def _applyPattern(self):
globStrings = encode_from_qstring(self.patternEdit.text())
H5EXTS = OpStreamingHdf5SequenceReaderM.H5EXTS
filenames = []
# see if some glob strings include HDF5 files
globStrings = globStrings.split(os.path.pathsep)
pcs = [PathComponents(x) for x in globStrings]
ish5 = [x.extension in H5EXTS for x in pcs]
h5GlobStrings = os.path.pathsep.join(
[x for x, y in zip(globStrings, ish5) if y is True])
globStrings = os.path.pathsep.join(
[x for x, y in zip(globStrings, ish5) if y is False])
filenames.extend(OpStackLoader.expandGlobStrings(globStrings))
try:
OpStreamingHdf5SequenceReaderS.checkGlobString(h5GlobStrings)
# OK, if nothing raised there is a single h5 file in h5GlobStrings:
pathComponents = PathComponents(
h5GlobStrings.split(os.path.pathsep)[0])
h5file = h5py.File(pathComponents.externalPath, mode='r')
filenames.extend(
"{}/{}".format(pathComponents.externalPath, internal)
for internal in OpStreamingHdf5SequenceReaderS.
expandGlobStrings(h5file, h5GlobStrings))
except (OpStreamingHdf5SequenceReaderS.WrongFileTypeError,
OpStreamingHdf5SequenceReaderS.NotTheSameFileError,
OpStreamingHdf5SequenceReaderS.NoInternalPlaceholderError,
OpStreamingHdf5SequenceReaderS.ExternalPlaceholderError):
pass
try:
OpStreamingHdf5SequenceReaderM.checkGlobString(h5GlobStrings)
filenames.extend(
"{}/{}".format(external, internal)
for external, internal in zip(
*OpStreamingHdf5SequenceReaderM.expandGlobStrings(
h5GlobStrings)))
except (OpStreamingHdf5SequenceReaderM.WrongFileTypeError,
OpStreamingHdf5SequenceReaderM.SameFileError,
OpStreamingHdf5SequenceReaderM.NoExternalPlaceholderError,
OpStreamingHdf5SequenceReaderM.InternalPlaceholderError):
pass
self._updateFileList(filenames)
def _applyPattern(self):
globStrings = self.patternEdit.text()
H5EXTS = OpStreamingHdf5SequenceReaderM.H5EXTS
filenames = []
# see if some glob strings include HDF5 files
globStrings = globStrings.split(os.path.pathsep)
pcs = [PathComponents(x) for x in globStrings]
ish5 = [x.extension in H5EXTS for x in pcs]
h5GlobStrings = os.path.pathsep.join([x for x, y in zip(globStrings, ish5) if y is True])
globStrings = os.path.pathsep.join([x for x, y in zip(globStrings, ish5) if y is False])
filenames.extend(OpStackLoader.expandGlobStrings(globStrings))
try:
OpStreamingHdf5SequenceReaderS.checkGlobString(h5GlobStrings)
# OK, if nothing raised there is a single h5 file in h5GlobStrings:
pathComponents = PathComponents(h5GlobStrings.split(os.path.pathsep)[0])
h5file = h5py.File(pathComponents.externalPath, mode='r')
filenames.extend(
"{}/{}".format(pathComponents.externalPath, internal)
for internal in OpStreamingHdf5SequenceReaderS.expandGlobStrings(h5file, h5GlobStrings))
except (
OpStreamingHdf5SequenceReaderS.WrongFileTypeError,
OpStreamingHdf5SequenceReaderS.NotTheSameFileError,
OpStreamingHdf5SequenceReaderS.NoInternalPlaceholderError,
OpStreamingHdf5SequenceReaderS.ExternalPlaceholderError):
pass
try:
OpStreamingHdf5SequenceReaderM.checkGlobString(h5GlobStrings)
filenames.extend(
"{}/{}".format(external, internal)
for external, internal
in zip(*OpStreamingHdf5SequenceReaderM.expandGlobStrings(h5GlobStrings))
)
except (
OpStreamingHdf5SequenceReaderM.WrongFileTypeError,
OpStreamingHdf5SequenceReaderM.SameFileError,
OpStreamingHdf5SequenceReaderM.NoExternalPlaceholderError,
OpStreamingHdf5SequenceReaderM.InternalPlaceholderError):
pass
self._updateFileList(filenames)
def _attemptOpenAsHdf5Stack(self, filePath):
if not ('*' in filePath or os.path.pathsep in filePath):
return ([], None)
# Now use the .checkGlobString method of the stack readers
isSingleFile = True
try:
OpStreamingHdf5SequenceReaderS.checkGlobString(filePath)
except OpStreamingHdf5SequenceReaderS.WrongFileTypeError:
return ([], None)
except (OpStreamingHdf5SequenceReaderS.NoInternalPlaceholderError,
OpStreamingHdf5SequenceReaderS.NotTheSameFileError,
OpStreamingHdf5SequenceReaderS.ExternalPlaceholderError):
isSingleFile = False
isMultiFile = True
try:
OpStreamingHdf5SequenceReaderM.checkGlobString(filePath)
except (OpStreamingHdf5SequenceReaderM.NoExternalPlaceholderError,
OpStreamingHdf5SequenceReaderM.SameFileError,
OpStreamingHdf5SequenceReaderM.InternalPlaceholderError):
isMultiFile = False
assert (not (isMultiFile and isSingleFile))
if isSingleFile is True:
opReader = OpStreamingHdf5SequenceReaderS(parent=self)
elif isMultiFile is True:
opReader = OpStreamingHdf5SequenceReaderM(parent=self)
try:
opReader.SequenceAxis.connect(self.SequenceAxis)
opReader.GlobString.setValue(filePath)
return ([opReader], opReader.OutputImage)
except (OpStreamingHdf5SequenceReaderM.WrongFileTypeError,
OpStreamingHdf5SequenceReaderS.WrongFileTypeError):
return ([], None)
else:
return ([], None)
def test_3d_vigra_along_t(self):
"""Test if 3d volumes generated through vigra are recognized correctly"""
# Prepare some data set for this case
data = numpy.random.randint(0, 255,
(10, 15, 50, 100, 3)).astype(numpy.uint8)
axistags = vigra.defaultAxistags('zyxc')
expected_axistags = vigra.defaultAxistags('tzyxc')
op = OpStreamingHdf5SequenceReaderM(graph=self.graph)
with tempdir() as d:
try:
for sliceIndex, tSlice in enumerate(data):
testDataFileName = '{path}/test-{index:02d}.h5'.format(
path=d, index=sliceIndex)
# Write the dataset to an hdf5 file
# (Note: Don't use vigra to do this, which may reorder the axes)
h5File = h5py.File(testDataFileName)
try:
h5File.create_group('volume')
h5File['volume'].create_dataset("subvolume",
data=tSlice)
# Write the axistags attribute
current_path = 'volume/subvolume'
h5File[current_path].attrs[
'axistags'] = axistags.toJSON()
finally:
h5File.close()
# Read the data with an operator
hdf5GlobString = "{path}/test-*.h5/volume/subvolume".format(
path=d)
op.SequenceAxis.setValue('t')
op.GlobString.setValue(hdf5GlobString)
assert op.OutputImage.ready()
assert op.OutputImage.meta.axistags == expected_axistags
numpy.testing.assert_array_equal(
op.OutputImage[0:2, 5:10, 20:50, 40:70].wait(),
data[0:2, 5:10, 20:50, 40:70])
finally:
op.cleanUp()
def test_globStringValidity(self):
"""Check whether globStrings are correctly verified"""
testGlobString = '/tmp/test.h5/somedata'
with self.assertRaises(
OpStreamingHdf5SequenceReaderM.NoExternalPlaceholderError):
OpStreamingHdf5SequenceReaderM.checkGlobString(testGlobString)
testGlobString = '/tmp/test.jpg/*'
with self.assertRaises(
OpStreamingHdf5SequenceReaderM.WrongFileTypeError):
OpStreamingHdf5SequenceReaderM.checkGlobString(testGlobString)
testGlobString = '/tmp/test.h5/data' + os.pathsep + '/tmp/test.h5/data2'
with self.assertRaises(OpStreamingHdf5SequenceReaderM.SameFileError):
OpStreamingHdf5SequenceReaderM.checkGlobString(testGlobString)
testGlobString = '/tmp/test-*.h5/data*'
with self.assertRaises(
OpStreamingHdf5SequenceReaderM.InternalPlaceholderError):
OpStreamingHdf5SequenceReaderM.checkGlobString(testGlobString)
testGlobString = '/tmp/test-0.h5/data' + os.pathsep + '/tmp/test-1.h5/data*'
with self.assertRaises(
OpStreamingHdf5SequenceReaderM.InternalPlaceholderError):
OpStreamingHdf5SequenceReaderM.checkGlobString(testGlobString)
validGlobStrings = [
'/tmp/test-*.h5/data',
'/tmp/test-1.h5/data1' + os.pathsep + '/tmp/test-2.h5/data1',
]
for testGlobString in validGlobStrings:
OpStreamingHdf5SequenceReaderM.checkGlobString(testGlobString)
# Implicit test for validity; test fails if an exception is raised
self.assertTrue(True)