def do_export(self, settings, selected_features, progress_slot):
"""
Implements ExportOperator.do_export(settings, selected_features, progress_slot
Most likely called from ExportOperator.export_object_data
:param settings: the settings for the exporter, see
:param selected_features:
:param progress_slot:
:return:
"""
from ilastik.utility.exportFile import objects_per_frame, ExportFile, ilastik_ids, Mode, Default, \
flatten_dict, division_flatten_dict
selected_features = list(selected_features)
with_divisions = self.Parameters.value["withDivisions"] if self.Parameters.ready() else False
obj_count = list(objects_per_frame(self.LabelImage))
track_ids, extra_track_ids, divisions = self.export_track_ids()
self._setLabel2Color()
lineage = flatten_dict(self.label2color, obj_count)
multi_move_max = self.Parameters.value["maxObj"] if self.Parameters.ready() else 2
t_range = self.Parameters.value["time_range"] if self.Parameters.ready() else (0, 0)
ids = ilastik_ids(obj_count)
export_file = ExportFile(settings["file path"])
export_file.ExportProgress.subscribe(progress_slot)
export_file.InsertionProgress.subscribe(progress_slot)
export_file.add_columns("table", range(sum(obj_count)), Mode.List, Default.KnimeId)
export_file.add_columns("table", list(ids), Mode.List, Default.IlastikId)
export_file.add_columns("table", lineage, Mode.List, Default.Lineage)
export_file.add_columns("table", track_ids, Mode.IlastikTrackingTable,
{"max": multi_move_max, "counts": obj_count, "extra ids": extra_track_ids,
"range": t_range})
if with_divisions:
object_feature_slot = self.ObjectFeaturesWithDivFeatures
else:
object_feature_slot = self.ObjectFeatures
export_file.add_columns("table", object_feature_slot, Mode.IlastikFeatureTable,
{"selection": selected_features})
if with_divisions:
if divisions:
div_lineage = division_flatten_dict(divisions, self.label2color)
zips = zip(*divisions)
divisions = zip(zips[0], div_lineage, *zips[1:])
export_file.add_columns("divisions", divisions, Mode.List, Default.DivisionNames)
else:
logger.debug("No divisions occurred. Division Table will not be exported!")
if settings["file type"] == "h5":
export_file.add_rois(Default.LabelRoiPath, self.LabelImage, "table", settings["margin"], "labeling")
if settings["include raw"]:
export_file.add_image(Default.RawPath, self.RawImage)
else:
export_file.add_rois(Default.RawRoiPath, self.RawImage, "table", settings["margin"])
export_file.write_all(settings["file type"], settings["compression"])
export_file.ExportProgress.unsubscribe(progress_slot)
export_file.InsertionProgress.unsubscribe(progress_slot)
def do_export(self, settings, selected_features, progress_slot):
"""
Implements ExportOperator.do_export(settings, selected_features, progress_slot
Most likely called from ExportOperator.export_object_data
:param settings: the settings for the exporter, see
:param selected_features:
:param progress_slot:
:return:
"""
from ilastik.utility.exportFile import objects_per_frame, ExportFile, ilastik_ids, Mode, Default, \
flatten_dict, division_flatten_dict
obj_count = list(objects_per_frame(self.LabelImage))
track_ids, extra_track_ids, divisions = self.export_track_ids()
self._setLabel2Color()
lineage = flatten_dict(self.label2color, obj_count)
multi_move_max = self.Parameters.value["maxObj"] if self.Parameters.ready() else 2
multi_move_max = max(2, multi_move_max)
t_range = self.Parameters.value["time_range"] if self.Parameters.ready() else (0, 0)
ids = ilastik_ids(obj_count)
export_file = ExportFile(settings["file path"])
export_file.ExportProgress.subscribe(progress_slot)
export_file.InsertionProgress.subscribe(progress_slot)
export_file.add_columns("table", range(sum(obj_count)), Mode.List, Default.KnimeId)
export_file.add_columns("table", list(ids), Mode.List, Default.IlastikId)
export_file.add_columns("table", lineage, Mode.List, Default.Lineage)
export_file.add_columns("table", track_ids, Mode.IlastikTrackingTable,
{"max": multi_move_max, "counts": obj_count, "extra ids": extra_track_ids,
"range": t_range})
export_file.add_columns("table", self.ObjectFeatures, Mode.IlastikFeatureTable,
{"selection": selected_features})
if self.Parameters.value["withDivisions"] if self.Parameters.ready() else False:
try:
div_lineage = division_flatten_dict(divisions, self.label2color)
zips = zip(*divisions)
divisions = zip(zips[0], div_lineage, *zips[1:])
export_file.add_columns("divisions", divisions, Mode.List, Default.DivisionNames)
except Exception as e:
if hasattr(progress_slot, "safe_popup"):
progress_slot.safe_popup_noclose("warning", "Warning", "Cannot export divisions.\nContinuing ...",
e)
else:
print "\nWarning, Cannot export divisions"
if settings["file type"] == "h5":
export_file.add_rois(Default.LabelRoiPath, self.LabelImage, "table", settings["margin"], "labeling")
if settings["include raw"]:
export_file.add_image(Default.RawPath, self.RawImage)
else:
export_file.add_rois(Default.RawRoiPath, self.RawImage, "table", settings["margin"])
export_file.write_all(settings["file type"], settings["compression"])
export_file.ExportProgress.unsubscribe(progress_slot)
export_file.InsertionProgress.unsubscribe(progress_slot)
def _do_export_impl(self, settings, selected_features, progress_slot, object_feature_slot, label_image_slot, lane_index, filename_suffix=""):
from ilastik.utility.exportFile import objects_per_frame, ExportFile, ilastik_ids, Mode, Default, \
flatten_dict, division_flatten_dict
selected_features = list(selected_features)
with_divisions = self.Parameters.value["withDivisions"] if self.Parameters.ready() else False
obj_count = list(objects_per_frame(label_image_slot))
track_ids, extra_track_ids, divisions = self.export_track_ids()
self._setLabel2Color()
lineage = flatten_dict(self.label2color, obj_count)
multi_move_max = self.Parameters.value["maxObj"] if self.Parameters.ready() else 2
t_range = self.Parameters.value["time_range"] if self.Parameters.ready() else (0, 0)
ids = ilastik_ids(obj_count)
file_path = settings["file path"]
if filename_suffix:
path, ext = os.path.splitext(file_path)
file_path = path + "-" + filename_suffix + ext
export_file = ExportFile(file_path)
export_file.ExportProgress.subscribe(progress_slot)
export_file.InsertionProgress.subscribe(progress_slot)
export_file.add_columns("table", range(sum(obj_count)), Mode.List, Default.KnimeId)
export_file.add_columns("table", list(ids), Mode.List, Default.IlastikId)
export_file.add_columns("table", lineage, Mode.List, Default.Lineage)
export_file.add_columns("table", track_ids, Mode.IlastikTrackingTable,
{"max": multi_move_max, "counts": obj_count, "extra ids": extra_track_ids,
"range": t_range})
export_file.add_columns("table", object_feature_slot, Mode.IlastikFeatureTable,
{"selection": selected_features})
if with_divisions:
if divisions:
div_lineage = division_flatten_dict(divisions, self.label2color)
zips = zip(*divisions)
divisions = zip(zips[0], div_lineage, *zips[1:])
export_file.add_columns("divisions", divisions, Mode.List, Default.DivisionNames)
else:
logger.debug("No divisions occurred. Division Table will not be exported!")
if settings["file type"] == "h5":
export_file.add_rois(Default.LabelRoiPath, label_image_slot, "table", settings["margin"], "labeling")
if settings["include raw"]:
export_file.add_image(Default.RawPath, self.RawImage)
else:
export_file.add_rois(Default.RawRoiPath, self.RawImage, "table", settings["margin"])
export_file.write_all(settings["file type"], settings["compression"])
export_file.ExportProgress.unsubscribe(progress_slot)
export_file.InsertionProgress.unsubscribe(progress_slot)
def _do_export_impl(self, settings, selected_features, progress_slot, object_feature_slot, label_image_slot, lane_index, filename_suffix=""):
from ilastik.utility.exportFile import objects_per_frame, ExportFile, ilastik_ids, Mode, Default, \
flatten_dict, division_flatten_dict
selected_features = list(selected_features)
with_divisions = self.Parameters.value["withDivisions"] if self.Parameters.ready() else False
obj_count = list(objects_per_frame(label_image_slot))
track_ids, extra_track_ids, divisions = self.export_track_ids()
self._setLabel2Color()
lineage = flatten_dict(self.label2color, obj_count)
multi_move_max = self.Parameters.value["maxObj"] if self.Parameters.ready() else 2
t_range = self.Parameters.value["time_range"] if self.Parameters.ready() else (0, 0)
ids = ilastik_ids(obj_count)
file_path = settings["file path"]
if filename_suffix:
path, ext = os.path.splitext(file_path)
file_path = path + "-" + filename_suffix + ext
export_file = ExportFile(file_path)
export_file.ExportProgress.subscribe(progress_slot)
export_file.InsertionProgress.subscribe(progress_slot)
export_file.add_columns("table", range(sum(obj_count)), Mode.List, Default.KnimeId)
export_file.add_columns("table", list(ids), Mode.List, Default.IlastikId)
export_file.add_columns("table", lineage, Mode.List, Default.Lineage)
export_file.add_columns("table", track_ids, Mode.IlastikTrackingTable,
{"max": multi_move_max, "counts": obj_count, "extra ids": extra_track_ids,
"range": t_range})
export_file.add_columns("table", object_feature_slot, Mode.IlastikFeatureTable,
{"selection": selected_features})
if with_divisions:
if divisions:
div_lineage = division_flatten_dict(divisions, self.label2color)
zips = zip(*divisions)
divisions = zip(zips[0], div_lineage, *zips[1:])
export_file.add_columns("divisions", divisions, Mode.List, Default.DivisionNames)
else:
logger.debug("No divisions occurred. Division Table will not be exported!")
if settings["file type"] == "h5":
export_file.add_rois(Default.LabelRoiPath, label_image_slot, "table", settings["margin"], "labeling")
if settings["include raw"]:
export_file.add_image(Default.RawPath, self.RawImage)
else:
export_file.add_rois(Default.RawRoiPath, self.RawImage, "table", settings["margin"])
export_file.write_all(settings["file type"], settings["compression"])
export_file.ExportProgress.unsubscribe(progress_slot)
export_file.InsertionProgress.unsubscribe(progress_slot)
def do_export(self, settings, selected_features, progress_slot):
"""
Implements ExportOperator.do_export(settings, selected_features, progress_slot
Most likely called from ExportOperator.export_object_data
:param settings: the settings for the exporter, see
:param selected_features:
:param progress_slot:
:return:
"""
from ilastik.utility.exportFile import objects_per_frame, ExportFile, ilastik_ids, Mode, Default, \
flatten_dict, division_flatten_dict
selected_features = list(selected_features)
with_divisions = self.Parameters.value[
"withDivisions"] if self.Parameters.ready() else False
obj_count = list(objects_per_frame(self.LabelImage))
track_ids, extra_track_ids, divisions = self.export_track_ids()
self._setLabel2Color()
lineage = flatten_dict(self.label2color, obj_count)
multi_move_max = self.Parameters.value[
"maxObj"] if self.Parameters.ready() else 2
t_range = self.Parameters.value["time_range"] if self.Parameters.ready(
) else (0, 0)
ids = ilastik_ids(obj_count)
export_file = ExportFile(settings["file path"])
export_file.ExportProgress.subscribe(progress_slot)
export_file.InsertionProgress.subscribe(progress_slot)
export_file.add_columns("table", range(sum(obj_count)), Mode.List,
Default.KnimeId)
export_file.add_columns("table", list(ids), Mode.List,
Default.IlastikId)
export_file.add_columns("table", lineage, Mode.List, Default.Lineage)
export_file.add_columns(
"table", track_ids, Mode.IlastikTrackingTable, {
"max": multi_move_max,
"counts": obj_count,
"extra ids": extra_track_ids,
"range": t_range
})
if with_divisions:
object_feature_slot = self.ObjectFeaturesWithDivFeatures
else:
object_feature_slot = self.ObjectFeatures
export_file.add_columns("table", object_feature_slot,
Mode.IlastikFeatureTable,
{"selection": selected_features})
if with_divisions:
if divisions:
div_lineage = division_flatten_dict(divisions,
self.label2color)
zips = zip(*divisions)
divisions = zip(zips[0], div_lineage, *zips[1:])
export_file.add_columns("divisions", divisions, Mode.List,
Default.DivisionNames)
else:
logger.debug(
"No divisions occurred. Division Table will not be exported!"
)
if settings["file type"] == "h5":
export_file.add_rois(Default.LabelRoiPath, self.LabelImage,
"table", settings["margin"], "labeling")
if settings["include raw"]:
export_file.add_image(Default.RawPath, self.RawImage)
else:
export_file.add_rois(Default.RawRoiPath, self.RawImage,
"table", settings["margin"])
export_file.write_all(settings["file type"], settings["compression"])
export_file.ExportProgress.unsubscribe(progress_slot)
export_file.InsertionProgress.unsubscribe(progress_slot)
def do_export(self, settings, selected_features, progress_slot, lane_index, filename_suffix=""):
"""
Implements ExportOperator.do_export(settings, selected_features, progress_slot
Most likely called from ExportOperator.export_object_data
:param settings: the settings for the exporter, see
:param selected_features:
:param progress_slot:
:param lane_index: Ignored. (This is a single-lane operator. It is the caller's responsibility to make sure he's calling the right lane.)
:param filename_suffix: If provided, appended to the filename (before the extension).
:return:
"""
assert lane_index == 0, "This has only been tested in tracking workflows with a single image."
from ilastik.utility.exportFile import objects_per_frame, ExportFile, ilastik_ids, Mode, Default, \
flatten_dict, division_flatten_dict
selected_features = list(selected_features)
with_divisions = self.Parameters.value["withDivisions"] if self.Parameters.ready() else False
obj_count = list(objects_per_frame(self.LabelImage))
track_ids, extra_track_ids, divisions = self.export_track_ids()
self._setLabel2Color()
lineage = flatten_dict(self.label2color, obj_count)
multi_move_max = self.Parameters.value["maxObj"] if self.Parameters.ready() else 2
t_range = self.Parameters.value["time_range"] if self.Parameters.ready() else (0, 0)
ids = ilastik_ids(obj_count)
file_path = settings["file path"]
if filename_suffix:
path, ext = os.path.splitext(file_path)
file_path = path + "-" + filename_suffix + ext
export_file = ExportFile(file_path)
export_file.ExportProgress.subscribe(progress_slot)
export_file.InsertionProgress.subscribe(progress_slot)
export_file.add_columns("table", range(sum(obj_count)), Mode.List, Default.KnimeId)
export_file.add_columns("table", list(ids), Mode.List, Default.IlastikId)
export_file.add_columns("table", lineage, Mode.List, Default.Lineage)
export_file.add_columns("table", track_ids, Mode.IlastikTrackingTable,
{"max": multi_move_max, "counts": obj_count, "extra ids": extra_track_ids,
"range": t_range})
if with_divisions:
object_feature_slot = self.ObjectFeaturesWithDivFeatures
else:
object_feature_slot = self.ObjectFeatures
export_file.add_columns("table", object_feature_slot, Mode.IlastikFeatureTable,
{"selection": selected_features})
if with_divisions:
if divisions:
div_lineage = division_flatten_dict(divisions, self.label2color)
zips = zip(*divisions)
divisions = zip(zips[0], div_lineage, *zips[1:])
export_file.add_columns("divisions", divisions, Mode.List, Default.DivisionNames)
else:
logger.debug("No divisions occurred. Division Table will not be exported!")
if settings["file type"] == "h5":
export_file.add_rois(Default.LabelRoiPath, self.LabelImage, "table", settings["margin"], "labeling")
if settings["include raw"]:
export_file.add_image(Default.RawPath, self.RawImage)
else:
export_file.add_rois(Default.RawRoiPath, self.RawImage, "table", settings["margin"])
export_file.write_all(settings["file type"], settings["compression"])
export_file.ExportProgress.unsubscribe(progress_slot)
export_file.InsertionProgress.unsubscribe(progress_slot)
