def step_segmentation(self, operation: SegmentationProfile,
children: List[CalculationTree]):
"""
Perform segmentation and iterate over ``children`` nodes
:param SegmentationProfile operation: Specification of segmentation operation
:param List[CalculationTree] children: list of nodes to iterate over after perform segmentation
"""
segmentation_class = analysis_algorithm_dict.get(
operation.algorithm, None)
if segmentation_class is None:
raise ValueError(
f"Segmentation class {operation.algorithm} do not found")
segmentation_algorithm: RestartableAlgorithm = segmentation_class()
segmentation_algorithm.set_image(self.image)
segmentation_algorithm.set_mask(self.mask)
segmentation_algorithm.set_parameters(**operation.values)
result = segmentation_algorithm.calculation_run(report_empty_fun)
backup_data = self.segmentation, self.additional_layers, self.algorithm_parameters
self.segmentation = result.segmentation
self.additional_layers = result.additional_layers
self.algorithm_parameters = {
"algorithm_name": operation.algorithm,
"values": operation.values
}
self.iterate_over(children)
self.segmentation, self.additional_layers, self.algorithm_parameters = backup_data
def step_measurement(self, operation: MeasurementCalculate):
"""
Calculate measurement defined in current operation.
:param MeasurementCalculate operation: definition of measurement to calculate
"""
channel = operation.channel
if channel == -1:
segmentation_class: Type[
SegmentationAlgorithm] = analysis_algorithm_dict.get(
self.algorithm_parameters["algorithm_name"], None)
if segmentation_class is None:
raise ValueError(
f"Segmentation class {self.algorithm_parameters['algorithm_name']} do not found"
)
channel = self.algorithm_parameters["values"][
segmentation_class.get_channel_parameter_name()]
image_channel = self.image.get_channel(channel)
# FIXME use additional information
measurement = operation.statistic_profile.calculate(
image_channel,
self.segmentation,
self.mask,
self.image.spacing,
operation.units,
)
self.measurement.append(measurement)
def step_measurement(self, operation: MeasurementCalculate):
"""
Calculate measurement defined in current operation.
:param MeasurementCalculate operation: definition of measurement to calculate
"""
channel = operation.channel
if channel == -1:
segmentation_class: Type[
SegmentationAlgorithm] = analysis_algorithm_dict.get(
self.algorithm_parameters["algorithm_name"], None)
if segmentation_class is None: # pragma: no cover
raise ValueError(
f"Segmentation class {self.algorithm_parameters['algorithm_name']} do not found"
)
channel = self.algorithm_parameters["values"][
segmentation_class.get_channel_parameter_name()]
# FIXME use additional information
old_mask = self.image.mask
self.image.set_mask(self.mask)
measurement = operation.measurement_profile.calculate(
self.image,
channel,
self.roi_info,
operation.units,
)
self.measurement.append(measurement)
self.image.set_mask(old_mask)