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status](https://github.com/OpenGATE/GateTools/actions/workflows/main.yml/badge.svg)](https://github.com/OpenGATE/GateTools/actions/workflows/main.yml)\n[![PyPI](https://img.shields.io/pypi/v/gatetools)](https://pypi.org/project/gatetools/)\n\n**Tools for [GATE](https://github.com/OpenGATE/Gate/) simulations.**\n\nInstall with : `pip install gatetools`\n\nClone the repository with `git clone --recursive https://github.com/OpenGATE/GateTools.git`\n(or `git submodule update --init` to update)\nthen `cd GateTools`, then `pip install -e .`\n\nExample of usage:\n```\ngt_gate_info\ngt_image_convert input.dcm -o output.mhd\ngt_image_convert input.mhd -o output_float.mhd -p float\ngt_image_arithm *.mhd -o output.mhd -O sum\ngt_gamma_index dose.mhd gate-DoseToWater.mhd -o gamma.mhd --dd 2 --dta 2.5 -u \"%\" -T 0.2\n```\n\nUse the flag `-h` to get print the help of each tool. Here is the current list of command line tools.\n\n| Tool                          | Comment                                                   |\n| -------------                 | -------------                                             |\n| `gt_affine_transform`         | Resample (resize, rotate) an image                        |\n| `gt_dicom_info`               | Print tag values of a dicom file                          |\n| `gt_dicom_rt_pbs2gate`        | Convert Dicom RT proton plan for Gate                     |\n| `gt_dicom_rt_struct_to_image` | Turn Dicom RT Struct contours into mask image             |\n| `gt_dvh`                      | Create Dose Volume Histogram                              |\n| `gt_gamma_index`              | Compute gamma index between images                        |\n| `gt_gate_info`                | Display info about current Gate/G4 version                |\n| `gt_hausdorff`                | Compute Hausdorff distance                                |\n| `gt_image_arithm`             | Pixel- or voxel-wise arithmetic operations                |\n| `gt_image_convert`            | Convert image file format (**dicom**, mhd, hdr, nii ... ) |\n| `gt_image_crop`               | Crop an image                                             |\n| `gt_image_gauss`              | Blur an image using gaussian filter                       |\n| `gt_image_resize`             | Resize an image                                           |\n| `gt_image_statistics`         | Statistics of an image                                    |\n| `gt_image_to_dicom_rt_struct` | Convert mask image to Dicom RTStruct                      |\n| `gt_image_uncertainty`        | Compute statistical uncertainty                           |\n| `gt_merge_root`               | Merge root files                                          |\n| `gt_morpho_math`              | Compute morphological operation                           |\n| `gt_phsp_convert`             | Convert a phase space file from root to npy               |\n| `gt_phsp_info`                | Display information about a phase space file              |\n| `gt_phsp_merge`               | Merge two phase space files (output in npy only)          |\n| `gt_phps_peaks`               | Try to detect photopeaks (experimental)                   |\n| `gt_phsp_plot`                | Plot marginal distributions form a phase space file       |\n| `gt_write_dicom`              | Convert image (mhd, nii, ...) to dicom                    |\n| `gt_digi_mac_converter`       | Convert old digitizer macros to the new commands (Gate9.3)|\n\nAll tools are also available to be use within your own Python script with, for example:\n```\nimport gatetools as gt\ngt.image_convert(inputImage, pixeltype)\n```\n\nTests: run\n```\npython -m unittest gatetools -v\npython -m unittest gatetools.phsp -v\n```\n\nClasses and function documentation. Use the following command to open a browser for documentation (it is still not very convenient ; will be improved later).\n```\npydoc -b\n```\n\nFor developers, please have a look at the [readme_dev.md](readme_dev.md) file.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopengate%2Fgatetools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fopengate%2Fgatetools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopengate%2Fgatetools/lists"}