gatetools

Tools for GATE simulations.

Install with : pip install gatetools

Clone the repository with git clone --recursive https://github.com/OpenGATE/GateTools.git (or git submodule update --init to update) then cd GateTools, then pip install -e .

Example of usage:

gt_gate_info
gt_image_convert input.dcm -o output.mhd
gt_image_convert input.mhd -o output_float.mhd -p float
gt_image_arithm *.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_affine_transform	Resample (resize, rotate) an image
gt_dicom_info	Print tag values of a dicom file
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_dvh	Create Dose Volume Histogram
gt_gamma_index	Compute gamma index between images
gt_gate_info	Display info about current Gate/G4 version
gt_hausdorff	Compute Hausdorff distance
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_gauss	Blur an image using gaussian filter
gt_image_resize	Resize an image
gt_image_statistics	Statistics of an image
gt_image_to_dicom_rt_struct	Convert mask image to Dicom RTStruct
gt_image_uncertainty	Compute statistical uncertainty
gt_merge_root	Merge root files
gt_morpho_math	Compute morphological operation
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
gt_write_dicom	Convert image (mhd, nii, ...) to dicom
gt_digi_mac_converter	Convert old digitizer macros to the new commands (Gate9.3)

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.