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        "author": "Paul McCarthy",
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        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: zlib/libpng License",
            "Programming Language :: C",
            "Programming Language :: Cython",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 3",
            "Topic :: System :: Archiving :: Compression"
        ],
        "description": "# indexed_gzip\n\n\n[![Travis build status](https://travis-ci.org/pauldmccarthy/indexed_gzip.svg?branch=master)](https://travis-ci.org/pauldmccarthy/indexed_gzip/) [![Appveyor build status](https://ci.appveyor.com/api/projects/status/github/indexed_gzip)](https://ci.appveyor.com/project/pauldmccarthy/indexed-gzip) [![PyPi version](https://img.shields.io/pypi/v/indexed_gzip.svg)](https://pypi.python.org/pypi/indexed_gzip/) [![Anaconda version](https://anaconda.org/conda-forge/indexed_gzip/badges/version.svg)](https://anaconda.org/conda-forge/indexed_gzip/)\n\n\n *Fast random access of gzip files in Python*\n\n\n * [Overview](#overview)\n * [Installation](#installation)\n * [Usage](#usage)\n * [Using with `nibabel`](#using-with-nibabel)\n * [Index import/export](#index-import-export)\n * [Write support](#write-support)\n * [Performance](#performance)\n * [Acknowledgements](#acknowledgements)\n * [License](#license)\n\n\n## Overview\n\n\nThe `indexed_gzip` project is a Python extension which aims to provide a\ndrop-in replacement for the built-in Python `gzip.GzipFile` class, the\n`IndexedGzipFile`.\n\n\n`indexed_gzip` was written to allow fast random access of compressed\n[NIFTI](http://nifti.nimh.nih.gov/) image files (for which GZIP is the\nde-facto compression standard), but will work with any GZIP file.\n`indexed_gzip` is easy to use with `nibabel` (http://nipy.org/nibabel/).\n\n\nThe standard `gzip.GzipFile` class exposes a random access-like interface (via\nits `seek` and `read` methods), but every time you seek to a new point in the\nuncompressed data stream, the `GzipFile` instance has to start decompressing\nfrom the beginning of the file, until it reaches the requested location.\n\n\nAn `IndexedGzipFile` instance gets around this performance limitation by\nbuilding an index, which contains *seek points*, mappings between\ncorresponding locations in the compressed and uncompressed data streams. Each\nseek point is accompanied by a chunk (32KB) of uncompressed data which is used\nto initialise the decompression algorithm, allowing us to start reading from\nany seek point. If the index is built with a seek point spacing of 1MB, we\nonly have to decompress (on average) 512KB of data to read from any location\nin the file.\n\n\n## Installation\n\n\n`indexed_gzip` is available on [PyPi](https://pypi.python.org/pypi) - to\ninstall, simply type:\n```sh\npip install indexed_gzip\n```\n\n\nYou can also install `indexed_gzip` from conda-forge:\n\n```sh\nconda install -c conda-forge indexed_gzip\n```\n\nTo compile `indexed_gzip`, make sure you have [cython](http://cython.org/)\ninstalled (and `numpy` if you want to compile the tests), and then run:\n```sh\npython setup.py develop\n```\n\n\nTo run the tests, type the following; you will need `numpy` and `pytest`\ninstalled:\n```sh\npytest\n```\n\n## Usage\n\n\nYou can use the `indexed_gzip` module directly:\n\n\n```python\nimport indexed_gzip as igzip\n\n# You can create an IndexedGzipFile instance\n# by specifying a file name, or an open file\n# handle. For the latter use, the file handle\n# must be opened in read-only binary mode.\n# Write support is currently non-existent.\nmyfile = igzip.IndexedGzipFile('big_file.gz')\n\nsome_offset_into_uncompressed_data = 234195\n\n# The index will be automatically\n# built on-demand when seeking or\n# reading.\nmyfile.seek(some_offset_into_uncompressed_data)\ndata = myfile.read(1048576)\n```\n\n\n## Using with `nibabel`\n\n\nYou can use `indexed_gzip` with `nibabel`. `nibabel` >= 2.3.0 will\nautomatically use `indexed_gzip` if it is present:\n\n\n```python\nimport nibabel as nib\n\nimage = nib.load('big_image.nii.gz')\n```\n\n\nIf you are using `nibabel` 2.2.x, you need to explicitly set the `keep_file_open`\nflag:\n\n\n```python\nimport nibabel as nib\n\nimage = nib.load('big_image.nii.gz', keep_file_open='auto')\n```\n\n\nTo use `indexed_gzip` with `nibabel` 2.1.0 or older, you need to do a little\nmore work:\n\n\n```python\nimport nibabel      as nib\nimport indexed_gzip as igzip\n\n# Here we are using 4MB spacing between\n# seek points, and using a larger read\n# buffer (than the default size of 16KB).\nfobj = igzip.IndexedGzipFile(\n    filename='big_image.nii.gz',\n    spacing=4194304,\n    readbuf_size=131072)\n\n# Create a nibabel image using\n# the existing file handle.\nfmap = nib.Nifti1Image.make_file_map()\nfmap['image'].fileobj = fobj\nimage = nib.Nifti1Image.from_file_map(fmap)\n\n# Use the image ArrayProxy to access the\n# data - the index will automatically be\n# built as data is accessed.\nvol3 = image.dataobj[:, :, :, 3]\n```\n\n\n## Index import/export\n\n\nIf you have a large file, you may wish to pre-generate the index once, and\nsave it out to an index file:\n\n\n```python\nimport indexed_gzip as igzip\n\n# Load the file, pre-generate the\n# index, and save it out to disk.\nfobj = igzip.IndexedGzipFile('big_file.gz')\nfobj.build_full_index()\nfobj.export_index('big_file.gzidx')\n```\n\n\nThe next time you open the same file, you can load in the index:\n\n\n```python\nimport indexed_gip as igzip\nfobj = igzip.IndexedGzipFile('big_file.gz', index_file='big_file.gzidx')\n```\n\n\n## Write support\n\n\n`indexed_gzip` does not currently have any support for writing. Currently if you\nwish to write to a file, you will need to save the file by alternate means (e.g.\nvia `gzip` or `nibabel`), and then re-create a new `IndexedGzipFile` instance.\nFor example:\n\n\n```python\n\nimport nibabel as nib\n\n# Load the entire image into memory\nimage = nib.load('big_image.nii.gz')\ndata = image.get_data()\n\n# Make changes to the data\ndata[:, :, :, 5] *= 100\n\n# Save the image using nibabel\nnib.save(data, 'big_image.nii.gz')\n\n# Re-load the image\nimage = nib.load('big_image.nii.gz')\n```\n\n\n## Performance\n\n\nA small [test script](indexed_gzip/tests/benchmark.py) is included with\n`indexed_gzip`; this script compares the performance of the `IndexedGzipFile`\nclass with the `gzip.GzipFile` class. This script does the following:\n\n  1. Generates a test file.\n\n  2. Generates a specified number of seek locations, uniformly spaced\n     throughout the test file.\n\n  3. Randomly shuffles these locations\n\n  4. Seeks to each location, and reads a chunk of data from the file.\n\n\nThis plot shows the results of this test for a few compresed files of varying\nsizes, with 500 seeks:\n\n\n![Indexed gzip performance](./performance.png)\n\n\n## Acknowledgements\n\n\nThe `indexed_gzip` project is based upon the `zran.c` example (written by Mark\nAlder) which ships with the [zlib](http://www.zlib.net/) source code.\n\n\n`indexed_gzip` was originally inspired by Zalan Rajna's (@zrajna)\n[zindex](https://github.com/zrajna/zindex) project:\n\n    Z. Rajna, A. Keskinarkaus, V. Kiviniemi and T. Seppanen\n    \"Speeding up the file access of large compressed NIfTI neuroimaging data\"\n    Engineering in Medicine and Biology Society (EMBC), 2015 37th Annual\n    International Conference of the IEEE, Milan, 2015, pp. 654-657.\n\n    https://sourceforge.net/projects/libznzwithzindex/\n\n\nInitial work on `indexed_gzip` took place at\n[Brainhack](http://www.brainhack.org/) Paris, at the Institut Pasteur,\n24th-26th February 2016, with the support of the\n[FMRIB Centre](https://www.ndcn.ox.ac.uk/divisions/fmrib/), at the\nUniversity of Oxford, UK.\n\n\nMany thanks to the following contributors (listed chronologically):\n\n - Zalan Rajna (@zrajna): bug fixes (#2)\n - Martin Craig (@mcraig-ibme): porting `indexed_gzip` to Windows (#3)\n - Chris Markiewicz (@effigies): Option to drop file handles (#6)\n - Omer Ozarslan (@ozars): Index import/export (#8)\n\n\n## License\n\n\n`indexed_gzip` inherits the [zlib](http://www.zlib.net) license, available for\nperusal in the [LICENSE](LICENSE) file.\n\n",
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