Some thoughts about GateTools

Some thoughts about GateTools

GateTools: associated python scripts and tools for GATE.

• official name: GateTools ? other ideas ?

• single python package: pip install gatetools

  • dependencies (auto) : sitk itk uproot pydicom numpy matplotlib click etc
  • source code in OpenGate github as a third repo (GateTools), along with Gate and GateContrib
  • only 'official' tools here. User contributions will be in GateContrib (and may use this package as a module)
  • ideally with associated tests
  • docs as readthedocs rst
  • if needed: examples of usage in GateContrib

• tools should be both 1) as a command line ('à la' clitk), and 2) as a function callable from a python script. Example:

gate_image_arithm *.mhd -o sum.mhd -t 'sum'

or

import gatetools as g
g.gate_image_arithm(filenames, output_filename, operation_type)

Use of click python package for that.

List of tools: (prefixed by 'gate_' or 'gt_' ? with or without .py extension ?)

• gate_image_arithm
• gate_image_resample
• gate_image_uncertainty
• gate_image_crop
• gate_image_convert
• gate_dicom_plan_to_macro
• gate_dicom_convert
• gate_dicom_struct_to_binary_image
• gate_root_merge (WARNING: not sure if uproot can write .root Tree file)
• gate_root_convert_to_npy
• gate_stat_file_merge
• gate_split_and_run
• gate_run_merge

• organise in folders ?

  • image
  • cluster
  • rt_ion
  • misc

• how to:

  • DavidB + ThomasB + DavidS first, then add all volonteers
  • need one branch for every new tool
  • probably need one (or more) gate_helpers.py module with functions common to several tools
  • start by
    • make tools priority
    • pick one tool and code it
    • share, compare code before switching to another tool