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        "author": "Arve Seljebu",
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        "description": "DEPRECIATED\n===========\n\nThis software has been split up in smaller modules:\n\n-  `leicacam <https://github.com/arve0/leicacam>`__: Communicate with\n   Leica microscopes over CAM TCP/IP socket.\n-  `leicaexperiment <https://github.com/arve0/leicaexperiment>`__: Read\n   Leica LAS Matrix Screener experiments (output from scans).\n-  `leicascanningtemplate <https://github.com/arve0/leicascanningtemplate>`__:\n   Read Leica matrix screener scanning templates (define wells etc).\n-  `leicaautomator <https://github.com/arve0/leicaautomator>`__: Attempt\n   at fully automating a microscope scan.\n\nmatrixscreener\n==============\n\nThis is a python module for interfacing with *Leica LAS AF/X Matrix\nScreener*. It can read experiments and communicate with the microscope\nover network.\n\nThe module can be used to:\n\n-  stitch wells from an experiment exported with the *LAS AF Data\n   Exporter*\n-  batch compress images lossless\n-  programmatically select slides/wells/fields/images given by\n   attributes like\n\n   -  slide (S)\n   -  well position (U, V)\n   -  field position (X, Y)\n   -  z-stack position (Z)\n   -  channel (C)\n\n-  read experiment data from OME-XML\n\nThe module is developed on Mac OS X, but should work on Linux and\nWindows too. If you find any bugs, please report them as an\n`issue <https://github.com/arve0/matrixscreener/issues/new>`__ on\ngithub. Pull request are also welcome.\n\nFeatures\n--------\n\n-  Access experiment as a python object\n-  Compress to PNGs without loosing precision, metadata or colormap\n-  ImageJ stitching (Fiji is installed via\n   `fijibin <https://github.com/arve0/fijibin>`__)\n-  Communicate with microscope over CAM TCP/IP socket\n\nInstall\n-------\n\n::\n\n    pip install matrixscreener\n\nExamples\n--------\n\n**stitch experiment**\n\n.. code:: python\n\n    import matrixscreener\n    # create short hand\n    Experiment = matrixscreener.experiment.Experiment\n\n    # path should contain AditionalData and slide--S*\n    scan = Experiment('path/to/experiment')\n\n    print(matrixscreener.imagej._bin) # Fiji installed via package fijibin\n    matrixscreener.imagej._bin = '/path/to/imagej'\n\n    # if path is omitted, experiment path is used for output files\n    stitched_images = experiment.stitch('/path/to/output/files/')\n\n**stitch specific well**\n\n.. code:: python\n\n    from matrixscreener import experiment\n\n    # path should contain AditionalData and slide--S*\n    stitched_images = experiment.stitch('/path/to/well')\n\n**do stuff on all images**\n\n.. code:: python\n\n    from matrixscreener import experiment\n\n    scan = experiment.Experiment('path/to/experiment--')\n\n    for image in scan.images:\n        do stuff...\n\n**do stuff on specific wells/fields**\n\n.. code:: python\n\n    from matrixscreener import experiment\n\n    # select specific parts\n    selected_wells = [well for well in scan.wells if 'U00' in well]\n    for well in selected_wells:\n        do stuff...\n\n    def condition(path):\n        x_above = experiment.attribute(path, 'X') > 1\n        x_below = experiment.attribute(path, 'X') < 5\n        return x_above and x_below\n\n    selected_fields = [field for field in scan.fields if condition(field)]\n    for field in selected_fields:\n        do stuff..\n\n**subtract data**\n\n.. code:: python\n\n    from matrixscreener.experiment import attribute\n\n    # get all channels\n    channels = [attribute(image, 'C') for image in scan.images]\n    min_ch, max_ch = min(channels), max(channels)\n\n**communicate with microscope**\n\n.. code:: python\n\n    from matrixscreener.cam import CAM\n\n    cam = CAM()   # initiate and connect, default localhost:8895\n\n    # some commands are created as short hands\n    # start matrix scan\n    response = cam.start_scan()\n    print(response)\n\n    # but you could also create your own command with a list of tuples\n    command = [('cmd', 'enableall'),\n               ('value', 'true')]\n    response = cam.send(command)\n    print(response)\n\n    # or even send it as a bytes string (note the b)\n    command = b'/cmd:enableall /value:true'\n    response = cam.send(command)\n    print(response)\n\n**batch lossless compress of experiment**\n\n::\n\n    import matrixscreener as ms\n\n    e = ms.experiment.Experiment('/path/to/experiment')\n    pngs = ms.experiment.compress(e.images)\n    print(pngs)\n\nSee also `this\nnotebook <http://nbviewer.ipython.org/github/arve0/matrixscreener/tree/master/notebooks/compress.ipynb>`__.\n\nDevelop\n-------\n\n::\n\n    git clone https://github.com/arve0/matrixscreener.git\n    cd matrixscreener\n    # hack\n    ./setup.py install\n\nTesting\n-------\n\n::\n\n    pip install tox\n    tox\n\n**specific test, here compression test**\n\n::\n\n    pip install pytest numpy\n    py.test -k compression tests/test_experiment.py\n\n**specific test with extra output, jump into pdb upon error**\n\n::\n\n    DEBUG=matrixscreener py.test -k compression tests/test_experiment.py --pdb -s\n\nAPI Reference\n-------------\n\nAll commands should be documented in docstrings in `numpy\nformat <https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt>`__.\n\nAPI reference is available\n`online <http://matrixscreener.readthedocs.org>`__, can be read with\n`pydoc <https://docs.python.org/3.4/library/pydoc.html>`__ or any\neditor/repl that does autocomplete with docstrings.\n\nIn example:\n\n::\n\n    pydoc matrixscreener\n    pydoc matrixscreener.cam\n    pydoc matrixscreener.experiment\n    pydoc matrixscreener.imagej\n\nRelease procedure\n-----------------\n\n-  Create\n   `.pypirc <https://docs.python.org/3.5/distutils/packageindex.html#the-pypirc-file>`__\n   if missing.\n\n   ::\n\n       [distutils]\n       index-servers=\n               pypi\n               pypitest\n\n       [pypitest]\n       repository = https://testpypi.python.org/pypi\n       username = username\n       password = password\n\n       [pypi]\n       repository = https://pypi.python.org/pypi\n       username = username\n       password = password\n\n-  Update ``changelog.md``\n-  Update version in ``__init__.py``, ``setup.py`` and ``doc/conf.py``\n-  Git commit and tag version\n-  ``./generate-rst.sh`` (pandoc needed)\n-  Stage release:\n   ``python setup.py sdist bdist_wheel upload -r pypitest``\n-  Release: ``python setup.py sdist bdist_wheel upload``",
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