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    "info": {
        "author": "Tom Doel",
        "author_email": "t.doel@ucl.ac.uk",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Developers",
            "Intended Audience :: Healthcare Industry",
            "Intended Audience :: Information Technology",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: BSD License",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Image Recognition",
            "Topic :: Scientific/Engineering :: Information Analysis",
            "Topic :: Scientific/Engineering :: Medical Science Apps.",
            "Topic :: Scientific/Engineering :: Visualization"
        ],
        "description": "ImageSplit\n==========\n\n.. image:: https://cmiclab.cs.ucl.ac.uk/GIFT-Surg/ImageSplit/raw/master/giftsurg-icon.png\n    :height: 128px\n    :width: 128px\n    :target: https://cmiclab.cs.ucl.ac.uk/GIFT-Surg/ImageSplit\n\n\n.. image:: https://cmiclab.cs.ucl.ac.uk/GIFT-Surg/ImageSplit/badges/master/build.svg\n    :target: https://cmiclab.cs.ucl.ac.uk/GIFT-Surg/ImageSplit/commits/master\n    :alt: GitLab-CI test status\n\n.. image:: https://travis-ci.org/gift-surg/ImageSplit.svg?branch=master\n    :target: https://travis-ci.org/gift-surg/ImageSplit\n    :alt: Travis test status\n\n.. image:: https://cmiclab.cs.ucl.ac.uk/GIFT-Surg/ImageSplit/badges/master/coverage.svg\n    :target: https://cmiclab.cs.ucl.ac.uk/GIFT-Surg/ImageSplit/commits/master\n    :alt: Test coverage\n\n.. image:: https://readthedocs.org/projects/imagesplit/badge/?version=latest\n    :target: http://imagesplit.readthedocs.io/en/latest/?badge=latest\n    :alt: Documentation Status\n\nImageSplit is a utility for splitting very large image volumes into slices or multiple overlapping sub-volumes, and for recombining sub-volumes into a one or more volumes. ImageSplit can also convert the underlying data types.\n\nImageSplit is designed to prioritise low memory usage over performance, so that large volumes can be easily processed with limited memory resources.\n\nAuthor: Tom Doel\n\nImageSplit was developed as part of the `GIFT-Surg`_ project, at the `Translational Imaging Group (TIG)`_ in the `Centre for Medical Image Computing (CMIC)`_ at `University College London (UCL)`_.\n\n\nInstalling\n~~~~~~~~~~\n\n::\n\n    pip install imagesplit\n\nNotes:\n    * We recommend you use pip to install ImageSplit.\n    * Ensure you have Python 2.7 or 3.5 or later installed\n    * (especially for macOS users): we suggest you do not modify the system installation of Python 2.7. Instead install a separate version of Python for development purposes (for example, using Homebrew), or use `virtualenv` to create a python virtual environment which you can safely modify without affecting the system installation.\n    * If you have Python 2 and Python 3 insatlled, `pip2` may map to Python 2 and `pip3` may map to Python 3. This will depend on your installation\n    * If you get permission errors when using `pip`, you may be trying to modify the system Python installation. This is not recommended. Instead install a local version of Python for development, or use a virtual environment (`virtualenv`).\n\n\nExample usage\n~~~~~~~~~~~~~\n\nPlease see detailed usage below.\n\nHere is an example which splits files:\n\n::\n\n    imagesplit --input input_data/image.vge --out output_data/split_image -s c --format tiff -z --rescale -50 350 --type uchar\n\n\n\nThis command will:\n    * split the volume file with header `input_data/image.vge`\n    * into coronal slices (`-s c`)\n    * saving them in the `output_data` folder with the filenames `split_image_0000.tiff`, `split_image_0001.tiff` etc\n    * The file format is tiff (`--format tiff`)\n    * with default compression (`-z`)\n    * and data type unsigned char (`--type uchar`)\n    * The data will be normalised (rescaled) between minimum and maximum values `-50` and `350` (`--rescale -50 350`)\n\nHere is an example which combines files which are derived from files produced by a previous splitting:\n\n::\n\n    imagesplit --input input_data/split_mask.mhd --out output_data/combined_image --format mhd --descriptor output_data/split_image__info.imagesplit\n\nThis command will:\n    * Combine multiple images in the folder `input_data/split_mask_*.mhd` into a single output file output_data/combined_image.mhd\n    * The splitting of the input files is determined from the descriptor file `output_data/split_image__info.imagesplit` generated by a previous splitting command\n    * If you are recombining the files that were originally split, you don't need to specify `--input`. If however you are combining files that are not the ones that were originally split, but which are derived from those, then specify `--input` will modify the filenames in the descriptor to match the input files.\n      For example, if you split an image file into multiple subimages, and then compute a mask from each subimage, you can use the original descriptor file to assemble the masks into a combined mask volume. The descriptor is the one from the splitting, but the input filename points to the mask files to combine. The descriptor file will be loaded but the filenames modified to match the mask filenames.\n\n\nDetailed Usage\n~~~~~~~~~~~~~~\n\n::\n\n    imagesplit.py [-h] -i INPUT [-o OUT] [-l OVERLAP] [-m MAX [MAX ...]] [-x STARTINDEX] [-t TYPE] [-f FORMAT] [-r [RESCALE [RESCALE ...]]] [-z [COMPRESS]] [-s SLICE] [-a AXIS [AXIS ...]] [-d DESCRIPTOR] [--test]\n\n\n:warning: ImageSplit will overwrite existing output files. Make sure you have your images backed up before you use this utility, to prevent accidental data loss.\n\n\n\nArguments:\n\n\nInput and output filenames:\n\n    -i INPUT, --input INPUT  Name of input file, or filename prefix for a set of files. If you are combining multiple files using a descriptor, with filenames of the form `*_0001.mhd`, be sure to omit the `*_0001` from the input filename, as it will be appended automatically.\n\n    -o OUT, --out OUT        Name of output file, or filename prefix if more than one file is output\n\n    -x STARTINDEX, --startindex STARTINDEX\n                             Start index for filename suffix when loading or saving\n                             a sequence of files\n\n    -d DESCRIPTOR\n                             Specifies that the input files should be assembled using the file DESCRIPTOR as a guide. The DESCRIPTOR file (.imagesplit) is generated from a previous splitting, and stores file offsets which allow you to assemble subvolumes back into a volume.\n                             The filenames in the DESCRIPTOR file will be overridden by the specified INPUT file name.\n                             This allows you to combine files according to a template generated from a different file splitting.\n\nSpecify how to split the image:\n\n    -l OVERLAP, --overlap OVERLAP\n                             Number of voxels to overlap between output images. If\n                             not specified, output images will not overlap\n\n    -m MAX, --max MAX\n                             Maximum number of voxels in each dimension in each\n                             output file. MAX can be a scalar or vector corresponding\n                             to each image dimension. The file will be optimally\n                             split such that each file output dimension is less\n                             than or equal to this maximum.\n\n\nSpecify file format, data type, and whether data should be rescaled (normalised):\n\n    -t TYPE, --type TYPE  Output data type (default: same as input file datatype)\n\n    -f FORMAT, --format FORMAT  Output file format such as mhd, tiff (default: same as input file format)\n\n    -r RESCALE, --rescale RESCALE\n        Rescale image between the specified min and max\n        values. If no RESCALE values are specified, use the volume limits.\n\n    -z COMPRESS, --compress COMPRESS\n        Enables compression (default if -Z not specified: no compression). Valid\n        values depend on the output file format. -z with no\n        COMPRESS argument will choose a suitable compression for\n        this file format. For TIFF files, the default is Adboe\n        deflat and other valid values are those supported by PIL.\n\n\nSpecify output orientation:\n\n    -s SLICE, --slice SLICE\n        Divide image into slices along the specified axis.\n        Choose 1, 2, 3 etc to select an axis relative to the\n        current image orientation, or c, s, a to select an\n        absolute orientation.This argument cannot be used with --axis, --max or --overlap.\n\n    -a AXIS, --axis AXIS\n        Axis ordering (default 1 2 3). Specifies the global\n        axis corresponding to each dimension in the image\n        file. The first value is the global axis represented\n        by the first dimension in the file, and so on. One\n        value for each dimension, dimensions are numbered\n        1,2,3,... and a negative value means that axis is\n        flipped. This cannot be used with --slice\n\n\n\nHelp and testing:\n\n    --test      If set, no writing will be performed to the output files\n    -h, --help  Show this help message and exit\n\n\nContributing\n^^^^^^^^^^^^\n\nPlease see the `contributing guidelines`_.\n\n\nUseful links\n^^^^^^^^^^^^\n\n`Source code repository`_\n`Documentation`_\n\n\nLicensing and copyright\n-----------------------\n\nCopyright 2017-2018 University College London.\nImageSplit is released under the BSD-3 licence. Please see the `license file`_ for details.\n\n\nAcknowledgements\n----------------\n\nSupported by `Wellcome`_ and `EPSRC`_.\n\n\n.. _`Wellcome EPSRC Centre for Interventional and Surgical Sciences`: http://www.ucl.ac.uk/weiss\n.. _`source code repository`: https://cmiclab.cs.ucl.ac.uk/GIFT-Surg/ImageSplit\n.. _`Documentation`: https://imagesplit.readthedocs.io\n.. _`University College London (UCL)`: http://www.ucl.ac.uk/\n.. _`Translational Imaging Group (TIG)`: http://cmictig.cs.ucl.ac.uk/\n.. _`Centre for Medical Image Computing (CMIC)`: http://cmic.cs.ucl.ac.uk\n.. _`Wellcome`: https://wellcome.ac.uk/\n.. _`GIFT-Surg`: https://www.gift-surg.ac.uk\n.. _`EPSRC`: https://www.epsrc.ac.uk/\n.. _`contributing guidelines`: https://cmiclab.cs.ucl.ac.uk/GIFT-Surg/ImageSplit/blob/master/CONTRIBUTING.rst\n.. _`license file`: https://cmiclab.cs.ucl.ac.uk/GIFT-Surg/ImageSplit/blob/master/LICENSE\n\n\n\n\n\n\n\n\n\n\n\n\n",
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