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.