PartSegCore.analysis.measurement_calculation

class PartSegCore.analysis.measurement_calculation.ColocalizationMeasurement

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

This algorithm has following parameters:

• channel_fst (Channel)- Channel 1

• channel_scd (Channel)- Channel 2

• colocalization (CorrelationEnum)- Colocalization

• randomize (bool)- Randomize channel, If randomize orders of pixels in one channel

• randomize_repeat (int)- Randomize num, Number of repetitions for mean_calculate

classmethod calculate_property(area_array, colocalization, randomize=False, randomize_repeat=10, channel_fst=0, channel_scd=1, **kwargs)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

Return type

symbols

class PartSegCore.analysis.measurement_calculation.Compactness

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

static calculate_property(**kwargs)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

class PartSegCore.analysis.measurement_calculation.ComponentBoundingBox

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

static calculate_property(bounds_info, _component_num, **kwargs)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_starting_leaf()

This leaf is put on default list

classmethod get_units(ndim)

Return units for measurement. They are shown to user

class PartSegCore.analysis.measurement_calculation.ComponentsInfo(roi_components: numpy.ndarray, mask_components: numpy.ndarray, components_translation: Dict[int, List[int]])

Bases: NamedTuple

Class for storage information about relation between roi components and mask components

Variables

• roi_components (numpy.ndarray) – list of roi components

• mask_components (numpy.ndarray) – list of mask components

• components_translation (Dict[int, List[int]]) – mapping from roi components to mask components base on intersections

components_translation: Dict[int, List[int]]

Alias for field number 2

mask_components: numpy.ndarray

Alias for field number 1

roi_components: numpy.ndarray

Alias for field number 0

class PartSegCore.analysis.measurement_calculation.ComponentsNumber

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

static calculate_property(area_array, **_)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

class PartSegCore.analysis.measurement_calculation.CorrelationEnum(value)

Bases: str, enum.Enum

An enumeration.

class PartSegCore.analysis.measurement_calculation.Diameter

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

Class for calculate diameter of ROI in fast way. From Malandain, G., & Boissonnat, J. (2002). Computing the diameter of a point set, 12(6), 489-509. https://doi.org/10.1142/S0218195902001006

static calculate_property(area_array, voxel_size, result_scalar, **_)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

class PartSegCore.analysis.measurement_calculation.DiameterOld

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

n**2 calculate diameter of ROI

static calculate_property(area_array, voxel_size, result_scalar, **_)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

class PartSegCore.analysis.measurement_calculation.DistanceMaskROI

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

This algorithm has following parameters:

• distance_from_mask (DistancePoint)- Distance from mask

• distance_to_roi (DistancePoint)- Distance to ROI

static area_type(area)

Map chosen area type to proper area type. Allow to correct Area type.

classmethod calculate_property(channel, area_array, mask, voxel_size, result_scalar, distance_from_mask, distance_to_roi, *args, **kwargs)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_starting_leaf()

This leaf is put on default list

classmethod get_units(ndim)

Return units for measurement. They are shown to user

classmethod need_channel()

if need image data

class PartSegCore.analysis.measurement_calculation.DistancePoint(value)

Bases: enum.Enum

An enumeration.

class PartSegCore.analysis.measurement_calculation.DistanceROIROI

Bases: PartSegCore.analysis.measurement_calculation.DistanceMaskROI

This algorithm has following parameters:

• profile (ROIExtractionProfile)- ROI extraction profile

• distance_from_new_roi (DistancePoint)- Distance new ROI

• distance_to_roi (DistancePoint)- Distance to ROI

classmethod calculate_property(channel, image, area_array, profile, mask, voxel_size, result_scalar, distance_from_new_roi, distance_to_roi, **kwargs)

Main function for calculating measurement

Parameters

• channel (ndarray) – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array (ndarray) – array representing current area returned by area_type()

• roi – array representing roi

• mask (Optional[ndarray]) – array representing mask (upper level roi)

• voxel_size (Sequence[float]) – size of single voxel in meters

• result_scalar (float) – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_starting_leaf()

This leaf is put on default list

class PartSegCore.analysis.measurement_calculation.FirstPrincipalAxisLength

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

static calculate_property(**kwargs)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

classmethod need_channel()

if need image data

class PartSegCore.analysis.measurement_calculation.GetROIAnnotationType

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

This algorithm has following parameters:

• name (str)- Name

static calculate_property(roi_annotation, name, _component_num, **kwargs)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_starting_leaf()

This leaf is put on default list

classmethod get_units(ndim)

Return units for measurement. They are shown to user

class PartSegCore.analysis.measurement_calculation.Haralick

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

This algorithm has following parameters:

• feature (HaralickEnum)- Feature

• distance (ConstrainedIntValue)- Distance

classmethod calculate_property(area_array, channel, distance, feature, _cache=False, **kwargs)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

Return type

symbols

classmethod need_channel()

if need image data

class PartSegCore.analysis.measurement_calculation.HaralickEnum(value)

Bases: enum.Enum

An enumeration.

PartSegCore.analysis.measurement_calculation.MEASUREMENT_DICT

Register with all measurements algorithms

Need class methods: get_description, is_component, calculate_property, get_starting_leaf, get_units, need_channel

Default content:

• Volume - Volume

• Diameter - Diameter

• Pixel brightness sum - PixelBrightnessSum

• Component Bounding Box - ComponentBoundingBox

• annotation by name - GetROIAnnotationType

• Components number - ComponentsNumber

• Maximum pixel brightness - MaximumPixelBrightness

• Minimum pixel brightness - MinimumPixelBrightness

• Mean pixel brightness - MeanPixelBrightness

• Median pixel brightness - MedianPixelBrightness

• Standard deviation of pixel brightness - StandardDeviationOfPixelBrightness

• Colocalization - ColocalizationMeasurement

• Moment - Moment

• First principal axis length - FirstPrincipalAxisLength

• Second principal axis length - SecondPrincipalAxisLength

• Third principal axis length - ThirdPrincipalAxisLength

• Compactness - Compactness

• Sphericity - Sphericity

• Surface - Surface

• rim volume - RimVolume

• rim pixel brightness sum - RimPixelBrightnessSum

• Neighbourhood new ROI presence - ROINeighbourhoodROI

• ROI distance - DistanceMaskROI

• to new ROI distance - DistanceROIROI

• distance splitting volume - SplitOnPartVolume

• distance splitting pixel brightness sum - SplitOnPartPixelBrightnessSum

• Voxels - Voxels

• Haralick - Haralick

• Voxel size - VoxelSize

class PartSegCore.analysis.measurement_calculation.MaximumPixelBrightness

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

static calculate_property(area_array, channel, **_)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

classmethod need_channel()

if need image data

class PartSegCore.analysis.measurement_calculation.MeanPixelBrightness

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

static calculate_property(area_array, channel, **_)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

classmethod need_channel()

if need image data

class PartSegCore.analysis.measurement_calculation.MeasurementResult(components_info)

Bases: MutableMapping[str, Tuple[Union[float, List[float], str], str]]

Class for storage measurements info.

get_component_info(all_components=False)

Get information which type of components are in storage.

Return type

Tuple[bool, bool]

Returns

has_mask_components, has_segmentation_components

get_global_names()

Get names for only parameters which are not ‘PerComponent.Yes’

get_global_parameters()

Get only parameters which are not ‘PerComponent.Yes’

get_labels(expand=True, all_components=False)

If expand is false return list of keys of this storage. Otherwise return labels for measurement. Base are keys of this storage. If has mask components, or has segmentation_components then add this labels

Return type

List[str]

get_separated(all_components=False)

Get measurements separated for each component

Return type

List[List[Union[float, List[float], str]]]

set_filename(path_fo_file)

Set name of file to be presented as first position.

class PartSegCore.analysis.measurement_calculation.MedianPixelBrightness

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

static calculate_property(area_array, channel, **_)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

classmethod need_channel()

if need image data

class PartSegCore.analysis.measurement_calculation.MinimumPixelBrightness

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

static calculate_property(area_array, channel, **_)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

classmethod need_channel()

if need image data

class PartSegCore.analysis.measurement_calculation.Moment

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

static calculate_property(area_array, channel, voxel_size, **_)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

classmethod need_channel()

if need image data

class PartSegCore.analysis.measurement_calculation.PixelBrightnessSum

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

static calculate_property(area_array, channel, **_)

Parameters

• area_array (ndarray) – mask for area

• channel (ndarray) – data. same shape like area_type

Returns

Pixels brightness sum on given area

classmethod get_units(ndim)

Return units for measurement. They are shown to user

classmethod need_channel()

if need image data

exception PartSegCore.analysis.measurement_calculation.ProhibitedDivision

Bases: Exception

class PartSegCore.analysis.measurement_calculation.ROINeighbourhoodROI

Bases: PartSegCore.analysis.measurement_calculation.DistanceMaskROI

This algorithm has following parameters:

• profile (ROIExtractionProfile)- ROI extraction profile

• distance (ConstrainedFloatValue)- Distance

• units (Units)- Units

classmethod calculate_property(image, area_array, profile, mask, voxel_size, distance, units, **kwargs)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array (ndarray) – array representing current area returned by area_type()

• roi – array representing roi

• mask (Optional[ndarray]) – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_starting_leaf()

This leaf is put on default list

class PartSegCore.analysis.measurement_calculation.RimPixelBrightnessSum

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

This algorithm has following parameters:

• distance (ConstrainedFloatValue)- Distance

• units (Units)- Units

static area_type(area)

Map chosen area type to proper area type. Allow to correct Area type.

static calculate_property(channel, area_array, **kwargs)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_starting_leaf()

This leaf is put on default list

classmethod get_units(ndim)

Return units for measurement. They are shown to user

classmethod need_channel()

if need image data

class PartSegCore.analysis.measurement_calculation.RimVolume

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

This algorithm has following parameters:

• distance (ConstrainedFloatValue)- Distance

• units (Units)- Units

static area_type(area)

Map chosen area type to proper area type. Allow to correct Area type.

static calculate_property(area_array, voxel_size, result_scalar, **kwargs)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_starting_leaf()

This leaf is put on default list

classmethod get_units(ndim)

Return units for measurement. They are shown to user

class PartSegCore.analysis.measurement_calculation.SecondPrincipalAxisLength

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

static calculate_property(**kwargs)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

classmethod need_channel()

if need image data

class PartSegCore.analysis.measurement_calculation.SettingsValue(function, help_message, arguments, is_component, default_area)

Bases: NamedTuple

arguments: Optional[dict]

Alias for field number 2

default_area: Optional[PartSegCore.analysis.measurement_base.AreaType]

Alias for field number 4

function: Callable

Alias for field number 0

help_message: str

Alias for field number 1

is_component: bool

Alias for field number 3

class PartSegCore.analysis.measurement_calculation.Sphericity

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

static calculate_property(**kwargs)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

class PartSegCore.analysis.measurement_calculation.SplitOnPartPixelBrightnessSum

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

This algorithm has following parameters:

• num_of_parts (ConstrainedIntValue)- Number of Parts

• equal_volume (bool)- Equal Volume, If split should be done in respect of parts volume of parts thickness.

• part_selection (ConstrainedIntValue)- Which part (from border)

static area_type(area)

Map chosen area type to proper area type. Allow to correct Area type.

static calculate_property(part_selection, channel, area_array, **kwargs)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_starting_leaf()

This leaf is put on default list

classmethod get_units(ndim)

Return units for measurement. They are shown to user

classmethod need_channel()

if need image data

class PartSegCore.analysis.measurement_calculation.SplitOnPartVolume

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

This algorithm has following parameters:

• num_of_parts (ConstrainedIntValue)- Number of Parts

• equal_volume (bool)- Equal Volume, If split should be done in respect of parts volume of parts thickness.

• part_selection (ConstrainedIntValue)- Which part (from border)

static area_type(area)

Map chosen area type to proper area type. Allow to correct Area type.

static calculate_property(part_selection, area_array, voxel_size, result_scalar, **kwargs)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_starting_leaf()

This leaf is put on default list

classmethod get_units(ndim)

Return units for measurement. They are shown to user

class PartSegCore.analysis.measurement_calculation.StandardDeviationOfPixelBrightness

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

static calculate_property(area_array, channel, **_)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

classmethod need_channel()

if need image data

class PartSegCore.analysis.measurement_calculation.Surface

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

static calculate_property(area_array, voxel_size, result_scalar, **_)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

class PartSegCore.analysis.measurement_calculation.ThirdPrincipalAxisLength

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

static calculate_property(**kwargs)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

classmethod need_channel()

if need image data

class PartSegCore.analysis.measurement_calculation.Volume

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

classmethod calculate_property(area_array, voxel_size, result_scalar, **_)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

class PartSegCore.analysis.measurement_calculation.VoxelSize

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

classmethod calculate_property(voxel_size, result_scalar, **kwargs)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

Return type

symbols

class PartSegCore.analysis.measurement_calculation.Voxels

Bases: PartSegCore.analysis.measurement_base.MeasurementMethodBase

classmethod calculate_property(area_array, **_)

Main function for calculating measurement

Parameters

• channel – main channel selected for measurement

• channel_{i} – for channel requested using get_fields() AlgorithmProperty("channel", "Channel", 0, value_type=Channel)

• area_array – array representing current area returned by area_type()

• roi – array representing roi

• mask – array representing mask (upper level roi)

• voxel_size – size of single voxel in meters

• result_scalar – scalar to get proper units in result

• roi_alternative – dict with alternative roi representation (for plugin specific mapping)

• roi_annotation – dict with roi annotations (for plugin specific mapping)

List incomplete.

classmethod get_units(ndim)

Return units for measurement. They are shown to user

PartSegCore.analysis.measurement_calculation.double_normal(point_index, point_positions, points_array)

Parameters

• point_index (int) – index of starting points

• point_positions (ndarray) – points array of size (points_num, number of dimensions)

• points_array (ndarray) – bool matrix with information about which points are in set

Returns

PartSegCore.analysis.measurement_calculation.empty_fun(_a0=None, _a1=None)

This function is being used as dummy reporting function.

PartSegCore.analysis.measurement_calculation.hash_fun_call_name(fun, arguments, area, per_component, channel, components_num)

Calculate string for properly cache measurements result.

Parameters

• fun (Union[Callable, MeasurementMethodBase]) – method for which hash string should be calculated

• arguments (Dict) – its additional arguments

• area (AreaType) – type of rea

• per_component (PerComponent) – If it is per component

• channel (Channel) – channel number on which calculation is performed

Return type

str

Returns

unique string for such set of arguments

PartSegCore.analysis.measurement_calculation.iterative_double_normal(points_positions)

Parameters

points_positions (ndarray) – points array of size (points_num, number of dimensions)

Returns

square power of diameter, 2-tuple of points index gave information which points ar chosen