def get_islands(self, props=['area', 'maxwidth', 'major_axis_length',
'minor_axis_length', 'surrounding_links'],
connectivity=2):
"""
Finds all the islands in the binary mask and computes their morphological
properties. Can be used to help "clean" masks of small islands. Must
run compute_network() first.
Parameters
----------
props : list, optional
Properties to compute for each island. Properties can be any of those
provided by rivgraph.im_utils.regionprops.
The default is ['area', 'maxwidth', 'major_axis_length', 'minor_axis_length'].
connectivity : int, optional
If 1, 4-connectivity will be used to determine connected blobs. If
2, 8-connectivity will be used. The default is 2.
Returns
-------
islands : geopandas GeoDataFrame
Contains the polygons of each island with the requested property
attributes as columns. An additional 'remove' attribute is
initialized to make thresholding easier.
"""
do_surr = False
if 'surrounding_links' in props:
props.remove('surrounding_links')
if hasattr(self, 'links') is True:
do_surr = True
else:
logger.info('Cannot compute surrounding island links without first computing the network. Skipping.')
logger.info('Getting island properties...')
islands, Iislands = mu.get_island_properties(self.Imask, self.pixlen, self.pixarea, self.crs, self.gt, props, connectivity=connectivity)
logger.info('got island properties.')
if do_surr is True:
if hasattr(self.links, 'wid_adj') is False:
self.compute_link_width_and_length()
logger.info('Computing surrounding links for each island...')
islands = mu.surrounding_link_properties(self.links, self.nodes, self.Imask, islands, Iislands, self.pixlen, self.pixarea)
logger.info('surrounding links computed.')
# Add a column to be used for thresholding
islands['remove'] = [False for i in range(len(islands))]
return islands, Iislands
def test_no_props(self, test_net):
"""Test, no island properties."""
props = []
gdf, Ilabel = mask_utils.get_island_properties(test_net.Imask,
test_net.pixlen,
test_net.pixarea,
test_net.crs,
test_net.gt, props)
# assert image mask size same as labeled image size
assert Ilabel.shape == test_net.Imask.shape
# make assertion about gdf shape
assert np.shape(gdf) == (99, 2)
def test_islandprops(self, test_net):
"""Test given island properties."""
props = ['area', 'major_axis_length', 'minor_axis_length',
'perim_len', 'convex_area']
gdf, Ilabel = mask_utils.get_island_properties(test_net.Imask,
test_net.pixlen,
test_net.pixarea,
test_net.crs,
test_net.gt,
props)
# assert image mask size same as labeled image size
assert Ilabel.shape == test_net.Imask.shape
# make assertion about gdf shape
assert np.shape(gdf) == (99, 7)