Python code to place fiducial markers into slicer

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1

I am trying to place fiducial markers down, but not with the widget or GUI. I am wondering how I can do this in my python code. I have a text file with a list of coordinates, and I want to place the markers at those coordinates. Any help would be appreciated. Thanks.

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Here’s one way to do it: Read your text file into a Nx3 numpy array (here: arr), then create or get the desired fiducial node (here: nfids, class: slicer.vtkMRMLMarkupsFiducialNode). With these two, you can use the following function to place fiducials into that node (with or without names):

def fiducialListFromArray(nfids, arr, listFidNames=None):
    nrfids = arr.shape[0]
    if listFidNames is None:
        listFidNames = ['%s-%d'%(nfids.GetName(),i+1) for i in range(nrfids)]
    for i in range(nrfids):
        nfids.AddFiducial(arr[i,0], arr[i,1], arr[i,2], listFidNames[i])
    return nfids
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slicer.modules.markups.logic().AddFiducial(x, y, z)

I think this will work right?

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@mxtt Reading the Markups section of the “Script Repository” should help you move forward:
https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#markups

place fiducial markers down, but not with the widget or GUI. […] do this in my python code

More specifically, the entry Adding control points Programmatically