fissa.readimagejrois module

Based on code originally written by Luis Pedro Coelho <luis@luispedro.org>, 2012, available at https://gist.github.com/luispedro/3437255, distributed under the MIT License.

Modified

• 2014 by Jeffrey Zaremba (@jzaremba), https://github.com/losonczylab/sima
• 2015 by Scott Lowe (@scottclowe) and Sander Keemink (@swkeemink).

fissa.readimagejrois.read_imagej_roi_zip(filename)

Reads an ImageJ ROI zip set and parses each ROI individually

Parameters:filename (str) – Path to the ImageJ ROis zip file Returns:roi_list – List of the parsed ImageJ ROIs Return type:list

fissa.readimagejrois.read_roi(roi_obj)

Parses an individual ImageJ ROI

This is based on the Java implementation: http://rsbweb.nih.gov/ij/developer/source/ij/io/RoiDecoder.java.html

Parameters:

roi_obj (file object) – File object containing a single ImageJ ROI

Returns:

Returns a parsed ROI object, a dictionary with either a ‘polygons’ or a ‘mask’ field.

Return type:

dict

Raises:

• IOError – If there is an error reading the roi file object
• ValueError – If unable to parse ROI