| Name | pyclesperanto JSON |
| Version |
0.16.0
JSON |
| download |
| home_page | None |
| Summary | GPU-accelerated image processing in python using OpenCL |
| upload_time | 2024-11-21 17:38:30 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | Copyright 2024 Stéphane Rigaud, Robert Haase, Institut Pasteur Paris, Max Planck Institute for Molecular Cell Biology and Genetics Dresden, ScaDS.AI, Leipzig University Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| keywords |
image processing
gpu
opencl
scientific computing
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# py-clesperanto
[](https://anaconda.org/conda-forge/pyclesperanto)
[](https://pypi.org/project/pyclesperanto)
[](https://github.com/clEsperanto/pyclesperanto/raw/main/LICENSE)
[](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha)
[](https://github.com/clEsperanto/pyclesperanto/actions/workflows/build.yml)
[](https://codecov.io/gh/clesperanto/pyclesperanto)
[](https://python.org)
[](https://github.com/psf/black)
[](https://github.com/clEsperanto/pyclesperanto)
[](https://github.com/clEsperanto/pyclesperanto)
[](https://doi.org/10.5281/zenodo.13853800)
pyclesperanto is the python package of [clEsperanto] - a multi-language framework for GPU-accelerated image processing.
It relies on a familly of [OpenCL kernels] originated from [CLIJ].
This package is developped in python and C++ wrapped using [PyBind11], and uses the C++ [CLIc] library as a processing backend.
### Reference and examples
An in-depth API reference and package documentation can be found [here](https://clesperanto.github.io/pyclesperanto/), and several demonstration notebook on how to use the library and major functionnality are available in the [demos folder](https://github.com/clEsperanto/pyclesperanto/tree/main/demos)
## __Installation__
* Get a conda/python environment, e.g. via [__mamba-forge__](https://github.com/conda-forge/miniforge#mambaforge).
* If you never used python/conda environments before, please follow [these instructions](https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html) first.
* Create a new environment and activate it:
```
mamba create --name cle
mamba activate cle
```
* Install pyclesperanto using [__mamba / conda__](https://focalplane.biologists.com/2022/12/08/managing-scientific-python-environments-using-conda-mamba-and-friends/):
```
mamba install -c conda-forge pyclesperanto
```
__MacOS__ users may need to install the following package: `mamba install -c conda-forge ocl_icd_wrapper_apple`
__Linux__ users may need to install the following package: `mamba install -c conda-forge ocl-icd-system`
**NOTE:** It is also possible to install pyclesperanto with `pip`
## Troubleshooting: Graphics cards drivers
In case you encounter one of the following error messages:
* `"ImportError: DLL load failed while importing cl: The specified procedure could not be found"` [see also](https://github.com/clEsperanto/pyclesperanto_prototype/issues/55)
* `"clGetPlatformIDs failed: PLATFORM_NOT_FOUND_KHR"`
* `"No backend available. Please install either OpenCL or CUDA on your system."`
* `"No device available. Please install either OpenCL or CUDA on your system."`
please install recent drivers for your graphics card and/or OpenCL device. Select the right driver source depending on your hardware from this list:
* [AMD drivers](https://www.amd.com/en/support)
* [NVidia drivers](https://www.nvidia.com/download/index.aspx)
* [Intel GPU drivers](https://www.intel.com/content/www/us/en/download/726609/intel-arc-graphics-windows-dch-driver.html)
* [Microsoft Windows OpenCL support](https://www.microsoft.com/en-us/p/opencl-and-opengl-compatibility-pack/9nqpsl29bfff)
Linux user may have to install packages such as `intel-opencl-icd` or `rocm-opencl-runtime` depending on their GPU.
## __Code Example__
```python
import pyclesperanto as cle
from skimage.io import imread, imsave
# initialize GPU
device = cle.select_device()
print("Used GPU: ", device)
image = imread("https://samples.fiji.sc/blobs.png")
# push image to device memory
input_image = cle.push(image)
# process the image
inverted = cle.subtract_image_from_scalar(input_image, scalar=255)
blurred = cle.gaussian_blur(inverted, sigma_x=1, sigma_y=1)
binary = cle.threshold_otsu(blurred)
labeled = cle.connected_components_labeling(binary)
# The maxmium intensity in a label image corresponds to the number of objects
num_labels = cle.maximum_of_all_pixels(labeled)
# print out result
print("Num objects in the image: " + str(num_labels))
# read image from device memory
output_image = cle.pull(labeled)
imsave("result.tif", output_image)
```
## __Examples & Demos gallery__
<table border="0">
<tr><td>
<img src="https://github.com/clEsperanto/pyclesperanto/raw/main/demos/images/labeled_blobs.png" width="300"/>
</td><td>
[Segment + analyze blobs](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/basics/count_blobs.ipynb)
</td></tr>
<tr><td>
<img src="https://github.com/clEsperanto/pyclesperanto/raw/main/demos/images/cell_segmentation.png" width="300"/>
</td><td>
[Cell segmentation + Voronoi labeling](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/cell_segmentation.ipynb)
</td></tr>
<tr><td>
<img src="https://github.com/clEsperanto/pyclesperanto/raw/main/demos/images/image_filtering.png" width="300"/>
</td><td>
[3D image filtering](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/image_filtering.ipynb)
</td></tr>
<tr><td>
<img src="https://github.com/clEsperanto/pyclesperanto/raw/main/demos/images/find_local_maxima.png" width="300"/>
</td><td>
[Find local maxima](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/find_local_maxima.ipynb)
</td></tr>
<tr><td>
<img src="https://github.com/clEsperanto/pyclesperanto/raw/main/demos/images/tribolium3d_segmentation.png" width="300"/>
</td><td>
[3D Tribolium nuclei segmentation](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/process_tribolium.ipynb)
</td></tr>
<tr><td>
<img src="https://github.com/clEsperanto/pyclesperanto/raw/main/demos/images/explore_API.png" width="300"/>
</td><td>
[Explore application programming interface (API)](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/explore_API.ipynb)
</td></tr>
<!--
<tr><td>
<img src="https://raw.githubusercontent.com/clEsperanto/pyclesperanto/main/demos/images/multi-gpu.png" width="300"/>
</td><td>
[Multi-GPU developer_docs](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/multi_gpu_demo.ipynb)
</td></tr>
-->
</table>
More usage and example can be found as notebooks in the [demos](./user_docs) folder
# __Contributing and Feedback__
clEsperanto is developed in the open because we believe in the [open source community].
Feel free to drop feedback as [github issue] or via [image.sc forum].
Contribution are also very welcome. Please read our [community guidelines] before you start and get in touch with us so that we can help you get started.
If you liked our work, star the repository, share it with your friends, and use it to make cool stuff!
## Acknowledgements
We acknowledge support by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy (EXC2068) Cluster of Excellence Physics of Life of TU Dresden.
This project has been made possible in part by grant number 2021-237734 ([GPU-accelerating Fiji and friends using distributed CLIJ, NEUBIAS-style, EOSS4](https://chanzuckerberg.com/eoss/proposals/gpu-accelerating-fiji-and-friends-using-distributed-clij-neubias-style/)) from the Chan Zuckerberg Initiative DAF, an advised fund of the Silicon Valley Community Foundation.
[clEsperanto]: http://clesperanto.net/
[OpenCL kernels]: https://github.com/clEsperanto/clij-opencl-kernels/tree/clesperanto_kernels
[CLIJ]: http://clij.github.io/
[CLIc]: https://github.com/clEsperanto/CLIc
[community guidelines]: https://clij.github.io/clij2-docs/community_guidelines
[github issue]: https://github.com/clEsperanto/pyclesperanto/issues
[image.sc forum]: https://forum.image.sc/
[PyBind11]: https://github.com/pybind
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"author_email": "Stephane Rigaud <stephane.rigaud@pasteur.fr>, Robert Haase <robert.haase@uni-leipzig.de>",
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"description": "# py-clesperanto\n[](https://anaconda.org/conda-forge/pyclesperanto)\n[](https://pypi.org/project/pyclesperanto)\n[](https://github.com/clEsperanto/pyclesperanto/raw/main/LICENSE)\n[](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha)\n[](https://github.com/clEsperanto/pyclesperanto/actions/workflows/build.yml)\n[](https://codecov.io/gh/clesperanto/pyclesperanto)\n[](https://python.org)\n[](https://github.com/psf/black)\n[](https://github.com/clEsperanto/pyclesperanto)\n[](https://github.com/clEsperanto/pyclesperanto)\n[](https://doi.org/10.5281/zenodo.13853800)\n\n\npyclesperanto is the python package of [clEsperanto] - a multi-language framework for GPU-accelerated image processing.\nIt relies on a familly of [OpenCL kernels] originated from [CLIJ].\nThis package is developped in python and C++ wrapped using [PyBind11], and uses the C++ [CLIc] library as a processing backend.\n\n### Reference and examples\n\nAn in-depth API reference and package documentation can be found [here](https://clesperanto.github.io/pyclesperanto/), and several demonstration notebook on how to use the library and major functionnality are available in the [demos folder](https://github.com/clEsperanto/pyclesperanto/tree/main/demos)\n\n## __Installation__\n\n* Get a conda/python environment, e.g. via [__mamba-forge__](https://github.com/conda-forge/miniforge#mambaforge).\n * If you never used python/conda environments before, please follow [these instructions](https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html) first.\n* Create a new environment and activate it:\n\n```\nmamba create --name cle\nmamba activate cle\n```\n\n* Install pyclesperanto using [__mamba / conda__](https://focalplane.biologists.com/2022/12/08/managing-scientific-python-environments-using-conda-mamba-and-friends/):\n\n```\nmamba install -c conda-forge pyclesperanto\n```\n\n__MacOS__ users may need to install the following package: `mamba install -c conda-forge ocl_icd_wrapper_apple`\n__Linux__ users may need to install the following package: `mamba install -c conda-forge ocl-icd-system`\n\n**NOTE:** It is also possible to install pyclesperanto with `pip`\n\n## Troubleshooting: Graphics cards drivers\n\nIn case you encounter one of the following error messages:\n* `\"ImportError: DLL load failed while importing cl: The specified procedure could not be found\"` [see also](https://github.com/clEsperanto/pyclesperanto_prototype/issues/55)\n* `\"clGetPlatformIDs failed: PLATFORM_NOT_FOUND_KHR\"`\n* `\"No backend available. Please install either OpenCL or CUDA on your system.\"`\n* `\"No device available. Please install either OpenCL or CUDA on your system.\"`\n\nplease install recent drivers for your graphics card and/or OpenCL device. Select the right driver source depending on your hardware from this list:\n\n* [AMD drivers](https://www.amd.com/en/support)\n* [NVidia drivers](https://www.nvidia.com/download/index.aspx)\n* [Intel GPU drivers](https://www.intel.com/content/www/us/en/download/726609/intel-arc-graphics-windows-dch-driver.html)\n* [Microsoft Windows OpenCL support](https://www.microsoft.com/en-us/p/opencl-and-opengl-compatibility-pack/9nqpsl29bfff)\n\nLinux user may have to install packages such as `intel-opencl-icd` or `rocm-opencl-runtime` depending on their GPU.\n\n## __Code Example__\n\n```python\nimport pyclesperanto as cle\nfrom skimage.io import imread, imsave\n\n# initialize GPU\ndevice = cle.select_device()\nprint(\"Used GPU: \", device)\n\nimage = imread(\"https://samples.fiji.sc/blobs.png\")\n\n# push image to device memory\ninput_image = cle.push(image)\n\n# process the image\ninverted = cle.subtract_image_from_scalar(input_image, scalar=255)\nblurred = cle.gaussian_blur(inverted, sigma_x=1, sigma_y=1)\nbinary = cle.threshold_otsu(blurred)\nlabeled = cle.connected_components_labeling(binary)\n\n# The maxmium intensity in a label image corresponds to the number of objects\nnum_labels = cle.maximum_of_all_pixels(labeled)\n\n# print out result\nprint(\"Num objects in the image: \" + str(num_labels))\n\n# read image from device memory\noutput_image = cle.pull(labeled)\nimsave(\"result.tif\", output_image)\n```\n\n## __Examples & Demos gallery__\n\n<table border=\"0\">\n\n<tr><td>\n<img src=\"https://github.com/clEsperanto/pyclesperanto/raw/main/demos/images/labeled_blobs.png\" width=\"300\"/>\n</td><td>\n\n[Segment + analyze blobs](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/basics/count_blobs.ipynb)\n\n</td></tr>\n\n<tr><td>\n<img src=\"https://github.com/clEsperanto/pyclesperanto/raw/main/demos/images/cell_segmentation.png\" width=\"300\"/>\n</td><td>\n\n[Cell segmentation + Voronoi labeling](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/cell_segmentation.ipynb)\n\n</td></tr>\n\n<tr><td>\n<img src=\"https://github.com/clEsperanto/pyclesperanto/raw/main/demos/images/image_filtering.png\" width=\"300\"/>\n</td><td>\n\n[3D image filtering](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/image_filtering.ipynb)\n\n</td></tr>\n\n\n<tr><td>\n<img src=\"https://github.com/clEsperanto/pyclesperanto/raw/main/demos/images/find_local_maxima.png\" width=\"300\"/>\n</td><td>\n\n[Find local maxima](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/find_local_maxima.ipynb)\n\n</td></tr>\n\n<tr><td>\n<img src=\"https://github.com/clEsperanto/pyclesperanto/raw/main/demos/images/tribolium3d_segmentation.png\" width=\"300\"/>\n</td><td>\n\n[3D Tribolium nuclei segmentation](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/process_tribolium.ipynb)\n\n</td></tr>\n\n<tr><td>\n<img src=\"https://github.com/clEsperanto/pyclesperanto/raw/main/demos/images/explore_API.png\" width=\"300\"/>\n</td><td>\n\n[Explore application programming interface (API)](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/explore_API.ipynb)\n\n</td></tr>\n\n<!--\n<tr><td>\n\n<img src=\"https://raw.githubusercontent.com/clEsperanto/pyclesperanto/main/demos/images/multi-gpu.png\" width=\"300\"/>\n\n</td><td>\n\n[Multi-GPU developer_docs](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/multi_gpu_demo.ipynb)\n\n</td></tr>\n-->\n</table>\n\nMore usage and example can be found as notebooks in the [demos](./user_docs) folder\n\n# __Contributing and Feedback__\n\nclEsperanto is developed in the open because we believe in the [open source community].\nFeel free to drop feedback as [github issue] or via [image.sc forum].\nContribution are also very welcome. Please read our [community guidelines] before you start and get in touch with us so that we can help you get started.\nIf you liked our work, star the repository, share it with your friends, and use it to make cool stuff!\n\n## Acknowledgements\n\nWe acknowledge support by the Deutsche Forschungsgemeinschaft under Germany\u2019s Excellence Strategy (EXC2068) Cluster of Excellence Physics of Life of TU Dresden.\nThis project has been made possible in part by grant number 2021-237734 ([GPU-accelerating Fiji and friends using distributed CLIJ, NEUBIAS-style, EOSS4](https://chanzuckerberg.com/eoss/proposals/gpu-accelerating-fiji-and-friends-using-distributed-clij-neubias-style/)) from the Chan Zuckerberg Initiative DAF, an advised fund of the Silicon Valley Community Foundation.\n\n\n[clEsperanto]: http://clesperanto.net/\n[OpenCL kernels]: https://github.com/clEsperanto/clij-opencl-kernels/tree/clesperanto_kernels\n[CLIJ]: http://clij.github.io/\n[CLIc]: https://github.com/clEsperanto/CLIc\n[community guidelines]: https://clij.github.io/clij2-docs/community_guidelines\n[github issue]: https://github.com/clEsperanto/pyclesperanto/issues\n[image.sc forum]: https://forum.image.sc/\n[PyBind11]: https://github.com/pybind\n",
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"license": "Copyright 2024 St\u00e9phane Rigaud, Robert Haase, Institut Pasteur Paris, Max Planck Institute for Molecular Cell Biology and Genetics Dresden, ScaDS.AI, Leipzig University Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.",
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