def _applyPattern(self):
globStrings = self.patternEdit.text()
H5EXTS = OpStreamingH5N5SequenceReaderM.H5EXTS
N5EXTS = OpStreamingH5N5SequenceReaderM.N5EXTS
filenames = []
# see if some glob strings include HDF5 and/or N5 files
globStrings = globStrings.split(os.path.pathsep)
pcs = [PathComponents(x) for x in globStrings]
is_h5_n5 = [x.extension in (H5EXTS + N5EXTS) for x in pcs]
h5GlobStrings = os.path.pathsep.join(
[x for x, y in zip(globStrings, is_h5_n5) if y is True])
globStrings = os.path.pathsep.join(
[x for x, y in zip(globStrings, is_h5_n5) if y is False])
filenames.extend(OpStackLoader.expandGlobStrings(globStrings))
try:
OpStreamingH5N5SequenceReaderS.checkGlobString(h5GlobStrings)
# OK, if nothing raised there is a single h5 file in h5GlobStrings:
pathComponents = PathComponents(
h5GlobStrings.split(os.path.pathsep)[0])
h5file = OpStreamingH5N5Reader.get_h5_n5_file(
pathComponents.externalPath, mode="r")
filenames.extend(
"{}/{}".format(pathComponents.externalPath, internal)
for internal in OpStreamingH5N5SequenceReaderS.
expandGlobStrings(h5file, h5GlobStrings))
except (
OpStreamingH5N5SequenceReaderS.WrongFileTypeError,
OpStreamingH5N5SequenceReaderS.NotTheSameFileError,
OpStreamingH5N5SequenceReaderS.NoInternalPlaceholderError,
OpStreamingH5N5SequenceReaderS.ExternalPlaceholderError,
):
pass
try:
OpStreamingH5N5SequenceReaderM.checkGlobString(h5GlobStrings)
filenames.extend(
"{}/{}".format(external, internal)
for external, internal in zip(
*OpStreamingH5N5SequenceReaderM.expandGlobStrings(
h5GlobStrings)))
except (
OpStreamingH5N5SequenceReaderM.WrongFileTypeError,
OpStreamingH5N5SequenceReaderM.SameFileError,
OpStreamingH5N5SequenceReaderM.NoExternalPlaceholderError,
OpStreamingH5N5SequenceReaderM.InternalPlaceholderError,
):
pass
self._updateFileList(filenames)
def _applyPattern(self):
globStrings = self.patternEdit.text()
H5EXTS = OpStreamingH5N5SequenceReaderM.H5EXTS
N5EXTS = OpStreamingH5N5SequenceReaderM.N5EXTS
filenames = []
# see if some glob strings include HDF5 and/or N5 files
globStrings = globStrings.split(os.path.pathsep)
pcs = [PathComponents(x) for x in globStrings]
is_h5_n5 = [x.extension in (H5EXTS + N5EXTS) for x in pcs]
h5GlobStrings = os.path.pathsep.join([x for x, y in zip(globStrings, is_h5_n5) if y is True])
globStrings = os.path.pathsep.join([x for x, y in zip(globStrings, is_h5_n5) if y is False])
filenames.extend(OpStackLoader.expandGlobStrings(globStrings))
try:
OpStreamingH5N5SequenceReaderS.checkGlobString(h5GlobStrings)
# OK, if nothing raised there is a single h5 file in h5GlobStrings:
pathComponents = PathComponents(h5GlobStrings.split(os.path.pathsep)[0])
h5file = OpStreamingH5N5Reader.get_h5_n5_file(pathComponents.externalPath, mode='r')
filenames.extend(
"{}/{}".format(pathComponents.externalPath, internal)
for internal in OpStreamingH5N5SequenceReaderS.expandGlobStrings(h5file, h5GlobStrings))
except (
OpStreamingH5N5SequenceReaderS.WrongFileTypeError,
OpStreamingH5N5SequenceReaderS.NotTheSameFileError,
OpStreamingH5N5SequenceReaderS.NoInternalPlaceholderError,
OpStreamingH5N5SequenceReaderS.ExternalPlaceholderError):
pass
try:
OpStreamingH5N5SequenceReaderM.checkGlobString(h5GlobStrings)
filenames.extend(
"{}/{}".format(external, internal)
for external, internal
in zip(*OpStreamingH5N5SequenceReaderM.expandGlobStrings(h5GlobStrings))
)
except (
OpStreamingH5N5SequenceReaderM.WrongFileTypeError,
OpStreamingH5N5SequenceReaderM.SameFileError,
OpStreamingH5N5SequenceReaderM.NoExternalPlaceholderError,
OpStreamingH5N5SequenceReaderM.InternalPlaceholderError):
pass
self._updateFileList(filenames)
def _attemptOpenAsH5N5Stack(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:
OpStreamingH5N5SequenceReaderS.checkGlobString(filePath)
except OpStreamingH5N5SequenceReaderS.WrongFileTypeError:
return ([], None)
except (
OpStreamingH5N5SequenceReaderS.NoInternalPlaceholderError,
OpStreamingH5N5SequenceReaderS.NotTheSameFileError,
OpStreamingH5N5SequenceReaderS.ExternalPlaceholderError,
):
isSingleFile = False
isMultiFile = True
try:
OpStreamingH5N5SequenceReaderM.checkGlobString(filePath)
except (
OpStreamingH5N5SequenceReaderM.NoExternalPlaceholderError,
OpStreamingH5N5SequenceReaderM.SameFileError,
OpStreamingH5N5SequenceReaderM.InternalPlaceholderError,
):
isMultiFile = False
assert not (isMultiFile and isSingleFile)
if isSingleFile is True:
opReader = OpStreamingH5N5SequenceReaderS(parent=self)
elif isMultiFile is True:
opReader = OpStreamingH5N5SequenceReaderM(parent=self)
try:
opReader.SequenceAxis.connect(self.SequenceAxis)
opReader.GlobString.setValue(filePath)
return ([opReader], opReader.OutputImage)
except (OpStreamingH5N5SequenceReaderM.WrongFileTypeError,
OpStreamingH5N5SequenceReaderS.WrongFileTypeError):
return ([], None)
def test_globStringValidity(self):
"""Check whether globStrings are correctly verified"""
testGlobString = "/tmp/test.h5"
with self.assertRaises(
OpStreamingH5N5SequenceReaderS.NoInternalPlaceholderError):
OpStreamingH5N5SequenceReaderS.checkGlobString(testGlobString)
testGlobString = "/tmp/test.n5"
with self.assertRaises(
OpStreamingH5N5SequenceReaderS.NoInternalPlaceholderError):
OpStreamingH5N5SequenceReaderS.checkGlobString(testGlobString)
testGlobString = "/tmp/test.h5/a" + os.pathsep + "/tmp/test2.h5/a"
with self.assertRaises(
OpStreamingH5N5SequenceReaderS.NotTheSameFileError):
OpStreamingH5N5SequenceReaderS.checkGlobString(testGlobString)
testGlobString = "/tmp/test.n5/a" + os.pathsep + "/tmp/test2.n5/a"
with self.assertRaises(
OpStreamingH5N5SequenceReaderS.NotTheSameFileError):
OpStreamingH5N5SequenceReaderS.checkGlobString(testGlobString)
testGlobString = "/tmp/test*.h5/a" + os.pathsep + "/tmp/test*.h5/a"
with self.assertRaises(
OpStreamingH5N5SequenceReaderS.ExternalPlaceholderError):
OpStreamingH5N5SequenceReaderS.checkGlobString(testGlobString)
testGlobString = "/tmp/test*.n5/a" + os.pathsep + "/tmp/test*.n5/a"
with self.assertRaises(
OpStreamingH5N5SequenceReaderS.ExternalPlaceholderError):
OpStreamingH5N5SequenceReaderS.checkGlobString(testGlobString)
testGlobString = "/tmp/test.jpg/*"
with self.assertRaises(
OpStreamingH5N5SequenceReaderS.WrongFileTypeError):
OpStreamingH5N5SequenceReaderS.checkGlobString(testGlobString)
validGlobStrings = [
"/tmp/test.h5/*",
"/tmp/test.h5/data1" + os.pathsep + "/tmp/test.h5/data2",
"/tmp/test.h5/data*",
"/tmp/test.n5/*",
"/tmp/test.n5/data1" + os.pathsep + "/tmp/test.n5/data2",
"/tmp/test.n5/data*",
]
# Implicit test for validity; test fails if an exception is raised
for testGlobString in validGlobStrings:
OpStreamingH5N5SequenceReaderS.checkGlobString(testGlobString)
self.assertTrue(True)
def test_globStringValidity(self):
"""Check whether globStrings are correctly verified"""
testGlobString = "/tmp/test.h5"
with self.assertRaises(OpStreamingH5N5SequenceReaderS.NoInternalPlaceholderError):
OpStreamingH5N5SequenceReaderS.checkGlobString(testGlobString)
testGlobString = "/tmp/test.n5"
with self.assertRaises(OpStreamingH5N5SequenceReaderS.NoInternalPlaceholderError):
OpStreamingH5N5SequenceReaderS.checkGlobString(testGlobString)
testGlobString = "/tmp/test.h5/a" + os.pathsep + "/tmp/test2.h5/a"
with self.assertRaises(OpStreamingH5N5SequenceReaderS.NotTheSameFileError):
OpStreamingH5N5SequenceReaderS.checkGlobString(testGlobString)
testGlobString = "/tmp/test.n5/a" + os.pathsep + "/tmp/test2.n5/a"
with self.assertRaises(OpStreamingH5N5SequenceReaderS.NotTheSameFileError):
OpStreamingH5N5SequenceReaderS.checkGlobString(testGlobString)
testGlobString = "/tmp/test*.h5/a" + os.pathsep + "/tmp/test*.h5/a"
with self.assertRaises(OpStreamingH5N5SequenceReaderS.ExternalPlaceholderError):
OpStreamingH5N5SequenceReaderS.checkGlobString(testGlobString)
testGlobString = "/tmp/test*.n5/a" + os.pathsep + "/tmp/test*.n5/a"
with self.assertRaises(OpStreamingH5N5SequenceReaderS.ExternalPlaceholderError):
OpStreamingH5N5SequenceReaderS.checkGlobString(testGlobString)
testGlobString = "/tmp/test.jpg/*"
with self.assertRaises(OpStreamingH5N5SequenceReaderS.WrongFileTypeError):
OpStreamingH5N5SequenceReaderS.checkGlobString(testGlobString)
validGlobStrings = [
"/tmp/test.h5/*",
"/tmp/test.h5/data1" + os.pathsep + "/tmp/test.h5/data2",
"/tmp/test.h5/data*",
"/tmp/test.n5/*",
"/tmp/test.n5/data1" + os.pathsep + "/tmp/test.n5/data2",
"/tmp/test.n5/data*",
]
# Implicit test for validity; test fails if an exception is raised
for testGlobString in validGlobStrings:
OpStreamingH5N5SequenceReaderS.checkGlobString(testGlobString)
self.assertTrue(True)