# slicerutil
A package containing usefull functions for working with common nodes in 3D Slicer as NumPyArrays.
## Table of Contents
- [Installation](#Installation)
- [License](#License)
- [Requirements](#Requirements)
- [Setup](#Setup)
- [Tutorial](#Description)
- [Example patients](#Examples)
- [Acknowledgements](#Acknowledgements)
## Installation
**!!!! Please install this package in a Slicer python environment through 3D Slicer's python terminal !!!!**
### Install dependencies:
* Python >= 3
* [NumPy](https://numpy.org/doc/stable/index.html)
* [Matplotlib](https://matplotlib.org)
### Install slicerutil
``` python
import pip
pip.main(['install', 'slicerutil'])
```
### Import the package
After installing the package use the following to import:
``` python
import slicerutil as su
```
or if you want to use the package in function mode (without oop):
``` python
import slicerutil.basic_functions as bf
```
## License
The following repository is under MIT license. For more information, visit [LICENSE](/LICENSE).
## Setup
### Downloading the 3D slicer application & supporting software
Please follow the steps provided bellow:
1. Visit [slicer](https://download.slicer.org) to download the application.
2. Visit [anaconda](https://www.anaconda.com/download) to download python3/ jupyter notebook.
3. Visit [Visual Studio Code](https://code.visualstudio.com/Download) to download the source-code editor (optional).
4. From the Extensions Manager widget, download the SlicerJupyter, MeshToLabelMap, PETDICOMExtension (if working with PET DICOMS), SlicerRT (if working with radiotherapy data).
- The Slicer application needs to restart to install the extensions.
### Set up the SlicerJupyter
1. Using the search widget in Slicer, open the SlicerJupyter extension by searching for JupyterKernel.
2. Click the "Start Jupyter Server" button. A JupyterLab notebook will open when the setup is complete.
3. Click the "Jupyter server in external Python environment" and copy the command to clipboard.
4. Open the anaconda prompt (Terminal if on mac) and paste the command.
5. (Optional) open an external environment (Visual Studio Code) and select the Slicer kernel!
## Acknowledgements
The slicer scripting tutorial would not be possible without the following open source software:
- [Slicer](https://github.com/Slicer/Slicer)
- [Numpy](https://github.com/numpy/numpy)
- [Matplotlib](https://github.com/matplotlib/matplotlib)
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"description": "\n\n# slicerutil\nA package containing usefull functions for working with common nodes in 3D Slicer as NumPyArrays. \n\n## Table of Contents\n- [Installation](#Installation)\n- [License](#License)\n- [Requirements](#Requirements)\n- [Setup](#Setup)\n- [Tutorial](#Description)\n- [Example patients](#Examples)\n- [Acknowledgements](#Acknowledgements)\n\n## Installation\n**!!!! Please install this package in a Slicer python environment through 3D Slicer's python terminal !!!!**\n\n### Install dependencies:\n* Python >= 3\n* [NumPy](https://numpy.org/doc/stable/index.html)\n* [Matplotlib](https://matplotlib.org)\n\n### Install slicerutil\n``` python\nimport pip\n\npip.main(['install', 'slicerutil'])\n```\n\n### Import the package\nAfter installing the package use the following to import:\n``` python\nimport slicerutil as su\n```\n\nor if you want to use the package in function mode (without oop):\n``` python\nimport slicerutil.basic_functions as bf\n```\n\n## License\nThe following repository is under MIT license. For more information, visit [LICENSE](/LICENSE).\n\n## Setup\n\n### Downloading the 3D slicer application & supporting software\n\nPlease follow the steps provided bellow:\n1. Visit [slicer](https://download.slicer.org) to download the application.\n2. Visit [anaconda](https://www.anaconda.com/download) to download python3/ jupyter notebook.\n3. Visit [Visual Studio Code](https://code.visualstudio.com/Download) to download the source-code editor (optional).\n4. From the Extensions Manager widget, download the SlicerJupyter, MeshToLabelMap, PETDICOMExtension (if working with PET DICOMS), SlicerRT (if working with radiotherapy data).\n - The Slicer application needs to restart to install the extensions.\n\n### Set up the SlicerJupyter\n1. Using the search widget in Slicer, open the SlicerJupyter extension by searching for JupyterKernel.\n\n \n2. Click the \"Start Jupyter Server\" button. A JupyterLab notebook will open when the setup is complete.\n3. Click the \"Jupyter server in external Python environment\" and copy the command to clipboard.\n4. Open the anaconda prompt (Terminal if on mac) and paste the command.\n5. (Optional) open an external environment (Visual Studio Code) and select the Slicer kernel!\n\n\n## Acknowledgements\nThe slicer scripting tutorial would not be possible without the following open source software:\n- [Slicer](https://github.com/Slicer/Slicer)\n- [Numpy](https://github.com/numpy/numpy)\n- [Matplotlib](https://github.com/matplotlib/matplotlib)\n",
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