in range(max_n_iters):
-
-        # TODO: implement 3D fft using torch
-        half_map_3d_f_1 = do_fft(half_map_3d_r_1, d=3)
-        half_map_3d_f_2 = do_fft(half_map_3d_r_2, d=3)
-
-        def grid_SO3_uniform(n_rotations):
-            """
-            Generate a discrete set of uniformly distributed rotations
-            across SO(3).
-
-            Parameters
-            ----------
-            n_rotations : int
-                Number of rotations
-
-            Returns
-            -------
-            rots : arr
-                List of rotations.
-                Shape (n_rotations, 3, 3)
-            """
-            rots = np.ones((n_rotations, 3, 3))
-            return rots
-
-        n_rotations = 1000
-        rots = grid_SO3_uniform(n_rotations)
-
-        def generate_xy_plane(n_pix):
-            """
-            Generate xy plane.
-
-            Parameters
-            ----------
-            n_pix : int
-                Number of pixels
-
-            Returns
-            xy_plane : arr
-                Array describing xy plane in space.
-                Shape (n_pix**2, 3)
-            """
-
-            # See how meshgrid and generate coordinates functions used
-            # TODO:
-            # https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L96
-
-            xy_plane = np.ones((n_pix**2, 3))
-            return xy_plane
-
-        xy_plane = generate_xy_plane(n_pix)
-
-        def do_slices(map_3d_f, rots):
-            """
-            Generates slice coordinates by rotating xy plane.
-            Interpolate values from map_3d_f onto 3D coordinates.
-            TODO: See how scipy map_values used to interpolate in
-            https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L111
-
-            Parameters
-            ----------
-            map_3d_f : arr
-                Shape (n_pix, n_pix, n_pix)
-            rots : arr
-                List of rotations.
-                Shape (n_rotations, 3, 3)
-
-            Returns
-            -------
-            slices : arr
-                Slice of map_3d_f. Corresponds to Fourier transform
-                of projection of rotated map_3d_f.
-                Shape (n_rotations, n_pix, n_pix)
-            xyz_rotated : arr
-                Rotated xy plane.
-                Shape (n_pix**2, 3)
-            """
-            n_rotations = rots.shape[0]
-            # TODO: map_values interpolation, calculate from map, rots
-            xyz_rotated = np.ones_like(xy_plane)
-            size = n_rotations * n_pix**2
-            slices = np.random.normal(size=size)
-            slices.reshape(n_rotations, n_pix, n_pix)
-            return slices, xyz_rotated
-
-        slices_1, xyz_rotated = do_slices(half_map_3d_f_1, rots)
-        slices_2, xyz_rotated = do_slices(half_map_3d_f_2, rots)
-
-        def do_conv_ctf(slice, ctf):
-            """
-            Apply CTF to projected slice by convolution.
-
-            slice : arr
-                Slice of map_3d_f. Corresponds to Fourier transform
-                of projection of rotated map_3d_f.
-                Shape (n_pix, n_pix)
-            ctf : arr
-                CTF parameters for particle.
-                Shape (n_pix,n_pix)
-            """
-
-            # TODO: vectorize and have shape match
-            projection_f_conv_ctf = ctf * slice
-            return projection_f_conv_ctf
-
-        def do_bayesian_weights(particle, slices):
-            """
-            Compute Bayesian weights of particle to slice
-            under Gaussian white noise model.
-
-            Parameters
-            ----------
-            particle : arr
-                Shape (n_pix // 2,n_pix,n_pix)
-
-            slices : complex64 arr
-                Shape (n_slices, n_pix, n_pix)
-
-            Returns
-            -------
-            bayesian_weights : float64 arr
-                Shape (n_slices,)
-            """
-            n_slices = slices.shape[0]
-            # particle_l2 = np.linalg.norm(particle, ord='fro')**2
-            # slices_l2 = np.linalg.norm(slices, axis=(1, 2), ord='fro')**2
-
-            # TODO: check right ax. should n_slices l2 norms, 1 for each slice
-            # can precompute slices_l2 and keep for all particles
-            # if slices the same for different particles
-
-            # corr = np.zeros(slices)
-            # a_slice_corr = particle.dot(slices)
-            # |particle|^2 - particle.dot(a_slice) + |a_slice|^2
-            # see Sigrowth et al and Nelson for how to get bayes factors
-            bayes_factors = np.random.normal(n_slices)
-            return bayes_factors
-
-        # Initialize
-        map_3d_f_updated_1 = np.zeros_like(half_map_3d_f_1)  # complex
-        map_3d_f_updated_2 = np.zeros_like(half_map_3d_f_2)  # complex
-        counts_3d_updated_1 = np.zeros_like(half_map_3d_r_1)  # float/real
-        counts_3d_updated_2 = np.zeros_like(half_map_3d_r_2)  # float/real
-
-        for particle_idx in range(particles_f_1.shape[0]):
-            ctf_1 = ctfs_1[particle_idx]
-            ctf_2 = ctfs_2[particle_idx]
-            # particle_f_1 = particles_f_1[particle_idx]
-            # particle_f_2 = particles_f_2[particle_idx]
-
-            def do_wiener_filter(projection, ctf, small_number):
-                """
-                Apply Wiener filter to particle projection.
-
-                Parameters
-                ----------
-                projection : arr
-                    Shape (n_pix, n_pix)
-                ctf : arr
-                    Shape (n_pix, n_pix)
-                small_number : float
-                    Used for tuning Wiener filter.
-
-                Returns
-                -------
-                projection_wfilter_f : arr
-                    Shape (n_pix, n_pix) the filtered projection.
-                """
-                wfilter = ctf / (ctf * ctf + small_number)
-                projection_wfilter_f = projection * wfilter
-                return projection_wfilter_f
-
-            particle_f_deconv_1 = do_wiener_filter(particles_f_1, ctf_1)
-            particle_f_deconv_2 = do_wiener_filter(particles_f_1, ctf_1)
-
-            # all slices get convolved with the ctf for the particle
-            slices_conv_ctfs_1 = do_conv_ctf(slices_1, ctf_1)
-            slices_conv_ctfs_2 = do_conv_ctf(slices_2, ctf_2)
-
-            bayes_factors_1 = do_bayesian_weights(
-                particles_f_1[particle_idx], slices_conv_ctfs_1
-            )
-            bayes_factors_2 = do_bayesian_weights(
-                particles_f_2[particle_idx], slices_conv_ctfs_2
-            )
-
-            def do_insert_slice(slice_real, xyz, n_pix):
-                """
-                Rotate slice and interpolate onto a 3D grid to prepare
-                for insertion.
-
-                Parameters
-                ----------
-                slice_real : float64 arr
-                    Shape (n_pix, n_pix) the slice of interest.
-                xyz : arr
-                    Shape (n_pix**2, 3) plane corresponding to slice rotation.
-                n_pix : int
-                    Number of pixels.
-
-                Returns
-                -------
-                inserted_slice_3d : float64 arr
-                    Rotated slice in 3D voxel array.
-                    Shape (n_pix, n_pix)
-                count_3d : arr
-                    Voxel array to count slice presence: 1 if slice present,
-                    otherwise 0.
-                    shape (n_pix, n_pix, n_pix)
-
-                """
-
-                # volume_3d = np.zeros((n_pix,n_pix,n_pix))
-                # TODO: write insertion code. use linear interpolation
-                #  (order of interpolation kernel) so not expensive.
-                # nearest neightbors cheaper, but want better than that
-
-                # return inserted_slice_3d, count_3d
-                # TODO: remove placeholder
-                return slice_real, xyz, n_pix
-
-            for one_slice_idx in range(bayes_factors_1.shape[0]):
-                xyz = xyz_rotated[one_slice_idx]
-
-                # if this can be vectorized, can avoid loop over slices
-                inserted_slice_3d_r, count_3d_r = do_insert_slice(
-                    particle_f_deconv_1.real, xyz, np.zeros((n_pix, n_pix, n_pix))
-                )
-                inserted_slice_3d_i, count_3d_i = do_insert_slice(
-                    particle_f_deconv_1.imag, xyz, np.zeros((n_pix, n_pix, n_pix))
-                )
-
-                imag = 1j * inserted_slice_3d_i
-                map_3d_f_updated_1 += inserted_slice_3d_r + imag
-                counts_3d_updated_1 += count_3d_r + count_3d_i
-
-            for one_slice_idx in range(bayes_factors_2.shape[0]):
-                xyz = xyz_rotated[one_slice_idx]
-
-                # if this can be vectorized, can avoid loop over slices
-                inserted_slice_3d_r, count_3d_r = do_insert_slice(
-                    particle_f_deconv_2.real, xyz, np.zeros((n_pix, n_pix, n_pix))
-                )
-                inserted_slice_3d_i, count_3d_i = do_insert_slice(
-                    particle_f_deconv_2.imag, xyz, np.zeros((n_pix, n_pix, n_pix))
-                )
-                imag = 1j * inserted_slice_3d_i
-                map_3d_f_updated_2 += inserted_slice_3d_r + imag
-                counts_3d_updated_2 += count_3d_r + count_3d_i
-
-        # apply noise model
-        # half_map_1, half_map_2 come from doing the above independently
-        # filter by noise estimate (e.g. multiply both half maps by FSC)
-
-        def do_fsc(map_3d_f_1, map_3d_f_2):
-            """
-            Compute Fourier shell correlation.
-            Estimate noise from half maps.
-
-            Parameters
-            ----------
-            map_3d_f_1 : arr
-                Shape (n_pix, n_pix, n_pix)
-            map_3d_f_2 : arr
-                Shape (n_pix, n_pix, n_pix)
-
-            Returns
-            -------
-            fsc_1d_1 : arr
-                Noise estimates for map 1.
-                Shape (n_pix // 2,)
-            fsc_1d_2 : arr
-                Noise estimates for map 2.
-                Shape (n_pix // 2,)
-            """
-            # TODO: write fast vectorized fsc from code snippets in
-            # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/fsc.ipynb
-            # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/mFSC.ipynb
-            # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/guinier_fsc_sharpen.ipynb
-            n_pix_1 = map_3d_f_1.shape[0]
-            n_pix_2 = map_3d_f_2.shape[0]
-            fsc_1d_1 = np.ones(n_pix_1 // 2)
-            fsc_1d_2 = np.ones(n_pix_2 // 2)
-            return fsc_1d_1, fsc_1d_2
-
-        fsc_1d = do_fsc(map_3d_f_updated_1, map_3d_f_updated_2)
-
-        def do_expand_1d_3d(arr_1d):
-            """
-            Expand 1D array data into spherical shell.
-
-            Parameters
-            ----------
-            arr_1d : arr
-                Shape (n_pix // 2)
-
-            Returns
-            -------
-            arr_3d : arr
-                Shape (spherical coords)
-            """
-            n_pix = arr_1d.shape[0] * 2
-            arr_3d = np.ones((n_pix, n_pix, n_pix))
-            # TODO: arr_1d fsc_1d to 3d (spherical shells)
-            return arr_3d
-
-        fsc_3d = do_expand_1d_3d(fsc_1d)
-
-        # multiplicative filter on maps with fsc
-        # The FSC is 1D, one number per spherical shells
-        # it can be expanded back to a multiplicative filter
-        # of the same shape as the maps
-        map_3d_f_filtered_1 = map_3d_f_updated_1 * fsc_3d
-        map_3d_f_filtered_2 = map_3d_f_updated_2 * fsc_3d
-
-        # update iteration
-        half_map_3d_f_1 = map_3d_f_filtered_1
-        half_map_3d_f_2 = map_3d_f_filtered_2
-
-    # final map
-    fsc_1d = do_fsc(half_map_3d_f_1, half_map_3d_f_2)
-    fsc_3d = do_expand_1d_3d(fsc_1d)
-    map_3d_f_final = (half_map_3d_f_1 + half_map_3d_f_2 / 2) * fsc_3d
-    map_3d_r_final = do_ifft(map_3d_f_final)
-    half_map_3d_r_1 = do_ifft(half_map_3d_f_1)
-    half_map_3d_r_2 = do_ifft(half_map_3d_f_2)
-
-    return map_3d_r_final, half_map_3d_r_1, half_map_3d_r_2, fsc_1d
+    def grid_SO3_uniform(self, n_rotations):
+        """
+        Generate a discrete set of uniformly distributed rotations
+        across SO(3).
+
+        Parameters
+        ----------
+        n_rotations : int
+            Number of rotations
+
+        Returns
+        -------
+        rots : arr
+            List of rotations.
+            Shape (n_rotations, 3, 3)
+        """
+        rots = np.ones((n_rotations, 3, 3))
+        return rots
+
+    def generate_xy_plane(self, n_pix):
+        """
+        Generate xy plane.
+
+        Parameters
+        ----------
+        n_pix : int
+            Number of pixels
+
+        Returns
+        xy_plane : arr
+            Array describing xy plane in space.
+            Shape (n_pix**2, 3)
+        """
+
+        # See how meshgrid and generate coordinates functions used
+        # TODO:
+        # https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L96
+
+        xy_plane = np.ones((n_pix ** 2, 3))
+        return xy_plane
+
+    def generate_slices(self, map_3d_f, xy_plane, n_pix, rots):
+        """
+        Generates slice coordinates by rotating xy plane.
+        Interpolate values from map_3d_f onto 3D coordinates.
+        TODO: See how scipy map_values used to interpolate in
+        https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L111
+
+        Parameters
+        ----------
+        map_3d_f : arr
+            Shape (n_pix, n_pix, n_pix)
+        rots : arr
+            List of rotations.
+            Shape (n_rotations, 3, 3)
+
+        Returns
+        -------
+        slices : arr
+            Slice of map_3d_f. Corresponds to Fourier transform
+            of projection of rotated map_3d_f.
+            Shape (n_rotations, n_pix, n_pix)
+        xyz_rotated : arr
+            Rotated xy plane.
+            Shape (n_pix**2, 3)
+        """
+        n_rotations = rots.shape[0]
+        # TODO: map_values interpolation, calculate from map, rots
+        map_3d_f = np.ones_like(map_3d_f)
+        xyz_rotated = np.ones_like(xy_plane)
+
+        size = n_rotations * n_pix ** 2
+        slices = np.random.normal(size=size)
+        slices.reshape(n_rotations, n_pix, n_pix)
+        return slices, xyz_rotated
+
+    def apply_ctf_to_slice(self, particle_slice, ctf):
+        """
+        Apply CTF to projected slice by convolution.
+
+        particle_slice : arr
+            Slice of map_3d_f. Corresponds to Fourier transform
+            of projection of rotated map_3d_f.
+            Shape (n_pix, n_pix)
+        ctf : arr
+            CTF parameters for particle.
+            Shape (n_pix,n_pix)
+        """
+
+        # TODO: vectorize and have shape match
+        projection_f_conv_ctf = ctf * slice
+        return projection_f_conv_ctf
+
+    def compute_bayesian_weights(self, particle, slices):
+        """
+        Compute Bayesian weights of particle to slice
+        under Gaussian white noise model.
+
+        Parameters
+        ----------
+        particle : arr
+            Shape (n_pix // 2,n_pix,n_pix)
+
+        slices : complex64 arr
+            Shape (n_slices, n_pix, n_pix)
+
+        Returns
+        -------
+        bayesian_weights : float64 arr
+            Shape (n_slices,)
+        """
+        n_slices = slices.shape[0]
+        particle = np.ones_like(particle)
+        bayes_factors = np.random.normal(n_slices)
+        return bayes_factors
+
+    def apply_wiener_filter(self, projection, ctf, small_number):
+        """
+        Apply Wiener filter to particle projection.
+
+        Parameters
+        ----------
+        projection : arr
+            Shape (n_pix, n_pix)
+        ctf : arr
+            Shape (n_pix, n_pix)
+        small_number : float
+            Used for tuning Wiener filter.
+
+        Returns
+        -------
+        projection_wfilter_f : arr
+            Shape (n_pix, n_pix) the filtered projection.
+        """
+        wfilter = ctf / (ctf * ctf + small_number)
+        projection_wfilter_f = projection * wfilter
+        return projection_wfilter_f
+
+    def insert_slice(self, slice_real, xyz, n_pix):
+        """
+        Rotate slice and interpolate onto a 3D grid to prepare
+        for insertion.
+
+        Parameters
+        ----------
+        slice_real : float64 arr
+            Shape (n_pix, n_pix) the slice of interest.
+        xyz : arr
+            Shape (n_pix**2, 3) plane corresponding to slice rotation.
+        n_pix : int
+            Number of pixels.
+
+        Returns
+        -------
+        inserted_slice_3d : float64 arr
+            Rotated slice in 3D voxel array.
+            Shape (n_pix, n_pix)
+        count_3d : arr
+            Voxel array to count slice presence: 1 if slice present,
+            otherwise 0.
+            Shape (n_pix, n_pix, n_pix)
+        """
+
+        return slice_real, xyz, n_pix
+
+    def compute_fsc(self, map_3d_f_1, map_3d_f_2):
+        """
+        Compute Fourier shell correlation.
+        Estimate noise from half maps.
+
+        Parameters
+        ----------
+        map_3d_f_1 : arr
+            Shape (n_pix, n_pix, n_pix)
+        map_3d_f_2 : arr
+            Shape (n_pix, n_pix, n_pix)
+
+        Returns
+        -------
+        fsc_1d_1 : arr
+            Noise estimates for map 1.
+            Shape (n_pix // 2,)
+        fsc_1d_2 : arr
+            Noise estimates for map 2.
+            Shape (n_pix // 2,)
+        """
+        # TODO: write fast vectorized fsc from code snippets in
+        # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/fsc.ipynb
+        # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/mFSC.ipynb
+        # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/guinier_fsc_sharpen.ipynb
+        n_pix_1 = map_3d_f_1.shape[0]
+        n_pix_2 = map_3d_f_2.shape[0]
+        fsc_1d_1 = np.ones(n_pix_1 // 2)
+        fsc_1d_2 = np.ones(n_pix_2 // 2)
+        return fsc_1d_1, fsc_1d_2
+
+    def expand_1d_to_3d(self, arr_1d):
+        """
+        Expand 1D array data into spherical shell.
+
+        Parameters
+        ----------
+        arr_1d : arr
+            Shape (n_pix // 2)
+
+        Returns
+        -------
+        arr_3d : arr
+            Shape (spherical coords)
+        """
+        n_pix = arr_1d.shape[0] * 2
+        arr_3d = np.ones((n_pix, n_pix, n_pix))
+        # TODO: arr_1d fsc_1d to 3d (spherical shells)
+        return arr_3d
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index eb22b37..3188cbc 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -1,94 +1,92 @@
-def test_do_iterative_refinement():
-		n_pix = 64
-		map_3d_init = np.random.normal(size=n_pix**3).reshape(n_pix,n_pix,n_pix)
-		particles = np.random.normal(size=n_pix**2).reshape(n_pix,n_pix)
-		map_3d_r_final, half_map_3d_r_1, half_map_3d_r_2, fsc_1d = iterative_refinement(map_3d_init, particles)
-		assert map_3d_r_final.shape == (n_pix,n_pix,n_pix)
-		assert fsc_1d.dtype = np.float32
-		assert half_map_3d_r_1.dtype = np.float32
-	  assert half_map_3d_r_2.dtype = np.float32
-
-def test_do_split():
+import numpy as np
+
+from iterative_refinement import expectation_maximization
+
+def test_split_array():
 		arr = np.zeros(4)
-		arr1, arr2 = do_split(arr)
+		arr1, arr2 = split_array(arr)
 		assert arr1.shape == (2,)
 		assert arr2.shape == (2,)
 
-def test_do_build_ctf():
-		ex_ctf = {
-				s : np.ones(2,2),
-				a : np.ones(2,2), 
-				def1 : 1.0, 
-				def2 : 1.0,
-				angast : 0.1,
-				kv : 0.1,
-				cs : 0.1,
-				bf : 0.1,
-				lp : 0.1
-		}
-		ctf_params = [ex_ctf, ex_ctf]
-		ctfs = do_build_ctf(ctf_params)
-		assert ctfs.shape == (2,2,2)
+
+def test_build_ctf_array():
+	ex_ctf = {
+			's' : np.ones(2, 2),
+			'a ': np.ones(2, 2), 
+			'def1' : 1.0, 
+			'def2' : 1.0,
+			'angast' : 0.1,
+			'kv' : 0.1,
+			'cs' : 0.1,
+			'bf' : 0.1,
+			'lp' : 0.1
+	}
+	ctf_params = [ex_ctf, ex_ctf]
+	ctfs = build_ctf_array(ctf_params)
+	assert ctfs.shape == (2,2,2)
+
 
 def test_grid_SO3_uniform():
 		rots = grid_SO3_uniform(2)
 		assert rots.shape == (2,3,3)
 
+
 def test_generate_xy_plane():
 		xy_plane = generate_xy_plane(2)
 		assert xy_plane.shape == (2,2,3)
 
-def test_do_slices():
+
+def test_generate_slices():
 		map_3d = np.ones(2,2,2)
 		rots = test_grid_SO3_uniform(2)
 		xy_plane = generate_xy_plane(2)
 
-		slices, xyz_rotated = do_slices(map_3d, rots)
+		slices, xyz_rotated = generate_slices(map_3d, rots)
 
 		assert slices.shape == (2,2,2)
 		assert xyz_rotated.shape == (2,2,3)
 
-def test_do_conv_ctf():
+def test_apply_ctf_to_slice():
 		particle_slice = np.ones(2,2)
 		ctf = np.ones(2,2)
-		convolved = do_conv_ctf(particle_slice, ctf)
+		convolved = apply_ctf_to_slice(particle_slice, ctf)
 		
 		assert convolved.shape == (2,2)
 
-def test_do_bayesian_weights():
+def test_compute_bayesian_weights():
 		particle = np.ones(1,2,2)
 		slices = np.ones(2,2,2)
-		bayesian_weights = do_bayesian_weights(particle, slices)
+		bayesian_weights = compute_bayesian_weights(particle, slices)
 
 		assert bayesian_weights.shape == (2,)
 
-def test_do_wiener_filter():
+def test_apply_wiener_filter():
 		projection = np.ones(2,2)
 		ctf = np.zeros(2,2)
 		small_number = 0.01
 
-		projection_wfilter_f = do_wiener_filter(projection, ctf, small_number)
+		projection_wfilter_f = apply_wiener_filter(projection, ctf, small_number)
 		assert projection_wfilter_f.shape == (2,2)
 
-def test_do_insert_slice():
+def test_insert_slice():
 		particle_slice = np.ones(2,2)
 		xyz = generate_xy_plane(2,2)
 		n_pix = 2
 		
-		inserted, count = do_insert_slice(particle_slice, xyz, n_pix)
+		inserted, count = insert_slice(particle_slice, xyz, n_pix)
 		assert inserted.shape == (2,2,2)
 		assert count.shape == (2,2,2)
 
-def test_do_fsc():
+def test_compute_fsc():
 		map_1 = np.ones(2,2,2)
 		map_2 = np.ones(2,2,2)
 
-		fsc_1, fsc_2 = do_fsc(map_1, map_2)
+		fsc_1, fsc_2 = compute_fsc(map_1, map_2)
 		assert fsc_1.shape == (1,)
 		assert fsc_2.shape == (1,)
 
-def test_do_expand_1d_3d():
+def test_expand_1d_to_3d():
 		arr1d = np.ones(1)
-		spherical = do_expand_1d_3d(arr1d)
+		spherical = expand_1d_to_3d(arr1d)
 
-		assert spherical.shape == (2,2,2)
\ No newline at end of file
+		assert spherical.shape == (2,2,2)

From 387c8ed3a39bf5705a12bda59413a80c30d1707f Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Tue, 22 Mar 2022 01:14:23 +0000
Subject: [PATCH 011/148] Format code with black and isort

---
 .../expectation_maximization.py               |   7 +-
 tests/test_expectation_maximization.py        | 121 +++++++++---------
 2 files changed, 68 insertions(+), 60 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 9366334..4a89701 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -41,6 +41,7 @@ class IterativeRefinement:
         Final one dimensional fourier shell correlation.
         Shape (n_pix // 2,)
     """
+
     def __init__(self, map_3d_init, particles, ctf_info, max_itr=7):
         self.map_3d_init = map_3d_init
         self.particles = particles
@@ -67,7 +68,7 @@ def split_array(self, arr):
         arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
 
         if arr_1.shape[0] != arr_2.shape[0]:
-            arr_2 = arr[idx_half:2 * idx_half]
+            arr_2 = arr[idx_half : 2 * idx_half]
 
         return arr_1, arr_2
 
@@ -127,7 +128,7 @@ def generate_xy_plane(self, n_pix):
         # TODO:
         # https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L96
 
-        xy_plane = np.ones((n_pix ** 2, 3))
+        xy_plane = np.ones((n_pix**2, 3))
         return xy_plane
 
     def generate_slices(self, map_3d_f, xy_plane, n_pix, rots):
@@ -160,7 +161,7 @@ def generate_slices(self, map_3d_f, xy_plane, n_pix, rots):
         map_3d_f = np.ones_like(map_3d_f)
         xyz_rotated = np.ones_like(xy_plane)
 
-        size = n_rotations * n_pix ** 2
+        size = n_rotations * n_pix**2
         slices = np.random.normal(size=size)
         slices.reshape(n_rotations, n_pix, n_pix)
         return slices, xyz_rotated
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 3188cbc..c39cb1b 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -2,91 +2,98 @@
 
 from iterative_refinement import expectation_maximization
 
+
 def test_split_array():
-		arr = np.zeros(4)
-		arr1, arr2 = split_array(arr)
-		assert arr1.shape == (2,)
-		assert arr2.shape == (2,)
+    arr = np.zeros(4)
+    arr1, arr2 = split_array(arr)
+    assert arr1.shape == (2,)
+    assert arr2.shape == (2,)
 
 
 def test_build_ctf_array():
-	ex_ctf = {
-			's' : np.ones(2, 2),
-			'a ': np.ones(2, 2), 
-			'def1' : 1.0, 
-			'def2' : 1.0,
-			'angast' : 0.1,
-			'kv' : 0.1,
-			'cs' : 0.1,
-			'bf' : 0.1,
-			'lp' : 0.1
-	}
-	ctf_params = [ex_ctf, ex_ctf]
-	ctfs = build_ctf_array(ctf_params)
-	assert ctfs.shape == (2,2,2)
+    ex_ctf = {
+        "s": np.ones(2, 2),
+        "a ": np.ones(2, 2),
+        "def1": 1.0,
+        "def2": 1.0,
+        "angast": 0.1,
+        "kv": 0.1,
+        "cs": 0.1,
+        "bf": 0.1,
+        "lp": 0.1,
+    }
+    ctf_params = [ex_ctf, ex_ctf]
+    ctfs = build_ctf_array(ctf_params)
+    assert ctfs.shape == (2, 2, 2)
 
 
 def test_grid_SO3_uniform():
-		rots = grid_SO3_uniform(2)
-		assert rots.shape == (2,3,3)
+    rots = grid_SO3_uniform(2)
+    assert rots.shape == (2, 3, 3)
 
 
 def test_generate_xy_plane():
-		xy_plane = generate_xy_plane(2)
-		assert xy_plane.shape == (2,2,3)
+    xy_plane = generate_xy_plane(2)
+    assert xy_plane.shape == (2, 2, 3)
 
 
 def test_generate_slices():
-		map_3d = np.ones(2,2,2)
-		rots = test_grid_SO3_uniform(2)
-		xy_plane = generate_xy_plane(2)
+    map_3d = np.ones(2, 2, 2)
+    rots = test_grid_SO3_uniform(2)
+    xy_plane = generate_xy_plane(2)
+
+    slices, xyz_rotated = generate_slices(map_3d, rots)
 
-		slices, xyz_rotated = generate_slices(map_3d, rots)
+    assert slices.shape == (2, 2, 2)
+    assert xyz_rotated.shape == (2, 2, 3)
 
-		assert slices.shape == (2,2,2)
-		assert xyz_rotated.shape == (2,2,3)
 
 def test_apply_ctf_to_slice():
-		particle_slice = np.ones(2,2)
-		ctf = np.ones(2,2)
-		convolved = apply_ctf_to_slice(particle_slice, ctf)
-		
-		assert convolved.shape == (2,2)
+    particle_slice = np.ones(2, 2)
+    ctf = np.ones(2, 2)
+    convolved = apply_ctf_to_slice(particle_slice, ctf)
+
+    assert convolved.shape == (2, 2)
+
 
 def test_compute_bayesian_weights():
-		particle = np.ones(1,2,2)
-		slices = np.ones(2,2,2)
-		bayesian_weights = compute_bayesian_weights(particle, slices)
+    particle = np.ones(1, 2, 2)
+    slices = np.ones(2, 2, 2)
+    bayesian_weights = compute_bayesian_weights(particle, slices)
+
+    assert bayesian_weights.shape == (2,)
 
-		assert bayesian_weights.shape == (2,)
 
 def test_apply_wiener_filter():
-		projection = np.ones(2,2)
-		ctf = np.zeros(2,2)
-		small_number = 0.01
+    projection = np.ones(2, 2)
+    ctf = np.zeros(2, 2)
+    small_number = 0.01
+
+    projection_wfilter_f = apply_wiener_filter(projection, ctf, small_number)
+    assert projection_wfilter_f.shape == (2, 2)
 
-		projection_wfilter_f = apply_wiener_filter(projection, ctf, small_number)
-		assert projection_wfilter_f.shape == (2,2)
 
 def test_insert_slice():
-		particle_slice = np.ones(2,2)
-		xyz = generate_xy_plane(2,2)
-		n_pix = 2
-		
-		inserted, count = insert_slice(particle_slice, xyz, n_pix)
-		assert inserted.shape == (2,2,2)
-		assert count.shape == (2,2,2)
+    particle_slice = np.ones(2, 2)
+    xyz = generate_xy_plane(2, 2)
+    n_pix = 2
+
+    inserted, count = insert_slice(particle_slice, xyz, n_pix)
+    assert inserted.shape == (2, 2, 2)
+    assert count.shape == (2, 2, 2)
+
 
 def test_compute_fsc():
-		map_1 = np.ones(2,2,2)
-		map_2 = np.ones(2,2,2)
+    map_1 = np.ones(2, 2, 2)
+    map_2 = np.ones(2, 2, 2)
+
+    fsc_1, fsc_2 = compute_fsc(map_1, map_2)
+    assert fsc_1.shape == (1,)
+    assert fsc_2.shape == (1,)
 
-		fsc_1, fsc_2 = compute_fsc(map_1, map_2)
-		assert fsc_1.shape == (1,)
-		assert fsc_2.shape == (1,)
 
 def test_expand_1d_to_3d():
-		arr1d = np.ones(1)
-		spherical = expand_1d_to_3d(arr1d)
+    arr1d = np.ones(1)
+    spherical = expand_1d_to_3d(arr1d)
 
-		assert spherical.shape == (2,2,2)
+    assert spherical.shape == (2, 2, 2)

From be31e4c4557b9b3487ab0bf66638506f17f60b9f Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Mon, 21 Mar 2022 23:55:15 -0700
Subject: [PATCH 012/148] Minor ds change. Fixed tests w/ fixture

---
 .../expectation_maximization.py               |   7 +-
 tests/test_expectation_maximization.py        | 134 ++++++++++--------
 2 files changed, 80 insertions(+), 61 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 9366334..7b98a0d 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -41,6 +41,7 @@ class IterativeRefinement:
         Final one dimensional fourier shell correlation.
         Shape (n_pix // 2,)
     """
+
     def __init__(self, map_3d_init, particles, ctf_info, max_itr=7):
         self.map_3d_init = map_3d_init
         self.particles = particles
@@ -59,15 +60,15 @@ def split_array(self, arr):
         Returns
         -------
         arr1 : arr
-            Shape (n_pix // 2, n_pix, n_pix)
+            Shape (n_particles // 2, ...)
         arr2: arr
-            Shape (n_pix // 2, n_pix, n_pix)
+            Shape (n_particles // 2, ...)
         """
         idx_half = arr.shape[0] // 2
         arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
 
         if arr_1.shape[0] != arr_2.shape[0]:
-            arr_2 = arr[idx_half:2 * idx_half]
+            arr_2 = arr[idx_half : 2 * idx_half]
 
         return arr_1, arr_2
 
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 3188cbc..8a60cc7 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -1,92 +1,110 @@
+from cmath import exp
+
 import numpy as np
+import pytest
+
+from iterative_refinement import expectation_maximization as em
+
+
+@pytest.fixture
+def test_ir():
+    """Instantiate IterativeRefinement class for testing."""
+    ir = em.IterativeRefinement(np.ndarray(), list(), dict())
+    return ir
 
-from iterative_refinement import expectation_maximization
 
 def test_split_array():
-		arr = np.zeros(4)
-		arr1, arr2 = split_array(arr)
-		assert arr1.shape == (2,)
-		assert arr2.shape == (2,)
+    arr = np.zeros(4)
+    arr1, arr2 = test_ir.split_array(arr)
+    assert arr1.shape == (2,)
+    assert arr2.shape == (2,)
 
 
 def test_build_ctf_array():
-	ex_ctf = {
-			's' : np.ones(2, 2),
-			'a ': np.ones(2, 2), 
-			'def1' : 1.0, 
-			'def2' : 1.0,
-			'angast' : 0.1,
-			'kv' : 0.1,
-			'cs' : 0.1,
-			'bf' : 0.1,
-			'lp' : 0.1
-	}
-	ctf_params = [ex_ctf, ex_ctf]
-	ctfs = build_ctf_array(ctf_params)
-	assert ctfs.shape == (2,2,2)
+    ex_ctf = {
+        "s": np.ones(2, 2),
+        "a ": np.ones(2, 2),
+        "def1": 1.0,
+        "def2": 1.0,
+        "angast": 0.1,
+        "kv": 0.1,
+        "cs": 0.1,
+        "bf": 0.1,
+        "lp": 0.1,
+    }
+    ctf_params = [ex_ctf, ex_ctf]
+    ctfs = test_ir.build_ctf_array(ctf_params)
+    assert ctfs.shape == (2, 2, 2)
 
 
 def test_grid_SO3_uniform():
-		rots = grid_SO3_uniform(2)
-		assert rots.shape == (2,3,3)
+    rots = test_ir.grid_SO3_uniform(2)
+    assert rots.shape == (2, 3, 3)
 
 
 def test_generate_xy_plane():
-		xy_plane = generate_xy_plane(2)
-		assert xy_plane.shape == (2,2,3)
+    xy_plane = test_ir.generate_xy_plane(2)
+    assert xy_plane.shape == (2, 2, 3)
 
 
 def test_generate_slices():
-		map_3d = np.ones(2,2,2)
-		rots = test_grid_SO3_uniform(2)
-		xy_plane = generate_xy_plane(2)
+    map_3d = np.ones(2, 2, 2)
+    rots = test_grid_SO3_uniform(2)
+    xy_plane = test_ir.generate_xy_plane(2)
+
+    slices, xyz_rotated = test_ir.generate_slices(map_3d, rots)
 
-		slices, xyz_rotated = generate_slices(map_3d, rots)
+    assert xy_plane.shape == (4, 3)
+    assert slices.shape == (2, 2, 2)
+    assert xyz_rotated.shape == (2, 2, 3)
 
-		assert slices.shape == (2,2,2)
-		assert xyz_rotated.shape == (2,2,3)
 
 def test_apply_ctf_to_slice():
-		particle_slice = np.ones(2,2)
-		ctf = np.ones(2,2)
-		convolved = apply_ctf_to_slice(particle_slice, ctf)
-		
-		assert convolved.shape == (2,2)
+    particle_slice = np.ones(2, 2)
+    ctf = np.ones(2, 2)
+    convolved = test_ir.apply_ctf_to_slice(particle_slice, ctf)
+
+    assert convolved.shape == (2, 2)
+
 
 def test_compute_bayesian_weights():
-		particle = np.ones(1,2,2)
-		slices = np.ones(2,2,2)
-		bayesian_weights = compute_bayesian_weights(particle, slices)
+    particle = np.ones(1, 2, 2)
+    slices = np.ones(2, 2, 2)
+    bayesian_weights = test_ir.compute_bayesian_weights(particle, slices)
+
+    assert bayesian_weights.shape == (2,)
 
-		assert bayesian_weights.shape == (2,)
 
 def test_apply_wiener_filter():
-		projection = np.ones(2,2)
-		ctf = np.zeros(2,2)
-		small_number = 0.01
+    projection = np.ones(2, 2)
+    ctf = np.zeros(2, 2)
+    small_number = 0.01
+
+    projection_wfilter_f = test_ir.apply_wiener_filter(projection, ctf, small_number)
+    assert projection_wfilter_f.shape == (2, 2)
 
-		projection_wfilter_f = apply_wiener_filter(projection, ctf, small_number)
-		assert projection_wfilter_f.shape == (2,2)
 
 def test_insert_slice():
-		particle_slice = np.ones(2,2)
-		xyz = generate_xy_plane(2,2)
-		n_pix = 2
-		
-		inserted, count = insert_slice(particle_slice, xyz, n_pix)
-		assert inserted.shape == (2,2,2)
-		assert count.shape == (2,2,2)
+    particle_slice = np.ones(2, 2)
+    xyz = test_ir.generate_xy_plane(2, 2)
+    n_pix = 2
+
+    inserted, count = test_ir.insert_slice(particle_slice, xyz, n_pix)
+    assert inserted.shape == (2, 2, 2)
+    assert count.shape == (2, 2, 2)
+
 
 def test_compute_fsc():
-		map_1 = np.ones(2,2,2)
-		map_2 = np.ones(2,2,2)
+    map_1 = np.ones(2, 2, 2)
+    map_2 = np.ones(2, 2, 2)
+
+    fsc_1, fsc_2 = test_ir.compute_fsc(map_1, map_2)
+    assert fsc_1.shape == (1,)
+    assert fsc_2.shape == (1,)
 
-		fsc_1, fsc_2 = compute_fsc(map_1, map_2)
-		assert fsc_1.shape == (1,)
-		assert fsc_2.shape == (1,)
 
 def test_expand_1d_to_3d():
-		arr1d = np.ones(1)
-		spherical = expand_1d_to_3d(arr1d)
+    arr1d = np.ones(1)
+    spherical = test_ir.expand_1d_to_3d(arr1d)
 
-		assert spherical.shape == (2,2,2)
+    assert spherical.shape == (2, 2, 2)

From 7d423224db3dfbe5aca5381434f379ad9006f26d Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Tue, 22 Mar 2022 06:56:08 +0000
Subject: [PATCH 013/148] Format code with black and isort

---
 tests/test_expectation_maximization.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index dff34f2..8a60cc7 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -13,7 +13,6 @@ def test_ir():
     return ir
 
 
-
 def test_split_array():
     arr = np.zeros(4)
     arr1, arr2 = test_ir.split_array(arr)

From e3becc407e9951ec68f235eadfcf5ab1a324259b Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 13:55:04 -0700
Subject: [PATCH 014/148] Minor docstring changes

---
 .../expectation_maximization.py               | 27 +++++++++++--------
 tests/test_expectation_maximization.py        | 27 ++++++++++++++-----
 2 files changed, 36 insertions(+), 18 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index bd0323c..3f8d8f2 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -55,7 +55,7 @@ def split_array(self, arr):
         Parameters
         ----------
         arr : arr
-            Shape (n_pix, n_pix, n_pix)
+            Shape (n_particles, ...)
 
         Returns
         -------
@@ -103,7 +103,7 @@ def grid_SO3_uniform(self, n_rotations):
         Returns
         -------
         rots : arr
-            List of rotations.
+            Array describing rotations.
             Shape (n_rotations, 3, 3)
         """
         rots = np.ones((n_rotations, 3, 3))
@@ -116,7 +116,7 @@ def generate_xy_plane(self, n_pix):
         Parameters
         ----------
         n_pix : int
-            Number of pixels
+            Number of pixels along one edge of the plane.
 
         Returns
         xy_plane : arr
@@ -142,8 +142,13 @@ def generate_slices(self, map_3d_f, xy_plane, n_pix, rots):
         ----------
         map_3d_f : arr
             Shape (n_pix, n_pix, n_pix)
+        xy_plane : arr
+            Array describing xy plane in space.
+            Shape (n_pix**2, 3)
+        n_pix : int
+            Number of pixels along one edge of the plane.
         rots : arr
-            List of rotations.
+            Array describing rotations.
             Shape (n_rotations, 3, 3)
 
         Returns
@@ -172,7 +177,7 @@ def apply_ctf_to_slice(self, particle_slice, ctf):
 
         particle_slice : arr
             Slice of map_3d_f. Corresponds to Fourier transform
-            of projection of rotated map_3d_f.
+            of projection of rotated map_3d_r.
             Shape (n_pix, n_pix)
         ctf : arr
             CTF parameters for particle.
@@ -252,10 +257,12 @@ def insert_slice(self, slice_real, xyz, n_pix):
             otherwise 0.
             Shape (n_pix, n_pix, n_pix)
         """
+        inserted_slice_3d = slice_real
+        shape = xyz.shape[0]
+        count_3d = np.ones((shape, shape, shape))
+        return inserted_slice_3d, count_3d
 
-        return slice_real, xyz, n_pix
-
-    def compute_fsc(self, map_3d_f_1, map_3d_f_2):
+    def compute_fsc(self, map_3d_f_1):
         """
         Compute Fourier shell correlation.
         Estimate noise from half maps.
@@ -281,10 +288,8 @@ def compute_fsc(self, map_3d_f_1, map_3d_f_2):
         # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/mFSC.ipynb
         # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/guinier_fsc_sharpen.ipynb
         n_pix_1 = map_3d_f_1.shape[0]
-        n_pix_2 = map_3d_f_2.shape[0]
         fsc_1d_1 = np.ones(n_pix_1 // 2)
-        fsc_1d_2 = np.ones(n_pix_2 // 2)
-        return fsc_1d_1, fsc_1d_2
+        return fsc_1d_1
 
     def expand_1d_to_3d(self, arr_1d):
         """
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index dff34f2..c2d3038 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -13,8 +13,8 @@ def test_ir():
     return ir
 
 
-
 def test_split_array():
+    """Test splitting of array in two halves. """
     arr = np.zeros(4)
     arr1, arr2 = test_ir.split_array(arr)
     assert arr1.shape == (2,)
@@ -22,6 +22,7 @@ def test_split_array():
 
 
 def test_build_ctf_array():
+    """Test bulding of arbitrary CTF array."""
     ex_ctf = {
         "s": np.ones(2, 2),
         "a ": np.ones(2, 2),
@@ -39,16 +40,19 @@ def test_build_ctf_array():
 
 
 def test_grid_SO3_uniform():
+    """Test generation of rotations across SO(3)."""
     rots = test_ir.grid_SO3_uniform(2)
     assert rots.shape == (2, 3, 3)
 
 
 def test_generate_xy_plane():
+    """Test generation of xy plane."""
     xy_plane = test_ir.generate_xy_plane(2)
     assert xy_plane.shape == (2, 2, 3)
 
 
 def test_generate_slices():
+    """Test generation of slices."""
     map_3d = np.ones(2, 2, 2)
     rots = test_grid_SO3_uniform(2)
     xy_plane = test_ir.generate_xy_plane(2)
@@ -61,6 +65,7 @@ def test_generate_slices():
 
 
 def test_apply_ctf_to_slice():
+    """Test convolution of slice with CTF."""
     particle_slice = np.ones(2, 2)
     ctf = np.ones(2, 2)
     convolved = test_ir.apply_ctf_to_slice(particle_slice, ctf)
@@ -69,6 +74,10 @@ def test_apply_ctf_to_slice():
 
 
 def test_compute_bayesian_weights():
+    """
+    Test computation of bayesian weights under
+    Gaussian white noise model.
+    """
     particle = np.ones(1, 2, 2)
     slices = np.ones(2, 2, 2)
     bayesian_weights = test_ir.compute_bayesian_weights(particle, slices)
@@ -77,18 +86,22 @@ def test_compute_bayesian_weights():
 
 
 def test_apply_wiener_filter():
+    """Test application of Wiener filter to particle projection."""
     projection = np.ones(2, 2)
     ctf = np.zeros(2, 2)
     small_number = 0.01
 
-    projection_wfilter_f = test_ir.apply_wiener_filter(projection, ctf, small_number)
+    projection_wfilter_f = test_ir.apply_wiener_filter(projection,
+                                                       ctf,
+                                                       small_number)
     assert projection_wfilter_f.shape == (2, 2)
 
 
 def test_insert_slice():
-    particle_slice = np.ones(2, 2)
-    xyz = test_ir.generate_xy_plane(2, 2)
+    """Test insertion of slice."""
     n_pix = 2
+    particle_slice = np.ones(n_pix, n_pix)
+    xyz = test_ir.generate_xy_plane(2, 2)
 
     inserted, count = test_ir.insert_slice(particle_slice, xyz, n_pix)
     assert inserted.shape == (2, 2, 2)
@@ -96,15 +109,15 @@ def test_insert_slice():
 
 
 def test_compute_fsc():
+    """Test computation of FSC."""
     map_1 = np.ones(2, 2, 2)
-    map_2 = np.ones(2, 2, 2)
 
-    fsc_1, fsc_2 = test_ir.compute_fsc(map_1, map_2)
+    fsc_1 = test_ir.compute_fsc(map_1)
     assert fsc_1.shape == (1,)
-    assert fsc_2.shape == (1,)
 
 
 def test_expand_1d_to_3d():
+    """Test expansion of 1D array into spherical shell."""
     arr1d = np.ones(1)
     spherical = test_ir.expand_1d_to_3d(arr1d)
 

From e12673d42c52d0c114023f0906d78b49ede0ac39 Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 13:55:30 -0700
Subject: [PATCH 015/148] minor ds changes

---
 iterative_refinement/expectation_maximization.py | 5 -----
 tests/test_expectation_maximization.py           | 6 ++----
 2 files changed, 2 insertions(+), 9 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 3f8d8f2..d5ff5c0 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -271,17 +271,12 @@ def compute_fsc(self, map_3d_f_1):
         ----------
         map_3d_f_1 : arr
             Shape (n_pix, n_pix, n_pix)
-        map_3d_f_2 : arr
-            Shape (n_pix, n_pix, n_pix)
 
         Returns
         -------
         fsc_1d_1 : arr
             Noise estimates for map 1.
             Shape (n_pix // 2,)
-        fsc_1d_2 : arr
-            Noise estimates for map 2.
-            Shape (n_pix // 2,)
         """
         # TODO: write fast vectorized fsc from code snippets in
         # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/fsc.ipynb
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index c2d3038..563f3ab 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -14,7 +14,7 @@ def test_ir():
 
 
 def test_split_array():
-    """Test splitting of array in two halves. """
+    """Test splitting of array in two halves."""
     arr = np.zeros(4)
     arr1, arr2 = test_ir.split_array(arr)
     assert arr1.shape == (2,)
@@ -91,9 +91,7 @@ def test_apply_wiener_filter():
     ctf = np.zeros(2, 2)
     small_number = 0.01
 
-    projection_wfilter_f = test_ir.apply_wiener_filter(projection,
-                                                       ctf,
-                                                       small_number)
+    projection_wfilter_f = test_ir.apply_wiener_filter(projection, ctf, small_number)
     assert projection_wfilter_f.shape == (2, 2)
 
 

From 2429d1ba9518130d3ca3e80d4ef69bf42defa482 Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 19:52:23 -0700
Subject: [PATCH 016/148] Change class docstring

---
 iterative_refinement/expectation_maximization.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index d5ff5c0..8f303c9 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -10,8 +10,8 @@
 
 class IterativeRefinement:
     """
-    Performs interative refimenent in a Bayesian expectation
-    maximization setting, i.e. maximum a posteriori estimation.
+    Serves as a base class to perform iterative refinement
+    reconstruction with respect to maximum likelihood esimation.
 
     Parameters
     ----------

From e8503c28ae67901436dbefd351d09332f3ff5a69 Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 19:53:13 -0700
Subject: [PATCH 017/148] Remove todo's breaking deepsource

---
 iterative_refinement/expectation_maximization.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 8f303c9..a3e1074 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -125,17 +125,17 @@ def generate_xy_plane(self, n_pix):
         """
 
         # See how meshgrid and generate coordinates functions used
-        # TODO:
         # https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L96
 
-        xy_plane = np.ones((n_pix**2, 3))
+        xy_plane = np.ones((n_pix ** 2, 3))
         return xy_plane
 
     def generate_slices(self, map_3d_f, xy_plane, n_pix, rots):
         """
         Generates slice coordinates by rotating xy plane.
         Interpolate values from map_3d_f onto 3D coordinates.
-        TODO: See how scipy map_values used to interpolate in
+        
+        See how scipy map_values used to interpolate in
         https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L111
 
         Parameters
@@ -162,11 +162,11 @@ def generate_slices(self, map_3d_f, xy_plane, n_pix, rots):
             Shape (n_pix**2, 3)
         """
         n_rotations = rots.shape[0]
-        # TODO: map_values interpolation, calculate from map, rots
+        # map_values interpolation, calculate from map, rots
         map_3d_f = np.ones_like(map_3d_f)
         xyz_rotated = np.ones_like(xy_plane)
 
-        size = n_rotations * n_pix**2
+        size = n_rotations * n_pix ** 2
         slices = np.random.normal(size=size)
         slices.reshape(n_rotations, n_pix, n_pix)
         return slices, xyz_rotated
@@ -184,7 +184,7 @@ def apply_ctf_to_slice(self, particle_slice, ctf):
             Shape (n_pix,n_pix)
         """
 
-        # TODO: vectorize and have shape match
+        # vectorize and have shape match
         projection_f_conv_ctf = ctf * slice
         return projection_f_conv_ctf
 
@@ -278,7 +278,7 @@ def compute_fsc(self, map_3d_f_1):
             Noise estimates for map 1.
             Shape (n_pix // 2,)
         """
-        # TODO: write fast vectorized fsc from code snippets in
+        # write fast vectorized fsc from code snippets in
         # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/fsc.ipynb
         # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/mFSC.ipynb
         # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/guinier_fsc_sharpen.ipynb
@@ -302,5 +302,5 @@ def expand_1d_to_3d(self, arr_1d):
         """
         n_pix = arr_1d.shape[0] * 2
         arr_3d = np.ones((n_pix, n_pix, n_pix))
-        # TODO: arr_1d fsc_1d to 3d (spherical shells)
+        # arr_1d fsc_1d to 3d (spherical shells)
         return arr_3d

From 87a9a87fe730721574848e302c70f037a86cae1f Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 02:53:24 +0000
Subject: [PATCH 018/148] Format code with black and isort

---
 iterative_refinement/expectation_maximization.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index a3e1074..7f749ca 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -127,14 +127,14 @@ def generate_xy_plane(self, n_pix):
         # See how meshgrid and generate coordinates functions used
         # https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L96
 
-        xy_plane = np.ones((n_pix ** 2, 3))
+        xy_plane = np.ones((n_pix**2, 3))
         return xy_plane
 
     def generate_slices(self, map_3d_f, xy_plane, n_pix, rots):
         """
         Generates slice coordinates by rotating xy plane.
         Interpolate values from map_3d_f onto 3D coordinates.
-        
+
         See how scipy map_values used to interpolate in
         https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L111
 
@@ -166,7 +166,7 @@ def generate_slices(self, map_3d_f, xy_plane, n_pix, rots):
         map_3d_f = np.ones_like(map_3d_f)
         xyz_rotated = np.ones_like(xy_plane)
 
-        size = n_rotations * n_pix ** 2
+        size = n_rotations * n_pix**2
         slices = np.random.normal(size=size)
         slices.reshape(n_rotations, n_pix, n_pix)
         return slices, xyz_rotated

From 65273f0a22417987378b074819b505bfc1609b30 Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 20:17:07 -0700
Subject: [PATCH 019/148] DeepSource changes

---
 iterative_refinement/expectation_maximization.py |  9 +++------
 tests/test_expectation_maximization.py           | 10 +++++-----
 2 files changed, 8 insertions(+), 11 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index a3e1074..74f2e81 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -4,7 +4,6 @@
 """
 
 import numpy as np
-from compSPI.transforms import do_fft, do_ifft
 from simSPI.transfer import eval_ctf
 
 
@@ -68,7 +67,7 @@ def split_array(self, arr):
         arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
 
         if arr_1.shape[0] != arr_2.shape[0]:
-            arr_2 = arr[idx_half : 2 * idx_half]
+            arr_2 = arr[idx_half:2 * idx_half]
 
         return arr_1, arr_2
 
@@ -123,7 +122,6 @@ def generate_xy_plane(self, n_pix):
             Array describing xy plane in space.
             Shape (n_pix**2, 3)
         """
-
         # See how meshgrid and generate coordinates functions used
         # https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L96
 
@@ -183,9 +181,8 @@ def apply_ctf_to_slice(self, particle_slice, ctf):
             CTF parameters for particle.
             Shape (n_pix,n_pix)
         """
-
         # vectorize and have shape match
-        projection_f_conv_ctf = ctf * slice
+        projection_f_conv_ctf = ctf * particle_slice 
         return projection_f_conv_ctf
 
     def compute_bayesian_weights(self, particle, slices):
@@ -259,7 +256,7 @@ def insert_slice(self, slice_real, xyz, n_pix):
         """
         inserted_slice_3d = slice_real
         shape = xyz.shape[0]
-        count_3d = np.ones((shape, shape, shape))
+        count_3d = np.ones((shape, n_pix, n_pix))
         return inserted_slice_3d, count_3d
 
     def compute_fsc(self, map_3d_f_1):
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 563f3ab..f5fef31 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -1,5 +1,3 @@
-from cmath import exp
-
 import numpy as np
 import pytest
 
@@ -9,7 +7,7 @@
 @pytest.fixture
 def test_ir():
     """Instantiate IterativeRefinement class for testing."""
-    ir = em.IterativeRefinement(np.ndarray(), list(), dict())
+    ir = em.IterativeRefinement(np.ndarray(), list(), dict(), 7)
     return ir
 
 
@@ -54,7 +52,7 @@ def test_generate_xy_plane():
 def test_generate_slices():
     """Test generation of slices."""
     map_3d = np.ones(2, 2, 2)
-    rots = test_grid_SO3_uniform(2)
+    rots = test_ir.grid_SO3_uniform(2)
     xy_plane = test_ir.generate_xy_plane(2)
 
     slices, xyz_rotated = test_ir.generate_slices(map_3d, rots)
@@ -91,7 +89,9 @@ def test_apply_wiener_filter():
     ctf = np.zeros(2, 2)
     small_number = 0.01
 
-    projection_wfilter_f = test_ir.apply_wiener_filter(projection, ctf, small_number)
+    projection_wfilter_f = test_ir.apply_wiener_filter(projection,
+                                                       ctf,
+                                                       small_number)
     assert projection_wfilter_f.shape == (2, 2)
 
 

From d5ea49741d1dcfa1dcd40f0d897e9a54a21bbd51 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 03:17:50 +0000
Subject: [PATCH 020/148] Format code with black and isort

---
 iterative_refinement/expectation_maximization.py | 4 ++--
 tests/test_expectation_maximization.py           | 4 +---
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index a14574a..331486a 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -67,7 +67,7 @@ def split_array(self, arr):
         arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
 
         if arr_1.shape[0] != arr_2.shape[0]:
-            arr_2 = arr[idx_half:2 * idx_half]
+            arr_2 = arr[idx_half : 2 * idx_half]
 
         return arr_1, arr_2
 
@@ -182,7 +182,7 @@ def apply_ctf_to_slice(self, particle_slice, ctf):
             Shape (n_pix,n_pix)
         """
         # vectorize and have shape match
-        projection_f_conv_ctf = ctf * particle_slice 
+        projection_f_conv_ctf = ctf * particle_slice
         return projection_f_conv_ctf
 
     def compute_bayesian_weights(self, particle, slices):
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index f5fef31..5314ca6 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -89,9 +89,7 @@ def test_apply_wiener_filter():
     ctf = np.zeros(2, 2)
     small_number = 0.01
 
-    projection_wfilter_f = test_ir.apply_wiener_filter(projection,
-                                                       ctf,
-                                                       small_number)
+    projection_wfilter_f = test_ir.apply_wiener_filter(projection, ctf, small_number)
     assert projection_wfilter_f.shape == (2, 2)
 
 

From 1a797729cd11aae073c8b8bcb1997fab76d8332e Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 20:23:42 -0700
Subject: [PATCH 021/148] literals removed

---
 tests/test_expectation_maximization.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index f5fef31..2d8cc13 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -7,7 +7,10 @@
 @pytest.fixture
 def test_ir():
     """Instantiate IterativeRefinement class for testing."""
-    ir = em.IterativeRefinement(np.ndarray(), list(), dict(), 7)
+    my_list = []
+    my_dict = {}
+    itr = 7
+    ir = em.IterativeRefinement(my_list, my_dict, itr)
     return ir
 
 

From 38a9a5ea907507577c3ee091e2b01fb90098aeab Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 20:26:50 -0700
Subject: [PATCH 022/148] add pre commit

---
 .pre-commit-config.yaml | 42 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 .pre-commit-config.yaml

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..e0b31c6
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,42 @@
+default_language_version :
+  python : python3
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.1.0
+    hooks:
+      - id: check-byte-order-marker
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-yaml
+      - id: mixed-line-ending
+        args:
+          - --fix=no
+      - id: no-commit-to-branch
+        args:
+          - --branch=master
+      - id: check-added-large-files
+        args:
+          - --maxkb=2048
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 21.8b0
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/isort
+    rev: 5.9.3
+    hooks:
+      - id : isort
+        args : ["--profile", "black", "--filter-files"]
+  - repo: https://github.com/asottile/blacken-docs
+    rev: v1.8.0
+    hooks:
+    -   id: blacken-docs
+        additional_dependencies: [black==20.8b0]
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.7.9
+    hooks:
+    - id: flake8
+      additional_dependencies:
+        - flake8-docstrings
+        - flake8-import-order
+      exclude: reconstructSPI/__init__.py,tests/__init__.py
\ No newline at end of file

From 7a4de6f4c4d2b08119a37b9f064b7b107a81a99c Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 22:28:03 -0700
Subject: [PATCH 023/148] Init tests

---
 tests/__init__.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 tests/__init__.py

diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000..e69de29

From df6c749be239c37778396f9743b0014a62e51d19 Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 22:37:51 -0700
Subject: [PATCH 024/148] temporary static methods

---
 iterative_refinement/expectation_maximization.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 331486a..50d8aed 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -3,6 +3,7 @@
 for reconstruction of particles.
 """
 
+from os import stat
 import numpy as np
 from simSPI.transfer import eval_ctf
 
@@ -47,6 +48,7 @@ def __init__(self, map_3d_init, particles, ctf_info, max_itr=7):
         self.ctf_info = ctf_info
         self.max_itr = max_itr
 
+    @staticmethod
     def split_array(self, arr):
         """
         Split array into two halves along 0th axis.
@@ -71,6 +73,7 @@ def split_array(self, arr):
 
         return arr_1, arr_2
 
+    @staticmethod
     def build_ctf_array(self):
         """
         Build 2D array of evaluated CTFs from inputted
@@ -89,6 +92,7 @@ def build_ctf_array(self):
 
         return ctfs
 
+    @staticmethod
     def grid_SO3_uniform(self, n_rotations):
         """
         Generate a discrete set of uniformly distributed rotations
@@ -108,6 +112,7 @@ def grid_SO3_uniform(self, n_rotations):
         rots = np.ones((n_rotations, 3, 3))
         return rots
 
+    @staticmethod
     def generate_xy_plane(self, n_pix):
         """
         Generate xy plane.
@@ -128,6 +133,7 @@ def generate_xy_plane(self, n_pix):
         xy_plane = np.ones((n_pix**2, 3))
         return xy_plane
 
+    @staticmethod
     def generate_slices(self, map_3d_f, xy_plane, n_pix, rots):
         """
         Generates slice coordinates by rotating xy plane.
@@ -169,6 +175,7 @@ def generate_slices(self, map_3d_f, xy_plane, n_pix, rots):
         slices.reshape(n_rotations, n_pix, n_pix)
         return slices, xyz_rotated
 
+    @staticmethod
     def apply_ctf_to_slice(self, particle_slice, ctf):
         """
         Apply CTF to projected slice by convolution.
@@ -185,6 +192,7 @@ def apply_ctf_to_slice(self, particle_slice, ctf):
         projection_f_conv_ctf = ctf * particle_slice
         return projection_f_conv_ctf
 
+    @staticmethod
     def compute_bayesian_weights(self, particle, slices):
         """
         Compute Bayesian weights of particle to slice
@@ -208,6 +216,7 @@ def compute_bayesian_weights(self, particle, slices):
         bayes_factors = np.random.normal(n_slices)
         return bayes_factors
 
+    @staticmethod
     def apply_wiener_filter(self, projection, ctf, small_number):
         """
         Apply Wiener filter to particle projection.
@@ -230,6 +239,7 @@ def apply_wiener_filter(self, projection, ctf, small_number):
         projection_wfilter_f = projection * wfilter
         return projection_wfilter_f
 
+    @staticmethod
     def insert_slice(self, slice_real, xyz, n_pix):
         """
         Rotate slice and interpolate onto a 3D grid to prepare
@@ -259,6 +269,7 @@ def insert_slice(self, slice_real, xyz, n_pix):
         count_3d = np.ones((shape, n_pix, n_pix))
         return inserted_slice_3d, count_3d
 
+    @staticmethod
     def compute_fsc(self, map_3d_f_1):
         """
         Compute Fourier shell correlation.
@@ -283,6 +294,7 @@ def compute_fsc(self, map_3d_f_1):
         fsc_1d_1 = np.ones(n_pix_1 // 2)
         return fsc_1d_1
 
+    @staticmethod
     def expand_1d_to_3d(self, arr_1d):
         """
         Expand 1D array data into spherical shell.

From 6849b0c9e6ff6d07c94ecf9e5e6ba18ed62dcea7 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 05:38:02 +0000
Subject: [PATCH 025/148] Format code with black and isort

---
 iterative_refinement/expectation_maximization.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 50d8aed..95495a6 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -4,6 +4,7 @@
 """
 
 from os import stat
+
 import numpy as np
 from simSPI.transfer import eval_ctf
 

From 4e927ab8230890f46ae141309a113339dafa619c Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 23:08:09 -0700
Subject: [PATCH 026/148] temporary static methods

---
 .../expectation_maximization.py               | 22 +++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 50d8aed..a3f59c1 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -42,14 +42,14 @@ class IterativeRefinement:
         Shape (n_pix // 2,)
     """
 
-    def __init__(self, map_3d_init, particles, ctf_info, max_itr=7):
+    def __init__(map_3d_init, particles, ctf_info, max_itr=7):
         self.map_3d_init = map_3d_init
         self.particles = particles
         self.ctf_info = ctf_info
         self.max_itr = max_itr
 
     @staticmethod
-    def split_array(self, arr):
+    def split_array(arr):
         """
         Split array into two halves along 0th axis.
 
@@ -93,7 +93,7 @@ def build_ctf_array(self):
         return ctfs
 
     @staticmethod
-    def grid_SO3_uniform(self, n_rotations):
+    def grid_SO3_uniform(n_rotations):
         """
         Generate a discrete set of uniformly distributed rotations
         across SO(3).
@@ -113,7 +113,7 @@ def grid_SO3_uniform(self, n_rotations):
         return rots
 
     @staticmethod
-    def generate_xy_plane(self, n_pix):
+    def generate_xy_plane(n_pix):
         """
         Generate xy plane.
 
@@ -134,7 +134,7 @@ def generate_xy_plane(self, n_pix):
         return xy_plane
 
     @staticmethod
-    def generate_slices(self, map_3d_f, xy_plane, n_pix, rots):
+    def generate_slices(map_3d_f, xy_plane, n_pix, rots):
         """
         Generates slice coordinates by rotating xy plane.
         Interpolate values from map_3d_f onto 3D coordinates.
@@ -176,7 +176,7 @@ def generate_slices(self, map_3d_f, xy_plane, n_pix, rots):
         return slices, xyz_rotated
 
     @staticmethod
-    def apply_ctf_to_slice(self, particle_slice, ctf):
+    def apply_ctf_to_slice(particle_slice, ctf):
         """
         Apply CTF to projected slice by convolution.
 
@@ -193,7 +193,7 @@ def apply_ctf_to_slice(self, particle_slice, ctf):
         return projection_f_conv_ctf
 
     @staticmethod
-    def compute_bayesian_weights(self, particle, slices):
+    def compute_bayesian_weights(particle, slices):
         """
         Compute Bayesian weights of particle to slice
         under Gaussian white noise model.
@@ -217,7 +217,7 @@ def compute_bayesian_weights(self, particle, slices):
         return bayes_factors
 
     @staticmethod
-    def apply_wiener_filter(self, projection, ctf, small_number):
+    def apply_wiener_filter(projection, ctf, small_number):
         """
         Apply Wiener filter to particle projection.
 
@@ -240,7 +240,7 @@ def apply_wiener_filter(self, projection, ctf, small_number):
         return projection_wfilter_f
 
     @staticmethod
-    def insert_slice(self, slice_real, xyz, n_pix):
+    def insert_slice(slice_real, xyz, n_pix):
         """
         Rotate slice and interpolate onto a 3D grid to prepare
         for insertion.
@@ -270,7 +270,7 @@ def insert_slice(self, slice_real, xyz, n_pix):
         return inserted_slice_3d, count_3d
 
     @staticmethod
-    def compute_fsc(self, map_3d_f_1):
+    def compute_fsc(map_3d_f_1):
         """
         Compute Fourier shell correlation.
         Estimate noise from half maps.
@@ -295,7 +295,7 @@ def compute_fsc(self, map_3d_f_1):
         return fsc_1d_1
 
     @staticmethod
-    def expand_1d_to_3d(self, arr_1d):
+    def expand_1d_to_3d(arr_1d):
         """
         Expand 1D array data into spherical shell.
 

From ea2c766c06e1900b39ee754fcdefc7f39fa98c2f Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 23:16:53 -0700
Subject: [PATCH 027/148] ds changes

---
 iterative_refinement/expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index ef5476c..a743bdd 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -75,7 +75,7 @@ def split_array(arr):
     def build_ctf_array(self):
         """
         Build 2D array of evaluated CTFs from inputted
-        CTF parameters for each particle.
+        CTF parameters for a particle.
 
         Returns
         -------

From 714b33d577cabba7f238ba2f9c8a129a28321876 Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 23:19:00 -0700
Subject: [PATCH 028/148] changed deepsource

---
 .deepsource.toml | 21 +++++----------------
 1 file changed, 5 insertions(+), 16 deletions(-)

diff --git a/.deepsource.toml b/.deepsource.toml
index 93a9d6f..6c238bf 100644
--- a/.deepsource.toml
+++ b/.deepsource.toml
@@ -1,24 +1,13 @@
 version = 1
 
-test_patterns = ["test/**"]
+test_patterns = ["tests/**"]
 
-exclude_patterns = ["README.md"]
-
-[[analyzers]]
-name = "python"
-enabled = true
-
-  [analyzers.meta]
-  runtime_version = "3.x.x"
+exclude_patterns = ["[\"README.md\"]"]
 
 [[analyzers]]
 name = "test-coverage"
 enabled = true
 
-[[transformers]]
-name = "isort"
-enabled = true
-
-[[transformers]]
-name = "black"
-enabled = true
+[[analyzers]]
+name = "python"
+enabled = true
\ No newline at end of file

From 5b4db6ed8ea68c1953637535e8eae7fbe0f43934 Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 23:20:25 -0700
Subject: [PATCH 029/148] lint

---
 iterative_refinement/expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index a743bdd..851dbc4 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -68,7 +68,7 @@ def split_array(arr):
         arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
 
         if arr_1.shape[0] != arr_2.shape[0]:
-            arr_2 = arr[idx_half : 2 * idx_half]
+            arr_2 = arr[idx_half:2 * idx_half]
 
         return arr_1, arr_2
 

From ccd0d04e42a96d37ea3e0211e021924e27fa898b Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 23:21:22 -0700
Subject: [PATCH 030/148] add black back

---
 .deepsource.toml | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/.deepsource.toml b/.deepsource.toml
index 6c238bf..0e75684 100644
--- a/.deepsource.toml
+++ b/.deepsource.toml
@@ -1,13 +1,21 @@
 version = 1
 
-test_patterns = ["tests/**"]
+test_patterns = ["test/**"]
 
-exclude_patterns = ["[\"README.md\"]"]
+exclude_patterns = ["README.md"]
 
 [[analyzers]]
-name = "test-coverage"
+name = "python"
 enabled = true
 
+  [analyzers.meta]
+  runtime_version = "3.x.x"
+
 [[analyzers]]
-name = "python"
-enabled = true
\ No newline at end of file
+name = "test-coverage"
+enabled = true
+
+[[transformers]]
+name = "black"
+enabled = true
+

From c8f3c60355d7190ae24db10f69bd027c8f42e890 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 06:21:32 +0000
Subject: [PATCH 031/148] Format code with black

---
 iterative_refinement/expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 851dbc4..a743bdd 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -68,7 +68,7 @@ def split_array(arr):
         arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
 
         if arr_1.shape[0] != arr_2.shape[0]:
-            arr_2 = arr[idx_half:2 * idx_half]
+            arr_2 = arr[idx_half : 2 * idx_half]
 
         return arr_1, arr_2
 

From c2726b2edd3d66c45d7a404331cac168b7759d02 Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 23:25:21 -0700
Subject: [PATCH 032/148] update toml

---
 .deepsource.toml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.deepsource.toml b/.deepsource.toml
index 0e75684..b4f754a 100644
--- a/.deepsource.toml
+++ b/.deepsource.toml
@@ -1,6 +1,6 @@
 version = 1
 
-test_patterns = ["test/**"]
+test_patterns = ["tests/**"]
 
 exclude_patterns = ["README.md"]
 
@@ -8,9 +8,6 @@ exclude_patterns = ["README.md"]
 name = "python"
 enabled = true
 
-  [analyzers.meta]
-  runtime_version = "3.x.x"
-
 [[analyzers]]
 name = "test-coverage"
 enabled = true

From 7f962739ee5ee9d32e9e26689cadeab11492996d Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 23:28:28 -0700
Subject: [PATCH 033/148] ds

---
 iterative_refinement/expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index a743bdd..ef5476c 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -75,7 +75,7 @@ def split_array(arr):
     def build_ctf_array(self):
         """
         Build 2D array of evaluated CTFs from inputted
-        CTF parameters for a particle.
+        CTF parameters for each particle.
 
         Returns
         -------

From 3d4ad77b13f829c260c05b4e813d0b5c97d1af85 Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 23:38:35 -0700
Subject: [PATCH 034/148] added .ini for pytest

---
 pytest.ini | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 pytest.ini

diff --git a/pytest.ini b/pytest.ini
new file mode 100644
index 0000000..cf93d60
--- /dev/null
+++ b/pytest.ini
@@ -0,0 +1,4 @@
+[pytest]
+testpaths = tests
+python_files = *.py
+python_functions = test_*
\ No newline at end of file

From b2931812134b249a4b5856285e7d3734dfaf0bd8 Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 23:40:02 -0700
Subject: [PATCH 035/148] init

---
 iterative_refinement/__init__.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 iterative_refinement/__init__.py

diff --git a/iterative_refinement/__init__.py b/iterative_refinement/__init__.py
new file mode 100644
index 0000000..e69de29

From 02eec0a59890cb5e0c5b8d0d9020b3cc08b2c6d9 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 23 Mar 2022 23:46:41 -0700
Subject: [PATCH 036/148] Codecov files

---
 .codecov.yml | 24 ++++++++++++++++++++++++
 .coveragerc  |  3 +++
 .flake8      |  6 ++++++
 3 files changed, 33 insertions(+)
 create mode 100644 .codecov.yml
 create mode 100644 .coveragerc
 create mode 100644 .flake8

diff --git a/.codecov.yml b/.codecov.yml
new file mode 100644
index 0000000..c576999
--- /dev/null
+++ b/.codecov.yml
@@ -0,0 +1,24 @@
+coverage:
+  round: up
+  precision: 2
+  status:
+    patch:
+      default:
+        # basic
+        target: 90%
+        threshold: 2%
+        base: auto
+        flags:
+          - unit
+        # advanced
+        branches:
+          - master
+        if_no_uploads: error
+        if_not_found: error
+        if_ci_failed: error
+        only_pulls: false
+
+# Files to ignore
+ignore:
+  - "data"
+  - "notebooks"
diff --git a/.coveragerc b/.coveragerc
new file mode 100644
index 0000000..94a9d5a
--- /dev/null
+++ b/.coveragerc
@@ -0,0 +1,3 @@
+[report]
+fail_under = 90
+show_missing = True
diff --git a/.flake8 b/.flake8
new file mode 100644
index 0000000..88932be
--- /dev/null
+++ b/.flake8
@@ -0,0 +1,6 @@
+[flake8]
+docstring-convention = numpy
+import_order_style = smarkets
+max-line-length = 88
+extend-ignore = E203,I202,I100
+exclude = ioSPI/__init__.py,tests/__init__.py,tests/test_iotools/__init__.py

From 49138c707beebe07cec29088865d5a0b772f7b1f Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 23 Mar 2022 23:49:25 -0700
Subject: [PATCH 037/148] Linting files

---
 .github/workflows/lint.yml | 54 +++++++++++++++++++++++++++++++++
 .github/workflows/test.yml | 62 ++++++++++++++++++++++++++++++++++++++
 2 files changed, 116 insertions(+)
 create mode 100644 .github/workflows/lint.yml
 create mode 100644 .github/workflows/test.yml

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
new file mode 100644
index 0000000..d78382a
--- /dev/null
+++ b/.github/workflows/lint.yml
@@ -0,0 +1,54 @@
+name: "Lint"
+
+on:
+  push:
+    branches: [master,github-actions-test]
+    paths-ignore:
+    - 'README.md'
+    - '.deepsource.toml'
+    - '.gitignore'
+    - 'setup.py'
+
+
+  pull_request:
+    branches: [master]
+    paths-ignore:
+    - 'README.md'
+    - '.deepsource.toml'
+    - '.gitignore'
+    - 'setup.py'
+
+
+jobs:
+  build:
+
+    runs-on: ${{matrix.os}}
+    strategy:
+      matrix:
+        os: [ubuntu-18.04]
+        python-version: [3.9]
+        test-folder : ['tests']
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Build using Python ${{matrix.python-version}}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{matrix.python-version}}
+      - name: install dependencies [pip]
+        run:  |
+          pip install --upgrade pip setuptools wheel
+          for req in dev-requirements.txt; do
+            pip install -q -r $req
+          done
+          pip install -e .
+      - name: linting [black and isort]
+        run: |
+          black . --check
+          isort --profile black --check .
+      - name: linting [flake8]
+        run: |
+          flake8 ioSPI tests
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 0000000..d957659
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,62 @@
+name: "Test"
+
+on:
+  push:
+    branches: [master,github-actions-test]
+    paths-ignore:
+    - 'README.md'
+    - '.deepsource.toml'
+    - '.gitignore'
+    - 'setup.py'
+
+
+  pull_request:
+    branches: [master]
+    paths-ignore:
+    - 'README.md'
+    - '.deepsource.toml'
+    - '.gitignore'
+    - 'setup.py'
+
+
+jobs:
+  build:
+
+    runs-on: ${{matrix.os}}
+    strategy:
+      matrix:
+        os: [ubuntu-18.04]
+        python-version: [3.7,3.8,3.9]
+        test-folder : ['tests']
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Build using Python ${{matrix.python-version}}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{matrix.python-version}}
+
+      - name: cache conda
+        uses: actions/cache@v1
+        with:
+          path: $CONDA
+          key: ${{ runner.os }}-conda-${{ hashFiles('environment.yml') }}
+          restore-keys: |
+            ${{ runner.os }}-conda-
+      - name: install dependencies [conda]
+        run:  |
+          # $CONDA is an environment variable pointing to the root of the miniconda directory
+          $CONDA/bin/conda env update --file environment.yml --name base
+          $CONDA/bin/pip install -e .
+      - name: unit testing [pytest]
+        env:
+          TEST_TOKEN: ${{ secrets.TEST_TOKEN }}
+        run: |
+          $CONDA/bin/pytest --cov-report term --cov-report xml:coverage.xml --cov=ioSPI ${{matrix.test-folder}}
+      - name: uploading code coverage [codecov]
+        if: ${{matrix.python-version == 3.7}}
+        run: |
+          bash <(curl -s https://codecov.io/bash) -c

From 6135c7257d0a5790231abe8bb0e8ec94db86051f Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 23 Mar 2022 23:50:59 -0700
Subject: [PATCH 038/148] Dev requirements

---
 dev-requirements.txt | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 dev-requirements.txt

diff --git a/dev-requirements.txt b/dev-requirements.txt
new file mode 100644
index 0000000..663cad4
--- /dev/null
+++ b/dev-requirements.txt
@@ -0,0 +1,5 @@
+black
+flake8
+flake8-docstrings
+isort
+pre-commit

From f54ece8a2a366923c1078e2e085cf02e407f7a83 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 23 Mar 2022 23:53:39 -0700
Subject: [PATCH 039/148] Environment config

---
 environment.yml | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 environment.yml

diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..01e8d5c
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,18 @@
+name: reconstructSPI
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - codecov
+  - coverage
+  - gemmi
+  - numba
+  - numpy
+  - pillow>=8.2.0
+  - pip
+  - pytest
+  - pytest-cov
+  - pytorch
+  - pip :
+      - git+https://github.com/compSPI/simSPI.git
+

From b9b540e576178cf92f18a3c7167b03e2dfda1905 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 23 Mar 2022 23:56:29 -0700
Subject: [PATCH 040/148] Added setup.py

---
 setup.py | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 setup.py

diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..9631ff3
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,23 @@
+"""Create instructions to build the reconstructSPI package."""
+
+import setuptools
+
+requirements = []
+
+setuptools.setup(
+    name="reconstructSPI",
+    maintainer="Frederic Poitevin",
+    version="0.0.1",
+    maintainer_email="frederic.poitevin@stanford.edu",
+    description="Reconstruction methods and tools for SPI",
+    long_description=open("README.md", encoding="utf8").read(),
+    long_description_content_type="text/markdown",
+    url="https://github.com/compSPI/reconstructSPI.git",
+    packages=setuptools.find_packages(),
+    install_requires=requirements,
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "Operating System :: OS Independent",
+    ],
+    zip_safe=False,
+)

From afd729079916630db2fab8bce0bc1d9b2d87fc70 Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Wed, 23 Mar 2022 23:57:46 -0700
Subject: [PATCH 041/148] env yaml

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 01e8d5c..9908d0c 100644
--- a/environment.yml
+++ b/environment.yml
@@ -14,5 +14,5 @@ dependencies:
   - pytest-cov
   - pytorch
   - pip :
-      - git+https://github.com/compSPI/simSPI.git
+      - git+https://github.com/compSPI/reconstructSPI.git
 

From 5a4a56e75d1cb3341a619f8911635101d81ca7af Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 00:19:41 -0700
Subject: [PATCH 042/148] Reformatted docstrings

---
 .../expectation_maximization.py               | 56 +++++++------------
 1 file changed, 21 insertions(+), 35 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index ef5476c..4723f99 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -1,16 +1,11 @@
-"""
-Iterative refinement in Bayesian expection maximization setting
-for reconstruction of particles.
-"""
+"""Iterative refinement with Bayesian expection maximization."""
 
 import numpy as np
 from simSPI.transfer import eval_ctf
 
 
 class IterativeRefinement:
-    """
-    Serves as a base class to perform iterative refinement
-    reconstruction with respect to maximum likelihood esimation.
+    """Perform iterative refinement with max likelihood esimation.
 
     Parameters
     ----------
@@ -49,8 +44,7 @@ def __init__(self, map_3d_init, particles, ctf_info, max_itr=7):
 
     @staticmethod
     def split_array(arr):
-        """
-        Split array into two halves along 0th axis.
+        """Split array into two halves along 0th axis.
 
         Parameters
         ----------
@@ -73,9 +67,9 @@ def split_array(arr):
         return arr_1, arr_2
 
     def build_ctf_array(self):
-        """
-        Build 2D array of evaluated CTFs from inputted
-        CTF parameters for each particle.
+        """Build 2D array of evaluated CTFs.
+		
+		Use inputted CTF parameters, act for each particle.
 
         Returns
         -------
@@ -92,9 +86,7 @@ def build_ctf_array(self):
 
     @staticmethod
     def grid_SO3_uniform(n_rotations):
-        """
-        Generate a discrete set of uniformly distributed rotations
-        across SO(3).
+        """Generate uniformly distributed rotations in SO(3).
 
         Parameters
         ----------
@@ -112,8 +104,7 @@ def grid_SO3_uniform(n_rotations):
 
     @staticmethod
     def generate_xy_plane(n_pix):
-        """
-        Generate xy plane.
+        """Generate xy plane.
 
         Parameters
         ----------
@@ -133,9 +124,9 @@ def generate_xy_plane(n_pix):
 
     @staticmethod
     def generate_slices(map_3d_f, xy_plane, n_pix, rots):
-        """
-        Generates slice coordinates by rotating xy plane.
-        Interpolate values from map_3d_f onto 3D coordinates.
+        """Generate slice coordinates by rotating xy plane.
+        
+		Interpolate values from map_3d_f onto 3D coordinates.
 
         See how scipy map_values used to interpolate in
         https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L111
@@ -175,8 +166,7 @@ def generate_slices(map_3d_f, xy_plane, n_pix, rots):
 
     @staticmethod
     def apply_ctf_to_slice(particle_slice, ctf):
-        """
-        Apply CTF to projected slice by convolution.
+        """Apply CTF to projected slice by convolution.
 
         particle_slice : arr
             Slice of map_3d_f. Corresponds to Fourier transform
@@ -192,9 +182,9 @@ def apply_ctf_to_slice(particle_slice, ctf):
 
     @staticmethod
     def compute_bayesian_weights(particle, slices):
-        """
-        Compute Bayesian weights of particle to slice
-        under Gaussian white noise model.
+        """Compute Bayesian weights of particle to slice.
+        
+		Use Gaussian white noise model.
 
         Parameters
         ----------
@@ -216,8 +206,7 @@ def compute_bayesian_weights(particle, slices):
 
     @staticmethod
     def apply_wiener_filter(projection, ctf, small_number):
-        """
-        Apply Wiener filter to particle projection.
+        """Apply Wiener filter to particle projection.
 
         Parameters
         ----------
@@ -239,9 +228,7 @@ def apply_wiener_filter(projection, ctf, small_number):
 
     @staticmethod
     def insert_slice(slice_real, xyz, n_pix):
-        """
-        Rotate slice and interpolate onto a 3D grid to prepare
-        for insertion.
+        """Rotate slice and interpolate onto a 3D grid.
 
         Parameters
         ----------
@@ -269,9 +256,9 @@ def insert_slice(slice_real, xyz, n_pix):
 
     @staticmethod
     def compute_fsc(map_3d_f_1):
-        """
-        Compute Fourier shell correlation.
-        Estimate noise from half maps.
+        """Compute Fourier shell correlation. 
+		
+		Estimate noise from half maps.
 
         Parameters
         ----------
@@ -294,8 +281,7 @@ def compute_fsc(map_3d_f_1):
 
     @staticmethod
     def expand_1d_to_3d(arr_1d):
-        """
-        Expand 1D array data into spherical shell.
+        """Expand 1D array data into spherical shell.
 
         Parameters
         ----------

From e504e32b1d848f066af1545c2872344d73276a1b Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 07:19:48 +0000
Subject: [PATCH 043/148] Format code with black

---
 .../expectation_maximization.py                | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 4723f99..78d2676 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -68,8 +68,8 @@ def split_array(arr):
 
     def build_ctf_array(self):
         """Build 2D array of evaluated CTFs.
-		
-		Use inputted CTF parameters, act for each particle.
+
+                Use inputted CTF parameters, act for each particle.
 
         Returns
         -------
@@ -125,8 +125,8 @@ def generate_xy_plane(n_pix):
     @staticmethod
     def generate_slices(map_3d_f, xy_plane, n_pix, rots):
         """Generate slice coordinates by rotating xy plane.
-        
-		Interpolate values from map_3d_f onto 3D coordinates.
+
+                Interpolate values from map_3d_f onto 3D coordinates.
 
         See how scipy map_values used to interpolate in
         https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L111
@@ -183,8 +183,8 @@ def apply_ctf_to_slice(particle_slice, ctf):
     @staticmethod
     def compute_bayesian_weights(particle, slices):
         """Compute Bayesian weights of particle to slice.
-        
-		Use Gaussian white noise model.
+
+                Use Gaussian white noise model.
 
         Parameters
         ----------
@@ -256,9 +256,9 @@ def insert_slice(slice_real, xyz, n_pix):
 
     @staticmethod
     def compute_fsc(map_3d_f_1):
-        """Compute Fourier shell correlation. 
-		
-		Estimate noise from half maps.
+        """Compute Fourier shell correlation.
+
+                Estimate noise from half maps.
 
         Parameters
         ----------

From a282ffc0ffecc68b2391e29c0ded0dcb35b88c16 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 00:23:01 -0700
Subject: [PATCH 044/148] Testing workspace changes

---
 .flake8                    | 2 +-
 .github/workflows/lint.yml | 2 +-
 .github/workflows/test.yml | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.flake8 b/.flake8
index 88932be..cbc6363 100644
--- a/.flake8
+++ b/.flake8
@@ -3,4 +3,4 @@ docstring-convention = numpy
 import_order_style = smarkets
 max-line-length = 88
 extend-ignore = E203,I202,I100
-exclude = ioSPI/__init__.py,tests/__init__.py,tests/test_iotools/__init__.py
+exclude = reconstructSPI/__init__.py,tests/__init__.py
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index d78382a..cfc5574 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -51,4 +51,4 @@ jobs:
           isort --profile black --check .
       - name: linting [flake8]
         run: |
-          flake8 ioSPI tests
+          flake8 reconstructSPI tests
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index d957659..49cc26f 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -55,7 +55,7 @@ jobs:
         env:
           TEST_TOKEN: ${{ secrets.TEST_TOKEN }}
         run: |
-          $CONDA/bin/pytest --cov-report term --cov-report xml:coverage.xml --cov=ioSPI ${{matrix.test-folder}}
+          $CONDA/bin/pytest --cov-report term --cov-report xml:coverage.xml --cov=reconstructSPI ${{matrix.test-folder}}
       - name: uploading code coverage [codecov]
         if: ${{matrix.python-version == 3.7}}
         run: |

From 1a0af09af3d0117ab1cc7e3af3935d8a43bcfc40 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 00:26:45 -0700
Subject: [PATCH 045/148] Fixed test docstrings

---
 tests/test_expectation_maximization.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index bfe9703..2b5f328 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -1,3 +1,5 @@
+"""Test bayesian expectation maximization process."""
+
 import numpy as np
 import pytest
 
@@ -75,9 +77,9 @@ def test_apply_ctf_to_slice():
 
 
 def test_compute_bayesian_weights():
-    """
-    Test computation of bayesian weights under
-    Gaussian white noise model.
+    """Test computation of bayesian weights.
+    
+	For use under Gaussian white noise model.
     """
     particle = np.ones(1, 2, 2)
     slices = np.ones(2, 2, 2)

From 3d1be9b4c5b976075c55cb2091ee0bc7e6aaa694 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 07:26:50 +0000
Subject: [PATCH 046/148] Format code with black

---
 tests/test_expectation_maximization.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 2b5f328..16b6612 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -78,8 +78,8 @@ def test_apply_ctf_to_slice():
 
 def test_compute_bayesian_weights():
     """Test computation of bayesian weights.
-    
-	For use under Gaussian white noise model.
+
+    For use under Gaussian white noise model.
     """
     particle = np.ones(1, 2, 2)
     slices = np.ones(2, 2, 2)

From 5268b738e5052d360fec112f59eeba805a381d36 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 00:27:54 -0700
Subject: [PATCH 047/148] Edited module name

---
 .github/workflows/lint.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index cfc5574..9240dcc 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -51,4 +51,4 @@ jobs:
           isort --profile black --check .
       - name: linting [flake8]
         run: |
-          flake8 reconstructSPI tests
+          flake8 iterative_refinement tests

From 984af8ada2e2dec2dfe5d068c24a168e2123e3d7 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 00:29:52 -0700
Subject: [PATCH 048/148] Linting fixes

---
 iterative_refinement/__init__.py                 | 1 +
 iterative_refinement/expectation_maximization.py | 1 +
 2 files changed, 2 insertions(+)

diff --git a/iterative_refinement/__init__.py b/iterative_refinement/__init__.py
index e69de29..9143076 100644
--- a/iterative_refinement/__init__.py
+++ b/iterative_refinement/__init__.py
@@ -0,0 +1 @@
+"""Iterative refinement reconstruction methods."""
\ No newline at end of file
diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 78d2676..bbb0090 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -112,6 +112,7 @@ def generate_xy_plane(n_pix):
             Number of pixels along one edge of the plane.
 
         Returns
+		-------
         xy_plane : arr
             Array describing xy plane in space.
             Shape (n_pix**2, 3)

From eecb97e4329a55b8111a9f6feaf131cf058f706c Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 07:29:58 +0000
Subject: [PATCH 049/148] Format code with black

---
 iterative_refinement/__init__.py                 | 2 +-
 iterative_refinement/expectation_maximization.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/iterative_refinement/__init__.py b/iterative_refinement/__init__.py
index 9143076..5500bfe 100644
--- a/iterative_refinement/__init__.py
+++ b/iterative_refinement/__init__.py
@@ -1 +1 @@
-"""Iterative refinement reconstruction methods."""
\ No newline at end of file
+"""Iterative refinement reconstruction methods."""
diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index bbb0090..844a57c 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -112,7 +112,7 @@ def generate_xy_plane(n_pix):
             Number of pixels along one edge of the plane.
 
         Returns
-		-------
+                -------
         xy_plane : arr
             Array describing xy plane in space.
             Shape (n_pix**2, 3)

From f7f98b4f32d983e279714d7cac2b7974da2145a3 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 00:32:30 -0700
Subject: [PATCH 050/148] Linting fixes

---
 iterative_refinement/expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index bbb0090..48213f0 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -112,7 +112,7 @@ def generate_xy_plane(n_pix):
             Number of pixels along one edge of the plane.
 
         Returns
-		-------
+        -------
         xy_plane : arr
             Array describing xy plane in space.
             Shape (n_pix**2, 3)

From d2faa259b84f876fd719a0193bc7b1825ac41515 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 00:36:48 -0700
Subject: [PATCH 051/148] Fixed imports

---
 environment.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/environment.yml b/environment.yml
index 9908d0c..80d0457 100644
--- a/environment.yml
+++ b/environment.yml
@@ -13,6 +13,4 @@ dependencies:
   - pytest
   - pytest-cov
   - pytorch
-  - pip :
-      - git+https://github.com/compSPI/reconstructSPI.git
 

From a3eedd61f10c791385f1ff4ac50bbe669ef16f5f Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 00:40:51 -0700
Subject: [PATCH 052/148] Readded simSPI import

---
 environment.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/environment.yml b/environment.yml
index 80d0457..01e8d5c 100644
--- a/environment.yml
+++ b/environment.yml
@@ -13,4 +13,6 @@ dependencies:
   - pytest
   - pytest-cov
   - pytorch
+  - pip :
+      - git+https://github.com/compSPI/simSPI.git
 

From c898048f737c2c2c629b77e52415090fc33aa858 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 00:44:30 -0700
Subject: [PATCH 053/148] Fixed function reference

---
 tests/test_expectation_maximization.py | 28 +++++++++++++-------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 16b6612..bcbb95b 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -19,7 +19,7 @@ def test_ir():
 def test_split_array():
     """Test splitting of array in two halves."""
     arr = np.zeros(4)
-    arr1, arr2 = test_ir.split_array(arr)
+    arr1, arr2 = test_ir().split_array(arr)
     assert arr1.shape == (2,)
     assert arr2.shape == (2,)
 
@@ -38,29 +38,29 @@ def test_build_ctf_array():
         "lp": 0.1,
     }
     ctf_params = [ex_ctf, ex_ctf]
-    ctfs = test_ir.build_ctf_array(ctf_params)
+    ctfs = test_ir().build_ctf_array(ctf_params)
     assert ctfs.shape == (2, 2, 2)
 
 
 def test_grid_SO3_uniform():
     """Test generation of rotations across SO(3)."""
-    rots = test_ir.grid_SO3_uniform(2)
+    rots = test_ir().grid_SO3_uniform(2)
     assert rots.shape == (2, 3, 3)
 
 
 def test_generate_xy_plane():
     """Test generation of xy plane."""
-    xy_plane = test_ir.generate_xy_plane(2)
+    xy_plane = test_ir().generate_xy_plane(2)
     assert xy_plane.shape == (2, 2, 3)
 
 
 def test_generate_slices():
     """Test generation of slices."""
     map_3d = np.ones(2, 2, 2)
-    rots = test_ir.grid_SO3_uniform(2)
-    xy_plane = test_ir.generate_xy_plane(2)
+    rots = test_ir().grid_SO3_uniform(2)
+    xy_plane = test_ir().generate_xy_plane(2)
 
-    slices, xyz_rotated = test_ir.generate_slices(map_3d, rots)
+    slices, xyz_rotated = test_ir().generate_slices(map_3d, rots)
 
     assert xy_plane.shape == (4, 3)
     assert slices.shape == (2, 2, 2)
@@ -71,7 +71,7 @@ def test_apply_ctf_to_slice():
     """Test convolution of slice with CTF."""
     particle_slice = np.ones(2, 2)
     ctf = np.ones(2, 2)
-    convolved = test_ir.apply_ctf_to_slice(particle_slice, ctf)
+    convolved = test_ir().apply_ctf_to_slice(particle_slice, ctf)
 
     assert convolved.shape == (2, 2)
 
@@ -83,7 +83,7 @@ def test_compute_bayesian_weights():
     """
     particle = np.ones(1, 2, 2)
     slices = np.ones(2, 2, 2)
-    bayesian_weights = test_ir.compute_bayesian_weights(particle, slices)
+    bayesian_weights = test_ir().compute_bayesian_weights(particle, slices)
 
     assert bayesian_weights.shape == (2,)
 
@@ -94,7 +94,7 @@ def test_apply_wiener_filter():
     ctf = np.zeros(2, 2)
     small_number = 0.01
 
-    projection_wfilter_f = test_ir.apply_wiener_filter(projection, ctf, small_number)
+    projection_wfilter_f = test_ir().apply_wiener_filter(projection, ctf, small_number)
     assert projection_wfilter_f.shape == (2, 2)
 
 
@@ -102,9 +102,9 @@ def test_insert_slice():
     """Test insertion of slice."""
     n_pix = 2
     particle_slice = np.ones(n_pix, n_pix)
-    xyz = test_ir.generate_xy_plane(2, 2)
+    xyz = test_ir().generate_xy_plane(2, 2)
 
-    inserted, count = test_ir.insert_slice(particle_slice, xyz, n_pix)
+    inserted, count = test_ir().insert_slice(particle_slice, xyz, n_pix)
     assert inserted.shape == (2, 2, 2)
     assert count.shape == (2, 2, 2)
 
@@ -113,13 +113,13 @@ def test_compute_fsc():
     """Test computation of FSC."""
     map_1 = np.ones(2, 2, 2)
 
-    fsc_1 = test_ir.compute_fsc(map_1)
+    fsc_1 = test_ir().compute_fsc(map_1)
     assert fsc_1.shape == (1,)
 
 
 def test_expand_1d_to_3d():
     """Test expansion of 1D array into spherical shell."""
     arr1d = np.ones(1)
-    spherical = test_ir.expand_1d_to_3d(arr1d)
+    spherical = test_ir().expand_1d_to_3d(arr1d)
 
     assert spherical.shape == (2, 2, 2)

From 71356a5393ccef52d56a473712976af7fc8ed185 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 00:48:01 -0700
Subject: [PATCH 054/148] Fixed test_build_ctf_array

---
 tests/test_expectation_maximization.py | 16 ++--------------
 1 file changed, 2 insertions(+), 14 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index bcbb95b..44eaf69 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -26,20 +26,8 @@ def test_split_array():
 
 def test_build_ctf_array():
     """Test bulding of arbitrary CTF array."""
-    ex_ctf = {
-        "s": np.ones(2, 2),
-        "a ": np.ones(2, 2),
-        "def1": 1.0,
-        "def2": 1.0,
-        "angast": 0.1,
-        "kv": 0.1,
-        "cs": 0.1,
-        "bf": 0.1,
-        "lp": 0.1,
-    }
-    ctf_params = [ex_ctf, ex_ctf]
-    ctfs = test_ir().build_ctf_array(ctf_params)
-    assert ctfs.shape == (2, 2, 2)
+    ctfs = test_ir().build_ctf_array()
+    assert ctfs.shape == (0, 0, 0)
 
 
 def test_grid_SO3_uniform():

From 0522a91f250492198faaf76b87d0e28bb45da480 Mon Sep 17 00:00:00 2001
From: jed <jed324@gmail.com>
Date: Thu, 24 Mar 2022 01:02:41 -0700
Subject: [PATCH 055/148] tets

---
 .../expectation_maximization.py               |  6 +-
 tests/test_expectation_maximization.py        | 82 ++++++++++---------
 2 files changed, 47 insertions(+), 41 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 48213f0..2edec9a 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -115,12 +115,12 @@ def generate_xy_plane(n_pix):
         -------
         xy_plane : arr
             Array describing xy plane in space.
-            Shape (n_pix**2, 3)
+            Shape (n_pix, n_pix, 3)
         """
         # See how meshgrid and generate coordinates functions used
         # https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L96
 
-        xy_plane = np.ones((n_pix**2, 3))
+        xy_plane = np.ones((n_pix, n_pix, 3))
         return xy_plane
 
     @staticmethod
@@ -160,7 +160,7 @@ def generate_slices(map_3d_f, xy_plane, n_pix, rots):
         map_3d_f = np.ones_like(map_3d_f)
         xyz_rotated = np.ones_like(xy_plane)
 
-        size = n_rotations * n_pix**2
+        size = n_rotations * n_pix ** 2
         slices = np.random.normal(size=size)
         slices.reshape(n_rotations, n_pix, n_pix)
         return slices, xyz_rotated
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 44eaf69..dbf230c 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -16,98 +16,104 @@ def test_ir():
     return ir
 
 
-def test_split_array():
+@pytest.fixture
+def n_pix():
+    """Get sample n_pix value."""
+    return 128
+
+
+def test_split_array(test_ir, n_pix):
     """Test splitting of array in two halves."""
-    arr = np.zeros(4)
-    arr1, arr2 = test_ir().split_array(arr)
-    assert arr1.shape == (2,)
-    assert arr2.shape == (2,)
+    arr = np.zeros(n_pix)
+    arr1, arr2 = test_ir.split_array(arr)
+    assert arr1.shape == (n_pix / 2,)
+    assert arr2.shape == (n_pix / 2,)
 
 
-def test_build_ctf_array():
+def test_build_ctf_array(test_ir):
     """Test bulding of arbitrary CTF array."""
-    ctfs = test_ir().build_ctf_array()
+    ctfs = test_ir.build_ctf_array()
     assert ctfs.shape == (0, 0, 0)
 
 
-def test_grid_SO3_uniform():
+def test_grid_SO3_uniform(test_ir):
     """Test generation of rotations across SO(3)."""
-    rots = test_ir().grid_SO3_uniform(2)
+    rots = test_ir.grid_SO3_uniform(2)
     assert rots.shape == (2, 3, 3)
 
 
-def test_generate_xy_plane():
+def test_generate_xy_plane(test_ir, n_pix):
     """Test generation of xy plane."""
-    xy_plane = test_ir().generate_xy_plane(2)
-    assert xy_plane.shape == (2, 2, 3)
+    xy_plane = test_ir.generate_xy_plane(n_pix)
+    assert xy_plane.shape == (n_pix, n_pix, 3)
 
 
-def test_generate_slices():
+def test_generate_slices(test_ir):
     """Test generation of slices."""
-    map_3d = np.ones(2, 2, 2)
-    rots = test_ir().grid_SO3_uniform(2)
-    xy_plane = test_ir().generate_xy_plane(2)
+    map_3d = np.ones((2, 2, 2))
+    rots = test_ir.grid_SO3_uniform(2)
+    xy_plane = test_ir.generate_xy_plane(2)
 
-    slices, xyz_rotated = test_ir().generate_slices(map_3d, rots)
+    slices, xyz_rotated = test_ir.generate_slices(map_3d, rots)
 
     assert xy_plane.shape == (4, 3)
     assert slices.shape == (2, 2, 2)
     assert xyz_rotated.shape == (2, 2, 3)
 
 
-def test_apply_ctf_to_slice():
+def test_apply_ctf_to_slice(test_ir):
     """Test convolution of slice with CTF."""
-    particle_slice = np.ones(2, 2)
-    ctf = np.ones(2, 2)
-    convolved = test_ir().apply_ctf_to_slice(particle_slice, ctf)
+    particle_slice = np.ones((2, 2))
+    ctf = np.ones((2, 2))
+    convolved = test_ir.apply_ctf_to_slice(particle_slice, ctf)
 
     assert convolved.shape == (2, 2)
 
 
-def test_compute_bayesian_weights():
+def test_compute_bayesian_weights(test_ir):
     """Test computation of bayesian weights.
 
     For use under Gaussian white noise model.
     """
-    particle = np.ones(1, 2, 2)
-    slices = np.ones(2, 2, 2)
-    bayesian_weights = test_ir().compute_bayesian_weights(particle, slices)
+    particle = np.ones((1, 2, 2))
+    slices = np.ones((2, 2, 2))
+    bayesian_weights = test_ir.compute_bayesian_weights(particle, slices)
 
     assert bayesian_weights.shape == (2,)
 
 
-def test_apply_wiener_filter():
+def test_apply_wiener_filter(test_ir):
     """Test application of Wiener filter to particle projection."""
-    projection = np.ones(2, 2)
-    ctf = np.zeros(2, 2)
+    projection = np.ones((2, 2))
+    ctf = np.zeros((2, 2))
     small_number = 0.01
 
-    projection_wfilter_f = test_ir().apply_wiener_filter(projection, ctf, small_number)
+    projection_wfilter_f = test_ir.apply_wiener_filter(projection, ctf, small_number)
     assert projection_wfilter_f.shape == (2, 2)
 
 
-def test_insert_slice():
+def test_insert_slice(test_ir):
     """Test insertion of slice."""
     n_pix = 2
-    particle_slice = np.ones(n_pix, n_pix)
-    xyz = test_ir().generate_xy_plane(2, 2)
+    particle_slice = np.ones((n_pix, n_pix))
+    xyz = test_ir.generate_xy_plane(2)
 
-    inserted, count = test_ir().insert_slice(particle_slice, xyz, n_pix)
+    inserted, count = test_ir.insert_slice(particle_slice, xyz, n_pix)
     assert inserted.shape == (2, 2, 2)
     assert count.shape == (2, 2, 2)
 
 
-def test_compute_fsc():
+def test_compute_fsc(test_ir):
     """Test computation of FSC."""
-    map_1 = np.ones(2, 2, 2)
+    map_1 = np.ones((2, 2, 2))
 
-    fsc_1 = test_ir().compute_fsc(map_1)
+    fsc_1 = test_ir.compute_fsc(map_1)
     assert fsc_1.shape == (1,)
 
 
-def test_expand_1d_to_3d():
+def test_expand_1d_to_3d(test_ir):
     """Test expansion of 1D array into spherical shell."""
     arr1d = np.ones(1)
-    spherical = test_ir().expand_1d_to_3d(arr1d)
+    spherical = test_ir.expand_1d_to_3d(arr1d)
 
     assert spherical.shape == (2, 2, 2)

From ee0ef8f832d883e963cab87b959a05adb7f23935 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 08:02:54 +0000
Subject: [PATCH 056/148] Format code with black

---
 iterative_refinement/expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 2edec9a..244c79d 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -160,7 +160,7 @@ def generate_slices(map_3d_f, xy_plane, n_pix, rots):
         map_3d_f = np.ones_like(map_3d_f)
         xyz_rotated = np.ones_like(xy_plane)
 
-        size = n_rotations * n_pix ** 2
+        size = n_rotations * n_pix**2
         slices = np.random.normal(size=size)
         slices.reshape(n_rotations, n_pix, n_pix)
         return slices, xyz_rotated

From 7141f373d9fe4b00d609c69d0e5db3babb82c6e3 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 10:15:07 -0700
Subject: [PATCH 057/148] Reworked tests to use consistent array sizing

---
 tests/test_expectation_maximization.py | 59 +++++++++++++-------------
 1 file changed, 30 insertions(+), 29 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index dbf230c..2c1fe1f 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -9,17 +9,18 @@
 @pytest.fixture
 def test_ir():
     """Instantiate IterativeRefinement class for testing."""
-    my_list = []
-    my_dict = {}
+	map = np.zeros((n_pix, n_pix, n_pix))
+    particles = np.zeros((n_pix, n_pix, n_pix))
+	ctf_info = [{},] * n_pix
     itr = 7
-    ir = em.IterativeRefinement(my_list, my_dict, itr)
+    ir = em.IterativeRefinement(map, particles, ctf_info, itr)
     return ir
 
 
 @pytest.fixture
 def n_pix():
     """Get sample n_pix value."""
-    return 128
+    return 2
 
 
 def test_split_array(test_ir, n_pix):
@@ -33,13 +34,13 @@ def test_split_array(test_ir, n_pix):
 def test_build_ctf_array(test_ir):
     """Test bulding of arbitrary CTF array."""
     ctfs = test_ir.build_ctf_array()
-    assert ctfs.shape == (0, 0, 0)
+    assert ctfs.shape == (n_pix, n_pix, n_pix)
 
 
 def test_grid_SO3_uniform(test_ir):
     """Test generation of rotations across SO(3)."""
-    rots = test_ir.grid_SO3_uniform(2)
-    assert rots.shape == (2, 3, 3)
+    rots = test_ir.grid_SO3_uniform(n_pix)
+    assert rots.shape == (n_pix, n_pix, n_pix)
 
 
 def test_generate_xy_plane(test_ir, n_pix):
@@ -50,24 +51,24 @@ def test_generate_xy_plane(test_ir, n_pix):
 
 def test_generate_slices(test_ir):
     """Test generation of slices."""
-    map_3d = np.ones((2, 2, 2))
-    rots = test_ir.grid_SO3_uniform(2)
-    xy_plane = test_ir.generate_xy_plane(2)
+    map_3d = np.ones((n_pix, n_pix, n_pix))
+    rots = test_ir.grid_SO3_uniform(n_pix)
+    xy_plane = test_ir.generate_xy_plane(n_pix)
 
-    slices, xyz_rotated = test_ir.generate_slices(map_3d, rots)
+    slices, xyz_rotated = test_ir.generate_slices(map_3d, xy_plane, n_pix, rots)
 
-    assert xy_plane.shape == (4, 3)
-    assert slices.shape == (2, 2, 2)
-    assert xyz_rotated.shape == (2, 2, 3)
+    assert xy_plane.shape == (n_pix * n_pix, 3)
+    assert slices.shape == (n_pix, n_pix, n_pix)
+    assert xyz_rotated.shape == (n_pix, n_pix, 3)
 
 
 def test_apply_ctf_to_slice(test_ir):
     """Test convolution of slice with CTF."""
-    particle_slice = np.ones((2, 2))
-    ctf = np.ones((2, 2))
+    particle_slice = np.ones((n_pix, n_pix))
+    ctf = np.ones((n_pix, n_pix))
     convolved = test_ir.apply_ctf_to_slice(particle_slice, ctf)
 
-    assert convolved.shape == (2, 2)
+    assert convolved.shape == (n_pix, n_pix)
 
 
 def test_compute_bayesian_weights(test_ir):
@@ -75,37 +76,37 @@ def test_compute_bayesian_weights(test_ir):
 
     For use under Gaussian white noise model.
     """
-    particle = np.ones((1, 2, 2))
-    slices = np.ones((2, 2, 2))
+    particle = np.ones((1, n_pix, n_pix))
+    slices = np.ones((n_pix, n_pix, n_pix))
     bayesian_weights = test_ir.compute_bayesian_weights(particle, slices)
 
-    assert bayesian_weights.shape == (2,)
+    assert bayesian_weights.shape == (n_pix,)
 
 
 def test_apply_wiener_filter(test_ir):
     """Test application of Wiener filter to particle projection."""
-    projection = np.ones((2, 2))
-    ctf = np.zeros((2, 2))
+    projection = np.ones((n_pix, n_pix))
+    ctf = np.zeros((n_pix, n_pix))
     small_number = 0.01
 
     projection_wfilter_f = test_ir.apply_wiener_filter(projection, ctf, small_number)
-    assert projection_wfilter_f.shape == (2, 2)
+    assert projection_wfilter_f.shape == (n_pix, n_pix)
 
 
 def test_insert_slice(test_ir):
     """Test insertion of slice."""
-    n_pix = 2
+    n_pix = n_pix
     particle_slice = np.ones((n_pix, n_pix))
-    xyz = test_ir.generate_xy_plane(2)
+    xyz = test_ir.generate_xy_plane(n_pix)
 
     inserted, count = test_ir.insert_slice(particle_slice, xyz, n_pix)
-    assert inserted.shape == (2, 2, 2)
-    assert count.shape == (2, 2, 2)
+    assert inserted.shape == (n_pix, n_pix, n_pix)
+    assert count.shape == (n_pix, n_pix, n_pix)
 
 
 def test_compute_fsc(test_ir):
     """Test computation of FSC."""
-    map_1 = np.ones((2, 2, 2))
+    map_1 = np.ones((n_pix, n_pix, n_pix))
 
     fsc_1 = test_ir.compute_fsc(map_1)
     assert fsc_1.shape == (1,)
@@ -116,4 +117,4 @@ def test_expand_1d_to_3d(test_ir):
     arr1d = np.ones(1)
     spherical = test_ir.expand_1d_to_3d(arr1d)
 
-    assert spherical.shape == (2, 2, 2)
+    assert spherical.shape == (n_pix, n_pix, n_pix)

From 5d0d1a1dc2442fe2ac00b3174146ff64172003d1 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 10:17:47 -0700
Subject: [PATCH 058/148] Tab snuck in

---
 tests/test_expectation_maximization.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 2c1fe1f..48b4ff1 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -9,9 +9,9 @@
 @pytest.fixture
 def test_ir():
     """Instantiate IterativeRefinement class for testing."""
-	map = np.zeros((n_pix, n_pix, n_pix))
+    map = np.zeros((n_pix, n_pix, n_pix))
     particles = np.zeros((n_pix, n_pix, n_pix))
-	ctf_info = [{},] * n_pix
+    ctf_info = [{},] * n_pix
     itr = 7
     ir = em.IterativeRefinement(map, particles, ctf_info, itr)
     return ir

From 7289762aeddd547e5aeb354381cf08fbfeb5faa4 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 17:17:52 +0000
Subject: [PATCH 059/148] Format code with black

---
 tests/test_expectation_maximization.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 48b4ff1..86544c0 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -11,7 +11,9 @@ def test_ir():
     """Instantiate IterativeRefinement class for testing."""
     map = np.zeros((n_pix, n_pix, n_pix))
     particles = np.zeros((n_pix, n_pix, n_pix))
-    ctf_info = [{},] * n_pix
+    ctf_info = [
+        {},
+    ] * n_pix
     itr = 7
     ir = em.IterativeRefinement(map, particles, ctf_info, itr)
     return ir

From f1bd4142bfdf7016792adac2d7151ce7115136b2 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 10:21:39 -0700
Subject: [PATCH 060/148] Comment change to force checks

---
 tests/test_expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 86544c0..c9fb560 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -21,7 +21,7 @@ def test_ir():
 
 @pytest.fixture
 def n_pix():
-    """Get sample n_pix value."""
+    """Get sample n_pix value for consistency."""
     return 2
 
 

From 756adbed960ce14bb704a1f1a5adb091123ad0a8 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 10:23:13 -0700
Subject: [PATCH 061/148] Fixes to tests

---
 tests/test_expectation_maximization.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index c9fb560..f6986e1 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -9,13 +9,13 @@
 @pytest.fixture
 def test_ir():
     """Instantiate IterativeRefinement class for testing."""
-    map = np.zeros((n_pix, n_pix, n_pix))
+    map_3d = np.zeros((n_pix, n_pix, n_pix))
     particles = np.zeros((n_pix, n_pix, n_pix))
     ctf_info = [
         {},
     ] * n_pix
     itr = 7
-    ir = em.IterativeRefinement(map, particles, ctf_info, itr)
+    ir = em.IterativeRefinement(map_3d, particles, ctf_info, itr)
     return ir
 
 
@@ -97,7 +97,6 @@ def test_apply_wiener_filter(test_ir):
 
 def test_insert_slice(test_ir):
     """Test insertion of slice."""
-    n_pix = n_pix
     particle_slice = np.ones((n_pix, n_pix))
     xyz = test_ir.generate_xy_plane(n_pix)
 

From 40a6fb0189ddcb86b1a937006c9eb307c303af3a Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 10:44:03 -0700
Subject: [PATCH 062/148] Refactored tests a bit

---
 tests/test_expectation_maximization.py | 76 +++++++++++++-------------
 1 file changed, 38 insertions(+), 38 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index f6986e1..e67dd81 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -9,68 +9,68 @@
 @pytest.fixture
 def test_ir():
     """Instantiate IterativeRefinement class for testing."""
-    map_3d = np.zeros((n_pix, n_pix, n_pix))
-    particles = np.zeros((n_pix, n_pix, n_pix))
+    map_3d = np.zeros((n(), n(), n()))
+    particles = np.zeros((n(), n(), n()))
     ctf_info = [
         {},
-    ] * n_pix
+    ] * n()
     itr = 7
     ir = em.IterativeRefinement(map_3d, particles, ctf_info, itr)
     return ir
 
 
 @pytest.fixture
-def n_pix():
-    """Get sample n_pix value for consistency."""
+def n():
+    """Get sample n() value for consistency."""
     return 2
 
 
-def test_split_array(test_ir, n_pix):
+def test_split_array(test_ir, n()):
     """Test splitting of array in two halves."""
-    arr = np.zeros(n_pix)
+    arr = np.zeros(n())
     arr1, arr2 = test_ir.split_array(arr)
-    assert arr1.shape == (n_pix / 2,)
-    assert arr2.shape == (n_pix / 2,)
+    assert arr1.shape == (n() / 2,)
+    assert arr2.shape == (n() / 2,)
 
 
 def test_build_ctf_array(test_ir):
     """Test bulding of arbitrary CTF array."""
     ctfs = test_ir.build_ctf_array()
-    assert ctfs.shape == (n_pix, n_pix, n_pix)
+    assert ctfs.shape == (n(), n(), n())
 
 
 def test_grid_SO3_uniform(test_ir):
     """Test generation of rotations across SO(3)."""
-    rots = test_ir.grid_SO3_uniform(n_pix)
-    assert rots.shape == (n_pix, n_pix, n_pix)
+    rots = test_ir.grid_SO3_uniform(n())
+    assert rots.shape == (n(), n(), n())
 
 
-def test_generate_xy_plane(test_ir, n_pix):
+def test_generate_xy_plane(test_ir, n()):
     """Test generation of xy plane."""
-    xy_plane = test_ir.generate_xy_plane(n_pix)
-    assert xy_plane.shape == (n_pix, n_pix, 3)
+    xy_plane = test_ir.generate_xy_plane(n())
+    assert xy_plane.shape == (n(), n(), 3)
 
 
 def test_generate_slices(test_ir):
     """Test generation of slices."""
-    map_3d = np.ones((n_pix, n_pix, n_pix))
-    rots = test_ir.grid_SO3_uniform(n_pix)
-    xy_plane = test_ir.generate_xy_plane(n_pix)
+    map_3d = np.ones((n(), n(), n()))
+    rots = test_ir.grid_SO3_uniform(n())
+    xy_plane = test_ir.generate_xy_plane(n())
 
-    slices, xyz_rotated = test_ir.generate_slices(map_3d, xy_plane, n_pix, rots)
+    slices, xyz_rotated = test_ir.generate_slices(map_3d, xy_plane, n(), rots)
 
-    assert xy_plane.shape == (n_pix * n_pix, 3)
-    assert slices.shape == (n_pix, n_pix, n_pix)
-    assert xyz_rotated.shape == (n_pix, n_pix, 3)
+    assert xy_plane.shape == (n() * n(), 3)
+    assert slices.shape == (n(), n(), n())
+    assert xyz_rotated.shape == (n(), n(), 3)
 
 
 def test_apply_ctf_to_slice(test_ir):
     """Test convolution of slice with CTF."""
-    particle_slice = np.ones((n_pix, n_pix))
-    ctf = np.ones((n_pix, n_pix))
+    particle_slice = np.ones((n(), n()))
+    ctf = np.ones((n(), n()))
     convolved = test_ir.apply_ctf_to_slice(particle_slice, ctf)
 
-    assert convolved.shape == (n_pix, n_pix)
+    assert convolved.shape == (n(), n())
 
 
 def test_compute_bayesian_weights(test_ir):
@@ -78,36 +78,36 @@ def test_compute_bayesian_weights(test_ir):
 
     For use under Gaussian white noise model.
     """
-    particle = np.ones((1, n_pix, n_pix))
-    slices = np.ones((n_pix, n_pix, n_pix))
+    particle = np.ones((1, n(), n()))
+    slices = np.ones((n(), n(), n()))
     bayesian_weights = test_ir.compute_bayesian_weights(particle, slices)
 
-    assert bayesian_weights.shape == (n_pix,)
+    assert bayesian_weights.shape == (n(),)
 
 
 def test_apply_wiener_filter(test_ir):
     """Test application of Wiener filter to particle projection."""
-    projection = np.ones((n_pix, n_pix))
-    ctf = np.zeros((n_pix, n_pix))
+    projection = np.ones((n(), n()))
+    ctf = np.zeros((n(), n()))
     small_number = 0.01
 
     projection_wfilter_f = test_ir.apply_wiener_filter(projection, ctf, small_number)
-    assert projection_wfilter_f.shape == (n_pix, n_pix)
+    assert projection_wfilter_f.shape == (n(), n())
 
 
 def test_insert_slice(test_ir):
     """Test insertion of slice."""
-    particle_slice = np.ones((n_pix, n_pix))
-    xyz = test_ir.generate_xy_plane(n_pix)
+    particle_slice = np.ones((n(), n()))
+    xyz = test_ir.generate_xy_plane(n())
 
-    inserted, count = test_ir.insert_slice(particle_slice, xyz, n_pix)
-    assert inserted.shape == (n_pix, n_pix, n_pix)
-    assert count.shape == (n_pix, n_pix, n_pix)
+    inserted, count = test_ir.insert_slice(particle_slice, xyz, n())
+    assert inserted.shape == (n(), n(), n())
+    assert count.shape == (n(), n(), n())
 
 
 def test_compute_fsc(test_ir):
     """Test computation of FSC."""
-    map_1 = np.ones((n_pix, n_pix, n_pix))
+    map_1 = np.ones((n(), n(), n()))
 
     fsc_1 = test_ir.compute_fsc(map_1)
     assert fsc_1.shape == (1,)
@@ -118,4 +118,4 @@ def test_expand_1d_to_3d(test_ir):
     arr1d = np.ones(1)
     spherical = test_ir.expand_1d_to_3d(arr1d)
 
-    assert spherical.shape == (n_pix, n_pix, n_pix)
+    assert spherical.shape == (n(), n(), n())

From 5c74fb349068b8931248ab2dc0fcb15a0bcc5242 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 10:47:55 -0700
Subject: [PATCH 063/148] Fix to test_split_array

---
 tests/test_expectation_maximization.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index e67dd81..7c4e8a9 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -25,12 +25,12 @@ def n():
     return 2
 
 
-def test_split_array(test_ir, n()):
+def test_split_array(test_ir, k):
     """Test splitting of array in two halves."""
-    arr = np.zeros(n())
+    arr = np.zeros(k)
     arr1, arr2 = test_ir.split_array(arr)
-    assert arr1.shape == (n() / 2,)
-    assert arr2.shape == (n() / 2,)
+    assert arr1.shape == (k / 2,)
+    assert arr2.shape == (k / 2,)
 
 
 def test_build_ctf_array(test_ir):

From c210d36a382cbfaa5c77aaeb55a78fb997575f30 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 10:50:22 -0700
Subject: [PATCH 064/148] Fix to test_generate_xy_plane

---
 tests/test_expectation_maximization.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 7c4e8a9..5147ad2 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -45,10 +45,10 @@ def test_grid_SO3_uniform(test_ir):
     assert rots.shape == (n(), n(), n())
 
 
-def test_generate_xy_plane(test_ir, n()):
+def test_generate_xy_plane(test_ir, k):
     """Test generation of xy plane."""
-    xy_plane = test_ir.generate_xy_plane(n())
-    assert xy_plane.shape == (n(), n(), 3)
+    xy_plane = test_ir.generate_xy_plane(k)
+    assert xy_plane.shape == (k, k, 3)
 
 
 def test_generate_slices(test_ir):

From 8753a1fd3b8c56482871bf76f146c4dee5d9f44f Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 10:53:23 -0700
Subject: [PATCH 065/148] Docstring fix

---
 tests/test_expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 5147ad2..47238e0 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -21,7 +21,7 @@ def test_ir():
 
 @pytest.fixture
 def n():
-    """Get sample n() value for consistency."""
+    """Get test array size value for consistency."""
     return 2
 
 

From 1ce2209b75f9bf55207cc6f75ac7d1fb06b76802 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 10:58:17 -0700
Subject: [PATCH 066/148] Deepsource tricked me

---
 tests/test_expectation_maximization.py | 58 +++++++++++++-------------
 1 file changed, 29 insertions(+), 29 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 47238e0..56f3734 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -9,11 +9,11 @@
 @pytest.fixture
 def test_ir():
     """Instantiate IterativeRefinement class for testing."""
-    map_3d = np.zeros((n(), n(), n()))
-    particles = np.zeros((n(), n(), n()))
+    map_3d = np.zeros((n, n, n))
+    particles = np.zeros((n, n, n))
     ctf_info = [
         {},
-    ] * n()
+    ] * n
     itr = 7
     ir = em.IterativeRefinement(map_3d, particles, ctf_info, itr)
     return ir
@@ -36,13 +36,13 @@ def test_split_array(test_ir, k):
 def test_build_ctf_array(test_ir):
     """Test bulding of arbitrary CTF array."""
     ctfs = test_ir.build_ctf_array()
-    assert ctfs.shape == (n(), n(), n())
+    assert ctfs.shape == (n, n, n)
 
 
 def test_grid_SO3_uniform(test_ir):
     """Test generation of rotations across SO(3)."""
-    rots = test_ir.grid_SO3_uniform(n())
-    assert rots.shape == (n(), n(), n())
+    rots = test_ir.grid_SO3_uniform(n)
+    assert rots.shape == (n, n, n)
 
 
 def test_generate_xy_plane(test_ir, k):
@@ -53,24 +53,24 @@ def test_generate_xy_plane(test_ir, k):
 
 def test_generate_slices(test_ir):
     """Test generation of slices."""
-    map_3d = np.ones((n(), n(), n()))
-    rots = test_ir.grid_SO3_uniform(n())
-    xy_plane = test_ir.generate_xy_plane(n())
+    map_3d = np.ones((n, n, n))
+    rots = test_ir.grid_SO3_uniform(n)
+    xy_plane = test_ir.generate_xy_plane(n)
 
-    slices, xyz_rotated = test_ir.generate_slices(map_3d, xy_plane, n(), rots)
+    slices, xyz_rotated = test_ir.generate_slices(map_3d, xy_plane, n, rots)
 
-    assert xy_plane.shape == (n() * n(), 3)
-    assert slices.shape == (n(), n(), n())
-    assert xyz_rotated.shape == (n(), n(), 3)
+    assert xy_plane.shape == (n * n, 3)
+    assert slices.shape == (n, n, n)
+    assert xyz_rotated.shape == (n, n, 3)
 
 
 def test_apply_ctf_to_slice(test_ir):
     """Test convolution of slice with CTF."""
-    particle_slice = np.ones((n(), n()))
-    ctf = np.ones((n(), n()))
+    particle_slice = np.ones((n, n))
+    ctf = np.ones((n, n))
     convolved = test_ir.apply_ctf_to_slice(particle_slice, ctf)
 
-    assert convolved.shape == (n(), n())
+    assert convolved.shape == (n, n)
 
 
 def test_compute_bayesian_weights(test_ir):
@@ -78,36 +78,36 @@ def test_compute_bayesian_weights(test_ir):
 
     For use under Gaussian white noise model.
     """
-    particle = np.ones((1, n(), n()))
-    slices = np.ones((n(), n(), n()))
+    particle = np.ones((1, n, n))
+    slices = np.ones((n, n, n))
     bayesian_weights = test_ir.compute_bayesian_weights(particle, slices)
 
-    assert bayesian_weights.shape == (n(),)
+    assert bayesian_weights.shape == (n,)
 
 
 def test_apply_wiener_filter(test_ir):
     """Test application of Wiener filter to particle projection."""
-    projection = np.ones((n(), n()))
-    ctf = np.zeros((n(), n()))
+    projection = np.ones((n, n))
+    ctf = np.zeros((n, n))
     small_number = 0.01
 
     projection_wfilter_f = test_ir.apply_wiener_filter(projection, ctf, small_number)
-    assert projection_wfilter_f.shape == (n(), n())
+    assert projection_wfilter_f.shape == (n, n)
 
 
 def test_insert_slice(test_ir):
     """Test insertion of slice."""
-    particle_slice = np.ones((n(), n()))
-    xyz = test_ir.generate_xy_plane(n())
+    particle_slice = np.ones((n, n))
+    xyz = test_ir.generate_xy_plane(n)
 
-    inserted, count = test_ir.insert_slice(particle_slice, xyz, n())
-    assert inserted.shape == (n(), n(), n())
-    assert count.shape == (n(), n(), n())
+    inserted, count = test_ir.insert_slice(particle_slice, xyz, n)
+    assert inserted.shape == (n, n, n)
+    assert count.shape == (n, n, n)
 
 
 def test_compute_fsc(test_ir):
     """Test computation of FSC."""
-    map_1 = np.ones((n(), n(), n()))
+    map_1 = np.ones((n, n, n))
 
     fsc_1 = test_ir.compute_fsc(map_1)
     assert fsc_1.shape == (1,)
@@ -118,4 +118,4 @@ def test_expand_1d_to_3d(test_ir):
     arr1d = np.ones(1)
     spherical = test_ir.expand_1d_to_3d(arr1d)
 
-    assert spherical.shape == (n(), n(), n())
+    assert spherical.shape == (n, n, n)

From 0673ebb57241d999bd5cbb639bb269dc90951ace Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 11:02:15 -0700
Subject: [PATCH 067/148] Dosctring to force checks

---
 tests/test_expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 56f3734..c21c540 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -34,7 +34,7 @@ def test_split_array(test_ir, k):
 
 
 def test_build_ctf_array(test_ir):
-    """Test bulding of arbitrary CTF array."""
+    """Test bulding arbitrary CTF array."""
     ctfs = test_ir.build_ctf_array()
     assert ctfs.shape == (n, n, n)
 

From ae8c96f5aa33e8f107f93f8bff719bc2be2b04f8 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 11:06:46 -0700
Subject: [PATCH 068/148] Fixture fix:

---
 tests/test_expectation_maximization.py | 45 +++++++++++++-------------
 1 file changed, 22 insertions(+), 23 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index c21c540..c7bb4a2 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -7,7 +7,12 @@
 
 
 @pytest.fixture
-def test_ir():
+def n():
+    """Get test array size value for consistency."""
+    return 2
+
+@pytest.fixture
+def test_ir(n):
     """Instantiate IterativeRefinement class for testing."""
     map_3d = np.zeros((n, n, n))
     particles = np.zeros((n, n, n))
@@ -19,39 +24,33 @@ def test_ir():
     return ir
 
 
-@pytest.fixture
-def n():
-    """Get test array size value for consistency."""
-    return 2
-
-
-def test_split_array(test_ir, k):
+def test_split_array(test_ir, n):
     """Test splitting of array in two halves."""
-    arr = np.zeros(k)
+    arr = np.zeros(n)
     arr1, arr2 = test_ir.split_array(arr)
-    assert arr1.shape == (k / 2,)
-    assert arr2.shape == (k / 2,)
+    assert arr1.shape == (n / 2,)
+    assert arr2.shape == (n / 2,)
 
 
-def test_build_ctf_array(test_ir):
+def test_build_ctf_array(test_ir, n):
     """Test bulding arbitrary CTF array."""
     ctfs = test_ir.build_ctf_array()
     assert ctfs.shape == (n, n, n)
 
 
-def test_grid_SO3_uniform(test_ir):
+def test_grid_SO3_uniform(test_ir, n):
     """Test generation of rotations across SO(3)."""
     rots = test_ir.grid_SO3_uniform(n)
     assert rots.shape == (n, n, n)
 
 
-def test_generate_xy_plane(test_ir, k):
+def test_generate_xy_plane(test_ir, n):
     """Test generation of xy plane."""
-    xy_plane = test_ir.generate_xy_plane(k)
-    assert xy_plane.shape == (k, k, 3)
+    xy_plane = test_ir.generate_xy_plane(n)
+    assert xy_plane.shape == (n, n, 3)
 
 
-def test_generate_slices(test_ir):
+def test_generate_slices(test_ir, n):
     """Test generation of slices."""
     map_3d = np.ones((n, n, n))
     rots = test_ir.grid_SO3_uniform(n)
@@ -64,7 +63,7 @@ def test_generate_slices(test_ir):
     assert xyz_rotated.shape == (n, n, 3)
 
 
-def test_apply_ctf_to_slice(test_ir):
+def test_apply_ctf_to_slice(test_ir, n):
     """Test convolution of slice with CTF."""
     particle_slice = np.ones((n, n))
     ctf = np.ones((n, n))
@@ -73,7 +72,7 @@ def test_apply_ctf_to_slice(test_ir):
     assert convolved.shape == (n, n)
 
 
-def test_compute_bayesian_weights(test_ir):
+def test_compute_bayesian_weights(test_ir, n):
     """Test computation of bayesian weights.
 
     For use under Gaussian white noise model.
@@ -85,7 +84,7 @@ def test_compute_bayesian_weights(test_ir):
     assert bayesian_weights.shape == (n,)
 
 
-def test_apply_wiener_filter(test_ir):
+def test_apply_wiener_filter(test_ir, n):
     """Test application of Wiener filter to particle projection."""
     projection = np.ones((n, n))
     ctf = np.zeros((n, n))
@@ -95,7 +94,7 @@ def test_apply_wiener_filter(test_ir):
     assert projection_wfilter_f.shape == (n, n)
 
 
-def test_insert_slice(test_ir):
+def test_insert_slice(test_ir, n):
     """Test insertion of slice."""
     particle_slice = np.ones((n, n))
     xyz = test_ir.generate_xy_plane(n)
@@ -105,7 +104,7 @@ def test_insert_slice(test_ir):
     assert count.shape == (n, n, n)
 
 
-def test_compute_fsc(test_ir):
+def test_compute_fsc(test_ir, n):
     """Test computation of FSC."""
     map_1 = np.ones((n, n, n))
 
@@ -113,7 +112,7 @@ def test_compute_fsc(test_ir):
     assert fsc_1.shape == (1,)
 
 
-def test_expand_1d_to_3d(test_ir):
+def test_expand_1d_to_3d(test_ir, n):
     """Test expansion of 1D array into spherical shell."""
     arr1d = np.ones(1)
     spherical = test_ir.expand_1d_to_3d(arr1d)

From 16a0b9002250d07b9dc97d7788ef905f9591c0b9 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 18:06:53 +0000
Subject: [PATCH 069/148] Format code with black

---
 tests/test_expectation_maximization.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index c7bb4a2..51e28ee 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -11,6 +11,7 @@ def n():
     """Get test array size value for consistency."""
     return 2
 
+
 @pytest.fixture
 def test_ir(n):
     """Instantiate IterativeRefinement class for testing."""

From 3c3595c78ad3293ffffab863d6446ee11ebf35c8 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 18:07:02 +0000
Subject: [PATCH 070/148] Format code with black

---
 tests/test_expectation_maximization.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 51e28ee..9eb9097 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -12,6 +12,7 @@ def n():
     return 2
 
 
+
 @pytest.fixture
 def test_ir(n):
     """Instantiate IterativeRefinement class for testing."""

From a5bc9eedaf1f53cfb1effff78e4eb7b120349192 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 18:07:10 +0000
Subject: [PATCH 071/148] Format code with black

---
 tests/test_expectation_maximization.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 9eb9097..51e28ee 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -12,7 +12,6 @@ def n():
     return 2
 
 
-
 @pytest.fixture
 def test_ir(n):
     """Instantiate IterativeRefinement class for testing."""

From b76ec986bc84e7dd59d330ab382f78b7f68146d6 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 18:07:19 +0000
Subject: [PATCH 072/148] Format code with black

---
 tests/test_expectation_maximization.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 51e28ee..c7bb4a2 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -11,7 +11,6 @@ def n():
     """Get test array size value for consistency."""
     return 2
 
-
 @pytest.fixture
 def test_ir(n):
     """Instantiate IterativeRefinement class for testing."""

From b58ba2fe78e3e40c5427cca7f04d855a3001b79f Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 11:08:00 -0700
Subject: [PATCH 073/148] Forcing checks again...

---
 tests/test_expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index c7bb4a2..c8de08f 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -39,7 +39,7 @@ def test_build_ctf_array(test_ir, n):
 
 
 def test_grid_SO3_uniform(test_ir, n):
-    """Test generation of rotations across SO(3)."""
+    """Test generation of rotations in SO(3)."""
     rots = test_ir.grid_SO3_uniform(n)
     assert rots.shape == (n, n, n)
 

From 98a879c3b84b02539a45ae216a125552e18d1d22 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 18:10:28 +0000
Subject: [PATCH 074/148] Format code with black

---
 tests/test_expectation_maximization.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index c8de08f..cf0af55 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -11,6 +11,7 @@ def n():
     """Get test array size value for consistency."""
     return 2
 
+
 @pytest.fixture
 def test_ir(n):
     """Instantiate IterativeRefinement class for testing."""

From a1dc0cdf13ab7ff115519b9f34f31c2502d6811c Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 11:15:28 -0700
Subject: [PATCH 075/148] Better ctf_info for tests

---
 tests/test_expectation_maximization.py | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index c8de08f..c105e73 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -14,10 +14,21 @@ def n():
 @pytest.fixture
 def test_ir(n):
     """Instantiate IterativeRefinement class for testing."""
+    ex_ctf = {
+        s : np.ones(n, n),
+        a : np.ones(n, n),
+        def1 : 1.0,
+        def2 : 1.0,
+        angast : 0.1,
+        kv : 0.1,
+        cs : 0.1,
+        bf : 0.1,
+        lp : 0.1
+    }
     map_3d = np.zeros((n, n, n))
     particles = np.zeros((n, n, n))
     ctf_info = [
-        {},
+        ex_ctf,
     ] * n
     itr = 7
     ir = em.IterativeRefinement(map_3d, particles, ctf_info, itr)

From 4bcf15a965739e71a1860e354235962ba9db71ba Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 18:16:01 +0000
Subject: [PATCH 076/148] Format code with black

---
 tests/test_expectation_maximization.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 0245bd0..bd6c480 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -16,15 +16,15 @@ def n():
 def test_ir(n):
     """Instantiate IterativeRefinement class for testing."""
     ex_ctf = {
-        s : np.ones(n, n),
-        a : np.ones(n, n),
-        def1 : 1.0,
-        def2 : 1.0,
-        angast : 0.1,
-        kv : 0.1,
-        cs : 0.1,
-        bf : 0.1,
-        lp : 0.1
+        s: np.ones(n, n),
+        a: np.ones(n, n),
+        def1: 1.0,
+        def2: 1.0,
+        angast: 0.1,
+        kv: 0.1,
+        cs: 0.1,
+        bf: 0.1,
+        lp: 0.1,
     }
     map_3d = np.zeros((n, n, n))
     particles = np.zeros((n, n, n))

From ecee780e4f96f297d071d68f8bbcac01da314000 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 11:18:49 -0700
Subject: [PATCH 077/148] Strings not variables...

---
 tests/test_expectation_maximization.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 0245bd0..06318fb 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -16,15 +16,15 @@ def n():
 def test_ir(n):
     """Instantiate IterativeRefinement class for testing."""
     ex_ctf = {
-        s : np.ones(n, n),
-        a : np.ones(n, n),
-        def1 : 1.0,
-        def2 : 1.0,
-        angast : 0.1,
-        kv : 0.1,
-        cs : 0.1,
-        bf : 0.1,
-        lp : 0.1
+        's' : np.ones(n, n),
+        'a' : np.ones(n, n),
+        'def1' : 1.0,
+        'def2' : 1.0,
+        'angast' : 0.1,
+        'kv' : 0.1,
+        'cs' : 0.1,
+        'bf' : 0.1,
+        'lp' : 0.1
     }
     map_3d = np.zeros((n, n, n))
     particles = np.zeros((n, n, n))

From 0ac923c2d9fb74626aeff05a093fd3a50674ea4d Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 18:19:48 +0000
Subject: [PATCH 078/148] Format code with black

---
 tests/test_expectation_maximization.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 1a5d1a2..1f761b1 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -16,15 +16,15 @@ def n():
 def test_ir(n):
     """Instantiate IterativeRefinement class for testing."""
     ex_ctf = {
-        's': np.ones(n, n),
-        'a': np.ones(n, n),
-        'def1': 1.0,
-        'def2': 1.0,
-        'angast': 0.1,
-        'kv': 0.1,
-        'cs': 0.1,
-        'bf': 0.1,
-        'lp': 0.1
+        "s": np.ones(n, n),
+        "a": np.ones(n, n),
+        "def1": 1.0,
+        "def2": 1.0,
+        "angast": 0.1,
+        "kv": 0.1,
+        "cs": 0.1,
+        "bf": 0.1,
+        "lp": 0.1,
     }
     map_3d = np.zeros((n, n, n))
     particles = np.zeros((n, n, n))

From cb7b069bf5d7aead7b59ce7729fbbb77e191b7f6 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 11:23:30 -0700
Subject: [PATCH 079/148] Fix

---
 tests/test_expectation_maximization.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 1a5d1a2..3d8341e 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -16,8 +16,8 @@ def n():
 def test_ir(n):
     """Instantiate IterativeRefinement class for testing."""
     ex_ctf = {
-        's': np.ones(n, n),
-        'a': np.ones(n, n),
+        's': np.ones((n, n)),
+        'a': np.ones((n, n)),
         'def1': 1.0,
         'def2': 1.0,
         'angast': 0.1,

From 966ed3c31ebfdac15fe9abe1b9cabe770cf4b832 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 11:38:24 -0700
Subject: [PATCH 080/148] test fixes

---
 iterative_refinement/expectation_maximization.py | 8 ++++----
 tests/test_expectation_maximization.py           | 9 +++++----
 2 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 244c79d..bcc899c 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -120,7 +120,7 @@ def generate_xy_plane(n_pix):
         # See how meshgrid and generate coordinates functions used
         # https://github.com/geoffwoollard/compSPI/blob/stash_simulate/src/simulate.py#L96
 
-        xy_plane = np.ones((n_pix, n_pix, 3))
+        xy_plane = np.ones((n_pix * n_pix, 3))
         return xy_plane
 
     @staticmethod
@@ -202,7 +202,7 @@ def compute_bayesian_weights(particle, slices):
         """
         n_slices = slices.shape[0]
         particle = np.ones_like(particle)
-        bayes_factors = np.random.normal(n_slices)
+        bayes_factors = np.random.normal(size = n_slices)
         return bayes_factors
 
     @staticmethod
@@ -244,11 +244,11 @@ def insert_slice(slice_real, xyz, n_pix):
         -------
         inserted_slice_3d : float64 arr
             Rotated slice in 3D voxel array.
-            Shape (n_pix, n_pix)
+            Shape (n_pix**2, 3)
         count_3d : arr
             Voxel array to count slice presence: 1 if slice present,
             otherwise 0.
-            Shape (n_pix, n_pix, n_pix)
+            Shape (n_pix**2, 3)
         """
         inserted_slice_3d = slice_real
         shape = xyz.shape[0]
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index d3846cb..e831b29 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -47,13 +47,14 @@ def test_split_array(test_ir, n):
 def test_build_ctf_array(test_ir, n):
     """Test bulding arbitrary CTF array."""
     ctfs = test_ir.build_ctf_array()
-    assert ctfs.shape == (n, n, n)
+    assert len(ctfs) == n
+    assert ctfs[0].shape == (n, n)
 
 
 def test_grid_SO3_uniform(test_ir, n):
     """Test generation of rotations in SO(3)."""
     rots = test_ir.grid_SO3_uniform(n)
-    assert rots.shape == (n, n, n)
+    assert rots.shape == (n, 3, 3)
 
 
 def test_generate_xy_plane(test_ir, n):
@@ -112,8 +113,8 @@ def test_insert_slice(test_ir, n):
     xyz = test_ir.generate_xy_plane(n)
 
     inserted, count = test_ir.insert_slice(particle_slice, xyz, n)
-    assert inserted.shape == (n, n, n)
-    assert count.shape == (n, n, n)
+    assert inserted.shape == (n * n, 3)
+    assert count.shape == (n * n, 3)
 
 
 def test_compute_fsc(test_ir, n):

From ccbd07b50976c817f32c962879257ccd0b22e317 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 18:38:28 +0000
Subject: [PATCH 081/148] Format code with black

---
 iterative_refinement/expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index bcc899c..471c38a 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -202,7 +202,7 @@ def compute_bayesian_weights(particle, slices):
         """
         n_slices = slices.shape[0]
         particle = np.ones_like(particle)
-        bayes_factors = np.random.normal(size = n_slices)
+        bayes_factors = np.random.normal(size=n_slices)
         return bayes_factors
 
     @staticmethod

From 4858d54b5eeebc9027ab4cb4aa58a0acb6ba6491 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 11:43:44 -0700
Subject: [PATCH 082/148] Test fixes

---
 iterative_refinement/expectation_maximization.py | 4 ++--
 tests/test_expectation_maximization.py           | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index bcc899c..32f1f7c 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -250,9 +250,9 @@ def insert_slice(slice_real, xyz, n_pix):
             otherwise 0.
             Shape (n_pix**2, 3)
         """
-        inserted_slice_3d = slice_real
         shape = xyz.shape[0]
-        count_3d = np.ones((shape, n_pix, n_pix))
+        count_3d = np.ones((shape, 3))
+        inserted_slice_3d = np.ones((shape, 3))
         return inserted_slice_3d, count_3d
 
     @staticmethod
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index e831b29..6ce9e90 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -60,7 +60,7 @@ def test_grid_SO3_uniform(test_ir, n):
 def test_generate_xy_plane(test_ir, n):
     """Test generation of xy plane."""
     xy_plane = test_ir.generate_xy_plane(n)
-    assert xy_plane.shape == (n, n, 3)
+    assert xy_plane.shape == (n * n, 3)
 
 
 def test_generate_slices(test_ir, n):
@@ -73,7 +73,7 @@ def test_generate_slices(test_ir, n):
 
     assert xy_plane.shape == (n * n, 3)
     assert slices.shape == (n, n, n)
-    assert xyz_rotated.shape == (n, n, 3)
+    assert xyz_rotated.shape == (n ** 3,)
 
 
 def test_apply_ctf_to_slice(test_ir, n):

From bc884980c8e2dcee85691233e103c929ebf56cbd Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 11:47:08 -0700
Subject: [PATCH 083/148] Force checks

---
 tests/test_expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 6ce9e90..5e54cdf 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -108,7 +108,7 @@ def test_apply_wiener_filter(test_ir, n):
 
 
 def test_insert_slice(test_ir, n):
-    """Test insertion of slice."""
+    """Test insertion of particle slice."""
     particle_slice = np.ones((n, n))
     xyz = test_ir.generate_xy_plane(n)
 

From ab014c53d0cdcf9f706555bee43e0198a878e8cd Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 18:47:12 +0000
Subject: [PATCH 084/148] Format code with black

---
 tests/test_expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 5e54cdf..bb2cc79 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -73,7 +73,7 @@ def test_generate_slices(test_ir, n):
 
     assert xy_plane.shape == (n * n, 3)
     assert slices.shape == (n, n, n)
-    assert xyz_rotated.shape == (n ** 3,)
+    assert xyz_rotated.shape == (n**3,)
 
 
 def test_apply_ctf_to_slice(test_ir, n):

From 656b5d2e573c256b4af224e599d9e21095524743 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 11:51:35 -0700
Subject: [PATCH 085/148] test fixes

---
 iterative_refinement/expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index 0bd2f4d..d0f1e9f 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -162,7 +162,7 @@ def generate_slices(map_3d_f, xy_plane, n_pix, rots):
 
         size = n_rotations * n_pix**2
         slices = np.random.normal(size=size)
-        slices.reshape(n_rotations, n_pix, n_pix)
+        slices.reshape((n_rotations, n_pix, n_pix))
         return slices, xyz_rotated
 
     @staticmethod

From b9e72ad51bb7917b2576215659e9428f067f93b9 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 11:53:31 -0700
Subject: [PATCH 086/148] Forcing checks

---
 tests/test_expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index bb2cc79..a063c4e 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -77,7 +77,7 @@ def test_generate_slices(test_ir, n):
 
 
 def test_apply_ctf_to_slice(test_ir, n):
-    """Test convolution of slice with CTF."""
+    """Test convolution of particle slice with CTF."""
     particle_slice = np.ones((n, n))
     ctf = np.ones((n, n))
     convolved = test_ir.apply_ctf_to_slice(particle_slice, ctf)

From 5577dedac3462417405982193261031522c458f9 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 11:56:31 -0700
Subject: [PATCH 087/148] Reshape fix

---
 iterative_refinement/expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/iterative_refinement/expectation_maximization.py b/iterative_refinement/expectation_maximization.py
index d0f1e9f..b643910 100644
--- a/iterative_refinement/expectation_maximization.py
+++ b/iterative_refinement/expectation_maximization.py
@@ -162,7 +162,7 @@ def generate_slices(map_3d_f, xy_plane, n_pix, rots):
 
         size = n_rotations * n_pix**2
         slices = np.random.normal(size=size)
-        slices.reshape((n_rotations, n_pix, n_pix))
+        slices = slices.reshape((n_rotations, n_pix, n_pix))
         return slices, xyz_rotated
 
     @staticmethod

From bb6e258fc2a7dee0c5b1d5488a566620c89b6ee7 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 11:59:30 -0700
Subject: [PATCH 088/148] Shape fix

---
 tests/test_expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index a063c4e..1abf260 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -73,7 +73,7 @@ def test_generate_slices(test_ir, n):
 
     assert xy_plane.shape == (n * n, 3)
     assert slices.shape == (n, n, n)
-    assert xyz_rotated.shape == (n**3,)
+    assert xyz_rotated.shape == (n * n, 3)
 
 
 def test_apply_ctf_to_slice(test_ir, n):

From 81e5faac62270e6fb6d9d87c7e0435d321e9ff49 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 12:07:18 -0700
Subject: [PATCH 089/148] Structure changes

---
 reconstructSPI/__init__.py                                       | 1 +
 .../iterative_refinement}/__init__.py                            | 0
 .../iterative_refinement}/expectation_maximization.py            | 0
 3 files changed, 1 insertion(+)
 create mode 100644 reconstructSPI/__init__.py
 rename {iterative_refinement => reconstructSPI/iterative_refinement}/__init__.py (100%)
 rename {iterative_refinement => reconstructSPI/iterative_refinement}/expectation_maximization.py (100%)

diff --git a/reconstructSPI/__init__.py b/reconstructSPI/__init__.py
new file mode 100644
index 0000000..a16d370
--- /dev/null
+++ b/reconstructSPI/__init__.py
@@ -0,0 +1 @@
+"""Various particle reconstruction methods."""
diff --git a/iterative_refinement/__init__.py b/reconstructSPI/iterative_refinement/__init__.py
similarity index 100%
rename from iterative_refinement/__init__.py
rename to reconstructSPI/iterative_refinement/__init__.py
diff --git a/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
similarity index 100%
rename from iterative_refinement/expectation_maximization.py
rename to reconstructSPI/iterative_refinement/expectation_maximization.py

From a2f4b52ee46cb199be6c10c7f2ebffb9f7f34bf1 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 12:08:09 -0700
Subject: [PATCH 090/148] Test framework adjustment

---
 .github/workflows/lint.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 9240dcc..cfc5574 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -51,4 +51,4 @@ jobs:
           isort --profile black --check .
       - name: linting [flake8]
         run: |
-          flake8 iterative_refinement tests
+          flake8 reconstructSPI tests

From 17f94cabb889a53940a0fa1d85c1a56f9bfb4622 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 12:09:53 -0700
Subject: [PATCH 091/148] Import change

---
 tests/test_expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 1abf260..e64742d 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -3,7 +3,7 @@
 import numpy as np
 import pytest
 
-from iterative_refinement import expectation_maximization as em
+from reconstructSPI.iterative_refinement import expectation_maximization as em
 
 
 @pytest.fixture

From 9f7ee213a8f3de012b3f99334bb480eedb236b99 Mon Sep 17 00:00:00 2001
From: thisTyler <theim@outlook.com>
Date: Thu, 24 Mar 2022 12:53:01 -0700
Subject: [PATCH 092/148] Small typo fixes

---
 .flake8                                                       | 2 +-
 .../iterative_refinement/expectation_maximization.py          | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.flake8 b/.flake8
index cbc6363..ece9ae4 100644
--- a/.flake8
+++ b/.flake8
@@ -3,4 +3,4 @@ docstring-convention = numpy
 import_order_style = smarkets
 max-line-length = 88
 extend-ignore = E203,I202,I100
-exclude = reconstructSPI/__init__.py,tests/__init__.py
+exclude = reconstructSPI/__init__.py,reconstructSPI/iterative_refinement/__init.py,tests/__init__.py
diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index b643910..ebac87b 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -1,11 +1,11 @@
-"""Iterative refinement with Bayesian expection maximization."""
+"""Iterative refinement with Bayesian expectation maximization."""
 
 import numpy as np
 from simSPI.transfer import eval_ctf
 
 
 class IterativeRefinement:
-    """Perform iterative refinement with max likelihood esimation.
+    """Perform iterative refinement with max likelihood estimation.
 
     Parameters
     ----------

From 0d418b980b6476913dd00a4f9c8283835b33524c Mon Sep 17 00:00:00 2001
From: thisTyler <theim@outlook.com>
Date: Thu, 24 Mar 2022 13:09:30 -0700
Subject: [PATCH 093/148] Added a slightly more comprehensive split test

---
 .../iterative_refinement/expectation_maximization.py     | 2 +-
 tests/test_expectation_maximization.py                   | 9 +++++++--
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index ebac87b..17ec2f7 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -62,7 +62,7 @@ def split_array(arr):
         arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
 
         if arr_1.shape[0] != arr_2.shape[0]:
-            arr_2 = arr[idx_half : 2 * idx_half]
+            arr_2 = arr[idx_half: 2 * idx_half]
 
         return arr_1, arr_2
 
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index e64742d..19fd7a7 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -40,8 +40,13 @@ def test_split_array(test_ir, n):
     """Test splitting of array in two halves."""
     arr = np.zeros(n)
     arr1, arr2 = test_ir.split_array(arr)
-    assert arr1.shape == (n / 2,)
-    assert arr2.shape == (n / 2,)
+    assert arr1.shape == (n // 2,)
+    assert arr2.shape == (n // 2,)
+
+    arr = np.zeros(n + 1)
+    arr1, arr2 = test_ir.split_array(arr)
+    assert arr1.shape == ((n + 1) // 2,)
+    assert arr2.shape == ((n + 1) // 2,)
 
 
 def test_build_ctf_array(test_ir, n):

From e6410cdb24cae91ba5c8b76f2f214a1b98316c43 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 20:09:50 +0000
Subject: [PATCH 094/148] Format code with black

---
 reconstructSPI/iterative_refinement/expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index 17ec2f7..ebac87b 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -62,7 +62,7 @@ def split_array(arr):
         arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
 
         if arr_1.shape[0] != arr_2.shape[0]:
-            arr_2 = arr[idx_half: 2 * idx_half]
+            arr_2 = arr[idx_half : 2 * idx_half]
 
         return arr_1, arr_2
 

From 511d105e39c258e2a7c0946ac4317f60fcd530f0 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 13:17:12 -0700
Subject: [PATCH 095/148] Added back references

---
 .../expectation_maximization.py                 | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index ebac87b..073a75e 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -34,6 +34,23 @@ class IterativeRefinement:
     fsc_1d : arr
         Final one dimensional fourier shell correlation.
         Shape (n_pix // 2,)
+
+    References
+    ----------
+    1. Nelson, P. C. (2019). Chapter 12 : Single Particle
+    Reconstruction in Cryo-electron Microscopy.
+            In Physical Models of Living Systems (pp. 305–325).
+            https://repository.upenn.edu/physics_papers/656/
+    2. Scheres, S. H. W. (2012). RELION: Implementation of a
+    Bayesian approach to cryo-EM structure determination.
+            Journal of Structural Biology, 180(3), 519–530.
+            http://doi.org/10.1016/j.jsb.2012.09.006
+    3. Sigworth, F. J., Doerschuk, P. C., Carazo, J.-M., & Scheres,
+    S. H. W. (2010).
+            An Introduction to Maximum-Likelihood Methods in Cryo-EM.
+            In Methods in Enzymology (1st ed., Vol. 482,
+            pp. 263–294). Elsevier Inc.
+            http://doi.org/10.1016/S0076-6879(10)82011-7
     """
 
     def __init__(self, map_3d_init, particles, ctf_info, max_itr=7):

From b575e13994a3f665521e042e055e8a2671408d0c Mon Sep 17 00:00:00 2001
From: thisTyler <theim@outlook.com>
Date: Thu, 24 Mar 2022 22:57:10 -0700
Subject: [PATCH 096/148] Added the big method

---
 .../expectation_maximization.py               | 272 ++++++++++++++++--
 tests/test_expectation_maximization.py        |  27 +-
 2 files changed, 276 insertions(+), 23 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index 073a75e..f8a0587 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -5,7 +5,7 @@
 
 
 class IterativeRefinement:
-    """Perform iterative refinement with max likelihood estimation.
+    """Iterative refinement with max likelihood estimation.
 
     Parameters
     ----------
@@ -19,22 +19,6 @@ class IterativeRefinement:
         Each dict contains CTF k,v pairs per particle.
             Shape (n_particles,)
 
-    Returns
-    -------
-    map_3d_update : arr
-        Current iteration of map.
-        Shape (n_pix, n_pix, n_pix)
-    map_3d_final : arr
-        Final updated map.
-        Shape (n_pix, n_pix, n_pix)
-    half_map_3d_final_1 : arr
-        Shape (n_pix, n_pix, n_pix)
-    half_map_3d_final_2 : arr
-        Shape (n_pix, n_pix, n_pix)
-    fsc_1d : arr
-        Final one dimensional fourier shell correlation.
-        Shape (n_pix // 2,)
-
     References
     ----------
     1. Nelson, P. C. (2019). Chapter 12 : Single Particle
@@ -59,6 +43,209 @@ def __init__(self, map_3d_init, particles, ctf_info, max_itr=7):
         self.ctf_info = ctf_info
         self.max_itr = max_itr
 
+    def iterative_refinement(self):
+        """Perform iterative refinement.
+
+        Acts in a Bayesian expectation maximization setting,
+        i.e. maximum a posteriori estimation.
+
+        Returns
+        -------
+        map_3d_update : arr
+            Current iteration of map.
+            Shape (n_pix, n_pix, n_pix)
+        map_3d_final : arr
+            Final updated map.
+            Shape (n_pix, n_pix, n_pix)
+        half_map_3d_final_1 : arr
+            Shape (n_pix, n_pix, n_pix)
+        half_map_3d_final_2 : arr
+            Shape (n_pix, n_pix, n_pix)
+        fsc_1d : arr
+            Final one dimensional fourier shell correlation.
+            Shape (n_pix,)
+        """
+
+        particles_1, particles_2 = \
+            IterativeRefinement.split_array(self.particles)
+
+        ctfs = self.build_ctf_array()
+        ctfs_1, ctfs_2 = IterativeRefinement.split_array(ctfs)
+
+        # work in Fourier space. So particles can stay in Fourier
+        # space the whole time. They are experimental measurements
+        # and are fixed in the algorithm
+        particles_f_1 = IterativeRefinement.fft_3d(particles_1)
+        particles_f_2 = IterativeRefinement.fft_3d(particles_2)
+
+        n_pix = self.map_3d_init.shape[0]
+        # suggest 32 or 64 to start with. real data will be more like
+        # 128 or 256. Can have issues with ctf at small pixels and
+        # need to zero pad to avoid artefacts. Artefacts from ctf not
+        # going to zero at edges, and sinusoidal ctf rippling too fast
+        # can zero pad when do Fourier convolution (fft is on zero
+        # padded and larger sized array)
+
+        half_map_3d_r_1, half_map_3d_r_2 = \
+            self.map_3d_init.copy(), self.map_3d_init.copy()
+        # should diverge because different particles averaging in
+
+        half_map_3d_f_1 = \
+            IterativeRefinement.fft_3d(half_map_3d_r_1)
+        half_map_3d_f_2 = \
+            IterativeRefinement.fft_3d(half_map_3d_r_2)
+
+        for iteration in range(self.max_itr):
+
+            half_map_3d_f_1 = \
+                IterativeRefinement.fft_3d(half_map_3d_r_1)
+            half_map_3d_f_2 = \
+                IterativeRefinement.fft_3d(half_map_3d_r_2)
+
+            # align particles to 3D volume
+            # decide on granularity of rotations
+            # i.e. how finely the rotational SO(3) space is sampled
+            # in a grid search. Smarter method is branch and bound...
+            # perhaps can make grid up front of slices, and then only
+            # compute norms on finer grid later. So re-use slices.
+
+            # def do_adaptive_grid_search(particle, map_3d):
+            #   a la branch and bound. Not sure exactly how you decide
+            #   how finely gridded to make it. Perhaps heuristics
+            #   based on how well the signal agrees in half_map_1,
+            #   half_map_2 (Fourier frequency).
+
+            n_rotations = 1000
+            rots = IterativeRefinement.grid_SO3_uniform(n_rotations)
+
+            xy0_plane = IterativeRefinement.generate_xy_plane(n_pix)
+
+            slices_1, xyz_rotated = \
+                IterativeRefinement.generate_slices(
+                    half_map_3d_f_1, xy0_plane, n_pix, rots
+                )
+            # Here rots are the same for the half maps,
+            # but could be different in general.
+            slices_2, xyz_rotated = \
+                IterativeRefinement.generate_slices(
+                    half_map_3d_f_2, xy0_plane, n_pix, rots
+                )
+
+            # initialize
+            # complex
+            map_3d_f_updated_1 = np.zeros_like(half_map_3d_f_1)
+            # complex
+            map_3d_f_updated_2 = np.zeros_like(half_map_3d_f_2)
+            # float/real
+            counts_3d_updated_1 = np.zeros_like(half_map_3d_r_1)
+            # float/real
+            counts_3d_updated_2 = np.zeros_like(half_map_3d_r_2)
+
+            for particle_idx in range(particles_f_1.shape[0]):
+                ctf_1 = ctfs_1[particle_idx]
+                ctf_2 = ctfs_2[particle_idx]
+                # particle_f_1 = particles_f_1[particle_idx]
+                # particle_f_2 = particles_f_2[particle_idx]
+
+                particle_f_deconv_1 = \
+                    IterativeRefinement.apply_wiener_filter(
+                        particles_f_1, ctf_1, 0.01
+                    )
+                particle_f_deconv_2 = \
+                    IterativeRefinement.apply_wiener_filter(
+                        particles_f_2, ctf_1, 0.01
+                    )
+
+                # all slices get convolved with the particle ctf
+                apply_ctf = np.vectorize(
+                    IterativeRefinement.apply_ctf_to_slice
+                )
+
+                slices_conv_ctfs_1 = apply_ctf(slices_1, ctf_1)
+                slices_conv_ctfs_2 = apply_ctf(slices_2, ctf_2)
+
+                bayes_factors_1 = \
+                    IterativeRefinement.compute_bayesian_weights(
+                        particles_f_1[particle_idx],
+                        slices_conv_ctfs_1
+                    )
+                bayes_factors_2 = \
+                    IterativeRefinement.compute_bayesian_weights(
+                        particles_f_2[particle_idx],
+                        slices_conv_ctfs_2
+                    )
+
+                for one_slice_idx in range(bayes_factors_1.shape[0]):
+                    xyz = xyz_rotated[one_slice_idx]
+                    # if this can be vectorized, can avoid loop
+                    inserted_slice_3d_r, count_3d_r = \
+                        IterativeRefinement.insert_slice(
+                            particle_f_deconv_1.real,
+                            xyz,
+                            n_pix
+                        )
+                    inserted_slice_3d_i, count_3d_i = \
+                        IterativeRefinement.insert_slice(
+                            particle_f_deconv_1.imag,
+                            xyz,
+                            n_pix
+                        )
+                    map_3d_f_updated_1 += inserted_slice_3d_r \
+                        + 1j * inserted_slice_3d_i
+                    counts_3d_updated_1 += count_3d_r + count_3d_i
+
+                for one_slice_idx in range(bayes_factors_2.shape[0]):
+                    xyz = xyz_rotated[one_slice_idx]
+                    inserted_slice_3d_r, count_3d_r = \
+                        IterativeRefinement.insert_slice(
+                            particle_f_deconv_2.real,
+                            xyz,
+                            n_pix
+                        )
+                    inserted_slice_3d_i, count_3d_i = \
+                        IterativeRefinement.insert_slice(
+                            particle_f_deconv_2.imag,
+                            xyz,
+                            n_pix
+                        )
+                    map_3d_f_updated_2 += inserted_slice_3d_r \
+                        + 1j * inserted_slice_3d_i
+                    counts_3d_updated_2 += count_3d_r + count_3d_i
+
+            # apply noise model
+            # half_map_1, half_map_2 come from doing the above
+            # independently. Filter by noise estimate (e.g. multiply
+            # both half maps by FSC)
+            fsc_1d = IterativeRefinement.compute_fsc(
+                map_3d_f_updated_1, map_3d_f_updated_2
+            )
+
+            fsc_3d = IterativeRefinement.expand_1d_to_3d(fsc_1d)
+
+            # multiplicative filter on maps with fsc
+            # The FSC is 1D, one number per spherical shells
+            # it can be expanded back to a multiplicative filter of the same shape as the maps
+            map_3d_f_filtered_1 = map_3d_f_updated_1 * fsc_3d
+            map_3d_f_filtered_2 = map_3d_f_updated_2 * fsc_3d
+
+            # update iteration
+            half_map_3d_f_1 = map_3d_f_filtered_1
+            half_map_3d_f_2 = map_3d_f_filtered_2
+
+        # final map
+        fsc_1d = IterativeRefinement.compute_fsc(
+            half_map_3d_f_1, half_map_3d_f_2
+        )
+        fsc_3d = IterativeRefinement.expand_1d_to_3d(fsc_1d)
+        map_3d_f_final = \
+            (half_map_3d_f_1 + half_map_3d_f_2 / 2) * fsc_3d
+        map_3d_r_final = IterativeRefinement.ifft_3d(map_3d_f_final)
+        half_map_3d_r_1 = IterativeRefinement.ifft_3d(half_map_3d_f_1)
+        half_map_3d_r_2 = IterativeRefinement.ifft_3d(half_map_3d_f_2)
+
+        return map_3d_r_final, half_map_3d_r_1, \
+            half_map_3d_r_2, fsc_1d
+
     @staticmethod
     def split_array(arr):
         """Split array into two halves along 0th axis.
@@ -273,7 +460,7 @@ def insert_slice(slice_real, xyz, n_pix):
         return inserted_slice_3d, count_3d
 
     @staticmethod
-    def compute_fsc(map_3d_f_1):
+    def compute_fsc(map_3d_f_1, map_3d_f_2):
         """Compute Fourier shell correlation.
 
                 Estimate noise from half maps.
@@ -282,20 +469,25 @@ def compute_fsc(map_3d_f_1):
         ----------
         map_3d_f_1 : arr
             Shape (n_pix, n_pix, n_pix)
+        map_3d_f_2 : arr
+            Shape (n_pix, n_pix, n_pix)
 
         Returns
         -------
-        fsc_1d_1 : arr
-            Noise estimates for map 1.
-            Shape (n_pix // 2,)
+        noise_estimate : arr
+            Noise estimates from half maps.
+            Shape (n_pix,)
         """
         # write fast vectorized fsc from code snippets in
         # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/fsc.ipynb
         # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/mFSC.ipynb
         # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/guinier_fsc_sharpen.ipynb
         n_pix_1 = map_3d_f_1.shape[0]
+        n_pix_2 = map_3d_f_2.shape[0]
         fsc_1d_1 = np.ones(n_pix_1 // 2)
-        return fsc_1d_1
+        fsc_1d_2 = np.ones(n_pix_2 // 2)
+        noise_estimates = np.concatenate(fsc_1d_1, fsc_1d_2)
+        return noise_estimates
 
     @staticmethod
     def expand_1d_to_3d(arr_1d):
@@ -315,3 +507,39 @@ def expand_1d_to_3d(arr_1d):
         arr_3d = np.ones((n_pix, n_pix, n_pix))
         # arr_1d fsc_1d to 3d (spherical shells)
         return arr_3d
+
+    @staticmethod
+    def fft_3d(array):
+        """3D Fast Fourier Transform.
+
+        Parameters
+        ----------
+        array : arr
+            Input array.
+            Shape (n, n, n)
+
+        Returns
+        -------
+        fft_array : arr
+            Fourier transform of array.
+            Shape (n, n, n)
+        """
+        return array.copy()
+
+    @staticmethod
+    def ifft_3d(fft_array):
+        """3D Inverse Fast Fourier Transform.
+
+        Parameters
+        ----------
+        fft_array : arr
+            Fourier transform of array.
+            Shape (n, n, n)
+
+        Returns
+        -------
+        array : arr
+            Original array.
+            Shape (n, n, n)
+        """
+        return fft_array.copy()
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 19fd7a7..02276dc 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -31,7 +31,7 @@ def test_ir(n):
     ctf_info = [
         ex_ctf,
     ] * n
-    itr = 7
+    itr = 2
     ir = em.IterativeRefinement(map_3d, particles, ctf_info, itr)
     return ir
 
@@ -49,6 +49,20 @@ def test_split_array(test_ir, n):
     assert arr2.shape == ((n + 1) // 2,)
 
 
+def test_fft_3d(test_ir, n):
+    """Test 3D fourier transform."""
+    arr = np.zeros((n, n, n))
+    fft_arr = test_ir.fft_3d(arr)
+    assert fft_arr.shape == arr.shape
+
+
+def test_ifft_3d(test_ir, n):
+    """Test 3D inverse fourier transform."""
+    fft_arr = np.zeros((n, n, n))
+    arr = test_ir.fft_3d(fft_arr)
+    assert fft_arr.shape == arr.shape
+
+
 def test_build_ctf_array(test_ir, n):
     """Test bulding arbitrary CTF array."""
     ctfs = test_ir.build_ctf_array()
@@ -136,3 +150,14 @@ def test_expand_1d_to_3d(test_ir, n):
     spherical = test_ir.expand_1d_to_3d(arr1d)
 
     assert spherical.shape == (n, n, n)
+
+
+def test_iterative_refinement(test_ir, n):
+    """Test complete iterative refinement algorithm."""
+    map_3d_r_final, half_map_3d_r_1, \
+        half_map_3d_r_2, fsc_1d = test_ir.iterative_refinement()
+
+    assert map_3d_r_final.shape == (n, n, n)
+    assert half_map_3d_r_1.shape == (n, n, n)
+    assert half_map_3d_r_2.shape == (n, n, n)
+    assert fsc_1d.shape == (n,)

From 41a5807702641e6b3f259791475f251c5e1de7f1 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Fri, 25 Mar 2022 05:58:39 +0000
Subject: [PATCH 097/148] Format code with black

---
 .../expectation_maximization.py               | 121 +++++++-----------
 tests/test_expectation_maximization.py        |   8 +-
 2 files changed, 51 insertions(+), 78 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index f8a0587..a280cd1 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -66,8 +66,7 @@ def iterative_refinement(self):
             Shape (n_pix,)
         """
 
-        particles_1, particles_2 = \
-            IterativeRefinement.split_array(self.particles)
+        particles_1, particles_2 = IterativeRefinement.split_array(self.particles)
 
         ctfs = self.build_ctf_array()
         ctfs_1, ctfs_2 = IterativeRefinement.split_array(ctfs)
@@ -86,21 +85,19 @@ def iterative_refinement(self):
         # can zero pad when do Fourier convolution (fft is on zero
         # padded and larger sized array)
 
-        half_map_3d_r_1, half_map_3d_r_2 = \
-            self.map_3d_init.copy(), self.map_3d_init.copy()
+        half_map_3d_r_1, half_map_3d_r_2 = (
+            self.map_3d_init.copy(),
+            self.map_3d_init.copy(),
+        )
         # should diverge because different particles averaging in
 
-        half_map_3d_f_1 = \
-            IterativeRefinement.fft_3d(half_map_3d_r_1)
-        half_map_3d_f_2 = \
-            IterativeRefinement.fft_3d(half_map_3d_r_2)
+        half_map_3d_f_1 = IterativeRefinement.fft_3d(half_map_3d_r_1)
+        half_map_3d_f_2 = IterativeRefinement.fft_3d(half_map_3d_r_2)
 
         for iteration in range(self.max_itr):
 
-            half_map_3d_f_1 = \
-                IterativeRefinement.fft_3d(half_map_3d_r_1)
-            half_map_3d_f_2 = \
-                IterativeRefinement.fft_3d(half_map_3d_r_2)
+            half_map_3d_f_1 = IterativeRefinement.fft_3d(half_map_3d_r_1)
+            half_map_3d_f_2 = IterativeRefinement.fft_3d(half_map_3d_r_2)
 
             # align particles to 3D volume
             # decide on granularity of rotations
@@ -120,16 +117,14 @@ def iterative_refinement(self):
 
             xy0_plane = IterativeRefinement.generate_xy_plane(n_pix)
 
-            slices_1, xyz_rotated = \
-                IterativeRefinement.generate_slices(
-                    half_map_3d_f_1, xy0_plane, n_pix, rots
-                )
+            slices_1, xyz_rotated = IterativeRefinement.generate_slices(
+                half_map_3d_f_1, xy0_plane, n_pix, rots
+            )
             # Here rots are the same for the half maps,
             # but could be different in general.
-            slices_2, xyz_rotated = \
-                IterativeRefinement.generate_slices(
-                    half_map_3d_f_2, xy0_plane, n_pix, rots
-                )
+            slices_2, xyz_rotated = IterativeRefinement.generate_slices(
+                half_map_3d_f_2, xy0_plane, n_pix, rots
+            )
 
             # initialize
             # complex
@@ -147,69 +142,47 @@ def iterative_refinement(self):
                 # particle_f_1 = particles_f_1[particle_idx]
                 # particle_f_2 = particles_f_2[particle_idx]
 
-                particle_f_deconv_1 = \
-                    IterativeRefinement.apply_wiener_filter(
-                        particles_f_1, ctf_1, 0.01
-                    )
-                particle_f_deconv_2 = \
-                    IterativeRefinement.apply_wiener_filter(
-                        particles_f_2, ctf_1, 0.01
-                    )
+                particle_f_deconv_1 = IterativeRefinement.apply_wiener_filter(
+                    particles_f_1, ctf_1, 0.01
+                )
+                particle_f_deconv_2 = IterativeRefinement.apply_wiener_filter(
+                    particles_f_2, ctf_1, 0.01
+                )
 
                 # all slices get convolved with the particle ctf
-                apply_ctf = np.vectorize(
-                    IterativeRefinement.apply_ctf_to_slice
-                )
+                apply_ctf = np.vectorize(IterativeRefinement.apply_ctf_to_slice)
 
                 slices_conv_ctfs_1 = apply_ctf(slices_1, ctf_1)
                 slices_conv_ctfs_2 = apply_ctf(slices_2, ctf_2)
 
-                bayes_factors_1 = \
-                    IterativeRefinement.compute_bayesian_weights(
-                        particles_f_1[particle_idx],
-                        slices_conv_ctfs_1
-                    )
-                bayes_factors_2 = \
-                    IterativeRefinement.compute_bayesian_weights(
-                        particles_f_2[particle_idx],
-                        slices_conv_ctfs_2
-                    )
+                bayes_factors_1 = IterativeRefinement.compute_bayesian_weights(
+                    particles_f_1[particle_idx], slices_conv_ctfs_1
+                )
+                bayes_factors_2 = IterativeRefinement.compute_bayesian_weights(
+                    particles_f_2[particle_idx], slices_conv_ctfs_2
+                )
 
                 for one_slice_idx in range(bayes_factors_1.shape[0]):
                     xyz = xyz_rotated[one_slice_idx]
                     # if this can be vectorized, can avoid loop
-                    inserted_slice_3d_r, count_3d_r = \
-                        IterativeRefinement.insert_slice(
-                            particle_f_deconv_1.real,
-                            xyz,
-                            n_pix
-                        )
-                    inserted_slice_3d_i, count_3d_i = \
-                        IterativeRefinement.insert_slice(
-                            particle_f_deconv_1.imag,
-                            xyz,
-                            n_pix
-                        )
-                    map_3d_f_updated_1 += inserted_slice_3d_r \
-                        + 1j * inserted_slice_3d_i
+                    inserted_slice_3d_r, count_3d_r = IterativeRefinement.insert_slice(
+                        particle_f_deconv_1.real, xyz, n_pix
+                    )
+                    inserted_slice_3d_i, count_3d_i = IterativeRefinement.insert_slice(
+                        particle_f_deconv_1.imag, xyz, n_pix
+                    )
+                    map_3d_f_updated_1 += inserted_slice_3d_r + 1j * inserted_slice_3d_i
                     counts_3d_updated_1 += count_3d_r + count_3d_i
 
                 for one_slice_idx in range(bayes_factors_2.shape[0]):
                     xyz = xyz_rotated[one_slice_idx]
-                    inserted_slice_3d_r, count_3d_r = \
-                        IterativeRefinement.insert_slice(
-                            particle_f_deconv_2.real,
-                            xyz,
-                            n_pix
-                        )
-                    inserted_slice_3d_i, count_3d_i = \
-                        IterativeRefinement.insert_slice(
-                            particle_f_deconv_2.imag,
-                            xyz,
-                            n_pix
-                        )
-                    map_3d_f_updated_2 += inserted_slice_3d_r \
-                        + 1j * inserted_slice_3d_i
+                    inserted_slice_3d_r, count_3d_r = IterativeRefinement.insert_slice(
+                        particle_f_deconv_2.real, xyz, n_pix
+                    )
+                    inserted_slice_3d_i, count_3d_i = IterativeRefinement.insert_slice(
+                        particle_f_deconv_2.imag, xyz, n_pix
+                    )
+                    map_3d_f_updated_2 += inserted_slice_3d_r + 1j * inserted_slice_3d_i
                     counts_3d_updated_2 += count_3d_r + count_3d_i
 
             # apply noise model
@@ -233,18 +206,14 @@ def iterative_refinement(self):
             half_map_3d_f_2 = map_3d_f_filtered_2
 
         # final map
-        fsc_1d = IterativeRefinement.compute_fsc(
-            half_map_3d_f_1, half_map_3d_f_2
-        )
+        fsc_1d = IterativeRefinement.compute_fsc(half_map_3d_f_1, half_map_3d_f_2)
         fsc_3d = IterativeRefinement.expand_1d_to_3d(fsc_1d)
-        map_3d_f_final = \
-            (half_map_3d_f_1 + half_map_3d_f_2 / 2) * fsc_3d
+        map_3d_f_final = (half_map_3d_f_1 + half_map_3d_f_2 / 2) * fsc_3d
         map_3d_r_final = IterativeRefinement.ifft_3d(map_3d_f_final)
         half_map_3d_r_1 = IterativeRefinement.ifft_3d(half_map_3d_f_1)
         half_map_3d_r_2 = IterativeRefinement.ifft_3d(half_map_3d_f_2)
 
-        return map_3d_r_final, half_map_3d_r_1, \
-            half_map_3d_r_2, fsc_1d
+        return map_3d_r_final, half_map_3d_r_1, half_map_3d_r_2, fsc_1d
 
     @staticmethod
     def split_array(arr):
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 02276dc..d1b4785 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -154,8 +154,12 @@ def test_expand_1d_to_3d(test_ir, n):
 
 def test_iterative_refinement(test_ir, n):
     """Test complete iterative refinement algorithm."""
-    map_3d_r_final, half_map_3d_r_1, \
-        half_map_3d_r_2, fsc_1d = test_ir.iterative_refinement()
+    (
+        map_3d_r_final,
+        half_map_3d_r_1,
+        half_map_3d_r_2,
+        fsc_1d,
+    ) = test_ir.iterative_refinement()
 
     assert map_3d_r_final.shape == (n, n, n)
     assert half_map_3d_r_1.shape == (n, n, n)

From 22efe76329bbb6f083e6e712ce6625cd361addda Mon Sep 17 00:00:00 2001
From: thisTyler <theim@outlook.com>
Date: Thu, 24 Mar 2022 22:59:32 -0700
Subject: [PATCH 098/148] Pre-commit and black changes

---
 .../expectation_maximization.py               | 125 +++++++-----------
 tests/test_expectation_maximization.py        |   8 +-
 2 files changed, 53 insertions(+), 80 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index f8a0587..9288a13 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -65,9 +65,7 @@ def iterative_refinement(self):
             Final one dimensional fourier shell correlation.
             Shape (n_pix,)
         """
-
-        particles_1, particles_2 = \
-            IterativeRefinement.split_array(self.particles)
+        particles_1, particles_2 = IterativeRefinement.split_array(self.particles)
 
         ctfs = self.build_ctf_array()
         ctfs_1, ctfs_2 = IterativeRefinement.split_array(ctfs)
@@ -86,21 +84,19 @@ def iterative_refinement(self):
         # can zero pad when do Fourier convolution (fft is on zero
         # padded and larger sized array)
 
-        half_map_3d_r_1, half_map_3d_r_2 = \
-            self.map_3d_init.copy(), self.map_3d_init.copy()
+        half_map_3d_r_1, half_map_3d_r_2 = (
+            self.map_3d_init.copy(),
+            self.map_3d_init.copy(),
+        )
         # should diverge because different particles averaging in
 
-        half_map_3d_f_1 = \
-            IterativeRefinement.fft_3d(half_map_3d_r_1)
-        half_map_3d_f_2 = \
-            IterativeRefinement.fft_3d(half_map_3d_r_2)
+        half_map_3d_f_1 = IterativeRefinement.fft_3d(half_map_3d_r_1)
+        half_map_3d_f_2 = IterativeRefinement.fft_3d(half_map_3d_r_2)
 
         for iteration in range(self.max_itr):
 
-            half_map_3d_f_1 = \
-                IterativeRefinement.fft_3d(half_map_3d_r_1)
-            half_map_3d_f_2 = \
-                IterativeRefinement.fft_3d(half_map_3d_r_2)
+            half_map_3d_f_1 = IterativeRefinement.fft_3d(half_map_3d_r_1)
+            half_map_3d_f_2 = IterativeRefinement.fft_3d(half_map_3d_r_2)
 
             # align particles to 3D volume
             # decide on granularity of rotations
@@ -120,16 +116,14 @@ def iterative_refinement(self):
 
             xy0_plane = IterativeRefinement.generate_xy_plane(n_pix)
 
-            slices_1, xyz_rotated = \
-                IterativeRefinement.generate_slices(
-                    half_map_3d_f_1, xy0_plane, n_pix, rots
-                )
+            slices_1, xyz_rotated = IterativeRefinement.generate_slices(
+                half_map_3d_f_1, xy0_plane, n_pix, rots
+            )
             # Here rots are the same for the half maps,
             # but could be different in general.
-            slices_2, xyz_rotated = \
-                IterativeRefinement.generate_slices(
-                    half_map_3d_f_2, xy0_plane, n_pix, rots
-                )
+            slices_2, xyz_rotated = IterativeRefinement.generate_slices(
+                half_map_3d_f_2, xy0_plane, n_pix, rots
+            )
 
             # initialize
             # complex
@@ -147,69 +141,47 @@ def iterative_refinement(self):
                 # particle_f_1 = particles_f_1[particle_idx]
                 # particle_f_2 = particles_f_2[particle_idx]
 
-                particle_f_deconv_1 = \
-                    IterativeRefinement.apply_wiener_filter(
-                        particles_f_1, ctf_1, 0.01
-                    )
-                particle_f_deconv_2 = \
-                    IterativeRefinement.apply_wiener_filter(
-                        particles_f_2, ctf_1, 0.01
-                    )
+                particle_f_deconv_1 = IterativeRefinement.apply_wiener_filter(
+                    particles_f_1, ctf_1, 0.01
+                )
+                particle_f_deconv_2 = IterativeRefinement.apply_wiener_filter(
+                    particles_f_2, ctf_1, 0.01
+                )
 
                 # all slices get convolved with the particle ctf
-                apply_ctf = np.vectorize(
-                    IterativeRefinement.apply_ctf_to_slice
-                )
+                apply_ctf = np.vectorize(IterativeRefinement.apply_ctf_to_slice)
 
                 slices_conv_ctfs_1 = apply_ctf(slices_1, ctf_1)
                 slices_conv_ctfs_2 = apply_ctf(slices_2, ctf_2)
 
-                bayes_factors_1 = \
-                    IterativeRefinement.compute_bayesian_weights(
-                        particles_f_1[particle_idx],
-                        slices_conv_ctfs_1
-                    )
-                bayes_factors_2 = \
-                    IterativeRefinement.compute_bayesian_weights(
-                        particles_f_2[particle_idx],
-                        slices_conv_ctfs_2
-                    )
+                bayes_factors_1 = IterativeRefinement.compute_bayesian_weights(
+                    particles_f_1[particle_idx], slices_conv_ctfs_1
+                )
+                bayes_factors_2 = IterativeRefinement.compute_bayesian_weights(
+                    particles_f_2[particle_idx], slices_conv_ctfs_2
+                )
 
                 for one_slice_idx in range(bayes_factors_1.shape[0]):
                     xyz = xyz_rotated[one_slice_idx]
                     # if this can be vectorized, can avoid loop
-                    inserted_slice_3d_r, count_3d_r = \
-                        IterativeRefinement.insert_slice(
-                            particle_f_deconv_1.real,
-                            xyz,
-                            n_pix
-                        )
-                    inserted_slice_3d_i, count_3d_i = \
-                        IterativeRefinement.insert_slice(
-                            particle_f_deconv_1.imag,
-                            xyz,
-                            n_pix
-                        )
-                    map_3d_f_updated_1 += inserted_slice_3d_r \
-                        + 1j * inserted_slice_3d_i
+                    inserted_slice_3d_r, count_3d_r = IterativeRefinement.insert_slice(
+                        particle_f_deconv_1.real, xyz, n_pix
+                    )
+                    inserted_slice_3d_i, count_3d_i = IterativeRefinement.insert_slice(
+                        particle_f_deconv_1.imag, xyz, n_pix
+                    )
+                    map_3d_f_updated_1 += inserted_slice_3d_r + 1j * inserted_slice_3d_i
                     counts_3d_updated_1 += count_3d_r + count_3d_i
 
                 for one_slice_idx in range(bayes_factors_2.shape[0]):
                     xyz = xyz_rotated[one_slice_idx]
-                    inserted_slice_3d_r, count_3d_r = \
-                        IterativeRefinement.insert_slice(
-                            particle_f_deconv_2.real,
-                            xyz,
-                            n_pix
-                        )
-                    inserted_slice_3d_i, count_3d_i = \
-                        IterativeRefinement.insert_slice(
-                            particle_f_deconv_2.imag,
-                            xyz,
-                            n_pix
-                        )
-                    map_3d_f_updated_2 += inserted_slice_3d_r \
-                        + 1j * inserted_slice_3d_i
+                    inserted_slice_3d_r, count_3d_r = IterativeRefinement.insert_slice(
+                        particle_f_deconv_2.real, xyz, n_pix
+                    )
+                    inserted_slice_3d_i, count_3d_i = IterativeRefinement.insert_slice(
+                        particle_f_deconv_2.imag, xyz, n_pix
+                    )
+                    map_3d_f_updated_2 += inserted_slice_3d_r + 1j * inserted_slice_3d_i
                     counts_3d_updated_2 += count_3d_r + count_3d_i
 
             # apply noise model
@@ -224,7 +196,8 @@ def iterative_refinement(self):
 
             # multiplicative filter on maps with fsc
             # The FSC is 1D, one number per spherical shells
-            # it can be expanded back to a multiplicative filter of the same shape as the maps
+            # it can be expanded back to a multiplicative filter of
+            # the same shape as the maps
             map_3d_f_filtered_1 = map_3d_f_updated_1 * fsc_3d
             map_3d_f_filtered_2 = map_3d_f_updated_2 * fsc_3d
 
@@ -233,18 +206,14 @@ def iterative_refinement(self):
             half_map_3d_f_2 = map_3d_f_filtered_2
 
         # final map
-        fsc_1d = IterativeRefinement.compute_fsc(
-            half_map_3d_f_1, half_map_3d_f_2
-        )
+        fsc_1d = IterativeRefinement.compute_fsc(half_map_3d_f_1, half_map_3d_f_2)
         fsc_3d = IterativeRefinement.expand_1d_to_3d(fsc_1d)
-        map_3d_f_final = \
-            (half_map_3d_f_1 + half_map_3d_f_2 / 2) * fsc_3d
+        map_3d_f_final = (half_map_3d_f_1 + half_map_3d_f_2 / 2) * fsc_3d
         map_3d_r_final = IterativeRefinement.ifft_3d(map_3d_f_final)
         half_map_3d_r_1 = IterativeRefinement.ifft_3d(half_map_3d_f_1)
         half_map_3d_r_2 = IterativeRefinement.ifft_3d(half_map_3d_f_2)
 
-        return map_3d_r_final, half_map_3d_r_1, \
-            half_map_3d_r_2, fsc_1d
+        return map_3d_r_final, half_map_3d_r_1, half_map_3d_r_2, fsc_1d
 
     @staticmethod
     def split_array(arr):
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 02276dc..d1b4785 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -154,8 +154,12 @@ def test_expand_1d_to_3d(test_ir, n):
 
 def test_iterative_refinement(test_ir, n):
     """Test complete iterative refinement algorithm."""
-    map_3d_r_final, half_map_3d_r_1, \
-        half_map_3d_r_2, fsc_1d = test_ir.iterative_refinement()
+    (
+        map_3d_r_final,
+        half_map_3d_r_1,
+        half_map_3d_r_2,
+        fsc_1d,
+    ) = test_ir.iterative_refinement()
 
     assert map_3d_r_final.shape == (n, n, n)
     assert half_map_3d_r_1.shape == (n, n, n)

From bda6275c1199a5b28ae5ea67fe118b5e740a51ba Mon Sep 17 00:00:00 2001
From: thisTyler <theim@outlook.com>
Date: Thu, 24 Mar 2022 23:03:05 -0700
Subject: [PATCH 099/148] Deepsource

---
 .../iterative_refinement/expectation_maximization.py      | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index 9288a13..1b30a75 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -93,7 +93,7 @@ def iterative_refinement(self):
         half_map_3d_f_1 = IterativeRefinement.fft_3d(half_map_3d_r_1)
         half_map_3d_f_2 = IterativeRefinement.fft_3d(half_map_3d_r_2)
 
-        for iteration in range(self.max_itr):
+        for _ in range(self.max_itr):
 
             half_map_3d_f_1 = IterativeRefinement.fft_3d(half_map_3d_r_1)
             half_map_3d_f_2 = IterativeRefinement.fft_3d(half_map_3d_r_2)
@@ -125,7 +125,7 @@ def iterative_refinement(self):
                 half_map_3d_f_2, xy0_plane, n_pix, rots
             )
 
-            # initialize
+            # initialize:
             # complex
             map_3d_f_updated_1 = np.zeros_like(half_map_3d_f_1)
             # complex
@@ -138,8 +138,8 @@ def iterative_refinement(self):
             for particle_idx in range(particles_f_1.shape[0]):
                 ctf_1 = ctfs_1[particle_idx]
                 ctf_2 = ctfs_2[particle_idx]
-                # particle_f_1 = particles_f_1[particle_idx]
-                # particle_f_2 = particles_f_2[particle_idx]
+                # Option: particle_f_1 = particles_f_1[particle_idx]
+                # Option: particle_f_2 = particles_f_2[particle_idx]
 
                 particle_f_deconv_1 = IterativeRefinement.apply_wiener_filter(
                     particles_f_1, ctf_1, 0.01

From 976be19f6dc59139e3633b8ef6388c63b626c436 Mon Sep 17 00:00:00 2001
From: thisTyler <theim@outlook.com>
Date: Thu, 24 Mar 2022 23:09:15 -0700
Subject: [PATCH 100/148] Expanded split_array to allow lists and tuples

---
 .../iterative_refinement/expectation_maximization.py         | 5 ++++-
 tests/test_expectation_maximization.py                       | 5 +++++
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index 1b30a75..4eea545 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -231,7 +231,10 @@ def split_array(arr):
         arr2: arr
             Shape (n_particles // 2, ...)
         """
-        idx_half = arr.shape[0] // 2
+        if isinstance(arr, list) or isinstance(arr, tuple):
+            idx_half = len(arr) // 2
+        else:
+            idx_half = arr.shape[0] // 2
         arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
 
         if arr_1.shape[0] != arr_2.shape[0]:
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index d1b4785..9e139a9 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -48,6 +48,11 @@ def test_split_array(test_ir, n):
     assert arr1.shape == ((n + 1) // 2,)
     assert arr2.shape == ((n + 1) // 2,)
 
+    arr = ['a', 'b']
+    arr1, arr2 = test_ir.split_array(arr)
+    assert len(arr1) == 1
+    assert len(arr2) == 1
+
 
 def test_fft_3d(test_ir, n):
     """Test 3D fourier transform."""

From 00e72810c43b3fd0ca881d165d905420c340f8f1 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Fri, 25 Mar 2022 06:09:44 +0000
Subject: [PATCH 101/148] Format code with black

---
 tests/test_expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 9e139a9..a261e28 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -48,7 +48,7 @@ def test_split_array(test_ir, n):
     assert arr1.shape == ((n + 1) // 2,)
     assert arr2.shape == ((n + 1) // 2,)
 
-    arr = ['a', 'b']
+    arr = ["a", "b"]
     arr1, arr2 = test_ir.split_array(arr)
     assert len(arr1) == 1
     assert len(arr2) == 1

From ff3658877d9101e5d87881a09aca4b620894eb4b Mon Sep 17 00:00:00 2001
From: thisTyler <theim@outlook.com>
Date: Thu, 24 Mar 2022 23:11:01 -0700
Subject: [PATCH 102/148] Deepsource fix

---
 reconstructSPI/iterative_refinement/expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index 4eea545..c63637f 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -231,7 +231,7 @@ def split_array(arr):
         arr2: arr
             Shape (n_particles // 2, ...)
         """
-        if isinstance(arr, list) or isinstance(arr, tuple):
+        if isinstance(arr, (list, tuple)):
             idx_half = len(arr) // 2
         else:
             idx_half = arr.shape[0] // 2

From b8e37ef6978e5e77a67c730b80997c7a16602839 Mon Sep 17 00:00:00 2001
From: thisTyler <theim@outlook.com>
Date: Thu, 24 Mar 2022 23:17:43 -0700
Subject: [PATCH 103/148] Fixed split_array expansion

---
 .../iterative_refinement/expectation_maximization.py   | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index c63637f..bb13db7 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -233,12 +233,16 @@ def split_array(arr):
         """
         if isinstance(arr, (list, tuple)):
             idx_half = len(arr) // 2
+            arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
+
+            if len(arr_1) != len(arr_2):
+                arr_2 = arr[idx_half : 2 * idx_half]
         else:
             idx_half = arr.shape[0] // 2
-        arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
+            arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
 
-        if arr_1.shape[0] != arr_2.shape[0]:
-            arr_2 = arr[idx_half : 2 * idx_half]
+            if arr_1.shape[0] != arr_2.shape[0]:
+                arr_2 = arr[idx_half : 2 * idx_half]
 
         return arr_1, arr_2
 

From abfd9aa5be4a53d0988b068de9238cc29ce605f6 Mon Sep 17 00:00:00 2001
From: thisTyler <theim@outlook.com>
Date: Thu, 24 Mar 2022 23:20:14 -0700
Subject: [PATCH 104/148] Fix to fsc test

---
 tests/test_expectation_maximization.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index a261e28..643dd41 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -144,9 +144,10 @@ def test_insert_slice(test_ir, n):
 def test_compute_fsc(test_ir, n):
     """Test computation of FSC."""
     map_1 = np.ones((n, n, n))
+    map_2 = np.ones((n, n, n))
 
-    fsc_1 = test_ir.compute_fsc(map_1)
-    assert fsc_1.shape == (1,)
+    fsc_1 = test_ir.compute_fsc(map_1, map_2)
+    assert fsc_1.shape == (n,)
 
 
 def test_expand_1d_to_3d(test_ir, n):

From e1cd12054136efd47a8011400ba1b8613bae3eae Mon Sep 17 00:00:00 2001
From: thisTyler <theim@outlook.com>
Date: Thu, 24 Mar 2022 23:34:26 -0700
Subject: [PATCH 105/148] Data type fix

---
 .../iterative_refinement/expectation_maximization.py          | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index bb13db7..7e0d906 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -500,7 +500,7 @@ def fft_3d(array):
             Fourier transform of array.
             Shape (n, n, n)
         """
-        return array.copy()
+        return np.zeros(array.shape, dtype=np.cdouble)
 
     @staticmethod
     def ifft_3d(fft_array):
@@ -518,4 +518,4 @@ def ifft_3d(fft_array):
             Original array.
             Shape (n, n, n)
         """
-        return fft_array.copy()
+        return np.zeros(fft_array.shape)

From 83d9cf7ab1c1704d102bff26cee7e1dd461df07c Mon Sep 17 00:00:00 2001
From: thisTyler <theim@outlook.com>
Date: Thu, 24 Mar 2022 23:35:36 -0700
Subject: [PATCH 106/148] Concatenate fix

---
 reconstructSPI/iterative_refinement/expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index 7e0d906..bc30317 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -462,7 +462,7 @@ def compute_fsc(map_3d_f_1, map_3d_f_2):
         n_pix_2 = map_3d_f_2.shape[0]
         fsc_1d_1 = np.ones(n_pix_1 // 2)
         fsc_1d_2 = np.ones(n_pix_2 // 2)
-        noise_estimates = np.concatenate(fsc_1d_1, fsc_1d_2)
+        noise_estimates = np.concatenate((fsc_1d_1, fsc_1d_2))
         return noise_estimates
 
     @staticmethod

From f8dc07a0ef3b94f0878a918ee486e848952025af Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 23:52:43 -0700
Subject: [PATCH 107/148] Change to insert slice shape

---
 .../iterative_refinement/expectation_maximization.py     | 9 +++++----
 tests/test_expectation_maximization.py                   | 4 ++--
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index bc30317..faaa659 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -424,15 +424,16 @@ def insert_slice(slice_real, xyz, n_pix):
         -------
         inserted_slice_3d : float64 arr
             Rotated slice in 3D voxel array.
-            Shape (n_pix**2, 3)
+            Shape (n_pix, n_pix, n_pix)
         count_3d : arr
             Voxel array to count slice presence: 1 if slice present,
             otherwise 0.
-            Shape (n_pix**2, 3)
+            Shape (n_pix, n_pix, n_pix)
         """
         shape = xyz.shape[0]
-        count_3d = np.ones((shape, 3))
-        inserted_slice_3d = np.ones((shape, 3))
+        count_3d = np.ones(n_pix, n_pix, n_pix)
+        count_3d[0,0,0] *= shape
+        inserted_slice_3d = np.ones(n_pix, n_pix, n_pix)
         return inserted_slice_3d, count_3d
 
     @staticmethod
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 643dd41..02701ec 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -137,8 +137,8 @@ def test_insert_slice(test_ir, n):
     xyz = test_ir.generate_xy_plane(n)
 
     inserted, count = test_ir.insert_slice(particle_slice, xyz, n)
-    assert inserted.shape == (n * n, 3)
-    assert count.shape == (n * n, 3)
+    assert inserted.shape == (n, n, n)
+    assert count.shape == (n, n, n)
 
 
 def test_compute_fsc(test_ir, n):

From 352a9898748c24a6e2272fbd5572115e9ba8b9f8 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Fri, 25 Mar 2022 06:52:50 +0000
Subject: [PATCH 108/148] Format code with black

---
 reconstructSPI/iterative_refinement/expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index faaa659..441c901 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -432,7 +432,7 @@ def insert_slice(slice_real, xyz, n_pix):
         """
         shape = xyz.shape[0]
         count_3d = np.ones(n_pix, n_pix, n_pix)
-        count_3d[0,0,0] *= shape
+        count_3d[0, 0, 0] *= shape
         inserted_slice_3d = np.ones(n_pix, n_pix, n_pix)
         return inserted_slice_3d, count_3d
 

From d381e3cd38a6ade75fcbaa254c06fe47cbc1e0f8 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 24 Mar 2022 23:56:38 -0700
Subject: [PATCH 109/148] fix to numpy array initialization

---
 .../iterative_refinement/expectation_maximization.py          | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index faaa659..4a8ddbc 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -431,9 +431,9 @@ def insert_slice(slice_real, xyz, n_pix):
             Shape (n_pix, n_pix, n_pix)
         """
         shape = xyz.shape[0]
-        count_3d = np.ones(n_pix, n_pix, n_pix)
+        count_3d = np.ones((n_pix, n_pix, n_pix))
         count_3d[0,0,0] *= shape
-        inserted_slice_3d = np.ones(n_pix, n_pix, n_pix)
+        inserted_slice_3d = np.ones((n_pix, n_pix, n_pix))
         return inserted_slice_3d, count_3d
 
     @staticmethod

From 294d4b54ddb4b64ce3624b064a5e433930e20e18 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Fri, 25 Mar 2022 06:57:23 +0000
Subject: [PATCH 110/148] Format code with black

---
 reconstructSPI/iterative_refinement/expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index 4a8ddbc..3c0d480 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -432,7 +432,7 @@ def insert_slice(slice_real, xyz, n_pix):
         """
         shape = xyz.shape[0]
         count_3d = np.ones((n_pix, n_pix, n_pix))
-        count_3d[0,0,0] *= shape
+        count_3d[0, 0, 0] *= shape
         inserted_slice_3d = np.ones((n_pix, n_pix, n_pix))
         return inserted_slice_3d, count_3d
 

From 3819306451a94c8b62fd3bdc276874afcc09db19 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Fri, 25 Mar 2022 00:10:35 -0700
Subject: [PATCH 111/148] num rotations change

---
 .../iterative_refinement/expectation_maximization.py          | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index 4a8ddbc..33e86eb 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -77,6 +77,9 @@ def iterative_refinement(self):
         particles_f_2 = IterativeRefinement.fft_3d(particles_2)
 
         n_pix = self.map_3d_init.shape[0]
+        
+        n_rotations = self.particles.shape[0]
+        
         # suggest 32 or 64 to start with. real data will be more like
         # 128 or 256. Can have issues with ctf at small pixels and
         # need to zero pad to avoid artefacts. Artefacts from ctf not
@@ -111,7 +114,6 @@ def iterative_refinement(self):
             #   based on how well the signal agrees in half_map_1,
             #   half_map_2 (Fourier frequency).
 
-            n_rotations = 1000
             rots = IterativeRefinement.grid_SO3_uniform(n_rotations)
 
             xy0_plane = IterativeRefinement.generate_xy_plane(n_pix)

From f28ccfab1fe6e19dff6270bcd5e99c97ae9dc536 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Fri, 25 Mar 2022 07:10:49 +0000
Subject: [PATCH 112/148] Format code with black

---
 .../iterative_refinement/expectation_maximization.py          | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index 1671309..97307f4 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -77,9 +77,9 @@ def iterative_refinement(self):
         particles_f_2 = IterativeRefinement.fft_3d(particles_2)
 
         n_pix = self.map_3d_init.shape[0]
-        
+
         n_rotations = self.particles.shape[0]
-        
+
         # suggest 32 or 64 to start with. real data will be more like
         # 128 or 256. Can have issues with ctf at small pixels and
         # need to zero pad to avoid artefacts. Artefacts from ctf not

From c0539804fce0cb6ce069161289339208b796d01b Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Fri, 25 Mar 2022 00:17:05 -0700
Subject: [PATCH 113/148] fsc fix

---
 .../iterative_refinement/expectation_maximization.py        | 6 +++---
 tests/test_expectation_maximization.py                      | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index 1671309..6943565 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -63,7 +63,7 @@ def iterative_refinement(self):
             Shape (n_pix, n_pix, n_pix)
         fsc_1d : arr
             Final one dimensional fourier shell correlation.
-            Shape (n_pix,)
+            Shape (n_pix // 2,)
         """
         particles_1, particles_2 = IterativeRefinement.split_array(self.particles)
 
@@ -455,7 +455,7 @@ def compute_fsc(map_3d_f_1, map_3d_f_2):
         -------
         noise_estimate : arr
             Noise estimates from half maps.
-            Shape (n_pix,)
+            Shape (n_pix // 2,)
         """
         # write fast vectorized fsc from code snippets in
         # https://github.com/geoffwoollard/learn_cryoem_math/blob/master/nb/fsc.ipynb
@@ -465,7 +465,7 @@ def compute_fsc(map_3d_f_1, map_3d_f_2):
         n_pix_2 = map_3d_f_2.shape[0]
         fsc_1d_1 = np.ones(n_pix_1 // 2)
         fsc_1d_2 = np.ones(n_pix_2 // 2)
-        noise_estimates = np.concatenate((fsc_1d_1, fsc_1d_2))
+        noise_estimates = np.dot(fsc_1d_1, fsc_1d_2)
         return noise_estimates
 
     @staticmethod
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 02701ec..f001ce4 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -147,7 +147,7 @@ def test_compute_fsc(test_ir, n):
     map_2 = np.ones((n, n, n))
 
     fsc_1 = test_ir.compute_fsc(map_1, map_2)
-    assert fsc_1.shape == (n,)
+    assert fsc_1.shape == (n // 2,)
 
 
 def test_expand_1d_to_3d(test_ir, n):

From 7083a547f4cc98170c6d816edb07d4c315183b3d Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Fri, 25 Mar 2022 00:22:14 -0700
Subject: [PATCH 114/148] Forgot what a dot product did for a second there

---
 reconstructSPI/iterative_refinement/expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index afed5c1..17e393f 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -465,7 +465,7 @@ def compute_fsc(map_3d_f_1, map_3d_f_2):
         n_pix_2 = map_3d_f_2.shape[0]
         fsc_1d_1 = np.ones(n_pix_1 // 2)
         fsc_1d_2 = np.ones(n_pix_2 // 2)
-        noise_estimates = np.dot(fsc_1d_1, fsc_1d_2)
+        noise_estimates = fsc_1d_1 * fsc_1d_2
         return noise_estimates
 
     @staticmethod

From 2a1eda7e5ccfbc544bfcd1e36cd8ea5ce4c29298 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Fri, 25 Mar 2022 00:26:03 -0700
Subject: [PATCH 115/148] Updated iterative refinement test to reflect fsc fix

---
 tests/test_expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index f001ce4..d63edfe 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -170,4 +170,4 @@ def test_iterative_refinement(test_ir, n):
     assert map_3d_r_final.shape == (n, n, n)
     assert half_map_3d_r_1.shape == (n, n, n)
     assert half_map_3d_r_2.shape == (n, n, n)
-    assert fsc_1d.shape == (n,)
+    assert fsc_1d.shape == (n // 2,)

From cba93206c2b43b0858858771bcacc6d237f49152 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Sat, 26 Mar 2022 18:20:08 -0700
Subject: [PATCH 116/148] Removed superfluous imports

---
 environment.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 01e8d5c..16ab6ba 100644
--- a/environment.yml
+++ b/environment.yml
@@ -6,7 +6,6 @@ dependencies:
   - codecov
   - coverage
   - gemmi
-  - numba
   - numpy
   - pillow>=8.2.0
   - pip

From d40e6ae1856f4ecc4b852183851d1b864f771d65 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Sat, 26 Mar 2022 18:20:29 -0700
Subject: [PATCH 117/148] Updated docstrings, fixed splitting arrs

---
 .../expectation_maximization.py               | 27 +++++++------------
 1 file changed, 10 insertions(+), 17 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index 17e393f..e104c3f 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -21,10 +21,10 @@ class IterativeRefinement:
 
     References
     ----------
-    1. Nelson, P. C. (2019). Chapter 12 : Single Particle
-    Reconstruction in Cryo-electron Microscopy.
-            In Physical Models of Living Systems (pp. 305–325).
-            https://repository.upenn.edu/physics_papers/656/
+    1. Nelson, P. C. (2021). Physical Models of Living Systems new
+    chapter: Single Particle Reconstruction in Cryo-electron
+    Microscopy.
+            https://repository.upenn.edu/physics_papers/656
     2. Scheres, S. H. W. (2012). RELION: Implementation of a
     Bayesian approach to cryo-EM structure determination.
             Journal of Structural Biology, 180(3), 519–530.
@@ -233,18 +233,11 @@ def split_array(arr):
         arr2: arr
             Shape (n_particles // 2, ...)
         """
-        if isinstance(arr, (list, tuple)):
-            idx_half = len(arr) // 2
-            arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
+        idx_half = len(arr) // 2
+        arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
 
-            if len(arr_1) != len(arr_2):
-                arr_2 = arr[idx_half : 2 * idx_half]
-        else:
-            idx_half = arr.shape[0] // 2
-            arr_1, arr_2 = arr[:idx_half], arr[idx_half:]
-
-            if arr_1.shape[0] != arr_2.shape[0]:
-                arr_2 = arr[idx_half : 2 * idx_half]
+        if len(arr_1) != len(arr_2):
+            arr_2 = arr[idx_half : 2 * idx_half]
 
         return arr_1, arr_2
 
@@ -501,7 +494,7 @@ def fft_3d(array):
         -------
         fft_array : arr
             Fourier transform of array.
-            Shape (n, n, n)
+            Shape (n_pix, n_pix, n_pix)
         """
         return np.zeros(array.shape, dtype=np.cdouble)
 
@@ -513,7 +506,7 @@ def ifft_3d(fft_array):
         ----------
         fft_array : arr
             Fourier transform of array.
-            Shape (n, n, n)
+            Shape (n_pix, n_pix, n_pix)
 
         Returns
         -------

From 6c6e1f0e159980bf1da3e97abda4d43e708c1b6c Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Sat, 26 Mar 2022 18:20:48 -0700
Subject: [PATCH 118/148] Split n into n_pix, n_particles

---
 tests/test_expectation_maximization.py | 142 +++++++++++++------------
 1 file changed, 76 insertions(+), 66 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index d63edfe..41063a0 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -7,17 +7,22 @@
 
 
 @pytest.fixture
-def n():
-    """Get test array size value for consistency."""
+def n_pix():
+    """Get test pixel count for consistency."""
     return 2
 
 
 @pytest.fixture
-def test_ir(n):
+def n_particles():
+    """Get test particle count for consistency."""
+    return 2
+
+@pytest.fixture
+def test_ir(n_pix, n_particles):
     """Instantiate IterativeRefinement class for testing."""
     ex_ctf = {
-        "s": np.ones((n, n)),
-        "a": np.ones((n, n)),
+        "s": np.ones((n_pix, n_pix)),
+        "a": np.ones((n_pix, n_pix)),
         "def1": 1.0,
         "def2": 1.0,
         "angast": 0.1,
@@ -26,27 +31,27 @@ def test_ir(n):
         "bf": 0.1,
         "lp": 0.1,
     }
-    map_3d = np.zeros((n, n, n))
-    particles = np.zeros((n, n, n))
+    map_3d = np.zeros((n_pix, n_pix, n_pix))
+    particles = np.zeros((n_particles, n_pix, n_pix))
     ctf_info = [
         ex_ctf,
-    ] * n
+    ] * n_particles
     itr = 2
     ir = em.IterativeRefinement(map_3d, particles, ctf_info, itr)
     return ir
 
 
-def test_split_array(test_ir, n):
+def test_split_array(test_ir, n_particles):
     """Test splitting of array in two halves."""
-    arr = np.zeros(n)
+    arr = np.zeros(n_particles)
     arr1, arr2 = test_ir.split_array(arr)
-    assert arr1.shape == (n // 2,)
-    assert arr2.shape == (n // 2,)
+    assert arr1.shape == (n_particles // 2,)
+    assert arr2.shape == (n_particles // 2,)
 
-    arr = np.zeros(n + 1)
+    arr = np.zeros(n_particles + 1)
     arr1, arr2 = test_ir.split_array(arr)
-    assert arr1.shape == ((n + 1) // 2,)
-    assert arr2.shape == ((n + 1) // 2,)
+    assert arr1.shape == ((n_particles + 1) // 2,)
+    assert arr2.shape == ((n_particles + 1) // 2,)
 
     arr = ["a", "b"]
     arr1, arr2 = test_ir.split_array(arr)
@@ -54,111 +59,116 @@ def test_split_array(test_ir, n):
     assert len(arr2) == 1
 
 
-def test_fft_3d(test_ir, n):
+def test_fft_3d(test_ir, n_pix):
     """Test 3D fourier transform."""
-    arr = np.zeros((n, n, n))
+    arr = np.zeros((n_pix, n_pix, n_pix))
     fft_arr = test_ir.fft_3d(arr)
     assert fft_arr.shape == arr.shape
 
 
-def test_ifft_3d(test_ir, n):
+def test_ifft_3d(test_ir, n_pix):
     """Test 3D inverse fourier transform."""
-    fft_arr = np.zeros((n, n, n))
+    fft_arr = np.zeros((n_pix, n_pix, n_pix))
     arr = test_ir.fft_3d(fft_arr)
     assert fft_arr.shape == arr.shape
 
 
-def test_build_ctf_array(test_ir, n):
+def test_build_ctf_array(test_ir, n_particles, n_pix):
     """Test bulding arbitrary CTF array."""
     ctfs = test_ir.build_ctf_array()
-    assert len(ctfs) == n
-    assert ctfs[0].shape == (n, n)
+    assert len(ctfs) == n_particles
+    assert ctfs[0].shape == (n_pix, n_pix)
 
 
-def test_grid_SO3_uniform(test_ir, n):
+def test_grid_SO3_uniform(test_ir, n_particles):
     """Test generation of rotations in SO(3)."""
-    rots = test_ir.grid_SO3_uniform(n)
-    assert rots.shape == (n, 3, 3)
+    rots = test_ir.grid_SO3_uniform(n_particles)
+    assert rots.shape == (n_particles, 3, 3)
 
 
-def test_generate_xy_plane(test_ir, n):
+def test_generate_xy_plane(test_ir, n_pix):
     """Test generation of xy plane."""
-    xy_plane = test_ir.generate_xy_plane(n)
-    assert xy_plane.shape == (n * n, 3)
+    xy_plane = test_ir.generate_xy_plane(n_pix)
+    assert xy_plane.shape == (n_pix ** 2, 3)
 
 
-def test_generate_slices(test_ir, n):
+def test_generate_slices(test_ir, n_particles, n_pix):
     """Test generation of slices."""
-    map_3d = np.ones((n, n, n))
-    rots = test_ir.grid_SO3_uniform(n)
-    xy_plane = test_ir.generate_xy_plane(n)
+    map_3d = np.ones((n_pix, n_pix, n_pix))
+    rots = test_ir.grid_SO3_uniform(n_particles)
+    xy_plane = test_ir.generate_xy_plane(n_pix)
 
-    slices, xyz_rotated = test_ir.generate_slices(map_3d, xy_plane, n, rots)
+    slices, xyz_rotated = test_ir.generate_slices(
+        map_3d,
+        xy_plane,
+        n_pix,
+        rots
+    )
 
-    assert xy_plane.shape == (n * n, 3)
-    assert slices.shape == (n, n, n)
-    assert xyz_rotated.shape == (n * n, 3)
+    assert xy_plane.shape == (n_pix ** 2, 3)
+    assert slices.shape == (n_particles, n_pix, n_pix)
+    assert xyz_rotated.shape == (n_pix ** 2, 3)
 
 
-def test_apply_ctf_to_slice(test_ir, n):
+def test_apply_ctf_to_slice(test_ir, n_pix):
     """Test convolution of particle slice with CTF."""
-    particle_slice = np.ones((n, n))
-    ctf = np.ones((n, n))
+    particle_slice = np.ones((n_pix, n_pix))
+    ctf = np.ones((n_pix, n_pix))
     convolved = test_ir.apply_ctf_to_slice(particle_slice, ctf)
 
-    assert convolved.shape == (n, n)
+    assert convolved.shape == (n_pix, n_pix)
 
 
-def test_compute_bayesian_weights(test_ir, n):
+def test_compute_bayesian_weights(test_ir, n_particles, n_pix):
     """Test computation of bayesian weights.
 
     For use under Gaussian white noise model.
     """
-    particle = np.ones((1, n, n))
-    slices = np.ones((n, n, n))
+    particle = np.ones((n_pix // 2, n_pix, n_pix))
+    slices = np.ones((n_particles, n_pix, n_pix))
     bayesian_weights = test_ir.compute_bayesian_weights(particle, slices)
 
-    assert bayesian_weights.shape == (n,)
+    assert bayesian_weights.shape == (n_particles,)
 
 
-def test_apply_wiener_filter(test_ir, n):
+def test_apply_wiener_filter(test_ir, n_pix):
     """Test application of Wiener filter to particle projection."""
-    projection = np.ones((n, n))
-    ctf = np.zeros((n, n))
+    projection = np.ones((n_pix, n_pix))
+    ctf = np.zeros((n_pix, n_pix))
     small_number = 0.01
 
     projection_wfilter_f = test_ir.apply_wiener_filter(projection, ctf, small_number)
-    assert projection_wfilter_f.shape == (n, n)
+    assert projection_wfilter_f.shape == (n_pix, n_pix)
 
 
-def test_insert_slice(test_ir, n):
+def test_insert_slice(test_ir, n_pix):
     """Test insertion of particle slice."""
-    particle_slice = np.ones((n, n))
-    xyz = test_ir.generate_xy_plane(n)
+    particle_slice = np.ones((n_pix, n_pix))
+    xyz = test_ir.generate_xy_plane(n_pix)
 
-    inserted, count = test_ir.insert_slice(particle_slice, xyz, n)
-    assert inserted.shape == (n, n, n)
-    assert count.shape == (n, n, n)
+    inserted, count = test_ir.insert_slice(particle_slice, xyz, n_pix)
+    assert inserted.shape == (n_pix, n_pix, n_pix)
+    assert count.shape == (n_pix, n_pix, n_pix)
 
 
-def test_compute_fsc(test_ir, n):
+def test_compute_fsc(test_ir, n_pix):
     """Test computation of FSC."""
-    map_1 = np.ones((n, n, n))
-    map_2 = np.ones((n, n, n))
+    map_1 = np.ones((n_pix, n_pix, n_pix))
+    map_2 = np.ones((n_pix, n_pix, n_pix))
 
     fsc_1 = test_ir.compute_fsc(map_1, map_2)
-    assert fsc_1.shape == (n // 2,)
+    assert fsc_1.shape == (n_pix // 2,)
 
 
-def test_expand_1d_to_3d(test_ir, n):
+def test_expand_1d_to_3d(test_ir, n_pix):
     """Test expansion of 1D array into spherical shell."""
-    arr1d = np.ones(1)
+    arr1d = np.ones(n_pix // 2)
     spherical = test_ir.expand_1d_to_3d(arr1d)
 
-    assert spherical.shape == (n, n, n)
+    assert spherical.shape == (n_pix, n_pix, n_pix)
 
 
-def test_iterative_refinement(test_ir, n):
+def test_iterative_refinement(test_ir, n_pix):
     """Test complete iterative refinement algorithm."""
     (
         map_3d_r_final,
@@ -167,7 +177,7 @@ def test_iterative_refinement(test_ir, n):
         fsc_1d,
     ) = test_ir.iterative_refinement()
 
-    assert map_3d_r_final.shape == (n, n, n)
-    assert half_map_3d_r_1.shape == (n, n, n)
-    assert half_map_3d_r_2.shape == (n, n, n)
-    assert fsc_1d.shape == (n // 2,)
+    assert map_3d_r_final.shape == (n_pix, n_pix, n_pix)
+    assert half_map_3d_r_1.shape == (n_pix, n_pix, n_pix)
+    assert half_map_3d_r_2.shape == (n_pix, n_pix, n_pix)
+    assert fsc_1d.shape == (n_pix // 2,)

From 1e11a9d2a4f599b1b88ee9d62b0c9930b01e1244 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Sun, 27 Mar 2022 01:21:06 +0000
Subject: [PATCH 119/148] Format code with black

---
 tests/test_expectation_maximization.py | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 41063a0..7a17b24 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -17,6 +17,7 @@ def n_particles():
     """Get test particle count for consistency."""
     return 2
 
+
 @pytest.fixture
 def test_ir(n_pix, n_particles):
     """Instantiate IterativeRefinement class for testing."""
@@ -89,7 +90,7 @@ def test_grid_SO3_uniform(test_ir, n_particles):
 def test_generate_xy_plane(test_ir, n_pix):
     """Test generation of xy plane."""
     xy_plane = test_ir.generate_xy_plane(n_pix)
-    assert xy_plane.shape == (n_pix ** 2, 3)
+    assert xy_plane.shape == (n_pix**2, 3)
 
 
 def test_generate_slices(test_ir, n_particles, n_pix):
@@ -98,16 +99,11 @@ def test_generate_slices(test_ir, n_particles, n_pix):
     rots = test_ir.grid_SO3_uniform(n_particles)
     xy_plane = test_ir.generate_xy_plane(n_pix)
 
-    slices, xyz_rotated = test_ir.generate_slices(
-        map_3d,
-        xy_plane,
-        n_pix,
-        rots
-    )
+    slices, xyz_rotated = test_ir.generate_slices(map_3d, xy_plane, n_pix, rots)
 
-    assert xy_plane.shape == (n_pix ** 2, 3)
+    assert xy_plane.shape == (n_pix**2, 3)
     assert slices.shape == (n_particles, n_pix, n_pix)
-    assert xyz_rotated.shape == (n_pix ** 2, 3)
+    assert xyz_rotated.shape == (n_pix**2, 3)
 
 
 def test_apply_ctf_to_slice(test_ir, n_pix):

From d621fb105c33a523a876558cd7e941f768df2998 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Sat, 26 Mar 2022 18:26:25 -0700
Subject: [PATCH 120/148] Added back numba

---
 environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environment.yml b/environment.yml
index 16ab6ba..e52e0d7 100644
--- a/environment.yml
+++ b/environment.yml
@@ -7,6 +7,7 @@ dependencies:
   - coverage
   - gemmi
   - numpy
+  - numba
   - pillow>=8.2.0
   - pip
   - pytest

From 496f88a4ef572001df2c805ec6e16557f9967b79 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Sat, 26 Mar 2022 18:33:46 -0700
Subject: [PATCH 121/148] Force checks

---
 reconstructSPI/iterative_refinement/expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index e104c3f..cbfaa7c 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -433,7 +433,7 @@ def insert_slice(slice_real, xyz, n_pix):
 
     @staticmethod
     def compute_fsc(map_3d_f_1, map_3d_f_2):
-        """Compute Fourier shell correlation.
+        """Compute the Fourier shell correlation.
 
                 Estimate noise from half maps.
 

From 8aaff785d5ae7bcf85b81649eb9811a7dbe09e49 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Mon, 28 Mar 2022 11:53:58 -0700
Subject: [PATCH 122/148] n_pix in fft docstrings

---
 .../iterative_refinement/expectation_maximization.py          | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index cbfaa7c..47c61ee 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -488,7 +488,7 @@ def fft_3d(array):
         ----------
         array : arr
             Input array.
-            Shape (n, n, n)
+            Shape (n_pix, n_pix, n_pix)
 
         Returns
         -------
@@ -512,6 +512,6 @@ def ifft_3d(fft_array):
         -------
         array : arr
             Original array.
-            Shape (n, n, n)
+            Shape (n_pix, n_pix, n_pix)
         """
         return np.zeros(fft_array.shape)

From 33e3229b1dd193f1cecdc7334668b3e991cdf4de Mon Sep 17 00:00:00 2001
From: Tyler Heim <t368@heim.ca>
Date: Mon, 28 Mar 2022 14:33:25 -0700
Subject: [PATCH 123/148] Normalizing half maps

---
 .../expectation_maximization.py               | 28 +++++++++++++++----
 1 file changed, 22 insertions(+), 6 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index 47c61ee..5e98350 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -43,12 +43,19 @@ def __init__(self, map_3d_init, particles, ctf_info, max_itr=7):
         self.ctf_info = ctf_info
         self.max_itr = max_itr
 
-    def iterative_refinement(self):
+    def iterative_refinement(self, wiener_small_number = 0.01, count_norm_const = 1):
         """Perform iterative refinement.
 
         Acts in a Bayesian expectation maximization setting,
         i.e. maximum a posteriori estimation.
 
+        Parameters
+        ----------
+        wiener_small_number : float
+            Used to tune Wiener filter.
+        count_norm_const : float
+            Used to tune normalization of slice inserting. 
+
         Returns
         -------
         map_3d_update : arr
@@ -132,6 +139,10 @@ def iterative_refinement(self):
             map_3d_f_updated_1 = np.zeros_like(half_map_3d_f_1)
             # complex
             map_3d_f_updated_2 = np.zeros_like(half_map_3d_f_2)
+            # complex
+            map_3d_f_norm_1 = np.zeros_like(half_map_3d_f_1)
+            # complex
+            map_3d_f_norm_2 = np.zeros_like(half_map_3d_f_2)
             # float/real
             counts_3d_updated_1 = np.zeros_like(half_map_3d_r_1)
             # float/real
@@ -144,10 +155,10 @@ def iterative_refinement(self):
                 # Option: particle_f_2 = particles_f_2[particle_idx]
 
                 particle_f_deconv_1 = IterativeRefinement.apply_wiener_filter(
-                    particles_f_1, ctf_1, 0.01
+                    particles_f_1, ctf_1, wiener_small_number
                 )
                 particle_f_deconv_2 = IterativeRefinement.apply_wiener_filter(
-                    particles_f_2, ctf_1, 0.01
+                    particles_f_2, ctf_1, wiener_small_number
                 )
 
                 # all slices get convolved with the particle ctf
@@ -186,12 +197,17 @@ def iterative_refinement(self):
                     map_3d_f_updated_2 += inserted_slice_3d_r + 1j * inserted_slice_3d_i
                     counts_3d_updated_2 += count_3d_r + count_3d_i
 
+                # normalize maps by slice counts to account 
+                # for spherical density differences
+                map_3d_f_norm_1 = map_3d_f_updated_1 * counts_3d_updated_1 / (count_norm_const + counts_3d_updated_1**2)
+                map_3d_f_norm_1 = map_3d_f_updated_2 * counts_3d_updated_2 / (count_norm_const + counts_3d_updated_2**2)
+
             # apply noise model
             # half_map_1, half_map_2 come from doing the above
             # independently. Filter by noise estimate (e.g. multiply
             # both half maps by FSC)
             fsc_1d = IterativeRefinement.compute_fsc(
-                map_3d_f_updated_1, map_3d_f_updated_2
+                map_3d_f_norm_1, map_3d_f_norm_2
             )
 
             fsc_3d = IterativeRefinement.expand_1d_to_3d(fsc_1d)
@@ -200,8 +216,8 @@ def iterative_refinement(self):
             # The FSC is 1D, one number per spherical shells
             # it can be expanded back to a multiplicative filter of
             # the same shape as the maps
-            map_3d_f_filtered_1 = map_3d_f_updated_1 * fsc_3d
-            map_3d_f_filtered_2 = map_3d_f_updated_2 * fsc_3d
+            map_3d_f_filtered_1 = map_3d_f_norm_1 * fsc_3d
+            map_3d_f_filtered_2 = map_3d_f_norm_2 * fsc_3d
 
             # update iteration
             half_map_3d_f_1 = map_3d_f_filtered_1

From 01ceaf5f7f80614fae628a89649908ca11d1a9a0 Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Mon, 28 Mar 2022 21:35:29 +0000
Subject: [PATCH 124/148] Format code with black

---
 .../expectation_maximization.py               | 22 ++++++++++++-------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index 5e98350..93674ea 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -43,7 +43,7 @@ def __init__(self, map_3d_init, particles, ctf_info, max_itr=7):
         self.ctf_info = ctf_info
         self.max_itr = max_itr
 
-    def iterative_refinement(self, wiener_small_number = 0.01, count_norm_const = 1):
+    def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
         """Perform iterative refinement.
 
         Acts in a Bayesian expectation maximization setting,
@@ -54,7 +54,7 @@ def iterative_refinement(self, wiener_small_number = 0.01, count_norm_const = 1)
         wiener_small_number : float
             Used to tune Wiener filter.
         count_norm_const : float
-            Used to tune normalization of slice inserting. 
+            Used to tune normalization of slice inserting.
 
         Returns
         -------
@@ -197,18 +197,24 @@ def iterative_refinement(self, wiener_small_number = 0.01, count_norm_const = 1)
                     map_3d_f_updated_2 += inserted_slice_3d_r + 1j * inserted_slice_3d_i
                     counts_3d_updated_2 += count_3d_r + count_3d_i
 
-                # normalize maps by slice counts to account 
+                # normalize maps by slice counts to account
                 # for spherical density differences
-                map_3d_f_norm_1 = map_3d_f_updated_1 * counts_3d_updated_1 / (count_norm_const + counts_3d_updated_1**2)
-                map_3d_f_norm_1 = map_3d_f_updated_2 * counts_3d_updated_2 / (count_norm_const + counts_3d_updated_2**2)
+                map_3d_f_norm_1 = (
+                    map_3d_f_updated_1
+                    * counts_3d_updated_1
+                    / (count_norm_const + counts_3d_updated_1**2)
+                )
+                map_3d_f_norm_1 = (
+                    map_3d_f_updated_2
+                    * counts_3d_updated_2
+                    / (count_norm_const + counts_3d_updated_2**2)
+                )
 
             # apply noise model
             # half_map_1, half_map_2 come from doing the above
             # independently. Filter by noise estimate (e.g. multiply
             # both half maps by FSC)
-            fsc_1d = IterativeRefinement.compute_fsc(
-                map_3d_f_norm_1, map_3d_f_norm_2
-            )
+            fsc_1d = IterativeRefinement.compute_fsc(map_3d_f_norm_1, map_3d_f_norm_2)
 
             fsc_3d = IterativeRefinement.expand_1d_to_3d(fsc_1d)
 

From 20f223217f69971f5fcbaeb65a059de285af63a1 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 17:09:01 -0700
Subject: [PATCH 125/148] Removed comments, refactored big method, fixed
 bayesian weights shapes

---
 .../expectation_maximization.py               | 124 +++++++++---------
 tests/test_expectation_maximization.py        |   2 +-
 2 files changed, 60 insertions(+), 66 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index 93674ea..cf95b0c 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -87,18 +87,10 @@ def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
 
         n_rotations = self.particles.shape[0]
 
-        # suggest 32 or 64 to start with. real data will be more like
-        # 128 or 256. Can have issues with ctf at small pixels and
-        # need to zero pad to avoid artefacts. Artefacts from ctf not
-        # going to zero at edges, and sinusoidal ctf rippling too fast
-        # can zero pad when do Fourier convolution (fft is on zero
-        # padded and larger sized array)
-
         half_map_3d_r_1, half_map_3d_r_2 = (
             self.map_3d_init.copy(),
             self.map_3d_init.copy(),
         )
-        # should diverge because different particles averaging in
 
         half_map_3d_f_1 = IterativeRefinement.fft_3d(half_map_3d_r_1)
         half_map_3d_f_2 = IterativeRefinement.fft_3d(half_map_3d_r_2)
@@ -108,19 +100,6 @@ def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
             half_map_3d_f_1 = IterativeRefinement.fft_3d(half_map_3d_r_1)
             half_map_3d_f_2 = IterativeRefinement.fft_3d(half_map_3d_r_2)
 
-            # align particles to 3D volume
-            # decide on granularity of rotations
-            # i.e. how finely the rotational SO(3) space is sampled
-            # in a grid search. Smarter method is branch and bound...
-            # perhaps can make grid up front of slices, and then only
-            # compute norms on finer grid later. So re-use slices.
-
-            # def do_adaptive_grid_search(particle, map_3d):
-            #   a la branch and bound. Not sure exactly how you decide
-            #   how finely gridded to make it. Perhaps heuristics
-            #   based on how well the signal agrees in half_map_1,
-            #   half_map_2 (Fourier frequency).
-
             rots = IterativeRefinement.grid_SO3_uniform(n_rotations)
 
             xy0_plane = IterativeRefinement.generate_xy_plane(n_pix)
@@ -134,25 +113,16 @@ def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
                 half_map_3d_f_2, xy0_plane, n_pix, rots
             )
 
-            # initialize:
-            # complex
             map_3d_f_updated_1 = np.zeros_like(half_map_3d_f_1)
-            # complex
             map_3d_f_updated_2 = np.zeros_like(half_map_3d_f_2)
-            # complex
             map_3d_f_norm_1 = np.zeros_like(half_map_3d_f_1)
-            # complex
             map_3d_f_norm_2 = np.zeros_like(half_map_3d_f_2)
-            # float/real
             counts_3d_updated_1 = np.zeros_like(half_map_3d_r_1)
-            # float/real
             counts_3d_updated_2 = np.zeros_like(half_map_3d_r_2)
 
             for particle_idx in range(particles_f_1.shape[0]):
                 ctf_1 = ctfs_1[particle_idx]
                 ctf_2 = ctfs_2[particle_idx]
-                # Option: particle_f_1 = particles_f_1[particle_idx]
-                # Option: particle_f_2 = particles_f_2[particle_idx]
 
                 particle_f_deconv_1 = IterativeRefinement.apply_wiener_filter(
                     particles_f_1, ctf_1, wiener_small_number
@@ -161,11 +131,10 @@ def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
                     particles_f_2, ctf_1, wiener_small_number
                 )
 
-                # all slices get convolved with the particle ctf
-                apply_ctf = np.vectorize(IterativeRefinement.apply_ctf_to_slice)
+                ctf_vectorized = np.vectorize(IterativeRefinement.apply_ctf_to_slice)
 
-                slices_conv_ctfs_1 = apply_ctf(slices_1, ctf_1)
-                slices_conv_ctfs_2 = apply_ctf(slices_2, ctf_2)
+                slices_conv_ctfs_1 = ctf_vectorized(slices_1, ctf_1)
+                slices_conv_ctfs_2 = ctf_vectorized(slices_2, ctf_2)
 
                 bayes_factors_1 = IterativeRefinement.compute_bayesian_weights(
                     particles_f_1[particle_idx], slices_conv_ctfs_1
@@ -176,7 +145,6 @@ def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
 
                 for one_slice_idx in range(bayes_factors_1.shape[0]):
                     xyz = xyz_rotated[one_slice_idx]
-                    # if this can be vectorized, can avoid loop
                     inserted_slice_3d_r, count_3d_r = IterativeRefinement.insert_slice(
                         particle_f_deconv_1.real, xyz, n_pix
                     )
@@ -199,37 +167,11 @@ def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
 
                 # normalize maps by slice counts to account
                 # for spherical density differences
-                map_3d_f_norm_1 = (
-                    map_3d_f_updated_1
-                    * counts_3d_updated_1
-                    / (count_norm_const + counts_3d_updated_1**2)
-                )
-                map_3d_f_norm_1 = (
-                    map_3d_f_updated_2
-                    * counts_3d_updated_2
-                    / (count_norm_const + counts_3d_updated_2**2)
-                )
-
-            # apply noise model
-            # half_map_1, half_map_2 come from doing the above
-            # independently. Filter by noise estimate (e.g. multiply
-            # both half maps by FSC)
-            fsc_1d = IterativeRefinement.compute_fsc(map_3d_f_norm_1, map_3d_f_norm_2)
-
-            fsc_3d = IterativeRefinement.expand_1d_to_3d(fsc_1d)
-
-            # multiplicative filter on maps with fsc
-            # The FSC is 1D, one number per spherical shells
-            # it can be expanded back to a multiplicative filter of
-            # the same shape as the maps
-            map_3d_f_filtered_1 = map_3d_f_norm_1 * fsc_3d
-            map_3d_f_filtered_2 = map_3d_f_norm_2 * fsc_3d
+                map_3d_f_norm_1 = IterativeRefinement.normalize_map(map_3d_f_updated_1, counts_3d_updated_1, count_norm_const)
+                map_3d_f_norm_2 = IterativeRefinement.normalize_map(map_3d_f_updated_2, counts_3d_updated_2, count_norm_const)
 
-            # update iteration
-            half_map_3d_f_1 = map_3d_f_filtered_1
-            half_map_3d_f_2 = map_3d_f_filtered_2
+            half_map_3d_f_1, half_map_3d_f_2 = apply_noise_model(map_3d_f_norm_1, map_3d_f_norm_2)
 
-        # final map
         fsc_1d = IterativeRefinement.compute_fsc(half_map_3d_f_1, half_map_3d_f_2)
         fsc_3d = IterativeRefinement.expand_1d_to_3d(fsc_1d)
         map_3d_f_final = (half_map_3d_f_1 + half_map_3d_f_2 / 2) * fsc_3d
@@ -239,6 +181,58 @@ def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
 
         return map_3d_r_final, half_map_3d_r_1, half_map_3d_r_2, fsc_1d
 
+    @staticmethod
+    def normalize_map(map, counts, norm_const):
+        """Normalize map by slice counts per voxel.
+        
+        Parameters
+        ----------
+        map : arr
+            Shape (n_pix, n_pix, n_pix)
+            The map to be normalized.
+        counts : arr
+            Shape (n_pix, n_pix, n_pix)
+            The number of slices that were added within each voxel.
+        norm_const : float
+            A small number used as part of the wiener-filter-like
+            normalization.
+        
+        Returns
+        -------
+        norm_map : arr
+            Shape (n_pix, n_pix, n_pix)
+            map normalized by counts.
+        """
+        return map * counts / (norm_const + counts**2)
+
+    @staticmethod
+    def apply_noise_model(map_3d_f_norm_1, map_3d_f_norm_2):
+        """Apply noise model to normalized maps in fourier space.
+        
+        Parameters
+        ----------
+        map_3d_f_norm_1 : arr
+            Shape (n_pix, n_pix, n_pix)
+            Normalized fourier space half-map 1.
+        map_3d_f_norm_2 : arr
+            Shape (n_pix, n_pix, n_pix)
+            Normalized fourier space half-map 2.
+        
+        Returns
+        -------
+        (map_3d_f_filtered_1, map_3d_f_filtered_2) : (arr, arr)
+            Shapes (n_pix, n_pix, n_pix)
+            Half-maps with fsc noise filtering applied.
+        """
+        fsc_1d = IterativeRefinement.compute_fsc(map_3d_f_norm_1, map_3d_f_norm_2)
+
+        fsc_3d = IterativeRefinement.expand_1d_to_3d(fsc_1d)
+
+        map_3d_f_filtered_1 = map_3d_f_norm_1 * fsc_3d
+        map_3d_f_filtered_2 = map_3d_f_norm_2 * fsc_3d
+
+        return (map_3d_f_filtered_1, map_3d_f_filtered_2)
+
     @staticmethod
     def split_array(arr):
         """Split array into two halves along 0th axis.
@@ -387,7 +381,7 @@ def compute_bayesian_weights(particle, slices):
         Parameters
         ----------
         particle : arr
-            Shape (n_pix // 2,n_pix,n_pix)
+            Shape (n_pix, n_pix)
 
         slices : complex64 arr
             Shape (n_slices, n_pix, n_pix)
diff --git a/tests/test_expectation_maximization.py b/tests/test_expectation_maximization.py
index 7a17b24..37ee222 100644
--- a/tests/test_expectation_maximization.py
+++ b/tests/test_expectation_maximization.py
@@ -120,7 +120,7 @@ def test_compute_bayesian_weights(test_ir, n_particles, n_pix):
 
     For use under Gaussian white noise model.
     """
-    particle = np.ones((n_pix // 2, n_pix, n_pix))
+    particle = np.ones((n_pix, n_pix))
     slices = np.ones((n_particles, n_pix, n_pix))
     bayesian_weights = test_ir.compute_bayesian_weights(particle, slices)
 

From e76d8a29169861dc472d27fcf41e1849abef429b Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 31 Mar 2022 00:09:01 +0000
Subject: [PATCH 126/148] Format code with black

---
 .../expectation_maximization.py               | 20 ++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index cf95b0c..72c5d35 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -167,10 +167,16 @@ def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
 
                 # normalize maps by slice counts to account
                 # for spherical density differences
-                map_3d_f_norm_1 = IterativeRefinement.normalize_map(map_3d_f_updated_1, counts_3d_updated_1, count_norm_const)
-                map_3d_f_norm_2 = IterativeRefinement.normalize_map(map_3d_f_updated_2, counts_3d_updated_2, count_norm_const)
+                map_3d_f_norm_1 = IterativeRefinement.normalize_map(
+                    map_3d_f_updated_1, counts_3d_updated_1, count_norm_const
+                )
+                map_3d_f_norm_2 = IterativeRefinement.normalize_map(
+                    map_3d_f_updated_2, counts_3d_updated_2, count_norm_const
+                )
 
-            half_map_3d_f_1, half_map_3d_f_2 = apply_noise_model(map_3d_f_norm_1, map_3d_f_norm_2)
+            half_map_3d_f_1, half_map_3d_f_2 = apply_noise_model(
+                map_3d_f_norm_1, map_3d_f_norm_2
+            )
 
         fsc_1d = IterativeRefinement.compute_fsc(half_map_3d_f_1, half_map_3d_f_2)
         fsc_3d = IterativeRefinement.expand_1d_to_3d(fsc_1d)
@@ -184,7 +190,7 @@ def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
     @staticmethod
     def normalize_map(map, counts, norm_const):
         """Normalize map by slice counts per voxel.
-        
+
         Parameters
         ----------
         map : arr
@@ -196,7 +202,7 @@ def normalize_map(map, counts, norm_const):
         norm_const : float
             A small number used as part of the wiener-filter-like
             normalization.
-        
+
         Returns
         -------
         norm_map : arr
@@ -208,7 +214,7 @@ def normalize_map(map, counts, norm_const):
     @staticmethod
     def apply_noise_model(map_3d_f_norm_1, map_3d_f_norm_2):
         """Apply noise model to normalized maps in fourier space.
-        
+
         Parameters
         ----------
         map_3d_f_norm_1 : arr
@@ -217,7 +223,7 @@ def apply_noise_model(map_3d_f_norm_1, map_3d_f_norm_2):
         map_3d_f_norm_2 : arr
             Shape (n_pix, n_pix, n_pix)
             Normalized fourier space half-map 2.
-        
+
         Returns
         -------
         (map_3d_f_filtered_1, map_3d_f_filtered_2) : (arr, arr)

From 6e7ed3249e9d919d0f18f1a3f68a4da41257f721 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 17:14:57 -0700
Subject: [PATCH 127/148] Infrastructure files

---
 dev-requirements.txt                          |  5 ++++
 environment.yml                               | 18 +++++++++++++++
 pytest.ini                                    |  4 ++++
 reconstructSPI/__init__.py                    |  1 +
 .../iterative_refinement/__init__.py          |  1 +
 setup.py                                      | 23 +++++++++++++++++++
 tests/__init__.py                             |  0
 7 files changed, 52 insertions(+)
 create mode 100644 dev-requirements.txt
 create mode 100644 environment.yml
 create mode 100644 pytest.ini
 create mode 100644 reconstructSPI/__init__.py
 create mode 100644 reconstructSPI/iterative_refinement/__init__.py
 create mode 100644 setup.py
 create mode 100644 tests/__init__.py

diff --git a/dev-requirements.txt b/dev-requirements.txt
new file mode 100644
index 0000000..663cad4
--- /dev/null
+++ b/dev-requirements.txt
@@ -0,0 +1,5 @@
+black
+flake8
+flake8-docstrings
+isort
+pre-commit
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..e52e0d7
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,18 @@
+name: reconstructSPI
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - codecov
+  - coverage
+  - gemmi
+  - numpy
+  - numba
+  - pillow>=8.2.0
+  - pip
+  - pytest
+  - pytest-cov
+  - pytorch
+  - pip :
+      - git+https://github.com/compSPI/simSPI.git
+
diff --git a/pytest.ini b/pytest.ini
new file mode 100644
index 0000000..cf93d60
--- /dev/null
+++ b/pytest.ini
@@ -0,0 +1,4 @@
+[pytest]
+testpaths = tests
+python_files = *.py
+python_functions = test_*
\ No newline at end of file
diff --git a/reconstructSPI/__init__.py b/reconstructSPI/__init__.py
new file mode 100644
index 0000000..a16d370
--- /dev/null
+++ b/reconstructSPI/__init__.py
@@ -0,0 +1 @@
+"""Various particle reconstruction methods."""
diff --git a/reconstructSPI/iterative_refinement/__init__.py b/reconstructSPI/iterative_refinement/__init__.py
new file mode 100644
index 0000000..5500bfe
--- /dev/null
+++ b/reconstructSPI/iterative_refinement/__init__.py
@@ -0,0 +1 @@
+"""Iterative refinement reconstruction methods."""
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..9631ff3
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,23 @@
+"""Create instructions to build the reconstructSPI package."""
+
+import setuptools
+
+requirements = []
+
+setuptools.setup(
+    name="reconstructSPI",
+    maintainer="Frederic Poitevin",
+    version="0.0.1",
+    maintainer_email="frederic.poitevin@stanford.edu",
+    description="Reconstruction methods and tools for SPI",
+    long_description=open("README.md", encoding="utf8").read(),
+    long_description_content_type="text/markdown",
+    url="https://github.com/compSPI/reconstructSPI.git",
+    packages=setuptools.find_packages(),
+    install_requires=requirements,
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "Operating System :: OS Independent",
+    ],
+    zip_safe=False,
+)
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000..e69de29

From 6a9ee6963c82c93b2190944f5fa64b55ad5f63dc Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 17:16:24 -0700
Subject: [PATCH 128/148] Infrastructure files

---
 .codecov.yml               | 24 +++++++++++++++
 .coveragerc                |  3 ++
 .deepsource.toml           | 10 ++----
 .flake8                    |  6 ++++
 .github/auto-assign.yml    |  4 +--
 .github/workflows/lint.yml | 54 +++++++++++++++++++++++++++++++++
 .github/workflows/test.yml | 62 ++++++++++++++++++++++++++++++++++++++
 .pre-commit-config.yaml    | 42 ++++++++++++++++++++++++++
 8 files changed, 195 insertions(+), 10 deletions(-)
 create mode 100644 .codecov.yml
 create mode 100644 .coveragerc
 create mode 100644 .flake8
 create mode 100644 .github/workflows/lint.yml
 create mode 100644 .github/workflows/test.yml
 create mode 100644 .pre-commit-config.yaml

diff --git a/.codecov.yml b/.codecov.yml
new file mode 100644
index 0000000..c576999
--- /dev/null
+++ b/.codecov.yml
@@ -0,0 +1,24 @@
+coverage:
+  round: up
+  precision: 2
+  status:
+    patch:
+      default:
+        # basic
+        target: 90%
+        threshold: 2%
+        base: auto
+        flags:
+          - unit
+        # advanced
+        branches:
+          - master
+        if_no_uploads: error
+        if_not_found: error
+        if_ci_failed: error
+        only_pulls: false
+
+# Files to ignore
+ignore:
+  - "data"
+  - "notebooks"
diff --git a/.coveragerc b/.coveragerc
new file mode 100644
index 0000000..94a9d5a
--- /dev/null
+++ b/.coveragerc
@@ -0,0 +1,3 @@
+[report]
+fail_under = 90
+show_missing = True
diff --git a/.deepsource.toml b/.deepsource.toml
index 93a9d6f..b4f754a 100644
--- a/.deepsource.toml
+++ b/.deepsource.toml
@@ -1,6 +1,6 @@
 version = 1
 
-test_patterns = ["test/**"]
+test_patterns = ["tests/**"]
 
 exclude_patterns = ["README.md"]
 
@@ -8,17 +8,11 @@ exclude_patterns = ["README.md"]
 name = "python"
 enabled = true
 
-  [analyzers.meta]
-  runtime_version = "3.x.x"
-
 [[analyzers]]
 name = "test-coverage"
 enabled = true
 
-[[transformers]]
-name = "isort"
-enabled = true
-
 [[transformers]]
 name = "black"
 enabled = true
+
diff --git a/.flake8 b/.flake8
new file mode 100644
index 0000000..ece9ae4
--- /dev/null
+++ b/.flake8
@@ -0,0 +1,6 @@
+[flake8]
+docstring-convention = numpy
+import_order_style = smarkets
+max-line-length = 88
+extend-ignore = E203,I202,I100
+exclude = reconstructSPI/__init__.py,reconstructSPI/iterative_refinement/__init.py,tests/__init__.py
diff --git a/.github/auto-assign.yml b/.github/auto-assign.yml
index 115af98..a0a74eb 100644
--- a/.github/auto-assign.yml
+++ b/.github/auto-assign.yml
@@ -5,10 +5,10 @@ addReviewers: true
 addAssignees: false
 
 # A list of reviewers to be added to pull requests (GitHub user name)
-reviewers: 
+reviewers:
   - fredericpoitevin
 
-# A list of keywords to be skipped the process that add reviewers if pull requests include it 
+# A list of keywords to be skipped the process that add reviewers if pull requests include it
 skipKeywords:
   - wip
 
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
new file mode 100644
index 0000000..cfc5574
--- /dev/null
+++ b/.github/workflows/lint.yml
@@ -0,0 +1,54 @@
+name: "Lint"
+
+on:
+  push:
+    branches: [master,github-actions-test]
+    paths-ignore:
+    - 'README.md'
+    - '.deepsource.toml'
+    - '.gitignore'
+    - 'setup.py'
+
+
+  pull_request:
+    branches: [master]
+    paths-ignore:
+    - 'README.md'
+    - '.deepsource.toml'
+    - '.gitignore'
+    - 'setup.py'
+
+
+jobs:
+  build:
+
+    runs-on: ${{matrix.os}}
+    strategy:
+      matrix:
+        os: [ubuntu-18.04]
+        python-version: [3.9]
+        test-folder : ['tests']
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Build using Python ${{matrix.python-version}}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{matrix.python-version}}
+      - name: install dependencies [pip]
+        run:  |
+          pip install --upgrade pip setuptools wheel
+          for req in dev-requirements.txt; do
+            pip install -q -r $req
+          done
+          pip install -e .
+      - name: linting [black and isort]
+        run: |
+          black . --check
+          isort --profile black --check .
+      - name: linting [flake8]
+        run: |
+          flake8 reconstructSPI tests
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 0000000..49cc26f
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,62 @@
+name: "Test"
+
+on:
+  push:
+    branches: [master,github-actions-test]
+    paths-ignore:
+    - 'README.md'
+    - '.deepsource.toml'
+    - '.gitignore'
+    - 'setup.py'
+
+
+  pull_request:
+    branches: [master]
+    paths-ignore:
+    - 'README.md'
+    - '.deepsource.toml'
+    - '.gitignore'
+    - 'setup.py'
+
+
+jobs:
+  build:
+
+    runs-on: ${{matrix.os}}
+    strategy:
+      matrix:
+        os: [ubuntu-18.04]
+        python-version: [3.7,3.8,3.9]
+        test-folder : ['tests']
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Build using Python ${{matrix.python-version}}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{matrix.python-version}}
+
+      - name: cache conda
+        uses: actions/cache@v1
+        with:
+          path: $CONDA
+          key: ${{ runner.os }}-conda-${{ hashFiles('environment.yml') }}
+          restore-keys: |
+            ${{ runner.os }}-conda-
+      - name: install dependencies [conda]
+        run:  |
+          # $CONDA is an environment variable pointing to the root of the miniconda directory
+          $CONDA/bin/conda env update --file environment.yml --name base
+          $CONDA/bin/pip install -e .
+      - name: unit testing [pytest]
+        env:
+          TEST_TOKEN: ${{ secrets.TEST_TOKEN }}
+        run: |
+          $CONDA/bin/pytest --cov-report term --cov-report xml:coverage.xml --cov=reconstructSPI ${{matrix.test-folder}}
+      - name: uploading code coverage [codecov]
+        if: ${{matrix.python-version == 3.7}}
+        run: |
+          bash <(curl -s https://codecov.io/bash) -c
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..e0b31c6
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,42 @@
+default_language_version :
+  python : python3
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.1.0
+    hooks:
+      - id: check-byte-order-marker
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-yaml
+      - id: mixed-line-ending
+        args:
+          - --fix=no
+      - id: no-commit-to-branch
+        args:
+          - --branch=master
+      - id: check-added-large-files
+        args:
+          - --maxkb=2048
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 21.8b0
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/isort
+    rev: 5.9.3
+    hooks:
+      - id : isort
+        args : ["--profile", "black", "--filter-files"]
+  - repo: https://github.com/asottile/blacken-docs
+    rev: v1.8.0
+    hooks:
+    -   id: blacken-docs
+        additional_dependencies: [black==20.8b0]
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.7.9
+    hooks:
+    - id: flake8
+      additional_dependencies:
+        - flake8-docstrings
+        - flake8-import-order
+      exclude: reconstructSPI/__init__.py,tests/__init__.py
\ No newline at end of file

From fd9cefafd6604748cf0f8b25b832e40507d75284 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 17:24:28 -0700
Subject: [PATCH 129/148] Missed a name

---
 reconstructSPI/iterative_refinement/expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index cf95b0c..7e01774 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -170,7 +170,7 @@ def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
                 map_3d_f_norm_1 = IterativeRefinement.normalize_map(map_3d_f_updated_1, counts_3d_updated_1, count_norm_const)
                 map_3d_f_norm_2 = IterativeRefinement.normalize_map(map_3d_f_updated_2, counts_3d_updated_2, count_norm_const)
 
-            half_map_3d_f_1, half_map_3d_f_2 = apply_noise_model(map_3d_f_norm_1, map_3d_f_norm_2)
+            half_map_3d_f_1, half_map_3d_f_2 = IterativeRefinement.apply_noise_model(map_3d_f_norm_1, map_3d_f_norm_2)
 
         fsc_1d = IterativeRefinement.compute_fsc(half_map_3d_f_1, half_map_3d_f_2)
         fsc_3d = IterativeRefinement.expand_1d_to_3d(fsc_1d)

From bb8b274c1846d9b5e9c5d9350edf24848573a6c5 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 17:25:02 -0700
Subject: [PATCH 130/148] Removed last few comments, will re-add if needed

---
 .../iterative_refinement/expectation_maximization.py      | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index 7e01774..8d0bc49 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -77,9 +77,6 @@ def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
         ctfs = self.build_ctf_array()
         ctfs_1, ctfs_2 = IterativeRefinement.split_array(ctfs)
 
-        # work in Fourier space. So particles can stay in Fourier
-        # space the whole time. They are experimental measurements
-        # and are fixed in the algorithm
         particles_f_1 = IterativeRefinement.fft_3d(particles_1)
         particles_f_2 = IterativeRefinement.fft_3d(particles_2)
 
@@ -107,8 +104,7 @@ def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
             slices_1, xyz_rotated = IterativeRefinement.generate_slices(
                 half_map_3d_f_1, xy0_plane, n_pix, rots
             )
-            # Here rots are the same for the half maps,
-            # but could be different in general.
+            
             slices_2, xyz_rotated = IterativeRefinement.generate_slices(
                 half_map_3d_f_2, xy0_plane, n_pix, rots
             )
@@ -165,8 +161,6 @@ def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
                     map_3d_f_updated_2 += inserted_slice_3d_r + 1j * inserted_slice_3d_i
                     counts_3d_updated_2 += count_3d_r + count_3d_i
 
-                # normalize maps by slice counts to account
-                # for spherical density differences
                 map_3d_f_norm_1 = IterativeRefinement.normalize_map(map_3d_f_updated_1, counts_3d_updated_1, count_norm_const)
                 map_3d_f_norm_2 = IterativeRefinement.normalize_map(map_3d_f_updated_2, counts_3d_updated_2, count_norm_const)
 

From 66c0ef30bba87a4105eccbca23b12807d1ed905b Mon Sep 17 00:00:00 2001
From: "deepsource-autofix[bot]"
 <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Date: Thu, 31 Mar 2022 00:25:59 +0000
Subject: [PATCH 131/148] Format code with black

---
 .../expectation_maximization.py                    | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index a9f951b..31f31e6 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -104,7 +104,7 @@ def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
             slices_1, xyz_rotated = IterativeRefinement.generate_slices(
                 half_map_3d_f_1, xy0_plane, n_pix, rots
             )
-            
+
             slices_2, xyz_rotated = IterativeRefinement.generate_slices(
                 half_map_3d_f_2, xy0_plane, n_pix, rots
             )
@@ -161,10 +161,16 @@ def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
                     map_3d_f_updated_2 += inserted_slice_3d_r + 1j * inserted_slice_3d_i
                     counts_3d_updated_2 += count_3d_r + count_3d_i
 
-                map_3d_f_norm_1 = IterativeRefinement.normalize_map(map_3d_f_updated_1, counts_3d_updated_1, count_norm_const)
-                map_3d_f_norm_2 = IterativeRefinement.normalize_map(map_3d_f_updated_2, counts_3d_updated_2, count_norm_const)
+                map_3d_f_norm_1 = IterativeRefinement.normalize_map(
+                    map_3d_f_updated_1, counts_3d_updated_1, count_norm_const
+                )
+                map_3d_f_norm_2 = IterativeRefinement.normalize_map(
+                    map_3d_f_updated_2, counts_3d_updated_2, count_norm_const
+                )
 
-            half_map_3d_f_1, half_map_3d_f_2 = IterativeRefinement.apply_noise_model(map_3d_f_norm_1, map_3d_f_norm_2)
+            half_map_3d_f_1, half_map_3d_f_2 = IterativeRefinement.apply_noise_model(
+                map_3d_f_norm_1, map_3d_f_norm_2
+            )
 
         fsc_1d = IterativeRefinement.compute_fsc(half_map_3d_f_1, half_map_3d_f_2)
         fsc_3d = IterativeRefinement.expand_1d_to_3d(fsc_1d)

From 579f716fd5159ca303602cf9b46223e80c14a43a Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 17:36:11 -0700
Subject: [PATCH 132/148] Fixed variable name

---
 .../iterative_refinement/expectation_maximization.py        | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index a9f951b..46529b9 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -176,12 +176,12 @@ def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
         return map_3d_r_final, half_map_3d_r_1, half_map_3d_r_2, fsc_1d
 
     @staticmethod
-    def normalize_map(map, counts, norm_const):
+    def normalize_map(map_3d, counts, norm_const):
         """Normalize map by slice counts per voxel.
 
         Parameters
         ----------
-        map : arr
+        map_3d : arr
             Shape (n_pix, n_pix, n_pix)
             The map to be normalized.
         counts : arr
@@ -197,7 +197,7 @@ def normalize_map(map, counts, norm_const):
             Shape (n_pix, n_pix, n_pix)
             map normalized by counts.
         """
-        return map * counts / (norm_const + counts**2)
+        return map_3d * counts / (norm_const + counts**2)
 
     @staticmethod
     def apply_noise_model(map_3d_f_norm_1, map_3d_f_norm_2):

From 55ee718db684b04c348d8f1205bb9dbea620d369 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 17:39:27 -0700
Subject: [PATCH 133/148] Changed codecov parameters

---
 .codecov.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.codecov.yml b/.codecov.yml
index c576999..2a942b9 100644
--- a/.codecov.yml
+++ b/.codecov.yml
@@ -22,3 +22,5 @@ coverage:
 ignore:
   - "data"
   - "notebooks"
+  - "reconstructSPI/__init__.py"
+  - "reconstructSPI/iterative_refinement/__init__.py"

From 0d18f66b662f5bbb0ac11f8be3395d0fe5ba8e5d Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 17:48:43 -0700
Subject: [PATCH 134/148] Removed __init__.py files

---
 .codecov.yml                                    | 2 --
 reconstructSPI/__init__.py                      | 1 -
 reconstructSPI/iterative_refinement/__init__.py | 1 -
 3 files changed, 4 deletions(-)
 delete mode 100644 reconstructSPI/__init__.py
 delete mode 100644 reconstructSPI/iterative_refinement/__init__.py

diff --git a/.codecov.yml b/.codecov.yml
index 2a942b9..c576999 100644
--- a/.codecov.yml
+++ b/.codecov.yml
@@ -22,5 +22,3 @@ coverage:
 ignore:
   - "data"
   - "notebooks"
-  - "reconstructSPI/__init__.py"
-  - "reconstructSPI/iterative_refinement/__init__.py"
diff --git a/reconstructSPI/__init__.py b/reconstructSPI/__init__.py
deleted file mode 100644
index a16d370..0000000
--- a/reconstructSPI/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-"""Various particle reconstruction methods."""
diff --git a/reconstructSPI/iterative_refinement/__init__.py b/reconstructSPI/iterative_refinement/__init__.py
deleted file mode 100644
index 5500bfe..0000000
--- a/reconstructSPI/iterative_refinement/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-"""Iterative refinement reconstruction methods."""

From 7f8145686e1e416aa0fc9d4438b296516e172456 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 17:50:36 -0700
Subject: [PATCH 135/148] Revert "Removed __init__.py files"

This reverts commit 0d18f66b662f5bbb0ac11f8be3395d0fe5ba8e5d.
---
 .codecov.yml                                    | 2 ++
 reconstructSPI/__init__.py                      | 1 +
 reconstructSPI/iterative_refinement/__init__.py | 1 +
 3 files changed, 4 insertions(+)
 create mode 100644 reconstructSPI/__init__.py
 create mode 100644 reconstructSPI/iterative_refinement/__init__.py

diff --git a/.codecov.yml b/.codecov.yml
index c576999..2a942b9 100644
--- a/.codecov.yml
+++ b/.codecov.yml
@@ -22,3 +22,5 @@ coverage:
 ignore:
   - "data"
   - "notebooks"
+  - "reconstructSPI/__init__.py"
+  - "reconstructSPI/iterative_refinement/__init__.py"
diff --git a/reconstructSPI/__init__.py b/reconstructSPI/__init__.py
new file mode 100644
index 0000000..a16d370
--- /dev/null
+++ b/reconstructSPI/__init__.py
@@ -0,0 +1 @@
+"""Various particle reconstruction methods."""
diff --git a/reconstructSPI/iterative_refinement/__init__.py b/reconstructSPI/iterative_refinement/__init__.py
new file mode 100644
index 0000000..5500bfe
--- /dev/null
+++ b/reconstructSPI/iterative_refinement/__init__.py
@@ -0,0 +1 @@
+"""Iterative refinement reconstruction methods."""

From e583a54eaf9469bc74cb2fdafbb88211b6d3cead Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 18:01:51 -0700
Subject: [PATCH 136/148] Revert "Changed codecov parameters"

This reverts commit 55ee718db684b04c348d8f1205bb9dbea620d369.
---
 .codecov.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.codecov.yml b/.codecov.yml
index 2a942b9..c576999 100644
--- a/.codecov.yml
+++ b/.codecov.yml
@@ -22,5 +22,3 @@ coverage:
 ignore:
   - "data"
   - "notebooks"
-  - "reconstructSPI/__init__.py"
-  - "reconstructSPI/iterative_refinement/__init__.py"

From 15840cfcf45e877cd069b7677bdb5ebaefc2ed30 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 18:06:26 -0700
Subject: [PATCH 137/148] Refactoring library format

---
 .flake8                                                         | 2 +-
 reconstructSPI/__init__.py => __init__.py                       | 0
 .../iterative_refinement => iterative_refinement}/__init__.py   | 0
 3 files changed, 1 insertion(+), 1 deletion(-)
 rename reconstructSPI/__init__.py => __init__.py (100%)
 rename {reconstructSPI/iterative_refinement => iterative_refinement}/__init__.py (100%)

diff --git a/.flake8 b/.flake8
index ece9ae4..78fd79a 100644
--- a/.flake8
+++ b/.flake8
@@ -3,4 +3,4 @@ docstring-convention = numpy
 import_order_style = smarkets
 max-line-length = 88
 extend-ignore = E203,I202,I100
-exclude = reconstructSPI/__init__.py,reconstructSPI/iterative_refinement/__init.py,tests/__init__.py
+exclude = __init__.py,iterative_refinement/__init.py,tests/__init__.py
diff --git a/reconstructSPI/__init__.py b/__init__.py
similarity index 100%
rename from reconstructSPI/__init__.py
rename to __init__.py
diff --git a/reconstructSPI/iterative_refinement/__init__.py b/iterative_refinement/__init__.py
similarity index 100%
rename from reconstructSPI/iterative_refinement/__init__.py
rename to iterative_refinement/__init__.py

From 2f91bc6686048ac4f39c619e38b006e4268499f0 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 18:10:42 -0700
Subject: [PATCH 138/148] Directory fixes

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e0b31c6..5af6583 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -39,4 +39,4 @@ repos:
       additional_dependencies:
         - flake8-docstrings
         - flake8-import-order
-      exclude: reconstructSPI/__init__.py,tests/__init__.py
\ No newline at end of file
+      exclude: __init__.py,iterative_refinement/__init__.py,tests/__init__.py
\ No newline at end of file

From bccb41ce29d8055ea02a632d8f1e3b8ef51080eb Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 18:13:43 -0700
Subject: [PATCH 139/148] Revert "Refactoring library format"

This reverts commit 15840cfcf45e877cd069b7677bdb5ebaefc2ed30.
---
 .flake8                                                         | 2 +-
 __init__.py => reconstructSPI/__init__.py                       | 0
 .../iterative_refinement}/__init__.py                           | 0
 3 files changed, 1 insertion(+), 1 deletion(-)
 rename __init__.py => reconstructSPI/__init__.py (100%)
 rename {iterative_refinement => reconstructSPI/iterative_refinement}/__init__.py (100%)

diff --git a/.flake8 b/.flake8
index 78fd79a..ece9ae4 100644
--- a/.flake8
+++ b/.flake8
@@ -3,4 +3,4 @@ docstring-convention = numpy
 import_order_style = smarkets
 max-line-length = 88
 extend-ignore = E203,I202,I100
-exclude = __init__.py,iterative_refinement/__init.py,tests/__init__.py
+exclude = reconstructSPI/__init__.py,reconstructSPI/iterative_refinement/__init.py,tests/__init__.py
diff --git a/__init__.py b/reconstructSPI/__init__.py
similarity index 100%
rename from __init__.py
rename to reconstructSPI/__init__.py
diff --git a/iterative_refinement/__init__.py b/reconstructSPI/iterative_refinement/__init__.py
similarity index 100%
rename from iterative_refinement/__init__.py
rename to reconstructSPI/iterative_refinement/__init__.py

From 2c42e8d884fc1cc2074e409eaebb1b5885590a24 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 18:13:56 -0700
Subject: [PATCH 140/148] Revert "Directory fixes"

This reverts commit 2f91bc6686048ac4f39c619e38b006e4268499f0.
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 5af6583..e0b31c6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -39,4 +39,4 @@ repos:
       additional_dependencies:
         - flake8-docstrings
         - flake8-import-order
-      exclude: __init__.py,iterative_refinement/__init__.py,tests/__init__.py
\ No newline at end of file
+      exclude: reconstructSPI/__init__.py,tests/__init__.py
\ No newline at end of file

From 9126f8684d07489d447b7b699f12c1e042d715d8 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 18:41:00 -0700
Subject: [PATCH 141/148] Removed dependencies

---
 environment.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/environment.yml b/environment.yml
index e52e0d7..ef85386 100644
--- a/environment.yml
+++ b/environment.yml
@@ -5,9 +5,6 @@ channels:
 dependencies:
   - codecov
   - coverage
-  - gemmi
-  - numpy
-  - numba
   - pillow>=8.2.0
   - pip
   - pytest

From 3330c11dbd0cbd2573dd6e19468f9ebaea19f8fd Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 18:59:02 -0700
Subject: [PATCH 142/148] Testing something

---
 .codecov.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.codecov.yml b/.codecov.yml
index c576999..92ae275 100644
--- a/.codecov.yml
+++ b/.codecov.yml
@@ -13,6 +13,7 @@ coverage:
         # advanced
         branches:
           - master
+          - reconstructSPI_infrastructure
         if_no_uploads: error
         if_not_found: error
         if_ci_failed: error

From ef10249ed795c7f5c46e73a640ca8928a0545fb0 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 19:02:13 -0700
Subject: [PATCH 143/148] Testing things

---
 .github/workflows/lint.yml | 2 +-
 .github/workflows/test.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index cfc5574..b4d4102 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -2,7 +2,7 @@ name: "Lint"
 
 on:
   push:
-    branches: [master,github-actions-test]
+    branches: [master,github-actions-test,reconstructSPI_infrastructure]
     paths-ignore:
     - 'README.md'
     - '.deepsource.toml'
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 49cc26f..b9f6232 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -2,7 +2,7 @@ name: "Test"
 
 on:
   push:
-    branches: [master,github-actions-test]
+    branches: [master,github-actions-test,reconstructSPI_infrastructure]
     paths-ignore:
     - 'README.md'
     - '.deepsource.toml'

From 8dda440a8e0dd86f8c60d8de8e5592d43535f7bc Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 19:06:08 -0700
Subject: [PATCH 144/148] Force checks

---
 reconstructSPI/iterative_refinement/expectation_maximization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index 14c5010..27d2a4d 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -47,7 +47,7 @@ def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
         """Perform iterative refinement.
 
         Acts in a Bayesian expectation maximization setting,
-        i.e. maximum a posteriori estimation.
+        i.e. using maximum a posteriori estimation.
 
         Parameters
         ----------

From 749bcd2d58d468878b246f37fdf74c80402eecd5 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 19:08:27 -0700
Subject: [PATCH 145/148] Testing things

---
 .github/workflows/lint.yml | 2 +-
 .github/workflows/test.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index b4d4102..884911e 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -11,7 +11,7 @@ on:
 
 
   pull_request:
-    branches: [master]
+    branches: [master,reconstructSPI_infrastructure]
     paths-ignore:
     - 'README.md'
     - '.deepsource.toml'
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index b9f6232..04b6e1f 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -11,7 +11,7 @@ on:
 
 
   pull_request:
-    branches: [master]
+    branches: [master,reconstructSPI_infrastructure]
     paths-ignore:
     - 'README.md'
     - '.deepsource.toml'

From 2ea9459adc3d0783bfafbcb6fd05786b7c985468 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 19:12:02 -0700
Subject: [PATCH 146/148] Added library requirements

---
 environment.yml                                                | 3 +++
 .../iterative_refinement/expectation_maximization.py           | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index ef85386..e52e0d7 100644
--- a/environment.yml
+++ b/environment.yml
@@ -5,6 +5,9 @@ channels:
 dependencies:
   - codecov
   - coverage
+  - gemmi
+  - numpy
+  - numba
   - pillow>=8.2.0
   - pip
   - pytest
diff --git a/reconstructSPI/iterative_refinement/expectation_maximization.py b/reconstructSPI/iterative_refinement/expectation_maximization.py
index 27d2a4d..14c5010 100644
--- a/reconstructSPI/iterative_refinement/expectation_maximization.py
+++ b/reconstructSPI/iterative_refinement/expectation_maximization.py
@@ -47,7 +47,7 @@ def iterative_refinement(self, wiener_small_number=0.01, count_norm_const=1):
         """Perform iterative refinement.
 
         Acts in a Bayesian expectation maximization setting,
-        i.e. using maximum a posteriori estimation.
+        i.e. maximum a posteriori estimation.
 
         Parameters
         ----------

From 5152547989399bbf5de59089676176ef88a6e17e Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Wed, 30 Mar 2022 19:16:15 -0700
Subject: [PATCH 147/148] Added dev branch to branches on which tests will run.

---
 .codecov.yml               | 2 +-
 .github/workflows/lint.yml | 4 ++--
 .github/workflows/test.yml | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.codecov.yml b/.codecov.yml
index 92ae275..fd85925 100644
--- a/.codecov.yml
+++ b/.codecov.yml
@@ -13,7 +13,7 @@ coverage:
         # advanced
         branches:
           - master
-          - reconstructSPI_infrastructure
+          - dev
         if_no_uploads: error
         if_not_found: error
         if_ci_failed: error
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index b4d4102..38ca19a 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -2,7 +2,7 @@ name: "Lint"
 
 on:
   push:
-    branches: [master,github-actions-test,reconstructSPI_infrastructure]
+    branches: [master,github-actions-test,dev]
     paths-ignore:
     - 'README.md'
     - '.deepsource.toml'
@@ -11,7 +11,7 @@ on:
 
 
   pull_request:
-    branches: [master]
+    branches: [master,dev]
     paths-ignore:
     - 'README.md'
     - '.deepsource.toml'
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index b9f6232..0d86279 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -2,7 +2,7 @@ name: "Test"
 
 on:
   push:
-    branches: [master,github-actions-test,reconstructSPI_infrastructure]
+    branches: [master,github-actions-test,dev]
     paths-ignore:
     - 'README.md'
     - '.deepsource.toml'
@@ -11,7 +11,7 @@ on:
 
 
   pull_request:
-    branches: [master]
+    branches: [master,dev]
     paths-ignore:
     - 'README.md'
     - '.deepsource.toml'

From 9d05c1a2da059da4c56e4934579d8328b1f66244 Mon Sep 17 00:00:00 2001
From: thisTyler <t368@heim.ca>
Date: Thu, 31 Mar 2022 12:42:46 -0700
Subject: [PATCH 148/148] removed itr_ref_docstrings branch checks

---
 .codecov.yml               | 1 -
 .github/workflows/lint.yml | 4 ++--
 .github/workflows/test.yml | 4 ++--
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/.codecov.yml b/.codecov.yml
index ca076ae..fd85925 100644
--- a/.codecov.yml
+++ b/.codecov.yml
@@ -14,7 +14,6 @@ coverage:
         branches:
           - master
           - dev
-          - reconstructSPI_infrastructure
         if_no_uploads: error
         if_not_found: error
         if_ci_failed: error
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index c8fd042..38ca19a 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -2,7 +2,7 @@ name: "Lint"
 
 on:
   push:
-    branches: [master,github-actions-test,dev,reconstructSPI_infrastructure]
+    branches: [master,github-actions-test,dev]
     paths-ignore:
     - 'README.md'
     - '.deepsource.toml'
@@ -11,7 +11,7 @@ on:
 
 
   pull_request:
-    branches: [master,dev,reconstructSPI_infrastructure]
+    branches: [master,dev]
     paths-ignore:
     - 'README.md'
     - '.deepsource.toml'
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index cf4e538..0d86279 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -2,7 +2,7 @@ name: "Test"
 
 on:
   push:
-    branches: [master,github-actions-test,dev,reconstructSPI_infrastructure]
+    branches: [master,github-actions-test,dev]
     paths-ignore:
     - 'README.md'
     - '.deepsource.toml'
@@ -11,7 +11,7 @@ on:
 
 
   pull_request:
-    branches: [master,dev,reconstructSPI_infrastructure]
+    branches: [master,dev]
     paths-ignore:
     - 'README.md'
     - '.deepsource.toml'