Load DICOM series using python

Ben_George · June 21, 2018, 1:33pm

Hi

I am trying to create a python script that can import a DICOM image series from a folder, however I can’t seem to find a way to make this work.

I can load a single DICOM file (in my case an RTSTRUCT) using this code:

contour_fn = 'contours.dcm'
	
	# Add filename to list for DICOM-RT module
	contour_vtkFileList = vtk.vtkStringArray()
	contour_vtkFileList.InsertNextValue(slicer.util.toVTKString(contour_fn))
	
	# Examine files
	contour_loadablesCollection = vtk.vtkCollection()
	slicer.modules.dicomrtimportexport.logic().ExamineForLoad(contour_vtkFileList, contour_loadablesCollection)
	# Set name for when loaded
	contour_loadablesCollection.GetItemAsObject(0).SetName('RTSTRUCT')
	
	# Load file
	contour_success = slicer.modules.dicomrtimportexport.logic().LoadDicomRT(contour_loadablesCollection.GetItemAsObject(0))

However, if I create a list of filenames to load, it doesn’t seem to work correctly. Specifically, my ‘loadablesCollection’ is empty.

Is there a way to do this? I have seen options for loading patients from the DICOM browser, but I don’t want to have to import all the data through that if possible. Also, I’m not sure what the patient name will be, so don’t know how I would do a load by name/ID.

Many thanks

Ben

cpinter · June 21, 2018, 4:00pm

Hi Ben,

There are many convenience functions just for this in DICOMUtils. So you don’t need to go through the logic classes:

github.com

Slicer/Slicer/blob/master/Modules/Scripted/DICOMLib/DICOMUtils.py

import os
import vtk, qt, ctk, slicer
import logging

#########################################################
#
#
comment = """

  DICOMUtils is a collection of static-like DICOM
  utility functions facilitating convenient scripted
  use of the DICOM database

"""
#
#########################################################

#------------------------------------------------------------------------------
def loadPatientByUID(patientUID):
  """ Load patient by patient UID from DICOM database

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I see you want to load RT data. The code form this automated test might help:

github.com

SlicerRt/SlicerRT/blob/master/DicomRtImportExport/Testing/Python/DicomRtImportTest.py

import os
import unittest
import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import logging

class DicomRtImportTest(unittest.TestCase):
  def setUp(self):
    """ Do whatever is needed to reset the state - typically a scene clear will be enough.
    """
    slicer.mrmlScene.Clear(0)

    #TODO: Comment out
    #logFile = open('d:/pyTestLog.txt', 'a')
    #logFile.write(repr(slicer.modules.DicomRtImportTest) + '\n')
    #logFile.write(repr(slicer.modules.dicomrtimportexport) + '\n')
    #logFile.close()

  #------------------------------------------------------------------------------
  def runTest(self):

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or this

github.com

SlicerRt/SlicerRT/blob/master/Testing/Python/IGRTWorkflow_SelfTest.py

import os
import unittest
import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
from DICOMLib import DICOMUtils
import logging

#
# IGRTWorkflow_SelfTest
#
# IGRT: Calculate isocenter shifting, and evaluate its effect on the dose
#   1. Load planning DICOM-RT data and day 2 volumes
#   2. Add day 2 volumes in Subject Hierarchy
#   3. Compute isodose lines for both dose distributions
#   4. Register day 2 CT to planning CT using rigid registration
#   5. Transform day 2 dose volumes using the result transform
#   6. Compute difference dose using gamma comparison for
#     6A. Planning dose and unregistered day 2 dose
#     6B. Planning dose and registered day 2 dose
#   7. Accumulate

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Ben_George · June 22, 2018, 6:49am

Hi Csaba

Thanks for your response, I’ll take a look through the examples you suggested.

fedorov · July 30, 2018, 1:43pm

You can also take a look at this python module that provides a command line tool to essentially take a folder with DICOM data, and organize it into patient/study/series hierarchy of folders accompanied by volumetric reconstructions for each series. It does not handle RT, but it should be easy to add that. You can also find more details here: How can I convert DICOM series to NRRD files in batch mode?.

zgk110 · September 16, 2018, 3:40am

Hi, i am trying to import a dicom series directory by python scripting, i just found the command 'slicer.util.loadNodeFromFile /loadScene/loadVolume ’ , is there any other function to load the dicom series from directory ?

lassoan · September 16, 2018, 1:36pm

The post above has been moved here, as the same question has been discussed in this topic. If you have any follow-up questions please post them here.