Save files from loaded node ID in batch mode

Support
1

Hi guys,

I’m trying to follow the source codes for loading DICOM files as here:

Example: load all data from a DICOM folder (using a temporary DICOM database)
dicomDataDir = “c:/my/folder/with/dicom-files” # input folder with DICOM files
loadedNodeIDs = [] # this list will contain the list of all loaded node IDs
from DICOMLib import DICOMUtils
with DICOMUtils.TemporaryDICOMDatabase() as db:
DICOMUtils.importDicom(dicomDataDir, db)
patientUIDs = db.patients()
for patientUID in patientUIDs:
loadedNodeIDs.extend(DICOMUtils.loadPatientByUID(patientUID))

However, I’m not quite clear what will be the next steps. i.e., how can I use the list of “loadedNodeIDs” to obtain the loadable instances so that I can export to other file format?

2

Here is a slightly older example that just saves one node. You could extend this to loop over your loaded nodes and save them out.

3

You need to do something like this:

for loadedNodeID in loadedNodeIDs:
    slicer.util.saveNode(slicer.mrmlScene.GetNodeByID(loadedNodeID), ...set a filename here...)
4

Thanks Andras, the syntax is correct, however, for the DICOM series I tested, it says No patient found with DICOM database UID (u’1’,). However, using DICOMScalarVolumePlugin, I can successfully output the correct file. What I did was the following:
plugin = slicer.modules.dicomPlugins’DICOMScalarVolumePlugin’
if plugin:
loadables = plugin.examineFiles(fileNames)
volume = plugin.load(loadables[0])
output_path = os.path.join(output_directory,output_filename+output_extension)
try:
slicer.util.saveNode(volume, output_path)
except Exception as e:
print(e)
exit()
I’m not sure if this is robust enough to process most DICOM files as Slicer did.

5

Using the scalar volume plugin directly is fine, as long as you only need to load simple 3D volumes (not 4D volumes, structure sets, segmentation objects, registration objects, etc.).

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