next release v2.4.0

.github/workflows/test.yml

@@ -69,8 +69,6 @@ jobs:
         gpg_key: ${{ secrets.GPG_KEY }}
         password: ${{ secrets.PYPI_TOKEN }}
         upload: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags') }}
-      env:
-        PATHTOOLS: ${{ github.workspace }}/NiftyPET_tools
     - id: meta
       name: Changelog
       run: |

README.rst

@@ -14,26 +14,22 @@ The upsampling is needed for more accurate extraction (sampling) of PET data usi
 
 PVC is needed to correct for the spill-in and spill-out of PET signal from defined ROIs (specific for any given application).
 
-In order to facilitate these operations, NIMPA relies on third-party software for image conversion from DICOM to NIfTI (dcm2niix) and image registration (NiftyReg).  The additional software is installed automatically to a user specified location.
-
 **Documentation with installation manual and tutorials**: https://niftypet.readthedocs.io/
 
 Quick Install
 ~~~~~~~~~~~~~
 
-Note that installation prompts for setting the path to ``NiftyPET_tools``.
-This can be avoided by setting the environment variables ``PATHTOOLS``.
-It's also recommended (but not required) to use `conda`.
+Note that it's recommended (but not required) to use `conda`.
 
 .. code:: sh
 
-    # optional (Linux syntax) to avoid prompts
-    export PATHTOOLS=$HOME/NiftyPET_tools
     # cross-platform install
     conda install -c conda-forge python=3 \
-      ipykernel numpy scipy scikit-image matplotlib ipywidgets
+      ipykernel numpy scipy scikit-image matplotlib ipywidgets dcm2niix
     pip install "nimpa>=2"
 
+For optional `dcm2niix <https://github.com/rordenlab/dcm2niix>`_ (image conversion from DICOM to NIfTI) and/or `niftyreg <https://github.com/KCL-BMEIS/niftyreg>`_ (image registration) support, simply install them separately (``pip install dcm2niix niftyreg``).
+
 External CMake Projects
 ~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -68,7 +64,7 @@ Licence
 Copyright 2018-21
 
 - `Pawel J. Markiewicz <https://github.com/pjmark>`__ @ University College London
-- `Casper O. da Costa-Luis <https://github.com/casperdcl>`__ @ King's College London
+- `Casper O. da Costa-Luis <https://github.com/casperdcl>`__ @ University College London/King's College London
 - `Contributors <https://github.com/NiftyPET/NIMPA/graphs/contributors>`__
 
 .. |Docs| image:: https://readthedocs.org/projects/niftypet/badge/?version=latest

niftypet/nimpa/__init__.py

@@ -30,14 +30,17 @@
     'centre_mass_img', 'centre_mass_corr', 'coreg_spm', 'coreg_vinci',
     'create_dir', 'create_mask', 'ct2mu',
     'dcm2im', 'dcm2nii', 'dcmanonym', 'dcminfo', 'dcmsort',
-    'dice_coeff', 'dice_coeff_multiclass', 'fwhm2sig', 'getnii',
+    'dice_coeff', 'dice_coeff_multiclass', 'fwhm2sig', 'getmgh', 'getnii', 'mgh2nii',
     'getnii_descr', 'im_cut', 'imfill', 'imsmooth', 'iyang', 'motion_reg', 'nii_gzip',
     'nii_modify', 'nii_ugzip', 'niisort', 'orientnii', 'pet2pet_rigid', 'pick_t1w',
     'psf_gaussian', 'psf_measured', 'pvc_iyang', 'realign_mltp_spm', 'resample_fsl',
     'resample_mltp_spm', 'resample_niftyreg', 'resample_spm', 'resample_vinci', 'resample_dipy',
     'time_stamp'] # yapf: disable
 
-from numcu import add, div, mul
+try:
+    from numcu import add, div, mul
+except ImportError:
+    pass
 from pkg_resources import resource_filename
 
 from niftypet.ninst import cudasetup as cs
@@ -68,13 +71,15 @@
     dice_coeff,
     dice_coeff_multiclass,
     fwhm2sig,
+    getmgh,
     getnii,
     getnii_descr,
     im_cut,
     imfill,
     imsmooth,
     isub,
     iyang,
+    mgh2nii,
     motion_reg,
     nii_gzip,
     nii_modify,

niftypet/nimpa/prc/__init__.py

@@ -2,8 +2,8 @@
 __all__ = [
     # imio
     'array2nii', 'create_dir', 'dcm2im', 'dcm2nii', 'dcmanonym', 'dcminfo', 'dcmsort', 'fwhm2sig',
-    'getnii', 'getnii_descr', 'nii_gzip', 'nii_ugzip', 'niisort', 'orientnii', 'pick_t1w',
-    'time_stamp',
+    'mgh2nii', 'getmgh', 'getnii', 'getnii_descr', 'nii_gzip', 'nii_ugzip', 'niisort', 'orientnii',
+    'pick_t1w', 'time_stamp',
     # prc
     'bias_field_correction', 'centre_mass_img', 'centre_mass_corr', 'ct2mu', 'im_cut',
     'imsmooth', 'imtrimup',
@@ -26,8 +26,10 @@
     dcminfo,
     dcmsort,
     fwhm2sig,
+    getmgh,
     getnii,
     getnii_descr,
+    mgh2nii,
     nii_gzip,
     nii_ugzip,
     niisort,

niftypet/nimpa/prc/imio.py

@@ -1,6 +1,7 @@
 """image input/output functionalities."""
 import datetime
 import logging
+import numbers
 import os
 import pathlib
 import re
@@ -50,6 +51,107 @@ def fwhm2sig(fwhm, voxsize=2.0):
     return (fwhm/voxsize) / (2 * (2 * np.log(2))**.5)
 
 
+def mgh2nii(fim, fout=None, output=None):
+    ''' Convert `*.mgh` or `*.mgz` FreeSurfer image to NIfTI.
+        Arguments:
+            fim: path to the input MGH file
+            fout: path to the output NIfTI file, if None then
+                  creates based on `fim`
+            output: if not None and an applicable string it will
+            output a dictionary or an array (see below)
+        Return:
+            None: returns nothing
+            'image' or 'im': outputs just the image
+            'affine': outputs just the affine matrix
+            'all': outputs all as a dictionary
+    '''
+
+    if not os.path.isfile(fim):
+        raise ValueError('The input path is incorrect!')
+
+    # > get the image dictionary
+    mghd = getmgh(fim, output='all')
+    im = mghd['im']
+
+    # > sort out the output
+    if fout is None:
+        fout = fim.parent / (fim.name.split('.')[0] + '.nii.gz')
+
+    out = fout
+    if output == 'image' or output == 'im':
+        out = fout, im
+    elif output == 'affine':
+        out = fout, mghd['affine']
+    elif output == 'all':
+        out = mghd
+        out['fout'] = fout
+
+    array2nii(
+        mghd['im'], mghd['affine'], fout,
+        trnsp=(mghd['transpose'].index(0), mghd['transpose'].index(1), mghd['transpose'].index(2)),
+        flip=mghd['flip'])
+
+    return out
+
+
+def getmgh(fim, nan_replace=None, output='image'):
+    '''
+    Get image from `*.mgz` or `*.mgh` file (FreeSurfer).
+    Arguments:
+        fim: input file name for the MGH/Z image
+        output: option for choosing output: 'image', 'affine' matrix or
+                'all' for a dictionary with all the info.
+    Return:
+        'image': outputs just the image
+        'affine': outputs just the affine matrix
+        'all': outputs all as a dictionary
+    '''
+
+    if not os.path.isfile(fim):
+        raise ValueError('The input path is incorrect!')
+
+    mgh = nib.freesurfer.load(str(fim))
+
+    if output == 'image' or output == 'all':
+
+        imr = np.asanyarray(mgh.dataobj)
+        # replace NaNs if requested
+        if isinstance(nan_replace, numbers.Number):
+            imr[np.isnan(imr)] = nan_replace
+
+        imr = np.squeeze(imr)
+        dimno = imr.ndim
+
+        # > get orientations from the affine
+        ornt = nib.io_orientation(mgh.affine)
+        trnsp = tuple(np.flip(np.argsort(ornt[:, 0])))
+        flip = tuple(np.int8(ornt[:, 1]))
+
+        # > flip y-axis and z-axis and then transpose
+        if dimno == 4:   # dynamic
+            imr = np.transpose(imr[::-flip[0], ::-flip[1], ::-flip[2], :], (3,) + trnsp)
+        elif dimno == 3: # static
+            imr = np.transpose(imr[::-flip[0], ::-flip[1], ::-flip[2]], trnsp)
+
+        # # > voxel size
+        # voxsize = mgh.header.get('pixdim')[1:mgh.header.get('dim')[0] + 1]
+        # # > rearrange voxel size according to the orientation
+        # voxsize = voxsize[np.array(trnsp)]
+
+    if output == 'all':
+        out = {
+            'im': imr, 'affine': mgh.affine, 'fim': fim, 'dtype': mgh.get_data_dtype(),
+            'shape': imr.shape, 'hdr': mgh.header, 'transpose': trnsp, 'flip': flip}
+    elif output == 'image':
+        out = imr
+    elif output == 'affine':
+        out = mgh.affine
+    else:
+        raise NameError("Unrecognised output request!")
+
+    return out
+
+
 def getnii_descr(fim):
     '''Extracts the custom description header field to dictionary'''
     nim = nib.load(fim)
@@ -183,6 +285,11 @@ def dcminfo(dcmvar, Cnt=None, output='detail', t1_name='mprage'):
         cmmnt = dhdr[0x0020, 0x4000].value
         log.debug('   Comments: {}'.format(cmmnt))
 
+    # > institution
+    inst = ''
+    if [0x008, 0x080] in dhdr:
+        inst = dhdr[0x008, 0x080].value
+
     prtcl = ''
     if [0x18, 0x1030] in dhdr:
         prtcl = dhdr[0x18, 0x1030].value
@@ -297,7 +404,7 @@ def dcminfo(dcmvar, Cnt=None, output='detail', t1_name='mprage'):
 
     if validTs:
         mrdct = {
-            'series': srs, 'protocol': prtcl, 'units': unt, 'study_time': study_time,
+            'series': srs, 'protocol': prtcl, 'units': unt, 'study_time': study_time, 'inst': inst,
             'series_time': series_time, 'acq_time': acq_time, 'scanner_id': scanner_id, 'TR': TR,
             'TE': TE}
     # ---------------------------------------------
@@ -324,11 +431,11 @@ def dcminfo(dcmvar, Cnt=None, output='detail', t1_name='mprage'):
     elif isPET:
         petdct = {
             'series': srs, 'protocol': prtcl, 'study_time': study_time, 'series_time': series_time,
-            'acq_time': acq_time, 'scanner_id': scanner_id, 'type': srs_type, 'units': unt,
-            'recon': recon, 'decay_corr': decay_corr, 'dcf': dcf, 'attenuation': atten,
-            'scatter': scat, 'scf': scf, 'randoms': rand, 'dose_calib': dscf, 'dead_time': dt,
-            'tracer': tracer, 'total_dose': tdose, 'half_life': hlife, 'positron_fract': pfract,
-            'radio_start_time': ttime0, 'radio_stop_time': ttime1}
+            'inst': inst, 'acq_time': acq_time, 'scanner_id': scanner_id, 'type': srs_type,
+            'units': unt, 'recon': recon, 'decay_corr': decay_corr, 'dcf': dcf,
+            'attenuation': atten, 'scatter': scat, 'scf': scf, 'randoms': rand, 'dose_calib': dscf,
+            'dead_time': dt, 'tracer': tracer, 'total_dose': tdose, 'half_life': hlife,
+            'positron_fract': pfract, 'radio_start_time': ttime0, 'radio_stop_time': ttime1}
 
         out = ['pet', tracer.lower(), srs_type.lower(), scanner_id, petdct]
 

niftypet/nimpa/prc/prc.py

@@ -727,7 +727,6 @@ def pvc_iyang(
                 ft1w,
                 outpath=os.path.join(outpath, 'PET', 'positioning'),
                 fcomment=fcomment,
-                executable=Cnt['REGPATH'],
                 omp=multiprocessing.cpu_count() / 2,
                 rigOnly=True,
                 affDirect=False,
@@ -1286,6 +1285,9 @@ def bias_field_correction(fmr, fimout='', outpath='', fcomment='_N4bias', execut
 
     if len(outdct['fim']) == 1:
         outdct['fim'] = outdct['fim'][0]
+        if 'fmsk' in outdct:
+            outdct['fmsk'] = outdct['fmsk'][0]
+
     return outdct
 
 

niftypet/nimpa/prc/regseg.py

@@ -7,6 +7,7 @@
 import os
 import shutil
 import sys
+from os import fspath
 from subprocess import call
 from textwrap import dedent
 
@@ -276,7 +277,7 @@ def affine_niftyreg(
     fname_aff='',
     pickname='ref',
     fcomment='',
-    executable='',
+    executable=None,
     omp=1,
     rigOnly=False,
     affDirect=False,
@@ -294,10 +295,13 @@ def affine_niftyreg(
     fthrsh=0.05,
     verbose=True,
 ):
-
-    # check if the executable exists:
+    if not executable:
+        executable = getattr(rs, 'REGPATH', None)
+        if not executable:
+            from niftyreg import bin_path
+            executable = fspath(next(bin_path.glob("reg_aladin*")))
     if not os.path.isfile(executable):
-        raise IOError('Incorrect path to executable file for registration.')
+        raise IOError(f"executable not found:{executable}")
 
     # create a folder for images registered to ref
     if outpath != '':
@@ -377,16 +381,16 @@ def resample_niftyreg(
     fcomment='',
     pickname='ref',
     intrp=1,
-    executable='',
+    executable=None,
     verbose=True,
 ):
-
-    # check if the executable exists:
-    # if executable=='' and 'RESPATH' in Cnt and os.path.isfile(Cnt['RESPATH']):
-    #     executable = Cnt['RESPATH']
-
+    if not executable:
+        executable = getattr(rs, 'RESPATH', None)
+        if not executable:
+            from niftyreg import bin_path
+            executable = fspath(next(bin_path.glob("reg_resample*")))
     if not os.path.isfile(executable):
-        raise IOError('Incorrect path to executable file for registration.')
+        raise IOError(f"executable not found:{executable}")
 
     # > output path
     if outpath == '' and fimout != '':

pyproject.toml

@@ -1,6 +1,7 @@
 [build-system]
+# cuvec>=2.8.0
 requires = ["setuptools>=42", "wheel", "setuptools_scm[toml]>=3.4",
-            "ninst>=0.8.0", "cuvec>=2.8.0", "miutil[cuda]>=0.4.0",
+            "ninst>=0.9.0", "cuvec-base", "miutil[cuda]>=0.4.0",
             "scikit-build>=0.11.0", "cmake>=3.18", "ninja"]
 
 [tool.setuptools_scm]

setup.cfg

@@ -39,26 +39,12 @@ setup_requires=
     setuptools>=42
     wheel
     setuptools_scm[toml]
-    ninst>=0.8.0
+    ninst>=0.9.0
     scikit-build>=0.11.0
     cmake>=3.18
     ninja
-    cuvec>=2.8.0
+    cuvec-base
     miutil[cuda]>=0.4.0
-install_requires=
-    cuvec>=2.3.1
-    pydcm2niix>=1.0.20220116
-    dipy>=1.3.0
-    miutil[nii]>=0.10.0
-    nibabel>=2.4.0
-    ninst>=0.4.0
-    numcu
-    numpy>=1.14
-    pydicom>=1.0.2
-    scipy
-    setuptools
-    spm12
-    # SimpleITK>=1.2.0
 python_requires=>=3.6
 [options.extras_require]
 dev=
@@ -68,6 +54,9 @@ dev=
     pytest-timeout
     pytest-xdist
 plot=miutil[plot]
+cuda=cuvec>=2.3.1; numcu
+dcm2niix=dcm2niix>=1.0.20220116
+niftyreg=niftyreg
 
 [flake8]
 max_line_length=99