# pyDICOS
[](https://opensource.org/licenses/MIT)
[](https://github.com/Auxilia-tech/pyDICOS/actions/workflows/publish-pypi-deploy.yml)
[](https://github.com/Auxilia-tech/pyDICOS/actions/workflows/tests.yml)
[](https://codecov.io/gh/Auxilia-tech/pyDICOS)
## Motivations
This project was initiated to enable the usage of DICOS data in machine learning workflows.
PyDICOS is intended to be a simple python wrapper of Stratovan's C++ [DICOS library](https://www.stratovan.com/products/dicos-toolkit).
Note that this is **NOT** an open source implementation of the DICOS standard.
PyDICOS relies on [pybind11](https://github.com/pybind/pybind11) to wrap DICOS user-level API to python.
It depends on numpy to load data in python and can easily be installed _via_ `pip`.
PyDICOS is unrelated to [pydicom](https://github.com/pydicom/pydicom) in its implementation and contributors,
while being similar in its core spirit (enabling python data manipulations).
## Open Architecture
We firmly believe that by releasing this library, we will encourage and support the [Open Architecture framework](https://www.aci-europe.org/downloads/resources/TSA-230504-7_4.1%20Attachment%201%20OA%20for%20Airport%20Security%20Systems%202nd%20Edition%20%20FINAL.pdf). We welcome all actors of airport security to review and use this library.
## Scope
- Provide a pythonized API for the DICOS toolkit
- [x] First release : read/write functions for CT, DX and TDR, user-level API
- [x] First releases : DICOS protocol, client/server functions
- [x] Future release : more pure python functions to shave off heavy cpp signatures (`get_data`, `set_data` and `CT::generate_tdr`)
- [x] Future release : library indexed in Pypi
- [ ] Out of scope for now : Windows release
- [ ] Out of scope for now : AIT2D, AIT3D, QR
- [ ] Out of scope for now : Module and Tag level APIs
- Stay up to date with Stratovan latest releases
- Currently tested and supported DICOS version : `v3`
## Install
⚠️ pyDICOS is currently only available for linux on x86 platform.
### ✨ NEW ✨ Using Pypi index (recommended)
Using [pip](https://pip.pypa.io/en/stable/) directly from Pypi index :
```bash
pip install pydicos
```
### Building from source (dev mode)
To setup the build environment, clone the repository, create your virtual environment and install required dependencies
```bash
git clone https://github.com/Auxilia-tech/pyDICOS
cd pyDICOS
python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt
```
Install the [Stratovan toolkit](https://www.stratovan.com/products/dicos-toolkit) in the `opt` folder. If the library is already installed in another folder, skip this step and change the SDICOS path variable in `setup.sh`.
```bash
chmod +x ./sdicos_lin_ubuntu-20-{version}.run
./sdicos_lin_ubuntu-20-{version}.run --unattendedmodeui none --mode unattended --prefix /opt/stratovan/sdicos
chmod 755 -R /opt/stratovan/sdicos
```
To generate a python wheel :
```bash
chmod +x setup.sh
./setup.sh
```
The lib wheel should be produced in the `dist` folder and can be installed _via_ `pip` in any local virtual environment.
## Usage
### Concept diagram
<div align="center">
<img width="850" src="assets/DICOS.svg">
</div>
### Script usage
Refer to our [exemple files](https://github.com/Auxilia-tech/pyDICOS/tests) to explore the binded methods.
The stratovan exemple files were entirely translated in python.
Here is a quick exemple for a script that reads and rewrites a CT and DX scan, and a TDR.
```python
from pydicos import dcsread, dcswrite
ct = dcsread("SimpleCT/SimpleCT.dcs")
data = ct.get_data() # list of 3-dimentionnal numpy arrays
dcswrite(ct, "SimpleCT/SimpleCT_2.dcs")
dx = dcsread("DXFiles/SimpleDX.dcs")
data = dx.get_data() # 2-dimentionnal numpy array
dcswrite(dx, "DXFiles/SimpleDX_2.dcs")
tdr = dcsread("SimpleTDR/SimpleTDR.dcs")
data = tdr.get_data() # dictionnay of metadata
dcswrite(tdr, "SimpleTDR/SimpleTDR_2.dcs")
```
✨ NEW ✨ : refer to [our notebook](notebooks/tutorial.ipynb) tutorial for instructions and examples to change an object main attribute.
### Advanced usage
More complex operations can be addressed by using the C++ functions directly.
They can be invoked using the `pyDICOS` modules. For example, the previous
script would look like this :
```python
from pyDICOS import CT, DX, TDR, ErrorLog, Filename
ct, err, file = CT(), ErrorLog(), Filename("SimpleCT/SimpleCT.dcs")
if not ct.Read(file, err, None):
raise RuntimeError(f"Failed to read DICOS file: {file.Get()}\n{err.GetErrorLog().Get()}")
data = ... # This is very long, refer to pydicos._loaders::CTLoader.get_data for full script
if not ct.Write(Filename("SimpleCT/SimpleCT_2.dcs"), err):
raise RuntimeError(f"Failed to write DICOS file: SimpleCT/SimpleCT_2.dcs\n{err.GetErrorLog().Get()}")
dx, err, file = DX(), ErrorLog(), Filename("SimpleDX/SimpleDX.dcs")
if not dx.Read(file, err, None):
raise RuntimeError(f"Failed to read DICOS file: {file.Get()}\n{err.GetErrorLog().Get()}")
data = np.array(dx.GetXRayData().GetUnsigned16(), copy=False)
if not dx.Write(Filename("SimpleDX/SimpleDX_2.dcs"), err):
raise RuntimeError(f"Failed to write DICOS file: SimpleDX/SimpleDX_2.dcs\n{err.GetErrorLog().Get()}")
tdr, err, file = TDR(), ErrorLog(), Filename("SimpleTDR/SimpleTDR.dcs")
if not tdr.Read(file, err, None):
raise RuntimeError(f"Failed to read DICOS file: {filename}\n{err.GetErrorLog().Get()}")
data = ... # This is very long, refer to pydicos._loaders::TDRLoader.get_data for full script
if not tdr.Write(Filename("SimpleTDR/SimpleTDR_2.dcs"), err):
raise RuntimeError(f"Failed to write DICOS file: SimpleTDR/SimpleTDR_2.dcs\n{err.GetErrorLog().Get()}")
```
As you can see, `pyDICOS` is the direct translation of the C++ classes and in-place method signatures.
The objects of the `pydicos` library inherit the methods available in `pyDICOS`.
More details in [architecture](pydicos/README.md).
### Testing
The library can be tested via `pytest`
```bash
pytest tests/
```
## Contributing
As our resources are limited, we very much value your contributions, be it bug fixes, new core features, or documentation improvements.
For more information, please read our [contribution guide](CONTRIBUTING.md).
### Contributors acknowledgement
Many thanks to our main contributors :
- [Ahmad Audi](https://github.com/AAUDI) is a freelance developper specialized in C++ and python. He is available for similar work on [upwork](https://www.upwork.com/freelancers/~01a066bd29ed6d1a64). [LinkedIn](https://www.linkedin.com/in/ahmadaudi/)
- [Louis Combaldieu](https://github.com/lcombaldieu) is the cofounder and CTO of Auxilia. He specializes in deep learning and computer vision. Get in touch with him through our [contact form](https://www.auxilia-tech.com/contact) to learn more about pyDICOS and Auxilia's line of products.
## License
This software is released under the [MIT license](https://opensource.org/licenses/MIT).
### Stratovan inherited disclaimer
##############################################################################
### Stratovan Corporation Copyright and Disclaimer Notice:
###
### Copyright (c) 2014 Stratovan Corporation. All Rights Reserved.
###
### Permission to use, copy, modify, and distribute this software and its
### documentation without a signed licensing agreement, is hereby granted,
### provided that this copyright notice, this paragraph and the following two
### paragraphs appear in all copies, modifications, and distributions.
###
### IN NO EVENT SHALL STRATOVAN BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT,
### SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS,
### ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF
### STRATOVAN HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
###
### STRATOVAN SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED
### TO, THE IMPLIED WARRANTIES OF USE AND FITNESS FOR A PARTICULAR PURPOSE. THE
### SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS
### PROVIDED "AS IS". STRATOVAN HAS NO OBLIGATION TO PROVIDE MAINTENANCE,
### SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS UNLESS DIRECTED BY THE
### U.S. GOVERNMENT'S TRANSPORTATION SECURITY ADMINISTRATION (TSA).
###
##############################################################################
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"author_email": "louis.combaldieu@auxilia-tech.com",
"download_url": "https://github.com/Auxilia-tech/pydicos/",
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"description": "# pyDICOS\n\n[](https://opensource.org/licenses/MIT)\n[](https://github.com/Auxilia-tech/pyDICOS/actions/workflows/publish-pypi-deploy.yml)\n[](https://github.com/Auxilia-tech/pyDICOS/actions/workflows/tests.yml)\n[](https://codecov.io/gh/Auxilia-tech/pyDICOS)\n\n## Motivations\n\nThis project was initiated to enable the usage of DICOS data in machine learning workflows. \nPyDICOS is intended to be a simple python wrapper of Stratovan's C++ [DICOS library](https://www.stratovan.com/products/dicos-toolkit).\nNote that this is **NOT** an open source implementation of the DICOS standard.\n\nPyDICOS relies on [pybind11](https://github.com/pybind/pybind11) to wrap DICOS user-level API to python.\nIt depends on numpy to load data in python and can easily be installed _via_ `pip`.\n\nPyDICOS is unrelated to [pydicom](https://github.com/pydicom/pydicom) in its implementation and contributors, \nwhile being similar in its core spirit (enabling python data manipulations).\n\n## Open Architecture\n\nWe firmly believe that by releasing this library, we will encourage and support the [Open Architecture framework](https://www.aci-europe.org/downloads/resources/TSA-230504-7_4.1%20Attachment%201%20OA%20for%20Airport%20Security%20Systems%202nd%20Edition%20%20FINAL.pdf). We welcome all actors of airport security to review and use this library.\n\n## Scope\n\n - Provide a pythonized API for the DICOS toolkit\n - [x] First release : read/write functions for CT, DX and TDR, user-level API\n - [x] First releases : DICOS protocol, client/server functions\n - [x] Future release : more pure python functions to shave off heavy cpp signatures (`get_data`, `set_data` and `CT::generate_tdr`)\n - [x] Future release : library indexed in Pypi \n - [ ] Out of scope for now : Windows release\n - [ ] Out of scope for now : AIT2D, AIT3D, QR\n - [ ] Out of scope for now : Module and Tag level APIs\n - Stay up to date with Stratovan latest releases\n - Currently tested and supported DICOS version : `v3`\n\n## Install\n\n\u26a0\ufe0f pyDICOS is currently only available for linux on x86 platform.\n\n### \u2728 NEW \u2728 Using Pypi index (recommended)\n\nUsing [pip](https://pip.pypa.io/en/stable/) directly from Pypi index :\n```bash\npip install pydicos\n```\n\n### Building from source (dev mode)\n\nTo setup the build environment, clone the repository, create your virtual environment and install required dependencies\n\n```bash\ngit clone https://github.com/Auxilia-tech/pyDICOS\ncd pyDICOS\npython3 -m venv venv\nsource venv/bin/activate\npip install -r requirements.txt\n```\n\nInstall the [Stratovan toolkit](https://www.stratovan.com/products/dicos-toolkit) in the `opt` folder. If the library is already installed in another folder, skip this step and change the SDICOS path variable in `setup.sh`.\n```bash\nchmod +x ./sdicos_lin_ubuntu-20-{version}.run\n./sdicos_lin_ubuntu-20-{version}.run --unattendedmodeui none --mode unattended --prefix /opt/stratovan/sdicos\nchmod 755 -R /opt/stratovan/sdicos\n```\n\nTo generate a python wheel :\n\n```bash\nchmod +x setup.sh\n./setup.sh\n```\n\nThe lib wheel should be produced in the `dist` folder and can be installed _via_ `pip` in any local virtual environment.\n\n## Usage\n\n### Concept diagram\n\n<div align=\"center\">\n<img width=\"850\" src=\"assets/DICOS.svg\">\n</div>\n\n### Script usage\n\nRefer to our [exemple files](https://github.com/Auxilia-tech/pyDICOS/tests) to explore the binded methods.\nThe stratovan exemple files were entirely translated in python.\n\nHere is a quick exemple for a script that reads and rewrites a CT and DX scan, and a TDR.\n\n```python\nfrom pydicos import dcsread, dcswrite\n\nct = dcsread(\"SimpleCT/SimpleCT.dcs\")\ndata = ct.get_data() # list of 3-dimentionnal numpy arrays\ndcswrite(ct, \"SimpleCT/SimpleCT_2.dcs\")\n\ndx = dcsread(\"DXFiles/SimpleDX.dcs\")\ndata = dx.get_data() # 2-dimentionnal numpy array\ndcswrite(dx, \"DXFiles/SimpleDX_2.dcs\")\n\ntdr = dcsread(\"SimpleTDR/SimpleTDR.dcs\")\ndata = tdr.get_data() # dictionnay of metadata\ndcswrite(tdr, \"SimpleTDR/SimpleTDR_2.dcs\")\n```\n\n\u2728 NEW \u2728 : refer to [our notebook](notebooks/tutorial.ipynb) tutorial for instructions and examples to change an object main attribute.\n\n### Advanced usage\n\nMore complex operations can be addressed by using the C++ functions directly. \nThey can be invoked using the `pyDICOS` modules. For example, the previous \nscript would look like this :\n\n```python\nfrom pyDICOS import CT, DX, TDR, ErrorLog, Filename\n \nct, err, file = CT(), ErrorLog(), Filename(\"SimpleCT/SimpleCT.dcs\")\nif not ct.Read(file, err, None):\n raise RuntimeError(f\"Failed to read DICOS file: {file.Get()}\\n{err.GetErrorLog().Get()}\")\ndata = ... # This is very long, refer to pydicos._loaders::CTLoader.get_data for full script\nif not ct.Write(Filename(\"SimpleCT/SimpleCT_2.dcs\"), err):\n raise RuntimeError(f\"Failed to write DICOS file: SimpleCT/SimpleCT_2.dcs\\n{err.GetErrorLog().Get()}\")\n\ndx, err, file = DX(), ErrorLog(), Filename(\"SimpleDX/SimpleDX.dcs\")\nif not dx.Read(file, err, None):\n raise RuntimeError(f\"Failed to read DICOS file: {file.Get()}\\n{err.GetErrorLog().Get()}\")\ndata = np.array(dx.GetXRayData().GetUnsigned16(), copy=False)\nif not dx.Write(Filename(\"SimpleDX/SimpleDX_2.dcs\"), err):\n raise RuntimeError(f\"Failed to write DICOS file: SimpleDX/SimpleDX_2.dcs\\n{err.GetErrorLog().Get()}\")\n\ntdr, err, file = TDR(), ErrorLog(), Filename(\"SimpleTDR/SimpleTDR.dcs\")\nif not tdr.Read(file, err, None):\n raise RuntimeError(f\"Failed to read DICOS file: {filename}\\n{err.GetErrorLog().Get()}\")\ndata = ... # This is very long, refer to pydicos._loaders::TDRLoader.get_data for full script\nif not tdr.Write(Filename(\"SimpleTDR/SimpleTDR_2.dcs\"), err):\n raise RuntimeError(f\"Failed to write DICOS file: SimpleTDR/SimpleTDR_2.dcs\\n{err.GetErrorLog().Get()}\")\n```\nAs you can see, `pyDICOS` is the direct translation of the C++ classes and in-place method signatures. \nThe objects of the `pydicos` library inherit the methods available in `pyDICOS`. \nMore details in [architecture](pydicos/README.md).\n\n### Testing\n\nThe library can be tested via `pytest`\n```bash\npytest tests/\n```\n\n## Contributing\n\nAs our resources are limited, we very much value your contributions, be it bug fixes, new core features, or documentation improvements.\nFor more information, please read our [contribution guide](CONTRIBUTING.md).\n\n### Contributors acknowledgement\n\nMany thanks to our main contributors :\n\n - [Ahmad Audi](https://github.com/AAUDI) is a freelance developper specialized in C++ and python. He is available for similar work on [upwork](https://www.upwork.com/freelancers/~01a066bd29ed6d1a64). [LinkedIn](https://www.linkedin.com/in/ahmadaudi/)\n - [Louis Combaldieu](https://github.com/lcombaldieu) is the cofounder and CTO of Auxilia. He specializes in deep learning and computer vision. Get in touch with him through our [contact form](https://www.auxilia-tech.com/contact) to learn more about pyDICOS and Auxilia's line of products.\n\n## License\n\nThis software is released under the [MIT license](https://opensource.org/licenses/MIT).\n\n### Stratovan inherited disclaimer\n\n ##############################################################################\n ### Stratovan Corporation Copyright and Disclaimer Notice:\n ###\n ### Copyright (c) 2014 Stratovan Corporation. All Rights Reserved.\n ###\n ### Permission to use, copy, modify, and distribute this software and its\n ### documentation without a signed licensing agreement, is hereby granted,\n ### provided that this copyright notice, this paragraph and the following two\n ### paragraphs appear in all copies, modifications, and distributions.\n ###\n ### IN NO EVENT SHALL STRATOVAN BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT,\n ### SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS,\n ### ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF\n ### STRATOVAN HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n ###\n ### STRATOVAN SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED\n ### TO, THE IMPLIED WARRANTIES OF USE AND FITNESS FOR A PARTICULAR PURPOSE. THE\n ### SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS\n ### PROVIDED \"AS IS\". STRATOVAN HAS NO OBLIGATION TO PROVIDE MAINTENANCE,\n ### SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS UNLESS DIRECTED BY THE\n ### U.S. GOVERNMENT'S TRANSPORTATION SECURITY ADMINISTRATION (TSA).\n ###\n ##############################################################################\n",
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