Metadata-Version: 2.1
Name: biorad1sc_reader
Version: 0.7.0
Summary: Allows reading Bio-Rad *.1sc image/analysis files.
Home-page: https://github.com/itsayellow/biorad1sc_reader
Author: Matthew A. Clapp
Author-email: Matthew Clapp <itsayellow+dev@gmail.com>
License: MIT
Description: ================
        biorad1sc_reader
        ================
        
        Python Package to read, parse, convert \*.1sc files generated by Bio-Rad
        Quantity One software.
        
        Documentation at: http://biorad1sc-reader.readthedocs.io/
        
        An optional dependency: **numpy**.  If present, image operations in
        biorad1sc_reader will run 4x to 5x faster.
        
        Also installs the following command-line executables:
        
        ``bio1sc2tiff``
            converts \*.1sc files to \*.tif images. (type ``bio1sc2tiff --help``)
        ``bio1scmeta``
            reports all metadata contained in each \*.1sc file to a text file.
            (type ``bio1scmeta --help``)
        ``bio1scread``
            reports details on a \*.1sc file's internal structure.
            (type ``bio1scread --help``)
        
        **************
        Current Status
        **************
        
        * "Alpha" quality software
        
          * API subject to change
          * No known problems in operation.
        
        * 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()
          * Reader.get_metadata_compact()
        
        * Reading certain image Metadata from Data Block 7 OK
        
          * Reader.get_img_summary()
          * Includes:
        
            * 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. :)
        
        ********
        Examples
        ********
        
        .. code:: bash
        
            # setup reader with input file
            import bio1sc_reader
            myreader = bio1sc_reader.Reader("my_biorad_file.1sc")
            
            # get list/dict of all metadata in 1sc file
            my_img_metadata = myreader.get_metadata()
        
            # get a more succinct data structure of all metadata in 1sc file
            my_img_metadata = myreader.get_metadata_compact()
        
            # get a quick summary of some metadata about the image in the 1sc file
            my_img_metadata = myreader.get_img_summary()
        
            # 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)
        
        **************************
        File Format Documentation
        **************************
        
        * `File Specification for Bio-Rad 1sc files <http://biorad1sc-doc.readthedocs.io/>`_
        
        ************
        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/5.9.0/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>`_
        
Keywords: biorad,1sc,biology,scientific,imaging,image
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
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: >=3.6
Description-Content-Type: text/x-rst
