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Python tools for GATE, see https://github.com/OpenGATE/Gate

Project description

Tools for GATE simulations. Build Status

Install with : pip install gatetools

Example of usage:

gt_gate_info
gt_image_convert -i input.dcm -o output.mhd
gt_image_convert -i input.mhd -o output_float.mhd -p float
gt_image_arithm -i *.mhd -o output.mhd -O sum
gt_gamma_index dose.mhd gate-DoseToWater.mhd -o gamma.mhd --dd 2 --dta 2.5 -u "%" -T 0.2

Use the flag -h to get print the help of each tool. Here is the current list of command line tools.

Tool Comment
gt_dicom_rt_pbs2gate Convert Dicom RT proton plan for Gate
gt_dicom_rt_struct_to_image Turn Dicom RT Struct contours into mask image
gt_gamma_index Compute gamma index between images
gt_gate_info Display info about current Gate/G4 version
gt_image_arithm Pixel- or voxel-wise arithmetic operations
gt_image_convert Convert image file format (dicom, mhd, hdr, nii ... )
gt_image_crop Crop an image
gt_image_uncertainty Compute statistical uncertainty
gt_phsp_convert Convert a phase space file from root to npy
gt_phsp_info Display information about a phase space file
gt_phsp_merge Merge two phase space files (output in npy only)
gt_phps_peaks Try to detect photopeaks (experimental)
gt_phsp_plot Plot marginal distributions form a phase space file

All tools are also available to be use within your own Python script with, for example:

import gatetools as gt
gt.image_convert(inputImage, pixeltype)

Tests: run

python -m unittest gatetools -v
python -m unittest gatetools.phsp -v

Classes and function documentation. Use the following command to open a browser for documentation (it is still not very convenient ; will be improved later).

pydoc -b

For developers, please have a look at the readme_dev.md file.

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