https://github.com/opengate/gatetools
Python tools and functions for Gate
https://github.com/opengate/gatetools
Last synced: 8 months ago
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Python tools and functions for Gate
- Host: GitHub
- URL: https://github.com/opengate/gatetools
- Owner: OpenGATE
- License: lgpl-3.0
- Created: 2019-02-15T14:44:35.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2025-07-09T14:47:17.000Z (12 months ago)
- Last Synced: 2025-10-21T05:50:59.280Z (8 months ago)
- Language: Python
- Homepage:
- Size: 639 KB
- Stars: 34
- Watchers: 11
- Forks: 25
- Open Issues: 8
-
Metadata Files:
- Readme: readme.md
- License: LICENSE.md
- Authors: AUTHORS
Awesome Lists containing this project
README
[](https://github.com/OpenGATE/GateTools/actions/workflows/main.yml)
[](https://pypi.org/project/gatetools/)
**Tools for [GATE](https://github.com/OpenGATE/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](readme_dev.md) file.