fissa.ROI module¶

The functions below were adapted from the sima package http://www.losonczylab.org/sima version 1.3.0.

License¶

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.

fissa.ROI.poly2mask(polygons, im_size)[source]¶

Converts polygons to a sparse binary mask.

>>> from fissa.ROI import poly2mask
>>> poly1 = [[0,0], [0,1], [1,1], [1,0]]
>>> poly2 = [[0,1], [0,2], [2,2], [2,1]]
>>> mask = poly2mask([poly1, poly2], (3, 3))
>>> mask[0].todense()
matrix([[ True, False, False],
        [ True,  True, False],
        [False, False, False]], dtype=bool)

Parameters:	polygons (sequence of coordinates or sequence of Polygons) – A sequence of polygons where each is either a sequence of (x,y) or (x,y,z) coordinate pairs, an Nx2 or Nx3 numpy array, or a Polygon object. im_size (tuple) – Final size of the resulting mask
Returns:	masks – A list of sparse binary masks of the points contained within the polygons, one mask per plane. Each mask is in linked list sparse matrix format.
Return type:	list of sparse matrices