def expandGlobStrings(h5N5File, globStrings):
"""Matches a list of globStrings to internal paths of files
Args:
h5N5File: h5py or z5py File object, or path(string). If a string is given,
the file is opened and closed in this method.
globStrings: string. glob or path strings delimited by os.pathsep
Returns:
List of internal paths matching the globstrings that were found in
the provided h5py.File object
"""
if not isinstance(h5N5File, (h5py.File, z5py.N5File)):
with OpStreamingH5N5Reader.get_h5_n5_file(h5N5File, mode="r") as f:
ret = OpStreamingH5N5SequenceReaderS.expandGlobStrings(
f, globStrings)
return ret
ret = []
# Parse list into separate globstrings and combine them
for globString in globStrings.split(os.path.pathsep):
s = globString.strip()
components = PathComponents(s)
ret += sorted(
globH5N5(h5N5File, components.internalPath.lstrip("/")))
return ret
def testHdf5Glob(self):
hdf5File = self.createHdf5Data()
globString = "here/is/the/data/test-*"
expectedPaths = ["here/is/the/data/test-{index:02d}".format(index=index) for index in range(5)]
globbedPaths = globH5N5(hdf5File, globString)
assert all([a == b for a, b in zip(globbedPaths, expectedPaths)])
def globInternalPaths(cls, file_path: str, glob_str: str, cwd: str = None) -> List[str]:
glob_str = glob_str.lstrip("/")
internal_paths = set()
for path in cls.expand_path(file_path, cwd=cwd):
f = None
try:
if cls.pathIsNpz(path):
internal_paths |= set(globNpz(path, glob_str))
continue
elif cls.pathIsHdf5(path):
f = h5py.File(path, "r")
elif cls.pathIsN5(path):
f = z5py.N5File(path) # FIXME
else:
raise Exception(f"{path} is not an 'n5' or 'h5' file")
internal_paths |= set(globH5N5(f, glob_str))
finally:
if f is not None:
f.close()
return sorted(internal_paths)
def expandGlobStrings(h5N5File, globStrings):
"""Matches a list of globStrings to internal paths of files
Args:
h5N5File: h5py or z5py File object, or path(string). If a string is given,
the file is opened and closed in this method.
globStrings: string. glob or path strings delimited by os.pathsep
Returns:
List of internal paths matching the globstrings that were found in
the provided h5py.File object
"""
if not isinstance(h5N5File, (h5py.File, z5py.N5File)):
with OpStreamingH5N5Reader.get_h5_n5_file(h5N5File, mode="r") as f:
ret = OpStreamingH5N5SequenceReaderS.expandGlobStrings(f, globStrings)
return ret
ret = []
# Parse list into separate globstrings and combine them
for globString in globStrings.split(os.path.pathsep):
s = globString.strip()
components = PathComponents(s)
ret += sorted(globH5N5(h5N5File, components.internalPath.lstrip("/")))
return ret