def test_proxies(self): mzs = np.array([ 0.0, 1.0, 2.0, 3.0, 4.0, 5.0 ]).reshape(-1,1) ones = np.ones_like(mzs) peaks = np.hstack((mzs, ones)) spec = Spectrum(peaks, 0.0, 1, "0") spec.peaks[:, 0] += 1.0 assert np.linalg.norm(spec.peaks[:, 0] - mzs.flatten(), 1) == 6.0 def check(fun, spec=spec): before = spec.uniqueId() exec(fun, dict(spec=spec)) assert "unique_id" not in spec.meta after = spec.uniqueId() assert before != after check("spec.peaks[:, 0] += 1") check("spec.peaks += 1") check("spec.peaks -= 1") check("spec.peaks /= 2.1") check("spec.peaks //= 2.1") check("spec.peaks *= 2") check("spec.peaks %= 1.1") check("spec.peaks **= 2") check("spec.rt += 1") check("spec.msLevel += 1") check("spec.precursors = [(1, 1, 0)]") check("spec.polarity = '+'") pm = PeakMap([spec]) before = pm.uniqueId() pm.spectra[0].rt += 2 after = spec.uniqueId() assert before != after from cPickle import loads, dumps back = loads(dumps(pm)) back.meta.pop("unique_id", None) pm.meta.pop("unique_id", None) assert back.uniqueId() == pm.uniqueId() # this was broken after pickling, the callback was not pickled and calling # it whein operatin on peaks rose an excepion for s in back: s.peaks += 1 # this was broken because it creates a view which is not continous: s.peaks = s.peaks[1:-1:2] assert s.uniqueId() spec_new = loads(dumps(spec)) assert spec_new.scan_number == spec.scan_number assert spec_new.rt == spec.rt assert spec_new.msLevel == spec.msLevel assert spec_new.precursors == spec.precursors assert spec_new.polarity == spec.polarity assert np.linalg.norm(spec_new.peaks - spec.peaks) == 0.0
def test_proxies(self): mzs = np.array([0.0, 1.0, 2.0, 3.0, 4.0, 5.0]).reshape(-1, 1) ones = np.ones_like(mzs) peaks = np.hstack((mzs, ones)) spec = Spectrum(peaks, 0.0, 1, "0") spec.peaks[:, 0] += 1.0 assert np.linalg.norm(spec.peaks[:, 0] - mzs.flatten(), 1) == 6.0 def check(fun, spec=spec): before = spec.uniqueId() exec(fun, dict(spec=spec)) assert "unique_id" not in spec.meta after = spec.uniqueId() assert before != after check("spec.peaks[:, 0] += 1") check("spec.peaks += 1") check("spec.peaks -= 1") check("spec.peaks /= 2.1") check("spec.peaks //= 2.1") check("spec.peaks *= 2") check("spec.peaks %= 1.1") check("spec.peaks **= 2") check("spec.rt += 1") check("spec.msLevel += 1") check("spec.precursors = [(1, 1, 0)]") check("spec.polarity = '+'") pm = PeakMap([spec]) before = pm.uniqueId() pm.spectra[0].rt += 2 after = spec.uniqueId() assert before != after from cPickle import loads, dumps back = loads(dumps(pm)) back.meta.pop("unique_id", None) pm.meta.pop("unique_id", None) assert back.uniqueId() == pm.uniqueId() # this was broken after pickling, the callback was not pickled and calling # it whein operatin on peaks rose an excepion for s in back: s.peaks += 1 # this was broken because it creates a view which is not continous: s.peaks = s.peaks[1:-1:2] assert s.uniqueId() spec_new = loads(dumps(spec)) assert spec_new.scan_number == spec.scan_number assert spec_new.rt == spec.rt assert spec_new.msLevel == spec.msLevel assert spec_new.precursors == spec.precursors assert spec_new.polarity == spec.polarity assert np.linalg.norm(spec_new.peaks - spec.peaks) == 0.0
def testFilterIntensity(self, regtest): data = np.array([ 0.0, 1.0, 2.0, 3.0, 4.0, 5.0 ]).reshape(-1,1) intensities = np.array([ 10.0, 11.0, 12.0, 13.0, 14.0, 15.0 ]).reshape(-1,1) peaks = np.hstack((data, intensities)) assert peaks.shape == (6,2) spec1 = Spectrum(peaks, 0.0, 1, "0") spec2 = Spectrum(peaks, 0.0, 2, "0") assert spec1.maxIntensity() == 15.0 pm = PeakMap([spec1, spec2]) pm_x = pm.extract(mslevelmin=1) assert len(pm_x) == 2 pm_x = pm.extract(mslevelmin=2) assert len(pm_x) == 1 pm_x = pm.extract(mslevelmin=3) assert len(pm_x) == 0 pm_x = pm.extract(mslevelmax=1, imin=10.0, imax=15.0) assert len(pm_x) == 1 assert pm_x[0].peaks.shape == (6, 2) for spec in pm_x: print >> regtest, spec.peaks pm_x = pm.extract(mslevelmax=1, imin=10.0) assert len(pm_x) == 1 assert pm_x[0].peaks.shape == (6, 2) for spec in pm_x: print >> regtest, spec.peaks pm_x = pm.extract(mslevelmax=1, imax=15.0) assert len(pm_x) == 1 assert pm_x[0].peaks.shape == (6, 2) for spec in pm_x: print >> regtest, spec.peaks pm_x = pm.extract(mslevelmax=1, imin=10.0) assert len(pm_x) == 1 assert pm_x[0].peaks.shape == (6, 2) for spec in pm_x: print >> regtest, spec.peaks pm_x = pm.extract(mslevelmax=1, imin=11.0) assert len(pm_x) == 1 assert pm_x[0].peaks.shape == (5, 2) for spec in pm_x: print >> regtest, spec.peaks pm_x = pm.extract(mslevelmax=1, imin=11.0, imax = 13.5) assert len(pm_x) == 1 assert pm_x[0].peaks.shape == (3, 2) for spec in pm_x: print >> regtest, spec.peaks
def test_uniuqe_id(): ti = emzed.utils.toTable("id", [1, 1, 2]) t = emzed.utils.toTable("t", (ti, ti, None)) # peakmap unique id already tested by compression of peakmap: t.addColumn("pm", PeakMap([])) t.addColumn("blob", Blob("data")) assert t.uniqueId() == "a03470ffc2876f1c12becb55e5f82f4fd59d9f906afe6f07484755755c4807e0"
def test_remove(self): mzs = np.array([0.0, 1.0, 2.0, 3.0, 4.0, 5.0]).reshape(-1, 1) ones = np.ones_like(mzs) peaks = np.hstack((mzs, ones)) spectra = [ Spectrum(peaks, 0.0, 1, "0"), Spectrum(peaks, 1.0, 1, "0"), Spectrum(peaks, 1.5, 2, "0"), Spectrum(peaks, 2.0, 1, "0") ] pm = PeakMap(spectra) pmt = copy.deepcopy(pm) pmt.remove(0.0, 10.0, 0.0, 2.0) assert len(pmt) == 1 assert pmt.spectra[0] == Spectrum(peaks, 1.5, 2, "0") pmt = copy.deepcopy(pm) pmt.remove(1.0, 3.2, 1.0, 2.0) assert len(pmt) == 4 assert np.all(pmt.spectra[0].peaks == peaks) assert np.all( pmt.spectra[1].peaks.flatten() == [0., 1.0, 4.0, 1.0, 5.0, 1.0]) assert np.all(pmt.spectra[2].peaks == peaks) assert np.all( pmt.spectra[3].peaks.flatten() == [0., 1.0, 4.0, 1.0, 5.0, 1.0])
def testCompress(self): t = toTable("a", []) import numpy t.compressPeakMaps() s = Spectrum( numpy.arange(12, dtype="float64").reshape(-1, 2), 1.0, 1, "+") pm = PeakMap([s]) s = Spectrum( numpy.arange(12, dtype="float64").reshape(-1, 2), 1.0, 1, "+") pm2 = PeakMap([s]) t = toTable("pm", [pm, pm2]) assert len(set(map(id, t.pm.values))) == 2 t.compressPeakMaps() assert len(set(map(id, t.pm.values))) == 1
def test_proxies(self): mzs = np.array([ 0.0, 1.0, 2.0, 3.0, 4.0, 5.0 ]).reshape(-1,1) ones = np.ones_like(mzs) peaks = np.hstack((mzs, ones)) spec = Spectrum(peaks, 0.0, 1, "0") spec.peaks[:, 0] += 1.0 assert np.linalg.norm(spec.peaks[:, 0] - mzs.flatten(), 1) == 6.0 def check(fun, spec=spec): before = spec.uniqueId() exec(fun, dict(spec=spec)) assert "unique_id" not in spec.meta after = spec.uniqueId() assert before != after check("spec.peaks[:, 0] += 1") check("spec.peaks += 1") check("spec.peaks -= 1") check("spec.peaks /= 2.1") check("spec.peaks //= 2.1") check("spec.peaks *= 2") check("spec.peaks %= 1.1") check("spec.peaks **= 2") check("spec.rt += 1") check("spec.msLevel += 1") check("spec.precursors = [(1, 1)]") check("spec.polarity = '+'") pm = PeakMap([spec]) before = pm.uniqueId() pm.spectra[0].rt += 2 after = spec.uniqueId() assert before != after from cPickle import loads, dumps back = loads(dumps(pm)) back.meta.pop("unique_id", None) pm.meta.pop("unique_id", None) assert back.uniqueId() == pm.uniqueId()
def testTrapezIntegrationSimple(): p0 = np.array((1.0, 1.0, 2.0, 2.0)).reshape(-1,2) p1 = np.array((2.0, 2.0, 3.0, 3.0)).reshape(-1,2) p2 = np.array((1.0, 1.0, 2.0, 2.0, 3.0, 3.0)).reshape(-1,2) p3 = np.array((3.0, 3.0)).reshape(-1,2) s0 = Spectrum(p0, 0.0, 1, '0') s1 = Spectrum(p1, 1.0, 1, '0') s2 = Spectrum(p2, 2.0, 1, '0') s3 = Spectrum(p3, 3.0, 1, '0') pm = PeakMap([s0,s1,s2,s3]) integrator = dict(emzed._algorithm_configs.peakIntegrators)["trapez"] integrator.setPeakMap(pm) assert integrator.integrate(1.4, 2.5, 0, 3)["area"] == 5.0 assert integrator.integrate(1.4, 2.5, 0, 2)["area"] == 4.0 assert integrator.integrate(0.4, 2.5, 0, 3)["area"] == 6.5 assert integrator.integrate(0.4, 2.5, 0, 2)["area"] == 5.0 assert integrator.integrate(0.4, 3.0, 0, 3)["area"] == 14 # one level 2 spec: s1 = Spectrum(p1, 1.0, 2, '0') pm = PeakMap([s0,s1,s2,s3]) integrator.setPeakMap(pm) assert integrator.integrate(1.4, 2.5, 0, 3, msLevel=1)["area"] == 5.0 assert integrator.integrate(1.4, 2.5, 0, 2, msLevel=1)["area"] == 4.0 assert integrator.integrate(0.4, 2.5, 0, 3, msLevel=1)["area"] == 7.5 assert integrator.integrate(0.4, 2.5, 0, 2, msLevel=1)["area"] == 6.0 assert integrator.integrate(0.4, 3.0, 0, 3, msLevel=1)["area"] == 13.5 # multiple levels shall rise exception: ex(lambda: integrator.integrate(0.4, 3.0, 0, 3))
def test_proxies(self): mzs = np.array([0.0, 1.0, 2.0, 3.0, 4.0, 5.0]).reshape(-1, 1) ones = np.ones_like(mzs) peaks = np.hstack((mzs, ones)) spec = Spectrum(peaks, 0.0, 1, "0") spec.peaks[:, 0] += 1.0 assert np.linalg.norm(spec.peaks[:, 0] - mzs.flatten(), 1) == 6.0 def check(fun, spec=spec): before = spec.uniqueId() exec(fun, dict(spec=spec)) assert "unique_id" not in spec.meta after = spec.uniqueId() assert before != after check("spec.peaks[:, 0] += 1") check("spec.peaks += 1") check("spec.peaks -= 1") check("spec.peaks /= 2.1") check("spec.peaks //= 2.1") check("spec.peaks *= 2") check("spec.peaks %= 1.1") check("spec.peaks **= 2") check("spec.rt += 1") check("spec.msLevel += 1") check("spec.precursors = [(1, 1)]") check("spec.polarity = '+'") pm = PeakMap([spec]) before = pm.uniqueId() pm.spectra[0].rt += 2 after = spec.uniqueId() assert before != after from cPickle import loads, dumps back = loads(dumps(pm)) back.meta.pop("unique_id", None) pm.meta.pop("unique_id", None) assert back.uniqueId() == pm.uniqueId()
def test_unique_id(regtest): ti = emzed.utils.toTable("id", [1, 1, 2]) t = emzed.utils.toTable("t", (ti, ti, None)) # peakmap unique id already tested by compression of peakmap: t.addColumn("pm", PeakMap([]), type_=object) t.addColumn("blob", Blob("data")) print(t.uniqueId(), file=regtest) ti = emzed.utils.toTable("id", [1, 1, 2]) t = emzed.utils.toTable("t", (ti, ti, None)) # peakmap unique id already tested by compression of peakmap: t.addColumn("pm", PeakMap([]), type_=PeakMap) t.addColumn("blob", Blob("data")) print(t.uniqueId(), file=regtest) ti = emzed.utils.toTable("id", [1, 1, 2]) t = emzed.utils.toTable("t", (ti, ti, None)) # peakmap unique id already tested by compression of peakmap: t.addColumn("pm", PeakMap([])) t.addColumn("blob", Blob("data")) print(t.uniqueId(), file=regtest)
def testNoIntegration(): integrator = dict(emzed._algorithm_configs.peakIntegrators)["no_integration"] integrator.setPeakMap(PeakMap([])) result = integrator.integrate(0.0, 100.0, 0, 300, 1) assert result.get("area") is None assert result.get("rmse") is None assert result.get("params") is None # assert result.get("eic") is None assert result.get("baseline") is None rts = range(0, 600) x, y = integrator.getSmoothed(rts, result.get("params")) assert x == [] assert y == []
def _testIntegration(path, n_cpus, integrator_id, check_values=True): # test with and without unicode: ft = io.loadTable(path("data/features.table")) # an invalid row should not stop integration, but result # in None values for emzed.utils.integrate generated columns ftr = utils.integrate(ft, integrator_id, n_cpus=n_cpus, min_size_for_parallel_execution=1) assert len(ftr) == len(ft) assert "area" in ftr.getColNames() assert "rmse" in ftr.getColNames() if check_values: assert ftr.area.values[0] >= 0, ftr.area.values[0] assert ftr.rmse.values[0] >= 0, ftr.rmse.values[0] assert ftr.params.values[0] is not None assert ftr.method.values[0] is not None ft.setValue(ft.rows[0], "mzmin", None) ft._addColumnWithoutNameCheck("mzmin__0", ft.mzmin) ft._addColumnWithoutNameCheck("mzmax__0", ft.mzmax) ft._addColumnWithoutNameCheck("rtmin__0", ft.rtmin) ft._addColumnWithoutNameCheck("rtmax__0", ft.rtmax) ft._addColumnWithoutNameCheck("peakmap__0", ft.peakmap) ft.addColumn("mzminX", ft.mzmin) ft.addColumn("mzmaxX", ft.mzmax) ft.addColumn("rtminX", ft.rtmin) ft.addColumn("rtmaxX", ft.rtmax) ft.addColumn("peakmapX", ft.peakmap) ftr = utils.integrate(ft, integrator_id, n_cpus=n_cpus, min_size_for_parallel_execution=1) assert len(ftr) == len(ft) assert "area" in ftr.getColNames() assert "rmse" in ftr.getColNames() # assert "eic" in ftr.getColNames() assert "area__0" in ftr.getColNames() assert "rmse__0" in ftr.getColNames() # assert "eic__0" in ftr.getColNames() assert "areaX" in ftr.getColNames() assert "rmseX" in ftr.getColNames() assert "rmseX" in ftr.getColNames() # assert "eicX" in ftr.getColNames() if check_values: assert ftr.area.values[0] is None assert ftr.rmse.values[0] is None assert ftr.params.values[0] is None assert ftr.method.values[0] is not None # assert ftr.eic.values[0] is None assert ftr.area.values[1] is not None assert ftr.rmse.values[1] is not None assert ftr.params.values[1] is not None assert ftr.method.values[1] is not None # assert len(ftr.eic.values[1]) == 2 assert ftr.area__0.values[0] is None assert ftr.rmse__0.values[0] is None assert ftr.params__0.values[0] is None assert ftr.method__0.values[0] is not None # assert ftr.eic__0.values[0] is None assert ftr.area__0.values[1] is not None assert ftr.rmse__0.values[1] is not None assert ftr.params__0.values[1] is not None assert ftr.method__0.values[1] is not None # assert len(ftr.eic__0.values[1]) == 2 assert ftr.areaX.values[0] is None assert ftr.rmseX.values[0] is None assert ftr.paramsX.values[0] is None assert ftr.methodX.values[0] is not None # assert ftr.eicX.values[0] is None assert ftr.areaX.values[1] is not None assert ftr.rmseX.values[1] is not None assert ftr.paramsX.values[1] is not None assert ftr.methodX.values[1] is not None # assert len(ftr.eicX.values[1]) == 2 # test with empty chromatograms s0 = ft.peakmap.values[0].spectra[0] rt0 = s0.rt pm = PeakMap([s0]) rts, iis = pm.chromatogram(0, 10000, rt0 + 20, rt0 + 30) assert len(rts) == 0 assert len(iis) == 0 ft.replaceColumn("peakmap", pm) ft.replaceColumn("rtmin", rt0 + 10) ft.replaceColumn("rtmax", rt0 + 20) ftr2 = utils.integrate(ft, integrator_id, n_cpus=n_cpus, min_size_for_parallel_execution=1) # assert set(ftr2.eic.values) == {None} return ftr
def testEmptyPeakMap(self): pm = PeakMap([]) assert pm.extract(0, 9999, 0, 10000).spectra == () assert pm.filter(lambda t: True).spectra == () assert pm.specsInRange(0, 10e6) == [] assert pm.levelNSpecsInRange(1, 0, 10e6) == [] assert pm.chromatogram(0, 10e6, 0, 10e6) == ([], []) assert pm.chromatogram(0, 10e6) == ([], []) assert pm.msNPeaks(1, 0, 10e6).tolist() == [] assert pm.allRts() == [] assert pm.levelOneRts() == [] assert pm.levelNSpecs(1,2) == []
def testActions(): t = buildTable() n = len(t) recorder = RecordingObject() model = TableModel(t, recorder) t_orig = t.copy() action = DeleteRowsAction(model, [0], [0]) action.do() assert len(model.table) == len(t_orig) - 1 assert model.table.rows[0] == t_orig.rows[1] action.undo() assert len(model.table) == len(t_orig) assert model.table.rows[0] == t_orig.rows[0] action = CloneRowAction(model, 0, 0) action.do() assert model.table.rows[0] == t_orig.rows[0] assert model.table.rows[1] == t_orig.rows[0] assert model.table.rows[2] == t_orig.rows[1] assert len(model.table) == n + 1 action.undo() assert len(model.table) == n assert model.table.rows[0] == t_orig.rows[0] assert model.table.rows[1] == t_orig.rows[1] action = SortTableAction(model, [("mz", True)]) action.do() assert model.table.mz.values == (None, 1.0, 2.0) action.undo() assert model.table.mz.values == t_orig.mz.values action = SortTableAction(model, [("mz", False)]) action.do() assert model.table.mz.values == (2.0, 1.0, None) action.undo() assert model.table.mz.values == t_orig.mz.values class Index(object): def row(self): return 0 def column(self): return 0 action = ChangeValueAction(model, Index(), 0, 0, 3.0) action.do() assert model.table.rows[0][0] == 3.0 action.undo() assert model.table.rows[0][0] == 1.0 t = buildTable() import numpy peak = numpy.array(((1.0, 100.0), )) specs = [Spectrum(peak, rt, 1, "+") for rt in range(9, 15)] pm = PeakMap(specs) t.replaceColumn("peakmap", pm) model.table = emzed.utils.integrate(t, "no_integration") action = IntegrateAction(model, 0, "", "trapez", 0, 100, {0: 0}) action.do() assert model.table.area.values[0] == 500.0 action.undo() assert model.table.area.values[0] == None
def testFilterIntensity(self, regtest): data = np.array([0.0, 1.0, 2.0, 3.0, 4.0, 5.0]).reshape(-1, 1) intensities = np.array([10.0, 11.0, 12.0, 13.0, 14.0, 15.0]).reshape(-1, 1) peaks = np.hstack((data, intensities)) assert peaks.shape == (6, 2) spec1 = Spectrum(peaks, 0.0, 1, "0") spec2 = Spectrum(peaks, 0.0, 2, "0") assert spec1.maxIntensity() == 15.0 pm = PeakMap([spec1, spec2]) pm_x = pm.extract(mslevelmin=1) assert len(pm_x) == 2 pm_x = pm.extract(mslevelmin=2) assert len(pm_x) == 1 pm_x = pm.extract(mslevelmin=3) assert len(pm_x) == 0 pm_x = pm.extract(mslevelmax=1, imin=10.0, imax=15.0) assert len(pm_x) == 1 assert pm_x[0].peaks.shape == (6, 2) for spec in pm_x: print >> regtest, spec.peaks pm_x = pm.extract(mslevelmax=1, imin=10.0) assert len(pm_x) == 1 assert pm_x[0].peaks.shape == (6, 2) for spec in pm_x: print >> regtest, spec.peaks pm_x = pm.extract(mslevelmax=1, imax=15.0) assert len(pm_x) == 1 assert pm_x[0].peaks.shape == (6, 2) for spec in pm_x: print >> regtest, spec.peaks pm_x = pm.extract(mslevelmax=1, imin=10.0) assert len(pm_x) == 1 assert pm_x[0].peaks.shape == (6, 2) for spec in pm_x: print >> regtest, spec.peaks pm_x = pm.extract(mslevelmax=1, imin=11.0) assert len(pm_x) == 1 assert pm_x[0].peaks.shape == (5, 2) for spec in pm_x: print >> regtest, spec.peaks pm_x = pm.extract(mslevelmax=1, imin=11.0, imax=13.5) assert len(pm_x) == 1 assert pm_x[0].peaks.shape == (3, 2) for spec in pm_x: print >> regtest, spec.peaks
def testEmptyPeakMap(self): pm = PeakMap([]) assert pm.extract(0, 9999, 0, 10000).spectra == () assert pm.filter(lambda t: True).spectra == () assert pm.specsInRange(0, 10e6) == [] assert pm.levelNSpecsInRange(1, 0, 10e6) == [] assert pm.chromatogram(0, 10e6, 0, 10e6) == ([], []) assert pm.chromatogram(0, 10e6) == ([], []) assert pm.msNPeaks(1, 0, 10e6).tolist() == [] assert pm.allRts() == [] assert pm.levelOneRts() == [] assert pm.levelNSpecs(1, 2) == []
def test001(self): exp = MSExperiment() basename = "SHORT_MS2_FILE.mzData" here = os.path.dirname(os.path.abspath(__file__)) FileHandler().loadExperiment(os.path.join(here, "data", basename), exp) assert exp.size() > 0 pc = Precursor() pc.setMZ(1.0) pc.setIntensity(100) s0 = exp[0] s0.setPrecursors([pc]) s0.setMSLevel(2) spec = Spectrum.fromMSSpectrum(s0) settings = InstrumentSettings() settings.setPolarity(IonSource.Polarity.POSITIVE) s0.setInstrumentSettings(settings) self.compare_specs(spec, s0) specneu = Spectrum.fromMSSpectrum(spec.toMSSpectrum()) self.compare_specs(specneu, s0) pm = PeakMap.fromMSExperiment(exp) assert os.path.basename(pm.meta["source"]) == basename rtmin, rtmax = pm.rtRange(None) ms1s = pm.msNPeaks(1, rtmin, rtmax) assert ms1s.shape == (1797, 2), ms1s.shape ms1s2 = pm.msNPeaks(1, rtmax=rtmax) assert np.all(ms1s == ms1s2) ms1s3 = pm.msNPeaks(1, rtmin=0) assert np.all(ms1s == ms1s3) spec = pm.spectra[0] assert len(list(spec)) == len(spec) # calls iter allrts = pm.allRts() assert allrts[0] <= pm.rtRange()[0] assert allrts[-1] >= pm.rtRange()[1] assert len(allrts) == 41, len(allrts) level1 = pm.levelNSpecs(1, 1) level2 = pm.levelNSpecs(2, 2) level12 = pm.levelNSpecs(1, 2) assert len(level1) > 0 assert len(level2) > 0 assert len(level1) + len(level2) == len(level12) == len(pm) assert level1[0].msLevel == 1 assert level2[0].msLevel == 2 # use default arg: nmax = nmin if not provided: level1 = pm.levelNSpecs(1) level2 = pm.levelNSpecs(2) assert len(level1) > 0 assert len(level2) > 0 assert len(level1) + len(level2) == len(level12) == len(pm) assert level1[0].msLevel == 1 assert level2[0].msLevel == 2 lone = pm.levelOneRts() assert len(lone) == len(level1) self.compare_exp(pm, exp, basename) pm2 = PeakMap.fromMSExperiment(pm.toMSExperiment()) self.compare_exp(pm2, exp, basename) pm2 = pm.extract(rtmin=rtmin + .000001) assert len(pm2) == len(pm) - 1 pm2 = pm2.extract(rtmax=rtmax - 0.000001) assert len(pm2) == len(pm) - 2 mzmin, mzmax = pm.mzRange(2) assert mzmin < 250 assert mzmax > 860 mzmin, mzmax = pm.mzRange(1) assert mzmin >= 700 assert mzmax <= 1050 pm2 = pm.extract(rtmin + 0.00001, mzmin=300) mzmin2, mzmax2 = pm2.mzRange() assert mzmin2 >= 300 assert mzmax2 == mzmax pm2 = pm.extract(rtmin=rtmin + 0.000001, mzmin=300, mzmax=1000) mzmin2, mzmax2 = pm2.mzRange() assert mzmin2 >= 300 assert mzmax2 <= 1000 with pytest.raises(Exception): pm.spectra[0].peaksInRange() pp1 = pm.spectra[0].peaksInRange(mzmax=10000) pp2 = pm.spectra[0].peaksInRange(mzmin=0) assert np.all(pp1 == pp2) specs0 = list(pm.spectra) specs1 = pm.specsInRange(0, 99999) specs2 = pm.specsInRange(0, specs0[0].rt) specs3 = pm.specsInRange(specs0[-1].rt, 999999) assert specs0 == specs1 assert specs2 == [specs0[0]] assert specs3 == [specs0[-1]] pm.spectra[0].polarity = "+" pm.spectra[1].polarity = "-" pm = PeakMap(pm.spectra) mz = pm.representingMzPeak(0, 99999, 0, 99999) assert abs(mz - 831.86538) < 0.0001
def test001(self): exp = MSExperiment() basename = "SHORT_MS2_FILE.mzData" here = os.path.dirname(os.path.abspath(__file__)) FileHandler().loadExperiment(os.path.join(here, "data", basename), exp) assert exp.size()>0 pc = Precursor() pc.setMZ(1.0) pc.setIntensity(100) s0 = exp[0] s0.setPrecursors([pc]) s0.setMSLevel(2) spec = Spectrum.fromMSSpectrum(s0) settings = InstrumentSettings() settings.setPolarity(IonSource.Polarity.POSITIVE) s0.setInstrumentSettings(settings) self.compare_specs(spec, s0) specneu = Spectrum.fromMSSpectrum(spec.toMSSpectrum()) self.compare_specs(specneu, s0) pm = PeakMap.fromMSExperiment(exp) assert os.path.basename(pm.meta["source"]) == basename rtmin, rtmax = pm.rtRange(None) ms1s = pm.msNPeaks(1, rtmin, rtmax) assert ms1s.shape == (1797, 2), ms1s.shape ms1s2 = pm.msNPeaks(1, rtmax=rtmax) assert np.all(ms1s == ms1s2) ms1s3 = pm.msNPeaks(1, rtmin=0) assert np.all(ms1s == ms1s3) spec = pm.spectra[0] assert len(list(spec)) == len(spec) # calls iter allrts = pm.allRts() assert allrts[0] <= pm.rtRange()[0] assert allrts[-1] >= pm.rtRange()[1] assert len(allrts) == 41, len(allrts) level1 = pm.levelNSpecs(1, 1) level2 = pm.levelNSpecs(2, 2) level12 = pm.levelNSpecs(1, 2) assert len(level1) > 0 assert len(level2) > 0 assert len(level1) + len(level2) == len(level12) == len(pm) assert level1[0].msLevel == 1 assert level2[0].msLevel == 2 # use default arg: nmax = nmin if not provided: level1 = pm.levelNSpecs(1) level2 = pm.levelNSpecs(2) assert len(level1) > 0 assert len(level2) > 0 assert len(level1) + len(level2) == len(level12) == len(pm) assert level1[0].msLevel == 1 assert level2[0].msLevel == 2 lone = pm.levelOneRts() assert len(lone) == len(level1) self.compare_exp(pm, exp, basename) pm2 = PeakMap.fromMSExperiment(pm.toMSExperiment()) self.compare_exp(pm2, exp, basename) pm2 = pm.extract(rtmin=rtmin + .000001) assert len(pm2) == len(pm) - 1 pm2 = pm2.extract(rtmax=rtmax - 0.000001) assert len(pm2) == len(pm) - 2 mzmin, mzmax = pm.mzRange(2) assert mzmin < 250 assert mzmax > 860 mzmin, mzmax = pm.mzRange(1) assert mzmin >= 700 assert mzmax <= 1050 pm2 = pm.extract(rtmin+0.00001, mzmin=300) mzmin2, mzmax2 = pm2.mzRange() assert mzmin2 >= 300 assert mzmax2 == mzmax pm2 = pm.extract(rtmin = rtmin+0.000001, mzmin=300, mzmax=1000) mzmin2, mzmax2 = pm2.mzRange() assert mzmin2 >= 300 assert mzmax2 <= 1000 with pytest.raises(Exception): pm.spectra[0].peaksInRange() pp1 = pm.spectra[0].peaksInRange(mzmax = 10000) pp2 = pm.spectra[0].peaksInRange(mzmin = 0) assert np.all(pp1 == pp2) specs0 = list(pm.spectra) specs1 = pm.specsInRange(0, 99999) specs2 = pm.specsInRange(0, specs0[0].rt) specs3 = pm.specsInRange(specs0[-1].rt, 999999) assert specs0 == specs1 assert specs2 == [ specs0[0] ] assert specs3 == [ specs0[-1] ] pm.spectra[0].polarity = "+" pm.spectra[1].polarity = "-" pm = PeakMap(pm.spectra) mz = pm.representingMzPeak(0, 99999, 0, 99999) assert abs(mz-831.86538) < 0.0001