def test_1_3_8(path):
"""
the internal version of emzed 1.3.8 did not change since 1.3.2 so the "table version"
is 1.3.2, although the file was created using emzed 1.3.8
"""
t = loadTable(path("data/table_version_1_3_8.table"))
assert t.version == "1.3.2"
def setUp(self):
def path():
import os.path
here = os.path.dirname(os.path.abspath(__file__))
def j(*a):
return os.path.join(here, *a)
return j
ft = loadTable(path()("data", "features.table"))
# make copy and shift
ft2 = ft.copy()
def shift(t, col):
ix = t.getIndex(col)
for r in t.rows:
r[ix] += 2.0 + 0.1 * r[ix] - 0.005 * r[ix]*r[ix]
shift(ft2, "rt")
shift(ft2, "rtmin")
shift(ft2, "rtmax")
pms = set(ft2.getValue(row, "peakmap") for row in ft2.rows)
pmrtsbefore = []
assert len(pms) == 1
for pm in pms:
for spec in pm.spectra:
pmrtsbefore.append(spec.rt)
spec.rt += 2.0 + 0.1 * spec.rt - 0.005 * spec.rt * spec.rt
# delete one row, so ft should become reference map !
del ft2.rows[-1]
self.ft = ft
self.ft2 = ft2
def test_1_3_8(path):
"""
the internal version of emzed 1.3.8 did not change since 1.3.2 so the "table version"
is 1.3.2, although the file was created using emzed 1.3.8
"""
t = loadTable(path("data/table_version_1_3_8.table"))
assert t.version == "1.3.2"
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 test_2_7_5_table_with_peakmap(path):
"""the table under test had originally attributes rt, polarity, msLevel and peaks
which are now "proxied" (see impl. Spectrum class).
We check if this conversion worked.
"""
from emzed.core.data_types.ms_types import NDArrayProxy
t = loadTable(path("data/features.table"))
assert t.version == (2, 7, 5)
pm = t.peakmap.uniqueValue()
spec = pm.spectra[0]
for att in ("rt", "polarity", "msLevel", "precursors"):
assert hasattr(spec, "_" + att)
assert isinstance(spec.peaks, NDArrayProxy)
def test_2_7_5_table_with_peakmap(path):
"""the table under test had originally attributes rt, polarity, msLevel and peaks
which are now "proxied" (see impl. Spectrum class).
We check if this conversion worked.
"""
from emzed.core.data_types.ms_types import NDArrayProxy
t = loadTable(path("data/features.table"))
assert t.version == (2, 7, 5)
pm = t.peakmap.uniqueValue()
spec = pm.spectra[0]
for att in ("rt", "polarity", "msLevel", "precursors"):
assert hasattr(spec, "_" + att)
assert isinstance(spec.peaks, NDArrayProxy)
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 test_1_3_8(path):
print >> sys.stderr, "TEST LOADING OF TABLE FROM EMZED 1.3.8"
t = loadTable(path("data/feature_table_1.3.8.table"))
assert t.version == "1.3.8", "PLEASE READ cocepts/konzept_table_versions"
def test_2_7_5(path):
"""
in 2.7.5 we switched from cPickle to dill for serialization
"""
t = loadTable(path("data/table_version_2_7_5.table"))
assert t.version == (2, 7, 5)
def test_2_0_2(path):
t = loadTable(path("data/table_version_2_0_2.table"))
assert t.version == (2, 0, 2)
def test_2_7_5(path):
"""
in 2.7.5 we switched from cPickle to dill for serialization
"""
t = loadTable(path("data/table_version_2_7_5.table"))
assert t.version == (2, 7, 5)
def test_2_0_2(path):
t = loadTable(path("data/table_version_2_0_2.table"))
assert t.version == (2, 0, 2)