def testPoseClustering():
ft = ms.loadTable("data/features.table")
irt = ft.getIndex("rt")
# make copy and shift
ft2 = copy.deepcopy(ft)
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]
ftneu, ft2neu = ms.rtAlign([ft, ft2],
refTable=ft,
destination="temp_output",
nPeaks=9999,
numBreakpoints=5)
check(ft, ft2, ftneu, ft2neu)
ft2neu, ftneu = ms.rtAlign([ft2, ft],
refTable=ft,
destination="temp_output",
nPeaks=9999,
numBreakpoints=5)
check(ft, ft2, ftneu, ft2neu)
ftneu, ft2neu = ms.rtAlign([ft, ft2],
destination="temp_output",
nPeaks=9999,
numBreakpoints=5)
check(ft, ft2, ftneu, ft2neu)
def testAlignFeatureTables():
ft = ms.loadTable("data/features.table")
irt = ft.getIndex("rt")
# make copy and shift
ft2 = copy.deepcopy(ft)
ix = ft2.getIndex("rt")
for r in ft2.rows:
r[ix] += 2.0
# delete one row, so ft should become reference map !
del ft2.rows[-1]
ftneu, ft2neu = ms.rtAlign([ft, ft2],
destination="temp_output",
nPeaks=9999,
numBreakpoints=2)
irt = ft.getIndex("rt")
def getrt(t):
return np.array([r[irt] for r in t.rows])
# refmap ft should not be changed:
assert np.all(getrt(ftneu) == getrt(ft))
# but ft2 should:
assert np.linalg.norm(getrt(ft2neu) - getrt(ft2)) >= 7.9
# now ftneu and ft2neu should be very near.
# remenber: ft2 has not as much rows as ft, so:
assert np.linalg.norm(getrt(ft2neu) - getrt(ftneu)[:-1]) < 1e-6
# alignmen should produce alignment map:
assert osp.exists("temp_output/test_aligned.png")
def testAlignFeatureTables():
ft = ms.loadTable("data/features.table")
irt = ft.getIndex("rt")
# make copy and shift
ft2=copy.deepcopy(ft)
ix = ft2.getIndex("rt")
for r in ft2.rows:
r[ix] += 2.0
# delete one row, so ft should become reference map !
del ft2.rows[-1]
ftneu, ft2neu = ms.rtAlign([ft,ft2],
destination="temp_output",
nPeaks=9999,
numBreakpoints=2)
irt = ft.getIndex("rt")
def getrt(t):
return np.array([r[irt] for r in t.rows])
# refmap ft should not be changed:
assert np.all(getrt(ftneu) == getrt(ft))
# but ft2 should:
assert np.linalg.norm(getrt(ft2neu) - getrt(ft2)) >= 7.9
# now ftneu and ft2neu should be very near.
# remenber: ft2 has not as much rows as ft, so:
assert np.linalg.norm(getrt(ft2neu) - getrt(ftneu)[:-1]) < 1e-6
# alignmen should produce alignment map:
assert osp.exists("temp_output/test_aligned.png")
def testPoseClustering():
ft = ms.loadTable("data/features.table")
irt = ft.getIndex("rt")
# make copy and shift
ft2=copy.deepcopy(ft)
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]
ftneu, ft2neu = ms.rtAlign([ft,ft2], refTable=ft, destination="temp_output", nPeaks=9999,
numBreakpoints=5)
check(ft, ft2, ftneu, ft2neu)
ft2neu, ftneu = ms.rtAlign([ft2,ft], refTable=ft, destination="temp_output", nPeaks=9999,
numBreakpoints=5)
check(ft, ft2, ftneu, ft2neu)
ftneu, ft2neu = ms.rtAlign([ft,ft2], destination="temp_output", nPeaks=9999,
numBreakpoints=5)
check(ft, ft2, ftneu, ft2neu)
def test_ffm():
import ms
pm = ms.loadPeakMap("data/test.mzXML")
pm = pm.extract(rtmin=6, rtmax=12, mzmin=350, mzmax=400)
#ftab = ms.feature_detectors.runMetaboFeatureFinder(pm)
#assert len(ftab) == 19, len(ftab)
#ftab.print_()
#ftab2 = ms.feature_detectors.runMetaboFeatureFinder(pm, config_id="std")
#assert len(ftab2) == 30, len(ftab2)
#ftab2.print_()
ftab2 = ms.feature_detectors.runMetaboFeatureFinder(pm, ms_level=1)
assert len(ftab2) == 19, len(ftab2)
ftab2.print_()
al1, al2 = ms.rtAlign([ftab2, ftab2],
refTable=ftab2,
destination=".",
nPeaks=10)
def check(ft, ft2, ftneu, ft2neu):
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")) >= 7.9
assert np.linalg.norm(getrt(ft2neu, "rtmin") - getrt(ft2, "rtmin")) >= 7.9
assert np.linalg.norm(getrt(ft2neu, "rtmax") - getrt(ft2, "rtmax")) >= 7.9
# 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))) < 1
ex = None
try:
ftneu, ft2neu = ms.rtAlign([ftneu, ft2neu],
destination="temp_output",
nPeaks=9999,
numBreakpoints=2)
except Exception, e:
ex = e
def test_ffm():
import ms
pm = ms.loadPeakMap("data/test.mzXML")
pm = pm.extract(rtmin=6, rtmax=12, mzmin=350, mzmax=400)
#ftab = ms.feature_detectors.runMetaboFeatureFinder(pm)
#assert len(ftab) == 19, len(ftab)
#ftab.print_()
#ftab2 = ms.feature_detectors.runMetaboFeatureFinder(pm, config_id="std")
#assert len(ftab2) == 30, len(ftab2)
#ftab2.print_()
ftab2 = ms.feature_detectors.runMetaboFeatureFinder(pm, ms_level=1)
assert len(ftab2) == 19, len(ftab2)
ftab2.print_()
al1, al2 = ms.rtAlign([ftab2, ftab2], refTable=ftab2, destination=".",
nPeaks=10)
def check(ft, ft2, ftneu, ft2neu):
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")) >= 7.9
assert np.linalg.norm(getrt(ft2neu, "rtmin") - getrt(ft2, "rtmin")) >= 7.9
assert np.linalg.norm(getrt(ft2neu, "rtmax") - getrt(ft2, "rtmax")) >= 7.9
# 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))) < 1
ex = None
try:
ftneu, ft2neu = ms.rtAlign([ftneu,ft2neu], destination="temp_output", nPeaks=9999,
numBreakpoints=2)
except Exception, e:
ex = e