# pytransformix
A python3 wrapper for `transformix`, a command-line utility provided as part of the package [elastix](https://elastix.dev/index.php)
Currently runs on MacOS and Linux.
## Installation
### Step 1
**Either** `pip install` from [PyPI](https://pypi.org/project/transformix/):
pip install transformix
**or** first `git clone` the repo and then `pip install` from your clone:
cd ~/repos # Or wherever on your computer you want to download this code to
git clone https://github.com/jasper-tms/pytransformix.git
cd pytransformix
pip install .
### Step 2
Install [elastix](https://elastix.dev/download.php) by first downloading it from the [releases page](https://github.com/SuperElastix/elastix/releases). Operating system compatibility notes:
- Ubuntu 22.04: Use elastix-5.1.0 or the latest version.
- Ubuntu 20.04: Use elastix-5.0.1
- Ubuntu 18.04: Use elastix-5.0.0
- Ubuntu 16.04: Use elastix-4.9.0
- MacOS: elastix-5.0.1 worked on Big Sur, and I haven't tested other combinations. Probably safe to download the latest version.
Then extract the `.zip` or `.tar.gz` file you downloaded and put the folder somewhere on your computer. Then add that folder's `bin` subdirectory to your shell `PATH` and that folder's `lib` subdirectory to your shell `LD_LIBRARY_PATH`. For example, if you put the folder at `~/software/elastix-5.0.1-linux`, then add these three lines of text
export PATH=$HOME/software/elastix-5.0.1-linux/bin:$PATH
export LD_LIBRARY_PATH=$HOME/software/elastix-5.0.1-linux/lib${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH}
export DYLD_LIBRARY_PATH=$HOME/software/elastix-5.0.1-linux/lib${DYLD_LIBRARY_PATH+:$DYLD_LIBRARY_PATH}
to your shell config file (`~/.bashrc` for bash on Linux, `~/.bash_profile` for bash on Mac, or `~/.zshrc` for zsh on Mac). Then open up a new terminal and run `elastix`. If you see `Use "elastix --help" for information about elastix-usage.`, you're good to go. If not, feel free to [open an issue](https://github.com/jasper-tms/pytransformix/issues) and I can try to help.
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"description": "# pytransformix\n\nA python3 wrapper for `transformix`, a command-line utility provided as part of the package [elastix](https://elastix.dev/index.php)\n\nCurrently runs on MacOS and Linux.\n\n\n## Installation\n### Step 1\n**Either** `pip install` from [PyPI](https://pypi.org/project/transformix/):\n\n pip install transformix\n\n**or** first `git clone` the repo and then `pip install` from your clone:\n\n cd ~/repos # Or wherever on your computer you want to download this code to\n git clone https://github.com/jasper-tms/pytransformix.git\n cd pytransformix\n pip install .\n\n### Step 2\nInstall [elastix](https://elastix.dev/download.php) by first downloading it from the [releases page](https://github.com/SuperElastix/elastix/releases). Operating system compatibility notes:\n- Ubuntu 22.04: Use elastix-5.1.0 or the latest version.\n- Ubuntu 20.04: Use elastix-5.0.1\n- Ubuntu 18.04: Use elastix-5.0.0\n- Ubuntu 16.04: Use elastix-4.9.0\n- MacOS: elastix-5.0.1 worked on Big Sur, and I haven't tested other combinations. Probably safe to download the latest version.\n\nThen extract the `.zip` or `.tar.gz` file you downloaded and put the folder somewhere on your computer. Then add that folder's `bin` subdirectory to your shell `PATH` and that folder's `lib` subdirectory to your shell `LD_LIBRARY_PATH`. For example, if you put the folder at `~/software/elastix-5.0.1-linux`, then add these three lines of text\n\n export PATH=$HOME/software/elastix-5.0.1-linux/bin:$PATH\n export LD_LIBRARY_PATH=$HOME/software/elastix-5.0.1-linux/lib${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH}\n export DYLD_LIBRARY_PATH=$HOME/software/elastix-5.0.1-linux/lib${DYLD_LIBRARY_PATH+:$DYLD_LIBRARY_PATH}\n\nto your shell config file (`~/.bashrc` for bash on Linux, `~/.bash_profile` for bash on Mac, or `~/.zshrc` for zsh on Mac). Then open up a new terminal and run `elastix`. If you see `Use \"elastix --help\" for information about elastix-usage.`, you're good to go. If not, feel free to [open an issue](https://github.com/jasper-tms/pytransformix/issues) and I can try to help.\n\n\n",
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