def _createDatasetInfo(self, roleIndex, filePath, roi):
"""
Create a DatasetInfo object for the given filePath and roi.
roi may be None, in which case it is ignored.
"""
datasetInfo = DatasetInfo()
if roi is not None:
datasetInfo.subvolume_roi = roi
cwd = self.topLevelOperator.WorkingDirectory.value
absPath, relPath = getPathVariants(filePath, cwd)
# Relative by default, unless the file is in a totally different tree from the working directory.
if relPath is not None and len(os.path.commonprefix([cwd, absPath
])) > 1:
datasetInfo.filePath = relPath
else:
datasetInfo.filePath = absPath
datasetInfo.nickname = PathComponents(absPath).filenameBase
h5Exts = ['.ilp', '.h5', '.hdf5']
if os.path.splitext(datasetInfo.filePath)[1] in h5Exts:
datasetNames = self.getPossibleInternalPaths(absPath)
if len(datasetNames) == 0:
raise RuntimeError("HDF5 file %s has no image datasets" %
datasetInfo.filePath)
elif len(datasetNames) == 1:
datasetInfo.filePath += str(datasetNames[0])
else:
# If exactly one of the file's datasets matches a user's previous choice, use it.
if roleIndex not in self._default_h5_volumes:
self._default_h5_volumes[roleIndex] = set()
previous_selections = self._default_h5_volumes[roleIndex]
possible_auto_selections = previous_selections.intersection(
datasetNames)
if len(possible_auto_selections) == 1:
datasetInfo.filePath += str(
list(possible_auto_selections)[0])
else:
# Ask the user which dataset to choose
dlg = H5VolumeSelectionDlg(datasetNames, self)
if dlg.exec_() == QDialog.Accepted:
selected_index = dlg.combo.currentIndex()
selected_dataset = str(datasetNames[selected_index])
datasetInfo.filePath += selected_dataset
self._default_h5_volumes[roleIndex].add(
selected_dataset)
else:
raise DataSelectionGui.UserCancelledError()
# Allow labels by default if this gui isn't being used for batch data.
datasetInfo.allowLabels = (self.guiMode == GuiMode.Normal)
return datasetInfo
def _createDatasetInfo(self, roleIndex, filePath, roi):
"""
Create a DatasetInfo object for the given filePath and roi.
roi may be None, in which case it is ignored.
"""
datasetInfo = DatasetInfo()
if roi is not None:
datasetInfo.subvolume_roi = roi
cwd = self.topLevelOperator.WorkingDirectory.value
absPath, relPath = getPathVariants(filePath, cwd)
# Relative by default, unless the file is in a totally different tree from the working directory.
if relPath is not None and len(os.path.commonprefix([cwd, absPath])) > 1:
datasetInfo.filePath = relPath
else:
datasetInfo.filePath = absPath
datasetInfo.nickname = PathComponents(absPath).filenameBase
h5Exts = ['.ilp', '.h5', '.hdf5']
if os.path.splitext(datasetInfo.filePath)[1] in h5Exts:
datasetNames = self.getPossibleInternalPaths( absPath )
if len(datasetNames) == 0:
raise RuntimeError("HDF5 file %s has no image datasets" % datasetInfo.filePath)
elif len(datasetNames) == 1:
datasetInfo.filePath += str(datasetNames[0])
else:
# If exactly one of the file's datasets matches a user's previous choice, use it.
if roleIndex not in self._default_h5_volumes:
self._default_h5_volumes[roleIndex] = set()
previous_selections = self._default_h5_volumes[roleIndex]
possible_auto_selections = previous_selections.intersection(datasetNames)
if len(possible_auto_selections) == 1:
datasetInfo.filePath += str(list(possible_auto_selections)[0])
else:
# Ask the user which dataset to choose
dlg = H5VolumeSelectionDlg(datasetNames, self)
if dlg.exec_() == QDialog.Accepted:
selected_index = dlg.combo.currentIndex()
selected_dataset = str(datasetNames[selected_index])
datasetInfo.filePath += selected_dataset
self._default_h5_volumes[roleIndex].add( selected_dataset )
else:
raise DataSelectionGui.UserCancelledError()
# Allow labels by default if this gui isn't being used for batch data.
datasetInfo.allowLabels = ( self.guiMode == GuiMode.Normal )
return 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
def addFileNames(self, fileNames, roleIndex, startingLane=None, rois=None):
"""
Add the given filenames to both the GUI table and the top-level operator inputs.
If startingLane is None, the filenames will be *appended* to the role's list of files.
If rois is provided, it must be a list of (start,stop) tuples (one for each fileName)
"""
if rois is not None:
assert len(rois) == len(fileNames)
infos = []
if startingLane is None or startingLane == -1:
startingLane = len(self.topLevelOperator.DatasetGroup)
endingLane = startingLane+len(fileNames)-1
else:
assert startingLane < len(self.topLevelOperator.DatasetGroup)
max_files = len(self.topLevelOperator.DatasetGroup) - \
startingLane
if len(fileNames) > max_files:
msg = "You selected {num_selected} files for {num_slots} "\
"slots. To add new files use the 'Add new...' option "\
"in the context menu or the button in the last row."\
.format(num_selected=len(fileNames),
num_slots=max_files)
QMessageBox.critical( self, "Too many files", msg )
return
endingLane = min(startingLane+len(fileNames)-1,
len(self.topLevelOperator.DatasetGroup))
if self._max_lanes and endingLane >= self._max_lanes:
msg = "You may not add more than {} file(s) to this workflow. Please try again.".format( self._max_lanes )
QMessageBox.critical( self, "Too many files", msg )
return
# Assign values to the new inputs we just allocated.
# The GUI will be updated by callbacks that are listening to slot changes
for file_index, filePath in enumerate(fileNames):
datasetInfo = DatasetInfo()
if rois is not None:
datasetInfo.subvolume_roi = rois[file_index]
cwd = self.topLevelOperator.WorkingDirectory.value
absPath, relPath = getPathVariants(filePath, cwd)
# Relative by default, unless the file is in a totally different tree from the working directory.
if relPath is not None and len(os.path.commonprefix([cwd, absPath])) > 1:
datasetInfo.filePath = relPath
else:
datasetInfo.filePath = absPath
datasetInfo.nickname = PathComponents(absPath).filenameBase
h5Exts = ['.ilp', '.h5', '.hdf5']
if os.path.splitext(datasetInfo.filePath)[1] in h5Exts:
datasetNames = self.getPossibleInternalPaths( absPath )
if len(datasetNames) > 0:
datasetInfo.filePath += str(datasetNames[0])
else:
raise RuntimeError("HDF5 file %s has no image datasets" % datasetInfo.filePath)
# Allow labels by default if this gui isn't being used for batch data.
datasetInfo.allowLabels = ( self.guiMode == GuiMode.Normal )
infos.append(datasetInfo)
# if no exception was thrown, set up the operator now
opTop = self.topLevelOperator
originalSize = len(opTop.DatasetGroup)
if len( opTop.DatasetGroup ) < endingLane+1:
opTop.DatasetGroup.resize( endingLane+1 )
loaded_all = True
for laneIndex, info in zip(range(startingLane, endingLane+1), infos):
try:
self.topLevelOperator.DatasetGroup[laneIndex][roleIndex].setValue( info )
except DatasetConstraintError as ex:
return_val = [False]
# Give the user a chance to fix the problem
self.handleDatasetConstraintError(info, info.filePath, ex, roleIndex, laneIndex, return_val)
if not return_val[0]:
# Not successfully repaired. Roll back the changes and give up.
opTop.DatasetGroup.resize( originalSize )
loaded_all = False
break
except OpDataSelection.InvalidDimensionalityError as ex:
opTop.DatasetGroup.resize( originalSize )
QMessageBox.critical( self, "Dataset has different dimensionality", ex.message )
loaded_all = False
break
except Exception as ex:
loaded_all = False
msg = "Wasn't able to load your dataset into the workflow. See error log for details."
log_exception( logger, msg )
QMessageBox.critical( self, "Dataset Load Error", msg )
opTop.DatasetGroup.resize( originalSize )
# If we succeeded in adding all images, show the first one.
if loaded_all:
self.showDataset(startingLane, roleIndex)
# Notify the workflow that something that could affect applet readyness has occurred.
self.parentApplet.appletStateUpdateRequested.emit()
self.updateInternalPathVisiblity()