updated ims-cpp to latest

alexandrovteam · Aug 18, 2017 · ed386f7 · ed386f7
1 parent 3ac0e91
commit ed386f7
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Showing 5 changed files with 15 additions and 16 deletions.
diff --git a/cpyMSpec/legacy_interface.py b/cpyMSpec/legacy_interface.py
@@ -14,7 +14,7 @@ def complete_isodist(sf, sigma=0.001, cutoff_perc=0.1, charge=None, pts_per_mz=1
     cutoff = cutoff_perc / 100.0
     fwhm = sigma * 2.3548200450309493  # the exact ratio is 2 \sqrt{2 \log 2}
     abs_charge = max(1, abs(charge))
-    p = isotopePattern(str(sf), cutoff / 10.0)
+    p = isotopePattern(str(sf), 0.9999)
     p.addCharge(charge)
 
     mz = min(p.masses) / abs_charge

diff --git a/cpyMSpec/spectrum.py b/cpyMSpec/spectrum.py
@@ -298,16 +298,14 @@ def trimmed(self, n_peaks):
     def removeIntensitiesBelow(self, min_intensity):
         ims.spectrum_trim_intensity(self.ptr, min_intensity)
 
-def isotopePattern(sum_formula, threshold=1e-4, fft_threshold=1e-8):
+def isotopePattern(sum_formula, desired_prob=0.99999):
     """
     Calculates isotopic peaks for a sum formula.
 
     :param sum_formula: text representation of an atomic composition
     :type sum_formula: str
-    :param threshold: minimal abundance to keep in the final results
-    :param fft_threshold: minimal abundance to keep in intermediate
-           results (for each of the distinct atomic species)
+    :param desired_prob: total probability covered by the result
+    :type desired_prob: float
     """
-    s = ims.spectrum_new_from_sf(sum_formula.encode('ascii'),
-                                 threshold, fft_threshold)
+    s = ims.spectrum_new_from_sf(sum_formula.encode('ascii'), desired_prob)
     return _new_spectrum(TheoreticalSpectrum, s)
diff --git a/cpyMSpec/utils.py b/cpyMSpec/utils.py
@@ -17,4 +17,4 @@ def init_ffi():
 def load_shared_lib(ffi):
     return ffi.dlopen(full_filename(shared_lib("ms_cffi")))
 
-VERSION = "0.3.5"
+VERSION = "0.4.0"
diff --git a/ims-cpp b/ims-cpp
diff --git a/test/test_centroiding.py b/test/test_centroiding.py
@@ -2,22 +2,23 @@
 
 import pytest
 
-def assert_patterns_almost_equal(p1, p2):
+def assert_patterns_almost_equal(p1, p2, instr):
     peaks1 = list(zip(p1.masses, p1.intensities))
     peaks2 = list(zip(p2.masses, p2.intensities))
-    assert_peaks_almost_equal(peaks1[:5], peaks2[:5])
+    assert_peaks_almost_equal(peaks1[:5], peaks2[:5], instr)
 
-def assert_peaks_almost_equal(peaks1, peaks2):
+def assert_peaks_almost_equal(peaks1, peaks2, instr):
     for (m1, a1), (m2, a2) in zip(peaks1, peaks2):
-        assert abs(m1 - m2) < 1e-4
-        assert abs(a1 - a2) < 1e-3
+        ppm = m1 / instr.resolvingPowerAt(m1)
+        assert abs((m1 - m2) / m1) < 0.1 * ppm
+        assert abs((a1 - a2) / a2) < 1e-3
 
 formulas = ["C5H8O13Cl", "C3H5O7", "Fe2Cl3K5H7", "C44H28O32K", "C18Cl5Na3H22"]
 
 @pytest.mark.parametrize("f", formulas)
 @pytest.mark.parametrize("resolution", [10000, 30000, 50000, 80000, 100000])
 def test_centroiding(f, resolution):
-    p = isotopePattern(f, threshold=1e-7)
+    p = isotopePattern(f, 0.9999999)
     instr = InstrumentModel('tof', resolution)
     p1 = p.centroids(instr, points_per_fwhm=500)
     min_mz = min(p1.masses)
@@ -26,7 +27,7 @@ def test_centroiding(f, resolution):
     n_pts = int((max_mz + 2 - min_mz) / step)
     mzs = [min_mz - 1 + step * i for i in range(n_pts)]
     p2 = ProfileSpectrum(mzs, p.envelope(instr)(mzs)).centroids(window_size=15)
-    assert_patterns_almost_equal(p1, p2)
+    assert_patterns_almost_equal(p1, p2, instr)
 
 @pytest.mark.parametrize("f", formulas)
 @pytest.mark.parametrize("threshold", [1e-7, 1e-5, 1e-3])
+3 −21		CMakeLists.txt
+9 −9		Dockerfile
+1 −1		cffi/ims.h
+2 −2		cffi/isocalc.cpp
+495 −137		ms/isocalc.cpp
+2 −6		ms/isocalc.hpp
+24 −1		ms/periodic_table.hpp
+28 −2		ms/spectrum.cpp