def generateBatchPredictions(workflow, batchInputPaths, batchExportDir, batchOutputSuffix, exportedDatasetName):
"""
Compute the predictions for each of the specified batch input files,
and export them to corresponding h5 files.
"""
batchInputPaths = convertStacksToH5(batchInputPaths)
batchInputInfos = []
for p in batchInputPaths:
info = DatasetInfo()
info.location = DatasetInfo.Location.FileSystem
# Convert all paths to absolute
# (otherwise they are relative to the project file, which probably isn't what the user meant)
comp = PathComponents(p)
comp.externalPath = os.path.abspath(comp.externalPath)
info.filePath = comp.totalPath()
batchInputInfos.append(info)
# Configure batch input operator
opBatchInputs = workflow.batchInputApplet.topLevelOperator
opBatchInputs.Dataset.setValues( batchInputInfos )
# Configure batch export operator
opBatchResults = workflow.batchResultsApplet.topLevelOperator
opBatchResults.ExportDirectory.setValue(batchExportDir)
opBatchResults.Format.setValue(ExportFormat.H5)
opBatchResults.Suffix.setValue(batchOutputSuffix)
opBatchResults.InternalPath.setValue(exportedDatasetName)
opBatchResults.SelectedSlices.setValue([30])
logger.info( "Exporting data to " + opBatchResults.OutputDataPath[0].value )
# Set up progress display handling (just logging for now)
currentProgress = [None]
def handleProgress(percentComplete):
if currentProgress[0] != percentComplete:
currentProgress[0] = percentComplete
logger.info("Batch job: {}% complete.".format(percentComplete))
progressSignal = opBatchResults.ProgressSignal[0].value
progressSignal.subscribe( handleProgress )
# Make it happen!
result = opBatchResults.ExportResult[0].value
return result
def generateBatchPredictions(workflow, batchInputPaths, batchExportDir, batchOutputSuffix, exportedDatasetName, stackVolumeCacheDir):
"""
Compute the predictions for each of the specified batch input files,
and export them to corresponding h5 files.
"""
originalBatchInputPaths = list(batchInputPaths)
batchInputPaths = convertStacksToH5(batchInputPaths, stackVolumeCacheDir)
batchInputInfos = []
for p in batchInputPaths:
info = DatasetInfo()
info.location = DatasetInfo.Location.FileSystem
# Convert all paths to absolute
# (otherwise they are relative to the project file, which probably isn't what the user meant)
comp = PathComponents(p)
comp.externalPath = os.path.abspath(comp.externalPath)
info.filePath = comp.totalPath()
batchInputInfos.append(info)
# Also convert the export dir to absolute (for the same reason)
if batchExportDir != '':
batchExportDir = os.path.abspath( batchExportDir )
# Configure batch input operator
opBatchInputs = workflow.batchInputApplet.topLevelOperator
opBatchInputs.Dataset.setValues( batchInputInfos )
# Configure batch export operator
opBatchResults = workflow.batchResultsApplet.topLevelOperator
# By default, the output files from the batch export operator
# are named using the input file name.
# If we converted any stacks to hdf5, then the user won't recognize the input file name.
# Let's override the output file name using the *original* input file names.
outputFileNameBases = []
for origPath in originalBatchInputPaths:
outputFileNameBases.append( origPath.replace('*', 'STACKED') )
opBatchResults.OutputFileNameBase.setValues( outputFileNameBases )
opBatchResults.ExportDirectory.setValue(batchExportDir)
opBatchResults.Format.setValue(ExportFormat.H5)
opBatchResults.Suffix.setValue(batchOutputSuffix)
opBatchResults.InternalPath.setValue(exportedDatasetName)
logger.info( "Exporting data to " + opBatchResults.OutputDataPath[0].value )
# Set up progress display handling (just logging for now)
currentProgress = [None]
def handleProgress(percentComplete):
if currentProgress[0] != percentComplete:
currentProgress[0] = percentComplete
logger.info("Batch job: {}% complete.".format(percentComplete))
progressSignal = opBatchResults.ProgressSignal[0].value
progressSignal.subscribe( handleProgress )
# Make it happen!
result = opBatchResults.ExportResult[0].value
return result
def generateBatchPredictions(workflow, batchInputPaths, batchExportDir,
batchOutputSuffix, exportedDatasetName,
stackVolumeCacheDir):
"""
Compute the predictions for each of the specified batch input files,
and export them to corresponding h5 files.
"""
originalBatchInputPaths = list(batchInputPaths)
batchInputPaths = convertStacksToH5(batchInputPaths, stackVolumeCacheDir)
batchInputInfos = []
for p in batchInputPaths:
info = DatasetInfo()
info.location = DatasetInfo.Location.FileSystem
# Convert all paths to absolute
# (otherwise they are relative to the project file, which probably isn't what the user meant)
comp = PathComponents(p)
comp.externalPath = os.path.abspath(comp.externalPath)
info.filePath = comp.totalPath()
batchInputInfos.append(info)
# Also convert the export dir to absolute (for the same reason)
if batchExportDir != '':
batchExportDir = os.path.abspath(batchExportDir)
# Configure batch input operator
opBatchInputs = workflow.batchInputApplet.topLevelOperator
opBatchInputs.DatasetGroup.resize(len(batchInputInfos))
for info, multislot in zip(batchInputInfos, opBatchInputs.DatasetGroup):
# FIXME: This assumes that the workflow has exactly one dataset role.
multislot[0].setValue(info)
# Configure batch export operator
opBatchResults = workflow.batchResultsApplet.topLevelOperator
# By default, the output files from the batch export operator
# are named using the input file name.
# If we converted any stacks to hdf5, then the user won't recognize the input file name.
# Let's override the output file name using the *original* input file names.
outputFileNameBases = []
for origPath in originalBatchInputPaths:
outputFileNameBases.append(origPath.replace('*', 'STACKED'))
opBatchResults.OutputFileNameBase.setValues(outputFileNameBases)
opBatchResults.ExportDirectory.setValue(batchExportDir)
opBatchResults.Format.setValue(ExportFormat.H5)
opBatchResults.Suffix.setValue(batchOutputSuffix)
opBatchResults.InternalPath.setValue(exportedDatasetName)
logger.info("Exporting data to " + opBatchResults.OutputDataPath[0].value)
# Set up progress display handling (just logging for now)
currentProgress = [None]
def handleProgress(percentComplete):
if currentProgress[0] != percentComplete:
currentProgress[0] = percentComplete
logger.info("Batch job: {}% complete.".format(percentComplete))
progressSignal = opBatchResults.ProgressSignal[0].value
progressSignal.subscribe(handleProgress)
# Make it happen!
result = opBatchResults.ExportResult[0].value
return result
