def convertStacksToH5(cls, filePaths, stackVolumeCacheDir):
"""
If any of the files in filePaths appear to be globstrings for a stack,
convert the given stack to hdf5 format.
Return the filePaths list with globstrings replaced by the paths to the new hdf5 volumes.
"""
import hashlib
import pickle
import h5py
from lazyflow.graph import Graph
from lazyflow.operators.ioOperators import OpStackToH5Writer
filePaths = list(filePaths)
for i, path in enumerate(filePaths):
if not path or '*' not in path:
continue
globstring = path
# Embrace paranoia:
# We want to make sure we never re-use a stale cache file for a new dataset,
# even if the dataset is located in the same location as a previous one and has the same globstring!
# Create a sha-1 of the file name and modification date.
sha = hashlib.sha1()
files = [k.replace('\\', '/') for k in glob.glob(path)]
for f in files:
sha.update(f)
sha.update(pickle.dumps(os.stat(f).st_mtime))
stackFile = sha.hexdigest() + '.h5'
stackPath = os.path.join(stackVolumeCacheDir,
stackFile).replace('\\', '/')
# Overwrite original path
filePaths[i] = stackPath + "/volume/data"
# Generate the hdf5 if it doesn't already exist
if os.path.exists(stackPath):
logger.info(
"Using previously generated hdf5 volume for stack {}".
format(path))
logger.info("Volume path: {}".format(filePaths[i]))
else:
logger.info("Generating hdf5 volume for stack {}".format(path))
logger.info("Volume path: {}".format(filePaths[i]))
if not os.path.exists(stackVolumeCacheDir):
os.makedirs(stackVolumeCacheDir)
with h5py.File(stackPath) as f:
# Configure the conversion operator
opWriter = OpStackToH5Writer(graph=Graph())
opWriter.hdf5Group.setValue(f)
opWriter.hdf5Path.setValue("volume/data")
opWriter.GlobString.setValue(globstring)
# Initiate the write
success = opWriter.WriteImage.value
assert success, "Something went wrong when generating an hdf5 file from an image sequence."
return filePaths
def convertStacksToH5(filePaths):
"""
If any of the files in filePaths appear to be globstrings for a stack,
convert the given stack to hdf5 format.
Return the filePaths list with globstrings replaced by the paths to the new hdf5 volumes.
"""
filePaths = list(filePaths)
for i, path in enumerate(filePaths):
if '*' in path:
globstring = path
stackPath = os.path.splitext(globstring)[0]
stackPath.replace('*', "_VOLUME")
stackPath += ".h5"
# Overwrite original path
filePaths[i] = stackPath + "/volume/data"
# Generate the hdf5 if it doesn't already exist
if not os.path.exists(stackPath):
with h5py.File(stackPath) as f:
# Configure the conversion operator
opWriter = OpStackToH5Writer( graph=Graph() )
opWriter.hdf5Group.setValue(f)
opWriter.hdf5Path.setValue("volume/data")
opWriter.GlobString.setValue(globstring)
# Initiate the write
success = opWriter.WriteImage.value
return filePaths
def importStackAsLocalDataset(self, info):
"""
Add the given stack data to the project file as a local dataset.
Create a datainfo and append it to our operator.
"""
with Tracer(traceLogger):
try:
self.progressSignal.emit(0)
projectFileHdf5 = self.mainOperator.ProjectFile.value
topGroup = self.getOrCreateGroup(projectFileHdf5,
self.topGroupName)
localDataGroup = self.getOrCreateGroup(topGroup, 'local_data')
globstring = info.filePath
info.location = DatasetInfo.Location.ProjectInternal
opWriter = OpStackToH5Writer(graph=self.mainOperator.graph)
opWriter.hdf5Group.setValue(localDataGroup)
opWriter.hdf5Path.setValue(info.datasetId)
opWriter.GlobString.setValue(globstring)
# Forward progress from the writer directly to our applet
opWriter.progressSignal.subscribe(self.progressSignal.emit)
success = opWriter.WriteImage.value
numDatasets = len(self.mainOperator.Dataset)
self.mainOperator.Dataset.resize(numDatasets + 1)
self.mainOperator.Dataset[numDatasets].setValue(info)
finally:
self.progressSignal.emit(100)
return success
def importStackAsLocalDataset(self, info):
"""
Add the given stack data to the project file as a local dataset.
Does not update the topLevelOperator.
:param info: A DatasetInfo object.
Note: info.filePath must be a str which lists the stack files, delimited with os.path.pathsep
Note: info will be MODIFIED by this function. Use the modified info when assigning it to a dataset.
"""
try:
self.progressSignal.emit(0)
projectFileHdf5 = self.topLevelOperator.ProjectFile.value
topGroup = getOrCreateGroup(projectFileHdf5, self.topGroupName)
localDataGroup = getOrCreateGroup(topGroup, 'local_data')
globstring = info.filePath
info.location = DatasetInfo.Location.ProjectInternal
firstPathParts = PathComponents(
info.filePath.split(os.path.pathsep)[0])
info.filePath = firstPathParts.externalDirectory + '/??' + firstPathParts.extension
info.fromstack = True
# Use absolute path
cwd = self.topLevelOperator.WorkingDirectory
if os.path.pathsep not in globstring and not os.path.isabs(
globstring):
globstring = os.path.normpath(os.path.join(cwd, globstring))
opWriter = OpStackToH5Writer(parent=self.topLevelOperator.parent,
graph=self.topLevelOperator.graph)
opWriter.hdf5Group.setValue(localDataGroup)
opWriter.hdf5Path.setValue(info.datasetId)
opWriter.GlobString.setValue(globstring)
# Forward progress from the writer directly to our applet
opWriter.progressSignal.subscribe(self.progressSignal.emit)
success = opWriter.WriteImage.value
finally:
opWriter.cleanUp()
self.progressSignal.emit(100)
return success