Add combine_spectra and base_peak_mass functions

libgunshotmatch/consolidate/__init__.py

@@ -27,7 +27,7 @@
 #
 
 # stdlib
-from collections import Counter
+from collections import Counter, defaultdict
 from fnmatch import fnmatch
 from itertools import permutations
 from multiprocessing import Pool
@@ -61,6 +61,7 @@
 		"pairwise_ms_comparisons",
 		"ConsolidatedPeakFilter",
 		"InvertedFilter",
+		"combine_spectra",
 		)
 
 
@@ -804,3 +805,31 @@ def filter(self, consolidated_peaks: List[ConsolidatedPeak]) -> List[Consolidate
 				filtered_consolidated_peaks.append(cp)
 
 		return filtered_consolidated_peaks
+
+
+def combine_spectra(peak: ConsolidatedPeak) -> Tuple[List[int], List[float]]:
+	"""
+	Sum the intensities across all mass spectra in the given peak.
+
+	:param peak:
+
+	:returns: List of masses and list of corresponding intensities.
+
+	.. versionadded:: v0.11.0
+	"""
+
+	combined_ms_data: Dict[int, float] = defaultdict(float)
+
+	for ms in peak.ms_list:
+		if ms is not None:
+			for mass, intensity in zip(ms.mass_list, ms.intensity_list):
+				combined_ms_data[mass] += intensity
+
+	mass_list, intensity_list = [], []
+	for mass, intensity in combined_ms_data.items():
+		mass_list.append(mass)
+		intensity_list.append(intensity)
+
+	# mass_list, intensity_list = zip(*combined_ms_data.items())
+
+	return mass_list, intensity_list

libgunshotmatch/peak.py

@@ -55,6 +55,7 @@
 		"filter_peaks",
 		"peak_from_dict",
 		"write_alignment",
+		"base_peak_mass",
 		)
 
 
@@ -531,3 +532,25 @@ def _to_peak_list(a_list: List[Peak]) -> PeakList:
 		return a_list
 	else:
 		return PeakList(a_list)
+
+
+def base_peak_mass(peak: Peak) -> float:
+	"""
+	Returns the mass of the largest fragment in the peak's mass spectrum.
+
+	:param peak:
+
+	.. versionadded:: v0.11.0
+	"""
+
+	apex_mass_list = peak.mass_spectrum.mass_list
+	apex_mass_spec = peak.mass_spectrum.mass_spec
+
+	# Determine the intensity of the base peak in the mass spectrum
+	base_peak_intensity = max(apex_mass_spec)
+
+	# Determine the index of the base peak in the mass spectrum
+	base_peak_index = apex_mass_spec.index(base_peak_intensity)
+
+	# Finally, determine the mass of the base peak
+	return apex_mass_list[base_peak_index]

tests/conftest.py

@@ -1,4 +1,6 @@
 # 3rd party
+import numpy
+from coincidence.regressions import _representer_for
 from pytest_regressions.data_regression import RegressionYamlDumper
 from yaml.representer import RepresenterError
 
@@ -10,3 +12,21 @@ def represent_undefined(self, data):  # noqa: MAN001,MAN002
 
 
 RegressionYamlDumper.represent_undefined = represent_undefined  # type: ignore[method-assign]
+
+
+@_representer_for(
+		numpy.int64,
+		numpy.int32,
+		numpy.float64,
+		)
+def _represent_numpy(dumper: RegressionYamlDumper, data: int):  # noqa: MAN002
+	return dumper.represent_data(int(data))
+
+
+# @_representer_for(
+# 		numpy.float64,
+# 		)
+# def _represent_mappings(dumper: RegressionYamlDumper, data: float):  # noqa: MAN002
+# 	if data == 0:
+# 		return dumper.represent_data(0)
+# 	return dumper.represent_data(str(round_rt(data)))

tests/test_consolidate.py

@@ -3,32 +3,26 @@
 from typing import Optional
 
 # 3rd party
-import numpy
 import pyms_nist_search
 import pytest
-from coincidence.regressions import AdvancedDataRegressionFixture, AdvancedFileRegressionFixture, _representer_for
+from coincidence.regressions import AdvancedDataRegressionFixture, AdvancedFileRegressionFixture
 from domdf_python_tools.paths import PathPlus
 from domdf_python_tools.typing import PathLike
-from pytest_regressions.data_regression import RegressionYamlDumper
 from pytest_regressions.dataframe_regression import DataFrameRegressionFixture
 
 # this package
-from libgunshotmatch.consolidate import ConsolidatedPeakFilter, InvertedFilter, pairwise_ms_comparisons
+from libgunshotmatch.consolidate import (
+		ConsolidatedPeakFilter,
+		InvertedFilter,
+		combine_spectra,
+		pairwise_ms_comparisons
+		)
 from libgunshotmatch.consolidate._fields import _attrs_convert_reference_data
 from libgunshotmatch.project import Project
 
 # Test consolidate process from gsmp file
 
 
-@_representer_for(
-		numpy.int64,
-		numpy.int32,
-		numpy.float64,
-		)
-def _represent_numpy(dumper: RegressionYamlDumper, data: int):  # noqa: MAN002
-	return dumper.represent_data(int(data))
-
-
 class MockEngine(pyms_nist_search.Engine):
 	"""
 	Engine that returns :py:obj:`None` for the reference data.
@@ -197,3 +191,13 @@ def test__attrs_convert_reference_data():
 	with pytest.raises(TypeError, match="'reference_data' must be a `pyms_nist_search.ReferenceData` object,"):
 		# Wrong type
 		_attrs_convert_reference_data([])  # type: ignore[arg-type]
+
+
+def test_combine_spectra(advanced_data_regression: AdvancedDataRegressionFixture):
+	project = Project.from_file("tests/Eley Super Game.gsmp")
+	assert project.consolidated_peaks is not None
+
+	spectra = []
+	for peak in project.consolidated_peaks:
+		spectra.append(combine_spectra(peak))
+	advanced_data_regression.check(spectra)