def post_process_lane_export(self, lane_index):
# FIXME: This probably only works for the non-blockwise export slot.
# We should assert that the user isn't using the blockwise slot.
settings, selected_features = self.trackingApplet.topLevelOperator.getLane(lane_index).get_table_export_settings()
from lazyflow.utility import PathComponents, make_absolute, format_known_keys
if settings:
self.dataExportTrackingApplet.progressSignal.emit(-1)
raw_dataset_info = self.dataSelectionApplet.topLevelOperator.DatasetGroup[lane_index][0].value
project_path = self.shell.projectManager.currentProjectPath
project_dir = os.path.dirname(project_path)
dataset_dir = PathComponents(raw_dataset_info.filePath).externalDirectory
abs_dataset_dir = make_absolute(dataset_dir, cwd=project_dir)
known_keys = {}
known_keys['dataset_dir'] = abs_dataset_dir
nickname = raw_dataset_info.nickname.replace('*', '')
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(os.path.pathsep)[0]).fileNameBase
known_keys['nickname'] = nickname
# use partial formatting to fill in non-coordinate name fields
name_format = settings['file path']
partially_formatted_name = format_known_keys( name_format, known_keys )
settings['file path'] = partially_formatted_name
req = self.trackingApplet.topLevelOperator.getLane(lane_index).export_object_data(
lane_index,
# FIXME: Even in non-headless mode, we can't show the gui because we're running in a non-main thread.
# That's not a huge deal, because there's still a progress bar for the overall export.
show_gui=False)
req.wait()
self.dataExportTrackingApplet.progressSignal.emit(100)
def post_process_lane_export(self, lane_index):
# FIXME: This probably only works for the non-blockwise export slot.
# We should assert that the user isn't using the blockwise slot.
settings, selected_features = self.trackingApplet.topLevelOperator.getLane(lane_index).get_table_export_settings()
from lazyflow.utility import PathComponents, make_absolute, format_known_keys
if settings:
self.dataExportTrackingApplet.progressSignal.emit(-1)
raw_dataset_info = self.dataSelectionApplet.topLevelOperator.DatasetGroup[lane_index][0].value
project_path = self.shell.projectManager.currentProjectPath
project_dir = os.path.dirname(project_path)
dataset_dir = PathComponents(raw_dataset_info.filePath).externalDirectory
abs_dataset_dir = make_absolute(dataset_dir, cwd=project_dir)
known_keys = {}
known_keys['dataset_dir'] = abs_dataset_dir
nickname = raw_dataset_info.nickname.replace('*', '')
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(os.path.pathsep)[0]).fileNameBase
known_keys['nickname'] = nickname
# use partial formatting to fill in non-coordinate name fields
name_format = settings['file path']
partially_formatted_name = format_known_keys( name_format, known_keys )
settings['file path'] = partially_formatted_name
req = self.trackingApplet.topLevelOperator.getLane(lane_index).export_object_data(
lane_index,
# FIXME: Even in non-headless mode, we can't show the gui because we're running in a non-main thread.
# That's not a huge deal, because there's still a progress bar for the overall export.
show_gui=False)
req.wait()
self.dataExportTrackingApplet.progressSignal.emit(100)
def setupOutputs(self):
# FIXME: If RawData becomes unready() at the same time as RawDatasetInfo(), then
# we have no guarantees about which one will trigger setupOutputs() first.
# It is therefore possible for 'RawDatasetInfo' to appear ready() to us,
# even though it's upstream partner is UNready. We are about to get the
# unready() notification, but it will come too late to prevent our
# setupOutputs method from being called.
# Without proper graph setup transaction semantics, we have to use this
# hack as a workaround.
try:
rawInfo = self.RawDatasetInfo.value
except:
for oslot in list(self.outputs.values()):
if oslot.upstream_slot is None:
oslot.meta.NOTREADY = True
return
selection_index = self.InputSelection.value
if not self.Inputs[selection_index].ready():
for oslot in list(self.outputs.values()):
if oslot.upstream_slot is None:
oslot.meta.NOTREADY = True
return
self._opFormattedExport.Input.connect(self.Inputs[selection_index])
dataset_dir = str(rawInfo.default_output_dir)
abs_dataset_dir, _ = getPathVariants(dataset_dir, self.WorkingDirectory.value)
known_keys = {}
known_keys["dataset_dir"] = abs_dataset_dir
nickname = rawInfo.nickname.replace("*", "")
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(os.path.pathsep)[0]).fileNameBase
known_keys["nickname"] = nickname
result_types = self.SelectionNames.value
known_keys["result_type"] = result_types[selection_index]
self._opFormattedExport.TransactionSlot.disconnect()
# Blank the internal path while we manipulate the external path
# to avoid invalid intermediate states of ExportPath
self._opFormattedExport.OutputInternalPath.setValue("")
# use partial formatting to fill in non-coordinate name fields
name_format = self.OutputFilenameFormat.value
partially_formatted_name = format_known_keys(name_format, known_keys)
# Convert to absolute path before configuring the internal op
abs_path, _ = getPathVariants(partially_formatted_name, self.WorkingDirectory.value)
self._opFormattedExport.OutputFilenameFormat.setValue(abs_path)
# use partial formatting on the internal dataset name, too
internal_dataset_format = self.OutputInternalPath.value
partially_formatted_dataset_name = format_known_keys(internal_dataset_format, known_keys)
self._opFormattedExport.OutputInternalPath.setValue(partially_formatted_dataset_name)
# Re-connect to finish the 'transaction'
self._opFormattedExport.TransactionSlot.connect(self.TransactionSlot)
def format_path(self, path_template: str) -> str:
dataset_dir = str(self._dataset_info.default_output_dir)
abs_dataset_dir, _ = getPathVariants(dataset_dir, self._working_dir)
nickname = self._dataset_info.nickname.replace("*", "")
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(
os.path.pathsep)[0]).fileNameBase
known_keys = {"dataset_dir": abs_dataset_dir, "nickname": nickname}
if self._result_type:
known_keys["result_type"] = self._result_type
return format_known_keys(path_template, known_keys)
def getPartiallyFormattedName(self, lane_index, path_format_string):
''' Takes the format string for the output file, fills in the most important placeholders, and returns it '''
raw_dataset_info = self.dataSelectionApplet.topLevelOperator.DatasetGroup[lane_index][0].value
project_path = self.shell.projectManager.currentProjectPath
project_dir = os.path.dirname(project_path)
dataset_dir = PathComponents(raw_dataset_info.filePath).externalDirectory
abs_dataset_dir = make_absolute(dataset_dir, cwd=project_dir)
known_keys = {}
known_keys['dataset_dir'] = abs_dataset_dir
nickname = raw_dataset_info.nickname.replace('*', '')
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(os.path.pathsep)[0]).fileNameBase
known_keys['nickname'] = nickname
known_keys['result_type'] = self.dataExportTrackingApplet.topLevelOperator.SelectedPlugin._value
# use partial formatting to fill in non-coordinate name fields
partially_formatted_name = format_known_keys(path_format_string, known_keys)
return partially_formatted_name
def getPartiallyFormattedName(self, lane_index, path_format_string):
''' Takes the format string for the output file, fills in the most important placeholders, and returns it '''
raw_dataset_info = self.dataSelectionApplet.topLevelOperator.DatasetGroup[lane_index][0].value
project_path = self.shell.projectManager.currentProjectPath
project_dir = os.path.dirname(project_path)
dataset_dir = PathComponents(raw_dataset_info.filePath).externalDirectory
abs_dataset_dir = make_absolute(dataset_dir, cwd=project_dir)
known_keys = {}
known_keys['dataset_dir'] = abs_dataset_dir
nickname = raw_dataset_info.nickname.replace('*', '')
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(os.path.pathsep)[0]).fileNameBase
known_keys['nickname'] = nickname
known_keys['result_type'] = self.dataExportTrackingApplet.topLevelOperator.SelectedPlugin._value
# use partial formatting to fill in non-coordinate name fields
partially_formatted_name = format_known_keys(path_format_string, known_keys)
return partially_formatted_name
def post_process_lane_export(self, lane_index):
settings, selected_features = self.trackingApplet.topLevelOperator.getLane(
lane_index).get_table_export_settings()
if settings:
self.dataExportApplet.progressSignal.emit(0)
raw_dataset_info = self.dataSelectionApplet.topLevelOperator.DatasetGroup[
lane_index][0].value
project_path = self.shell.projectManager.currentProjectPath
project_dir = os.path.dirname(project_path)
dataset_dir = PathComponents(
raw_dataset_info.filePath).externalDirectory
abs_dataset_dir = make_absolute(dataset_dir, cwd=project_dir)
known_keys = {}
known_keys['dataset_dir'] = abs_dataset_dir
nickname = raw_dataset_info.nickname.replace('*', '')
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(
os.path.pathsep)[0]).fileNameBase
known_keys['nickname'] = nickname
# use partial formatting to fill in non-coordinate name fields
name_format = settings['file path']
partially_formatted_name = format_known_keys(
name_format, known_keys)
settings['file path'] = partially_formatted_name
req = self.trackingApplet.topLevelOperator.getLane(
lane_index
).export_object_data(
lane_index,
# FIXME: Even in non-headless mode, we can't show the gui because we're running in a non-main thread.
# That's not a huge deal, because there's still a progress bar for the overall export.
show_gui=False)
req.wait()
self.dataExportApplet.progressSignal.emit(100)
# Restore state of axis ranges
parameters = self.trackingApplet.topLevelOperator.Parameters.value
parameters['time_range'] = self.prev_time_range
parameters['x_range'] = self.prev_x_range
parameters['y_range'] = self.prev_y_range
parameters['z_range'] = self.prev_z_range
def getPartiallyFormattedName(self, lane_index: int, path_format_string: str) -> str:
''' Takes the format string for the output file, fills in the most important placeholders, and returns it '''
raw_dataset_info = self.topLevelOperator.RawDatasetInfo[lane_index].value
project_path = self.topLevelOperator.WorkingDirectory.value
dataset_dir = PathComponents(raw_dataset_info.filePath).externalDirectory
abs_dataset_dir = make_absolute(dataset_dir, cwd=project_path)
nickname = raw_dataset_info.nickname.replace('*', '')
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(os.path.pathsep)[0]).fileNameBase
known_keys = {
'dataset_dir': abs_dataset_dir,
'nickname': nickname,
'result_type': self.topLevelOperator.SelectedPlugin._value,
}
return format_known_keys(path_format_string, known_keys)
def post_process_lane_export(self, lane_index):
settings, selected_features = self.trackingApplet.topLevelOperator.getLane(lane_index).get_table_export_settings()
if settings:
self.dataExportApplet.progressSignal.emit(0)
raw_dataset_info = self.dataSelectionApplet.topLevelOperator.DatasetGroup[lane_index][0].value
project_path = self.shell.projectManager.currentProjectPath
project_dir = os.path.dirname(project_path)
dataset_dir = PathComponents(raw_dataset_info.filePath).externalDirectory
abs_dataset_dir = make_absolute(dataset_dir, cwd=project_dir)
known_keys = {}
known_keys['dataset_dir'] = abs_dataset_dir
nickname = raw_dataset_info.nickname.replace('*', '')
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(os.path.pathsep)[0]).fileNameBase
known_keys['nickname'] = nickname
# use partial formatting to fill in non-coordinate name fields
name_format = settings['file path']
partially_formatted_name = format_known_keys( name_format, known_keys )
settings['file path'] = partially_formatted_name
req = self.trackingApplet.topLevelOperator.getLane(lane_index).export_object_data(
lane_index,
# FIXME: Even in non-headless mode, we can't show the gui because we're running in a non-main thread.
# That's not a huge deal, because there's still a progress bar for the overall export.
show_gui=False)
req.wait()
self.dataExportApplet.progressSignal.emit(100)
# Restore state of axis ranges
parameters = self.trackingApplet.topLevelOperator.Parameters.value
parameters['time_range'] = self.prev_time_range
parameters['x_range'] = self.prev_x_range
parameters['y_range'] = self.prev_y_range
parameters['z_range'] = self.prev_z_range
def create_default_headless_dataset_info(cls, filepath):
"""
filepath may be a globstring or a full hdf5 path+dataset
"""
comp = PathComponents(filepath)
nickname = comp.filenameBase
# Remove globstring syntax.
if '*' in nickname:
nickname = nickname.replace('*', '')
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(os.path.pathsep)[0]).fileNameBase
info = DatasetInfo()
info.location = DatasetInfo.Location.FileSystem
info.nickname = nickname
info.filePath = filepath
# Convert all (non-url) paths to absolute
# (otherwise they are relative to the project file, which probably isn't what the user meant)
if not isUrl(filepath):
comp.externalPath = os.path.abspath(comp.externalPath)
info.filePath = comp.totalPath()
return info
def setupOutputs(self):
self.cleanupOnDiskView()
# FIXME: If RawData becomes unready() at the same time as RawDatasetInfo(), then
# we have no guarantees about which one will trigger setupOutputs() first.
# It is therefore possible for 'RawDatasetInfo' to appear ready() to us,
# even though it's upstream partner is UNready. We are about to get the
# unready() notification, but it will come too late to prevent our
# setupOutputs method from being called.
# Without proper graph setup transaction semantics, we have to use this
# hack as a workaround.
try:
rawInfo = self.RawDatasetInfo.value
except:
for oslot in self.outputs.values():
if oslot.partner is None:
oslot.meta.NOTREADY = True
return
selection_index = self.InputSelection.value
if not self.Inputs[selection_index].ready():
for oslot in self.outputs.values():
if oslot.partner is None:
oslot.meta.NOTREADY = True
return
self._opFormattedExport.Input.connect( self.Inputs[selection_index] )
dataset_dir = PathComponents(rawInfo.filePath).externalDirectory
abs_dataset_dir, _ = getPathVariants(dataset_dir, self.WorkingDirectory.value)
known_keys = {}
known_keys['dataset_dir'] = abs_dataset_dir
nickname = rawInfo.nickname.replace('*', '')
if '//' in nickname:
nickname = PathComponents(nickname.split('//')[0]).fileNameBase
known_keys['nickname'] = nickname
# Disconnect to open the 'transaction'
if self._opImageOnDiskProvider is not None:
self._opImageOnDiskProvider.TransactionSlot.disconnect()
self._opFormattedExport.TransactionSlot.disconnect()
# Blank the internal path while we manipulate the external path
# to avoid invalid intermediate states of ExportPath
self._opFormattedExport.OutputInternalPath.setValue( "" )
# use partial formatting to fill in non-coordinate name fields
name_format = self.OutputFilenameFormat.value
partially_formatted_name = format_known_keys( name_format, known_keys )
# Convert to absolute path before configuring the internal op
abs_path, _ = getPathVariants( partially_formatted_name, self.WorkingDirectory.value )
self._opFormattedExport.OutputFilenameFormat.setValue( abs_path )
# use partial formatting on the internal dataset name, too
internal_dataset_format = self.OutputInternalPath.value
partially_formatted_dataset_name = format_known_keys( internal_dataset_format, known_keys )
self._opFormattedExport.OutputInternalPath.setValue( partially_formatted_dataset_name )
# Re-connect to finish the 'transaction'
self._opFormattedExport.TransactionSlot.connect( self.TransactionSlot )
if self._opImageOnDiskProvider is not None:
self._opImageOnDiskProvider.TransactionSlot.connect( self.TransactionSlot )
self.setupOnDiskView()
def post_process_lane_export(self, lane_index, checkOverwriteFiles=False):
# FIXME: This probably only works for the non-blockwise export slot.
# We should assert that the user isn't using the blockwise slot.
# Plugin export if selected
logger.info("Export source is: " + self.dataExportTrackingApplet.
topLevelOperator.SelectedExportSource.value)
print "in post_process_lane_export"
if self.dataExportTrackingApplet.topLevelOperator.SelectedExportSource.value == OpTrackingBaseDataExport.PluginOnlyName:
logger.info("Export source plugin selected!")
selectedPlugin = self.dataExportTrackingApplet.topLevelOperator.SelectedPlugin.value
exportPluginInfo = pluginManager.getPluginByName(
selectedPlugin, category="TrackingExportFormats")
if exportPluginInfo is None:
logger.error("Could not find selected plugin %s" %
exportPluginInfo)
else:
exportPlugin = exportPluginInfo.plugin_object
logger.info("Exporting tracking result using %s" %
selectedPlugin)
name_format = self.dataExportTrackingApplet.topLevelOperator.getLane(
lane_index).OutputFilenameFormat.value
partially_formatted_name = self.getPartiallyFormattedName(
lane_index, name_format)
if exportPlugin.exportsToFile:
filename = partially_formatted_name
if os.path.basename(filename) == '':
filename = os.path.join(filename, 'pluginExport.txt')
else:
filename = os.path.dirname(partially_formatted_name)
if filename is None or len(str(filename)) == 0:
logger.error(
"Cannot export from plugin with empty output filename")
return
exportStatus = self.trackingApplet.topLevelOperator.getLane(
lane_index).exportPlugin(filename, exportPlugin,
checkOverwriteFiles)
if not exportStatus:
return False
logger.info("Export done")
return
# CSV Table export (only if plugin was not selected)
settings, selected_features = self.trackingApplet.topLevelOperator.getLane(
lane_index).get_table_export_settings()
from lazyflow.utility import PathComponents, make_absolute, format_known_keys
if settings:
self.dataExportTrackingApplet.progressSignal.emit(-1)
raw_dataset_info = self.dataSelectionApplet.topLevelOperator.DatasetGroup[
lane_index][0].value
project_path = self.shell.projectManager.currentProjectPath
project_dir = os.path.dirname(project_path)
dataset_dir = PathComponents(
raw_dataset_info.filePath).externalDirectory
abs_dataset_dir = make_absolute(dataset_dir, cwd=project_dir)
known_keys = {}
known_keys['dataset_dir'] = abs_dataset_dir
nickname = raw_dataset_info.nickname.replace('*', '')
if os.path.pathsep in nickname:
nickname = PathComponents(nickname.split(
os.path.pathsep)[0]).fileNameBase
known_keys['nickname'] = nickname
# use partial formatting to fill in non-coordinate name fields
name_format = settings['file path']
partially_formatted_name = format_known_keys(
name_format, known_keys)
settings['file path'] = partially_formatted_name
req = self.trackingApplet.topLevelOperator.getLane(
lane_index
).export_object_data(
lane_index,
# FIXME: Even in non-headless mode, we can't show the gui because we're running in a non-main thread.
# That's not a huge deal, because there's still a progress bar for the overall export.
show_gui=False)
req.wait()
self.dataExportTrackingApplet.progressSignal.emit(100)
