def _deserializeFromHdf5(self, topGroup, groupVersion, hdf5File,
projectFilePath):
with Tracer(traceLogger):
self._projectFilePath = projectFilePath
self.initWithoutTopGroup(hdf5File, projectFilePath)
infoDir = topGroup['infos']
self.mainOperator.Dataset.resize(len(infoDir))
for index, (infoGroupName,
infoGroup) in enumerate(sorted(infoDir.items())):
datasetInfo = DatasetInfo()
# Make a reverse-lookup of the location storage strings
LocationLookup = {
v: k
for k, v in self.LocationStrings.items()
}
datasetInfo.location = LocationLookup[str(
infoGroup['location'].value)]
# Write to the 'private' members to avoid resetting the dataset id
datasetInfo._filePath = str(infoGroup['filePath'].value)
datasetInfo._datasetId = str(infoGroup['datasetId'].value)
# Deserialize the "allow labels" flag
try:
datasetInfo.allowLabels = infoGroup['allowLabels'].value
except KeyError:
pass
# Deserialize the axisorder (if present)
try:
datasetInfo.axisorder = infoGroup['axisorder'].value
except KeyError:
if ilastik.utility.globals.ImportOptions.default_axis_order is not None:
datasetInfo.axisorder = ilastik.utility.globals.ImportOptions.default_axis_order
# If the data is supposed to be in the project,
# check for it now.
if datasetInfo.location == DatasetInfo.Location.ProjectInternal:
if not datasetInfo.datasetId in topGroup[
'local_data'].keys():
raise RuntimeError(
"Corrupt project file. Could not find data for " +
infoGroupName)
# If the data is supposed to exist outside the project, make sure it really does.
if datasetInfo.location == DatasetInfo.Location.FileSystem:
filePath = PathComponents(
datasetInfo.filePath,
os.path.split(projectFilePath)[0]).externalPath
if not os.path.exists(filePath):
raise RuntimeError("Could not find external data: " +
filePath)
# Give the new info to the operator
self.mainOperator.Dataset[index].setValue(datasetInfo)
self._dirty = False
def deserializeFromHdf5(self, hdf5File, projectFilePath, headless=False):
# Check the overall file version
ilastikVersion = hdf5File["ilastikVersion"].value
# This is the v0.5 import deserializer. Don't work with 0.6 projects (or anything else).
if ilastikVersion != 0.5:
return
# The 'working directory' for the purpose of constructing absolute
# paths from relative paths is the project file's directory.
projectDir = os.path.split(projectFilePath)[0]
self.topLevelOperator.WorkingDirectory.setValue(projectDir)
# Access the top group and the info group
try:
#dataset = hdf5File["DataSets"]["dataItem00"]["data"]
dataDir = hdf5File["DataSets"]
except KeyError:
# If our group (or subgroup) doesn't exist, then make sure the operator is empty
self.topLevelOperator.DatasetGroup.resize(0)
return
self.topLevelOperator.DatasetGroup.resize(len(dataDir))
for index, (datasetDirName,
datasetDir) in enumerate(sorted(dataDir.items())):
datasetInfo = DatasetInfo()
# We'll set up the link to the dataset in the old project file,
# but we'll set the location to ProjectInternal so that it will
# be copied to the new file when the project is saved.
datasetInfo.location = DatasetInfo.Location.ProjectInternal
# Some older versions of ilastik 0.5 stored the data in tzyxc order.
# Some power-users can enable a command-line flag that tells us to
# transpose the data back to txyzc order when we import the old project.
default_axis_order = ilastik.utility.globals.ImportOptions.default_axis_order
if default_axis_order is not None:
import warnings
warnings.warn(
"Using a strange axis order to import ilastik 0.5 projects: {}"
.format(default_axis_order))
datasetInfo.axistags = vigra.defaultAxistags(
default_axis_order)
# Write to the 'private' members to avoid resetting the dataset id
totalDatasetPath = str(projectFilePath + '/DataSets/' +
datasetDirName + '/data')
datasetInfo._filePath = totalDatasetPath
datasetInfo._datasetId = datasetDirName # Use the old dataset name as the new dataset id
datasetInfo.nickname = "{} (imported from v0.5)".format(
datasetDirName)
# Give the new info to the operator
self.topLevelOperator.DatasetGroup[index][0].setValue(datasetInfo)
def deserializeFromHdf5(self, hdf5File, projectFilePath):
with Tracer(traceLogger):
# Check the overall file version
ilastikVersion = hdf5File["ilastikVersion"].value
# This is the v0.5 import deserializer. Don't work with 0.6 projects (or anything else).
if ilastikVersion != 0.5:
return
# The 'working directory' for the purpose of constructing absolute
# paths from relative paths is the project file's directory.
projectDir = os.path.split(projectFilePath)[0]
self.mainOperator.WorkingDirectory.setValue(projectDir)
# These project file inputs are required, but are not used because the data is treated as "external"
self.mainOperator.ProjectDataGroup.setValue('DataSets')
self.mainOperator.ProjectFile.setValue(hdf5File)
# Access the top group and the info group
try:
#dataset = hdf5File["DataSets"]["dataItem00"]["data"]
dataDir = hdf5File["DataSets"]
except KeyError:
# If our group (or subgroup) doesn't exist, then make sure the operator is empty
self.mainOperator.Dataset.resize(0)
return
self.mainOperator.Dataset.resize(len(dataDir))
for index, (datasetDirName,
datasetDir) in enumerate(sorted(dataDir.items())):
datasetInfo = DatasetInfo()
# Since we are importing from a 0.5 file, all datasets will be external
# to the project (pulled in from the old file as hdf5 datasets)
datasetInfo.location = DatasetInfo.Location.FileSystem
# Some older versions of ilastik 0.5 stored the data in tzyxc order.
# Some power-users can enable a command-line flag that tells us to
# transpose the data back to txyzc order when we import the old project.
if ilastik.utility.globals.ImportOptions.default_axis_order is not None:
datasetInfo.axisorder = ilastik.utility.globals.ImportOptions.default_axis_order
# Write to the 'private' members to avoid resetting the dataset id
totalDatasetPath = projectFilePath + '/DataSets/' + datasetDirName + '/data'
datasetInfo._filePath = str(totalDatasetPath)
datasetInfo._datasetId = datasetDirName # Use the old dataset name as the new dataset id
# Give the new info to the operator
self.mainOperator.Dataset[index].setValue(datasetInfo)
def _readDatasetInfo(self, infoGroup, localDataGroup, projectFilePath, headless):
# Unready datasets are represented with an empty group.
if len( infoGroup ) == 0:
return None, False
datasetInfo = DatasetInfo()
# Make a reverse-lookup of the location storage strings
LocationLookup = { v:k for k,v in self.LocationStrings.items() }
datasetInfo.location = LocationLookup[ str(infoGroup['location'].value) ]
# Write to the 'private' members to avoid resetting the dataset id
datasetInfo._filePath = infoGroup['filePath'].value
datasetInfo._datasetId = infoGroup['datasetId'].value
try:
datasetInfo.allowLabels = infoGroup['allowLabels'].value
except KeyError:
pass
try:
datasetInfo.drange = tuple( infoGroup['drange'].value )
except KeyError:
pass
try:
datasetInfo.nickname = infoGroup['nickname'].value
except KeyError:
datasetInfo.nickname = PathComponents(datasetInfo.filePath).filenameBase
try:
datasetInfo.fromstack = infoGroup['fromstack'].value
except KeyError:
# Guess based on the storage setting and original filepath
datasetInfo.fromstack = ( datasetInfo.location == DatasetInfo.Location.ProjectInternal
and ( ('?' in datasetInfo._filePath) or (os.path.pathsep in datasetInfo._filePath) ) )
try:
tags = vigra.AxisTags.fromJSON( infoGroup['axistags'].value )
datasetInfo.axistags = tags
except KeyError:
# Old projects just have an 'axisorder' field instead of full axistags
try:
axisorder = infoGroup['axisorder'].value
datasetInfo.axistags = vigra.defaultAxistags(axisorder)
except KeyError:
pass
try:
start, stop = map( tuple, infoGroup['subvolume_roi'].value )
datasetInfo.subvolume_roi = (start, stop)
except KeyError:
pass
# If the data is supposed to be in the project,
# check for it now.
if datasetInfo.location == DatasetInfo.Location.ProjectInternal:
if not datasetInfo.datasetId in localDataGroup.keys():
raise RuntimeError("Corrupt project file. Could not find data for " + infoGroup.name)
dirty = False
# If the data is supposed to exist outside the project, make sure it really does.
if datasetInfo.location == DatasetInfo.Location.FileSystem and not isUrl(datasetInfo.filePath):
pathData = PathComponents( datasetInfo.filePath, os.path.split(projectFilePath)[0])
filePath = pathData.externalPath
if not os.path.exists(filePath):
if headless:
raise RuntimeError("Could not find data at " + filePath)
filt = "Image files (" + ' '.join('*.' + x for x in OpDataSelection.SupportedExtensions) + ')'
newpath = self.repairFile(filePath, filt)
if pathData.internalPath is not None:
newpath += pathData.internalPath
datasetInfo._filePath = getPathVariants(newpath , os.path.split(projectFilePath)[0])[0]
dirty = True
return datasetInfo, dirty