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        "author": "Casper da Costa-Luis",
        "author_email": "casper.dcl@physics.org",
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            "Development Status :: 4 - Beta",
            "Framework :: IPython",
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            "Programming Language :: Python",
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        "description": "The following example may be launched interactively via any of the following:\n\n- |Binder|\n- `Local file <README.ipynb>`__\n- `GitHub Preview <https://github.com/casperdcl/brainweb/blob/master/README.ipynb>`__\n\n.. |Binder| image:: https://mybinder.org/badge_logo.svg\n   :target: https://mybinder.org/v2/gh/casperdcl/brainweb/master?filepath=README.ipynb\n\nBrainWeb-based multimodal models of 20 normal brains\n====================================================\n\n|PyPI| |CI| |Quality| |DOI| |LICENCE|\n\n**Download and Preprocessing for PET-MR Simulations**\n\nThis notebook will not re-download/re-process files if they already\nexist.\n\n- Output data\n\n  - ``~/.brainweb/subject_*.npz``: dtype(shape): ``float32(127, 344, 344)``\n\n- `Raw data source <http://brainweb.bic.mni.mcgill.ca/brainweb/anatomic_normal_20.html>`__\n\n  - ``~/.brainweb/subject_*.bin.gz``: dtype(shape): ``uint16(362, 434, 362)``\n\n- Install\n\n  - ``pip install brainweb``\n\n--------------\n\n- Author: Casper da Costa-Luis <casper.dcl@physics.org>\n- Date: 2017-19\n- Licence: `MPLv2.0 <https://www.mozilla.org/MPL/2.0>`__\n\n.. |PyPI| image:: https://img.shields.io/pypi/v/brainweb.svg\n   :target: https://pypi.org/project/brainweb\n.. |CI| image:: https://travis-ci.org/casperdcl/brainweb.svg?branch=master\n   :target: https://travis-ci.org/casperdcl/brainweb\n.. |Quality| image:: https://api.codacy.com/project/badge/Grade/cdad13693b0141199c31d5b44c7ab185\n   :target: https://www.codacy.com/app/casper-dcl/brainweb\n.. |DOI| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3269888.svg\n   :target: https://doi.org/10.5281/zenodo.3269888\n.. |LICENCE| image:: https://img.shields.io/pypi/l/brainweb.svg?label=licence\n   :target: https://www.mozilla.org/MPL/2.0\n\n.. code:: python\n\n    from __future__ import print_function, division\n    %matplotlib notebook\n    import brainweb\n    from brainweb import volshow\n    import numpy as np\n    from os import path\n    from tqdm.auto import tqdm\n    import logging\n    logging.basicConfig(level=logging.INFO)\n\nRaw Data\n--------\n\n.. code:: python\n\n    # download\n    files = brainweb.get_files()\n\n    # read last file\n    data = brainweb.load_file(files[-1])\n\n    # show last subject\n    print(files[-1])\n    volshow(data, cmaps=['gist_ncar']);\n\n::\n\n    ~/.brainweb/subject_54.bin.gz\n\n.. image:: https://raw.githubusercontent.com/casperdcl/brainweb/master/raw.png\n\nTransform\n---------\n\nConvert raw image data:\n\n-  Siemens Biograph mMR resolution (~2mm) & dimensions (127, 344, 344)\n-  PET/T1/T2/uMap intensities\n-  randomised structure for PET/T1/T2\n-  t (1 + g [2 G_sigma(r) - 1]), where\n\n   -  r = rand(127, 344, 344) in [0, 1),\n   -  Gaussian smoothing sigma = 1,\n   -  g = 1 for PET; 0.75 for MR, and\n   -  t = the PET or MR piecewise constant phantom\n\n.. code:: python\n\n    brainweb.seed(1337)\n\n    for f in tqdm(files, desc=\"mMR ground truths\", unit=\"subject\"):\n        vol = brainweb.get_mmr_fromfile(\n            f,\n            petNoise=1, t1Noise=0.75, t2Noise=0.75,\n            petSigma=1, t1Sigma=1, t2Sigma=1)\n\n.. code:: python\n\n    # show last subject\n    print(f)\n    volshow([vol['PET' ][:, 100:-100, 100:-100],\n             vol['uMap'][:, 100:-100, 100:-100],\n             vol['T1'  ][:, 100:-100, 100:-100],\n             vol['T2'  ][:, 100:-100, 100:-100]],\n            cmaps=['hot', 'bone', 'Greys_r', 'Greys_r'],\n            titles=[\"PET\", \"uMap\", \"T1\", \"T2\"]);\n\n::\n\n    ~/.brainweb/subject_54.bin.gz\n\n.. image:: https://raw.githubusercontent.com/casperdcl/brainweb/master/mMR.png\n\n.. code:: python\n\n    # add some lesions\n    brainweb.seed(1337)\n    im3d = brainweb.add_lesions(vol['PET'])\n    volshow(im3d[:, 100:-100, 100:-100], cmaps=['hot']);\n\n.. image:: https://raw.githubusercontent.com/casperdcl/brainweb/master/lesions.png\n\n\n",
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