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        "author": "Talley Lambert",
        "author_email": "talley.lambert@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering",
            "Topic :: Scientific/Engineering :: Visualization"
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        "description": "# tifffolder\n\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n\nLazily read a subset of data from a folder of images using numpy slicing syntax.  Includes simplified but robust file pattern matching syntax and multithreaded file reading.  Note: this is not intended to promote a folder of tiffs as a useful way to store lots of information (things like hdf5/n5/klb are preferable).  But for data that begins as a folder of tiffs, tifffolder simplifies the process of parsing that folder into data along different axes (and could be used as an intermediate step in the coversion to a better format if desired).\n\n### Install with pip\n\n```bash\n$ pip install tifffolder\n```\n\n### Install with conda\n\n```bash\n$ conda install -c talley tifffolder\n```\n\n### Usage\n\n```python\n>>> from tifffolder import TiffFolder\n>>> tf = TiffFolder('/folder/of/tiffs', patterns={'t': '_stack{d4}', 'c': '_ch{d1}'})\n\n# get dataset shape and order of axes\n>>> tf.shape\n(10, 2, 65, 184, 157)  # (nt, nc, nz, ny, nx)\n>>> tf.axes\n'tczyx'\n\n# reorder data  (still experimental)\n>>> tf.axes = 'tzcxy'\n>>> tf.shape\n(10, 65, 2, 157, 184)\n\n# data is only read from disk when explicitly indexed\n# get the last 10 Z planes from every other timepoint, \n# in the first channel cropping to the middle half in Y\n>>> data = tf[::2, 0, -10:, tf.shape[-2] * 1 // 4 : tf.shape[-2] * 3 // 4 ]\n>>> data.shape\n(5, 10, 92, 157)   # (nt, nz, ny, nx)\n\n\n# Can also be used as an iterator/generator for lazily reading data\n>>> for timepoint in tf:\n>>>     do_something(timepoint)\n     \n# or just load the whole thing\n>>> alldata = tf.asarray()\n>>> alldata.shape == tf.shape\nTrue\n\n# asarray() also accepts any axis kwargs\n>>> somedata = tf.asarray(t=range(1,10), c=0)\n\n# Or just to select filenames along certain axes:\n>>> tf.select_filenames(t=range(1,10,2), c=0)\n['./test_ch0_stack0001_488nm.tif',\n './test_ch0_stack0003_488nm.tif',\n './test_ch0_stack0005_488nm.tif',\n './test_ch0_stack0007_488nm.tif',\n './test_ch0_stack0009_488nm.tif']\n```\n\n### Specifying filename patterns:\n\ntifffolder converts a simplified regex syntax into relatively robust lookahead regex that will match patterns in any order in the filename or fail elegantly.\n\nThe TiffFolder class accepts a `patterns` parameter (dict or list of two-tuples).  For each (key, value) in the `patterns` dict:\n* key = the axis name (e.g. `'x', 'y', 'z', 'c', 't', 's'`)\n* value = the simplified regex where:\n    - things in brackets `{}` will be captured\n    - things outside of brackest will be required to match, but not captured\n    - `{d}` means match any number of digits\n    - `{D}` means match any number of NON-digits\n    - `{}` means match any alphanumeric character (excluding underscore)\n    - `{d2}` means match exactly two digits (for example)\n\n\nFor example:\n\n```python\n>>> patterns = {\n    'rel': '_{d7}msec',\n    'w': '_{d3}nm',\n    't': '_stack{d4}',\n    'c': '_ch{d1}',\n    'cam': 'Cam{D1}'\n}\n>>> tf = TiffFolder('/folder/of/tiffs', patterns)\n>>> tf._parse_filename('cell1_ch0_stack0009_488nm_0034829msec.tif')\n{'rel': 34829, 'w': 488, 't': 9, 'c': 0, 'cam': None}\n\n>>> tf._parse_filename('cell1_CamA_ch2_stack0001_560nm_0034829msec.tif')\n{'rel': 34829, 'w': 560, 't': 1, 'c': 2, 'cam': 'A'}\n\n>>> tifffolder.build_regex('cam', 'Cam{}')\n'(?=.*Cam(?P<cam>[a-zA-Z0-9]+))?'\n\n>>> tifffolder.build_regex('c', '_ch{d1}')\n'(?=.*_ch(?P<c>\\\\d{1}))?'\n```\n\n\n##### todo\n* check axis reordering\n* check z planes across files",
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