Anywhere to find a list of required inputs for Python?

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1

Hello,

I am trying to write a Python script that can automate the export of a .stl model from a segmentation that is imported with the CT DICOM set.

I have pretty much everything by painfully looking through examples online, but I am stuck on how to do the final export.

I think this might be the code to use:

slicer.modules.models.logic().SaveModel()

But that code requires two arguments and I have no way of figuring out what they are supposed to be. This is an issue I have run into with many other commands. Is there some database I can access that says what all the arguments for a code are supposed to be?

All i get back in the traceback error is:

TypeError: SaveModel() takes exactly 2 arguments (0 given)

Which is next to useless as it doesnā€™t tell me what the arguments need to be.

2

You can use the help command to get documentation on any command. For example, enter this in the Python console:

help(slicer.modules.models.logic().SaveModel)

You can find full documentation of Slicerā€™s Python-wrapped C++ API at http://apidocs.slicer.org. Models module logic is documented here: http://apidocs.slicer.org/master/classvtkSlicerModelsLogic.html#ae7123e56a176f06e0eda54403f07f393

3

Thanks.

Iā€™m having difficulty finding the vtkMRMLModelNode for the model I want to save. Is there a way to list all available?

Also will the SaveModel() save as .stl format?

Itā€™s very confusing to me what stuff I have to use slicer.modules.models for and what stuff I have to use slicer.vtkMRMLModelNode() for

4

Get list of all model nodes in the scene: use slicer.util.getNodesByClass. For example:

models=slicer.util.getNodesByClass('vtkMRMLModelNode')
for model in models:   
  if not model.GetHideFromEditors():
    print(model.GetName())

Save model as STL:

slicer.util.saveNode(modelNode, "c:/tmp/test.stl")

Model node only stores the data, so youā€™ll only find methods in this class that are responsible getting/setting content. Any operation on the data is implemented in Models or other module logic classes or in utility functions.

5

Once again, Thanks so much for your help.

Sorry to be a bother, I hope this is the last I have to ask for help.
So I am trying to automate the step to export all segmentations as model that I can then save using the code you provided above.

So I have these segmentations. The Binary labelmap is currently master:

image
image800Ɨ327 14 KB

Then I have the following code to try to export them to models

>>>segmentations = slicer.util.getNodesByClass(ā€˜vtkMRMLSegmentationNodeā€™)
>>>modelHierarchyNode = slicer.vtkMRMLModelHierarchyNode()
>>>slicer.mrmlScene.AddNode(modelHierarchyNode)
>>>slicer.modules.segmentations.logic().ExportAllSegmentsToModelHierarchy(segmentations[0],slicer.util.getNodesByClass(ā€˜vtkMRMLModelHierarchyNodeā€™)[0])

After the final line, the console returns ā€œTrueā€ but no models appear, just this:

image
image802Ɨ454 9.32 KB

i am sure there is one step I am missingā€¦

6

Bump. Please see above. Iā€™ve tried trouble shooting and Iā€™m not sure where I am going wrong.

The ExportAllSegmentsToModelHierarchy() returns ā€œTrueā€, but no models appear under the ModelHierarchy node.

7

Thanks for the feedback. Youā€™ve discovered a bug in ExportAllSegmentsToModelHierarchy method that Iā€™ll fix in the nightly build today. Till then, or if you use the latest stable version, you can use ExportSegmentsToModelHierarchy method instead:

seg = getNode('Segmentation')
modelHierarchyNodeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLModelHierarchyNode')
segmentIds = vtk.vtkStringArray()
seg.GetSegmentation().GetSegmentIDs(segmentIds)
slicer.modules.segmentations.logic().ExportSegmentsToModelHierarchy(seg, segmentIds, modelHierarchyNodeNode)
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