matrixscreener 0.6.1
Python API for Leica LAS AF MatrixScreener
License: MIT

DEPRECIATED
===========

This software has been split up in smaller modules:

-  `leicacam <https://github.com/arve0/leicacam>`__: Communicate with
   Leica microscopes over CAM TCP/IP socket.
-  `leicaexperiment <https://github.com/arve0/leicaexperiment>`__: Read
   Leica LAS Matrix Screener experiments (output from scans).
-  `leicascanningtemplate <https://github.com/arve0/leicascanningtemplate>`__:
   Read Leica matrix screener scanning templates (define wells etc).
-  `leicaautomator <https://github.com/arve0/leicaautomator>`__: Attempt
   at fully automating a microscope scan.

matrixscreener
==============

This is a python module for interfacing with *Leica LAS AF/X Matrix
Screener*. It can read experiments and communicate with the microscope
over network.

The module can be used to:

-  stitch wells from an experiment exported with the *LAS AF Data
   Exporter*
-  batch compress images lossless
-  programmatically select slides/wells/fields/images given by
   attributes like

   -  slide (S)
   -  well position (U, V)
   -  field position (X, Y)
   -  z-stack position (Z)
   -  channel (C)

-  read experiment data from OME-XML

The module is developed on Mac OS X, but should work on Linux and
Windows too. If you find any bugs, please report them as an
`issue <https://github.com/arve0/matrixscreener/issues/new>`__ on
github. Pull request are also welcome.

Features
--------

-  Access experiment as a python object
-  Compress to PNGs without loosing precision, metadata or colormap
-  ImageJ stitching (Fiji is installed via
   `fijibin <https://github.com/arve0/fijibin>`__)
-  Communicate with microscope over CAM TCP/IP socket

Install
-------

::

    pip install matrixscreener

Examples
--------

**stitch experiment**

.. code:: python

    import matrixscreener
    # create short hand
    Experiment = matrixscreener.experiment.Experiment

    # path should contain AditionalData and slide--S*
    scan = Experiment('path/to/experiment')

    print(matrixscreener.imagej._bin) # Fiji installed via package fijibin
    matrixscreener.imagej._bin = '/path/to/imagej'

    # if path is omitted, experiment path is used for output files
    stitched_images = experiment.stitch('/path/to/output/files/')

**stitch specific well**

.. code:: python

    from matrixscreener import experiment

    # path should contain AditionalData and slide--S*
    stitched_images = experiment.stitch('/path/to/well')

**do stuff on all images**

.. code:: python

    from matrixscreener import experiment

    scan = experiment.Experiment('path/to/experiment--')

    for image in scan.images:
        do stuff...

**do stuff on specific wells/fields**

.. code:: python

    from matrixscreener import experiment

    # select specific parts
    selected_wells = [well for well in scan.wells if 'U00' in well]
    for well in selected_wells:
        do stuff...

    def condition(path):
        x_above = experiment.attribute(path, 'X') > 1
        x_below = experiment.attribute(path, 'X') < 5
        return x_above and x_below

    selected_fields = [field for field in scan.fields if condition(field)]
    for field in selected_fields:
        do stuff..

**subtract data**

.. code:: python

    from matrixscreener.experiment import attribute

    # get all channels
    channels = [attribute(image, 'C') for image in scan.images]
    min_ch, max_ch = min(channels), max(channels)

**communicate with microscope**

.. code:: python

    from matrixscreener.cam import CAM

    cam = CAM()   # initiate and connect, default localhost:8895

    # some commands are created as short hands
    # start matrix scan
    response = cam.start_scan()
    print(response)

    # but you could also create your own command with a list of tuples
    command = [('cmd', 'enableall'),
               ('value', 'true')]
    response = cam.send(command)
    print(response)

    # or even send it as a bytes string (note the b)
    command = b'/cmd:enableall /value:true'
    response = cam.send(command)
    print(response)

**batch lossless compress of experiment**

::

    import matrixscreener as ms

    e = ms.experiment.Experiment('/path/to/experiment')
    pngs = ms.experiment.compress(e.images)
    print(pngs)

See also `this
notebook <http://nbviewer.ipython.org/github/arve0/matrixscreener/tree/master/notebooks/compress.ipynb>`__.

Develop
-------

::

    git clone https://github.com/arve0/matrixscreener.git
    cd matrixscreener
    # hack
    ./setup.py install

Testing
-------

::

    pip install tox
    tox

**specific test, here compression test**

::

    pip install pytest numpy
    py.test -k compression tests/test_experiment.py

**specific test with extra output, jump into pdb upon error**

::

    DEBUG=matrixscreener py.test -k compression tests/test_experiment.py --pdb -s

API Reference
-------------

All commands should be documented in docstrings in `numpy
format <https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt>`__.

API reference is available
`online <http://matrixscreener.readthedocs.org>`__, can be read with
`pydoc <https://docs.python.org/3.4/library/pydoc.html>`__ or any
editor/repl that does autocomplete with docstrings.

In example:

::

    pydoc matrixscreener
    pydoc matrixscreener.cam
    pydoc matrixscreener.experiment
    pydoc matrixscreener.imagej

Release procedure
-----------------

-  Create
   `.pypirc <https://docs.python.org/3.5/distutils/packageindex.html#the-pypirc-file>`__
   if missing.

   ::

       [distutils]
       index-servers=
               pypi
               pypitest

       [pypitest]
       repository = https://testpypi.python.org/pypi
       username = username
       password = password

       [pypi]
       repository = https://pypi.python.org/pypi
       username = username
       password = password

-  Update ``changelog.md``
-  Update version in ``__init__.py``, ``setup.py`` and ``doc/conf.py``
-  Git commit and tag version
-  ``./generate-rst.sh`` (pandoc needed)
-  Stage release:
   ``python setup.py sdist bdist_wheel upload -r pypitest``
-  Release: ``python setup.py sdist bdist_wheel upload``