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 testRunnerTable():
with ExceptionTester():
Table(["a"],[np.float32],["%f"],[[32.0]])
#build table
names="int long float str object array".split()
types = [int, long, float, str, object, np.ndarray,]
formats = [ "%3d", "%d", "%.3f", "%s", "%r", "'array(%r)' % (o.shape,)" ]
row1 = [ 1, 12323L, 1.0, "hi", { 1: 1 }, np.array((1,2,3)) ]
row2 = [ 2, 22323L, 2.0, "hi2", [2,3,], np.array(((2,3,4),(1,2,3))) ]
row3 = [ 3, 32323L, 3.0, "hi3", (3,) , np.array(((3,3,4,5),(1,2,3,4))) ]
rows = [row1, row2, row3]
t=Table(names, types, formats, rows, "testtabelle", meta=dict(why=42))
run(t, names, [row1, row2, row3])
# test pickle
dat = pickle.dumps(t)
t = pickle.loads(dat)
run(t, names, [row1, row2, row3])
ms.storeTable(t, u"temp_output/test.table")
try:
ms.storeTable(t, "temp_output/test.table")
assert False, "no exception thrown althoug file should exist!"
except:
pass
ms.storeTable(t, "temp_output/test.table", True)
t = ms.loadTable("temp_output/test.table")
run(t, names, [row1, row2, row3])
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 testRunnerTable():
with ExceptionTester():
Table(["a"], [np.float32], ["%f"], [[32.0]])
#build table
names = "int long float str object array".split()
types = [
int,
long,
float,
str,
object,
np.ndarray,
]
formats = ["%3d", "%d", "%.3f", "%s", "%r", "'array(%r)' % (o.shape,)"]
row1 = [1, 12323L, 1.0, "hi", {1: 1}, np.array((1, 2, 3))]
row2 = [2, 22323L, 2.0, "hi2", [
2,
3,
], np.array(((2, 3, 4), (1, 2, 3)))]
row3 = [
3, 32323L, 3.0, "hi3", (3, ),
np.array(((3, 3, 4, 5), (1, 2, 3, 4)))
]
rows = [row1, row2, row3]
t = Table(names, types, formats, rows, "testtabelle", meta=dict(why=42))
run(t, names, [row1, row2, row3])
# test pickle
dat = pickle.dumps(t)
t = pickle.loads(dat)
run(t, names, [row1, row2, row3])
ms.storeTable(t, u"temp_output/test.table")
try:
ms.storeTable(t, "temp_output/test.table")
assert False, "no exception thrown althoug file should exist!"
except:
pass
ms.storeTable(t, "temp_output/test.table", True)
t = ms.loadTable("temp_output/test.table")
run(t, names, [row1, row2, row3])
def testMzAlign():
tab = ms.loadTable("data/ftab_for_mzalign.table")
pm = tab.peakmap.values[0]
s0 = pm.spectra[0].peaks[:,0]
import os
print os.getcwd()
print os.listdir("temp_output")
tab_aligned = ms.mzAlign(tab, interactive=False, minPoints=4, tol=14*MMU,
destination="temp_output")
after = tab_aligned.mz.values
pm = tab_aligned.peakmap.values[0]
s0 = pm.spectra[0].peaks[:,0]
assert abs(s0[0]-202.121231079) < 1e-5, float(s0[0])
assert abs(after[0]-272.199238673) < 1e-5, float(after[0])
assert len(glob.glob("temp_output/2011-10-06_054_PKTB*"))==4
# former errror: transformation resulted in numpy.float64 values
assert tab_aligned.get(tab_aligned.colTypes, "mz") == float
assert tab_aligned.get(tab_aligned.colTypes, "mzmin") == float
assert tab_aligned.get(tab_aligned.colTypes, "mzmax") == float
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 testMzAlign():
tab = ms.loadTable("data/ftab_for_mzalign.table")
pm = tab.peakmap.values[0]
s0 = pm.spectra[0].peaks[:, 0]
import os
print os.getcwd()
print os.listdir("temp_output")
tab_aligned = ms.mzAlign(tab,
interactive=False,
minPoints=4,
tol=14 * MMU,
destination="temp_output")
after = tab_aligned.mz.values
pm = tab_aligned.peakmap.values[0]
s0 = pm.spectra[0].peaks[:, 0]
assert abs(s0[0] - 202.121231079) < 1e-5, float(s0[0])
assert abs(after[0] - 272.199238673) < 1e-5, float(after[0])
assert len(glob.glob("temp_output/2011-10-06_054_PKTB*")) == 4
# former errror: transformation resulted in numpy.float64 values
assert tab_aligned.get(tab_aligned.colTypes, "mz") == float
assert tab_aligned.get(tab_aligned.colTypes, "mzmin") == float
assert tab_aligned.get(tab_aligned.colTypes, "mzmax") == float
def testIntegration():
# test with and without unicode:
ft = ms.loadTable(u"data/features.table")
# an invalid row should not stop integration, but result
# in None values for ms.integrate generated columns
ftr = ms.integrate(ft, "trapez")
assert len(ftr) == len(ft)
assert "area" in ftr.getColNames()
assert "rmse" in ftr.getColNames()
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 = ms.integrate(ft, "trapez")
ftr.info()
assert len(ftr) == len(ft)
assert "area" in ftr.getColNames()
assert "rmse" in ftr.getColNames()
assert "area__0" in ftr.getColNames()
assert "rmse__0" in ftr.getColNames()
assert "areaX" in ftr.getColNames()
assert "rmseX" in ftr.getColNames()
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.area.values[1] >= 0
assert ftr.rmse.values[1] >= 0
assert ftr.params.values[1] is not None
assert ftr.method.values[1] is not None
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.params__0.values[1] is not None
assert ftr.method__0.values[1] is not None
assert ftr.area__0.values[1] >= 0
assert ftr.rmse__0.values[1] >= 0
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.paramsX.values[1] is not None
assert ftr.methodX.values[1] is not None
assert ftr.areaX.values[1] >= 0
assert ftr.rmseX.values[1] >= 0
def test_old():
print >> sys.stderr, "TEST LOADING OF TABLE FROM EMZED BEFORE 1.3.2"
t = ms.loadTable("feature_table_before_1.3.2.table")
assert not hasattr(t, "version"),\
"PLEASE READ cocepts/konzept_table_versions"
import sys
sys.path.insert(0, "..")
import ms
t = ms.loadTable("integrated_features.table")
t2 = t.copy()
tj = t.join(t2, t.id == t2.id)
tj.rtmin__0 -= 20
tj.rtmax__0 -= 20
pm = tj.peakmap__0.values[0]
for s in pm.spectra:
s.rt -= 20
ms.inspect(tj)
def test_1_3_8():
print >> sys.stderr, "TEST LOADING OF TABLE FROM EMZED 1.3.8"
t = ms.loadTable("feature_table_1.3.8.table")
assert t.version == "1.3.8", "PLEASE READ cocepts/konzept_table_versions"
def test_old():
print >> sys.stderr, "TEST LOADING OF TABLE FROM EMZED BEFORE 1.3.2"
t = ms.loadTable("feature_table_before_1.3.2.table")
assert not hasattr(t, "version"),\
"PLEASE READ cocepts/konzept_table_versions"
def test_1_3_8():
print >> sys.stderr, "TEST LOADING OF TABLE FROM EMZED 1.3.8"
t = ms.loadTable("feature_table_1.3.8.table")
assert t.version == "1.3.8", "PLEASE READ cocepts/konzept_table_versions"
#encoding: utf-8
import sys
sys.path.insert(0, "..")
import ms
table = ms.loadTable("features.table")
print table.rows[0]
ms.inspect([table])
try:
table = ms.loadCSV(p)
except Exception, e:
import traceback
traceback.print_exc()
print "PARSING",p,"FAILED"
continue
name, _ = os.path.splitext(os.path.basename(p))
name = name.replace(" ","_")
table.title = name
exec("%s=table" % name)
print "LOADED", name, "FROM", p
# table files overrun csv files !
for p in glob.glob("%s/*.table" % path):
try:
table = ms.loadTable(p)
except Exception, e:
import traceback
traceback.print_exc()
print "PARSING",p,"FAILED"
continue
name, _ = os.path.splitext(os.path.basename(p))
name = name.replace(" ","_")
table.title = name
table.meta["loaded_from"] = os.path.abspath(p)
exec("%s=table" % name)
print "LOADED", name, "FROM", p
elements = Elements()
# next line only valid after execution of 100loadpubchem.py during
# startup:
#encoding: utf-8
import sys
sys.path.insert(0, "..")
import ms
table = ms.loadTable("features.table")
table2 = ms.loadTable("integrated_features.table")
ms.inspect([table, table2])
try:
table = ms.loadCSV(p)
except Exception, e:
import traceback
traceback.print_exc()
print "PARSING", p, "FAILED"
continue
name, _ = os.path.splitext(os.path.basename(p))
name = name.replace(" ", "_")
table.title = name
exec("%s=table" % name)
print "LOADED", name, "FROM", p
# table files overrun csv files !
for p in glob.glob("%s/*.table" % path):
try:
table = ms.loadTable(p)
except Exception, e:
import traceback
traceback.print_exc()
print "PARSING", p, "FAILED"
continue
name, _ = os.path.splitext(os.path.basename(p))
name = name.replace(" ", "_")
table.title = name
table.meta["loaded_from"] = os.path.abspath(p)
exec("%s=table" % name)
print "LOADED", name, "FROM", p
elements = Elements()
# next line only valid after execution of 100loadpubchem.py during
# startup:
def testIntegration():
# test with and without unicode:
ft = ms.loadTable(u"data/features.table")
# an invalid row should not stop integration, but result
# in None values for ms.integrate generated columns
ftr = ms.integrate(ft, "trapez")
assert len(ftr) == len(ft)
assert "area" in ftr.getColNames()
assert "rmse" in ftr.getColNames()
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 = ms.integrate(ft, "trapez")
ftr.info()
assert len(ftr) == len(ft)
assert "area" in ftr.getColNames()
assert "rmse" in ftr.getColNames()
assert "area__0" in ftr.getColNames()
assert "rmse__0" in ftr.getColNames()
assert "areaX" in ftr.getColNames()
assert "rmseX" in ftr.getColNames()
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.area.values[1] >= 0
assert ftr.rmse.values[1] >= 0
assert ftr.params.values[1] is not None
assert ftr.method.values[1] is not None
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.params__0.values[1] is not None
assert ftr.method__0.values[1] is not None
assert ftr.area__0.values[1] >= 0
assert ftr.rmse__0.values[1] >= 0
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.paramsX.values[1] is not None
assert ftr.methodX.values[1] is not None
assert ftr.areaX.values[1] >= 0
assert ftr.rmseX.values[1] >= 0