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 2018. |
| date: | Sep 11 2015 12:03 |
| dragonflyVersion: | |
| 3.1.0.286 (D) | |
| UUID: | 5bc96a00761e11e79055448a5b5d70c0 |
Class Code¶
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class
OrsPythonPlugins.OrsVolumeROITools.OrsVolumeROITools.OrsVolumeROITools(varname=None, managed=True)¶ -
UIDescriptors= [<ORSServiceClass.OrsPlugin.uidescriptor.UIDescriptor object>]¶
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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
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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
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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
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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
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canAddRangeToNewOnCurrentDataset()¶
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classmethod
canAddRemoveRange(listROIToModify, dataset, rangeMin, rangeMax)¶
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classmethod
canAddRemoveRangeCheckingOnlyRange(dataset, rangeMin, rangeMax)¶
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canAddRemoveRangeOnCurrentDataset(listROIToModify)¶
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classmethod
canAddRemoveRegionClipOnListOfROIs(listROIToModify)¶
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classmethod
canClear(listROIToModify)¶
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classmethod
canClose(listROIToModify, kernelShape, kernelDim, kernelSize, dataset, rangeMin, rangeMax, currentTime)¶
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canCloseOnCurrentDataset(listROIToModify, kernelShape, kernelDim, kernelSize, currentTime)¶
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classmethod
canCreateEmptyROIFromStructuredGrid(structuredGrid)¶
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classmethod
canCustomROITool(customROIToolName)¶
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classmethod
canDilate(listROIToModify, kernelShape, kernelDim, kernelSize, dataset, rangeMin, rangeMax, currentTime)¶
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canDilateOnCurrentDataset(listROIToModify, kernelShape, kernelDim, kernelSize, currentTime)¶
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classmethod
canErode(listROIToModify, kernelShape, kernelDim, kernelSize, dataset, rangeMin, rangeMax, currentTime)¶
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canErodeOnCurrentDataset(listROIToModify, kernelShape, kernelDim, kernelSize, currentTime)¶
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classmethod
canExportAsCubicMesh(listROIToExport)¶
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classmethod
canExportAsSampledMesh(listROIToExport, samplingX, samplingY, samplingZ, currentTime)¶
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classmethod
canExportAsSampledThicknessMesh(listROIToExport, samplingX, samplingY, samplingZ, currentTime)¶
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classmethod
canExportAsThicknessMesh(listROIToExport)¶
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classmethod
canFillInnerAreas(listROIToModify, fillInnerAreasMode, currentTime)¶
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classmethod
canOpen(listROIToModify, kernelShape, kernelDim, kernelSize, dataset, rangeMin, rangeMax, currentTime)¶
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canOpenOnCurrentDataset(listROIToModify, kernelShape, kernelDim, kernelSize, currentTime)¶
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classmethod
canOverwriteData(listROIToAnalyze, dataset)¶
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classmethod
canReverse(listROIToModify, currentTime)¶
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classmethod
canSkeletonize(listROIToModify)¶
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classmethod
canSplitAtOtsu(listROIToAnalyze, dataset, currentTime)¶
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classmethod
canUndo(listROIToModify)¶
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canUseRange()¶
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classmethod
chooseDataset()¶
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interfacemethod
clear(listROIToModify)¶ Clears the ROIs.
Parameters: listROIToModify (ORSModel.ors.ROI) [count=[1, None]] – ROI to clear
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closable= False¶
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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
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closeWidget(name)¶
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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
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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
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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
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contextualMenu(context)¶
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classmethod
createBestROIForROIs(listOfROIs)¶
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createDatasetFromMultiROI(aMultiROI)¶
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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
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createDistanceMapFromROIsAtCurrentTime(roiGUIDs, signed=False)¶
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interfacemethod
createEmptyROIFromStructuredGrid(structuredGrid, title, ROIColor)¶ Creates an empty ROI from a structured grid
Parameters: - structuredGrid (ORSModel.ors.StructuredGrid) – reference shape of the new ROI
- title (str) – title of the new ROI
- ROIColor (ORSModel.ors.Color) – color of the new ROI
Returns: output (ORSModel.ors.ROI) – created ROI
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interfacemethod
createLabeledROIFromROI(aROI, IProgress=None, includeDiagonal=False)¶ Computes the labelization of a ROI
Parameters: - aROI (ORSModel.ors.ROI) – ROI to compute the labelization on
- IProgress (ORSModel.ors.Progress) – progress object
- includeDiagonal (bool) – include diagonal 26 neighbor
Returns: labelizationMultiROI (ORSModel.ors.MultiROI) – MultiROI of the labelized ROI
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createLabeledROIFromROIAndPublish(aROI, includeDiagonal=False)¶
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createLabeledROIFromROIOrMultiROIAndPublish(aROIOrMultiROI, includeDiagonal=False)¶
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interfacemethod
createLabeledROIFromROIWithDiagonal(aROI, IProgress=None)¶ Computes the labelization of a ROI 26 neighbor
Parameters: - aROI (ORSModel.ors.ROI) – ROI to compute the labelization on
- IProgress (ORSModel.ors.Progress) – progress object
Returns: labelizationMultiROI (ORSModel.ors.MultiROI) – MultiROI of the labelized ROI
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createMeshFromMultiROI(aMultiROI)¶
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createMultiROIFromDataset(dataset)¶
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interfacemethod
createROIFromLabeledROI(aMultiROI, IProgress=None)¶ Creates a new ROI by taking all the voxels from all the labels of the MultiROI
Parameters: - aMultiROI (ORSModel.ors.MultiROI) – a MultiROI
- IProgress (ORSModel.ors.Progress) – progress object
Returns: aROI (ORSModel.ors.ROI) – a ROI
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createROIFromLabeledROIAndPublish(aMultiROI)¶
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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
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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
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interfacemethod
createVolumeThicknessFromROI(aROI, currentTime, IProgress=None)¶ Computes the volume thickness of a ROI
Parameters: - aROI (ORSModel.ors.ROI) – 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
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createVolumeThicknessFromROIAndPublish(aROI)¶
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interfacemethod
cutFromData(listROIToAnalyze, dataset)¶ Writes zeros 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
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deletePlugin(aWidget=None)¶
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dictCustomROITools= {}¶
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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
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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
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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
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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
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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
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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
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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
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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
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exportROIsAsCubicMesh(listROIToExport, currentTime)¶
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exportROIsAsSampledMesh(listROIToExport, samplingX, samplingY, samplingZ, currentTime=0)¶
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exportROIsAsSampledThicknessMesh(listROIToExport, samplingX, samplingY, samplingZ, currentTime=0, smoothingIterationsCount=0)¶
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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)¶
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exportROIsAsSmoothedThicknessMesh(listROIToExport, currentTime=0, smoothingMethod='Laplacian Smoothing', nbOfIterations=1, isBoundarySmoothedOn=False, isFeatureEdgeOn=False, featureAngle=0.5, passBandFactor=0.001)¶
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exportROIsAsThicknessMesh(listROIToExport, currentTime=0)¶
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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
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getCurrentChannel()¶
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getCurrentVisualChannel()¶
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classmethod
getCustomROIToolNames()¶
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classmethod
getListAvailableKernelDim()¶
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classmethod
getListAvailableKernelSize()¶
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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
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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
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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
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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
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getUseRange()¶
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classmethod
initializeCustomROITools()¶
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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
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classmethod
interpolateROIInBackground(listROIToInterpolate, axis=0, rbf=False, timeStep=0)¶
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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.
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keepAlive= False¶
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listCustomROIToolNames= []¶
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multiple= False¶
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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
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openWidget(name, dock=None, tab=None, x=-1, y=-1, w=-1, l=-1, order=-1)¶
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orsCurrentDisplayChange()¶
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orsSelectedObjectsChange()¶
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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
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classmethod
propagateDirtyAfterROIModification(listROIModified)¶
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classmethod
refreshDisplaysAfterROIModification(listROIModified)¶
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removeEmptyLabels(aMultiROI)¶
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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
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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
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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
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savable= True¶
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set2DWindowLevel2RangeOnCurrentVisual(rangeMinInPhysicalUnits, rangeMaxInPhysicalUnits, logging=True)¶
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setSecondLevelingStatusOnCurrentVisual(isEnabled)¶
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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
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interfacemethod
skeletonizeROI(aROI, IProgress=None)¶ Applies a skeletonize operation.
Parameters: - aROI (ORSModel.ors.ROI) – the ROI to skeletonize
- IProgress (ORSModel.ors.Progress) – progress object
Returns: skeletonROI (ORSModel.ors.ROI) – the skeletonization of the ROI
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skeletonizeROIAndPublish(aROI)¶
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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: - ROIToAnalyze (ORSModel.ors.ROI) – ROI over which the dataset will be analyzed
- dataset (ORSModel.ors.Channel) – Dataset to analyze
- currentTime (int) – Time step of the ROI and of the dataset
- IProgress (ORSModel.ors.Progress) – progress object
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
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classmethod
splitAtOtsuAndPublish(listROIToAnalyze, dataset, currentTime=0)¶
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thinFromMenu(roiGUIDs)¶
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interfacemethod
undo(listROIToModify)¶ Undo the last operation made on a ROI.
Parameters: listROIToModify (ORSModel.ors.ROI) [count=[1, None]] – ROI to modify
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updateHistogramDataOfCurrentChannel(histogramRange=None, axisUpdated=False)¶ Updates or creates an histogram data model object for the current range channel.
Return:
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updateVisualUsedForRange()¶
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