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| − | <noinclude>{{documentation/versioncheck}} | + | <noinclude>{{documentation/versioncheck}}</noinclude> |
| − | </noinclude> | |
| − | __TOC__
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| | | | |
| − | | + | {{documentation/banner |
| − | =Community-contributed modules=
| + | | text = [https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html This page has been moved to read-the-docs.] |
| − | | + | | background-color = 8FBC8F }} |
| − | The examples in this section are [[Documentation/{{documentation/version}}/Developers/Modules#Scripted_Modules| Scripted Modules]] that provide a user interface in the module panel along with specialized implementation logic.
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| − | | |
| − | Usage: save the .py file to a directory, add the directory to the additional module paths in the Slicer application settings (choose in the menu: Edit / Application settings, click Modules, click >> next to Additional module paths, click Add, and choose the .py file's location).
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| − | | |
| − | More information about python scripted modules and more usage examples can be found in the[[Documentation/{{documentation/version}}/Developers/Python_scripting | Python scripting]] wiki page.
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| − | | |
| − | ==Filters==
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| − | | |
| − | *[https://raw.github.com/pieper/VolumeMasker/master/VolumeMasker.py VolumeMasker.py]: Update a target volume with the results of setting all input volume voxels to 0 except for those that correspond to a selected label value in an input label map (Used for example in the volume rendering in [https://www.youtube.com/watch?v=dfu2gugHLHs this video).
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| − | | |
| − | ==DICOM==
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| − | | |
| − | *[https://gist.github.com/pieper/6186477 dicom header browser] to easily scroll through dicom files using dcmdump.
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| − | *[https://github.com/SlicerRt/SlicerRT/tree/master/BatchProcessing SlicerRT batch processing] to batch convert RT structure sets to labelmap NRRD files.
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| − | | |
| − | ==Informatics==
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| − | | |
| − | *[https://gist.github.com/lassoan/bf0954d93cacc8cbe27cd4a3ad503f2f MarkupsInfo.py]: Compute the total length between all the points of a markup list.
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| − | *[https://github.com/lassoan/SlicerLineProfile/blob/master/LineProfile/LineProfile.py LineProfile.py]: Compute intensity profile in a volume along a line.
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| − | | |
| − | =Community-contributed examples=
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| − | | |
| − | Usage: Copy-paste the shown code lines or linked .py file contents into Python console in Slicer. Or save them to a file and run them using execfile.
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| − | | |
| − | ==Get node object from the scene from node name or ID==
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| − | | |
| − | Examples in the script repository commonly use <code>slicer.util.getNode()</code> function for getting a node object from the scene. This method is only recommended for testing and interactive debugging.
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| − | | |
| − | *<code>slicer.util.getNode()</code> is recommended **only for interactive debugging** in the Python console/Jupyter notebook
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| − | **its input is intentionally defined vaguely (it can be either node ID or name and you can use wildcards such as <code>*</code>), which is good because it make it simpler to use, but the uncertain behavior is not good for general-purpose use in a module
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| − | **throws an exception so that the developer knows immediately that there was a typo or other unexpected error
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| − | *<code>slicer.mrmlScene.GetNodeByID()</code> is optimized for usage in modules:
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| − | **its behavior is more predictable: it only accepts node ID as input. <code>slicer.mrmlScene.GetFirstNodeByName()</code> can be used to get a node by its name, but since multiple nodes in the scene can have the same name, it is not recommended to keep reference to a node by its name.
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| − | **if node is not found it returns <code>None</code> (instead of throwing an exception), because this is often not considered an error in module code (it is just used to check existence of a node) and using return value for not-found nodes allows simpler syntax
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| − | | |
| − | ==Capture==
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| − | | |
| − | *Capture the full Slicer screen and save it into a file
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| − | | |
| − | img = qt.QPixmap.grabWidget(slicer.util.mainWindow()).toImage()
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| − | img.save('c:/tmp/test.png')
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| − | | |
| − | *Capture all the views save it into a file:
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| − | <pre>
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| − | import ScreenCapture
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| − | cap = ScreenCapture.ScreenCaptureLogic()
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| − | cap.showViewControllers(False)
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| − | cap.captureImageFromView(None,'c:/tmp/test.png')
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| − | cap.showViewControllers(True)
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| − | </pre>
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| − | | |
| − | *Capture a single view:
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| − | <pre>
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| − | viewNodeID = 'vtkMRMLViewNode1'
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| − | import ScreenCapture
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| − | cap = ScreenCapture.ScreenCaptureLogic()
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| − | view = cap.viewFromNode(slicer.mrmlScene.GetNodeByID(viewNodeID))
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| − | cap.captureImageFromView(view,'c:/tmp/test.png')
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| − | </pre>
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| − | Common values for viewNodeID: vtkMRMLSliceNodeRed, vtkMRMLSliceNodeYellow, vtkMRMLSliceNodeGreen, vtkMRMLViewNode1, vtkMRMLViewNode2.
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| − | The ScreenCapture module can also create video animations of rotating views, slice sweeps, etc.
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| − | | |
| − | *Capture a slice view sweep into a series of PNG files - for example, Red slice view, 30 images, from position -125.0 to 75.0, into c:/tmp folder, with name image_00001.png, image_00002.png, ...
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| − | | |
| − | <pre>
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| − | import ScreenCapture
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| − | ScreenCapture.ScreenCaptureLogic().captureSliceSweep(getNode('vtkMRMLSliceNodeRed'), -125.0, 75.0, 30, "c:/tmp", "image_%05d.png")
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| − | </pre>
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| − | | |
| − | *Capture 3D view into PNG file with transparent background
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| − | <pre>
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| − | renderWindow = slicer.app.layoutManager().threeDWidget(0).threeDView().renderWindow()
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| − | renderWindow.SetAlphaBitPlanes(1)
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| − | wti = vtk.vtkWindowToImageFilter()
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| − | wti.SetInputBufferTypeToRGBA()
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| − | wti.SetInput(renderWindow)
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| − | writer = vtk.vtkPNGWriter()
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| − | writer.SetFileName("c:/tmp/screenshot.png")
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| − | writer.SetInputConnection(wti.GetOutputPort())
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| − | writer.Write()
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| − | </pre>
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| − | | |
| − | ==Launching Slicer==
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| − | | |
| − | *How to open an .mrb file with Slicer at the command line?
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| − | | |
| − | Slicer.exe --python-code "slicer.util.loadScene( 'f:/2013-08-23-Scene.mrb' )"
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| − | | |
| − | *How to run a script in the Slicer environment in batch mode (without showing any graphical user interface)?
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| − | | |
| − | Slicer.exe --python-code "doSomething; doSomethingElse; etc." --testing --no-splash --no-main-window
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| − | | |
| − | ==Load volume from file==
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| − | | |
| − | <pre>
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| − | loadedVolumeNode = slicer.util.loadVolume('c:/Users/abc/Documents/MRHead.nrrd')
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| − | </pre>
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| − | | |
| − | Additional options may be specified in <code>properties</code> argument. For example, load an image stack by disabling <code>singleFile</code> option:
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| − | | |
| − | <pre>
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| − | loadedVolumeNode = slicer.util.loadVolume('c:/Users/abc/Documents/SomeImage/file001.png', {'singleFile': False})
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| − | </pre>
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| − | | |
| − | Get a MRML node in the scene based on the node name and call methods of that object. For the MRHead sample data:
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| − | | |
| − | vol=slicer.util.getNode('MR*')
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| − | vol.GetImageData().GetDimensions()
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| − | | |
| − | | |
| − | ==Load volume from URL==
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| − | | |
| − | Download a volume from a URL and load it into the scene using the code snippet below. Downloaded data is temporarily preserved in the application's cache folder and if the checksum of the already downloaded data matches the specified checksum (<algo>:<digest>) then the file is retrieved from the cache instead of being downloaded again. To compute digest with algo ''SHA256'', you can run <code>slicer.util.computeChecksum("SHA256", "path/to/file")</code>.
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| − | | |
| − | <pre>
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| − | import SampleData
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| − | sampleDataLogic = SampleData.SampleDataLogic()
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| − | loadedNodes = sampleDataLogic.downloadFromURL(
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| − | nodeNames='MRHead',
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| − | fileNames='MR-head25.nrrd',
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| − | uris='https://github.com/Slicer/SlicerTestingData/releases/download/SHA256/cc211f0dfd9a05ca3841ce1141b292898b2dd2d3f08286affadf823a7e58df93',
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| − | checksums='SHA256:cc211f0dfd9a05ca3841ce1141b292898b2dd2d3f08286affadf823a7e58df93')[0]
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| − | </pre>
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| − | | |
| − | With interruptible progress reporting using a progress bar:
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| − | | |
| − | <pre>
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| − | import SampleData
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| − | | |
| − | def reportProgress(msg, level=None):
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| − | # Print progress in the console
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| − | print("Loading... {0}%".format(sampleDataLogic.downloadPercent))
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| − | # Abort download if cancel is clicked in progress bar
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| − | if slicer.progressWindow.wasCanceled:
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| − | raise Exception('download aborted')
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| − | # Update progress window
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| − | slicer.progressWindow.show()
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| − | slicer.progressWindow.activateWindow()
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| − | slicer.progressWindow.setValue(int(sampleDataLogic.downloadPercent))
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| − | slicer.progressWindow.setLabelText("Downloading...")
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| − | # Process events to allow screen to refresh
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| − | slicer.app.processEvents()
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| − | | |
| − | try:
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| − | volumeNode = None
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| − | slicer.progressWindow = slicer.util.createProgressDialog()
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| − | sampleDataLogic = SampleData.SampleDataLogic()
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| − | sampleDataLogic.logMessage = reportProgress
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| − | loadedNodes = sampleDataLogic.downloadFromURL(
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| − | nodeNames='MRHead',
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| − | fileNames='MR-head25.nrrd',
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| − | uris='https://github.com/Slicer/SlicerTestingData/releases/download/SHA256/cc211f0dfd9a05ca3841ce1141b292898b2dd2d3f08286affadf823a7e58df93',
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| − | checksums='SHA256:cc211f0dfd9a05ca3841ce1141b292898b2dd2d3f08286affadf823a7e58df93')
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| − | volumeNode = loadedNodes[0]
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| − | finally:
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| − | slicer.progressWindow.close()
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| − | </pre>
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| − | | |
| − | ==Show volume rendering automatically when a volume is loaded==
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| − | | |
| − | To show volume rendering of a volume automatically when it is loaded, add the lines below to your
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| − | [[Documentation/{{documentation/version}}/Developers/Python_scripting#How_to_systematically_execute_custom_python_code_at_startup_.3F|.slicerrc file]].
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| − | | |
| − | <pre>
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| − | @vtk.calldata_type(vtk.VTK_OBJECT)
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| − | def onNodeAdded(caller, event, calldata):
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| − | node = calldata
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| − | if isinstance(node, slicer.vtkMRMLVolumeNode):
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| − | # Call showVolumeRendering using a timer instead of calling it directly
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| − | # to allow the volume loading to fully complete.
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| − | qt.QTimer.singleShot(0, lambda: showVolumeRendering(node))
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| − | | |
| − | def showVolumeRendering(volumeNode):
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| − | print("Show volume rendering of node "+volumeNode.GetName())
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| − | volRenLogic = slicer.modules.volumerendering.logic()
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| − | displayNode = volRenLogic.CreateDefaultVolumeRenderingNodes(volumeNode)
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| − | displayNode.SetVisibility(True)
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| − | scalarRange = volumeNode.GetImageData().GetScalarRange()
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| − | if scalarRange[1]-scalarRange[0] < 1500:
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| − | # small dynamic range, probably MRI
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| − | displayNode.GetVolumePropertyNode().Copy(volRenLogic.GetPresetByName('MR-Default'))
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| − | else:
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| − | # larger dynamic range, probably CT
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| − | displayNode.GetVolumePropertyNode().Copy(volRenLogic.GetPresetByName('CT-Chest-Contrast-Enhanced'))
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| − |
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| − | slicer.mrmlScene.AddObserver(slicer.vtkMRMLScene.NodeAddedEvent, onNodeAdded)
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| − | </pre>
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| − | | |
| − | ==Automatically load volumes that are copied into a folder==
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| − | | |
| − | This example shows how to implement a simple background task by using a timer. The background task is to check for any new volume files in folder and if there is any then automatically load it.
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| − | | |
| − | There are more efficient methods for file system monitoring or exchanging image data in real-time (for example, using OpenIGTLink), the example below is just for demonstration purposes.
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| − | | |
| − | <pre>
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| − | incomingVolumeFolder = "c:/tmp/incoming"
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| − | incomingVolumesProcessed = []
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| − | | |
| − | def checkForNewVolumes():
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| − | # Check if there is a new file in the
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| − | from os import listdir
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| − | from os.path import isfile, join
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| − | for f in listdir(incomingVolumeFolder):
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| − | if f in incomingVolumesProcessed:
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| − | # this is an incoming file, it was already there
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| − | continue
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| − | filePath = join(incomingVolumeFolder, f)
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| − | if not isfile(filePath):
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| − | # ignore directories
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| − | continue
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| − | logging.info("Loading new file: "+f)
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| − | incomingVolumesProcessed.append(f)
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| − | slicer.util.loadVolume(filePath)
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| − | # Check again in 3000ms
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| − | qt.QTimer.singleShot(3000, checkForNewVolumes)
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| − | | |
| − | # Start monitoring
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| − | checkForNewVolumes()
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| − | </pre>
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| − | | |
| − | ==DICOM==
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| − | ===How to load DICOM files into the scene from a folder===
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| − | | |
| − | This code loads all DICOM objects into the scene from a file folder. All the registered plugins are evaluated and the one with the highest confidence will be used to load the data. Files are imported into a temporary DICOM database, so the current Slicer DICOM database is not impacted.
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| − | | |
| − | <pre>
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| − | dicomDataDir = "c:/my/folder/with/dicom-files" # input folder with DICOM files
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| − | loadedNodeIDs = [] # this list will contain the list of all loaded node IDs
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| − |
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| − | from DICOMLib import DICOMUtils
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| − | with DICOMUtils.TemporaryDICOMDatabase() as db:
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| − | DICOMUtils.importDicom(dicomDataDir, db)
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| − | patientUIDs = db.patients()
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| − | for patientUID in patientUIDs:
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| − | loadedNodeIDs.extend(DICOMUtils.loadPatientByUID(patientUID))
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| − | </pre>
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| − | | |
| − | ===How to import DICOM files into the application's DICOM database===
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| − | | |
| − | This code snippet uses Slicer DICOM browser built-in indexer to import DICOM files into the database. Images are not loaded into the scene, but they show up in the DICOM browser. After import, data sets can be loaded using DICOMUtils functions (e.g., loadPatientByUID) - see above for an example.
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| − | | |
| − | <pre>
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| − | # instantiate a new DICOM browser
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| − | slicer.util.selectModule("DICOM")
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| − | dicomBrowser = slicer.modules.DICOMWidget.browserWidget.dicomBrowser
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| − | # use dicomBrowser.ImportDirectoryCopy to make a copy of the files (useful for importing data from removable storage)
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| − | dicomBrowser.importDirectory(dicomFilesDirectory, dicomBrowser.ImportDirectoryAddLink)
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| − | # wait for import to finish before proceeding (optional, if removed then import runs in the background)
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| − | dicomBrowser.waitForImportFinished()
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| − | </pre>
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| − | | |
| − | ===How to import DICOM files using DICOMweb===
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| − | | |
| − | Download and import DICOM data set using DICOMweb from [https://kheops.online/ Kheops], Google Health API, etc.
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| − | | |
| − | How to obtain accessToken:
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| − | | |
| − | *Google Cloud: Execute <code>gcloud auth print-access-token</code> once you have logged in
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| − | *Kheops: create an album, create a sharing link (somethin like <code>https://demo.kheops.online/view/TfYXwbKAW7JYbAgZ7MyISf</code>), the token is the string after the last slash
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| − | | |
| − | <pre>
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| − | slicer.util.selectModule("DICOM") # ensure DICOM database is initialized and
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| − | slicer.app.processEvents()
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| − | from DICOMLib import DICOMUtils
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| − | DICOMUtils.importFromDICOMWeb(
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| − | dicomWebEndpoint="http://demo.kheops.online/api",
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| − | studyInstanceUID="1.3.6.1.4.1.14519.5.2.1.8421.4009.985792766370191766692237040819",
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| − | accessToken="TfYXwbKAW7JYbAgZ7MyISf")
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| − | </pre>
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| − | | |
| − | ===How to access top level tags of DICOM images imported into Slicer?===
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| − | | |
| − | For example, to print the first patient's first study's first series' "0020,0032" field:
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| − | | |
| − | <pre>
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| − | db=slicer.dicomDatabase
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| − | patientList=db.patients()
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| − | studyList=db.studiesForPatient(patientList[0])
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| − | seriesList=db.seriesForStudy(studyList[0])
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| − | fileList=db.filesForSeries(seriesList[0])
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| − | # Note, fileValue accesses the database of cached top level tags
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| − | # (nested tags are not included)
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| − | print(db.fileValue(fileList[0],'0020,0032'))
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| − | # Get tag group,number from dicom dictionary
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| − | import pydicom as dicom
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| − | tagName = "StudyDate"
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| − | tagStr = str(dicom.tag.Tag(tagName))[1:-1].replace(' ','')
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| − | print(db.fileValue(fileList[0],tagStr))
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| − | </pre>
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| − | | |
| − | ===How to access DICOM tags nested in a sequence===
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| − | db=slicer.dicomDatabase
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| − | patientList=db.patients()
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| − | studyList=db.studiesForPatient(patientList[0])
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| − | seriesList=db.seriesForStudy(studyList[0])
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| − | fileList=db.filesForSeries(seriesList[0])
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| − | # use pydicom to access the full header, which requires
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| − | # re-reading the dataset instead of using the database cache
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| − | import pydicom
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| − | pydicom.dcmread(fileList[0])
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| − | ds.CTExposureSequence[0].ExposureModulationType
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| − | | |
| − | ===How to access tag of a volume loaded from DICOM? For example, get the patient position stored in a volume:===
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| − | volumeName='2: ENT IMRT'
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| − | n=slicer.util.getNode(volumeName)
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| − | instUids=n.GetAttribute('DICOM.instanceUIDs').split()
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| − | filename=slicer.dicomDatabase.fileForInstance(instUids[0])
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| − | print(slicer.dicomDatabase.fileValue(filename,'0018,5100'))
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| − | | |
| − | ===How to access tag of an item in the Subject Hierachy tree? For example, get the content time tag of a structure set:===
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| − | rtStructName = '3: RTSTRUCT: PROS'
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| − | rtStructNode = slicer.util.getNode(rtStructName)
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| − | shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
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| − | rtStructShItemID = shNode.GetItemByDataNode(rtStructNode)
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| − | ctSliceInstanceUids = shNode.GetItemAttribute(rtStructShItemID, 'DICOM.ReferencedInstanceUIDs').split()
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| − | filename = slicer.dicomDatabase.fileForInstance(ctSliceInstanceUids[0])
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| − | print(slicer.dicomDatabase.fileValue(filename,'0008,0033'))
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| − | | |
| − | ===How to get path and filename of a loaded DICOM volume?===
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| − | def pathFromNode(node):
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| − | storageNode=node.GetStorageNode()
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| − | if storageNode is not None: # loaded via drag-drop
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| − | filepath=storageNode.GetFullNameFromFileName()
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| − | else: # loaded via DICOM browser
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| − | instanceUIDs=node.GetAttribute('DICOM.instanceUIDs').split()
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| − | filepath=slicer.dicomDatabase.fileForInstance(instUids[0])
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| − | return filepath
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| − |
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| − | # example:
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| − | node=slicer.util.getNode('volume1')
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| − | path=self.pathFromNode(node)
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| − | print("DICOM path=%s" % path)
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| − | | |
| − | ===How can I convert DICOM to NRRD on the command line?===
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| − | | |
| − | /Applications/Slicer-4.6.2.app/Contents/MacOS/Slicer --no-main-window --python-code "node=slicer.util.loadVolume('/tmp/series/im0.dcm'); slicer.util.saveNode(node, '/tmp/output.nrrd'); exit()"
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| − | | |
| − | The same can be done on windows by using the top level Slicer.exe. Be sure to use forward slashes in the pathnames within quotes on the command line.
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| − | | |
| − | ===Export a volume to DICOM file format===
| |
| − | | |
| − | <pre>
| |
| − | volumeNode = getNode('CTChest')
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| − | outputFolder = "c:/tmp/dicom-output"
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| − | | |
| − | # Create patient and study and put the volume under the study
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| − | shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
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| − | patientItemID = shNode.CreateSubjectItem(shNode.GetSceneItemID(), "test patient")
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| − | studyItemID = shNode.CreateStudyItem(patientItemID, "test study")
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| − | volumeShItemID = shNode.GetItemByDataNode(volumeNode)
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| − | shNode.SetItemParent(volumeShItemID, studyItemID)
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| − | | |
| − | import DICOMScalarVolumePlugin
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| − | exporter = DICOMScalarVolumePlugin.DICOMScalarVolumePluginClass()
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| − | exportables = exporter.examineForExport(volumeShItemID)
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| − | for exp in exportables:
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| − | exp.directory = outputFolder
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| − | | |
| − | exporter.export(exportables)
| |
| − | </pre>
| |
| − | | |
| − | ===Export a segmentation to DICOM segmentation object===
| |
| − | | |
| − | <pre>
| |
| − | segmentationNode = ...
| |
| − | referenceVolumeNode = ...
| |
| − | outputFolder = "c:/tmp/dicom-output"
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| − | | |
| − | # Associate segmentation node with a reference volume node
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| − | shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
| |
| − | referenceVolumeShItem = shNode.GetItemByDataNode(referenceVolumeNode)
| |
| − | studyShItem = shNode.GetItemParent(referenceVolumeShItem)
| |
| − | segmentationShItem = shNode.GetItemByDataNode(segmentationNode)
| |
| − | shNode.SetItemParent(segmentationShItem, studyShItem)
| |
| − | | |
| − | # Export to DICOM
| |
| − | import DICOMSegmentationPlugin
| |
| − | exporter = DICOMSegmentationPlugin.DICOMSegmentationPluginClass()
| |
| − | exportables = exporter.examineForExport(segmentationShItem)
| |
| − | for exp in exportables:
| |
| − | exp.directory = outputFolder
| |
| − | | |
| − | exporter.export(exportables)
| |
| − | </pre>
| |
| − | | |
| − | ===Customize table columns in DICOM browser===
| |
| − | | |
| − | Documentation of methods for changing DICOM browser columns: https://github.com/commontk/CTK/blob/master/Libs/DICOM/Core/ctkDICOMDatabase.h#L354-L375
| |
| − | | |
| − | <pre>
| |
| − | # Get browser and database
| |
| − | dicomBrowser = slicer.modules.dicom.widgetRepresentation().self().browserWidget.dicomBrowser
| |
| − | dicomDatabase = dicomBrowser.database()
| |
| − | | |
| − | # Print list of available columns
| |
| − | print(dicomDatabase.patientFieldNames)
| |
| − | print(dicomDatabase.studyFieldNames)
| |
| − | print(dicomDatabase.seriesFieldNames)
| |
| − | | |
| − | # Change column order
| |
| − | dicomDatabase.setWeightForField('Series', 'SeriesDescription', 7)
| |
| − | dicomDatabase.setWeightForField('Studies', 'StudyDescription', 6)
| |
| − | # Change column visibility
| |
| − | dicomDatabase.setVisibilityForField('Patients', 'PatientsBirthDate', False)
| |
| − | dicomDatabase.setVisibilityForField('Patients', 'PatientsComments', True)
| |
| − | dicomDatabase.setWeightForField('Patients', 'PatientsComments', 8)
| |
| − | # Change column name
| |
| − | dicomDatabase.setDisplayedNameForField('Series', 'DisplayedCount', 'Number of images')
| |
| − | # Change column width to manual
| |
| − | dicomDatabase.setFormatForField('Series', 'SeriesDescription', '{"resizeMode":"interactive"}')
| |
| − | # Customize table manager in DICOM browser
| |
| − | dicomTableManager = dicomBrowser.dicomTableManager()
| |
| − | dicomTableManager.selectionMode = qt.QAbstractItemView.SingleSelection
| |
| − | dicomTableManager.autoSelectSeries = False
| |
| − | | |
| − | # Force database views update
| |
| − | dicomDatabase.closeDatabase()
| |
| − | dicomDatabase.openDatabase(dicomBrowser.database().databaseFilename)
| |
| − | </pre>
| |
| − | | |
| − | ==Toolbar functions==
| |
| − | | |
| − | *How to turn on slice intersections in the crosshair menu on the toolbar:
| |
| − | <pre>
| |
| − | viewNodes = slicer.util.getNodesByClass('vtkMRMLSliceCompositeNode')
| |
| − | for viewNode in viewNodes:
| |
| − | viewNode.SetSliceIntersectionVisibility(1)
| |
| − | </pre>
| |
| − | | |
| − | How to find similar functions? For this one I searched for "slice intersections" text in the whole slicer source code, found that the function is implemented in Base\QTGUI\qSlicerViewersToolBar.cxx, then translated the qSlicerViewersToolBarPrivate::setSliceIntersectionVisible(bool visible) method to Python.
| |
| − | | |
| − | ==Switch to a different module==
| |
| − | | |
| − | This utility function can be used to open a different module:
| |
| − | | |
| − | <pre>
| |
| − | slicer.util.selectModule('DICOM')
| |
| − | </pre>
| |
| − | | |
| − | ==Manipulating objects in the slice viewer==
| |
| − | | |
| − | ===How to define/edit a circular region of interest in a slice viewer?===
| |
| − | | |
| − | Drop two markup points on a slice view and copy-paste the code below into the Python console. After this, as you move the markups you’ll see a circle following the markups.
| |
| − | | |
| − | <pre>
| |
| − | # Update the sphere from the fiducial points
| |
| − | def UpdateSphere(param1, param2):
| |
| − | import math
| |
| − | centerPointCoord = [0.0, 0.0, 0.0]
| |
| − | markups.GetNthFiducialPosition(0,centerPointCoord)
| |
| − | circumferencePointCoord = [0.0, 0.0, 0.0]
| |
| − | markups.GetNthFiducialPosition(1,circumferencePointCoord)
| |
| − | sphere.SetCenter(centerPointCoord)
| |
| − | radius=math.sqrt((centerPointCoord[0]-circumferencePointCoord[0])**2+(centerPointCoord[1]-circumferencePointCoord[1])**2+(centerPointCoord[2]-circumferencePointCoord[2])**2)
| |
| − | sphere.SetRadius(radius)
| |
| − | sphere.SetPhiResolution(30)
| |
| − | sphere.SetThetaResolution(30)
| |
| − | sphere.Update()
| |
| − | | |
| − | # Get markup node from scene
| |
| − | markups=slicer.util.getNode('F')
| |
| − | sphere = vtk.vtkSphereSource()
| |
| − | UpdateSphere(0,0)
| |
| − |
| |
| − | # Create model node and add to scene
| |
| − | modelsLogic = slicer.modules.models.logic()
| |
| − | model = modelsLogic.AddModel(sphere.GetOutput())
| |
| − | model.GetDisplayNode().SetSliceIntersectionVisibility(True)
| |
| − | model.GetDisplayNode().SetSliceIntersectionThickness(3)
| |
| − | model.GetDisplayNode().SetColor(1,1,0)
| |
| − |
| |
| − | # Call UpdateSphere whenever the fiducials are changed
| |
| − | markups.AddObserver(slicer.vtkMRMLMarkupsNode.PointModifiedEvent, UpdateSphere, 2)
| |
| − | </pre>
| |
| − | | |
| − | ===Specify a sphere by multiple of markups points===
| |
| − | | |
| − | Drop multiple markup points at the boundary of the spherical object and and copy-paste the code below into the Python console to get best-fit sphere. Minimum 4 points are required, it is recommended to place the points far from each other for most accurate fit.
| |
| − | | |
| − | <pre>
| |
| − | # Get markup node from scene
| |
| − | markups = slicer.util.getNode('F')
| |
| − | | |
| − | from scipy.optimize import least_squares
| |
| − | import numpy
| |
| − | | |
| − | def fit_sphere_least_squares(x_values, y_values, z_values, initial_parameters, bounds=((-numpy.inf, -numpy.inf, -numpy.inf, -numpy.inf),(numpy.inf, numpy.inf, numpy.inf, numpy.inf))):
| |
| − | """
| |
| − | Source: https://github.com/thompson318/scikit-surgery-sphere-fitting/blob/master/sksurgeryspherefitting/algorithms/sphere_fitting.py
| |
| − | Uses scipy's least squares optimisor to fit a sphere to a set
| |
| − | of 3D Points
| |
| − | :return: x: an array containing the four fitted parameters
| |
| − | :return: ier: int An integer flag. If it is equal to 1, 2, 3 or 4, the
| |
| − | solution was found.
| |
| − | :param: (x,y,z) three arrays of equal length containing the x, y, and z
| |
| − | coordinates.
| |
| − | :param: an array containing four initial values (centre, and radius)
| |
| − | """
| |
| − | return least_squares(_calculate_residual_sphere, initial_parameters, bounds=bounds, method='trf', jac='3-point', args=(x_values, y_values, z_values))
| |
| − | | |
| − | def _calculate_residual_sphere(parameters, x_values, y_values, z_values):
| |
| − | """
| |
| − | Source: https://github.com/thompson318/scikit-surgery-sphere-fitting/blob/master/sksurgeryspherefitting/algorithms/sphere_fitting.py
| |
| − | Calculates the residual error for an x,y,z coordinates, fitted
| |
| − | to a sphere with centre and radius defined by the parameters tuple
| |
| − | :return: The residual error
| |
| − | :param: A tuple of the parameters to be optimised, should contain [x_centre, y_centre, z_centre, radius]
| |
| − | :param: arrays containing the x,y, and z coordinates.
| |
| − | """
| |
| − | #extract the parameters
| |
| − | x_centre, y_centre, z_centre, radius = parameters
| |
| − | #use numpy's sqrt function here, which works by element on arrays
| |
| − | distance_from_centre = numpy.sqrt((x_values - x_centre)**2 + (y_values - y_centre)**2 + (z_values - z_centre)**2)
| |
| − | return distance_from_centre - radius
| |
| − | | |
| − | # Fit a sphere to the markups fidicual points
| |
| − | markupsPositions = slicer.util.arrayFromMarkupsControlPoints(markups)
| |
| − | import numpy as np
| |
| − | # initial guess
| |
| − | center0 = np.mean(markupsPositions, 0)
| |
| − | radius0 = np.linalg.norm(np.amin(markupsPositions,0)-np.amax(markupsPositions,0))/2.0
| |
| − | fittingResult = fit_sphere_least_squares(markupsPositions[:,0], markupsPositions[:,1], markupsPositions[:,2], [center0[0], center0[1], center0[2], radius0])
| |
| − | [centerX, centerY, centerZ, radius] = fittingResult['x']
| |
| − | | |
| − | # Create a sphere using the fitted parameters
| |
| − | sphere = vtk.vtkSphereSource()
| |
| − | sphere.SetPhiResolution(30)
| |
| − | sphere.SetThetaResolution(30)
| |
| − | sphere.SetCenter(centerX, centerY, centerZ)
| |
| − | sphere.SetRadius(radius)
| |
| − | sphere.Update()
| |
| − |
| |
| − | # Add the sphere to the scene
| |
| − | modelsLogic = slicer.modules.models.logic()
| |
| − | model = modelsLogic.AddModel(sphere.GetOutput())
| |
| − | model.GetDisplayNode().SetSliceIntersectionVisibility(True)
| |
| − | model.GetDisplayNode().SetSliceIntersectionThickness(3)
| |
| − | model.GetDisplayNode().SetColor(1,1,0)
| |
| − | </pre>
| |
| − | | |
| − | ==Measure angle between two slice planes==
| |
| − | | |
| − | Measure angle between red and yellow slice nodes. Whenever any of the slice nodes are moved, the updated angle is printed on the console.
| |
| − | | |
| − | <pre>
| |
| − | sliceNodeIds = ['vtkMRMLSliceNodeRed', 'vtkMRMLSliceNodeYellow']
| |
| − | | |
| − | # Print angles between slice nodes
| |
| − | def ShowAngle(unused1=None, unused2=None):
| |
| − | sliceNormalVector = []
| |
| − | for sliceNodeId in sliceNodeIds:
| |
| − | sliceToRAS = slicer.mrmlScene.GetNodeByID(sliceNodeId).GetSliceToRAS()
| |
| − | sliceNormalVector.append([sliceToRAS.GetElement(0,2), sliceToRAS.GetElement(1,2), sliceToRAS.GetElement(2,2)])
| |
| − | angleRad = vtk.vtkMath.AngleBetweenVectors(sliceNormalVector[0], sliceNormalVector[1])
| |
| − | angleDeg = vtk.vtkMath.DegreesFromRadians(angleRad)
| |
| − | print('Angle between slice planes = {0:0.3f}'.format(angleDeg))
| |
| − | | |
| − | # Observe slice node changes
| |
| − | for sliceNodeId in sliceNodeIds:
| |
| − | slicer.mrmlScene.GetNodeByID(sliceNodeId).AddObserver(vtk.vtkCommand.ModifiedEvent, ShowAngle)
| |
| − | | |
| − | # Print current angle
| |
| − | ShowAngle()
| |
| − | </pre>
| |
| − | | |
| − | ==Measure angle between two markup planes==
| |
| − | | |
| − | Measure angle between two markup plane nodes. Whenever any of the plane nodes are moved, the updated angle is printed on the console.
| |
| − | | |
| − | <pre>
| |
| − | planeNodeNames = ['P', 'P_1']
| |
| − | | |
| − | # Print angles between slice nodes
| |
| − | def ShowAngle(unused1=None, unused2=None):
| |
| − | planeNormalVectors = []
| |
| − | for planeNodeName in planeNodeNames:
| |
| − | planeNode = slicer.util.getFirstNodeByClassByName('vtkMRMLMarkupsPlaneNode', planeNodeName)
| |
| − | planeNormalVector = [0.0, 0.0, 0.0]
| |
| − | planeNode.GetNormalWorld(planeNormalVector)
| |
| − | planeNormalVectors.append(planeNormalVector)
| |
| − | angleRad = vtk.vtkMath.AngleBetweenVectors(planeNormalVectors[0], planeNormalVectors[1])
| |
| − | angleDeg = vtk.vtkMath.DegreesFromRadians(angleRad)
| |
| − | print('Angle between planes {0} and {1} = {2:0.3f}'.format(planeNodeNames[0], planeNodeNames[1], angleDeg))
| |
| − | | |
| − | # Observe plane node changes
| |
| − | for planeNodeName in planeNodeNames:
| |
| − | planeNode = slicer.util.getFirstNodeByClassByName('vtkMRMLMarkupsPlaneNode', planeNodeName)
| |
| − | planeNode.AddObserver(slicer.vtkMRMLMarkupsPlaneNode.PointModifiedEvent, ShowAngle)
| |
| − | | |
| − | # Print current angle
| |
| − | ShowAngle()
| |
| − | </pre>
| |
| − | | |
| − | ==Measure angle between two markup lines==
| |
| − | | |
| − | Measure angle between two markup line nodes. Whenever either line is moved, the updated angle is printed on the console.
| |
| − | | |
| − | <pre>
| |
| − | lineNodeNames = ['L', 'L_1']
| |
| − | | |
| − | # Print angles between slice nodes
| |
| − | def ShowAngle(unused1=None, unused2=None):
| |
| − | import numpy as np
| |
| − | lineDirectionVectors = []
| |
| − | for lineNodeName in lineNodeNames:
| |
| − | lineNode = slicer.util.getFirstNodeByClassByName('vtkMRMLMarkupsLineNode', lineNodeName)
| |
| − | lineStartPos = np.zeros(3)
| |
| − | lineEndPos = np.zeros(3)
| |
| − | lineNode.GetNthControlPointPositionWorld(0, lineStartPos)
| |
| − | lineNode.GetNthControlPointPositionWorld(1, lineEndPos)
| |
| − | lineDirectionVector = (lineEndPos-lineStartPos)/np.linalg.norm(lineEndPos-lineStartPos)
| |
| − | lineDirectionVectors.append(lineDirectionVector)
| |
| − | angleRad = vtk.vtkMath.AngleBetweenVectors(lineDirectionVectors[0], lineDirectionVectors[1])
| |
| − | angleDeg = vtk.vtkMath.DegreesFromRadians(angleRad)
| |
| − | print('Angle between lines {0} and {1} = {2:0.3f}'.format(lineNodeNames[0], lineNodeNames[1], angleDeg))
| |
| − | | |
| − | # Observe line node changes
| |
| − | for lineNodeName in lineNodeNames:
| |
| − | lineNode = slicer.util.getFirstNodeByClassByName('vtkMRMLMarkupsLineNode', lineNodeName)
| |
| − | lineNode.AddObserver(slicer.vtkMRMLMarkupsLineNode.PointModifiedEvent, ShowAngle)
| |
| − | | |
| − | # Print current angle
| |
| − | ShowAngle()
| |
| − | </pre>
| |
| − | | |
| − | ==Set slice position and orientation from 3 markup fiducials==
| |
| − | | |
| − | Drop 3 markup points in the scene and copy-paste the code below into the Python console. After this, as you move the markups you’ll see the red slice view position and orientation will be set to make it fit to the 3 points.
| |
| − | | |
| − | <pre>
| |
| − | # Update plane from fiducial points
| |
| − | def UpdateSlicePlane(param1=None, param2=None):
| |
| − | # Get point positions as numpy array
| |
| − | import numpy as np
| |
| − | nOfFiduciallPoints = markups.GetNumberOfFiducials()
| |
| − | if nOfFiduciallPoints < 3:
| |
| − | return # not enough points
| |
| − | points = np.zeros([3,nOfFiduciallPoints])
| |
| − | for i in range(0, nOfFiduciallPoints):
| |
| − | markups.GetNthFiducialPosition(i, points[:,i])
| |
| − | # Compute plane position and normal
| |
| − | planePosition = points.mean(axis=1)
| |
| − | planeNormal = np.cross(points[:,1] - points[:,0], points[:,2] - points[:,0])
| |
| − | planeX = points[:,1] - points[:,0]
| |
| − | sliceNode.SetSliceToRASByNTP(planeNormal[0], planeNormal[1], planeNormal[2],
| |
| − | planeX[0], planeX[1], planeX[2],
| |
| − | planePosition[0], planePosition[1], planePosition[2], 0)
| |
| − | | |
| − | # Get markup node from scene
| |
| − | sliceNode = slicer.app.layoutManager().sliceWidget('Red').mrmlSliceNode()
| |
| − | markups = slicer.util.getNode('F')
| |
| − | | |
| − | # Update slice plane manually
| |
| − | UpdateSlicePlane()
| |
| − | | |
| − | # Update slice plane automatically whenever points are changed
| |
| − | markupObservation = [markups, markups.AddObserver(slicer.vtkMRMLMarkupsNode.PointModifiedEvent, UpdateSlicePlane, 2)]
| |
| − | </pre>
| |
| − | | |
| − | To stop automatic updates, run this:
| |
| − | <pre>
| |
| − | markupObservation[0].RemoveObserver(markupObservation[1])
| |
| − | </pre>
| |
| − | | |
| − | | |
| − | ==Set slice position and orientation from a normal vector and position==
| |
| − | | |
| − | This code snippet shows how to display a slice view defined by a normal vector and position in an anatomically sensible way: rotating slice view so that "up" direction (or "right" direction) is towards an anatomical axis.
| |
| − | | |
| − | <pre>
| |
| − | def setSlicePoseFromSliceNormalAndPosition(sliceNode, sliceNormal, slicePosition, defaultViewUpDirection=None, backupViewRightDirection=None):
| |
| − | """
| |
| − | Set slice pose from the provided plane normal and position. View up direction is determined automatically,
| |
| − | to make view up point towards defaultViewUpDirection.
| |
| − | :param defaultViewUpDirection Slice view will be spinned in-plane to match point approximately this up direction. Default: patient superior.
| |
| − | :param backupViewRightDirection Slice view will be spinned in-plane to match point approximately this right direction
| |
| − | if defaultViewUpDirection is too similar to sliceNormal. Default: patient left.
| |
| − | """
| |
| − | # Fix up input directions
| |
| − | if defaultViewUpDirection is None:
| |
| − | defaultViewUpDirection = [0,0,1]
| |
| − | if backupViewRightDirection is None:
| |
| − | backupViewRightDirection = [-1,0,0]
| |
| − | if sliceNormal[1]>=0:
| |
| − | sliceNormalStandardized = sliceNormal
| |
| − | else:
| |
| − | sliceNormalStandardized = [-sliceNormal[0], -sliceNormal[1], -sliceNormal[2]]
| |
| − | # Compute slice axes
| |
| − | sliceNormalViewUpAngle = vtk.vtkMath.AngleBetweenVectors(sliceNormalStandardized, defaultViewUpDirection)
| |
| − | angleTooSmallThresholdRad = 0.25 # about 15 degrees
| |
| − | if sliceNormalViewUpAngle > angleTooSmallThresholdRad and sliceNormalViewUpAngle < vtk.vtkMath.Pi() - angleTooSmallThresholdRad:
| |
| − | viewUpDirection = defaultViewUpDirection
| |
| − | sliceAxisY = viewUpDirection
| |
| − | sliceAxisX = [0, 0, 0]
| |
| − | vtk.vtkMath.Cross(sliceAxisY, sliceNormalStandardized, sliceAxisX)
| |
| − | else:
| |
| − | sliceAxisX = backupViewRightDirection
| |
| − | # Set slice axes
| |
| − | sliceNode.SetSliceToRASByNTP(sliceNormalStandardized[0], sliceNormalStandardized[1], sliceNormalStandardized[2],
| |
| − | sliceAxisX[0], sliceAxisX[1], sliceAxisX[2],
| |
| − | slicePosition[0], slicePosition[1], slicePosition[2], 0)
| |
| − | | |
| − | # Example usage:
| |
| − | sliceNode = getNode('vtkMRMLSliceNodeRed')
| |
| − | transformNode = getNode('Transform_3')
| |
| − | transformMatrix = vtk.vtkMatrix4x4()
| |
| − | transformNode.GetMatrixTransformToParent(transformMatrix)
| |
| − | sliceNormal = [transformMatrix.GetElement(0,2), transformMatrix.GetElement(1,2), transformMatrix.GetElement(2,2)]
| |
| − | slicePosition = [transformMatrix.GetElement(0,3), transformMatrix.GetElement(1,3), transformMatrix.GetElement(2,3)]
| |
| − | setSlicePoseFromSliceNormalAndPosition(sliceNode, sliceNormal, slicePosition)
| |
| − | </pre>
| |
| − | | |
| − | ==Extract randomly oriented slabs of given shape from a volume==
| |
| − | | |
| − | Returns a numpy array of sliceCount random tiles.
| |
| − | | |
| − | <pre>
| |
| − | def randomSlices(volume, sliceCount, sliceShape):
| |
| − | layoutManager = slicer.app.layoutManager()
| |
| − | redWidget = layoutManager.sliceWidget('Red')
| |
| − | sliceNode = redWidget.mrmlSliceNode()
| |
| − | sliceNode.SetDimensions(*sliceShape, 1)
| |
| − | sliceNode.SetFieldOfView(*sliceShape, 1)
| |
| − | bounds = [0]*6
| |
| − | volume.GetRASBounds(bounds)
| |
| − | imageReslice = redWidget.sliceLogic().GetBackgroundLayer().GetReslice()
| |
| − | | |
| − | sliceSize = sliceShape[0] * sliceShape[1]
| |
| − | X = numpy.zeros([sliceCount, sliceSize])
| |
| − | | |
| − | for sliceIndex in range(sliceCount):
| |
| − | position = numpy.random.rand(3) * 2 - 1
| |
| − | position = [bounds[0] + bounds[1]-bounds[0] * position[0],
| |
| − | bounds[2] + bounds[3]-bounds[2] * position[1],
| |
| − | bounds[4] + bounds[5]-bounds[4] * position[2]]
| |
| − | normal = numpy.random.rand(3) * 2 - 1
| |
| − | normal = normal / numpy.linalg.norm(normal)
| |
| − | transverse = numpy.cross(normal, [0,0,1])
| |
| − | orientation = 0
| |
| − | sliceNode.SetSliceToRASByNTP( normal[0], normal[1], normal[2],
| |
| − | transverse[0], transverse[1], transverse[2],
| |
| − | position[0], position[1], position[2],
| |
| − | orientation)
| |
| − | if sliceIndex % 100 == 0:
| |
| − | slicer.app.processEvents()
| |
| − | imageReslice.Update()
| |
| − | imageData = imageReslice.GetOutputDataObject(0)
| |
| − | array = vtk.util.numpy_support.vtk_to_numpy(imageData.GetPointData().GetScalars())
| |
| − | X[sliceIndex] = array
| |
| − | return X
| |
| − | </pre>
| |
| − | | |
| − | ==Switching to markup fiducial placement mode==
| |
| − | | |
| − | To activate a fiducial placement mode, both interaction mode has to be set and a fiducial node has to be selected:
| |
| − | | |
| − | <pre>
| |
| − | interactionNode = slicer.app.applicationLogic().GetInteractionNode()
| |
| − | selectionNode = slicer.app.applicationLogic().GetSelectionNode()
| |
| − | selectionNode.SetReferenceActivePlaceNodeClassName("vtkMRMLMarkupsFiducialNode")
| |
| − | fiducialNode = slicer.vtkMRMLMarkupsFiducialNode()
| |
| − | slicer.mrmlScene.AddNode(fiducialNode)
| |
| − | fiducialNode.CreateDefaultDisplayNodes()
| |
| − | selectionNode.SetActivePlaceNodeID(fiducialNode.GetID())
| |
| − | interactionNode.SetCurrentInteractionMode(interactionNode.Place)
| |
| − | </pre>
| |
| − | | |
| − | Alternatively, ''qSlicerMarkupsPlaceWidget'' widget can be used to initiate markup placement:
| |
| − | | |
| − | <pre>
| |
| − | # Temporary markups node
| |
| − | markupsNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsFiducialNode")
| |
| − | | |
| − | def placementModeChanged(active):
| |
| − | print("Placement: " +("active" if active else "inactive"))
| |
| − | # You can inspect what is in the markups node here, delete the temporary markup node, etc.
| |
| − | | |
| − | # Create and set up widget that contains a single "place markup" button. The widget can be placed in the module GUI.
| |
| − | placeWidget = slicer.qSlicerMarkupsPlaceWidget()
| |
| − | placeWidget.setMRMLScene(slicer.mrmlScene)
| |
| − | placeWidget.setCurrentNode(markupsNode)
| |
| − | placeWidget.buttonsVisible=False
| |
| − | placeWidget.placeButton().show()
| |
| − | placeWidget.connect('activeMarkupsFiducialPlaceModeChanged(bool)', placementModeChanged)
| |
| − | placeWidget.show()
| |
| − | </pre>
| |
| − | | |
| − | ==Change markup fiducial display properties==
| |
| − | | |
| − | Display properties are stored in display node(s) associated with the fiducial node.
| |
| − | | |
| − | <pre>
| |
| − | fiducialNode = getNode('F')
| |
| − | fiducialDisplayNode = fiducialNode.GetDisplayNode()
| |
| − | fiducialDisplayNode.SetVisibility(False) # Hide all points
| |
| − | fiducialDisplayNode.SetVisibility(True) # Show all points
| |
| − | fiducialDisplayNode.SetSelectedColor(1,1,0) # Set color to yellow
| |
| − | fiducialDisplayNode.SetViewNodeIDs(["vtkMRMLSliceNodeRed", "vtkMRMLViewNode1"]) # Only show in red slice view and first 3D view
| |
| − | </pre>
| |
| − | | |
| − | ==Get a notification if a markup point position is modified==
| |
| − | | |
| − | Event management of Slicer-4.11 version is still subject to change. The example below shows how point manipulation can be observed now.
| |
| − | | |
| − | <pre>
| |
| − | def onMarkupChanged(caller,event):
| |
| − | markupsNode = caller
| |
| − | sliceView = markupsNode.GetAttribute('Markups.MovingInSliceView')
| |
| − | movingMarkupIndex = markupsNode.GetDisplayNode().GetActiveControlPoint()
| |
| − | if movingMarkupIndex >= 0:
| |
| − | pos = [0,0,0]
| |
| − | markupsNode.GetNthFiducialPosition(movingMarkupIndex, pos)
| |
| − | isPreview = markupsNode.GetNthControlPointPositionStatus(movingMarkupIndex) == slicer.vtkMRMLMarkupsNode.PositionPreview
| |
| − | if isPreview:
| |
| − | logging.info("Point {0} is previewed at {1} in slice view {2}".format(movingMarkupIndex, pos, sliceView))
| |
| − | else:
| |
| − | logging.info("Point {0} was moved {1} in slice view {2}".format(movingMarkupIndex, pos, sliceView))
| |
| − | else:
| |
| − | logging.info("Points modified: slice view = {0}".format(sliceView))
| |
| − | | |
| − | def onMarkupStartInteraction(caller, event):
| |
| − | markupsNode = caller
| |
| − | sliceView = markupsNode.GetAttribute('Markups.MovingInSliceView')
| |
| − | movingMarkupIndex = markupsNode.GetDisplayNode().GetActiveControlPoint()
| |
| − | logging.info("Start interaction: point ID = {0}, slice view = {1}".format(movingMarkupIndex, sliceView))
| |
| − | | |
| − | def onMarkupEndInteraction(caller, event):
| |
| − | markupsNode = caller
| |
| − | sliceView = markupsNode.GetAttribute('Markups.MovingInSliceView')
| |
| − | movingMarkupIndex = markupsNode.GetDisplayNode().GetActiveControlPoint()
| |
| − | logging.info("End interaction: point ID = {0}, slice view = {1}".format(movingMarkupIndex, sliceView))
| |
| − | | |
| − | markupsNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsFiducialNode")
| |
| − | markupsNode.CreateDefaultDisplayNodes()
| |
| − | markupsNode.AddFiducial(0,0,0)
| |
| − | markupsNode.AddObserver(slicer.vtkMRMLMarkupsNode.PointModifiedEvent, onMarkupChanged)
| |
| − | markupsNode.AddObserver(slicer.vtkMRMLMarkupsNode.PointStartInteractionEvent, onMarkupStartInteraction)
| |
| − | markupsNode.AddObserver(slicer.vtkMRMLMarkupsNode.PointEndInteractionEvent, onMarkupEndInteraction)
| |
| − | </pre>
| |
| − | | |
| − | ==Get a notification if a transform is modified==
| |
| − | | |
| − | <pre>
| |
| − | def onTransformNodeModified(transformNode, unusedArg2=None, unusedArg3=None):
| |
| − | transformMatrix = vtk.vtkMatrix4x4()
| |
| − | transformNode.GetMatrixTransformToWorld(transformMatrix)
| |
| − | print("Position: [{0}, {1}, {2}]".format(transformMatrix.GetElement(0,3), transformMatrix.GetElement(1,3), transformMatrix.GetElement(2,3)))
| |
| − | | |
| − | transformNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLTransformNode")
| |
| − | transformNode.AddObserver(slicer.vtkMRMLTransformNode.TransformModifiedEvent, onTransformNodeModified)
| |
| − | </pre>
| |
| − | | |
| − | ==Rotate a node around a specified point==
| |
| − | | |
| − | Set up the scene:
| |
| − | | |
| − | *Add a markup fiducial node (centerOfRotationMarkupsNode) with a single point to specify center of rotation.
| |
| − | *Add a rotation transform (rotationTransformNode) that will be edited in Transforms module to specify rotation angles.
| |
| − | *Add a transform (finalTransformNode) and apply it (not harden) to those nodes (images, models, etc.) that you want to rotate around the center of rotation point.
| |
| − | | |
| − | Then run the script below, go to Transforms module, select rotationTransformNode, and move rotation sliders.
| |
| − | | |
| − | <pre>
| |
| − | # This markups fiducial node specifies the center of rotation
| |
| − | centerOfRotationMarkupsNode = getNode('F')
| |
| − | # This transform can be edited in Transforms module
| |
| − | rotationTransformNode = getNode('LinearTransform_3')
| |
| − | # This transform has to be applied to the image, model, etc.
| |
| − | finalTransformNode = getNode('LinearTransform_4')
| |
| − | | |
| − | def updateFinalTransform(unusedArg1=None, unusedArg2=None, unusedArg3=None):
| |
| − | rotationMatrix = vtk.vtkMatrix4x4()
| |
| − | rotationTransformNode.GetMatrixTransformToParent(rotationMatrix)
| |
| − | rotationCenterPointCoord = [0.0, 0.0, 0.0]
| |
| − | centerOfRotationMarkupsNode.GetNthControlPointPositionWorld(0, rotationCenterPointCoord)
| |
| − | finalTransform = vtk.vtkTransform()
| |
| − | finalTransform.Translate(rotationCenterPointCoord)
| |
| − | finalTransform.Concatenate(rotationMatrix)
| |
| − | finalTransform.Translate(-rotationCenterPointCoord[0], -rotationCenterPointCoord[1], -rotationCenterPointCoord[2])
| |
| − | finalTransformNode.SetAndObserveMatrixTransformToParent(finalTransform.GetMatrix())
| |
| − | | |
| − | # Manual initial update
| |
| − | updateFinalTransform()
| |
| − | | |
| − | # Automatic update when point is moved or transform is modified
| |
| − | rotationTransformNodeObserver = rotationTransformNode.AddObserver(slicer.vtkMRMLTransformNode.TransformModifiedEvent, updateFinalTransform)
| |
| − | centerOfRotationMarkupsNodeObserver = centerOfRotationMarkupsNode.AddObserver(slicer.vtkMRMLMarkupsNode.PointModifiedEvent, updateFinalTransform)
| |
| − | | |
| − | # Execute these lines to stop automatic updates:
| |
| − | # rotationTransformNode.RemoveObserver(rotationTransformNodeObserver)
| |
| − | # centerOfRotationMarkupsNode.RemoveObserver(centerOfRotationMarkupsNodeObserver)
| |
| − | | |
| − | </pre>
| |
| − | | |
| − | ==Rotate a node around a specified line==
| |
| − | | |
| − | Set up the scene:
| |
| − | | |
| − | *Add a markup line node (rotationAxisMarkupsNode) with 2 points to specify rotation axis.
| |
| − | *Add a rotation transform (rotationTransformNode) that will be edited in Transforms module to specify rotation angle.
| |
| − | *Add a transform (finalTransformNode) and apply it (not harden) to those nodes (images, models, etc.) that you want to rotate around the line.
| |
| − | | |
| − | Then run the script below, go to Transforms module, select rotationTransformNode, and move Edit / Rotation / IS slider.
| |
| − | | |
| − | <pre>
| |
| − | # This markups fiducial node specifies the center of rotation
| |
| − | rotationAxisMarkupsNode = getNode('L')
| |
| − | # This transform can be edited in Transforms module (Edit / Rotation / IS slider)
| |
| − | rotationTransformNode = getNode('LinearTransform_3')
| |
| − | # This transform has to be applied to the image, model, etc.
| |
| − | finalTransformNode = getNode('LinearTransform_4')
| |
| − | | |
| − | def updateFinalTransform(unusedArg1=None, unusedArg2=None, unusedArg3=None):
| |
| − | import numpy as np
| |
| − | rotationAxisPoint1_World = np.zeros(3)
| |
| − | rotationAxisMarkupsNode.GetNthControlPointPositionWorld(0, rotationAxisPoint1_World)
| |
| − | rotationAxisPoint2_World = np.zeros(3)
| |
| − | rotationAxisMarkupsNode.GetNthControlPointPositionWorld(1, rotationAxisPoint2_World)
| |
| − | axisDirectionZ_World = rotationAxisPoint2_World-rotationAxisPoint1_World
| |
| − | axisDirectionZ_World = axisDirectionZ_World/np.linalg.norm(axisDirectionZ_World)
| |
| − | # Get transformation between world coordinate system and rotation axis aligned coordinate system
| |
| − | worldToRotationAxisTransform = vtk.vtkMatrix4x4()
| |
| − | p=vtk.vtkPlaneSource()
| |
| − | p.SetNormal(axisDirectionZ_World)
| |
| − | axisOrigin = np.array(p.GetOrigin())
| |
| − | axisDirectionX_World = np.array(p.GetPoint1())-axisOrigin
| |
| − | axisDirectionY_World = np.array(p.GetPoint2())-axisOrigin
| |
| − | rotationAxisToWorldTransform = np.row_stack((np.column_stack((axisDirectionX_World, axisDirectionY_World, axisDirectionZ_World, rotationAxisPoint1_World)), (0, 0, 0, 1)))
| |
| − | rotationAxisToWorldTransformMatrix = slicer.util.vtkMatrixFromArray(rotationAxisToWorldTransform)
| |
| − | worldToRotationAxisTransformMatrix = slicer.util.vtkMatrixFromArray(np.linalg.inv(rotationAxisToWorldTransform))
| |
| − | # Compute transformation chain
| |
| − | rotationMatrix = vtk.vtkMatrix4x4()
| |
| − | rotationTransformNode.GetMatrixTransformToParent(rotationMatrix)
| |
| − | finalTransform = vtk.vtkTransform()
| |
| − | finalTransform.Concatenate(rotationAxisToWorldTransformMatrix)
| |
| − | finalTransform.Concatenate(rotationMatrix)
| |
| − | finalTransform.Concatenate(worldToRotationAxisTransformMatrix)
| |
| − | finalTransformNode.SetAndObserveMatrixTransformToParent(finalTransform.GetMatrix())
| |
| − | | |
| − | # Manual initial update
| |
| − | updateFinalTransform()
| |
| − | | |
| − | # Automatic update when point is moved or transform is modified
| |
| − | rotationTransformNodeObserver = rotationTransformNode.AddObserver(slicer.vtkMRMLTransformNode.TransformModifiedEvent, updateFinalTransform)
| |
| − | rotationAxisMarkupsNodeObserver = rotationAxisMarkupsNode.AddObserver(slicer.vtkMRMLMarkupsNode.PointModifiedEvent, updateFinalTransform)
| |
| − | | |
| − | # Execute these lines to stop automatic updates:
| |
| − | # rotationTransformNode.RemoveObserver(rotationTransformNodeObserver)
| |
| − | # rotationAxisMarkupsNode.RemoveObserver(rotationAxisMarkupsNodeObserver)
| |
| − | </pre>
| |
| − | | |
| − | ==Show a context menu when a markup point is clicked in a slice or 3D view==
| |
| − | | |
| − | Subject hierarchy plugins can offer actions in the view context menu when right-clicking objects that support such picking (such as Markups fiducials). A comprehensive [https://github.com/Slicer/Slicer/blob/master/Modules/Loadable/Annotations/SubjectHierarchyPlugins/AnnotationsSubjectHierarchyPlugin.py subject hierarchy plugin example] is for the Annotations module.
| |
| − | | |
| − | <pre>
| |
| − | | |
| − | def viewContextMenuActions(self):
| |
| − | return [self.doSomething]
| |
| − | | |
| − | def showViewContextMenuActionsForItem(self, itemID, eventData):
| |
| − | if not itemID:
| |
| − | logging.error('Invalid item for view context menu ' + str(itemID))
| |
| − | return
| |
| − | | |
| − | pluginHandlerSingleton = slicer.qSlicerSubjectHierarchyPluginHandler.instance()
| |
| − | shNode = pluginHandlerSingleton.subjectHierarchyNode()
| |
| − | if shNode is None:
| |
| − | logging.error('Failed to access subject hierarchy node')
| |
| − | return
| |
| − | | |
| − | associatedNode = shNode.GetItemDataNode(itemID)
| |
| − | if not associatedNode or not associatedNode.IsA("vtkMRMLMarkupsNode"):
| |
| − | return
| |
| − | | |
| − | self.viewMenuEventData = eventData
| |
| − | self.viewMenuEventData['NodeID'] = associatedNode.GetID()
| |
| − | | |
| − | def onDoSomething(self):
| |
| − | nodeID = self.viewMenuEventData['NodeID']
| |
| − | markupsNode = slicer.mrmlScene.GetNodeByID(nodeID)
| |
| − | if markupsNode is None or not markupsNode.IsA("vtkMRMLMarkupsNode"):
| |
| − | logging.error('Failed to get fiducial markups node by ID ' + str(nodeID))
| |
| − | return
| |
| − | | |
| − | componentIndex = self.viewMenuEventData['ComponentIndex']
| |
| − | markupID = markupsNode.GetNthMarkupID(componentIndex)
| |
| − |
| |
| − | # Do something with the clicked fiducial
| |
| − | | |
| − | </pre>
| |
| − | | |
| − | ==Write markup positions to JSON file==
| |
| − | | |
| − | <pre>
| |
| − | markupNode = getNode('F')
| |
| − | outputFileName = 'c:/tmp/test.json'
| |
| − | | |
| − | # Get markup positions
| |
| − | data = []
| |
| − | for fidIndex in range(markupNode.GetNumberOfFiducials()):
| |
| − | coords=[0,0,0]
| |
| − | markupNode.GetNthFiducialPosition(fidIndex,coords)
| |
| − | data.append({'label': markupNode.GetNthFiducialLabel(), 'position': coords})
| |
| − | | |
| − | import json
| |
| − | with open(outputFileName, 'w') as outfile:
| |
| − | json.dump(data, outfile)
| |
| − | </pre>
| |
| − | | |
| − | ==Write annotation ROI to JSON file==
| |
| − | | |
| − | <pre>
| |
| − | roiNode = getNode('R')
| |
| − | outputFileName = "c:/tmp/test.json"
| |
| − | | |
| − | # Get annotation ROI data
| |
| − | center = [0,0,0]
| |
| − | radius = [0,0,0]
| |
| − | roiNode.GetControlPointWorldCoordinates(0, center)
| |
| − | roiNode.GetControlPointWorldCoordinates(1, radius)
| |
| − | data = {'center': radius, 'radius': radius}
| |
| − | | |
| − | # Write to json file
| |
| − | import json
| |
| − | with open(outputFileName, 'w') as outfile:
| |
| − | json.dump(data, outfile)
| |
| − | </pre>
| |
| − | | |
| − | ==Show a simple surface mesh as a model node==
| |
| − | | |
| − | This example shows how to display a simple surface mesh (a box, created by a VTK source filter) as a model node.
| |
| − | | |
| − | <pre>
| |
| − | # Create and set up polydata source
| |
| − | box = vtk.vtkCubeSource()
| |
| − | box.SetXLength(30)
| |
| − | box.SetYLength(20)
| |
| − | box.SetZLength(15)
| |
| − | box.SetCenter(10,20,5)
| |
| − | | |
| − | # Create a model node that displays output of the source
| |
| − | boxNode = slicer.modules.models.logic().AddModel(box.GetOutputPort())
| |
| − | | |
| − | # Adjust display properties
| |
| − | boxNode.GetDisplayNode().SetColor(1,0,0)
| |
| − | boxNode.GetDisplayNode().SetOpacity(0.8)
| |
| − | </pre>
| |
| − | | |
| − | ==Measure distance of points from surface==
| |
| − | | |
| − | This example computes closest distance of points (markups fiducial 'F') from a surface (model node 'mymodel') and writes results into a table.
| |
| − | | |
| − | <pre>
| |
| − | markupsNode = getNode('F')
| |
| − | modelNode = getNode('mymodel')
| |
| − | | |
| − | # Transform model polydata to world coordinate system
| |
| − | if modelNode.GetParentTransformNode():
| |
| − | transformModelToWorld = vtk.vtkGeneralTransform()
| |
| − | slicer.vtkMRMLTransformNode.GetTransformBetweenNodes(modelNode.GetParentTransformNode(), None, transformModelToWorld)
| |
| − | polyTransformToWorld = vtk.vtkTransformPolyDataFilter()
| |
| − | polyTransformToWorld.SetTransform(transformModelToWorld)
| |
| − | polyTransformToWorld.SetInputData(modelNode.GetPolyData())
| |
| − | polyTransformToWorld.Update()
| |
| − | surface_World = polyTransformToWorld.GetOutput()
| |
| − | else:
| |
| − | surface_World = modelNode.GetPolyData()
| |
| − | | |
| − | # Create arrays to store results
| |
| − | indexCol = vtk.vtkIntArray()
| |
| − | indexCol.SetName("Index")
| |
| − | labelCol = vtk.vtkStringArray()
| |
| − | labelCol.SetName("Name")
| |
| − | distanceCol = vtk.vtkDoubleArray()
| |
| − | distanceCol.SetName("Distance")
| |
| − | | |
| − | distanceFilter = vtk.vtkImplicitPolyDataDistance()
| |
| − | distanceFilter.SetInput(surface_World);
| |
| − | nOfFiduciallPoints = markupsNode.GetNumberOfFiducials()
| |
| − | for i in range(0, nOfFiduciallPoints):
| |
| − | point_World = [0,0,0]
| |
| − | markupsNode.GetNthControlPointPositionWorld(i, point_World)
| |
| − | closestPointOnSurface_World = [0,0,0]
| |
| − | closestPointDistance = distanceFilter.EvaluateFunctionAndGetClosestPoint(point_World, closestPointOnSurface_World)
| |
| − | indexCol.InsertNextValue(i)
| |
| − | labelCol.InsertNextValue(markupsNode.GetNthControlPointLabel(i))
| |
| − | distanceCol.InsertNextValue(closestPointDistance)
| |
| − | | |
| − | # Create a table from result arrays
| |
| − | resultTableNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLTableNode", "Points from surface distance")
| |
| − | resultTableNode.AddColumn(indexCol)
| |
| − | resultTableNode.AddColumn(labelCol)
| |
| − | resultTableNode.AddColumn(distanceCol)
| |
| − | | |
| − | # Show table in view layout
| |
| − | slicer.app.layoutManager().setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpTableView)
| |
| − | slicer.app.applicationLogic().GetSelectionNode().SetReferenceActiveTableID(resultTableNode.GetID())
| |
| − | slicer.app.applicationLogic().PropagateTableSelection()
| |
| − | </pre>
| |
| − | | |
| − | ==Add a texture mapped plane to the scene as a model==
| |
| − | Note that model textures are not exposed in the GUI and are not saved in the scene
| |
| − | <pre>
| |
| − | # Create model node
| |
| − | planeSource = vtk.vtkPlaneSource()
| |
| − | planeSource.SetOrigin(-50.0, -50.0, 0.0)
| |
| − | planeSource.SetPoint1(50.0, -50.0, 0.0)
| |
| − | planeSource.SetPoint2(-50.0, 50.0, 0.0)
| |
| − | model = slicer.modules.models.logic().AddModel(planeSource.GetOutputPort())
| |
| − | | |
| − | # Tune display properties
| |
| − | modelDisplay = model.GetDisplayNode()
| |
| − | modelDisplay.SetColor(1,1,0) # yellow
| |
| − | modelDisplay.SetBackfaceCulling(0)
| |
| − | | |
| − | # Add texture (just use image of an ellipsoid)
| |
| − | e = vtk.vtkImageEllipsoidSource()
| |
| − | modelDisplay.SetTextureImageDataConnection(e.GetOutputPort())
| |
| − | </pre>
| |
| − | | |
| − | ==Get scalar values at surface of a model==
| |
| − | | |
| − | The following script allows getting selected scalar value at a selected position of a model. Position can be selected by moving the mouse while holding down Shift key.
| |
| − | | |
| − | <pre>
| |
| − | modelNode = getNode('sphere')
| |
| − | modelPointValues = modelNode.GetPolyData().GetPointData().GetArray("Normals")
| |
| − | markupsNode = slicer.mrmlScene.GetFirstNodeByName('F')
| |
| − | | |
| − | if not markupsNode:
| |
| − | markupsNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsFiducialNode","F")
| |
| − | | |
| − | pointsLocator = vtk.vtkPointLocator() # could try using vtk.vtkStaticPointLocator() if need to optimize
| |
| − | pointsLocator.SetDataSet(modelNode.GetPolyData())
| |
| − | pointsLocator.BuildLocator()
| |
| − | | |
| − | def onMouseMoved(observer,eventid):
| |
| − | ras=[0,0,0]
| |
| − | crosshairNode.GetCursorPositionRAS(ras)
| |
| − | if markupsNode.GetNumberOfFiducials() == 0:
| |
| − | markupsNode.AddFiducial(*ras)
| |
| − | else:
| |
| − | markupsNode.SetNthFiducialPosition(0,*ras)
| |
| − | closestPointId = pointsLocator.FindClosestPoint(ras)
| |
| − | closestPointValue = modelPointValues.GetTuple(closestPointId)
| |
| − | print("RAS = " + repr(ras) + " value = " + repr(closestPointValue))
| |
| − | | |
| − | crosshairNode=slicer.util.getNode('Crosshair')
| |
| − | observationId = crosshairNode.AddObserver(slicer.vtkMRMLCrosshairNode.CursorPositionModifiedEvent, onMouseMoved)
| |
| − | | |
| − | # To stop printing of values run this:
| |
| − | # crosshairNode.RemoveObserver(observationId)
| |
| − | </pre>
| |
| − | | |
| − | ==Select cells of a model using markups fiducial points==
| |
| − | | |
| − | The following script selects cells of a model node that are closest to positions of markups fiducial points.
| |
| − | | |
| − | <pre>
| |
| − | # Get input nodes
| |
| − | modelNode = slicer.util.getNode('Segment_1') # select cells in this model
| |
| − | markupsNode = slicer.util.getNode('F') # points will be selected at positions specified by this markups fiducial node
| |
| − | | |
| − | # Create scalar array that will store selection state
| |
| − | cellScalars = modelNode.GetMesh().GetCellData()
| |
| − | selectionArray = cellScalars.GetArray('selection')
| |
| − | if not selectionArray:
| |
| − | selectionArray = vtk.vtkIntArray()
| |
| − | selectionArray.SetName('selection')
| |
| − | selectionArray.SetNumberOfValues(modelNode.GetMesh().GetNumberOfCells())
| |
| − | selectionArray.Fill(0)
| |
| − | cellScalars.AddArray(selectionArray)
| |
| − | | |
| − | # Set up coloring by selection array
| |
| − | modelNode.GetDisplayNode().SetActiveScalar("selection", vtk.vtkAssignAttribute.CELL_DATA)
| |
| − | modelNode.GetDisplayNode().SetAndObserveColorNodeID("vtkMRMLColorTableNodeWarm1")
| |
| − | modelNode.GetDisplayNode().SetScalarVisibility(True)
| |
| − | | |
| − | # Initialize cell locator
| |
| − | cell = vtk.vtkCellLocator()
| |
| − | cell.SetDataSet(modelNode.GetMesh())
| |
| − | cell.BuildLocator()
| |
| − | | |
| − | def onPointsModified(observer=None, eventid=None):
| |
| − | global markupsNode, selectionArray
| |
| − | selectionArray.Fill(0) # set all cells to non-selected by default
| |
| − | markupPoints = slicer.util.arrayFromMarkupsControlPoints(markupsNode)
| |
| − | closestPoint = [0.0, 0.0, 0.0]
| |
| − | cellObj = vtk.vtkGenericCell()
| |
| − | cellId = vtk.mutable(0)
| |
| − | subId = vtk.mutable(0)
| |
| − | dist2 = vtk.mutable(0.0)
| |
| − | for markupPoint in markupPoints:
| |
| − | cell.FindClosestPoint(markupPoint, closestPoint, cellObj, cellId, subId, dist2)
| |
| − | closestCell = cellId.get()
| |
| − | if closestCell >=0:
| |
| − | selectionArray.SetValue(closestCell, 100) # set selected cell's scalar value to non-zero
| |
| − | selectionArray.Modified()
| |
| − | | |
| − | # Initial update
| |
| − | onPointsModified()
| |
| − | # Automatic update each time when a markup point is modified
| |
| − | markupsNodeObserverTag = markupsNode.AddObserver(slicer.vtkMRMLMarkupsFiducialNode.PointModifiedEvent, onPointsModified)
| |
| − | | |
| − | # To stop updating selection, run this:
| |
| − | # markupsNode.RemoveObserver(markupsNodeObserverTag)
| |
| − | </pre>
| |
| − | | |
| − | ==Load volume from .vti file==
| |
| − | | |
| − | Slicer does not provide reader for VTK XML image data file format (as they are not commonly used for storing medical images and they cannot store image axis directions) but such files can be read by using this script:
| |
| − | | |
| − | <pre>
| |
| − | reader=vtk.vtkXMLImageDataReader()
| |
| − | reader.SetFileName("/path/to/file.vti")
| |
| − | reader.Update()
| |
| − | imageData = reader.GetOutput()
| |
| − | spacing = imageData.GetSpacing()
| |
| − | origin = imageData.GetOrigin()
| |
| − | imageData.SetOrigin(0,0,0)
| |
| − | imageData.SetSpacing(1,1,1)
| |
| − | volumeNode=slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode")
| |
| − | volumeNode.SetAndObserveImageData(imageData)
| |
| − | volumeNode.SetSpacing(spacing)
| |
| − | volumeNode.SetOrigin(origin)
| |
| − | slicer.util.setSliceViewerLayers(volumeNode, fit=True)
| |
| − | </pre>
| |
| − | | |
| − | ==Export entire scene as VRML==
| |
| − | | |
| − | Save all surface meshes displayed in the scene (models, markups, etc). Solid colors and coloring by scalar is preserved. Textures are not supported.
| |
| − | | |
| − | <pre>
| |
| − | exporter = vtk.vtkVRMLExporter()
| |
| − | exporter.SetRenderWindow(slicer.app.layoutManager().threeDWidget(0).threeDView().renderWindow())
| |
| − | exporter.SetFileName('C:/tmp/something.wrl')
| |
| − | exporter.Write()
| |
| − | </pre>
| |
| − | | |
| − | ==Export model to Blender, including color by scalar==
| |
| − | | |
| − | <pre>
| |
| − | modelNode = getNode("Model")
| |
| − | plyFilePath = "c:/tmp/model.ply"
| |
| − | | |
| − | modelDisplayNode = modelNode.GetDisplayNode()
| |
| − | triangles = vtk.vtkTriangleFilter()
| |
| − | triangles.SetInputConnection(modelDisplayNode.GetOutputPolyDataConnection())
| |
| − | | |
| − | plyWriter = vtk.vtkPLYWriter()
| |
| − | plyWriter.SetInputConnection(triangles.GetOutputPort())
| |
| − | lut = vtk.vtkLookupTable()
| |
| − | lut.DeepCopy(modelDisplayNode.GetColorNode().GetLookupTable())
| |
| − | lut.SetRange(modelDisplayNode.GetScalarRange())
| |
| − | plyWriter.SetLookupTable(lut)
| |
| − | plyWriter.SetArrayName(modelDisplayNode.GetActiveScalarName())
| |
| − | | |
| − | plyWriter.SetFileName(plyFilePath)
| |
| − | plyWriter.Write()
| |
| − | </pre>
| |
| − | | |
| − | ==Export a tract (FiberBundle) to Blender, including color==
| |
| − | <div id="Export_a_fiber_tracts_to_Blender.2C_including_color"></div>
| |
| − | Note: an interactive version of this script is now included in the [http://dmri.slicer.org/ SlicerDMRI extension] ([https://github.com/SlicerDMRI/SlicerDMRI/tree/master/Modules/Scripted/TractographyExportPLY module code]).
| |
| − | After installing SlicerDMRI, go to ''Modules -> Diffusion -> Import and Export -> Export tractography to PLY (mesh)''.
| |
| − | | |
| − | The example below shows how to export a tractography "FiberBundleNode" to a PLY file:
| |
| − | | |
| − | <pre>
| |
| − | lineDisplayNode = getNode("*LineDisplay*")
| |
| − | plyFilePath = "/tmp/fibers.ply"
| |
| − | | |
| − | tuber = vtk.vtkTubeFilter()
| |
| − | tuber.SetInputData(lineDisplayNode.GetOutputPolyData())
| |
| − | tuber.Update()
| |
| − | tubes = tuber.GetOutputDataObject(0)
| |
| − | scalars = tubes.GetPointData().GetArray(0)
| |
| − | scalars.SetName("scalars")
| |
| − | | |
| − | triangles = vtk.vtkTriangleFilter()
| |
| − | triangles.SetInputData(tubes)
| |
| − | triangles.Update()
| |
| − | | |
| − | colorNode = lineDisplayNode.GetColorNode()
| |
| − | lookupTable = vtk.vtkLookupTable()
| |
| − | lookupTable.DeepCopy(colorNode.GetLookupTable())
| |
| − | lookupTable.SetTableRange(0,1)
| |
| − | | |
| − | plyWriter = vtk.vtkPLYWriter()
| |
| − | plyWriter.SetInputData(triangles.GetOutput())
| |
| − | plyWriter.SetLookupTable(lookupTable)
| |
| − | plyWriter.SetArrayName("scalars")
| |
| − | | |
| − | plyWriter.SetFileName(plyFilePath)
| |
| − | plyWriter.Write()
| |
| − | </pre>
| |
| − | | |
| − | ==Iterate over tract (FiberBundle) streamline points==
| |
| − | | |
| − | This example shows how to access the points in each line of a FiberBundle as a numpy array (view).
| |
| − | | |
| − | <pre>
| |
| − | from vtk.util.numpy_support import vtk_to_numpy
| |
| − | | |
| − | fb = getNode("FiberBundle_F") # <- fill in node ID here
| |
| − | | |
| − | # get point data as 1d array
| |
| − | points = slicer.util.arrayFromModelPoints(fb)
| |
| − | | |
| − | # get line cell ids as 1d array
| |
| − | line_ids = vtk_to_numpy(fb.GetPolyData().GetLines().GetData())
| |
| − | | |
| − | # VTK cell ids are stored as
| |
| − | # [ N0 c0_id0 ... c0_id0
| |
| − | # N1 c1_id0 ... c1_idN1 ]
| |
| − | # so we need to
| |
| − | # - read point count for each line (cell)
| |
| − | # - grab the ids in that range from `line_ids` array defined above
| |
| − | # - index the `points` array by those ids
| |
| − | cur_idx = 1
| |
| − | for _ in range(pd.GetLines().GetNumberOfCells()):
| |
| − | # - read point count for this line (cell)
| |
| − | count = lines[cur_idx - 1]
| |
| − | | |
| − | # - grab the ids in that range from `lines`
| |
| − | index_array = line_ids[ cur_idx : cur_idx + count]
| |
| − | # update to the next range
| |
| − | cur_idx += count + 1
| |
| − | | |
| − | # - index the point array by those ids
| |
| − | line_points = points[index_array]
| |
| − | | |
| − | # do work here
| |
| − | </pre>
| |
| − | | |
| − | ==Clone a node==
| |
| − | | |
| − | This example shows how to make a copy of any node that appears in Subject Hierarchy (in Data module).
| |
| − | | |
| − | <pre>
| |
| − | # Get a node from SampleData that we will clone
| |
| − | import SampleData
| |
| − | nodeToClone = SampleData.SampleDataLogic().downloadMRHead()
| |
| − | | |
| − | # Clone the node
| |
| − | shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
| |
| − | itemIDToClone = shNode.GetItemByDataNode(nodeToClone)
| |
| − | clonedItemID = slicer.modules.subjecthierarchy.logic().CloneSubjectHierarchyItem(shNode, itemIDToClone)
| |
| − | clonedNode = shNode.GetItemDataNode(clonedItemID)
| |
| − | </pre>
| |
| − | | |
| − | ==Clone a volume==
| |
| − | This example shows how to clone the MRHead sample volume, including its pixel data and display settings.
| |
| − | <pre>
| |
| − | sourceVolumeNode = slicer.util.getNode('MRHead')
| |
| − | volumesLogic = slicer.modules.volumes.logic()
| |
| − | clonedVolumeNode = volumesLogic.CloneVolume(slicer.mrmlScene, sourceVolumeNode, 'Cloned volume')
| |
| − | </pre>
| |
| − | | |
| − | ==Create a new volume==
| |
| − | This example shows how to create a new empty volume.
| |
| − | <pre>
| |
| − | nodeName = "MyNewVolume"
| |
| − | imageSize = [512, 512, 512]
| |
| − | voxelType=vtk.VTK_UNSIGNED_CHAR
| |
| − | imageOrigin = [0.0, 0.0, 0.0]
| |
| − | imageSpacing = [1.0, 1.0, 1.0]
| |
| − | imageDirections = [[1,0,0], [0,1,0], [0,0,1]]
| |
| − | fillVoxelValue = 0
| |
| − | | |
| − | # Create an empty image volume, filled with fillVoxelValue
| |
| − | imageData = vtk.vtkImageData()
| |
| − | imageData.SetDimensions(imageSize)
| |
| − | imageData.AllocateScalars(voxelType, 1)
| |
| − | imageData.GetPointData().GetScalars().Fill(fillVoxelValue)
| |
| − | # Create volume node
| |
| − | volumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode", nodeName)
| |
| − | volumeNode.SetOrigin(imageOrigin)
| |
| − | volumeNode.SetSpacing(imageSpacing)
| |
| − | volumeNode.SetIJKToRASDirections(imageDirections)
| |
| − | volumeNode.SetAndObserveImageData(imageData)
| |
| − | volumeNode.CreateDefaultDisplayNodes()
| |
| − | volumeNode.CreateDefaultStorageNode()
| |
| − | </pre>
| |
| − | | |
| − | ==Get value of a volume at specific voxel coordinates==
| |
| − | | |
| − | This example shows how to get voxel value of "volumeNode" at "ijk" volume voxel coordinates.
| |
| − | | |
| − | <pre>
| |
| − | volumeNode = slicer.util.getNode('MRHead')
| |
| − | ijk = [20,40,30] # volume voxel coordinates
| |
| − | | |
| − | voxels = slicer.util.arrayFromVolume(volumeNode) # get voxels as a numpy array
| |
| − | voxelValue = voxels[ijk[2], ijk[1], ijk[0]] # note that numpy array index order is kji (not ijk)
| |
| − | </pre>
| |
| − | | |
| − | ==Modify voxels in a volume==
| |
| − | | |
| − | Typically the fastest and simplest way of modifying voxels is by using numpy operators. Voxels can be retrieved in a numpy array using the `array` method and modified using standard numpy methods. For example, threshold a volume:
| |
| − | | |
| − | <pre>
| |
| − | nodeName = 'MRHead'
| |
| − | thresholdValue = 100
| |
| − | voxelArray = array(nodeName) # get voxels as numpy array
| |
| − | voxelArray[voxelArray < thresholdValue] = 0 # modify voxel values
| |
| − | getNode(nodeName).Modified() # at the end of all processing, notify Slicer that the image modification is completed
| |
| − | </pre>
| |
| − | | |
| − | This example shows how to change voxels values of the MRHead sample volume.
| |
| − | The values will be computed by function f(r,a,s,) = (r-10)*(r-10)+(a+15)*(a+15)+s*s.
| |
| − | <pre>
| |
| − | volumeNode=slicer.util.getNode('MRHead')
| |
| − | ijkToRas = vtk.vtkMatrix4x4()
| |
| − | volumeNode.GetIJKToRASMatrix(ijkToRas)
| |
| − | imageData=volumeNode.GetImageData()
| |
| − | extent = imageData.GetExtent()
| |
| − | for k in range(extent[4], extent[5]+1):
| |
| − | for j in range(extent[2], extent[3]+1):
| |
| − | for i in range(extent[0], extent[1]+1):
| |
| − | position_Ijk=[i, j, k, 1]
| |
| − | position_Ras=ijkToRas.MultiplyPoint(position_Ijk)
| |
| − | r=position_Ras[0]
| |
| − | a=position_Ras[1]
| |
| − | s=position_Ras[2]
| |
| − | functionValue=(r-10)*(r-10)+(a+15)*(a+15)+s*s
| |
| − | imageData.SetScalarComponentFromDouble(i,j,k,0,functionValue)
| |
| − | imageData.Modified()
| |
| − | </pre>
| |
| − | | |
| − | ==Get volume voxel coordinates from markup fiducial RAS coordinates==
| |
| − | | |
| − | This example shows how to get voxel coordinate of a volume corresponding to a markup fiducial point position.
| |
| − | | |
| − | <pre>
| |
| − | # Inputs
| |
| − | volumeNode = getNode('MRHead')
| |
| − | markupsNode = getNode('F')
| |
| − | markupsIndex = 0
| |
| − | | |
| − | # Get point coordinate in RAS
| |
| − | point_Ras = [0, 0, 0, 1]
| |
| − | markupsNode.GetNthFiducialWorldCoordinates(markupsIndex, point_Ras)
| |
| − | | |
| − | # If volume node is transformed, apply that transform to get volume's RAS coordinates
| |
| − | transformRasToVolumeRas = vtk.vtkGeneralTransform()
| |
| − | slicer.vtkMRMLTransformNode.GetTransformBetweenNodes(None, volumeNode.GetParentTransformNode(), transformRasToVolumeRas)
| |
| − | point_VolumeRas = transformRasToVolumeRas.TransformPoint(point_Ras[0:3])
| |
| − | | |
| − | # Get voxel coordinates from physical coordinates
| |
| − | volumeRasToIjk = vtk.vtkMatrix4x4()
| |
| − | volumeNode.GetRASToIJKMatrix(volumeRasToIjk)
| |
| − | point_Ijk = [0, 0, 0, 1]
| |
| − | volumeRasToIjk.MultiplyPoint(np.append(point_VolumeRas,1.0), point_Ijk)
| |
| − | point_Ijk = [ int(round(c)) for c in point_Ijk[0:3] ]
| |
| − | | |
| − | # Print output
| |
| − | print(point_Ijk)
| |
| − | </pre>
| |
| − | | |
| − | ==Get markup fiducial RAS coordinates from volume voxel coordinates==
| |
| − | | |
| − | This example shows how to get position of maximum intensity voxel of a volume (determined by numpy, in IJK coordinates) in RAS coordinates so that it can be marked with a markup fiducial.
| |
| − | | |
| − | <pre>
| |
| − | # Inputs
| |
| − | volumeNode = getNode('MRHead')
| |
| − | markupsNode = getNode('F')
| |
| − | | |
| − | # Get voxel position in IJK coordinate system
| |
| − | import numpy as np
| |
| − | volumeArray = slicer.util.arrayFromVolume(volumeNode)
| |
| − | # Get position of highest voxel value
| |
| − | point_Kji = np.where(volumeArray == volumeArray.max())
| |
| − | point_Ijk = [point_Kji[2][0], point_Kji[1][0], point_Kji[0][0]]
| |
| − | | |
| − | # Get physical coordinates from voxel coordinates
| |
| − | volumeIjkToRas = vtk.vtkMatrix4x4()
| |
| − | volumeNode.GetIJKToRASMatrix(volumeIjkToRas)
| |
| − | point_VolumeRas = [0, 0, 0, 1]
| |
| − | volumeIjkToRas.MultiplyPoint(np.append(point_Ijk,1.0), point_VolumeRas)
| |
| − | | |
| − | # If volume node is transformed, apply that transform to get volume's RAS coordinates
| |
| − | transformVolumeRasToRas = vtk.vtkGeneralTransform()
| |
| − | slicer.vtkMRMLTransformNode.GetTransformBetweenNodes(volumeNode.GetParentTransformNode(), None, transformVolumeRasToRas)
| |
| − | point_Ras = transformVolumeRasToRas.TransformPoint(point_VolumeRas[0:3])
| |
| − | | |
| − | # Add a markup at the computed position and print its coordinates
| |
| − | markupsNode.AddFiducial(point_Ras[0], point_Ras[1], point_Ras[2], "max")
| |
| − | print(point_Ras)
| |
| − | </pre>
| |
| − | | |
| − | ==Get the values of all voxels for a label value==
| |
| − | | |
| − | If you have a background image called ‘Volume’ and a mask called ‘Volume-label’ created with the Editor you could do something like this:
| |
| − | | |
| − | <pre>
| |
| − | | |
| − | import numpy
| |
| − | volume = array('Volume')
| |
| − | label = array('Volume-label')
| |
| − | points = numpy.where( label == 1 ) # or use another label number depending on what you segmented
| |
| − | values = volume[points] # this will be a list of the label values
| |
| − | values.mean() # should match the mean value of LabelStatistics calculation as a double-check
| |
| − | numpy.savetxt('values.txt', values)
| |
| − | </pre>
| |
| − | | |
| − | ==Access values in a DTI tensor volume==
| |
| − | This example shows how to access individual tensors at the voxel level.
| |
| − | | |
| − | First load your DWI volume and estimate tensors to produce a DTI volume called ‘Output DTI Volume’
| |
| − | | |
| − | Then open the python window: View->Python interactor
| |
| − | | |
| − | Use this command to access tensors through numpy:
| |
| − | | |
| − | <pre>
| |
| − | tensors = array('Output DTI Volume')
| |
| − | </pre>
| |
| − | | |
| − | Type the following code into the Python window to access all tensor components using vtk commands:
| |
| − | | |
| − | <pre>
| |
| − | volumeNode=slicer.util.getNode('Output DTI Volume')
| |
| − | imageData=volumeNode.GetImageData()
| |
| − | tensors = imageData.GetPointData().GetTensors()
| |
| − | extent = imageData.GetExtent()
| |
| − | idx = 0
| |
| − | for k in range(extent[4], extent[5]+1):
| |
| − | for j in range(extent[2], extent[3]+1):
| |
| − | for i in range(extent[0], extent[1]+1):
| |
| − | tensors.GetTuple9(idx)
| |
| − | idx += 1
| |
| − | </pre>
| |
| − | | |
| − | ==Change window/level (brightness/contrast) or colormap of a volume==
| |
| − | This example shows how to change window/level of the MRHead sample volume.
| |
| − | <pre>
| |
| − | volumeNode = getNode('MRHead')
| |
| − | displayNode = volumeNode.GetDisplayNode()
| |
| − | displayNode.AutoWindowLevelOff()
| |
| − | displayNode.SetWindow(50)
| |
| − | displayNode.SetLevel(100)
| |
| − | </pre>
| |
| − | | |
| − | Change color mapping from grayscale to rainbow:
| |
| − | <pre>
| |
| − | displayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeRainbow')
| |
| − | </pre>
| |
| − | | |
| − | ==Make mouse left-click and drag on the image adjust window/level==
| |
| − | | |
| − | In older Slicer versions, by default, left-click and drag in a slice view adjusted window/level of the displayed image. Window/level adjustment is now a new mouse mode that can be activated by clicking on its toolbar button or running this code:
| |
| − | | |
| − | <pre>
| |
| − | slicer.app.applicationLogic().GetInteractionNode().SetCurrentInteractionMode(slicer.vtkMRMLInteractionNode.AdjustWindowLevel)
| |
| − | </pre>
| |
| − | | |
| − | ==Create custom color table==
| |
| − | This example shows how to create a new color table, for example with inverted color range from the default Ocean color table.
| |
| − | <pre>
| |
| − | invertedocean = slicer.vtkMRMLColorTableNode()
| |
| − | invertedocean.SetTypeToUser()
| |
| − | invertedocean.SetNumberOfColors(256)
| |
| − | invertedocean.SetName("InvertedOcean")
| |
| − | | |
| − | for i in range(0,255):
| |
| − | invertedocean.SetColor(i, 0.0, 1 - (i+1e-16)/255.0, 1.0, 1.0)
| |
| − | | |
| − | slicer.mrmlScene.AddNode(invertedocean)
| |
| − | </pre>
| |
| − | | |
| − | ==Manipulate a Slice View==
| |
| − | | |
| − | ===Change slice offset===
| |
| − | | |
| − | Equivalent to moving the slider in slice view controller.
| |
| − | | |
| − | <pre>
| |
| − | layoutManager = slicer.app.layoutManager()
| |
| − | red = layoutManager.sliceWidget('Red')
| |
| − | redLogic = red.sliceLogic()
| |
| − | # Print current slice offset position
| |
| − | print(redLogic.GetSliceOffset())
| |
| − | # Change slice position
| |
| − | redLogic.SetSliceOffset(20)
| |
| − | </pre>
| |
| − | | |
| − | ===Change slice orientation===
| |
| − | | |
| − | Get 'Red' slice node and rotate around X and Y axes.
| |
| − | | |
| − | <pre>
| |
| − | sliceNode = slicer.app.layoutManager().sliceWidget('Red').mrmlSliceNode()
| |
| − | sliceToRas = sliceNode.GetSliceToRAS()
| |
| − | transform=vtk.vtkTransform()
| |
| − | transform.SetMatrix(SliceToRAS)
| |
| − | transform.RotateX(20)
| |
| − | transform.RotateY(15)
| |
| − | sliceToRas.DeepCopy(transform.GetMatrix())
| |
| − | sliceNode.UpdateMatrices()
| |
| − | </pre>
| |
| − | | |
| − | ===Show slice views in 3D window===
| |
| − | | |
| − | Equivalent to clicking 'eye' icon in the slice view controller.
| |
| − | | |
| − | <pre>
| |
| − | layoutManager = slicer.app.layoutManager()
| |
| − | for sliceViewName in layoutManager.sliceViewNames():
| |
| − | controller = layoutManager.sliceWidget(sliceViewName).sliceController()
| |
| − | controller.setSliceVisible(True)
| |
| − | </pre>
| |
| − | | |
| − | ===Reset field of view to show background volume maximized===
| |
| − | | |
| − | Equivalent to click small rectangle button ("Adjust the slice viewer's field of view...") in the slice view controller.
| |
| − | | |
| − | <pre>
| |
| − | slicer.util.resetSliceViews()
| |
| − | </pre>
| |
| − | | |
| − | ===Rotate slice views to volume plane===
| |
| − | | |
| − | Aligns slice views to volume axes, shows original image acquisition planes in slice views.
| |
| − | | |
| − | <pre>
| |
| − | volumeNode = slicer.util.getNode('MRHead')
| |
| − | layoutManager = slicer.app.layoutManager()
| |
| − | for sliceViewName in layoutManager.sliceViewNames():
| |
| − | layoutManager.sliceWidget(sliceViewName).mrmlSliceNode().RotateToVolumePlane(volumeNode)
| |
| − | </pre>
| |
| − | | |
| − | ===Iterate over current visible slice views, and set foreground and background images===
| |
| − | | |
| − | <pre>
| |
| − | slicer.util.setSliceViewerLayers(background=mrVolume, foreground=ctVolume)
| |
| − | </pre>
| |
| − | | |
| − | Internally, this method performs something like this:
| |
| − | | |
| − | <pre>
| |
| − | layoutManager = slicer.app.layoutManager()
| |
| − | for sliceViewName in layoutManager.sliceViewNames():
| |
| − | compositeNode = layoutManager.sliceWidget(sliceViewName).sliceLogic().GetSliceCompositeNode()
| |
| − | # setup background volume
| |
| − | compositeNode.SetBackgroundVolumeID(mrVolume.GetID())
| |
| − | # setup foreground volume
| |
| − | compositeNode.SetForegroundVolumeID(ctVolume.GetID())
| |
| − | # change opacity
| |
| − | compositeNode.SetForegroundOpacity(0.3)
| |
| − | </pre>
| |
| − | | |
| − | ==Show a volume in slice views==
| |
| − | | |
| − | Recommended:
| |
| − | | |
| − | <pre>
| |
| − | volumeNode = slicer.util.getNode('YourVolumeNode')
| |
| − | slicer.util.setSliceViewerLayers(background=volumeNode)
| |
| − | </pre>
| |
| − | | |
| − | or
| |
| − | | |
| − | Show volume in all visible views where volume selection propagation is enabled:
| |
| − | | |
| − | <pre>
| |
| − | volumeNode = slicer.util.getNode('YourVolumeNode')
| |
| − | applicationLogic = slicer.app.applicationLogic()
| |
| − | selectionNode = applicationLogic.GetSelectionNode()
| |
| − | selectionNode.SetSecondaryVolumeID(volumeNode.GetID())
| |
| − | applicationLogic.PropagateForegroundVolumeSelection(0)
| |
| − | </pre>
| |
| − | | |
| − | or
| |
| − | | |
| − | Show volume in selected views:
| |
| − | | |
| − | <pre>
| |
| − | n = slicer.util.getNode('YourVolumeNode')
| |
| − | for color in ['Red', 'Yellow', 'Green']:
| |
| − | slicer.app.layoutManager().sliceWidget(color).sliceLogic().GetSliceCompositeNode().SetForegroundVolumeID(n.GetID())
| |
| − | </pre>
| |
| − | | |
| − | ==Show comparison view of all model files a folder==
| |
| − | | |
| − | <pre>
| |
| − | # Inputs
| |
| − | modelDir = "c:/some/folder/containing/models"
| |
| − | modelFileExt = "stl"
| |
| − | numberOfColumns = 4
| |
| − | | |
| − | import math
| |
| − | import os
| |
| − | modelFiles = list(f for f in os.listdir(modelDir) if f.endswith('.' + modelFileExt))
| |
| − | | |
| − | # Create a custom layout
| |
| − | numberOfRows = int(math.ceil(len(modelFiles)/numberOfColumns))
| |
| − | customLayoutId=567 # we pick a random id that is not used by others
| |
| − | slicer.app.setRenderPaused(True)
| |
| − | customLayout = '<layout type="vertical">'
| |
| − | viewIndex = 0
| |
| − | for rowIndex in range(numberOfRows):
| |
| − | customLayout += '<item><layout type="horizontal">'
| |
| − | for colIndex in range(numberOfColumns):
| |
| − | name = os.path.basename(modelFiles[viewIndex]) if viewIndex < len(modelFiles) else "compare "+str(viewIndex)
| |
| − | customLayout += '<item><view class="vtkMRMLViewNode" singletontag="'+name
| |
| − | customLayout += '"><property name="viewlabel" action="default">'+name+'</property></view></item>'
| |
| − | viewIndex += 1
| |
| − | customLayout += '</layout></item>'
| |
| − | | |
| − | customLayout += '</layout>'
| |
| − | if not slicer.app.layoutManager().layoutLogic().GetLayoutNode().SetLayoutDescription(customLayoutId, customLayout):
| |
| − | slicer.app.layoutManager().layoutLogic().GetLayoutNode().AddLayoutDescription(customLayoutId, customLayout)
| |
| − | | |
| − | slicer.app.layoutManager().setLayout(customLayoutId)
| |
| − | | |
| − | # Load and show each model in a view
| |
| − | for modelIndex, modelFile in enumerate(modelFiles):
| |
| − | # Show only one model in each view
| |
| − | name = os.path.basename(modelFile)
| |
| − | viewNode = slicer.mrmlScene.GetSingletonNode(name, "vtkMRMLViewNode")
| |
| − | viewNode.LinkedControlOn()
| |
| − | modelNode = slicer.util.loadModel(modelDir+"/"+modelFile)
| |
| − | modelNode.GetDisplayNode().AddViewNodeID(viewNode.GetID())
| |
| − | | |
| − | slicer.app.setRenderPaused(False)
| |
| − | </pre>
| |
| − | | |
| − | ==Change opacity of foreground volume in slice views==
| |
| − | | |
| − | <pre>
| |
| − | slicer.util.setSliceViewerLayers(foregroundOpacity=0.4)
| |
| − | </pre>
| |
| − | | |
| − | or
| |
| − | | |
| − | Change opacity in a selected view
| |
| − | | |
| − | <pre>
| |
| − | lm = slicer.app.layoutManager()
| |
| − | sliceLogic = lm.sliceWidget('Red').sliceLogic()
| |
| − | compositeNode = sliceLogic.GetSliceCompositeNode()
| |
| − | compositeNode.SetForegroundOpacity(0.4)
| |
| − | </pre>
| |
| − | | |
| − | ==Fit slice plane to markup fiducials==
| |
| − | | |
| − | <pre>
| |
| − | sliceNode = slicer.mrmlScene.GetNodeByID("vtkMRMLSliceNodeRed")
| |
| − | markupsNode = slicer.mrmlScene.GetFirstNodeByName("F")
| |
| − | # Get markup point positions as numpy arrays
| |
| − | import numpy as np
| |
| − | p1 = np.zeros(3)
| |
| − | p2 = np.zeros(3)
| |
| − | p3 = np.zeros(3)
| |
| − | markupsNode.GetNthFiducialPosition(0, p1)
| |
| − | markupsNode.GetNthFiducialPosition(1, p2)
| |
| − | markupsNode.GetNthFiducialPosition(2, p3)
| |
| − | # Get plane axis directions
| |
| − | n = np.cross(p2-p1, p2-p3) # plane normal direction
| |
| − | n = n/np.linalg.norm(n)
| |
| − | t = np.cross([0.0, 0.0, 1], n) # plane transverse direction
| |
| − | t = t/np.linalg.norm(t)
| |
| − | # Set slice plane orientation and position
| |
| − | sliceNode.SetSliceToRASByNTP(n[0], n[1], n[2], t[0], t[1], t[2], p1[0], p1[1], p1[2], 0)
| |
| − | </pre>
| |
| − | | |
| − | ==Save a series of images from a Slice View==
| |
| − | | |
| − | You can use ScreenCapture module to capture series of images. To do it programmatically, save the following into a file such as '/tmp/record.py' and then in the slicer python console type "execfile('/tmp/record.py')"
| |
| − | | |
| − | <pre>
| |
| − | layoutName = 'Green'
| |
| − | imagePathPattern = '/tmp/image-%03d.png'
| |
| − | steps = 10
| |
| − | | |
| − | widget = slicer.app.layoutManager().sliceWidget(layoutName)
| |
| − | view = widget.sliceView()
| |
| − | logic = widget.sliceLogic()
| |
| − | bounds = [0,]*6
| |
| − | logic.GetSliceBounds(bounds)
| |
| − | | |
| − | for step in range(steps):
| |
| − | offset = bounds[4] + step/(1.*steps) * (bounds[5]-bounds[4])
| |
| − | logic.SetSliceOffset(offset)
| |
| − | view.forceRender()
| |
| − | image = qt.QPixmap.grabWidget(view).toImage()
| |
| − | image.save(imagePathPattern % step)
| |
| − | </pre>
| |
| − | | |
| − | ==Rasterize a model and save it to a series of image files==
| |
| − | | |
| − | This example shows how to generate a stack of image files from an STL file:
| |
| − | | |
| − | inputModelFile = "/some/input/folder/SomeShape.stl"
| |
| − | outputDir = "/some/output/folder"
| |
| − | outputVolumeLabelValue = 100
| |
| − | outputVolumeSpacingMm = [0.5, 0.5, 0.5]
| |
| − | outputVolumeMarginMm = [10.0, 10.0, 10.0]
| |
| − |
| |
| − | # Read model
| |
| − | inputModel = slicer.util.loadModel(inputModelFile)
| |
| − |
| |
| − | # Determine output volume geometry and create a corresponding reference volume
| |
| − | import math
| |
| − | import numpy as np
| |
| − | bounds = np.zeros(6)
| |
| − | inputModel.GetBounds(bounds)
| |
| − | imageData = vtk.vtkImageData()
| |
| − | imageSize = [ int((bounds[axis*2+1]-bounds[axis*2]+outputVolumeMarginMm[axis]*2.0)/outputVolumeSpacingMm[axis]) for axis in range(3) ]
| |
| − | imageOrigin = [ bounds[axis*2]-outputVolumeMarginMm[axis] for axis in range(3) ]
| |
| − | imageData.SetDimensions(imageSize)
| |
| − | imageData.AllocateScalars(vtk.VTK_UNSIGNED_CHAR, 1)
| |
| − | imageData.GetPointData().GetScalars().Fill(0)
| |
| − | referenceVolumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode")
| |
| − | referenceVolumeNode.SetOrigin(imageOrigin)
| |
| − | referenceVolumeNode.SetSpacing(outputVolumeSpacingMm)
| |
| − | referenceVolumeNode.SetAndObserveImageData(imageData)
| |
| − | referenceVolumeNode.CreateDefaultDisplayNodes()
| |
| − |
| |
| − | # Convert model to labelmap
| |
| − | seg = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSegmentationNode')
| |
| − | seg.SetReferenceImageGeometryParameterFromVolumeNode(referenceVolumeNode)
| |
| − | slicer.modules.segmentations.logic().ImportModelToSegmentationNode(inputModel, seg)
| |
| − | seg.CreateBinaryLabelmapRepresentation()
| |
| − | outputLabelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')
| |
| − | slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(seg, outputLabelmapVolumeNode, referenceVolumeNode)
| |
| − | outputLabelmapVolumeArray = (slicer.util.arrayFromVolume(outputLabelmapVolumeNode) * outputVolumeLabelValue).astype('int8')
| |
| − |
| |
| − | # Write labelmap volume to series of TIFF files
| |
| − | pip_install("imageio")
| |
| − | import imageio
| |
| − | for i in range(len(outputLabelmapVolumeArray)):
| |
| − | imageio.imwrite(f'{outputDir}/image_{i:03}.tiff', outputLabelmapVolumeArray[i])
| |
| − | | |
| − | ==Save the scene into a new directory==
| |
| − | | |
| − | <pre>
| |
| − | # Create a new directory where the scene will be saved into
| |
| − | import time
| |
| − | sceneSaveDirectory = slicer.app.temporaryPath + "/saved-scene-" + time.strftime("%Y%m%d-%H%M%S")
| |
| − | if not os.access(sceneSaveDirectory, os.F_OK):
| |
| − | os.makedirs(sceneSaveDirectory)
| |
| − | | |
| − | # Save the scene
| |
| − | if slicer.app.applicationLogic().SaveSceneToSlicerDataBundleDirectory(sceneSaveDirectory, None):
| |
| − | logging.info("Scene saved to: {0}".format(sceneSaveDirectory))
| |
| − | else:
| |
| − | logging.error("Scene saving failed")
| |
| − | </pre>
| |
| − | | |
| − | ==Save the scene into a single MRB file==
| |
| − | <pre>
| |
| − | # Generate file name
| |
| − | import time
| |
| − | sceneSaveFilename = slicer.app.temporaryPath + "/saved-scene-" + time.strftime("%Y%m%d-%H%M%S") + ".mrb"
| |
| − | | |
| − | # Save scene
| |
| − | if slicer.util.saveScene(sceneSaveFilename):
| |
| − | logging.info("Scene saved to: {0}".format(sceneSaveFilename))
| |
| − | else:
| |
| − | logging.error("Scene saving failed")
| |
| − | </pre>
| |
| − | | |
| − | ==Save a node to file==
| |
| − | | |
| − | Save a transform node to file (should work with any other node type, if file extension is set to a supported one):
| |
| − | | |
| − | <pre>
| |
| − | myNode = getNode("LinearTransform_3")
| |
| − | | |
| − | myStorageNode = myNode.CreateDefaultStorageNode()
| |
| − | myStorageNode.SetFileName("c:/tmp/something.tfm")
| |
| − | myStorageNode.WriteData(myNode)
| |
| − | </pre>
| |
| − | | |
| − | ==Override default scene save dialog==
| |
| − | | |
| − | Place this class in the scripted module file to override
| |
| − | | |
| − | <pre>
| |
| − | class MyModuleFileDialog ():
| |
| − | """This specially named class is detected by the scripted loadable
| |
| − | module and is the target for optional drag and drop operations.
| |
| − | See: Base/QTGUI/qSlicerScriptedFileDialog.h.
| |
| − | | |
| − | This class is used for overriding default scene save dialog
| |
| − | with simple saving the scene without asking anything.
| |
| − | """
| |
| − | | |
| − | def __init__(self,qSlicerFileDialog ):
| |
| − | self.qSlicerFileDialog = qSlicerFileDialog
| |
| − | qSlicerFileDialog.fileType = 'NoFile'
| |
| − | qSlicerFileDialog.description = 'Save scene'
| |
| − | qSlicerFileDialog.action = slicer.qSlicerFileDialog.Write
| |
| − | | |
| − | def execDialog(self):
| |
| − | # Implement custom scene save operation here.
| |
| − | # Return True if saving completed successfully,
| |
| − | # return False if saving was cancelled.
| |
| − | ...
| |
| − | return saved
| |
| − | </pre>
| |
| − | | |
| − | ==Override application close behavior==
| |
| − | | |
| − | When application close is requested then by default confirmation popup is displayed.
| |
| − | To customize this behavior (for example, allow application closing without displaying default confirmation popup)
| |
| − | an event filter can be installed for the close event on the main window:
| |
| − | | |
| − | <pre>
| |
| − | class CloseApplicationEventFilter(qt.QWidget):
| |
| − | def eventFilter(self, object, event):
| |
| − | if event.type() == qt.QEvent.Close:
| |
| − | event.accept()
| |
| − | return True
| |
| − | return False
| |
| − | | |
| − | filter = CloseApplicationEventFilter()
| |
| − | slicer.util.mainWindow().installEventFilter(filter)
| |
| − | </pre>
| |
| − | | |
| − | ==Center the 3D View on the Scene==
| |
| − | <pre>
| |
| − | layoutManager = slicer.app.layoutManager()
| |
| − | threeDWidget = layoutManager.threeDWidget(0)
| |
| − | threeDView = threeDWidget.threeDView()
| |
| − | threeDView.resetFocalPoint()
| |
| − | </pre>
| |
| − | | |
| − | ==Rotate the 3D View==
| |
| − | | |
| − | <pre>
| |
| − | layoutManager = slicer.app.layoutManager()
| |
| − | threeDWidget = layoutManager.threeDWidget(0)
| |
| − | threeDView = threeDWidget.threeDView()
| |
| − | threeDView.yaw()
| |
| − | </pre>
| |
| − | | |
| − | ==Display text in a 3D view or slice view==
| |
| − | | |
| − | The easiest way to show information overlaid on a viewer is to use corner annotations.
| |
| − | | |
| − | <pre>
| |
| − | view=slicer.app.layoutManager().threeDWidget(0).threeDView()
| |
| − | # Set text to "Something"
| |
| − | view.cornerAnnotation().SetText(vtk.vtkCornerAnnotation.UpperRight,"Something")
| |
| − | # Set color to red
| |
| − | view.cornerAnnotation().GetTextProperty().SetColor(1,0,0)
| |
| − | # Update the view
| |
| − | view.forceRender()
| |
| − | </pre>
| |
| − | | |
| − | To display text in slice views, replace the first line by this line (and consider hiding slice view annotations, to prevent them from overwriting the text you place there):
| |
| − | | |
| − | <pre>
| |
| − | view=slicer.app.layoutManager().sliceWidget("Red").sliceView()
| |
| − | </pre>
| |
| − | | |
| − | ==Hide slice view annotations (DataProbe)==
| |
| − | | |
| − | <pre>
| |
| − | # Disable slice annotations immediately
| |
| − | slicer.modules.DataProbeInstance.infoWidget.sliceAnnotations.sliceViewAnnotationsEnabled=False
| |
| − | slicer.modules.DataProbeInstance.infoWidget.sliceAnnotations.updateSliceViewFromGUI()
| |
| − | # Disable slice annotations persistently (after Slicer restarts)
| |
| − | settings = qt.QSettings()
| |
| − | settings.setValue('DataProbe/sliceViewAnnotations.enabled', 0)
| |
| − | </pre>
| |
| − | | |
| − | ==Turning off interpolation==
| |
| − | | |
| − | You can turn off interpolation for newly loaded volumes with this script from Steve Pieper.
| |
| − | | |
| − | <pre>
| |
| − | def NoInterpolate(caller,event):
| |
| − | for node in slicer.util.getNodes('*').values():
| |
| − | if node.IsA('vtkMRMLScalarVolumeDisplayNode'):
| |
| − | node.SetInterpolate(0)
| |
| − |
| |
| − | slicer.mrmlScene.AddObserver(slicer.mrmlScene.NodeAddedEvent, NoInterpolate)
| |
| − | </pre>
| |
| − | | |
| − | The below link explains how to put this in your startup script.
| |
| − | | |
| − | http://www.na-mic.org/Wiki/index.php/AHM2012-Slicer-Python#Refining_the_code_and_UI_with_slicerrc
| |
| − | | |
| − | | |
| − | ==Customize viewer layout==
| |
| − | | |
| − | Show a custom layout of a 3D view on top of the red slice view:
| |
| − | | |
| − | <pre>
| |
| − | customLayout = """
| |
| − | <layout type="vertical" split="true">
| |
| − | <item>
| |
| − | <view class="vtkMRMLViewNode" singletontag="1">
| |
| − | <property name="viewlabel" action="default">1</property>
| |
| − | </view>
| |
| − | </item>
| |
| − | <item>
| |
| − | <view class="vtkMRMLSliceNode" singletontag="Red">
| |
| − | <property name="orientation" action="default">Axial</property>
| |
| − | <property name="viewlabel" action="default">R</property>
| |
| − | <property name="viewcolor" action="default">#F34A33</property>
| |
| − | </view>
| |
| − | </item>
| |
| − | </layout>
| |
| − | """
| |
| − | | |
| − | # Built-in layout IDs are all below 100, so you can choose any large random number
| |
| − | # for your custom layout ID.
| |
| − | customLayoutId=501
| |
| − | | |
| − | layoutManager = slicer.app.layoutManager()
| |
| − | layoutManager.layoutLogic().GetLayoutNode().AddLayoutDescription(customLayoutId, customLayout)
| |
| − | | |
| − | # Switch to the new custom layout
| |
| − | layoutManager.setLayout(customLayoutId)
| |
| − | </pre>
| |
| − | | |
| − | See description of standard layouts (that can be used as examples) here:
| |
| − | https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Logic/vtkMRMLLayoutLogic.cxx
| |
| − | | |
| − | You can use this code snippet to add a button to the layout selector toolbar:
| |
| − | | |
| − | <pre>
| |
| − | # Add button to layout selector toolbar for this custom layout
| |
| − | viewToolBar = mainWindow().findChild('QToolBar', 'ViewToolBar')
| |
| − | layoutMenu = viewToolBar.widgetForAction(viewToolBar.actions()[0]).menu()
| |
| − | layoutSwitchActionParent = layoutMenu # use `layoutMenu` to add inside layout list, use `viewToolBar` to add next the standard layout list
| |
| − | layoutSwitchAction = layoutSwitchActionParent.addAction("My view") # add inside layout list
| |
| − | layoutSwitchAction.setData(layoutId)
| |
| − | layoutSwitchAction.setIcon(qt.QIcon(':Icons/Go.png'))
| |
| − | layoutSwitchAction.setToolTip('3D and slice view')
| |
| − | </pre>
| |
| − | | |
| − | ==Customize keyboard shortcuts==
| |
| − | | |
| − | Keyboard shortcuts can be specified for activating any Slicer feature by adding a couple of lines to your
| |
| − | [[Documentation/{{documentation/version}}/Developers/Python_scripting#How_to_systematically_execute_custom_python_code_at_startup_.3F|.slicerrc file]].
| |
| − | | |
| − | For example, this script registers ''Ctrl+b'', ''Ctrl+n'', ''Ctrl+m'', ''Ctrl+,'' keyboard shortcuts to switch between red, yellow, green, and 4-up view layouts.
| |
| − | | |
| − | <pre>
| |
| − | shortcuts = [
| |
| − | ('Ctrl+b', lambda: slicer.app.layoutManager().setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)),
| |
| − | ('Ctrl+n', lambda: slicer.app.layoutManager().setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpYellowSliceView)),
| |
| − | ('Ctrl+m', lambda: slicer.app.layoutManager().setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpGreenSliceView)),
| |
| − | ('Ctrl+,', lambda: slicer.app.layoutManager().setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView))
| |
| − | ]
| |
| − | | |
| − | for (shortcutKey, callback) in shortcuts:
| |
| − | shortcut = qt.QShortcut(slicer.util.mainWindow())
| |
| − | shortcut.setKey(qt.QKeySequence(shortcutKey))
| |
| − | shortcut.connect( 'activated()', callback)
| |
| − | </pre>
| |
| − | | |
| − | Here's an example for cycling through Segment Editor effects (requested [https://discourse.slicer.org/t/is-there-a-keystroke-to-cycle-through-effects-in-segment-editor/10117/2 on the forum] for the [http://slicermorph.org SlicerMorph] project).
| |
| − | <pre>
| |
| − | def cycleEffect(delta=1):
| |
| − | try:
| |
| − | orderedNames = list(slicer.modules.SegmentEditorWidget.editor.effectNameOrder())
| |
| − | allNames = slicer.modules.SegmentEditorWidget.editor.availableEffectNames()
| |
| − | for name in allNames:
| |
| − | try:
| |
| − | orderedNames.index(name)
| |
| − | except ValueError:
| |
| − | orderedNames.append(name)
| |
| − | orderedNames.insert(0, None)
| |
| − | activeEffect = slicer.modules.SegmentEditorWidget.editor.activeEffect()
| |
| − | if activeEffect:
| |
| − | activeName = slicer.modules.SegmentEditorWidget.editor.activeEffect().name
| |
| − | else:
| |
| − | activeName = None
| |
| − | newIndex = (orderedNames.index(activeName) + delta) % len(orderedNames)
| |
| − | slicer.modules.SegmentEditorWidget.editor.setActiveEffectByName(orderedNames[newIndex])
| |
| − | except AttributeError:
| |
| − | # module not active
| |
| − | pass
| |
| − | | |
| − | shortcuts = [
| |
| − | ('`', lambda: cycleEffect(-1)),
| |
| − | ('~', lambda: cycleEffect(1)),
| |
| − | ]
| |
| − | | |
| − | for (shortcutKey, callback) in shortcuts:
| |
| − | shortcut = qt.QShortcut(slicer.util.mainWindow())
| |
| − | shortcut.setKey(qt.QKeySequence(shortcutKey))
| |
| − | shortcut.connect( 'activated()', callback)
| |
| − | </pre>
| |
| − | | |
| − | ==Customize keyboard/mouse gestures in viewers==
| |
| − | | |
| − | Example for making the 3D view rotate using right-click-and-drag:
| |
| − | | |
| − | <pre>
| |
| − | threeDViewWidget = slicer.app.layoutManager().threeDWidget(0)
| |
| − | cameraDisplayableManager = threeDViewWidget.threeDView().displayableManagerByClassName('vtkMRMLCameraDisplayableManager')
| |
| − | cameraWidget = cameraDisplayableManager.GetCameraWidget()
| |
| − | | |
| − | # Remove old mapping from right-click-and-drag
| |
| − | cameraWidget.SetEventTranslationClickAndDrag(cameraWidget.WidgetStateIdle, vtk.vtkCommand.RightButtonPressEvent, vtk.vtkEvent.NoModifier,
| |
| − | cameraWidget.WidgetStateRotate, vtk.vtkWidgetEvent.NoEvent, vtk.vtkWidgetEvent.NoEvent)
| |
| − | | |
| − | # Make right-click-and-drag rotate the view
| |
| − | cameraWidget.SetEventTranslationClickAndDrag(cameraWidget.WidgetStateIdle, vtk.vtkCommand.RightButtonPressEvent, vtk.vtkEvent.NoModifier,
| |
| − | cameraWidget.WidgetStateRotate, cameraWidget.WidgetEventRotateStart, cameraWidget.WidgetEventRotateEnd)
| |
| − | </pre>
| |
| − | | |
| − | ==Disable certain user interactions in slice views==
| |
| − | | |
| − | For example, disable slice browsing using mouse wheel and keyboard shortcuts in the red slice viewer:
| |
| − | | |
| − | <pre>
| |
| − | interactorStyle = slicer.app.layoutManager().sliceWidget('Red').sliceView().sliceViewInteractorStyle()
| |
| − | interactorStyle.SetActionEnabled(interactorStyle.BrowseSlice, False)
| |
| − | </pre>
| |
| − | | |
| − | Hide all slice view controllers:
| |
| − | <pre>
| |
| − | lm = slicer.app.layoutManager()
| |
| − | for sliceViewName in lm.sliceViewNames():
| |
| − | lm.sliceWidget(sliceViewName).sliceController().setVisible(False)
| |
| − | </pre>
| |
| − | | |
| − | Hide all 3D view controllers:
| |
| − | <pre>
| |
| − | lm = slicer.app.layoutManager()
| |
| − | for viewIndex in range(slicer.app.layoutManager().threeDViewCount):
| |
| − | lm.threeDWidget(0).threeDController().setVisible(False)
| |
| − | </pre>
| |
| − | | |
| − | ==Change default slice view orientation==
| |
| − | | |
| − | You can left-right "flip" slice view orientation presets (show patient left side on left/right side of the screen) by copy-pasting the script below to your [[Documentation/{{documentation/version}}/Developers/FAQ/Python_Scripting#How_to_systematically_execute_custom_python_code_at_startup_.3F| .slicerrc.py file]].
| |
| − | | |
| − | <pre>
| |
| − | # Axial slice axes:
| |
| − | # 1 0 0
| |
| − | # 0 1 0
| |
| − | # 0 0 1
| |
| − | axialSliceToRas=vtk.vtkMatrix3x3()
| |
| − | | |
| − | # Coronal slice axes:
| |
| − | # 1 0 0
| |
| − | # 0 0 -1
| |
| − | # 0 1 0
| |
| − | coronalSliceToRas=vtk.vtkMatrix3x3()
| |
| − | coronalSliceToRas.SetElement(1,1, 0)
| |
| − | coronalSliceToRas.SetElement(1,2, -1)
| |
| − | coronalSliceToRas.SetElement(2,1, 1)
| |
| − | coronalSliceToRas.SetElement(2,2, 0)
| |
| − | | |
| − | # Replace orientation presets in all existing slice nodes and in the default slice node
| |
| − | sliceNodes = slicer.util.getNodesByClass('vtkMRMLSliceNode')
| |
| − | sliceNodes.append(slicer.mrmlScene.GetDefaultNodeByClass('vtkMRMLSliceNode'))
| |
| − | for sliceNode in sliceNodes:
| |
| − | orientationPresetName = sliceNode.GetOrientation()
| |
| − | sliceNode.RemoveSliceOrientationPreset("Axial")
| |
| − | sliceNode.AddSliceOrientationPreset("Axial", axialSliceToRas)
| |
| − | sliceNode.RemoveSliceOrientationPreset("Coronal")
| |
| − | sliceNode.AddSliceOrientationPreset("Coronal", coronalSliceToRas)
| |
| − | sliceNode.SetOrientation(orientationPresetName)
| |
| − | </pre>
| |
| − | | |
| − | | |
| − | ==Set all slice views linked by default==
| |
| − | | |
| − | You can make slice views linked by default (when application starts or the scene is cleared) by copy-pasting the script below to your [[Documentation/{{documentation/version}}/Developers/FAQ/Python_Scripting#How_to_systematically_execute_custom_python_code_at_startup_.3F| .slicerrc.py file]].
| |
| − | | |
| − | <pre>
| |
| − | # Set linked slice views in all existing slice composite nodes and in the default node
| |
| − | sliceCompositeNodes = slicer.util.getNodesByClass('vtkMRMLSliceCompositeNode')
| |
| − | defaultSliceCompositeNode = slicer.mrmlScene.GetDefaultNodeByClass('vtkMRMLSliceCompositeNode')
| |
| − | if not defaultSliceCompositeNode:
| |
| − | defaultSliceCompositeNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLSliceCompositeNode')
| |
| − | defaultSliceCompositeNode.UnRegister(None) # CreateNodeByClass is factory method, need to unregister the result to prevent memory leaks
| |
| − | slicer.mrmlScene.AddDefaultNode(defaultSliceCompositeNode)
| |
| − | sliceCompositeNodes.append(defaultSliceCompositeNode)
| |
| − | for sliceCompositeNode in sliceCompositeNodes:
| |
| − | sliceCompositeNode.SetLinkedControl(True)
| |
| − | </pre>
| |
| − | | |
| − | ==Set crosshair jump mode to centered by default==
| |
| − | | |
| − | You can change default slice jump mode (when application starts or the scene is cleared) by copy-pasting the script below to your [[Documentation/{{documentation/version}}/Developers/FAQ/Python_Scripting#How_to_systematically_execute_custom_python_code_at_startup_.3F| .slicerrc.py file]].
| |
| − | | |
| − | <pre>
| |
| − | crosshair=slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLCrosshairNode")
| |
| − | crosshair.SetCrosshairBehavior(crosshair.CenteredJumpSlice)
| |
| − | </pre>
| |
| − | | |
| − | ==Set up custom units in slice view ruler==
| |
| − | | |
| − | For microscopy or micro-CT images you may want to switch unit to micrometer instead of the default mm. To do that, 1. change the unit in Application settings / Units and 2. update ruler display settings using the script below (it can be copied to your Application startup script):
| |
| − | | |
| − | <pre>
| |
| − | lm = slicer.app.layoutManager()
| |
| − | for sliceViewName in lm.sliceViewNames():
| |
| − | sliceView = lm.sliceWidget(sliceViewName).sliceView()
| |
| − | displayableManager = sliceView.displayableManagerByClassName("vtkMRMLRulerDisplayableManager")
| |
| − | displayableManager.RemoveAllRulerScalePresets()
| |
| − | displayableManager.AddRulerScalePreset( 0.001, 5, 2, "nm", 1000.0)
| |
| − | displayableManager.AddRulerScalePreset( 0.010, 5, 2, "nm", 1000.0)
| |
| − | displayableManager.AddRulerScalePreset( 0.100, 5, 2, "nm", 1000.0)
| |
| − | displayableManager.AddRulerScalePreset( 0.500, 5, 1, "nm", 1000.0)
| |
| − | displayableManager.AddRulerScalePreset( 1.0, 5, 2, "um", 1.0)
| |
| − | displayableManager.AddRulerScalePreset( 5.0, 5, 1, "um", 1.0)
| |
| − | displayableManager.AddRulerScalePreset( 10.0, 5, 2, "um", 1.0)
| |
| − | displayableManager.AddRulerScalePreset( 50.0, 5, 1, "um", 1.0)
| |
| − | displayableManager.AddRulerScalePreset( 100.0, 5, 2, "um", 1.0)
| |
| − | displayableManager.AddRulerScalePreset( 500.0, 5, 1, "um", 1.0)
| |
| − | displayableManager.AddRulerScalePreset(1000.0, 5, 2, "mm", 0.001)
| |
| − | </pre>
| |
| − | | |
| − | ==Show orientation marker in all views==
| |
| − | | |
| − | <pre>
| |
| − | viewNodes = slicer.util.getNodesByClass('vtkMRMLAbstractViewNode')
| |
| − | for viewNode in viewNodes:
| |
| − | viewNode.SetOrientationMarkerType(slicer.vtkMRMLAbstractViewNode.OrientationMarkerTypeAxes)
| |
| − | </pre>
| |
| − | | |
| − | ==Show a slice view outside the view layout==
| |
| − | | |
| − | <pre>
| |
| − | layoutName = "TestSlice1"
| |
| − | layoutLabel = "TS1"
| |
| − | # ownerNode manages this view instead of the layout manager (it can be any node in the scene)
| |
| − | viewOwnerNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScriptedModuleNode")
| |
| − | | |
| − | # Create MRML nodes
| |
| − | viewNode = slicer.vtkMRMLSliceNode()
| |
| − | viewNode.SetName(layoutName)
| |
| − | viewNode.SetLayoutName(layoutName)
| |
| − | viewNode.SetLayoutLabel(layoutLabel)
| |
| − | viewNode.SetLayoutColor(1, 1, 0)
| |
| − | viewNode.SetAndObserveParentLayoutNodeID(viewOwnerNode.GetID())
| |
| − | viewNode = slicer.mrmlScene.AddNode(viewNode)
| |
| − | sliceCompositeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSliceCompositeNode")
| |
| − | sliceCompositeNode.SetLayoutName(layoutName)
| |
| − | | |
| − | # Create widget
| |
| − | viewWidget = slicer.qMRMLSliceWidget()
| |
| − | viewWidget.sliceViewName = layoutName
| |
| − | viewWidget.sliceViewLabel = layoutLabel
| |
| − | c = viewNode.GetLayoutColor()
| |
| − | viewWidget.sliceViewColor = qt.QColor.fromRgbF(c[0],c[1],c[2])
| |
| − | viewWidget.setMRMLScene(slicer.mrmlScene)
| |
| − | viewWidget.setMRMLSliceNode(viewNode)
| |
| − | sliceLogics = slicer.app.applicationLogic().GetSliceLogics()
| |
| − | viewWidget.setSliceLogics(sliceLogics)
| |
| − | sliceLogics.AddItem(viewWidget.sliceLogic())
| |
| − | viewWidget.show()
| |
| − | </pre>
| |
| − | | |
| − | ==Show a 3D view outside the view layout==
| |
| − | | |
| − | <pre>
| |
| − | layoutName = "Test3DView"
| |
| − | layoutLabel = "T3"
| |
| − | layoutColor = [1.0, 1.0, 0.0]
| |
| − | # ownerNode manages this view instead of the layout manager (it can be any node in the scene)
| |
| − | viewOwnerNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScriptedModuleNode")
| |
| − | | |
| − | # Create MRML node
| |
| − | viewNode = slicer.vtkMRMLViewNode()
| |
| − | viewNode.SetName(layoutName)
| |
| − | viewNode.SetLayoutName(layoutName)
| |
| − | viewNode.SetLayoutLabel(layoutLabel)
| |
| − | viewNode.SetLayoutColor(layoutColor)
| |
| − | viewNode.SetAndObserveParentLayoutNodeID(viewOwnerNode.GetID())
| |
| − | viewNode = slicer.mrmlScene.AddNode(viewNode)
| |
| − | | |
| − | # Create widget
| |
| − | viewWidget = slicer.qMRMLThreeDWidget()
| |
| − | viewWidget.viewLabel = layoutLabel
| |
| − | viewWidget.viewColor = qt.QColor.fromRgbF(*layoutColor)
| |
| − | viewWidget.setMRMLScene(slicer.mrmlScene)
| |
| − | viewWidget.setMRMLViewNode(viewNode)
| |
| − | viewWidget.show()
| |
| − | </pre>
| |
| − | | |
| − | ==Get displayable manager of a certain type for a certain view==
| |
| − | | |
| − | <pre>
| |
| − | threeDViewWidget = slicer.app.layoutManager().threeDWidget(0)
| |
| − | modelDisplayableManager = threeDViewWidget.threeDView().displayableManagerByClassName('vtkMRMLModelDisplayableManager')
| |
| − | if modelDisplayableManager is None:
| |
| − | logging.error('Failed to find the model displayable manager')
| |
| − | </pre>
| |
| − | | |
| − | ==Running an ITK filter in Python using SimpleITK==
| |
| − | Open the "Sample Data" module and download "MR Head", then paste the following snippet in Python interactor:
| |
| − | <pre>
| |
| − | import SampleData
| |
| − | import SimpleITK as sitk
| |
| − | import sitkUtils
| |
| − | | |
| − | # Get input volume node
| |
| − | inputVolumeNode = SampleData.SampleDataLogic().downloadMRHead()
| |
| − | # Create new volume node for output
| |
| − | outputVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLScalarVolumeNode', 'MRHeadFiltered')
| |
| − | | |
| − | # Run processing
| |
| − | inputImage = sitkUtils.PullVolumeFromSlicer(inputVolumeNode)
| |
| − | filter = sitk.SignedMaurerDistanceMapImageFilter()
| |
| − | outputImage = filter.Execute(inputImage)
| |
| − | sitkUtils.PushVolumeToSlicer(outputImage, outputVolumeNode)
| |
| − | | |
| − | # Show processing result
| |
| − | slicer.util.setSliceViewerLayers(background=outputVolumeNode)
| |
| − | </pre>
| |
| − | | |
| − | More information:
| |
| − | | |
| − | *See the SimpleITK documentation for SimpleITK examples: http://www.itk.org/SimpleITKDoxygen/html/examples.html
| |
| − | *sitkUtils in Slicer is used for pushing and pulling images from Slicer to SimpleITK: https://github.com/Slicer/Slicer/blob/master/Base/Python/sitkUtils.py
| |
| − | | |
| − | ==Get current mouse coordinates in a slice view==
| |
| − | | |
| − | You can get 3D (RAS) coordinates of the current mouse cursor from the crosshair singleton node as shown in the example below:
| |
| − | | |
| − | <pre>
| |
| − | def onMouseMoved(observer,eventid):
| |
| − | ras=[0,0,0]
| |
| − | crosshairNode.GetCursorPositionRAS(ras)
| |
| − | print(ras)
| |
| − | | |
| − | crosshairNode=slicer.util.getNode('Crosshair')
| |
| − | crosshairNode.AddObserver(slicer.vtkMRMLCrosshairNode.CursorPositionModifiedEvent, onMouseMoved)
| |
| − | </pre>
| |
| − | | |
| − | ==Get DataProbe text==
| |
| − | | |
| − | You can get the mouse location in pixel coordinates along with the pixel value at the mouse by hitting the '.' (period) key in a slice view after pasting in the following code.
| |
| − | | |
| − | <pre>
| |
| − | def printDataProbe():
| |
| − | infoWidget = slicer.modules.DataProbeInstance.infoWidget
| |
| − | for layer in ('B', 'F', 'L'):
| |
| − | print(infoWidget.layerNames[layer].text, infoWidget.layerIJKs[layer].text, infoWidget.layerValues[layer].text)
| |
| − | | |
| − | s = qt.QShortcut(qt.QKeySequence('.'), mainWindow())
| |
| − | s.connect('activated()', printDataProbe)
| |
| − | </pre>
| |
| − | | |
| − | ==Get axial slice as numpy array==
| |
| − | | |
| − | An axis-aligned (axial/sagittal/coronal/) slices of a volume can be extracted using simple numpy array indexing. For example:
| |
| − | | |
| − | <pre>
| |
| − | import SampleData
| |
| − | volumeNode = SampleData.SampleDataLogic().downloadMRHead()
| |
| − | sliceIndex = 12
| |
| − | | |
| − | voxels = slicer.util.arrayFromVolume(volumeNode) # Get volume as numpy array
| |
| − | slice = voxels[sliceIndex:,:] # Get one slice of the volume as numpy array
| |
| − | </pre>
| |
| − | | |
| − | ==Get reformatted image from a slice viewer as numpy array==
| |
| − | | |
| − | Set up 'red' slice viewer to show thick slab reconstructed from 3 slices:
| |
| − | <pre>
| |
| − | sliceNodeID = 'vtkMRMLSliceNodeRed'
| |
| − | | |
| − | # Get image data from slice view
| |
| − | sliceNode = slicer.mrmlScene.GetNodeByID(sliceNodeID)
| |
| − | appLogic = slicer.app.applicationLogic()
| |
| − | sliceLogic = appLogic.GetSliceLogic(sliceNode)
| |
| − | sliceLayerLogic = sliceLogic.GetBackgroundLayer()
| |
| − | reslice = sliceLayerLogic.GetReslice()
| |
| − | reslicedImage = vtk.vtkImageData()
| |
| − | reslicedImage.DeepCopy(reslice.GetOutput())
| |
| − | | |
| − | # Create new volume node using resliced image
| |
| − | volumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode")
| |
| − | volumeNode.SetIJKToRASMatrix(sliceNode.GetXYToRAS())
| |
| − | volumeNode.SetAndObserveImageData(reslicedImage)
| |
| − | volumeNode.CreateDefaultDisplayNodes()
| |
| − | volumeNode.CreateDefaultStorageNode()
| |
| − | | |
| − | # Get voxels as a numpy array
| |
| − | voxels = slicer.util.arrayFromVolume(volumeNode)
| |
| − | print(voxels.shape)
| |
| − | </pre>
| |
| − | | |
| − | ==Combine multiple volumes into one==
| |
| − | | |
| − | This example combines two volumes into a new one by subtracting one from the other.
| |
| − | | |
| − | <pre>
| |
| − | import SampleData
| |
| − | [input1Volume, input2Volume] = SampleData.SampleDataLogic().downloadDentalSurgery()
| |
| − | | |
| − | import slicer.util
| |
| − | a = slicer.util.arrayFromVolume(input1Volume)
| |
| − | b = slicer.util.arrayFromVolume(input2Volume)
| |
| − | | |
| − | # 'a' and 'b' are numpy arrays,
| |
| − | # they can be combined using any numpy array operations
| |
| − | # to produce the result array 'c'
| |
| − | c = b-a
| |
| − | | |
| − | volumeNode = slicer.modules.volumes.logic().CloneVolume(input1Volume, "Difference")
| |
| − | slicer.util.updateVolumeFromArray(volumeNode, c)
| |
| − | setSliceViewerLayers(background=volumeNode)
| |
| − | </pre>
| |
| − | | |
| − | ==Add noise to image==
| |
| − | | |
| − | This example shows how to add simulated noise to a volume.
| |
| − | | |
| − | <pre>
| |
| − | import SampleData
| |
| − | import numpy as np
| |
| − | | |
| − | # Get a sample input volume node
| |
| − | volumeNode = SampleData.SampleDataLogic().downloadMRHead()
| |
| − | | |
| − | # Get volume as numpy array and add noise
| |
| − | voxels = slicer.util.arrayFromVolume(volumeNode)
| |
| − | voxels[:] = voxels + np.random.normal(0.0, 20.0, size=voxels.shape)
| |
| − | slicer.util.arrayFromVolumeModified(volumeNode)
| |
| − | </pre>
| |
| − | | |
| − | | |
| − | ==Mask volume using segmentation==
| |
| − | | |
| − | This example shows how to blank out voxels of a volume outside all segments.
| |
| − | | |
| − | <pre>
| |
| − | # Input nodes
| |
| − | volumeNode = getNode('MRHead')
| |
| − | segmentationNode = getNode('Segmentation')
| |
| − | | |
| − | # Write segmentation to labelmap volume node with a geometry that matches the volume node
| |
| − | labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')
| |
| − | slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(segmentationNode, labelmapVolumeNode, volumeNode)
| |
| − | | |
| − | # Masking
| |
| − | import numpy as np
| |
| − | voxels = slicer.util.arrayFromVolume(volumeNode)
| |
| − | mask = slicer.util.arrayFromVolume(labelmapVolumeNode)
| |
| − | maskedVoxels = np.copy(voxels) # we don't want to modify the original volume
| |
| − | maskedVoxels[mask==0] = 0
| |
| − | | |
| − | # Write masked volume to volume node and show it
| |
| − | maskedVolumeNode = slicer.modules.volumes.logic().CloneVolume(volumeNode, "Masked")
| |
| − | slicer.util.updateVolumeFromArray(maskedVolumeNode, maskedVoxels)
| |
| − | slicer.util.setSliceViewerLayers(maskedVolumeNode)
| |
| − | </pre>
| |
| − | | |
| − | ==Apply random deformations to image==
| |
| − | | |
| − | This example shows how to apply random translation, rotation, and deformations to a volume to simulate variation in patient positioning, soft tissue motion, and random anatomical variations.
| |
| − | Control points are placed on a regularly spaced grid and then each control point is displaced by a random amount.
| |
| − | Thin-plate spline transform is computed from the original and transformed point list.
| |
| − | | |
| − | https://gist.github.com/lassoan/428af5285da75dc033d32ebff65ba940
| |
| − | | |
| − | ==Thick slab reconstruction and maximum/minimum intensity volume projections==
| |
| − | | |
| − | Set up 'red' slice viewer to show thick slab reconstructed from 3 slices:
| |
| − | <pre>
| |
| − | sliceNode = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeRed')
| |
| − | appLogic = slicer.app.applicationLogic()
| |
| − | sliceLogic = appLogic.GetSliceLogic(sliceNode)
| |
| − | sliceLayerLogic = sliceLogic.GetBackgroundLayer()
| |
| − | reslice = sliceLayerLogic.GetReslice()
| |
| − | reslice.SetSlabModeToMean()
| |
| − | reslice.SetSlabNumberOfSlices(10) # mean of 10 slices will computed
| |
| − | reslice.SetSlabSliceSpacingFraction(0.3) # spacing between each slice is 0.3 pixel (total 10 * 0.3 = 3 pixel neighborhood)
| |
| − | sliceNode.Modified()
| |
| − | </pre>
| |
| − | | |
| − | Set up 'red' slice viewer to show maximum intensity projection (MIP):
| |
| − | <pre>
| |
| − | sliceNode = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeRed')
| |
| − | appLogic = slicer.app.applicationLogic()
| |
| − | sliceLogic = appLogic.GetSliceLogic(sliceNode)
| |
| − | sliceLayerLogic = sliceLogic.GetBackgroundLayer()
| |
| − | reslice = sliceLayerLogic.GetReslice()
| |
| − | reslice.SetSlabModeToMax()
| |
| − | reslice.SetSlabNumberOfSlices(600) # use a large number of slices (600) to cover the entire volume
| |
| − | reslice.SetSlabSliceSpacingFraction(0.5) # spacing between slices are 0.5 pixel (supersampling is useful to reduce interpolation artifacts)
| |
| − | sliceNode.Modified()
| |
| − | </pre>
| |
| − | | |
| − | The projected image is available in a ''vtkImageData'' object by calling ''reslice.GetOutput()''.
| |
| − | | |
| − | ==Change default file type for nodes (that have never been saved yet)==
| |
| − | Default node can be specified that will be used as a basis of all new storage nodes. This can be used for setting default file extension. For example, change file format to STL for model nodes:
| |
| − | <pre>
| |
| − | defaultModelStorageNode = slicer.vtkMRMLModelStorageNode()
| |
| − | defaultModelStorageNode.SetDefaultWriteFileExtension('stl')
| |
| − | slicer.mrmlScene.AddDefaultNode(defaultModelStorageNode)
| |
| − | </pre>
| |
| − | | |
| − | To permanently change default file extension on your computer, copy-paste the code above into your application startup script (you can find its location in menu: Edit / Application settings / General / Application startup script).
| |
| − | | |
| − | ==Change file type for saving for all volumes (with already existing storage nodes)==
| |
| − | | |
| − | If it is not necessary to preserve file paths then the simplest is to configure default storage node (as shown in the example above), then delete all existing storage nodes. When save dialog is opened, default storage nodes will be recreated.
| |
| − | | |
| − | <pre>
| |
| − | # Delete existing model storage nodes so that they will be recreated with default settings
| |
| − | existingModelStorageNodes = slicer.util.getNodesByClass('vtkMRMLModelStorageNode')
| |
| − | for modelStorageNode in existingModelStorageNodes:
| |
| − | slicer.mrmlScene.RemoveNode(modelStorageNode)
| |
| − | </pre>
| |
| − | | |
| − | To update existing storage nodes to use new file extension (but keep all other parameters unchanged) you can use this approach (example is for volume storage):
| |
| − | | |
| − | <pre>
| |
| − | requiredFileExtension = '.nia'
| |
| − | originalFileExtension = '.nrrd'
| |
| − | volumeNodes = slicer.util.getNodesByClass('vtkMRMLScalarVolumeNode')
| |
| − | for volumeNode in volumeNodes:
| |
| − | volumeStorageNode = volumeNode.GetStorageNode()
| |
| − | if not volumeStorageNode:
| |
| − | volumeNode.AddDefaultStorageNode()
| |
| − | volumeStorageNode = volumeNode.GetStorageNode()
| |
| − | volumeStorageNode.SetFileName(volumeNode.GetName()+requiredFileExtension)
| |
| − | else:
| |
| − | volumeStorageNode.SetFileName(volumeStorageNode.GetFileName().replace(originalFileExtension, requiredFileExtension))
| |
| − | </pre>
| |
| − | | |
| − | To set all volume nodes to save uncompressed by default (add this to .slicerrc.py so it takes effect for the whole session):
| |
| − | <pre>
| |
| − | #set the default volume storage to not compress by default
| |
| − | defaultVolumeStorageNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
| |
| − | defaultVolumeStorageNode.SetUseCompression(0)
| |
| − | slicer.mrmlScene.AddDefaultNode(defaultVolumeStorageNode)
| |
| − | logging.info("Volume nodes will be stored uncompressed by default")
| |
| − | </pre>
| |
| − | | |
| − | Same thing as above, but applied to all segmentations instead of volumes:
| |
| − | <pre>
| |
| − | #set the default volume storage to not compress by default
| |
| − | defaultVolumeStorageNode = slicer.vtkMRMLSegmentationStorageNode()
| |
| − | defaultVolumeStorageNode.SetUseCompression(0)
| |
| − | slicer.mrmlScene.AddDefaultNode(defaultVolumeStorageNode)
| |
| − | logging.info("Segmentation nodes will be stored uncompressed
| |
| − | </pre>
| |
| − | | |
| − | ==Sequences==
| |
| − | | |
| − | ===Access voxels of a 4D volume as numpy array===
| |
| − | | |
| − | <pre>
| |
| − | # Get sequence node
| |
| − | import SampleData
| |
| − | sequenceNode = SampleData.SampleDataLogic().downloadSample('CTPCardioSeq')
| |
| − | # Alternatively, get the first sequence node in the scene:
| |
| − | # sequenceNode = slicer.util.getNodesByClass('vtkMRMLSequenceNode')[0]
| |
| − | | |
| − | # Get voxels of itemIndex'th volume as numpy array
| |
| − | itemIndex = 5
| |
| − | voxelArray = slicer.util.arrayFromVolume(sequenceNode.GetNthDataNode(itemIndex))
| |
| − | </pre>
| |
| − | | |
| − | ===Get index value===
| |
| − | | |
| − | <pre>
| |
| − | print("Index value of {0}th item: {1} = {2} {3}".format(
| |
| − | itemIndex,
| |
| − | sequenceNode.GetIndexName(),
| |
| − | sequenceNode.GetNthIndexValue(itemIndex),
| |
| − | sequenceNode.GetIndexUnit()))
| |
| − | </pre>
| |
| − | | |
| − | ===Browse a sequence and access currently displayed nodes===
| |
| − | | |
| − | <pre>
| |
| − | # Get a sequence node
| |
| − | import SampleData
| |
| − | sequenceNode = SampleData.SampleDataLogic().downloadSample('CTPCardioSeq')
| |
| − | | |
| − | # Find corresponding sequence browser node
| |
| − | browserNode = slicer.modules.sequences.logic().GetFirstBrowserNodeForSequenceNode(sequenceNode)
| |
| − | | |
| − | # Print sequence information
| |
| − | print("Number of items in the sequence: {0}".format(browserNode.GetNumberOfItems()))
| |
| − | print("Index name: {0}".format(browserNode.GetMasterSequenceNode().GetIndexName()))
| |
| − | | |
| − | # Jump to a selected sequence item
| |
| − | browserNode.SetSelectedItemNumber(5)
| |
| − | | |
| − | # Get currently displayed volume node voxels as numpy array
| |
| − | volumeNode = browserNode.GetProxyNode(sequenceNode)
| |
| − | voxelArray = slicer.util.arrayFromVolume(volumeNode)
| |
| − | ```
| |
| − | | |
| − | ===Concatenate all sequences in the scene into a new sequence===
| |
| − | | |
| − | <pre>
| |
| − | # Get all sequence nodes in the scene
| |
| − | sequenceNodes = slicer.util.getNodesByClass('vtkMRMLSequenceNode')
| |
| − | mergedSequenceNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSequenceNode', 'Merged sequence')
| |
| − | | |
| − | # Merge all sequence nodes into a new sequence node
| |
| − | mergedIndexValue = 0
| |
| − | for sequenceNode in sequenceNodes:
| |
| − | for itemIndex in range(sequenceNode.GetNumberOfDataNodes()):
| |
| − | dataNode = sequenceNode.GetNthDataNode(itemIndex)
| |
| − | mergedSequenceNode.SetDataNodeAtValue(dataNode, str(mergedIndexValue))
| |
| − | mergedIndexValue += 1
| |
| − | # Delete the sequence node we copied the data from, to prevent sharing of the same
| |
| − | # node by multiple sequences
| |
| − | slicer.mrmlScene.RemoveNode(sequenceNode)
| |
| − | | |
| − | # Create a sequence browser node for the new merged sequence
| |
| − | mergedSequenceBrowserNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSequenceBrowserNode', 'Merged')
| |
| − | mergedSequenceBrowserNode.AddSynchronizedSequenceNode(mergedSequenceNode)
| |
| − | slicer.modules.sequencebrowser.setToolBarActiveBrowserNode(mergedSequenceBrowserNode)
| |
| − | # Show proxy node in slice viewers
| |
| − | mergedProxyNode = mergedSequenceBrowserNode.GetProxyNode(mergedSequenceNode)
| |
| − | slicer.util.setSliceViewerLayers(background=mergedProxyNode)
| |
| − | </pre>
| |
| − | | |
| − | ==Segmentations==
| |
| − | | |
| − | ===Create a segmentation from a labelmap volume and display in 3D===
| |
| − | | |
| − | <pre>
| |
| − | labelmapVolumeNode = getNode('label')
| |
| − | seg = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSegmentationNode')
| |
| − | slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(labelmapVolumeNode, seg)
| |
| − | seg.CreateClosedSurfaceRepresentation()
| |
| − | slicer.mrmlScene.RemoveNode(labelmapVolumeNode)
| |
| − | </pre>
| |
| − | | |
| − | The last line is optional. It removes the original labelmap volume so that the same information is not shown twice.
| |
| − | | |
| − | ===Export labelmap node from segmentation node===
| |
| − | | |
| − | Export labelmap matching reference geometry of the segmentation:
| |
| − | | |
| − | <pre>
| |
| − | segmentationNode = getNode('Segmentation')
| |
| − | labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')
| |
| − | slicer.modules.segmentations.logic().ExportAllSegmentsToLabelmapNode(segmentationNode, labelmapVolumeNode, slicer.vtkSegmentation.EXTENT_REFERENCE_GEOMETRY)
| |
| − | </pre>
| |
| − | | |
| − | Export smallest possible labelmap:
| |
| − | | |
| − | <pre>
| |
| − | segmentationNode = getNode('Segmentation')
| |
| − | labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')
| |
| − | slicer.modules.segmentations.logic().ExportAllSegmentsToLabelmapNode(segmentationNode, labelmapVolumeNode)
| |
| − | </pre>
| |
| − | | |
| − | Export labelmap that matches geometry of a chosen reference volume:
| |
| − | | |
| − | <pre>
| |
| − | segmentationNode = getNode('Segmentation')
| |
| − | labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')
| |
| − | slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(segmentationNode, labelmapVolumeNode, referenceVolumeNode)
| |
| − | </pre>
| |
| − | | |
| − | Export a selection of segments (identified by their names):
| |
| − | | |
| − | <pre>
| |
| − | segmentNames = ["Prostate", "Urethra"]
| |
| − | segmentIds = vtk.vtkStringArray()
| |
| − | for segmentName in segmentNames:
| |
| − | segmentId = segmentationNode.GetSegmentation().GetSegmentIdBySegmentName(segmentName)
| |
| − | segmentIds.InsertNextValue(segmentId)
| |
| − | slicer.vtkSlicerSegmentationsModuleLogic.ExportSegmentsToLabelmapNode(segmentationNode, segmentIds, labelmapVolumeNode, referenceVolumeNode)
| |
| − | </pre>
| |
| − | | |
| − | Export to file by pressing Ctrl+Shift+S key:
| |
| − | | |
| − | <pre>
| |
| − | outputPath = "c:/tmp"
| |
| − | | |
| − | def exportLabelmap():
| |
| − | segmentationNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLSegmentationNode")
| |
| − | referenceVolumeNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLScalarVolumeNode")
| |
| − | labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')
| |
| − | slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(segmentationNode, labelmapVolumeNode, referenceVolumeNode)
| |
| − | filepath = outputPath + "/" + referenceVolumeNode.GetName()+"-label.nrrd"
| |
| − | slicer.util.saveNode(labelmapVolumeNode, filepath)
| |
| − | slicer.mrmlScene.RemoveNode(labelmapVolumeNode.GetDisplayNode().GetColorNode())
| |
| − | slicer.mrmlScene.RemoveNode(labelmapVolumeNode)
| |
| − | slicer.util.delayDisplay("Segmentation saved to "+filepath)
| |
| − | | |
| − | shortcut = qt.QShortcut(slicer.util.mainWindow())
| |
| − | shortcut.setKey(qt.QKeySequence('Ctrl+Shift+s'))
| |
| − | shortcut.connect( 'activated()', exportLabelmap)
| |
| − | </pre>
| |
| − | | |
| − | ===Export model nodes from segmentation node===
| |
| − | | |
| − | <pre>
| |
| − | segmentationNode = getNode("Segmentation")
| |
| − | shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
| |
| − | exportFolderItemId = shNode.CreateFolderItem(shNode.GetSceneItemID(), "Segments")
| |
| − | slicer.modules.segmentations.logic().ExportAllSegmentsToModels(segmentationNode, exportFolderItemId)
| |
| − | </pre>
| |
| − | | |
| − | ===Create a hollow model from boundary of solid segment===
| |
| − | | |
| − | In most cases, the most robust and flexible tool for creating empty shell models (e.g., vessel wall model from contrast agent segmentation) is the "Hollow" effect in Segment Editor module. However, for very thin shells, extrusion of the exported surface mesh representation may be just as robust and require less memory and computation time.
| |
| − | | |
| − | Example of creating a shell model from a segment (id="Segment_1") and convert it to a shell:
| |
| − | | |
| − | <pre>
| |
| − | # Get closed surface representation of the segment
| |
| − | shellThickness = 3.0 # mm
| |
| − | segmentationNode = getNode('Segmentation')
| |
| − | segmentationNode.CreateClosedSurfaceRepresentation()
| |
| − | polyData = segmentationNode.GetClosedSurfaceInternalRepresentation('Segment_1')
| |
| − | | |
| − | # Create shell
| |
| − | extrude = vtk.vtkLinearExtrusionFilter()
| |
| − | extrude.SetInputData(polyData)
| |
| − | extrude.SetExtrusionTypeToNormalExtrusion()
| |
| − | extrude.SetScaleFactor(shellThickness)
| |
| − | | |
| − | # Compute consistent surface normals
| |
| − | triangle_filter = vtk.vtkTriangleFilter()
| |
| − | triangle_filter.SetInputConnection(extrude.GetOutputPort())
| |
| − | normals = vtk.vtkPolyDataNormals()
| |
| − | normals.SetInputConnection(triangle_filter.GetOutputPort())
| |
| − | normals.FlipNormalsOn()
| |
| − | | |
| − | # Save result into new model node
| |
| − | slicer.modules.models.logic().AddModel(normals.GetOutputPort())
| |
| − | </pre>
| |
| − | | |
| − | ===Show a segmentation in 3D===
| |
| − | Segmentation can only be shown in 3D if closed surface representation (or other 3D-displayable representation) is available. To create closed surface representation:
| |
| − | <pre>
| |
| − | segmentation.CreateClosedSurfaceRepresentation()
| |
| − | </pre>
| |
| − | | |
| − | ===Get a representation of a segment===
| |
| − | Access binary labelmap stored in a segmentation node (without exporting it to a volume node) - if it does not exist, it will return None:
| |
| − | <pre>
| |
| − | image = slicer.vtkOrientedImageData()
| |
| − | segmentationNode.GetBinaryLabelmapRepresentation(segmentID, image)
| |
| − | </pre>
| |
| − | Get closed surface, if it does not exist, it will return None:
| |
| − | <pre>
| |
| − | outputPolyData = vtk.vtkPolyData()
| |
| − | segmentationNode.GetClosedSurfaceRepresentation(segmentID, outputPolyData)
| |
| − | </pre>
| |
| − | Get binary labelmap representation. If it does not exist then it will be created for that single segment. Applies parent transforms by default (if not desired, another argument needs to be added to the end: false):
| |
| − | <pre>
| |
| − | import vtkSegmentationCorePython as vtkSegmentationCore
| |
| − | outputOrientedImageData = vtkSegmentationCore.vtkOrientedImageData()
| |
| − | slicer.vtkSlicerSegmentationsModuleLogic.GetSegmentBinaryLabelmapRepresentation(segmentationNode, segmentID, outputOrientedImageData)
| |
| − | </pre>
| |
| − | Same as above, for closed surface representation:
| |
| − | <pre>
| |
| − | outputPolyData = vtk.vtkPolyData()
| |
| − | slicer.vtkSlicerSegmentationsModuleLogic.GetSegmentClosedSurfaceRepresentation(segmentationNode, segmentID, outputPolyData)
| |
| − | </pre>
| |
| − | | |
| − | ===Convert all segments using default path and conversion parameters===
| |
| − | <pre>
| |
| − | segmentationNode.CreateBinaryLabelmapRepresentation()
| |
| − | </pre>
| |
| − | | |
| − | ===Convert all segments using custom path or conversion parameters===
| |
| − | Change reference image geometry parameter based on an existing referenceImageData image:
| |
| − | <pre>
| |
| − | referenceGeometry = slicer.vtkSegmentationConverter.SerializeImageGeometry(referenceImageData)
| |
| − | segmentation.SetConversionParameter(slicer.vtkSegmentationConverter.GetReferenceImageGeometryParameterName(), referenceGeometry)
| |
| − | </pre>
| |
| − | | |
| − | ===Re-convert using a modified conversion parameter===
| |
| − | Changing smoothing factor for closed surface generation:
| |
| − | <pre>
| |
| − | import vtkSegmentationCorePython as vtkSegmentationCore
| |
| − | segmentation = getNode('Segmentation').GetSegmentation()
| |
| − | | |
| − | # Turn of surface smoothing
| |
| − | segmentation.SetConversionParameter('Smoothing factor','0.0')
| |
| − | | |
| − | # Recreate representation using modified parameters (and default conversion path)
| |
| − | segmentation.RemoveRepresentation(vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationClosedSurfaceRepresentationName())
| |
| − | segmentation.CreateRepresentation(vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationClosedSurfaceRepresentationName())
| |
| − | </pre>
| |
| − | | |
| − | ===Create keyboard shortcut for toggling sphere brush for paint and erase effects===
| |
| − | | |
| − | <pre>
| |
| − | def toggleSphereBrush():
| |
| − | segmentEditorWidget = slicer.modules.segmenteditor.widgetRepresentation().self().editor
| |
| − | paintEffect = segmentEditorWidget.effectByName("Paint")
| |
| − | isSphere = paintEffect.integerParameter('BrushSphere')
| |
| − | # BrushSphere is "common" parameter (shared between paint and erase)
| |
| − | paintEffect.setCommonParameter("BrushSphere", 0 if isSphere else 1)
| |
| − | | |
| − | shortcut = qt.QShortcut(slicer.util.mainWindow())
| |
| − | shortcut.setKey(qt.QKeySequence("s"))
| |
| − | shortcut.connect('activated()', toggleSphereBrush)
| |
| − | </pre>
| |
| − | | |
| − | ===Get centroid of a segment in world (RAS) coordinates===
| |
| − | | |
| − | This example shows how to get centroid of a segment in world coordinates and show that position in all slice views.
| |
| − | | |
| − | <pre>
| |
| − | segmentationNode = getNode('Segmentation')
| |
| − | segmentId = 'Segment_1'
| |
| − | | |
| − | # Get array voxel coordinates
| |
| − | import numpy as np
| |
| − | seg=arrayFromSegment(segmentation_node, segmentId)
| |
| − | # numpy array has voxel coordinates in reverse order (KJI instead of IJK)
| |
| − | # and the array is cropped to minimum size in the segmentation
| |
| − | mean_KjiCropped = [coords.mean() for coords in np.nonzero(seg)]
| |
| − | | |
| − | # Get segmentation voxel coordinates
| |
| − | segImage = segmentationNode.GetBinaryLabelmapRepresentation(segmentId)
| |
| − | segImageExtent = segImage.GetExtent()
| |
| − | # origin of the array in voxel coordinates is determined by the start extent
| |
| − | mean_Ijk = [mean_KjiCropped[2], mean_KjiCropped[1], mean_KjiCropped[0]] + np.array([segImageExtent[0], segImageExtent[2], segImageExtent[4]])
| |
| − | | |
| − | # Get segmentation physical coordinates
| |
| − | ijkToWorld = vtk.vtkMatrix4x4()
| |
| − | segImage.GetImageToWorldMatrix(ijkToWorld)
| |
| − | mean_World = [0, 0, 0, 1]
| |
| − | ijkToRas.MultiplyPoint(np.append(mean_Ijk,1.0), mean_World)
| |
| − | mean_World = mean_World[0:3]
| |
| − | | |
| − | # If segmentation node is transformed, apply that transform to get RAS coordinates
| |
| − | transformWorldToRas = vtk.vtkGeneralTransform()
| |
| − | slicer.vtkMRMLTransformNode.GetTransformBetweenNodes(segmentationNode.GetParentTransformNode(), None, transformWorldToRas)
| |
| − | mean_Ras = transformWorldToRas.TransformPoint(mean_World)
| |
| − | | |
| − | # Show mean position value and jump to it in all slice viewers
| |
| − | print(mean_Ras)
| |
| − | slicer.modules.markups.logic().JumpSlicesToLocation(mean_Ras[0], mean_Ras[1], mean_Ras[2], True)
| |
| − | </pre>
| |
| − | | |
| − | ===Get histogram of a segmented region===
| |
| − | | |
| − | <pre>
| |
| − | # Generate input data
| |
| − | ################################################
| |
| − | | |
| − | # Load master volume
| |
| − | import SampleData
| |
| − | sampleDataLogic = SampleData.SampleDataLogic()
| |
| − | masterVolumeNode = sampleDataLogic.downloadMRBrainTumor1()
| |
| − | | |
| − | # Create segmentation
| |
| − | segmentationNode = slicer.vtkMRMLSegmentationNode()
| |
| − | slicer.mrmlScene.AddNode(segmentationNode)
| |
| − | segmentationNode.CreateDefaultDisplayNodes() # only needed for display
| |
| − | segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)
| |
| − | | |
| − | # Create segment
| |
| − | tumorSeed = vtk.vtkSphereSource()
| |
| − | tumorSeed.SetCenter(-6, 30, 28)
| |
| − | tumorSeed.SetRadius(25)
| |
| − | tumorSeed.Update()
| |
| − | segmentationNode.AddSegmentFromClosedSurfaceRepresentation(tumorSeed.GetOutput(), "Segment A", [1.0,0.0,0.0])
| |
| − | | |
| − | # Compute histogram
| |
| − | ################################################
| |
| − | | |
| − | labelValue = 1 # label value of first segment
| |
| − | | |
| − | # Get segmentation as labelmap volume node
| |
| − | labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')
| |
| − | slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(segmentationNode, labelmapVolumeNode, masterVolumeNode)
| |
| − | | |
| − | # Extract all voxels of the segment as numpy array
| |
| − | volumeArray = slicer.util.arrayFromVolume(masterVolumeNode)
| |
| − | labelArray = slicer.util.arrayFromVolume(labelmapVolumeNode)
| |
| − | segmentVoxels = volumeArray[labelArray==labelValue]
| |
| − | | |
| − | # Compute histogram
| |
| − | import numpy as np
| |
| − | histogram = np.histogram(segmentVoxels, bins=50)
| |
| − | | |
| − | # Plot histogram
| |
| − | ################################################
| |
| − | | |
| − | slicer.util.plot(histogram, xColumnIndex = 1)
| |
| − | </pre>
| |
| − | | |
| − | ===Get segments visible at a selected position===
| |
| − | | |
| − | Show in the console names of segments visible at a markups fiducial position:
| |
| − | | |
| − | <pre>
| |
| − | segmentationNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLSegmentationNode")
| |
| − | markupsFiducialNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLMarkupsFiducialNode")
| |
| − | sliceViewLabel = "Red" # any slice view where segmentation node is visible works
| |
| − | | |
| − | def printSegmentNames(unused1=None, unused2=None):
| |
| − |
| |
| − | sliceViewWidget = slicer.app.layoutManager().sliceWidget(sliceViewLabel)
| |
| − | segmentationsDisplayableManager = sliceViewWidget.sliceView().displayableManagerByClassName('vtkMRMLSegmentationsDisplayableManager2D')
| |
| − | ras = [0,0,0]
| |
| − | markupsFiducialNode.GetNthControlPointPositionWorld(0, ras)
| |
| − | segmentIds = vtk.vtkStringArray()
| |
| − | segmentationsDisplayableManager.GetVisibleSegmentsForPosition(ras, segmentationNode.GetDisplayNode(), segmentIds)
| |
| − | for idIndex in range(segmentIds.GetNumberOfValues()):
| |
| − | segment = segmentationNode.GetSegmentation().GetSegment(segmentIds.GetValue(idIndex))
| |
| − | print('Segment found at position {0}: {1}'.format(ras, segment.GetName()))
| |
| − | | |
| − | # Observe markup node changes
| |
| − | markupsFiducialNode.AddObserver(slicer.vtkMRMLMarkupsPlaneNode.PointModifiedEvent, printSegmentNames)
| |
| − | printSegmentNames()
| |
| − | </pre>
| |
| − | | |
| − | ===Set default segmentation options===
| |
| − | | |
| − | Allow segments to overlap each other by default:
| |
| − | | |
| − | <pre>
| |
| − | defaultSegmentEditorNode = slicer.vtkMRMLSegmentEditorNode()
| |
| − | defaultSegmentEditorNode.SetOverwriteMode(slicer.vtkMRMLSegmentEditorNode.OverwriteNone)
| |
| − | slicer.mrmlScene.AddDefaultNode(defaultSegmentEditorNode)
| |
| − | </pre>
| |
| − | | |
| − | To always make this the default, add the lines above to your
| |
| − | [[Documentation/{{documentation/version}}/Developers/Python_scripting#How_to_systematically_execute_custom_python_code_at_startup_.3F|.slicerrc file]].
| |
| − | | |
| − | ===How to run segment editor effects from a script===
| |
| − | | |
| − | Editor effects are complex because they need to handle changing master volumes, undo/redo, masking operations, etc. Therefore, it is recommended to use the effect by instantiating a qMRMLSegmentEditorWidget or use/extract processing logic of the effect and use that from a script.
| |
| − | | |
| − | ====Use Segment editor effects from script (qMRMLSegmentEditorWidget)====
| |
| − | | |
| − | Examples:
| |
| − | | |
| − | *[https://gist.github.com/lassoan/2d5a5b73645f65a5eb6f8d5f97abf31b brain tumor segmentation using grow from seeds effect]
| |
| − | *[https://gist.github.com/lassoan/ef30bc27a22a648ead7f82243f5cc7d5 AI-assisted brain tumor segmentation]
| |
| − | *[https://gist.github.com/lassoan/1673b25d8e7913cbc245b4f09ed853f9 skin surface extraction using thresholding and smoothing]
| |
| − | *[https://gist.github.com/lassoan/2f5071c562108dac8efe277c78f2620f mask a volume with segments and compute histogram for each region]
| |
| − | *[https://gist.github.com/lassoan/5ad51c89521d3cd9c5faf65767506b37 create fat/muscle/bone segment by thresholding and report volume of each segment]
| |
| − | *[https://gist.github.com/lassoan/4d0b94bda52d5b099432e424e03aa2b1 segment cranial cavity automatically in dry bone skull CT]
| |
| − | *[https://gist.github.com/lassoan/84d1f9a093dbb6a46c0fcc89279d8088 remove patient table from CT image]
| |
| − | | |
| − | Description of effect parameters are available [https://slicer.readthedocs.io/en/latest/developer_guide/modules/segmenteditor.html#effect-parameters here].
| |
| − | | |
| − | ====Use logic of effect from a script====
| |
| − | | |
| − | This example shows how to perform operations on segmentations using VTK filters ''extracted'' from an effect: | |
| − | | |
| − | *[https://gist.github.com/lassoan/7c94c334653010696b2bf96abc0ac8e7 brain tumor segmentation using grow from seeds effect]
| |
| − | | |
| − | ===Process segment using a VTK filter===
| |
| − | | |
| − | This example shows how to apply a VTK filter to a segment that dilates the image by a specified margin.
| |
| − | | |
| − | <pre>
| |
| − | segmentationNode = getNode('Segmentation')
| |
| − | segmentId = "Segment_1"
| |
| − | kernelSize = [3,1,5]
| |
| − | | |
| − | # Export segment as vtkImageData (via temporary labelmap volume node)
| |
| − | segmentIds = vtk.vtkStringArray()
| |
| − | segmentIds.InsertNextValue(segmentId)
| |
| − | labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')
| |
| − | slicer.modules.segmentations.logic().ExportSegmentsToLabelmapNode(segmentationNode, segmentIds, labelmapVolumeNode)
| |
| − | | |
| − | # Process segmentation
| |
| − | segmentImageData = labelmapVolumeNode.GetImageData()
| |
| − | erodeDilate = vtk.vtkImageDilateErode3D()
| |
| − | erodeDilate.SetInputData(segmentImageData)
| |
| − | erodeDilate.SetDilateValue(1)
| |
| − | erodeDilate.SetErodeValue(0)
| |
| − | erodeDilate.SetKernelSize(*kernelSize)
| |
| − | erodeDilate.Update()
| |
| − | segmentImageData.DeepCopy(erodeDilate.GetOutput())
| |
| − | | |
| − | # Import segment from vtkImageData
| |
| − | slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(labelmapVolumeNode, segmentationNode, segmentIds)
| |
| − | | |
| − | # Cleanup temporary nodes
| |
| − | slicer.mrmlScene.RemoveNode(labelmapVolumeNode.GetDisplayNode().GetColorNode())
| |
| − | slicer.mrmlScene.RemoveNode(labelmapVolumeNode)
| |
| − | </pre>
| |
| − | | |
| − | ===Get information from segmentation nrrd file header===
| |
| − | | |
| − | You can use this code snippet to get information from segmentation (.seg.nrrd), for example when creating numpy arrays for generating training data for deep learning networks. This script can be used in any Python environment, not just inside Slicer.
| |
| − | | |
| − | <pre>
| |
| − | # pip_install('pynrrd')
| |
| − | | |
| − | def read_segmentation_info(filename):
| |
| − | import nrrd
| |
| − | header = nrrd.read_header(filename)
| |
| − | segmentation_info = {}
| |
| − | segments = []
| |
| − | segment_index = 0
| |
| − | while True:
| |
| − | prefix = "Segment{0}_".format(segment_index)
| |
| − | if not prefix + "ID" in header.keys():
| |
| − | break
| |
| − | segment = {}
| |
| − | segment["index"] = segment_index
| |
| − | segment["color"] = [float(i) for i in header[prefix + "Color"].split(" ")] # Segment0_Color:=0.501961 0.682353 0.501961
| |
| − | segment["colorAutoGenerated"] = int(header[prefix + "ColorAutoGenerated"]) != 0 # Segment0_ColorAutoGenerated:=1
| |
| − | segment["extent"] = [int(i) for i in header[prefix + "Extent"].split(" ")] # Segment0_Extent:=68 203 53 211 24 118
| |
| − | segment["id"] = header[prefix + "ID"] # Segment0_ID:=Segment_1
| |
| − | segment["labelValue"] = int(header[prefix + "LabelValue"]) # Segment0_LabelValue:=1
| |
| − | segment["layer"] = int(header[prefix + "Layer"]) # Segment0_Layer:=0
| |
| − | segment["name"] = header[prefix + "Name"] # Segment0_Name:=Segment_1
| |
| − | segment["nameAutoGenerated"] = int(header[prefix + "NameAutoGenerated"]) != 0 # Segment0_NameAutoGenerated:=1
| |
| − | # Segment0_Tags:=Segmentation.Status:inprogress|TerminologyEntry:Segmentation category and type - 3D Slicer General Anatomy list
| |
| − | # ~SCT^85756007^Tissue~SCT^85756007^Tissue~^^~Anatomic codes - DICOM master list~^^~^^|
| |
| − | tags = {}
| |
| − | tags_str = header[prefix + "Tags"].split("|")
| |
| − | for tag_str in tags_str:
| |
| − | tag_str = tag_str.strip()
| |
| − | if not tag_str:
| |
| − | continue
| |
| − | key, value = tag_str.split(":", maxsplit=1)
| |
| − | tags[key] = value
| |
| − | segment["tags"] = tags
| |
| − | segments.append(segment)
| |
| − | segment_index += 1
| |
| − | segmentation_info["segments"] = segments
| |
| − | return segmentation_info
| |
| − | | |
| − | def segment_from_name(segmentation_info, segment_name):
| |
| − | for segment in segmentation_info["segments"]:
| |
| − | if segment_name == segment["name"]:
| |
| − | return segment
| |
| − | raise KeyError('segment not found by name ' + segment_name)
| |
| − | | |
| − | def segment_names(segmentation_info):
| |
| − | names = []
| |
| − | for segment in segmentation_info["segments"]:
| |
| − | names.append(segment["name"])
| |
| − | return names
| |
| − | | |
| − | def extract_segments(voxels, header, segmentation_info, segment_names_to_label_values):
| |
| − | import numpy as np
| |
| − | # Create empty array from last 3 dimensions (output will be flattened to a 3D array)
| |
| − | output_voxels = np.zeros(voxels.shape[-3:])
| |
| − | # Copy non-segmentation fields to the extracted header
| |
| − | output_header = {}
| |
| − | for key in header.keys():
| |
| − | if not re.match("^Segment[0-9]+_.+", key):
| |
| − | output_header[key] = header[key]
| |
| − | # Copy extracted segments
| |
| − | dims = len(voxels.shape)
| |
| − | for output_segment_index, segment_name_to_label_value in enumerate(segment_names_to_label_values):
| |
| − | # Copy relabeled voxel data
| |
| − | segment = segment_from_name(segmentation_info, segment_name_to_label_value[0])
| |
| − | input_label_value = segment["labelValue"]
| |
| − | output_label_value = segment_name_to_label_value[1]
| |
| − | if dims == 3:
| |
| − | output_voxels[voxels == input_label_value] = output_label_value
| |
| − | elif dims == 4:
| |
| − | inputLayer = segment["layer"]
| |
| − | output_voxels[voxels[inputLayer,:,:,:] == input_label_value] = output_label_value
| |
| − | else:
| |
| − | raise ValueError("Voxel array dimension is invalid")
| |
| − | # Copy all segment fields corresponding to this segment
| |
| − | for key in header.keys():
| |
| − | prefix = "Segment{0}_".format(segment["index"])
| |
| − | matched = re.match("^"+prefix+"(.+)", key)
| |
| − | if matched:
| |
| − | field_name = matched.groups()[0]
| |
| − | if field_name == "LabelValue":
| |
| − | value = output_label_value
| |
| − | elif field_name == "Layer":
| |
| − | # output is a single layer (3D volume)
| |
| − | value = 0
| |
| − | else:
| |
| − | value = header[key]
| |
| − | output_header["Segment{0}_".format(output_segment_index) + field_name] = value
| |
| − | # Remove unnecessary 4th dimension (volume is collapsed into 3D)
| |
| − | if dims == 4:
| |
| − | # Remove "none" from "none (0,1,0) (0,0,-1) (-1.2999954223632812,0,0)"
| |
| − | output_header["space directions"] = output_header["space directions"][-3:,:]
| |
| − | # Remove "list" from "list domain domain domain"
| |
| − | output_header["kinds"] = output_header["kinds"][-3:]
| |
| − | return output_voxels, output_header
| |
| − | | |
| − | # Read segmentation and show some information about segments
| |
| − | filename = "c:/Users/andra/OneDrive/Projects/SegmentationPynrrd/SegmentationOverlapping.seg.nrrd"
| |
| − | segmentation_info = read_segmentation_info(filename)
| |
| − | number_of_segments = len(segmentation_info["segments"])
| |
| − | names = segment_names(segmentation_info)
| |
| − | label0 = segment_from_name(segmentation_info, names[0])["labelValue"]
| |
| − | print("Number of segments: " + str())
| |
| − | print("Segment names: " + str(names))
| |
| − | print("Label value of {0}: {1}".format(names[0], label0))
| |
| − | | |
| − | # Extract selected segments with chosen label values
| |
| − | extracted_filename = "c:/Users/andra/OneDrive/Projects/SegmentationPynrrd/SegmentationExtracted.seg.nrrd"
| |
| − | voxels, header = nrrd.read(filename)
| |
| − | segment_list = [("Segment_1", 10), ("Segment_3", 12), ("Segment_4", 6)]
| |
| − | extracted_voxels, extracted_header = extract_segments(voxels, header, segmentation_info, segment_list)
| |
| − | nrrd.write(extracted_filename, extracted_voxels, extracted_header)
| |
| − | </pre>
| |
| − | | |
| − | ==Quantifying segments==
| |
| − | | |
| − | ===Get centroid of each segment===
| |
| − | | |
| − | Place a markups fiducial point at the centroid of each segment.
| |
| − | | |
| − | <pre>
| |
| − | segmentationNode = getNode('Segmentation')
| |
| − | | |
| − | # Compute centroids
| |
| − | import SegmentStatistics
| |
| − | segStatLogic = SegmentStatistics.SegmentStatisticsLogic()
| |
| − | segStatLogic.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID())
| |
| − | segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.centroid_ras.enabled", str(True))
| |
| − | segStatLogic.computeStatistics()
| |
| − | stats = segStatLogic.getStatistics()
| |
| − | | |
| − | # Place a markup point in each centroid
| |
| − | markupsNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsFiducialNode")
| |
| − | markupsNode.CreateDefaultDisplayNodes()
| |
| − | for segmentId in stats['SegmentIDs']:
| |
| − | centroid_ras = stats[segmentId,"LabelmapSegmentStatisticsPlugin.centroid_ras"]
| |
| − | segmentName = segmentationNode.GetSegmentation().GetSegment(segmentId).GetName()
| |
| − | markupsNode.AddFiducialFromArray(centroid_ras, segmentName)
| |
| − | </pre>
| |
| − | | |
| − | ===Get size, position, and orientation of each segment===
| |
| − | | |
| − | This example computes oriented bounding box for each segment and displays them using annotation ROI.
| |
| − | <pre>
| |
| − | segmentationNode = getNode('Segmentation')
| |
| − | | |
| − | # Compute bounding boxes
| |
| − | import SegmentStatistics
| |
| − | segStatLogic = SegmentStatistics.SegmentStatisticsLogic()
| |
| − | segStatLogic.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID())
| |
| − | segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.obb_origin_ras.enabled",str(True))
| |
| − | segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.obb_diameter_mm.enabled",str(True))
| |
| − | segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.obb_direction_ras_x.enabled",str(True))
| |
| − | segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.obb_direction_ras_y.enabled",str(True))
| |
| − | segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.obb_direction_ras_z.enabled",str(True))
| |
| − | segStatLogic.computeStatistics()
| |
| − | stats = segStatLogic.getStatistics()
| |
| − | | |
| − | # Draw ROI for each oriented bounding box
| |
| − | import numpy as np
| |
| − | for segmentId in stats['SegmentIDs']:
| |
| − | # Get bounding box
| |
| − | obb_origin_ras = np.array(stats[segmentId,"LabelmapSegmentStatisticsPlugin.obb_origin_ras"])
| |
| − | obb_diameter_mm = np.array(stats[segmentId,"LabelmapSegmentStatisticsPlugin.obb_diameter_mm"])
| |
| − | obb_direction_ras_x = np.array(stats[segmentId,"LabelmapSegmentStatisticsPlugin.obb_direction_ras_x"])
| |
| − | obb_direction_ras_y = np.array(stats[segmentId,"LabelmapSegmentStatisticsPlugin.obb_direction_ras_y"])
| |
| − | obb_direction_ras_z = np.array(stats[segmentId,"LabelmapSegmentStatisticsPlugin.obb_direction_ras_z"])
| |
| − | # Create ROI
| |
| − | segment = segmentationNode.GetSegmentation().GetSegment(segmentId)
| |
| − | roi=slicer.mrmlScene.AddNewNodeByClass("vtkMRMLAnnotationROINode")
| |
| − | roi.SetName(segment.GetName()+' bounding box')
| |
| − | roi.SetXYZ(0.0, 0.0, 0.0)
| |
| − | roi.SetRadiusXYZ(*(0.5*obb_diameter_mm))
| |
| − | # Position and orient ROI using a transform
| |
| − | obb_center_ras = obb_origin_ras+0.5*(obb_diameter_mm[0] * obb_direction_ras_x + obb_diameter_mm[1] * obb_direction_ras_y + obb_diameter_mm[2] * obb_direction_ras_z)
| |
| − | boundingBoxToRasTransform = np.row_stack((np.column_stack((obb_direction_ras_x, obb_direction_ras_y, obb_direction_ras_z, obb_center_ras)), (0, 0, 0, 1)))
| |
| − | boundingBoxToRasTransformMatrix = slicer.util.vtkMatrixFromArray(boundingBoxToRasTransform)
| |
| − | transformNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLTransformNode')
| |
| − | transformNode.SetAndObserveMatrixTransformToParent(boundingBoxToRasTransformMatrix)
| |
| − | roi.SetAndObserveTransformNodeID(transformNode.GetID())
| |
| − | </pre>
| |
| − | | |
| − | Complete list of available parameters can be obtained by running <code>segStatLogic.getParameterNode().GetParameterNames()</code>.
| |
| − | | |
| − | ==Markups==
| |
| − | | |
| − | ===Load markups fiducial list from file===
| |
| − | | |
| − | Markups fiducials can be loaded from file:
| |
| − | | |
| − | <pre>
| |
| − | slicer.util.loadMarkupsFiducialList('/path/to/list/F.fcsv')
| |
| − | </pre>
| |
| − | | |
| − | ===Adding Fiducials Programatically===
| |
| − | | |
| − | Markups fiducials can be added to the currently active list from the python console by using the following module logic command:
| |
| − | | |
| − | <pre>
| |
| − | slicer.modules.markups.logic().AddFiducial()
| |
| − | </pre>
| |
| − | | |
| − | The command with no arguments will place a new fiducial at the origin. You can also pass it an initial location:
| |
| − | | |
| − | <pre>
| |
| − | slicer.modules.markups.logic().AddFiducial(1.0, -2.0, 3.3)
| |
| − | </pre>
| |
| − | | |
| − | ===Add a button to module GUI to activate fiducial placement===
| |
| − | | |
| − | This code snippet creates a toggle button, which activates fiducial placement when pressed (and deactivates when released).
| |
| − | | |
| − | The [http://apidocs.slicer.org/master/classqSlicerMarkupsPlaceWidget.html qSlicerMarkupsPlaceWidget widget] can automatically activate placement of multiple points and can show buttons for deleting points, changing colors, lock, and hide points.
| |
| − | | |
| − | <pre>
| |
| − | w=slicer.qSlicerMarkupsPlaceWidget()
| |
| − | w.setMRMLScene(slicer.mrmlScene)
| |
| − | markupsNodeID = slicer.modules.markups.logic().AddNewFiducialNode()
| |
| − | w.setCurrentNode(slicer.mrmlScene.GetNodeByID(markupsNodeID))
| |
| − | # Hide all buttons and only show place button
| |
| − | w.buttonsVisible=False
| |
| − | w.placeButton().show()
| |
| − | w.show()
| |
| − | </pre>
| |
| − | | |
| − | ===Adding Fiducials via Mouse Clicks===
| |
| − | | |
| − | You can also set the mouse mode into Markups fiducial placement by calling:
| |
| − | | |
| − | <pre>
| |
| − | placeModePersistence = 1
| |
| − | slicer.modules.markups.logic().StartPlaceMode(placeModePersistence)
| |
| − | </pre>
| |
| − | | |
| − | A lower level way to do this is via the selection and interaction nodes:
| |
| − | | |
| − | <pre>
| |
| − | selectionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLSelectionNodeSingleton")
| |
| − | selectionNode.SetReferenceActivePlaceNodeClassName("vtkMRMLMarkupsFiducialNode")
| |
| − | interactionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLInteractionNodeSingleton")
| |
| − | placeModePersistence = 1
| |
| − | interactionNode.SetPlaceModePersistence(placeModePersistence)
| |
| − | # mode 1 is Place, can also be accessed via slicer.vtkMRMLInteractionNode().Place
| |
| − | interactionNode.SetCurrentInteractionMode(1)
| |
| − | </pre>
| |
| − | | |
| − | To switch back to view transform once you're done placing fiducials:
| |
| − | | |
| − | <pre>
| |
| − | interactionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLInteractionNodeSingleton")
| |
| − | interactionNode.SwitchToViewTransformMode()
| |
| − | # also turn off place mode persistence if required
| |
| − | interactionNode.SetPlaceModePersistence(0)
| |
| − | </pre>
| |
| − | | |
| − | ===Access to Fiducial Properties===
| |
| − | | |
| − | Each vtkMRMLMarkupsFiducialNode has a vector of points in it which can be accessed from python:
| |
| − | | |
| − | <pre>
| |
| − | fidNode = getNode("vtkMRMLMarkupsFiducialNode1")
| |
| − | n = fidNode.AddFiducial(4.0, 5.5, -6.0)
| |
| − | fidNode.SetNthFiducialLabel(n, "new label")
| |
| − | # each markup is given a unique id which can be accessed from the superclass level
| |
| − | id1 = fidNode.GetNthMarkupID(n)
| |
| − | # manually set the position
| |
| − | fidNode.SetNthFiducialPosition(n, 6.0, 7.0, 8.0)
| |
| − | # set the label
| |
| − | fidNode.SetNthFiducialLabel(n, "New label")
| |
| − | # set the selected flag, only selected = 1 fiducials will be passed to CLIs
| |
| − | fidNode.SetNthFiducialSelected(n, 1)
| |
| − | # set the visibility flag
| |
| − | fidNode.SetNthFiducialVisibility(n, 0)
| |
| − | </pre>
| |
| − | | |
| − | You can loop over the fiducials in a list and get the coordinates:
| |
| − | | |
| − | <pre>
| |
| − | fidList = slicer.util.getNode('F')
| |
| − | numFids = fidList.GetNumberOfFiducials()
| |
| − | for i in range(numFids):
| |
| − | ras = [0,0,0]
| |
| − | fidList.GetNthFiducialPosition(i,ras)
| |
| − | # the world position is the RAS position with any transform matrices applied
| |
| − | world = [0,0,0,0]
| |
| − | fidList.GetNthFiducialWorldCoordinates(0,world)
| |
| − | print(i,": RAS =",ras,", world =",world)
| |
| − | </pre>
| |
| − | | |
| − | You can also look at the sample code in the [https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/Endoscopy/Endoscopy.py#L287 Endoscopy module] to see how python is used to access fiducials from a scripted module.
| |
| − | | |
| − | ==Accessing views, renderers, and cameras==
| |
| − | | |
| − | Iterate through all 3D views in current layout:
| |
| − | | |
| − | <pre>
| |
| − | layoutManager = slicer.app.layoutManager()
| |
| − | for threeDViewIndex in range(layoutManager.threeDViewCount) :
| |
| − | view = layoutManager.threeDWidget(threeDViewIndex).threeDView()
| |
| − | threeDViewNode = view.mrmlViewNode()
| |
| − | cameraNode = slicer.modules.cameras.logic().GetViewActiveCameraNode(threeDViewNode)
| |
| − | print('View node for 3D widget ' + str(threeDViewIndex))
| |
| − | print(' Name: ' + threeDViewNode .GetName())
| |
| − | print(' ID: ' + threeDViewNode .GetID())
| |
| − | print(' Camera ID: ' + cameraNode.GetID())
| |
| − | </pre>
| |
| − | | |
| − | Iterate through all slice views in current layout:
| |
| − | | |
| − | <pre>
| |
| − | layoutManager = slicer.app.layoutManager()
| |
| − | for sliceViewName in layoutManager.sliceViewNames():
| |
| − | view = layoutManager.sliceWidget(sliceViewName).sliceView()
| |
| − | sliceNode = view.mrmlSliceNode()
| |
| − | sliceLogic = slicer.app.applicationLogic().GetSliceLogic(sliceNode)
| |
| − | compositeNode = sliceLogic.GetSliceCompositeNode()
| |
| − | print('Slice view ' + str(sliceViewName))
| |
| − | print(' Name: ' + sliceNode.GetName())
| |
| − | print(' ID: ' + sliceNode.GetID())
| |
| − | print(' Background volume: {0}'.format(compositeNode.GetBackgroundVolumeID()))
| |
| − | print(' Foreground volume: {0} (opacity: {1})'.format(compositeNode.GetForegroundVolumeID(), compositeNode.GetForegroundOpacity()))
| |
| − | print(' Label volume: {0} (opacity: {1})'.format(compositeNode.GetLabelVolumeID(), compositeNode.GetLabelOpacity()))
| |
| − | </pre>
| |
| − | | |
| − | For low-level manipulation of views, it is possible to access VTK render windows, renderers and cameras of views in the current layout.
| |
| − | <pre>
| |
| − | renderWindow = view.renderWindow()
| |
| − | renderers = renderWindow.GetRenderers()
| |
| − | renderer = renderers.GetItemAsObject(0)
| |
| − | camera = cameraNode.GetCamera()
| |
| − | </pre>
| |
| − | | |
| − | ==Hide view controller bars==
| |
| − | | |
| − | <pre>
| |
| − | slicer.app.layoutManager().threeDWidget(0).threeDController().setVisible(False)
| |
| − | slicer.app.layoutManager().sliceWidget('Red').sliceController().setVisible(False)
| |
| − | slicer.app.layoutManager().plotWidget(0).plotController().setVisible(False)
| |
| − | slicer.app.layoutManager().tableWidget(0).tableController().setVisible(False)
| |
| − | </pre>
| |
| − | | |
| − | ==Customize widgets in view controller bars==
| |
| − | | |
| − | <pre>
| |
| − | sliceController = slicer.app.layoutManager().sliceWidget("Red").sliceController()
| |
| − | | |
| − | # hide what is not needed
| |
| − | sliceController.pinButton().hide()
| |
| − | #sliceController.viewLabel().hide()
| |
| − | sliceController.fitToWindowToolButton().hide()
| |
| − | sliceController.sliceOffsetSlider().hide()
| |
| − | | |
| − | # add custom widgets
| |
| − | myButton = qt.QPushButton("My custom button")
| |
| − | sliceController.barLayout().addWidget(myButton)
| |
| − | </pre>
| |
| − | | |
| − | ==Change 3D view background color==
| |
| − | | |
| − | <pre>
| |
| − | viewNode = slicer.app.layoutManager().threeDWidget(0).mrmlViewNode()
| |
| − | viewNode.SetBackgroundColor(1,0,0)
| |
| − | viewNode.SetBackgroundColor2(1,0,0)
| |
| − | | |
| − | </pre>
| |
| − | | |
| − | ==Hide Slicer logo from main window (to increase space)==
| |
| − | | |
| − | <pre>
| |
| − | slicer.util.findChild(slicer.util.mainWindow(), 'LogoLabel').visible = False
| |
| − | </pre>
| |
| − | | |
| − | ==Subject hierarchy==
| |
| − | ====Get the pseudo-singleton subject hierarchy node====
| |
| − | It manages the whole hierarchy and provides functions to access and manipulate
| |
| − | shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
| |
| − | | |
| − | ====Create subject hierarchy item====
| |
| − | # If it is for a data node, it is automatically created, but the create function can be used to set parent:
| |
| − | shNode.CreateItem(parentItemID, dataNode)
| |
| − | # If it is a hierarchy item without a data node, then the create function must be used:
| |
| − | shNode.CreateSubjectItem(parentItemID, name)
| |
| − | shNode.CreateFolderItem(parentItemID, name)
| |
| − | shNode.CreateHierarchyItem(parentItemID, name, level) # Advanced method to set level attribute manually (usually subject, study, or folder, but it can be a virtual branch for example)
| |
| − | | |
| − | ====Get subject hierarchy item====
| |
| − | Items in subject hierarchy are uniquely identified by integer IDs
| |
| − | # Get scene item ID first because it is the root item:
| |
| − | sceneItemID = shNode.GetSceneItemID()
| |
| − | # Get direct child by name
| |
| − | subjectItemID = shNode.GetItemChildWithName(sceneItemID, 'Subject_1')
| |
| − | # Get item for data node
| |
| − | itemID = shNode.GetItemByDataNode(dataNode)
| |
| − | # Get item by UID (such as DICOM)
| |
| − | itemID = shNode.GetItemByUID(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMUIDName(), seriesInstanceUid)
| |
| − | itemID = shNode.GetItemByUIDList(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMInstanceUIDName(), instanceUID)
| |
| − | # Invalid item ID for checking validity of a given ID (most functions return the invalid ID when item is not found)
| |
| − | invalidItemID = slicer.vtkMRMLSubjectHierarchyNode.GetInvalidItemID()
| |
| − | | |
| − | ====Traverse children of a subject hierarchy item====
| |
| − | children = vtk.vtkIdList()
| |
| − | shNode.GetItemChildren(parent, children)
| |
| − | for i in range(children.GetNumberOfIds()):
| |
| − | child = children.GetId(i)
| |
| − | ...
| |
| − | | |
| − | ====Manipulate subject hierarchy item====
| |
| − | Instead of node operations on the individual subject hierarchy nodes, item operations are performed on the one subject hierarchy node.
| |
| − | # Set item name
| |
| − | shNode.SetItemName(itemID, 'NewName')
| |
| − | # Set item parent (reparent)
| |
| − | shNode.SetItemParent(itemID, newParentItemID)
| |
| − | # Set visibility of data node associated to an item
| |
| − | shNode.SetItemDisplayVisibility(itemID, 1)
| |
| − | # Set visibility of whole branch
| |
| − | # Note: Folder-type items (fodler, subject, study, etc.) create their own display nodes when show/hiding from UI.
| |
| − | # The displayable managers use SH information to determine visibility of an item, so no need to show/hide individual leaf nodes any more.
| |
| − | # Once the folder display node is created, it can be shown hidden simply using shNode.SetItemDisplayVisibility
| |
| − | # From python, this is how to trigger creating a folder display node
| |
| − | pluginHandler = slicer.qSlicerSubjectHierarchyPluginHandler().instance()
| |
| − | folderPlugin = pluginHandler.pluginByName('Folder')
| |
| − | folderPlugin.setDisplayVisibility(folderItemID, 1)
| |
| − | | |
| − | ====Filter items in TreeView or ComboBox====
| |
| − | Displayed items can be filtered using ''setAttributeFilter'' method. An example of the usage can be found in the [https://github.com/Slicer/Slicer/blob/e66e3b08e35384526528e6ae678e9ec9f079f286/Applications/SlicerApp/Testing/Python/SubjectHierarchyGenericSelfTest.py#L352-L360 unit test]. Modified version here:
| |
| − | print(shTreeView.displayedItemCount()) # 5
| |
| − | shTreeView.setAttributeFilter('DICOM.Modality') # Nodes must have this attribute
| |
| − | print(shTreeView.displayedItemCount()) # 3
| |
| − | shTreeView.setAttributeFilter('DICOM.Modality','CT') # Have attribute and equal 'CT'
| |
| − | print(shTreeView.displayedItemCount()) # 1
| |
| − | shTreeView.removeAttributeFilter()
| |
| − | print(shTreeView.displayedItemCount()) # 5
| |
| − | | |
| − | ===Listen to subject hierarchy item events===
| |
| − | The subject hierarchy node sends the node item id as calldata. Item IDs are vtkIdType, which are NOT vtkObjects. You need to use vtk.calldata_type(vtk.VTK_LONG) (otherwise the application crashes).
| |
| − |
| |
| − | class MyListenerClass(VTKObservationMixin):
| |
| − | def __init__(self):
| |
| − | VTKObservationMixin.__init__(self)
| |
| − |
| |
| − | shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
| |
| − | self.addObserver(shNode, shNode.SubjectHierarchyItemModifiedEvent, self.shItemModifiedEvent)
| |
| − |
| |
| − | @vtk.calldata_type(vtk.VTK_LONG)
| |
| − | def shItemModifiedEvent(self, caller, eventId, callData):
| |
| − | print("SH Node modified")
| |
| − | print("SH item ID: {0}".format(callData))
| |
| − | | |
| − | ===Subject hierarchy plugin offering view context menu action===
| |
| − | If an object that supports view context menus (e.g. markups) is right-clicked in a slice or 3D view, it can offer custom actions. Due to internal limitations these plugins must be set up differently, as explained [https://github.com/Slicer/Slicer/blob/master/Modules/Loadable/Annotations/SubjectHierarchyPlugins/AnnotationsSubjectHierarchyPlugin.py#L96-L107 here]. This example makes it easier to create such a plugin.
| |
| − | <syntaxhighlight lang="python">
| |
| − | import vtk, qt, ctk, slicer
| |
| − | from slicer.ScriptedLoadableModule import *
| |
| − | from slicer.util import VTKObservationMixin
| |
| − | | |
| − | from SubjectHierarchyPlugins import AbstractScriptedSubjectHierarchyPlugin
| |
| − | | |
| − | class ViewContextMenu(ScriptedLoadableModule):
| |
| − | """Uses ScriptedLoadableModule base class, available at:
| |
| − | https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
| |
| − | """
| |
| − | | |
| − | def __init__(self, parent):
| |
| − | ScriptedLoadableModule.__init__(self, parent)
| |
| − | self.parent.title = "Markup Editor"
| |
| − | self.parent.categories = ["SlicerMorph", "Labs"]
| |
| − | self.parent.dependencies = []
| |
| − | self.parent.contributors = ["Steve Pieper (Isomics, Inc.)"]
| |
| − | self.parent.helpText = """
| |
| − | A tool to manipulate Markups using the Segment Editor as a geometry backend
| |
| − | """
| |
| − | self.parent.helpText += self.getDefaultModuleDocumentationLink()
| |
| − | self.parent.acknowledgementText = """
| |
| − | This module was developed by Steve Pieper, Sara Rolfe and Murat Maga,
| |
| − | through a NSF ABI Development grant, "An Integrated Platform for Retrieval,
| |
| − | Visualization and Analysis of 3D Morphology From Digital Biological Collections"
| |
| − | (Award Numbers: 1759883 (Murat Maga), 1759637 (Adam Summers), 1759839 (Douglas Boyer)).
| |
| − | This file was originally developed by Jean-Christophe Fillion-Robin, Kitware Inc.,
| |
| − | Andras Lasso, PerkLab, and Steve Pieper, Isomics, Inc.
| |
| − | and was partially funded by NIH grant 3P41RR013218-12S1.
| |
| − | """
| |
| − | | |
| − | #
| |
| − | # register subject hierarchy plugin once app is initialized
| |
| − | #
| |
| − | def onStartupCompleted():
| |
| − | import SubjectHierarchyPlugins
| |
| − | from ViewContextMenu import ViewContextMenuSubjectHierarchyPlugin
| |
| − | scriptedPlugin = slicer.qSlicerSubjectHierarchyScriptedPlugin(None)
| |
| − | scriptedPlugin.setPythonSource(ViewContextMenuSubjectHierarchyPlugin.filePath)
| |
| − | pluginHandler = slicer.qSlicerSubjectHierarchyPluginHandler.instance()
| |
| − | pluginHandler.registerPlugin(scriptedPlugin)
| |
| − | print('ViewContextMenuSubjectHierarchyPlugin loaded')
| |
| − | slicer.app.connect("startupCompleted()", onStartupCompleted)
| |
| − | | |
| − | | |
| − | class ViewContextMenuSubjectHierarchyPlugin(AbstractScriptedSubjectHierarchyPlugin):
| |
| − | | |
| − | # Necessary static member to be able to set python source to scripted subject hierarchy plugin
| |
| − | filePath = __file__
| |
| − | | |
| − | def __init__(self, scriptedPlugin):
| |
| − | self.viewAction = qt.QAction(f"CUSTOM VIEW ...", scriptedPlugin)
| |
| − | self.viewAction.objectName = 'CustomViewAction'
| |
| − | self.viewAction.connect("triggered()", self.onViewAction)
| |
| − | | |
| − | def onViewAction(self):
| |
| − | print(f"VIEW ACTION")
| |
| − | | |
| − | def viewContextMenuActions(self):
| |
| − | return [self.viewAction]
| |
| − | | |
| − | def showViewContextMenuActionsForItem(self, itemID, eventData=None):
| |
| − | pluginHandler = slicer.qSlicerSubjectHierarchyPluginHandler.instance()
| |
| − | pluginLogic = pluginHandler.pluginLogic()
| |
| − | menuActions = list(pluginLogic.availableViewMenuActionNames())
| |
| − | menuActions.append('CustomViewAction')
| |
| − | pluginLogic.setDisplayedViewMenuActionNames(menuActions)
| |
| − | self.viewAction.visible = True
| |
| − | </syntaxhighlight>
| |
| − | | |
| − | ===Use whitelist to customize view menu===
| |
| − | When right-clicking certain types of nodes in the 2D/3D views, a subject hierarchy menu pops up. If menu actions need to be removed, a whitelist can be used to specify the ones that should show up.
| |
| − | pluginHandler = slicer.qSlicerSubjectHierarchyPluginHandler.instance()
| |
| − | pluginLogic = pluginHandler.pluginLogic()
| |
| − | menuActions = pluginLogic.availableViewMenuActionNames()
| |
| − | # Returns ('RenamePointAction', 'DeletePointAction', 'ToggleSelectPointAction', 'EditPropertiesAction')
| |
| − | newActions = ['RenamePointAction']
| |
| − | pluginLogic.setDisplayedViewMenuActionNames(newActions)
| |
| − | | |
| − | ==Plotting==
| |
| − | | |
| − | ===Slicer plots displayed in view layout===
| |
| − | | |
| − | Create histogram plot of a volume and show it embedded in the view layout. More information: https://www.slicer.org/wiki/Documentation/Nightly/Developers/Plots
| |
| − | | |
| − | ====Using <code>slicer.util.plot</code> utility function====
| |
| − | | |
| − | <pre>
| |
| − | # Get a volume from SampleData and compute its histogram
| |
| − | import SampleData
| |
| − | import numpy as np
| |
| − | volumeNode = SampleData.SampleDataLogic().downloadMRHead()
| |
| − | histogram = np.histogram(arrayFromVolume(volumeNode), bins=50)
| |
| − | | |
| − | chartNode = slicer.util.plot(histogram, xColumnIndex = 1)
| |
| − | chartNode.SetYAxisRangeAuto(False)
| |
| − | chartNode.SetYAxisRange(0, 4e5)
| |
| − | </pre>
| |
| − | | |
| − | [[Image:SlicerPlot.png]]
| |
| − | | |
| − | ====Using MRML classes only====
| |
| − | | |
| − | <pre>
| |
| − | # Get a volume from SampleData
| |
| − | import SampleData
| |
| − | volumeNode = SampleData.SampleDataLogic().downloadMRHead()
| |
| − | | |
| − | # Compute histogram values
| |
| − | import numpy as np
| |
| − | histogram = np.histogram(arrayFromVolume(volumeNode), bins=50)
| |
| − | | |
| − | # Save results to a new table node
| |
| − | tableNode=slicer.mrmlScene.AddNewNodeByClass("vtkMRMLTableNode")
| |
| − | updateTableFromArray(tableNode, histogram)
| |
| − | tableNode.GetTable().GetColumn(0).SetName("Count")
| |
| − | tableNode.GetTable().GetColumn(1).SetName("Intensity")
| |
| − | | |
| − | # Create plot
| |
| − | plotSeriesNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLPlotSeriesNode", volumeNode.GetName() + ' histogram')
| |
| − | plotSeriesNode.SetAndObserveTableNodeID(tableNode.GetID())
| |
| − | plotSeriesNode.SetXColumnName("Intensity")
| |
| − | plotSeriesNode.SetYColumnName("Count")
| |
| − | plotSeriesNode.SetPlotType(plotSeriesNode.PlotTypeScatterBar)
| |
| − | plotSeriesNode.SetColor(0, 0.6, 1.0)
| |
| − | | |
| − | # Create chart and add plot
| |
| − | plotChartNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLPlotChartNode")
| |
| − | plotChartNode.AddAndObservePlotSeriesNodeID(plotSeriesNode.GetID())
| |
| − | plotChartNode.YAxisRangeAutoOff()
| |
| − | plotChartNode.SetYAxisRange(0, 500000)
| |
| − | | |
| − | # Show plot in layout
| |
| − | slicer.modules.plots.logic().ShowChartInLayout(plotChartNode)
| |
| − | </pre>
| |
| − | | |
| − | ===Using matplotlib===
| |
| − | | |
| − | Matplotlib may be used from within Slicer, but the default Tk backend locks up and crashes Slicer. However, Matplotlib may still be used through other backends. More details can be found on the [http://matplotlib.sourceforge.net/ MatPlotLib] pages.
| |
| − | | |
| − | ====Non-interactive plot====
| |
| − | | |
| − | <pre>
| |
| − | try:
| |
| − | import matplotlib
| |
| − | except ModuleNotFoundError:
| |
| − | pip_install('matplotlib')
| |
| − | import matplotlib
| |
| − | | |
| − | matplotlib.use('Agg')
| |
| − | from pylab import *
| |
| − | | |
| − | t1 = arange(0.0, 5.0, 0.1)
| |
| − | t2 = arange(0.0, 5.0, 0.02)
| |
| − | t3 = arange(0.0, 2.0, 0.01)
| |
| − | | |
| − | subplot(211)
| |
| − | plot(t1, cos(2*pi*t1)*exp(-t1), 'bo', t2, cos(2*pi*t2)*exp(-t2), 'k')
| |
| − | grid(True)
| |
| − | title('A tale of 2 subplots')
| |
| − | ylabel('Damped')
| |
| − | | |
| − | subplot(212)
| |
| − | plot(t3, cos(2*pi*t3), 'r--')
| |
| − | grid(True)
| |
| − | xlabel('time (s)')
| |
| − | ylabel('Undamped')
| |
| − | savefig('MatplotlibExample.png')
| |
| − | | |
| − | # Static image view
| |
| − | pm = qt.QPixmap("MatplotlibExample.png")
| |
| − | imageWidget = qt.QLabel()
| |
| − | imageWidget.setPixmap(pm)
| |
| − | imageWidget.setScaledContents(True)
| |
| − | imageWidget.show()
| |
| − | </pre>
| |
| − | | |
| − | [[Image:MatplotlibExample.png]]
| |
| − | | |
| − | ====Plot in Slicer Jupyter notebook====
| |
| − | | |
| − | <pre>
| |
| − | import JupyterNotebooksLib as slicernb
| |
| − | try:
| |
| − | import matplotlib
| |
| − | except ModuleNotFoundError:
| |
| − | pip_install('matplotlib')
| |
| − | import matplotlib
| |
| − | | |
| − | matplotlib.use('Agg')
| |
| − | | |
| − | import matplotlib.pyplot as plt
| |
| − | import numpy as np
| |
| − | | |
| − | def f(t):
| |
| − | s1 = np.cos(2*np.pi*t)
| |
| − | e1 = np.exp(-t)
| |
| − | return s1 * e1
| |
| − | | |
| − | t1 = np.arange(0.0, 5.0, 0.1)
| |
| − | t2 = np.arange(0.0, 5.0, 0.02)
| |
| − | t3 = np.arange(0.0, 2.0, 0.01)
| |
| − | | |
| − | | |
| − | fig, axs = plt.subplots(2, 1, constrained_layout=True)
| |
| − | axs[0].plot(t1, f(t1), 'o', t2, f(t2), '-')
| |
| − | axs[0].set_title('subplot 1')
| |
| − | axs[0].set_xlabel('distance (m)')
| |
| − | axs[0].set_ylabel('Damped oscillation')
| |
| − | fig.suptitle('This is a somewhat long figure title', fontsize=16)
| |
| − | | |
| − | axs[1].plot(t3, np.cos(2*np.pi*t3), '--')
| |
| − | axs[1].set_xlabel('time (s)')
| |
| − | axs[1].set_title('subplot 2')
| |
| − | axs[1].set_ylabel('Undamped')
| |
| − | | |
| − | slicernb.MatplotlibDisplay(matplotlib.pyplot)
| |
| − | </pre>
| |
| − | | |
| − | [[Image:JupyterNotebookMatplotlibExample.png]]
| |
| − | | |
| − | ====Interactive plot using wxWidgets GUI toolkit====
| |
| − | | |
| − | <pre>
| |
| − | try:
| |
| − | import matplotlib
| |
| − | import wx
| |
| − | except ModuleNotFoundError:
| |
| − | pip_install('matplotlib wxPython')
| |
| − | import matplotlib
| |
| − | | |
| − | # Get a volume from SampleData and compute its histogram
| |
| − | import SampleData
| |
| − | import numpy as np
| |
| − | volumeNode = SampleData.SampleDataLogic().downloadMRHead()
| |
| − | histogram = np.histogram(arrayFromVolume(volumeNode), bins=50)
| |
| − | | |
| − | # Set matplotlib to use WXAgg backend
| |
| − | import matplotlib
| |
| − | matplotlib.use('WXAgg')
| |
| − | | |
| − | # Show an interactive plot
| |
| − | import matplotlib.pyplot as plt
| |
| − | fig, ax = plt.subplots()
| |
| − | ax.plot(histogram[1][1:], histogram[0].astype(float))
| |
| − | ax.grid(True)
| |
| − | ax.set_ylim((0, 4e5))
| |
| − | plt.show(block=False)
| |
| − | </pre>
| |
| − | | |
| − | [[Image:InteractiveMatplotlibExample.png]]
| |
| − | | |
| − | ==Execute external applications==
| |
| − | | |
| − | How to run external applications from Slicer.
| |
| − | | |
| − | ===Run process in default environment===
| |
| − | | |
| − | When a process is launched from Slicer then by default Slicer's ITK, VTK, Qt, etc. libraries are used. If an external application has its own version of these libraries, then the application is expected to crash. To prevent crashing, the application must be run in the environment where Slicer started up (without all Slicer-specific library paths). This startup environment can be retrieved using ''slicer.util.startupEnvironment()''.
| |
| − | | |
| − | Example: run Python3 script from Slicer:
| |
| − | | |
| − | <pre>
| |
| − | command_to_execute = ["/usr/bin/python3", "-c", "print('hola')"]
| |
| − | from subprocess import check_output
| |
| − | check_output(
| |
| − | command_to_execute,
| |
| − | env=slicer.util.startupEnvironment()
| |
| − | )
| |
| − | </pre>
| |
| − | | |
| − | will output:
| |
| − | <pre>
| |
| − | 'hola\n'
| |
| − | </pre>
| |
| − | | |
| − | On some systems, ''shell=True'' must be specified as well.
| |
| − | | |
| − | ==Manage extensions==
| |
| − | | |
| − | ===Download and install extension===
| |
| − | | |
| − | <pre>
| |
| − | extensionName = 'SlicerIGT'
| |
| − | em = slicer.app.extensionsManagerModel()
| |
| − | if not em.isExtensionInstalled(extensionName):
| |
| − | extensionMetaData = em.retrieveExtensionMetadataByName(extensionName)
| |
| − | url = em.serverUrl().toString()+'/download/item/'+extensionMetaData['item_id']
| |
| − | extensionPackageFilename = slicer.app.temporaryPath+'/'+extensionMetaData['md5']
| |
| − | slicer.util.downloadFile(url, extensionPackageFilename)
| |
| − | em.installExtension(extensionPackageFilename)
| |
| − | slicer.util.restart()
| |
| − | </pre>
| |
| − | | |
| − | ===Install a module directly from a git repository===
| |
| − | This can be useful for sharing code in development without requiring a restart of Slicer.
| |
| − | | |
| − | https://gist.github.com/pieper/a9c0ba57de3833c9f5aea68247bda597
| |
