OrsVolumeROITools

Manages the tools applicable to Regions of Interest

author:ORS Team
contact:http://theobjects.com
email:info@theobjects.com
organization:Object Research Systems (ORS), Inc.
address:760 St-Paul West, suite 101, Montréal, Québec, Canada, H3C 1M4
copyright:Object Research Systems (ORS), Inc. All rights reserved 2019.
date:Sep 11 2015 12:03
dragonflyVersion:
 3.1.0.286 (D)
UUID:5bc96a00761e11e79055448a5b5d70c0

Class Code

class OrsPythonPlugins.OrsVolumeROITools.OrsVolumeROITools.OrsVolumeROITools(varname=None, managed=True)
UIDescriptors = [<ORSServiceClass.OrsPlugin.uidescriptor.UIDescriptor object>]
interfacemethod addRange(listROIToModify, dataset, rangeMin, rangeMax, timeStep=0)

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) – Dataset for range comparison
  • rangeMin (float) – minimal value of the range
  • rangeMax (float) – maximal value of the range
  • timeStep (int) – timeIndex
interfacemethod addRangeInterpolated(listROIToModify, dataset, rangeMin, rangeMax, cubicInterpolation, timeStep=0)

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) – 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, layoutFullName, dataset=None, rangeMin=0.0, rangeMax=0.0, add=True, currentTime=0)

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

Parameters:
  • listROIToModify (ORSModel.ors.ROI) [count=[1, None]] – ROI to modify
  • layoutFullName (str) – a genealogical name (the view in which the box is present)
  • dataset (ORSModel.ors.Channel) – 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
interfacemethod applyCustomTool(customToolName)

Applies a custom tool.

It is the responsibility of the custom tool to do the propagateDirty of the modified ROIs and to refresh the displays, because we don’t have access to the involved ROIs.

The “undo” is not taken care of here.

Parameters:customToolName (str) – name of the custom tool
canAddRangeToNewOnCurrentDataset()
classmethod canAddRemoveRange(listROIToModify, dataset, rangeMin, rangeMax)
classmethod canAddRemoveRangeCheckingOnlyRange(dataset, rangeMin, rangeMax)
canAddRemoveRangeOnCurrentDataset(listROIToModify)
classmethod canAddRemoveRegionClipOnListOfROIs(listROIToModify)
classmethod canClear(listROIToModify)
classmethod canClose(listROIToModify, kernelShape, kernelDim, kernelSize, dataset, rangeMin, rangeMax, currentTime)
canCloseOnCurrentDataset(listROIToModify, kernelShape, kernelDim, kernelSize, currentTime)
classmethod canCustomROITool(customROIToolName)
classmethod canDilate(listROIToModify, kernelShape, kernelDim, kernelSize, dataset, rangeMin, rangeMax, currentTime)
canDilateOnCurrentDataset(listROIToModify, kernelShape, kernelDim, kernelSize, currentTime)
classmethod canErode(listROIToModify, kernelShape, kernelDim, kernelSize, dataset, rangeMin, rangeMax, currentTime)
canErodeOnCurrentDataset(listROIToModify, kernelShape, kernelDim, kernelSize, currentTime)
classmethod canExportAsCubicMesh(listROIToExport)
classmethod canExportAsSampledMesh(listROIToExport, samplingX, samplingY, samplingZ, currentTime)
classmethod canExportAsSampledThicknessMesh(listROIToExport, samplingX, samplingY, samplingZ, currentTime)
classmethod canExportAsThicknessMesh(listROIToExport)
classmethod canFillInnerAreas(listROIToModify, fillInnerAreasMode, currentTime)
classmethod canOpen(listROIToModify, kernelShape, kernelDim, kernelSize, dataset, rangeMin, rangeMax, currentTime)
canOpenOnCurrentDataset(listROIToModify, kernelShape, kernelDim, kernelSize, currentTime)
classmethod canOverwriteData(listROIToAnalyze, dataset)
classmethod canReverse(listROIToModify, currentTime)
classmethod canSkeletonize(listROIToModify)
classmethod canSplitAtOtsu(listROIToAnalyze, dataset, currentTime)
classmethod canUndo(listROIToModify)
canUseRange()
classmethod chooseDataset()
interfacemethod clear(listROIToModify)

Clears the ROIs.

Parameters:listROIToModify (ORSModel.ors.ROI) [count=[1, None]] – ROI to clear
closable = False
interfacemethod close(listROIToModify, kernelShape, kernelDim, kernelSize, dataset=None, rangeMin=0.0, rangeMax=0.0, repetitionCount=1, currentTime=0)

Applies a morphological closing operation on a ROI.

Parameters:
  • listROIToModify (ORSModel.ors.ROI) [count=[1, None]] – ROI to modify
  • kernelShape (str) – Kernel shape (‘square’, ‘circle’ or ‘cross’)
  • kernelDim (int) – Kernel dimension (2 or 3)
  • kernelSize (int) – Kernel size (odd number between 1 and 33)
  • dataset (ORSModel.ors.Channel) – 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
closeWidget(name)
interfacemethod computeAnisotropyMIL(aROI, anisotropyMILRadius, anisotropyMILSampling, anisotropyMILOrientations, anisotropyMILMinIterations, anisotropyMILMaxIterations, anisotropyMILTolerance, IProgress=None)

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

Parameters:
  • aROI (ORSModel.ors.ROI) – 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
computeAnisotropyMILWithDialog(aROI)
interfacemethod computeAnisotropySVD(aROI, anisotropySVDRadius, anisotropySVDSampling, anisotropySVDOrientations, anisotropySVDMinIterations, anisotropySVDMaxIterations, anisotropySVDTolerance, IProgress=None)

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

Parameters:
  • aROI (ORSModel.ors.ROI) – 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
computeAnisotropySVDWithDialog(aROI)
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
interfacemethod computeWatershedFromMultiROI(aMultiROI, datasetForShape, timeStep)

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) – Dataset used to compute the edge map
  • timeStep (int) – time index of aMultiROI and of datasetForShape
interfacemethod computeWatershedFromROIs(listOfROIs, datasetForShape, timeStep)

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) – Dataset used to compute the edge map
  • timeStep (int) – time index of the input ROIs and of datasetForShape
contextualMenu(context)
classmethod createBestROIForROIs(listOfROIs)
createDatasetFromMultiROI(aMultiROI)
interfacemethod createDistanceMapFromROIs(ROIs, tIndex, IProgress=None)

Computes a distance map from a set of ROIs

Parameters:
  • ROIs (ORSModel.ors.ROI) [count=[1, None]] – 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
createDistanceMapFromROIsAtCurrentTime(roiGUIDs, signed=False)
interfacemethod createEmptyROIFromStructuredGrid(structuredGrid, title, ROIColor)

Creates an empty ROI from a structured grid

Parameters:
Returns:

output (ORSModel.ors.ROI) – created ROI
interfacemethod createEmptyROIFromVisualBox(aVisualBox, title, currentTime, ROIColor)

Creates an empty ROI from a structured grid

Parameters:
  • aVisualBox (ORSModel.ors.VisualBox) – 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
Returns:

output (ORSModel.ors.ROI) – created ROI
interfacemethod createLabeledROIFromROI(aROI, IProgress=None, includeDiagonal=False)

Computes the labelization of a ROI

Parameters:
Returns:

labelizationMultiROI (ORSModel.ors.MultiROI) – MultiROI of the labelized ROI
createLabeledROIFromROIAndPublish(aROI, includeDiagonal=False)
createLabeledROIFromROIOrMultiROIAndPublish(aROIOrMultiROI, includeDiagonal=False)
interfacemethod createLabeledROIFromROIWithDiagonal(aROI, IProgress=None)

Computes the labelization of a ROI 26 neighbor

Parameters:
Returns:

labelizationMultiROI (ORSModel.ors.MultiROI) – MultiROI of the labelized ROI
createMeshFromMultiROI(aMultiROI)
createMultiROIFromDataset(dataset)
interfacemethod createROIFromLabeledROI(aMultiROI, IProgress=None)

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

Parameters:
Returns:

aROI (ORSModel.ors.ROI) – a ROI
createROIFromLabeledROIAndPublish(aMultiROI)
interfacemethod createROIInRange(dataset, title, rangeMin, rangeMax, timeStep=0)

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

Parameters:
  • dataset (ORSModel.ors.Channel) – 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
Returns:

output (ORSModel.ors.ROI) – created ROI
interfacemethod createSignedDistanceMapFromROIs(ROIs, tIndex)

Computes a signed distance map from a set of ROIs

Parameters:
  • ROIs (ORSModel.ors.ROI) [count=[1, None]] – ROIs to compute the distance map from
  • tIndex (int) – time index of the ROIs to use
Returns:

distanceMapDataset (ORSModel.ors.Channel) – dataset of the computed distance map
interfacemethod createVolumeThicknessFromROI(aROI, currentTime, IProgress=None)

Computes the volume thickness of a ROI

Parameters:
Returns:

volumeThicknessChannel (ORSModel.ors.Channel) – Volume thickness
createVolumeThicknessFromROIAndPublish(aROI)
interfacemethod cutFromData(listROIToAnalyze, dataset)

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

Parameters:
deletePlugin(aWidget=None)
dictCustomROITools = {}
interfacemethod dilate(listROIToModify, kernelShape, kernelDim, kernelSize, dataset=None, rangeMin=0.0, rangeMax=0.0, repetitionCount=1, currentTime=0)

Applies a morphological dilation operation on a ROI.

Parameters:
  • listROIToModify (ORSModel.ors.ROI) [count=[1, None]] – ROI to modify
  • kernelShape (str) – Kernel shape (‘square’, ‘circle’ or ‘cross’)
  • kernelDim (int) – Kernel dimension (2 or 3)
  • kernelSize (int) – Kernel size (odd number between 1 and 33)
  • dataset (ORSModel.ors.Channel) – 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
interfacemethod erode(listROIToModify, kernelShape, kernelDim, kernelSize, dataset=None, rangeMin=0.0, rangeMax=0.0, repetitionCount=1, currentTime=0)

Applies a morphological erosion operation on a ROI.

Parameters:
  • listROIToModify (ORSModel.ors.ROI) [count=[1, None]] – ROI to modify
  • kernelShape (str) – Kernel shape (‘square’, ‘circle’ or ‘cross’)
  • kernelDim (int) – Kernel dimension (2 or 3)
  • kernelSize (int) – Kernel size (odd number between 1 and 33)
  • dataset (ORSModel.ors.Channel) – 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
interfacemethod exportROIAsALaplacianSmoothedAndSampledThicknessMesh(aROI, samplingX=1, samplingY=1, samplingZ=1, currentTime=0, nbOfIterations=1)

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) – 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, samplingX=1, samplingY=1, samplingZ=1, currentTime=0, nbOfIterations=2, isBoundarySmoothedOn=False, isFeatureEdgeOn=False, featureAngle=0.5, passBandFactor=0.001)

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) – 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) – smoothing iterations count
  • isFeatureEdgeOn (bool) – smoothing iterations count
  • featureAngle (float) – smoothing iterations count
  • passBandFactor (float) – 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
  • errorCode (int) – an error code
interfacemethod exportROIAsCubicMesh(aROI, currentTime)

Generates a cubic mesh from a ROI

No mesh is generated if the input ROI is empty.

Parameters:
  • aROI (ORSModel.ors.ROI) – the ROI to get a cubic mesh representation from
  • currentTime (int) – time index in the ROI
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, samplingX, samplingY, samplingZ, currentTime=0)

Generates a sampled mesh from a ROI

No mesh is generated if the input ROI is empty.

Parameters:
  • aROI (ORSModel.ors.ROI) – the ROI 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, currentTime=0)

Generates a thickness mesh from a ROI

No mesh is generated if the input ROI is empty.

Parameters:
  • aROI (ORSModel.ors.ROI) – 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, xSampling, ySampling, zSampling, currentTime, smoothingIterationsCount=0)

Generates a thickness mesh from a ROI

No mesh is generated if the input ROI is empty.

Parameters:
  • aROI (ORSModel.ors.ROI) – 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
exportROIsAsCubicMesh(listROIToExport, currentTime)
exportROIsAsSampledMesh(listROIToExport, samplingX, samplingY, samplingZ, currentTime=0)
exportROIsAsSampledThicknessMesh(listROIToExport, samplingX, samplingY, samplingZ, currentTime=0, smoothingIterationsCount=0)
exportROIsAsSmoothedSampledThicknessMesh(listROIToExport, samplingX=1, samplingY=1, samplingZ=1, currentTime=0, smoothingMethod='Laplacian Smoothing', nbOfIterations=1, isBoundarySmoothedOn=False, isFeatureEdgeOn=False, featureAngle=0.5, passBandFactor=0.001)
exportROIsAsSmoothedThicknessMesh(listROIToExport, currentTime=0, smoothingMethod='Laplacian Smoothing', nbOfIterations=1, isBoundarySmoothedOn=False, isFeatureEdgeOn=False, featureAngle=0.5, passBandFactor=0.001)
exportROIsAsThicknessMesh(listROIToExport, currentTime=0)
interfacemethod fillInnerAreas(listROIToModify, fillInnerAreasMode, currentTime=0)

Applies a filling of inner areas on a ROI.

Parameters:
  • listROIToModify (ORSModel.ors.ROI) [count=[1, None]] – ROI to modify
  • fillInnerAreasMode (str) – Filling mode (‘3D’, ‘2D (X)’, ‘2D (Y)’ or ‘2D (Z)’)
  • currentTime (int) – Time step of the ROI
getCurrentChannel()
getCurrentVisualChannel()
classmethod getCustomROIToolNames()
classmethod getListAvailableKernelDim()
classmethod getListAvailableKernelSize()
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
classmethod getOtsuThreshold(dataset, currentTime, mask)
interfacemethod getRange(channel)

Gets the range of a visual associated to a channel.

The returned values have no physical units.

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
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

See also

ORSServiceClass.OrsPlugin.orsPlugin.OrsPlugin.setState()

getUseRange()
classmethod initializeCustomROITools()
interfacemethod interpolateROI(listROIToInterpolate, axis=0, rbf=False, timeStep=0)

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

Parameters:
  • listROIToInterpolate (ORSModel.ors.ROI) [count=[1, None]] – ROI to modify
  • axis (int) – axis of interpolation
  • rbf (bool) – use rbf interpolation
  • timeStep (int) – timeIndex
classmethod interpolateROIInBackground(listROIToInterpolate, axis=0, rbf=False, timeStep=0)
isCurrentChannelInFloatingRepresentation()

Get the floating representation status of the current range channel.

Returns:isFloatingRepresentation (bool) – True if the channel has a float or double data type.
keepAlive = False
listCustomROIToolNames = []
multiple = False
interfacemethod open(listROIToModify, kernelShape, kernelDim, kernelSize, dataset=None, rangeMin=0.0, rangeMax=0.0, repetitionCount=1, currentTime=0)

Applies a morphological opening operation on a ROI.

Parameters:
  • listROIToModify (ORSModel.ors.ROI) [count=[1, None]] – ROI to modify
  • kernelShape (str) – Kernel shape (‘square’, ‘circle’ or ‘cross’)
  • kernelDim (int) – Kernel dimension (2 or 3)
  • kernelSize (int) – Kernel size (odd number between 1 and 33)
  • dataset (ORSModel.ors.Channel) – 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
openWidget(name, dock=None, tab=None, x=-1, y=-1, w=-1, l=-1, order=-1)
orsCurrentDisplayChange()
orsSelectedObjectsChange()
interfacemethod overwriteData(listROIToAnalyze, dataset, overwriteValue)

Writes a given value in a dataset at the location of the ROI.

Parameters:
  • listROIToAnalyze (ORSModel.ors.ROI) [count=[1, None]] – ROI over which the dataset will be written
  • dataset (ORSModel.ors.Channel) – Dataset to write in
  • overwriteValue (float) – Value to write in the dataset
classmethod propagateDirtyAfterROIModification(listROIModified)
classmethod refreshDisplaysAfterROIModification(listROIModified)
removeEmptyLabels(aMultiROI)
interfacemethod removeRange(listROIToModify, dataset, rangeMin, rangeMax, timeStep=0)

Removes 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) – Dataset for range comparison
  • rangeMin (float) – minimal value of the range
  • rangeMax (float) – maximal value of the range
  • timeStep (int) – timeIndex
interfacemethod removeRangeInterpolated(listROIToModify, dataset, rangeMin, rangeMax, cubicInterpolation, timeStep=0)

Removes 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) – 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
reset2DWindowLevel2RangeOnCurrentVisual(logging=True)
interfacemethod reverse(listROIToModify, currentTime=0)

Reverse the inclusion state of each voxel.

Parameters:
  • listROIToModify (ORSModel.ors.ROI) [count=[1, None]] – ROI to modify
  • currentTime (int) – Time step of the ROI
savable = True
set2DWindowLevel2RangeOnCurrentVisual(rangeMinInPhysicalUnits, rangeMaxInPhysicalUnits, logging=True)
interfacemethod setRangeAsLowerOtsu(dataset, iTIndex)

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

Parameters:
interfacemethod setRangeAsUpperOtsu(dataset, iTIndex)

Sets the range of the second leveling of a visual associated to a dataset to upper Otsu.

Parameters:
setSecondLevelingStatusOnCurrentVisual(isEnabled)
setState(state)

This method is called to set up the plugin when loading a session.

Note

This method is called only if the string returned by ORSServiceClass.OrsPlugin.orsPlugin.OrsPlugin.getState() at the saving of the session was not empty.

Parameters:state (str) – string of information as provided by the getState during the saving of the session
interfacemethod skeletonize(listROIToModify)

Applies a skeletonize operation.

Deprecated since version 4.0: Use skeletonizeROI.

Parameters:listROIToModify (ORSModel.ors.ROI) [count=[1, None]] – ROI to modify
interfacemethod skeletonizeROI(aROI, IProgress=None)

Applies a skeletonize operation.

Parameters:
Returns:

skeletonROI (ORSModel.ors.ROI) – the skeletonization of the ROI
skeletonizeROIAndPublish(aROI)
interfacemethod skeletonizeROIAsGraph(aROI, IProgress=None)

Applies a skeletonize operation and output the result as a graph.

Parameters:
Returns:

skeletonGraph (ORSModel.ors.Graph) – the skeletonization of the ROI as a Graph
skeletonizeROIAsGraphAndPublish(aROI)
interfacemethod smooth(ROIToModify, kernelShape, kernelDim, kernelSize, allowNewVoxels=True, dataset=None, rangeMin=0.0, rangeMax=0.0, currentTime=0, IProgress=None)

Applies a smoothing operation on a ROI.

Parameters:
  • ROIToModify (ORSModel.ors.ROI) – ROI to smooth
  • 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)
  • allowNewVoxels (bool) – if True, new voxels may be added by the smoothing operation; otherwise, the smoothing operation will only remove voxels.
  • dataset (ORSModel.ors.Channel) – 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
  • currentTime (int) – time step of the ROI
  • IProgress (ORSModel.ors.Progress) – progress object
classmethod smoothMultipleROIs(listROIToModify, kernelShape, kernelDim, kernelSize, allowNewVoxels=True, dataset=None, rangeMin=0.0, rangeMax=0.0, currentTime=0)
interfacemethod splitAtOtsu(ROIToAnalyze, dataset, currentTime=0, IProgress=None)

Creates the ROIs of the background and foreground obtained by the Otsu’s method. The values taken in the histogram are those where in the dataset at the location in the ROI.

Parameters:
Returns:
  • ROIBackground (ORSModel.ors.ROI) – the locations of the ROI to analyze where the dataset has the values lower than the Otsu threshold
  • ROIForeground (ORSModel.ors.ROI) – the locations of the ROI to analyze where the dataset has the values higher than the Otsu threshold
  • isComputationCancelled (bool) – flag to know if the computation has been cancelled by the user
classmethod splitAtOtsuAndPublish(listROIToAnalyze, dataset, currentTime=0)
interfacemethod undo(listROIToModify)

Undo the last operation made on a ROI.

Parameters:listROIToModify (ORSModel.ors.ROI) [count=[1, None]] – ROI to modify
updateHistogramDataOfCurrentChannel()

Updates or creates an histogram data model object for the current range channel.

Return:
updateVisualUsedForRange()