def openProjectFile(cls, projectFilePath):
"""
Class method.
Attempt to open the given path to an existing project file.
If it doesn't exist, raise a ``ProjectManager.FileMissingError``.
If its version is outdated, raise a ``ProjectManager.ProjectVersionError.``
"""
logger.info("Opening Project: " + projectFilePath)
if not os.path.exists(projectFilePath):
raise ProjectManager.FileMissingError()
# Open the file as an HDF5 file
try:
hdf5File = h5py.File(projectFilePath)
readOnly = False
except IOError:
# Maybe the project is read-only
hdf5File = h5py.File(projectFilePath, 'r')
readOnly = True
projectVersion = "0.5"
if "ilastikVersion" in hdf5File.keys():
projectVersion = hdf5File["ilastikVersion"].value
# FIXME: version comparison
if not isVersionCompatible(projectVersion):
# Must use _importProject() for old project files.
raise ProjectManager.ProjectVersionError(projectVersion, ilastik.__version__)
return (hdf5File, readOnly)
def deserializeFromHdf5(self, hdf5File, projectFilePath, headless=False):
"""Read the the current applet state from the given hdf5File
handle, which should already be open.
Subclasses should **not** override this method. Instead,
subclasses override the 'private' version,
*_deserializeFromHdf5*
:param hdf5File: An h5py.File handle to the project file,
which should already be open
:param projectFilePath: The path to the given file handle.
(Most serializers do not use this parameter.)
:param headless: Are we called in headless mode?
(in headless mode corrupted files cannot be fixed via the GUI)
"""
# Check the overall file version
fileVersion = hdf5File["ilastikVersion"].value
# Make sure we can find our way around the project tree
if not isVersionCompatible(fileVersion):
return
self.progressSignal.emit(0)
# If the top group isn't there, call initWithoutTopGroup
try:
topGroup = hdf5File[self.topGroupName]
groupVersion = topGroup['StorageVersion'][()]
except KeyError:
topGroup = None
groupVersion = None
try:
if topGroup is not None:
inc = self.progressIncrement()
for ss in self.serialSlots:
ss.deserialize(topGroup)
self.progressSignal.emit(inc)
# Call the subclass to do remaining work
if self.caresOfHeadless:
self._deserializeFromHdf5(topGroup, groupVersion, hdf5File,
projectFilePath, headless)
else:
self._deserializeFromHdf5(topGroup, groupVersion, hdf5File,
projectFilePath)
else:
self.initWithoutTopGroup(hdf5File, projectFilePath)
finally:
self.progressSignal.emit(100)
def deserializeFromHdf5(self, hdf5File, projectFilePath, headless = False):
"""Read the the current applet state from the given hdf5File
handle, which should already be open.
Subclasses should **not** override this method. Instead,
subclasses override the 'private' version,
*_deserializeFromHdf5*
:param hdf5File: An h5py.File handle to the project file,
which should already be open
:param projectFilePath: The path to the given file handle.
(Most serializers do not use this parameter.)
:param headless: Are we called in headless mode?
(in headless mode corrupted files cannot be fixed via the GUI)
"""
# Check the overall file version
fileVersion = hdf5File["ilastikVersion"].value
# Make sure we can find our way around the project tree
if not isVersionCompatible(fileVersion):
return
self.progressSignal.emit(0)
# If the top group isn't there, call initWithoutTopGroup
try:
topGroup = hdf5File[self.topGroupName]
groupVersion = topGroup['StorageVersion'][()]
except KeyError:
topGroup = None
groupVersion = None
try:
if topGroup is not None:
inc = self.progressIncrement()
for ss in self.serialSlots:
ss.deserialize(topGroup)
self.progressSignal.emit(inc)
# Call the subclass to do remaining work
if self.caresOfHeadless:
self._deserializeFromHdf5(topGroup, groupVersion, hdf5File, projectFilePath, headless)
else:
self._deserializeFromHdf5(topGroup, groupVersion, hdf5File, projectFilePath)
else:
self.initWithoutTopGroup(hdf5File, projectFilePath)
finally:
self.progressSignal.emit(100)
def openProjectFile(cls, projectFilePath, forceReadOnly=False):
"""
Class method.
Attempt to open the given path to an existing project file.
If it doesn't exist, raise a ``ProjectManager.FileMissingError``.
If its version is outdated, raise a ``ProjectManager.ProjectVersionError.``
"""
projectFilePath = os.path.expanduser(projectFilePath)
logger.info("Opening Project: " + projectFilePath)
if not os.path.exists(projectFilePath):
raise ProjectManager.FileMissingError(projectFilePath)
# Open the file as an HDF5 file
try:
if forceReadOnly:
mode = "r"
else:
mode = "r+"
hdf5File = h5py.File(projectFilePath, mode)
except IOError:
# Maybe we tried 'r+', but the project is read-only
hdf5File = h5py.File(projectFilePath, "r")
readOnly = hdf5File.mode == "r"
projectVersion = "0.5"
if "ilastikVersion" in list(hdf5File.keys()):
projectVersion = hdf5File["ilastikVersion"].value.decode("utf-8")
# FIXME: version comparison
if not isVersionCompatible(projectVersion):
# Must use _importProject() for old project files.
raise ProjectManager.ProjectVersionError(projectVersion,
ilastik.__version__)
workflow_class = None
if "workflowName" in list(hdf5File.keys()):
# if workflow is found in file, take it
workflowName = hdf5File["workflowName"].value.decode("utf-8")
workflow_class = getWorkflowFromName(workflowName)
return (hdf5File, workflow_class, readOnly)
def openProjectFile(cls, projectFilePath, forceReadOnly=False):
"""
Class method.
Attempt to open the given path to an existing project file.
If it doesn't exist, raise a ``ProjectManager.FileMissingError``.
If its version is outdated, raise a ``ProjectManager.ProjectVersionError.``
"""
projectFilePath = os.path.expanduser(projectFilePath)
logger.info("Opening Project: " + projectFilePath)
if not os.path.exists(projectFilePath):
raise ProjectManager.FileMissingError(projectFilePath)
# Open the file as an HDF5 file
try:
if forceReadOnly:
mode = 'r'
else:
mode = 'r+'
hdf5File = h5py.File(projectFilePath, mode)
except IOError:
# Maybe we tried 'r+', but the project is read-only
hdf5File = h5py.File(projectFilePath, 'r')
readOnly = (hdf5File.mode == 'r')
projectVersion = "0.5"
if "ilastikVersion" in hdf5File.keys():
projectVersion = hdf5File["ilastikVersion"].value
# FIXME: version comparison
if not isVersionCompatible(projectVersion):
# Must use _importProject() for old project files.
raise ProjectManager.ProjectVersionError(projectVersion, ilastik.__version__)
workflow_class = None
if "workflowName" in hdf5File.keys():
#if workflow is found in file, take it
workflowName = hdf5File["workflowName"].value
workflow_class = getWorkflowFromName(workflowName)
return (hdf5File, workflow_class, readOnly)
def serializeToHdf5(self, hdf5File, projectFilePath):
"""Serialize the current applet state to the given hdf5 file.
Subclasses should **not** override this method. Instead,
subclasses override the 'private' version, *_serializetoHdf5*
:param hdf5File: An h5py.File handle to the project file,
which should already be open
:param projectFilePath: The path to the given file handle.
(Most serializers do not use this parameter.)
"""
# Check the overall file version
fileVersion = hdf5File["ilastikVersion"].value
# Make sure we can find our way around the project tree
if not isVersionCompatible(fileVersion):
return
topGroup = getOrCreateGroup(hdf5File, self.topGroupName)
progress = 0
self.progressSignal.emit(progress)
# Set the version
key = 'StorageVersion'
deleteIfPresent(topGroup, key)
topGroup.create_dataset(key, data=self.version)
try:
inc = self.progressIncrement(topGroup)
for ss in self.serialSlots:
ss.serialize(topGroup)
progress += inc
self.progressSignal.emit(progress)
# Call the subclass to do remaining work, if any
self._serializeToHdf5(topGroup, hdf5File, projectFilePath)
finally:
self.progressSignal.emit(100)
def serializeToHdf5(self, hdf5File, projectFilePath):
"""Serialize the current applet state to the given hdf5 file.
Subclasses should **not** override this method. Instead,
subclasses override the 'private' version, *_serializetoHdf5*
:param hdf5File: An h5py.File handle to the project file,
which should already be open
:param projectFilePath: The path to the given file handle.
(Most serializers do not use this parameter.)
"""
# Check the overall file version
fileVersion = hdf5File["ilastikVersion"].value
# Make sure we can find our way around the project tree
if not isVersionCompatible(fileVersion):
return
topGroup = getOrCreateGroup(hdf5File, self.topGroupName)
progress = 0
self.progressSignal.emit(progress)
# Set the version
key = 'StorageVersion'
deleteIfPresent(topGroup, key)
topGroup.create_dataset(key, data=self.version)
try:
inc = self.progressIncrement(topGroup)
for ss in self.serialSlots:
ss.serialize(topGroup)
progress += inc
self.progressSignal.emit(progress)
# Call the subclass to do remaining work, if any
self._serializeToHdf5(topGroup, hdf5File, projectFilePath)
finally:
self.progressSignal.emit(100)
def openProjectFile(cls, projectFilePath):
"""
Class method.
Attempt to open the given path to an existing project file.
If it doesn't exist, raise a ``ProjectManager.FileMissingError``.
If its version is outdated, raise a ``ProjectManager.ProjectVersionError.``
"""
logger.info("Opening Project: " + projectFilePath)
if not os.path.exists(projectFilePath):
raise ProjectManager.FileMissingError()
# Open the file as an HDF5 file
try:
hdf5File = h5py.File(projectFilePath)
readOnly = False
except IOError:
# Maybe the project is read-only
hdf5File = h5py.File(projectFilePath, 'r')
readOnly = True
projectVersion = "0.5"
if "ilastikVersion" in hdf5File.keys():
projectVersion = hdf5File["ilastikVersion"].value
# FIXME: version comparison
if not isVersionCompatible(projectVersion):
# Must use _importProject() for old project files.
raise ProjectManager.ProjectVersionError(projectVersion,
ilastik.__version__)
workflow_class = None
if "workflowName" in hdf5File.keys():
#if workflow is found in file, take it
workflowName = hdf5File["workflowName"].value
workflow_class = getWorkflowFromName(workflowName)
return (hdf5File, workflow_class, readOnly)
