def test_four(self):
import emzed.utils
import tempfile, pytest
ft = emzed.utils.integrate(self.ft, "max")
tmpdir = tempfile.mkdtemp()
with pytest.raises(Exception):
ftneu, ft2neu = rtAlign([ft,self.ft2], destination=tmpdir, nPeaks=9999,
numBreakpoints=5)
ftneu, ft2neu = rtAlign([ft,self.ft2], destination=tmpdir, nPeaks=9999,
numBreakpoints=5, resetIntegration=True)
def realignment_should_fail(ft, ft2, ftneu, ft2neu, path, regtest):
ex = None
try:
ftneu, ft2neu = rtAlign([ftneu, ft2neu], destination=path, nPeaks=9999,
numBreakpoints=2)
except Exception, e:
ex = e
def test_three(input_tables, regtest, tmpdir):
tmpdir = tmpdir.strpath
ft, ft2 = input_tables
ftneu, ft2neu = rtAlign([ft, ft2], destination=tmpdir, nPeaks=9999,
numBreakpoints=3)
check(ft, ft2, ftneu, ft2neu, tmpdir, regtest)
def test_three(self):
import tempfile
tmpdir = tempfile.mkdtemp()
ft, ft2 = self.ft, self.ft2
ftneu, ft2neu = rtAlign([ft,ft2], destination=tmpdir, nPeaks=9999,
numBreakpoints=5)
check(ft, ft2, ftneu, ft2neu, tmpdir)
def test_four(input_tables, regtest, tmpdir):
import emzed.utils
ft, ft2 = input_tables
ft = emzed.utils.integrate(ft, "max")
tmpdir = tmpdir.strpath
# fails becaus one is integrated, after alignment the integration would be infeasible:
with pytest.raises(Exception):
ftneu, ft2neu = rtAlign([ft, ft2], destination=tmpdir, nPeaks=9999,
numBreakpoints=3)
assert ft.method.countNotNone() > 0
assert ft.area.countNotNone() > 0
assert ft.params.countNotNone() > 0
# enforces alignment, but sets integration related columns to None
ftneu, ft2neu = rtAlign([ft, ft2], destination=tmpdir, nPeaks=9999,
numBreakpoints=5, resetIntegration=True)
# all Nones:
assert ftneu.method.countNotNone() == 0
assert ftneu.area.countNotNone() == 0
assert ftneu.params.countNotNone() == 0
def check(ft, ft2, ftneu, ft2neu, path):
def getrt(t, what):
return np.array([t.getValue(row, what) for row in t.rows])
# refmap ft should not be changed:
assert np.all(getrt(ftneu, "rt") == getrt(ft, "rt"))
assert np.all(getrt(ftneu, "rtmin") == getrt(ft, "rtmin"))
assert np.all(getrt(ftneu, "rtmax") == getrt(ft, "rtmax"))
# but ft2 should:
assert np.linalg.norm(getrt(ft2neu, "rt") - getrt(ft2, "rt")) >= 2.0
assert np.linalg.norm(getrt(ft2neu, "rtmin") - getrt(ft2, "rtmin")) >= 2.0
assert np.linalg.norm(getrt(ft2neu, "rtmax") - getrt(ft2, "rtmax")) >= 2.0
# now ftneu and ft2neu should be very near.
# remenber: ft2 has not as much rows as ft, so:
assert np.linalg.norm(getrt(ft2neu, "rt") - getrt(ftneu, "rt")[:-1]) < 1e-4
assert max(abs(getrt(ft2neu, "rtmin")- getrt(ftneu, "rtmin")[:-1])) < 0.2
assert max(abs(getrt(ft2neu, "rtmax")[:-1] - getrt(ftneu, "rtmax")[:-2])) < 1e-3
def getrtsfrompeakmap(table):
pms = set(table.getValue(row, "peakmap") for row in table.rows)
assert len(pms) == 1
pm = pms.pop()
return np.array([ spec.rt for spec in pm.spectra])
assert max(abs(getrtsfrompeakmap(ft2neu)- getrtsfrompeakmap(ftneu))) < 2.2
ex = None
try:
ftneu, ft2neu = rtAlign([ftneu,ft2neu], destination=path, nPeaks=9999,
numBreakpoints=2)
except Exception, e:
ex = e
