Merge pull request #219 from scottclowe/api_ROI-to-polygons

API: Rename module ROI -> polygons

CREDITS.rst

@@ -18,7 +18,7 @@ Testing
 
 External Code
 -------------
-* `ROI.py <https://github.com/rochefort-lab/fissa/blob/master/fissa/ROI.py>`_
+* `polygons.py <https://github.com/rochefort-lab/fissa/blob/master/fissa/polygons.py>`_
   was adapted from code contained in the `SIMA <http://www.losonczylab.org/sima/>`_ package
   under the `GNU GPL v2 License <https://www.gnu.org/licenses/gpl-2.0.html>`_.
 * `NIH ImageJ ROI parsing <https://github.com/rochefort-lab/fissa/blob/master/fissa/readimagejrois.py>`_

fissa/ROI.py → fissa/polygons.py

@@ -1,11 +1,15 @@
 """
 Polygon tools.
 
+.. versionchanged:: 1.0.0
+    Module renamed from ``fissa.ROI`` to ``fissa.polygons``.
+
 The functions below were adapted from the sima package
-http://www.losonczylab.org/sima version 1.3.0.
+http://www.losonczylab.org/sima, version 1.3.0.
+https://github.com/losonczylab/sima/blob/1.3.0/sima/ROI.py
+
+**License**
 
-License
--------
 This file is Copyright (C) 2014 The Trustees of Columbia University in the
 City of New York.
 
@@ -34,7 +38,7 @@ def poly2mask(polygons, im_size):
     """
     Convert polygons to a sparse binary mask.
 
-    >>> from fissa.ROI import poly2mask
+    >>> from fissa.polygons 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))

fissa/roitools.py

@@ -16,8 +16,8 @@
 except ImportError:
     import collections as abc
 
+from .polygons import poly2mask
 from .readimagejrois import read_imagej_roi_zip
-from .ROI import poly2mask
 
 
 def get_mask_com(mask):

fissa/tests/test_ROI.py → fissa/tests/test_polygons.py

@@ -1,9 +1,8 @@
 """
-Tests for the ROI module.
+Tests for the polygons module.
 
 This test was taken from the sima package
-http://www.losonczylab.org/sima
-version 1.3.0
+http://www.losonczylab.org/sima, v1.3.0:
 https://github.com/losonczylab/sima/blob/6d2cd4f071e4/sima/tests/test_ROI.py
 
 License
@@ -34,13 +33,13 @@
 # run properly, regardless of how python is started.
 from numpy.testing import assert_equal
 
-from .. import ROI
+from .. import polygons
 
 
 def test_poly2mask():
     poly1 = [[0, 0], [0, 1], [1, 1], [1, 0]]
     poly2 = [[0, 1], [0, 2], [2, 2], [2, 1]]
-    masks = ROI.poly2mask([poly1, poly2], (3, 3))
+    masks = polygons.poly2mask([poly1, poly2], (3, 3))
     assert_equal(
         masks[0].todense(),
         np.array(