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Development plan

As agreed on a Skype call last week, we start collecting here the list of tools from the VV/clitk collection that we would like to pythonize, for use in a python-based Gate workflow.

• clitkDicom2Image: convert DICOM CT images to MHD
• clitkDicomRTPlan2Gate: convert DICOM PBS pencil beam plan to Gate text input file
• clitkCropImage: crop image to within given bounding box
• clitkDicomRTStruct2Image: convert ROI to a binary (or fuzzy) mask for given image
• clitkGammaIndex: compute gamma index for 2D or 3D images (or any other dose grid)
• clitkGateSimulation2Dicom: convert MHD dose image into DICOM dose image
• clitkImage2DicomDose: convert DICOM dose image into MHD dose image
• clitkExtractPatient (kinda): replace everything outside the patient with air, optionally crop image to external
• clitkImageArithm: add, subtract, divide, multiply, scale
• clitkImageConvert: change pixel value type and/or image storage format
• clitkSetBackground: set a constant value to outside (unmasked) or inside (masked) voxels

Naming issue

For consistency and similar reasons, we could use the same names for classes/functions in Python, except maybe the "clitk" replaced with "py". But some names are just not so good. For instance, clitkGateSimulation2Dicom and clitkImage2DicomDose are each other's inverse, functionally speaking, it would be good to make that more clear in their names.

One suggestion: prefix all command line tools with 'gate_': gate_dicom_to_image, gate_gamma_index, gate_image_to_dicom_dose, gate_dicom_dose_to_image etc. In python, the package will be import gatetools as gate, allowing use of function such that gate.dicom_to_image etc

First tools to develop

1. gate_image_arithm: perform image to image arithmetic operation. Useful to merge output from several jobs
2. gate_merge_uncertainty: merge two (several) uncertainty images from DoseActor
3. gate_image_convert: convert file format (mhd, hdr, dicom), and/or pixel type (float, char etc).