Metadata-Version: 2.0
Name: biorad1sc-reader
Version: 0.2
Summary: Allows reading Bio-Rad *.1sc image/analysis files.
Home-page: http://github.com/itsayellow/biorad1sc_reader/
Author: Matthew A. Clapp
Author-email: itsayellow+dev@gmail.com
License: MIT
Description-Content-Type: UNKNOWN
Keywords: biorad 1sc biology scientific imaging
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Multimedia :: Graphics
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3
Requires-Dist: Pillow

================
biorad1sc_reader
================

Python Package to read, parse, convert \*.1sc files generated by Bio-Rad
Quantity One software.

Also installs ``bio1sc2tiff`` command-line executable to convert \*.1sc files
to \*.tif images.

Also installs ``bio1scmeta`` command-line executable to report all metadata
contained in each \*.1sc file to a text file.

An optional dependency: **numpy**.  If present, biorad1sc_reader will run 4x to 5x faster.

**************
Current Status
**************

* Version 0.2
* "Alpha" quality software
    * API subject to change
    * No known problems in operation.
* Installs command-line executables
    * bio1sc2tiff (type 'bio1sc2tiff --help')
    * bio1scmeta (type 'bio1scmeta --help')
* Reading Image Data OK
* Saving Image from file to new TIFF file OK
    * Reader.save_img_as_tiff()
    * Reader.save_img_as_tiff_sc()
* Reading all metadata OK
    * Reader.get_metadata()
* Reading Image Metadata from Data Block 7 OK
    * Reader.get_img_summary()
    * Current info
        * Scanner Name: <Scanner Name>
        * Number of Pixels: (<img_size_x> x <img_size_y>)
        * Image Area: (<img_size_x> mm x <img_size_y> mm)
        * Scan Memory Size: <total_img_size> Kb
        * Old file name: <old_file_name>
        * New file name: <new_file_name>
        * <File Directory>
        * New Image Acquired
        * Save As...
        * Quantity One <Quantity One Version String>
* python2 (lack of) support
    * I'm currently unwilling to support python2
    * If you'd like python2 support, it's DIY. :)

*************
Documentation
*************

* `File Specification for Bio-Rad 1sc files <https://github.com/itsayellow/biorad1sc_doc/blob/master/file_1sc_spec.md>`_

********
Examples
********

::

    # setup reader with input file
    import bio1sc_reader
    myreader = bio1sc_reader.Reader("my_biorad_file.1sc")

    # get list/dict of metadata in 1sc file
    my_img_metadata = myreader.get_metadata()

    # Different options for writing image data out as a TIFF file
    myreader.save_img_as_tif("unscaled_brightness.tif")
    myreader.save_img_as_tif("unscaled_inverted_brightness.tif", invert=True)
    myreader.save_img_as_tif_sc("scaled_brightness.tif")
    myreader.save_img_as_tif_sc("scaled_brightness_more.tif", scale=0.8)
    myreader.save_img_as_tif_sc("scaled_inverted_brightness.tif", invert=True)

************
Related Info
************
* `Bio-Rad Image Lab Software <http://www.bio-rad.com/en-cn/product/image-lab-software>`_
    * For Mac, only version 5.x supports 1sc files. (Click on the Download tab to find it.)
* `Bio-Rad Quantity One Software <http://www.bio-rad.com/en-cn/product/quantity-one-1-d-analysis-software>`_
    * Generates 1sc files from Bio-Rad instruments.
* `Bio Formats: Bio-Rad Gel 1sc file format <https://docs.openmicroscopy.org/bio-formats/5.6.0/formats/bio-rad-gel.html>`_
* `BioRadGelReader.java source <https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/BioRadGelReader.java>`_
* `Forum post: Bio-Format 1sc to jpg batch conversion <https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=2400>`_
* `reStructuredText Syntax <http://docutils.sourceforge.net/rst.html>`_


