{ "info": { "author": "", "author_email": "", "bugtrack_url": null, "classifiers": [ "License :: OSI Approved :: BSD License", "Operating System :: MacOS", "Operating System :: Microsoft :: Windows", "Operating System :: POSIX", "Operating System :: Unix", "Programming Language :: Python", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3 :: Only", "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Scientific/Engineering :: Information Analysis", "Topic :: Scientific/Engineering :: Visualization", "Topic :: Utilities" ], "description": "# ReconstructOrder\nReconstruct birefringence, slow axis, bright-field, and degree of polarization from polarization-resolved images. The core algorithm employs Stokes representation for reconstruction and background correction. The repository also provides utilities for batch analysis of multi-dimensional datasets acquired with Micro-Manager (https://micro-manager.org/) and OpenPolScope acquisition plugin (https://openpolscope.org/).\n\n## Installation\n\n### Create a new conda environment (optional, but recommended)\n>Install conda package management system by installing anaconda or miniconda (https://conda.io/). \n>Creating a conda environment dedicated to ReconstructOrder will avoid version conflicts among packages required by ReconstructOrder and packages required by other python software.\n>\n>```buildoutcfg\n>conda create -n python=3.7\n>conda activate \n>```\n\n#### All code blocks below assume you are in the above environment\n\n### Option 1: install released version via pip\n>ReconstructOrder is available on pip. Running pip install will also install dependencies.\n>From your environment created above, type:\n>```buildoutcfg\n>pip install ReconstructOrder\n>```\n\n### Option 2: install developer version via git\n>Install the git version control system git : https://git-scm.com/book/en/v2/Getting-Started-Installing-Git\n>\n>Use git to clone this repository to your current directory:\n>```buildoutcfg\n>git clone https://github.com/czbiohub/ReconstructOrder.git\n>```\n\n> * #### install dependencies\n> You have two options to install dependencies: via pip (python index package) or via docker\n>\n>> * ##### install dependencies via pip\n>> If you are running ReconstructOrder on your own machine, navigate to the cloned repository \n>> and install python library dependencies:\n>>\n>> ```buildoutcfg\n>> pip install -r requirements.txt\n>> ```\n\n>> * ##### install dependencies via docker\n>>\n>> If you are running ReconstructOrder on a compute node (e.g., fry2@czbiohub), it is recommended to run it in \na Docker container. \nDocker is the virtual environment with all the required libraries pre-installed so you can run your copy of \nReconstructOrder without recreating the environment.\nThe docker image for ReconstructOrder has been built on fry2@czbiohub. \nIf you are running ReconstructOrder on other servers, you can build the docker image after cloning the repository \nby doing : \n\n>> ```buildoutcfg\n>> docker build -t reconstruct_order:py37 -f Dockerfile.ReconstructOrder .\n>> ```\n\n>> Now, to start a docker container, do \n>> ```buildoutcfg\n>> docker run -it -v /data//:/ -v ~/ReconstructOrder:/ReconstructOrder reconstruct_order:py37 bash\n>> ```\n\n\n\n## Usage\n>To run reconstruction, you will need to create a configuration file. The configuration file is a .yml file and specifies parameters for:\n> * 'dataset'\n> * 'processing'\n> * 'plotting'\n>\n> Examples can be found https://github.com/czbiohub/ReconstructOrder under \"examples/example_configs\" folder\n> \n> See /ReconstructOrder/config/config_example.yml for an example config file with detailed explanation of parameters. \n>\n> Before running, you should modify the dataset:data_dir and dataset:processed_dir paths to point to source data path and output path, respectively. Example data is located at examples/example_data \n>\n> #### There are two ways to run reconstruction:\n>>* #### from command line\n>> If you pip installed the library, from any folder, simply type:\n>> ```buildoutcfg\n>> runReconstruction --config path-and-name-to-your-config.yml\n>> ```\n>>\n>> If you cloned the developer repo, navigate to the repo and call the script:\n>> ```buildoutcfg\n>> (C:\\ReconstructOrder\\) python runReconstruction.py --config path-and-name-to-your-config.yml\n>> ```\n>\n>>* #### from IPython\n>> If you are writing your own code and want to use the ReconstructOrder library, you can reconstruct as follows:\n>> ```buildoutcfg\n>> import ReconstructOrder.workflow as wf\n>> wf.reconstructBatch('path-and-name-to-your-config.yml')\n>> ```\n\n\n## License\nChan Zuckerberg Biohub Software License\n\nThis software license is the 2-clause BSD license plus clause a third clause\nthat prohibits redistribution and use for commercial purposes without further\npermission.\n\nCopyright \u00a9 2019. Chan Zuckerberg Biohub.\nAll rights reserved.\n\nRedistribution and use in source and binary forms, with or without\nmodification, are permitted provided that the following conditions are met:\n\n1.\tRedistributions of source code must retain the above copyright notice,\nthis list of conditions and the following disclaimer.\n\n2.\tRedistributions in binary form must reproduce the above copyright notice,\nthis list of conditions and the following disclaimer in the documentation\nand/or other materials provided with the distribution.\n\n3.\tRedistributions and use for commercial purposes are not permitted without\nthe Chan Zuckerberg Biohub's written permission. For purposes of this license,\ncommercial purposes are the incorporation of the Chan Zuckerberg Biohub's\nsoftware into anything for which you will charge fees or other compensation or\nuse of the software to perform a commercial service for a third party.\nContact ip@czbiohub.org for commercial licensing opportunities.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\nAND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\nIMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\nDISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE\nFOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL\nDAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\nSERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER\nCAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\nOR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\nOF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. \n\n\n", "description_content_type": "text/markdown", "docs_url": null, "download_url": "https://github.com/czbiohub/ReconstructOrder", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "", "keywords": "", "license": "Chan Zuckerberg Biohub Software License", "maintainer": "", "maintainer_email": "", "name": "ReconstructOrder", "package_url": "https://pypi.org/project/ReconstructOrder/", "platform": "", "project_url": "https://pypi.org/project/ReconstructOrder/", "project_urls": { "Download": "https://github.com/czbiohub/ReconstructOrder" }, "release_url": "https://pypi.org/project/ReconstructOrder/0.0.1/", "requires_dist": [ "numpy (>=1.10.0)", "opencv-python (>=3.4.2.16)", "pandas (>=0.24.2)", "pyyaml (>=3.13)", "matplotlib (>=3.0.3)", "scikit-image (>=0.15)", "scipy (>=1.2.1)" ], "requires_python": ">=3.6", "summary": "Reconstruct birefringence, slow axis, bright-field, and degree of polarization from polarization-resolved images.", "version": "0.0.1" }, "last_serial": 5214931, "releases": { "0.0.1": [ { "comment_text": "", "digests": { "md5": "fe80ec77ab29b27b2ee52da2f77d9270", "sha256": "0f8187b3df5272b96f75860dcfbe8a9c1f8432ffa7c542c11fe313cdab87d6be" }, "downloads": -1, "filename": "ReconstructOrder-0.0.1-py3-none-any.whl", "has_sig": false, "md5_digest": "fe80ec77ab29b27b2ee52da2f77d9270", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3.6", "size": 32509, "upload_time": "2019-05-02T00:15:02", "url": "https://files.pythonhosted.org/packages/bd/4a/2cfbb74bcef9d544d77b23df0431416579a3968f361b10380e1ca4336fed/ReconstructOrder-0.0.1-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "977d8ca52895d96cd4714803bcae777b", "sha256": "13c2610eeadc7c0341e128955212d17cfebeb7846cd611ab8858671c7abbdabb" }, "downloads": -1, "filename": "ReconstructOrder-0.0.1.tar.gz", "has_sig": false, "md5_digest": "977d8ca52895d96cd4714803bcae777b", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.6", "size": 29131, "upload_time": "2019-05-02T00:15:05", "url": "https://files.pythonhosted.org/packages/38/fd/759d882bca491da0a571b1707fd698b99ddca405424a55f2beeb018af69f/ReconstructOrder-0.0.1.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "fe80ec77ab29b27b2ee52da2f77d9270", "sha256": "0f8187b3df5272b96f75860dcfbe8a9c1f8432ffa7c542c11fe313cdab87d6be" }, "downloads": -1, "filename": "ReconstructOrder-0.0.1-py3-none-any.whl", "has_sig": false, "md5_digest": "fe80ec77ab29b27b2ee52da2f77d9270", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3.6", "size": 32509, "upload_time": "2019-05-02T00:15:02", "url": "https://files.pythonhosted.org/packages/bd/4a/2cfbb74bcef9d544d77b23df0431416579a3968f361b10380e1ca4336fed/ReconstructOrder-0.0.1-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "977d8ca52895d96cd4714803bcae777b", "sha256": "13c2610eeadc7c0341e128955212d17cfebeb7846cd611ab8858671c7abbdabb" }, "downloads": -1, "filename": "ReconstructOrder-0.0.1.tar.gz", "has_sig": false, "md5_digest": "977d8ca52895d96cd4714803bcae777b", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.6", "size": 29131, "upload_time": "2019-05-02T00:15:05", "url": "https://files.pythonhosted.org/packages/38/fd/759d882bca491da0a571b1707fd698b99ddca405424a55f2beeb018af69f/ReconstructOrder-0.0.1.tar.gz" } ] }