nipype.interfaces.slicer.surface module¶
Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.
GrayscaleModelMaker¶
Bases: SEMLikeCommandLine
Wrapped executable:
GrayscaleModelMaker.title: Grayscale Model Maker
category: Surface Models
description: Create 3D surface models from grayscale data. This module uses Marching Cubes to create an isosurface at a given threshold. The resulting surface consists of triangles that separate a volume into regions below and above the threshold. The resulting surface can be smoothed and decimated. This model works on continuous data while the module Model Maker works on labeled (or discrete) data.
version: 3.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/GrayscaleModelMaker
license: slicer3
contributor: Nicole Aucoin (SPL, BWH), Bill Lorensen (GE)
acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.
- Optional Inputs:
InputVolume (a pathlike object or string representing an existing file) – Volume containing the input grayscale data. Maps to a command-line argument:
%s(position: -2).OutputGeometry (a boolean or a pathlike object or string representing a file) – Output that contains geometry model. Maps to a command-line argument:
%s(position: -1).args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.decimate (a float) – Target reduction during decimation, as a decimal percentage reduction in the number of polygons. If 0, no decimation will be done. Maps to a command-line argument:
--decimate %f.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})name (a string) – Name to use for this model. Maps to a command-line argument:
--name %s.pointnormals (a boolean) – Calculate the point normals? Calculated point normals make the surface appear smooth. Without point normals, the surface will appear faceted. Maps to a command-line argument:
--pointnormals.smooth (an integer) – Number of smoothing iterations. If 0, no smoothing will be done. Maps to a command-line argument:
--smooth %d.splitnormals (a boolean) – Splitting normals is useful for visualizing sharp features. However it creates holes in surfaces which affect measurements. Maps to a command-line argument:
--splitnormals.threshold (a float) – Grayscale threshold of isosurface. The resulting surface of triangles separates the volume into voxels that lie above (inside) and below (outside) the threshold. Maps to a command-line argument:
--threshold %f.- Outputs:
OutputGeometry (a pathlike object or string representing an existing file) – Output that contains geometry model.
LabelMapSmoothing¶
Bases: SEMLikeCommandLine
Wrapped executable:
LabelMapSmoothing.title: Label Map Smoothing
category: Surface Models
description: This filter smoothes a binary label map. With a label map as input, this filter runs an anti-alising algorithm followed by a Gaussian smoothing algorithm. The output is a smoothed label map.
version: 1.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/LabelMapSmoothing
contributor: Dirk Padfield (GE), Josh Cates (Utah), Ross Whitaker (Utah)
acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. This filter is based on work developed at the University of Utah, and implemented at GE Research.
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})gaussianSigma (a float) – The standard deviation of the Gaussian kernel. Maps to a command-line argument:
--gaussianSigma %f.inputVolume (a pathlike object or string representing an existing file) – Input label map to smooth. Maps to a command-line argument:
%s(position: -2).labelToSmooth (an integer) – The label to smooth. All others will be ignored. If no label is selected by the user, the maximum label in the image is chosen by default. Maps to a command-line argument:
--labelToSmooth %d.maxRMSError (a float) – The maximum RMS error. Maps to a command-line argument:
--maxRMSError %f.numberOfIterations (an integer) – The number of iterations of the level set AntiAliasing algorithm. Maps to a command-line argument:
--numberOfIterations %d.outputVolume (a boolean or a pathlike object or string representing a file) – Smoothed label map. Maps to a command-line argument:
%s(position: -1).- Outputs:
outputVolume (a pathlike object or string representing an existing file) – Smoothed label map.
MergeModels¶
Bases: SEMLikeCommandLine
Wrapped executable:
MergeModels.title: Merge Models
category: Surface Models
description: Merge the polydata from two input models and output a new model with the added polydata. Uses the vtkAppendPolyData filter. Works on .vtp and .vtk surface files.
version: $Revision$
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/MergeModels
contributor: Nicole Aucoin (SPL, BWH), Ron Kikinis (SPL, BWH), Daniel Haehn (SPL, BWH)
acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.
- Optional Inputs:
Model1 (a pathlike object or string representing an existing file) – Model. Maps to a command-line argument:
%s(position: -3).Model2 (a pathlike object or string representing an existing file) – Model. Maps to a command-line argument:
%s(position: -2).ModelOutput (a boolean or a pathlike object or string representing a file) – Model. Maps to a command-line argument:
%s(position: -1).args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})- Outputs:
ModelOutput (a pathlike object or string representing an existing file) – Model.
ModelMaker¶
Bases: SEMLikeCommandLine
Wrapped executable:
ModelMaker.title: Model Maker
category: Surface Models
description: Create 3D surface models from segmented data.<p>Models are imported into Slicer under a model hierarchy node in a MRML scene. The model colors are set by the color table associated with the input volume (these colours will only be visible if you load the model scene file).</p><p><b>Create Multiple:</b></p><p>If you specify a list of Labels, it will over ride any start/end label settings.</p><p>If you click<i>Generate All</i>it will over ride the list of labels and any start/end label settings.</p><p><b>Model Maker Settings:</b></p><p>You can set the number of smoothing iterations, target reduction in number of polygons (decimal percentage). Use 0 and 1 if you wish no smoothing nor decimation.<br>You can set the flags to split normals or generate point normals in this pane as well.<br>You can save a copy of the models after intermediate steps (marching cubes, smoothing, and decimation if not joint smoothing, otherwise just after decimation); these models are not saved in the mrml file, turn off deleting temporary files first in the python window:<br><i>slicer.modules.modelmaker.cliModuleLogic().DeleteTemporaryFilesOff()</i></p>
version: 4.1
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ModelMaker
license: slicer4
contributor: Nicole Aucoin (SPL, BWH), Ron Kikinis (SPL, BWH), Bill Lorensen (GE)
acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.
- Optional Inputs:
InputVolume (a pathlike object or string representing an existing file) – Input label map. The Input Volume drop down menu is populated with the label map volumes that are present in the scene, select one from which to generate models. Maps to a command-line argument:
%s(position: -1).args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.color (a pathlike object or string representing an existing file) – Color table to make labels to colors and objects. Maps to a command-line argument:
--color %s.debug (a boolean) – Turn this flag on in order to see debugging output (look in the Error Log window that is accessed via the View menu). Maps to a command-line argument:
--debug.decimate (a float) – Chose the target reduction in number of polygons as a decimal percentage (between 0 and 1) of the number of polygons. Specifies the percentage of triangles to be removed. For example, 0.1 means 10% reduction and 0.9 means 90% reduction. Maps to a command-line argument:
--decimate %f.end (an integer) – If you want to specify a continuous range of labels from which to generate models, enter the higher label here. Voxel value up to which to continue making models. Skip any values with zero voxels. Maps to a command-line argument:
--end %d.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})filtertype (‘Sinc’ or ‘Laplacian’) – You can control the type of smoothing done on the models by selecting a filter type of either Sinc or Laplacian. Maps to a command-line argument:
--filtertype %s.generateAll (a boolean) – Generate models for all labels in the input volume. select this option if you want to create all models that correspond to all values in a labelmap volume (using the Joint Smoothing option below is useful with this option). Ignores Labels, Start Label, End Label settings. Skips label 0. Maps to a command-line argument:
--generateAll.jointsmooth (a boolean) – This will ensure that all resulting models fit together smoothly, like jigsaw puzzle pieces. Otherwise the models will be smoothed independently and may overlap. Maps to a command-line argument:
--jointsmooth.labels (a list of items which are an integer) – A comma separated list of label values from which to make models. f you specify a list of Labels, it will override any start/end label settings. If you click Generate All Models it will override the list of labels and any start/end label settings. Maps to a command-line argument:
--labels %s.modelSceneFile (a boolean or a list of items which are a pathlike object or string representing a file) – Generated models, under a model hierarchy node. Models are imported into Slicer under a model hierarchy node, and their colors are set by the color table associated with the input label map volume. The model hierarchy node must be created before running the model maker, by selecting Create New ModelHierarchy from the Models drop down menu. If you’re running from the command line, a model hierarchy node in a new mrml scene will be created for you. Maps to a command-line argument:
--modelSceneFile %s....name (a string) – Name to use for this model. Any text entered in the entry box will be the starting string for the created model file names. The label number and the color name will also be part of the file name. If making multiple models, use this as a prefix to the label and color name. Maps to a command-line argument:
--name %s.pad (a boolean) – Pad the input volume with zero value voxels on all 6 faces in order to ensure the production of closed surfaces. Sets the origin translation and extent translation so that the models still line up with the unpadded input volume. Maps to a command-line argument:
--pad.pointnormals (a boolean) – Turn this flag on if you wish to calculate the normal vectors for the points. Maps to a command-line argument:
--pointnormals.saveIntermediateModels (a boolean) – You can save a copy of the models after each of the intermediate steps (marching cubes, smoothing, and decimation if not joint smoothing, otherwise just after decimation). These intermediate models are not saved in the mrml file, you have to load them manually after turning off deleting temporary files in they python console (View ->Python Interactor) using the following command slicer.modules.modelmaker.cliModuleLogic().DeleteTemporaryFilesOff(). Maps to a command-line argument:
--saveIntermediateModels.skipUnNamed (a boolean) – Select this to not generate models from labels that do not have names defined in the color look up table associated with the input label map. If true, only models which have an entry in the color table will be generated. If false, generate all models that exist within the label range. Maps to a command-line argument:
--skipUnNamed.smooth (an integer) – Here you can set the number of smoothing iterations for Laplacian smoothing, or the degree of the polynomial approximating the windowed Sinc function. Use 0 if you wish no smoothing. . Maps to a command-line argument:
--smooth %d.splitnormals (a boolean) – Splitting normals is useful for visualizing sharp features. However it creates holes in surfaces which affects measurements. Maps to a command-line argument:
--splitnormals.start (an integer) – If you want to specify a continuous range of labels from which to generate models, enter the lower label here. Voxel value from which to start making models. Used instead of the label list to specify a range (make sure the label list is empty or it will over ride this). Maps to a command-line argument:
--start %d.- Outputs:
modelSceneFile (a list of items which are a pathlike object or string representing an existing file) – Generated models, under a model hierarchy node. Models are imported into Slicer under a model hierarchy node, and their colors are set by the color table associated with the input label map volume. The model hierarchy node must be created before running the model maker, by selecting Create New ModelHierarchy from the Models drop down menu. If you’re running from the command line, a model hierarchy node in a new mrml scene will be created for you.
ModelToLabelMap¶
Bases: SEMLikeCommandLine
Wrapped executable:
ModelToLabelMap.title: Model To Label Map
category: Surface Models
description: Intersects an input model with an reference volume and produces an output label map.
version: 0.1.0.$Revision: 8643 $(alpha)
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/PolyDataToLabelMap
contributor: Nicole Aucoin (SPL, BWH), Xiaodong Tao (GE)
acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.
- Optional Inputs:
InputVolume (a pathlike object or string representing an existing file) – Input volume. Maps to a command-line argument:
%s(position: -3).OutputVolume (a boolean or a pathlike object or string representing a file) – The label volume. Maps to a command-line argument:
%s(position: -1).args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.distance (a float) – Sample distance. Maps to a command-line argument:
--distance %f.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})surface (a pathlike object or string representing an existing file) – Model. Maps to a command-line argument:
%s(position: -2).- Outputs:
OutputVolume (a pathlike object or string representing an existing file) – The label volume.
ProbeVolumeWithModel¶
Bases: SEMLikeCommandLine
Wrapped executable:
ProbeVolumeWithModel.title: Probe Volume With Model
category: Surface Models
description: Paint a model by a volume (using vtkProbeFilter).
version: 0.1.0.$Revision: 1892 $(alpha)
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ProbeVolumeWithModel
contributor: Lauren O’Donnell (SPL, BWH)
acknowledgements: BWH, NCIGT/LMI
- Optional Inputs:
InputModel (a pathlike object or string representing an existing file) – Input model. Maps to a command-line argument:
%s(position: -2).InputVolume (a pathlike object or string representing an existing file) – Volume to use to ‘paint’ the model. Maps to a command-line argument:
%s(position: -3).OutputModel (a boolean or a pathlike object or string representing a file) – Output ‘painted’ model. Maps to a command-line argument:
%s(position: -1).args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})- Outputs:
OutputModel (a pathlike object or string representing an existing file) – Output ‘painted’ model.