Is it possible to create/clone a node keeping the same location in the hierarchy of the father node?

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1

Basically I have a big subject hierarchy (several folders), and inside each I have nodes (volumes, segmentations, transformations). I want to create a table for instance and place it in the same location of the generating data, or clone one of the volumes, make some calculation and save as a new volume in the same hierarchy.

When I do this

    volumeNode = slicer.vtkSlicerVolumesLogic().CloneVolume(slicer.mrmlScene, fatherNode, nodename, True)
    util.updateVolumeFromArray(volumeNode, new_arr)
    volumeNode.Modified()

the created volume is outside of the hierarchy so I have to move it manually. Is there a way to tell the new volume to be placed where the father is located??

2

This feature is already available in Data module. You can convert file folder hierarchy to subject hierarchy by clicking on the empty area of the subject hierarchy tree:

For example, you load a number of images from a folder structure (folder names a, b, c, d, e):

image

results in:

image

1 Like
3

I have already a hierarchy:

image

what I need is to coy the object to perform some operations and keep bpoth the new and the old volumes, I am doing like this

    shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
    itemID = shNode.GetItemByDataNode(node)
    newname = name.replace('CTCT', 'DENS')
    clonedItemID = slicer.modules.subjecthierarchy.logic().CloneSubjectHierarchyItem(shNode, itemID, newname)
    vox_arr = np.array(slicer.util.array(newname)).copy()
    vox_arr = np.where(vox_arr<0, 0.0009990791851848257 * vox_arr + 1, 0.0005116346986394071 * vox_arr + 1)
    clonedNode = shNode.GetItemDataNode(clonedItemID)
    slicer.util.updateVolumeFromArray(clonedNode, vox_arr)
    clonedNode.Modified()

But then when I visualize both images, THEY ARE BOTH CHANGED!!

image

I need to preserve the hierarchy path, but also to create a new volume and modify it without changing the original. This code preserves the hierarchy, but modifies both volumes:

image

the code in the original post creates a new volume you can modify safely without modifying the original but it does not preserve the hierarchy.

So how to do this?

4

Cloning a volume using CloneSubjectHierarchyItem creates a shallow copy of the image data. You can either use Volume module’s CloneVolume method or modify your code above to clone the image data by adding clonedNode.SetAndObserveImageData(vtk.vtkImageData()) before slicer.util.updateVolumeFromArray(clonedNode, vox_arr).

5

yes, that worked!
image

not trivial line BTW! Thanks

6

Yes, that’s why we added the clone volume example in the script repository.