OrsVolumeROITools¶

Manages the tools applicable to Regions of Interest

author:: Dragonfly Team
contact:: https://dragonfly.comet.tech
email:: support.dragonfly@comet.tech
organization:: Comet Technologies Canada Inc.
address:: 460 Ste-Catherine Ouest, suite 600, Montréal, Québec, Canada, H3B 1A7
copyright:: Comet Technologies Canada Inc. All rights reserved 2023.
date:: Sep 11 2015 12:03
dragonflyVersion:: 3.1.0.286 (D)
UUID:: 5bc96a00761e11e79055448a5b5d70c0

Class Code¶

class OrsPythonPlugins.OrsVolumeROITools.OrsVolumeROITools.OrsVolumeROITools(*args, **kwargs)¶

SobelWatershedFromMultiROI2D(aMultiROI, dataset=None, mask=None)¶

Entry point for computing watershed 2D on a MultiROI or from a list of ROIs

Parameters:

orsObject – MultiROI
roiForShape – ROI

interfacemethod addRange(listROIToModify: List[Union[ROI, MultiROI]], dataset: Channel, rangeMin: float, rangeMax: float, timeStep: int = 0) → None¶

Adds each voxel where the intensity in the dataset is included in the given range.

Parameters:

listROIToModify (ORSModel.ors.ROI, ORSModel.ors.MultiROI) [count=[1, None]] – ROI or MultiROI to modify
dataset (ORSModel.ors.Channel) [const] – Dataset for range comparison
rangeMin (float) – minimal value of the range
rangeMax (float) – maximal value of the range
timeStep (int) – timeIndex, or -1 for all time

interfacemethod addRangeInterpolated(listROIToModify: List[ROI], dataset: Channel, rangeMin: float, rangeMax: float, cubicInterpolation: bool, timeStep: int = 0) → None¶

Adds each voxel where the intensity in the dataset is included in the given range.

Parameters:

listROIToModify (ORSModel.ors.ROI) [count=[1, None]] – ROI to modify
dataset (ORSModel.ors.Channel) [const] – Dataset for range comparison
rangeMin (float) – minimal value of the range
rangeMax (float) – maximal value of the range
cubicInterpolation (bool) – use cubic interpolation
timeStep (int) – timeIndex

interfacemethod addRemoveRegionClip(listROIToModify: List[Union[ROI, MultiROI]], layoutFullName: str, dataset: Channel = None, rangeMin: float = 0.0, rangeMax: float = 0.0, add: bool = True, currentTime: int = 0) → None¶

Adds or removes an area determined by a clipping box on a ROI or a MultiROI.

Parameters:

listROIToModify (ORSModel.ors.ROI, ORSModel.ors.MultiROI) [count=[1, None]] – ROI or MultiROI to modify
layoutFullName (str) – a genealogical name (the view in which the box is present)
dataset (ORSModel.ors.Channel) [const] – Dataset for range comparison (if application should be restricted to a range)
rangeMin (float) – minimal value of the range
rangeMax (float) – maximal value of the range
add (bool) – if True, an addition will be done; if False, a removal will be done.
currentTime (int) – Time step of the ROI

cleanup()¶: Deletes the variables managed by the plugin. It is the place to remove callbacks and other references to Python objects that would prevent them to be garbage collected. This method is called during the process of deletion of the plugin. It calls for the cleanup and deletion of the forms.

classmethod clear(listROIToModify, currentTime=0)¶

Clears the ROIs and/or MultiROIs

Parameters:

listROIToModify (ORSModel.ors.ROI, ORSModel.ors.MultiROI) [count=[1, None]] – ROIs or MultiROIs to clear
currentTime (int) – time step of the ROI, or -1 for all time

classmethod clearForAllTimeSteps(listROIToModify)¶

Clears the ROIs and/or MultiROIs

Parameters:: listROIToModify (ORSModel.ors.ROI, ORSModel.ors.MultiROI) [count=[1, None]] – ROIs or MultiROIs to clear

interfacemethod clearSingleROI(aROI: Union[ROI, MultiROI], timeStep: int = 0) → None¶

Clears a ROI or MultiROI for a specific timestep

Parameters:

aROI (ORSModel.ors.ROI, ORSModel.ors.MultiROI) – the ROI or MultiROI to clear
timeStep (int) – time step of the ROI or MultiROI

interfacemethod clearSingleROIForAllTimeSteps(aROI: Union[ROI, MultiROI]) → None¶

Clears a ROI or MultiROI for All timeSteps

Parameters:: aROI (ORSModel.ors.ROI, ORSModel.ors.MultiROI) – the ROI or MultiROI to clear

interfacemethod close(aROIToModify: Union[ROI, MultiROI] = None, kernelShape: str = 'square', kernelDim: int = 3, kernelSize: int = 3, dataset: Channel = None, rangeMin: float = 0.0, rangeMax: float = 0.0, repetitionCount: int = 1, currentTime: int = 0, axis: int = 2, sliceIndicesExpr: str = '', listROIToModify: List[Union[ROI, MultiROI]] = None, sliceIndices: SequenceableCollection = None) → None¶

Applies a morphological closing operation on a ROI or a MultiROI.

Changed in version -: Argument listToModify (list) is replaced by aROIToModify (single instance) - Argument sliceIndices (Array) is replaced by sliceIndicesExpr (string expression)

Parameters:

aROIToModify (ORSModel.ors.ROI, ORSModel.ors.MultiROI) – ROI or MultiROI to modify
kernelShape (str) – Kernel shape (‘square’, ‘circle’ or ‘cross’)
kernelDim (int) – Kernel dimension (2 or 3)
kernelSize (int) – Kernel size (odd number between 3 and 33)
dataset (ORSModel.ors.Channel) [const] – Dataset for range comparison (if application should be restricted to a range)
rangeMin (float) – minimal value of the range
rangeMax (float) – maximal value of the range
repetitionCount (int) – Count of repetition to be applied
currentTime (int) – Time step of the ROI
axis (int) – axis of operation if 2D kernel 0=X, 1=Y, 2=Z of the StructuredGrid
sliceIndicesExpr (str) – slices to work on in the given axis (string expression, 1-based, e.g. ‘1,2,3-5,4-20/3’)
listROIToModify (ORSModel.ors.ROI, ORSModel.ors.MultiROI) [count=[1, None]] [deprecated: use aROIToModify instead] – ROI or MultiROI to modify
sliceIndices (ORSModel.ors.SequenceableCollection) [deprecated: use sliceIndicesExpr instead] – collection of slices to work on in the given axis

interfacemethod computeAdaptiveWatershed(aROI: ROI, tStep: int, IProgress: Progress = None) → MultiROI¶

Compute the adaptive watershed

Sun, H.Q., and Y.J.Luo. Adaptive watershed segmentation of binary particle image. Journal of microscopy 233.2(2009): 326 - 330.

Parameters:

aROI (ORSModel.ors.ROI) – the dataset to copy
tStep (int) – a tStep value
IProgress (ORSModel.ors.Progress) – progress object

Returns:

newMultiROI (ORSModel.ors.MultiROI) – the Watershed result MultiROI

interfacemethod computeAdaptiveWatershed2D(aROI: ROI, tStep, IProgress=None)¶

Compute the adaptive watershed 2D by processing each slice individually

Based on: Sun, H.Q., and Y.J.Luo. Adaptive watershed segmentation of binary particle image. Journal of microscopy 233.2(2009): 326 - 330.

Parameters:

aROI (ORSModel.ors.ROI) – the dataset to process
tStep (int) – a tStep value
IProgress (ORSModel.ors.Progress) – progress object

Returns:

newMultiROI (ORSModel.ors.MultiROI) – the Watershed result MultiROI

classmethod computeAdaptiveWatershed2D_fromMenu(aROI: ROI)¶

Menu action method for the Adaptive Watershed 2D menu item

Parameters:: aROI (ORSModel.ors.ROI) – The ROI to process

interfacemethod computeAnisotropyMIL(aROI: ROI, anisotropyMILRadius: float, anisotropyMILSampling: float, anisotropyMILOrientations: int, anisotropyMILMinIterations: int, anisotropyMILMaxIterations: int, anisotropyMILTolerance: float, IProgress: Progress = None) → float¶

Computes the measurement of the anisotropy using the Mean Intercept Length (MIL).

Parameters:

aROI (ORSModel.ors.ROI) [const] – ROI to analyze
anisotropyMILRadius (float) – radius to analyze per orientation per star
anisotropyMILSampling (float) – distance between each sample on the line of analysis
anisotropyMILOrientations (int) – count of lines to analyze per star
anisotropyMILMinIterations (int) – minimal count of star to iterate on
anisotropyMILMaxIterations (int) – maximal count of star to iterate on
anisotropyMILTolerance (float) – smallest variance of anisotropy to reach before ending the iterations
IProgress (ORSModel.ors.Progress) – a Progress object

Returns:

anisotropyMIL (float) – measurement of the anisotropy

interfacemethod computeAnisotropySVD(aROI: ROI, anisotropySVDRadius: float, anisotropySVDSampling: float, anisotropySVDOrientations: int, anisotropySVDMinIterations: int, anisotropySVDMaxIterations: int, anisotropySVDTolerance: float, IProgress: Progress = None) → float¶

Computes the measurement of the anisotropy using the Star Volume Distribution (SVD).

Parameters:

aROI (ORSModel.ors.ROI) [const] – ROI to analyze
anisotropySVDRadius (float) – radius to analyze per orientation per star
anisotropySVDSampling (float) – distance between each sample on the line of analysis
anisotropySVDOrientations (int) – count of lines to analyze per star
anisotropySVDMinIterations (int) – minimal count of star to iterate on
anisotropySVDMaxIterations (int) – maximal count of star to iterate on
anisotropySVDTolerance (float) – smallest variance of anisotropy to reach before ending the iterations
IProgress (ORSModel.ors.Progress) – a Progress object

Returns:

anisotropySVD (float) – measurement of the anisotropy

interfacemethod computeSobelWatershedFromMultiROI2D(aMultiROI: MultiROI, dataset: Channel, mask: ROI, timeStep: int, IProgress: Optional[Progress] = None) → MultiROI¶

Computes the 2D watershed from a MultiROI

Parameters:

aMultiROI (ORSModel.ors.MultiROI) – MultiROI to compute the watershed from. The watershed result is put in that same object.
dataset (ORSModel.ors.Channel) – Channel used to compute the edge map
mask (ORSModel.ors.ROI) – ROI used as a mask to compute the watershed
timeStep (int) – time index of aMultiROI and of datasetForShape
IProgress (ORSModel.ors.Progress) – progress object

Returns:

newMultiROI (ORSModel.ors.MultiROI) – the Watershed result MultiROI

classmethod computeSparseGraphFromROI2D(aROI: ROI, aProgress: Progress = None, tStep: int = 0) → Graph¶

Computes the connectivity sparse graph from 2D slices of a ROI

Parameters:

aROI (ORSModel.ors.ROI) – source ROI
aProgress (ORSModel.ors.Progress) – progress object
tStep (int) – time step

Returns:

aGraph (ORSModel.ors.Graph) – resulting graph

classmethod computeSparseGraphFromROI2DAndPublish(aROI: ROI)¶

Computes the connectivity sparse graph from 2D slices of a ROI and publishes the result as a graph.

Parameters:: aROI (ORSModel.ors.ROI) – the ROI to skeletonize

classmethod computeWatershed(orsObject, datasetForShape=None)¶

Entry point for computing watershed on a MultiROI or from a list of ROIs

Parameters:: orsObject – MultiROI, or list of ROIs

computeWatershed2D(aMultiROI, roiForShape=None)¶

Entry point for computing watershed 2D on a MultiROI or from a list of ROIs

Parameters:

orsObject – MultiROI
roiForShape – ROI

interfacemethod computeWatershedFromMultiROI(aMultiROI: MultiROI, datasetForShape: Channel, timeStep: int) → None¶

Computes the watershed from a MultiROI

Parameters:

aMultiROI (ORSModel.ors.MultiROI) – MultiROI to compute the watershed from. The watershed result is put in that same object.
datasetForShape (ORSModel.ors.Channel) [const] – Dataset used to compute the edge map
timeStep (int) – time index of aMultiROI and of datasetForShape

interfacemethod computeWatershedFromMultiROI2D(aMultiROI: MultiROI, roiForShape: ROI, timeStep: int) → None¶

Computes the 2D watershed from a MultiROI

Deprecated since version 2022.2: use computeWatershedFromMultiROI2DFromGenealogicalName instead

Parameters:

aMultiROI (ORSModel.ors.MultiROI) – MultiROI to compute the watershed from. The watershed result is put in that same object.
roiForShape (ORSModel.ors.ROI) [const] – ROI used to compute the edge map
timeStep (int) – time index of aMultiROI and of datasetForShape

interfacemethod computeWatershedFromMultiROI2DFromGenealogicalName(aMultiROI: MultiROI, roiForShape: ROI, aViewGenealogicalName: str, timeStep: int) → None¶

Computes the watershed from a MultiROI

Parameters:

aMultiROI (ORSModel.ors.MultiROI) – MultiROI to compute the watershed from. The watershed result is put in that same object.
roiForShape (ORSModel.ors.ROI) [const] – ROI used to compute the edge map
aViewGenealogicalName (str) – a layout genealogical name
timeStep (int) – time index of aMultiROI and of datasetForShape

interfacemethod computeWatershedFromMultiROI2DFromPlane(aMultiROI: MultiROI, roiForShape: ROI, aPlane: Plane, timeStep: int) → None¶

Computes watershed 2D from a MultiROI using a plane

Parameters:

aMultiROI (ORSModel.ors.MultiROI) – MultiROI to compute the watershed from. The watershed result is put in that same object.
roiForShape (ORSModel.ors.ROI) [const] – ROI used to compute the edge map
aPlane (ORSModel.ors.Plane) – the plane on which the watershed 2D will take place
timeStep (int) – time index of aMultiROI and of datasetForShape

interfacemethod computeWatershedFromROIs(listOfROIs: List[ROI], datasetForShape: Channel, timeStep: int) → None¶

Computes the watershed from a list of ROIs

Parameters:

listOfROIs (ORSModel.ors.ROI) [count=[2, None]] – list of ROIs to compute the watershed from. The watershed result is put in these same objects.
datasetForShape (ORSModel.ors.Channel) [const] – Dataset used to compute the edge map
timeStep (int) – time index of the input ROIs and of datasetForShape

interfacemethod create2DDistanceMapFromROIs(ROIs: List[ROI], tIndex: int, signed: bool = False, IProgress: Progress = None) → Channel¶

Computes 2D distance map from a set of ROIs

Parameters:

ROIs (ORSModel.ors.ROI) [count=[1, None]] [const] – ROIs to compute the distance map from
tIndex (int) – time index of the ROIs to use
signed (bool) – is the distance map signed or not
IProgress (ORSModel.ors.Progress) – progress object

Returns:

distanceMapDataset (ORSModel.ors.Channel) – dataset of the computed distance map

interfacemethod createDistanceMapFromROIs(ROIs: List[ROI], tIndex: int, IProgress: Progress = None) → Channel¶

Computes a distance map from a set of ROIs

Parameters:

ROIs (ORSModel.ors.ROI) [count=[1, None]] [const] – ROIs to compute the distance map from
tIndex (int) – time index of the ROIs to use
IProgress (ORSModel.ors.Progress) – progress object

Returns:

distanceMapDataset (ORSModel.ors.Channel) – dataset of the computed distance map

classmethod createEmptyROIFromStructuredGrid(structuredGrid, title, ROIColor, createAsMultiROI)¶

Creates an empty ROI or MultiROI from a StructuredGrid

Deprecated since version 2021.3: Use createROIFromStructuredGrid or createMultiROIFromStructuredGrid instead

Parameters:

structuredGrid (ORSModel.ors.StructuredGrid) [const] – reference shape of the new ROI
title (str) – title of the new ROI
ROIColor (ORSModel.ors.Color) – color of the new ROI
createAsMultiROI (bool) – create a MultiROI if True, a ROI if False

Returns:

output (ORSModel.ors.ROI, ORSModel.ors.MultiROI) – created ROI

classmethod createEmptyROIFromVisualBox(aVisualBox, title, currentTime, ROIColor, createAsMultiROI)¶

Creates an empty ROI or MultiROI from a VisualBox

Deprecated since version 2021.3: Use createROIFromVisualBox or createMultiROIFromVisualBox instead

Parameters:

aVisualBox (ORSModel.ors.VisualBox) [const] – reference shape of the new ROI
title (str) – title of the new ROI
currentTime (int) – currentTime to get the box of the visual box
ROIColor (ORSModel.ors.Color) – color of the new ROI
createAsMultiROI (bool) – create a MultiROI if True, a ROI if False

Returns:

output (ORSModel.ors.ROI, ORSModel.ors.MultiROI) – created ROI or MultiROI

interfacemethod createLabeledROIFromLabeledROI(aMultiROI: MultiROI, IProgress: Progress = None, includeDiagonal: bool = False, perSlice: bool = False) → MultiROI¶

Computes the labelization of a labeled ROI by extracting each label, labelizing them and concatenating the results.

Parameters:

aMultiROI (ORSModel.ors.MultiROI) [const] – MultiROI to compute the labelization on
IProgress (ORSModel.ors.Progress) – progress object
includeDiagonal (bool) – include diagonal 26 neighbor (or 8 in 2D or when saelecting per slice)
perSlice (bool) – do a 2D connected component

Returns:

labelizationMultiROI (ORSModel.ors.MultiROI) – MultiROI of the labelized ROI

interfacemethod createLabeledROIFromROI(aROI: ROI, IProgress: Progress = None, includeDiagonal: bool = False, perSlice: bool = False) → MultiROI¶

Computes the labelization of a ROI

Parameters:

aROI (ORSModel.ors.ROI) [const] – ROI to compute the labelization on
IProgress (ORSModel.ors.Progress) – progress object
includeDiagonal (bool) – include diagonal 26 neighbor
perSlice (bool) – do a 2D connected component

Returns:

labelizationMultiROI (ORSModel.ors.MultiROI) – MultiROI of the labelized ROI

interfacemethod createLabeledROIFromROIWithDiagonal(aROI: ROI, IProgress: Progress = None) → MultiROI¶

Computes the labelization of a ROI 26 neighbor

Parameters:

aROI (ORSModel.ors.ROI) [const] – ROI to compute the labelization on
IProgress (ORSModel.ors.Progress) – progress object

Returns:

labelizationMultiROI (ORSModel.ors.MultiROI) – MultiROI of the labelized ROI

interfacemethod createMultiROIFromStructuredGrid(aStructuredGrid: StructuredGrid, title: str, classCount: int) → MultiROI¶

Creates an empty MultiROI from a StructuredGrid

Parameters:

aStructuredGrid (ORSModel.ors.StructuredGrid) [const] – reference shape of the new MultiROI
title (str) – title of the new MultiROI
classCount (int) – class count

Anonymize title:

True

Returns:

output (ORSModel.ors.MultiROI) – created MultiROI

interfacemethod createMultiROIFromVisualBox(aVisualBox: VisualBox, title: str, currentTime: int, classCount: int) → MultiROI¶

Creates an empty MultiROI from a VisualBox

Parameters:

aVisualBox (ORSModel.ors.VisualBox) [const] – reference shape of the new MultiROI
title (str) – title of the new MultiROI
currentTime (int) – currentTime to get the box of the visual box
classCount (int) – class count

Anonymize title:

True

Returns:

output (ORSModel.ors.MultiROI) – created MultiROI

interfacemethod createROIFromLabeledROI(aMultiROI: MultiROI, IProgress: Progress = None) → ROI¶

Creates a new ROI by taking all the voxels from all the labels of the MultiROI

Parameters:

aMultiROI (ORSModel.ors.MultiROI) [const] – a MultiROI
IProgress (ORSModel.ors.Progress) – progress object

Returns:

aROI (ORSModel.ors.ROI) – a ROI

interfacemethod createROIFromStructuredGrid(aStructuredGrid: StructuredGrid, title: str, ROIColor: Color) → ROI¶

Creates an empty ROI from a StructuredGrid

Parameters:

aStructuredGrid (ORSModel.ors.StructuredGrid) [const] – reference shape of the new ROI
title (str) – title of the new ROI
ROIColor (ORSModel.ors.Color) – color of the new ROI

Anonymize title:

True

Returns:

output (ORSModel.ors.ROI) – created ROI

interfacemethod createROIFromVisualBox(aVisualBox: VisualBox, title: str, currentTime: int, ROIColor: Color) → ROI¶

Creates an empty ROI from a VisualBox

Parameters:

aVisualBox (ORSModel.ors.VisualBox) [const] – reference shape of the new ROI
title (str) – title of the new ROI
currentTime (int) – currentTime to get the box of the visual box
ROIColor (ORSModel.ors.Color) – color of the new ROI

Anonymize title:

True

Returns:

output (ORSModel.ors.ROI) – created ROI

interfacemethod createROIInRange(dataset: Channel, title: str, rangeMin: float, rangeMax: float, timeStep: int = 0) → ROI¶

Creates a ROI from a dataset and a range of intensities.

Parameters:

dataset (ORSModel.ors.Channel) [const] – dataset of reference
title (str) – title of the new ROI
rangeMin (float) – minimal value of the dataset intensity to include in the ROI
rangeMax (float) – maximal value of the dataset intensity to include in the ROI
timeStep (int) – timeIndex, or -1 for all time

Anonymize title:

True

Returns:

output (ORSModel.ors.ROI) – created ROI

interfacemethod createSignedDistanceMapFromROIs(ROIs: List[ROI], tIndex: int, IProgress: Progress = None) → Channel¶

Computes a signed distance map from a set of ROIs

Parameters:

ROIs (ORSModel.ors.ROI) [count=[1, None]] [const] – ROIs to compute the distance map from
tIndex (int) – time index of the ROIs to use
IProgress (ORSModel.ors.Progress) – progress object

Returns:

distanceMapDataset (ORSModel.ors.Channel) – dataset of the computed distance map

interfacemethod createVolumeThicknessFromROI(aROI: ROI, currentTime: int, IProgress: Progress = None) → Channel¶

Computes the volume thickness of a ROI

Parameters:

aROI (ORSModel.ors.ROI) [const] – ROI to compute the volume thickness on
currentTime (int) – Time step of the ROI
IProgress (ORSModel.ors.Progress) – progress object

Returns:

volumeThicknessChannel (ORSModel.ors.Channel) – Volume thickness

interfacemethod cutFromData(listROIToAnalyze: List[ROI], dataset: Channel) → None¶

Writes zeros in a dataset at the location of the ROI.

Parameters:

listROIToAnalyze (ORSModel.ors.ROI) [count=[1, None]] [const] – ROI over which the dataset will be written
dataset (ORSModel.ors.Channel) – Dataset to write in

interfacemethod dilate(aROIToModify: Union[ROI, MultiROI] = None, kernelShape: str = 'square', kernelDim: int = 3, kernelSize: int = 3, dataset: Channel = None, rangeMin: float = 0.0, rangeMax: float = 0.0, repetitionCount: int = 1, currentTime: int = 0, axis: int = 2, sliceIndicesExpr: str = '', listROIToModify: List[Union[ROI, MultiROI]] = None, sliceIndices: SequenceableCollection = None) → None¶

Applies a morphological dilation operation on a ROI or a MultiROI.

Changed in version -: Argument listToModify (list) is replaced by aROIToModify (single instance) - Argument sliceIndices (Array) is replaced by sliceIndicesExpr (string expression)

Parameters:

aROIToModify (ORSModel.ors.ROI, ORSModel.ors.MultiROI) – ROI or MultiROI to modify
kernelShape (str) – Kernel shape (‘square’, ‘circle’ or ‘cross’)
kernelDim (int) – Kernel dimension (2 or 3)
kernelSize (int) – Kernel size (odd number between 3 and 33)
dataset (ORSModel.ors.Channel) [const] – Dataset for range comparison (if application should be restricted to a range)
rangeMin (float) – minimal value of the range
rangeMax (float) – maximal value of the range
repetitionCount (int) – Count of repetition to be applied
currentTime (int) – Time step of the ROI
axis (int) – axis of operation if 2D kernel 0=X, 1=Y, 2=Z of the StructuredGrid
sliceIndicesExpr (str) – slices to work on in the given axis (string expression, 1-based, e.g. ‘1,2,3-5,4-20/3’)
listROIToModify (ORSModel.ors.ROI, ORSModel.ors.MultiROI) [count=[1, None]] [deprecated: use aROIToModify instead] – ROI or MultiROI to modify
sliceIndices (ORSModel.ors.SequenceableCollection) [deprecated: use sliceIndicesExpr instead] – collection of slices to work on in the given axis

interfacemethod erode(aROIToModify: Union[ROI, MultiROI] = None, kernelShape: str = 'square', kernelDim: int = 3, kernelSize: int = 3, dataset: Channel = None, rangeMin: float = 0.0, rangeMax: float = 0.0, repetitionCount: int = 1, currentTime: int = 0, axis: int = 2, sliceIndicesExpr: str = '', listROIToModify: List[Union[ROI, MultiROI]] = None, sliceIndices: SequenceableCollection = None) → None¶

Applies a morphological erosion operation on a ROI or a MultiROI.

Changed in version -: Argument listToModify (list) is replaced by aROIToModify (single instance) - Argument sliceIndices (Array) is replaced by sliceIndicesExpr (string expression)

Parameters:

aROIToModify (ORSModel.ors.ROI, ORSModel.ors.MultiROI) – ROI or MultiROI to modify
kernelShape (str) – Kernel shape (‘square’, ‘circle’ or ‘cross’)
kernelDim (int) – Kernel dimension (2 or 3)
kernelSize (int) – Kernel size (odd number between 3 and 33)
dataset (ORSModel.ors.Channel) [const] – Dataset for range comparison (if application should be restricted to a range)
rangeMin (float) – minimal value of the range
rangeMax (float) – maximal value of the range
repetitionCount (int) – Count of repetition to be applied
currentTime (int) – Time step of the ROI
axis (int) – axis of operation if 2D kernel 0=X, 1=Y, 2=Z of the StructuredGrid
sliceIndicesExpr (str) – slices to work on in the given axis (string expression, 1-based, e.g. ‘1,2,3-5,4-20/3’)
listROIToModify (ORSModel.ors.ROI, ORSModel.ors.MultiROI) [count=[1, None]] [deprecated: use aROIToModify instead] – ROI or MultiROI to modify
sliceIndices (ORSModel.ors.SequenceableCollection) [deprecated: use sliceIndicesExpr instead] – collection of slices to work on in the given axis

interfacemethod exportROIAsALaplacianSmoothedAndSampledThicknessMesh(aROI: ROI, samplingX: int = 1, samplingY: int = 1, samplingZ: int = 1, currentTime: int = 0, nbOfIterations: int = 1) → Tuple[Mesh, bool]¶

Generates a smoothed thickness mesh from a ROI

The smoothing algorithm is a Laplacian.

No mesh is generated if the input ROI is empty.

Parameters:

aROI (ORSModel.ors.ROI) [const] – the ROI to get a thickness mesh representation from
samplingX (int) – sampling in X
samplingY (int) – sampling in Y
samplingZ (int) – sampling in Z
currentTime (int) – time index in the ROI
nbOfIterations (int) – smoothing iterations count

Returns:

mesh (ORSModel.ors.Mesh) – the generated thickness mesh
isThicknessMeshComputationCancelled (bool) – flag to know if the computation has been cancelled by the user

interfacemethod exportROIAsAWindowedSmoothedAndSampledThicknessMesh(aROI: ROI, samplingX: int = 1, samplingY: int = 1, samplingZ: int = 1, currentTime: int = 0, nbOfIterations: int = 2, isBoundarySmoothedOn: bool = False, isFeatureEdgeOn: bool = False, featureAngle: float = 0.5, passBandFactor: float = 0.001) → Tuple[Mesh, bool, int]¶

Generates a smoothed thickness mesh from a ROI

The smoothing algorithm is vtkWindowedSynFilter

No mesh is generated if the input ROI is empty.

Parameters:

aROI (ORSModel.ors.ROI) [const] – the ROI to get a thickness mesh representation from
samplingX (int) – sampling in X
samplingY (int) – sampling in Y
samplingZ (int) – sampling in Z
currentTime (int) – time index in the ROI
nbOfIterations (int) – smoothing iterations count
isBoundarySmoothedOn (bool) – if True, smoothing of vertices on the boundary of the mesh is performed
isFeatureEdgeOn (bool) – if True, smoothing along sharp interior edges is performed
featureAngle (float) – feature angle for sharp edge identification (in degree)
passBandFactor (float) – pass band value for the windowed filter

Returns:

mesh (ORSModel.ors.Mesh) – the generated thickness mesh
isThicknessMeshComputationCancelled (bool) – flag to know if the computation has been cancelled by the user
errorCode (int) – an error code

interfacemethod exportROIAsCubicMesh(aROI: Union[ROI, MultiROI], currentTime: int) → Tuple[Mesh, bool]¶

Generates a cubic mesh from a ROI or a MultiROI

No mesh is generated if the input ROI or MultiROI is empty.

Parameters:

aROI (ORSModel.ors.ROI, ORSModel.ors.MultiROI) [const] – the ROI or MultiROI to get a cubic mesh representation from
currentTime (int) – time index in the ROI or MultiROI

Returns:

mesh (ORSModel.ors.Mesh) – the generated cubic mesh
isCubicMeshComputationCancelled (bool) – flag to know if the computation has been cancelled by the user

interfacemethod exportROIAsSampledMesh(aROI: Union[ROI, MultiROI], samplingX: int, samplingY: int, samplingZ: int, currentTime: int = 0) → Tuple[Mesh, bool]¶

Generates a sampled mesh from a ROI or a MultiROI

No mesh is generated if the input ROI or MultiROI is empty.

Parameters:

aROI (ORSModel.ors.ROI, ORSModel.ors.MultiROI) [const] – the ROI or MultiROI to get a sampled mesh representation from
samplingX (int) – sampling in X
samplingY (int) – sampling in Y
samplingZ (int) – sampling in Z
currentTime (int) – time index in the ROI

Returns:

mesh (ORSModel.ors.Mesh) – the generated sampled mesh
isSampledMeshComputationCancelled (bool) – flag to know if the computation has been cancelled by the user

interfacemethod exportROIAsThicknessMesh(aROI: ROI, currentTime: int = 0) → Tuple[Mesh, bool]¶

Generates a thickness mesh from a ROI

No mesh is generated if the input ROI is empty.

Parameters:

aROI (ORSModel.ors.ROI) [const] – the ROI to get a thickness mesh representation from
currentTime (int) – time index in the ROI

Returns:

mesh (ORSModel.ors.Mesh) – the generated thickness mesh
isThicknessMeshComputationCancelled (bool) – flag to know if the computation has been cancelled by the user

interfacemethod exportROIAsThicknessMeshSample(aROI: ROI, xSampling: int, ySampling: int, zSampling: int, currentTime: int, smoothingIterationsCount: int = 0) → Tuple[Mesh, bool]¶

Generates a thickness mesh from a ROI

No mesh is generated if the input ROI is empty.

Parameters:

aROI (ORSModel.ors.ROI) [const] – the ROI to get a thickness mesh representation from
xSampling (int) – sampling in X
ySampling (int) – sampling in Y
zSampling (int) – sampling in Z
currentTime (int) – time index in the ROI
smoothingIterationsCount (int) – smoothing iterations count

Returns:

mesh (ORSModel.ors.Mesh) – the generated thickness mesh
isThicknessMeshComputationCancelled (bool) – flag to know if the computation has been cancelled by the user

classmethod extractSliceAsMultiROI(multiROI, sliceIndex, timestep, IProgress=None)¶: Extract a single slice from a MultiROI as a new MultiROI.

interfacemethod fillInnerAreas(aROIToModify: Union[ROI, MultiROI] = None, fillInnerAreasMode: str = '3D', currentTime: int = 0, listToModify: List[Union[ROI, MultiROI]] = None) → None¶

Applies a filling of inner areas on a ROI or a MultiROI.

Changed in version -: Argument listToModify (list) is replaced by aROIToModify (single instance) - Progress should be managed externally

Parameters:

aROIToModify (ORSModel.ors.ROI, ORSModel.ors.MultiROI) – ROI or MultiROI to modify
fillInnerAreasMode (str) – Filling mode (‘3D’, ‘2D (YZ)’, ‘2D (XZ)’ or ‘2D (XY)’)
currentTime (int) – Time step of the operation
listToModify (ORSModel.ors.ROI, ORSModel.ors.MultiROI) [count=[1, None]] [deprecated: use aROIToModify instead] – ROI or MultiROI to modify

classmethod get2DWindowLevel2Opacity(channel)¶

Gets the opacity of the range.

Parameters:: channel (ORSModel.ors.Channel) – associated channel to the visual
Returns:: rangeOpacity (float) – range opacity

interfacemethod getGridMultiROIFromROI(aROI: ROI, binX: int = 4, binY: int = 4, binZ: int = 4, IProgress: Progress = None) → MultiROI¶

Construct a MultiROi from a ROI where each label is the content of the ROI intersecting a cell of a uniform grid

Parameters:

aROI (ORSModel.ors.ROI) – the roi to grid
binX (int) – an int x cell size
binY (int) – an int y cell size
binZ (int) – an int z cell size
IProgress (ORSModel.ors.Progress) – progress object

Returns:

newMultiROI (ORSModel.ors.MultiROI) – the gridded ROI as a MultiROI

interfacemethod getGridMultiROIFromStructuredGrtid(aStructuredGrid: StructuredGrid, binX: int = 4, binY: int = 4, binZ: int = 4, IProgress: Progress = None) → MultiROI¶

Construct a MultiROi from a aStructuredGrid with an uniform grid

Parameters:

aStructuredGrid (ORSModel.ors.StructuredGrid) – aStructuredGrid to use as shape
binX (int) – an int x cell size
binY (int) – an int y cell size
binZ (int) – an int z cell size
IProgress (ORSModel.ors.Progress) – progress object

Returns:

newMultiROI (ORSModel.ors.MultiROI) – the gridded ROI as a MultiROI

classmethod getMainFormClass()¶

Gets the class of the main form

Returns:: output –

getMinMaxCurrentChannel()¶

Gets the minimal and maximal value of the current range channel.

Returns:

minValue (float) – minimal value of the current range channel
maxValue (float) – maximal value of the current range channel

interfacemethod getOtsuThreshold(dataset: Channel, currentTime: int, mask: ROI, useRange: bool = False, lowerRange: float = 0, upperRange: float = 0) → float¶

Get the otsu threshold of a dataset

Changed in version -: Argument useRange has been added - Argument lowerRange has been added - Argument upperRange has been added

Parameters:

dataset (ORSModel.ors.Channel) [const] – a dataset
currentTime (int) – timestep
mask (ORSModel.ors.ROI) [const] – a mask
useRange (bool) – if the range should be used
lowerRange (float) – lower range
upperRange (float) – upper range

Returns:

otsuThreshold (float) – the threshold value

interfacemethod getOtsuThresholdGivenRange(dataset: Channel, currentTime: int, mask: ROI, lowerRange: float, upperRange: float) → None¶

Gets the range of the second leveling of a visual associated to a dataset to lower Otsu value.

Parameters:

dataset (ORSModel.ors.Channel) – associated dataset
currentTime (int) – current time
mask (ORSModel.ors.ROI) – a mask
lowerRange (float) – lower range
upperRange (float) – upper range

interfacemethod getRange(channel: Channel) → Tuple[float, float]¶

Gets the range of a visual associated to a channel.

The returned values have no physical units.

Deprecated since version 4.5: Use getRangeInLayoutOfView.

Parameters:

channel (ORSModel.ors.Channel) – associated channel to the visual

Returns:

rangeMin (float) – minimal value of the range
rangeMax (float) – maximal value of the range

interfacemethod getRangeInLayoutOfView(channel: Channel, viewName: str) → Tuple[float, float]¶

Gets the range of a visual associated to a channel.

The returned values have no physical units.

Parameters:

channel (ORSModel.ors.Channel) [const] – associated channel to the visual
viewName (str) – a genealogical name

Returns:

rangeMin (float) – minimal value of the range
rangeMax (float) – maximal value of the range

getRangeInPhysicalUnitsOfCurrentVisual()¶

Gets the range (window level 2) of a visual in physical units and the slope and offset of the associated channel.

Returns:

rangeMinInPhysicalUnits (float) – minimal value of the range in physical units
rangeMaxInPhysicalUnits (float) – maximal value of the range in physical units
slope (float) – slope value in the channel
offset (float) – offset value in the channel

getRangeNoPhysicalUnitsOfCurrentVisual()¶

Gets the range (window level 2) of a visual without the physical units.

Returns:

rangeMinNoPhysicalUnits (float) – minimal value of the range without physical units
rangeMaxNoPhysicalUnits (float) – maximal value of the range without physical units

getState()¶

This method is called when saving a plugin instance in a session to obtain the information required to set up the plugin at the loading of the session.

The plugin needs to be savable (see ORSServiceClass.OrsPlugin.abstractPlugin.AbstractPlugin.savable).

Return:: a string of information that will be sent back to the setState method
Rtype:: str

Note

The usage of the character " is not permitted, unless escaped.

OrsVolumeROITools¶

Class Code¶

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