def test_integrate_empty_table(path, regtest):
# test with and without unicode:
ft = io.loadTable(path("data/features.table"))
ft = ft[:0]
# an invalid row should not stop integration, but result
# in None values for emzed.utils.integrate generated columns
print(ft, file=regtest)
ftr = utils.integrate(ft, "trapez", n_cpus=1)
print(ftr, file=regtest)
assert len(ftr) == len(ft)
print(file=regtest)
ftr = utils.integrate(ft, "trapez", n_cpus=2)
print(ftr, file=regtest)
assert len(ftr) == len(ft)
def main():
with measure("load pm"):
# pm = emzed.io.loadPeakMap("141208_pos001.mzXML")
pm = emzed.io.loadPeakMap("Danu.mzML")
t0 = emzed.utils.toTable("peakmap", (pm, ), type_=object)
path = "pm_only.hdf5"
with atomic_hdf5_writer(path) as add:
add(t0)
peaks = runMetaboFeatureFinder(pm)
peaks = integrate(peaks)
peaks.info()
with atomic_hdf5_writer("peaks.hdf5") as add:
add(peaks)
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
