def test_potrace_minsize(self):
""" Trace line with minsize smaller and larger than box """
geoimg = self.create_image_with_box()
# check that minsize did not filter out box
lines = vectorize.potrace(geoimg[0], minsize=100, geoloc=False)
self.assertEqual(len(lines[0]), len(self.truth_coords))
# check that minsize does filter out box
lines = vectorize.potrace(geoimg[0], minsize=200)
self.assertEqual(len(lines), 0)
def test_save_shapefile(self):
""" Save shapefile """
geoimg = self.create_image_with_box()
lines = vectorize.potrace(geoimg[0])
fout = os.path.join(os.path.dirname(__file__), 'test-shapefile')
vectorize.save_shapefile(lines, fout + '.shp')
[os.remove(f) for f in glob.glob(fout + '.*')]
def test_potrace_empty_image(self):
""" Trace image that is empty """
geoimg = create_image(empty=True)
lines = vectorize.potrace(geoimg[0], geoloc=False)
self.assertEqual(len(lines), 0)
geoj = vectorize.to_geojson(lines)
self.assertEqual(len(geoj['features']), 0)
def invoke(self):
# Get inputs
img = self.get_input_data_port('image')
threshold = self.get_input_string_port('threshold')
result_dir = self.get_output_data_port('result')
os.makedirs(result_dir)
# vectorize threshdolded (ie now binary) image
all_lower = glob2.glob('%s/**/*.tif' % img)
for img_file in all_lower:
geoimg = gippy.GeoImage(img_file, True)
coastline = bfvec.potrace(geoimg[0] > float(threshold),
minsize=defaults['minsize'],
close=defaults['close'],
alphamax=defaults['smooth'])
# convert coordinates to GeoJSON
geojson = bfvec.to_geojson(coastline, source=geoimg.basename())
# write geojson output file
with open(os.path.join(result_dir, 'result.geojson'), 'w') as f:
f.write(json.dumps(geojson))
self.reason = 'Successfully traced raster'
def test_close_line_strings_real(self):
""" Close line strings """
geoimg = download_image(self.test_url)
geoimg.set_nodata(0)
lines = vectorize.potrace(geoimg[0] > 9500, close=5)
fout = os.path.splitext(os.path.join(os.path.dirname(__file__), os.path.basename(self.test_url)))[0] + '_closed.geojson'
vectorize.save_geojson(lines, fout)
print('\nPerform visual inspection on %s' % fout)
def test_potrace_box(self):
""" Trace image of box """
geoimg = self.create_image_with_box()
lines = vectorize.potrace(geoimg[0], geoloc=True)
# check returned geometry
self.assertEqual(len(lines[0]), len(self.truth_coords))
for c in lines[0]:
self.assertTrue(c in self.truth_coords)
def test_potrace_image(self):
""" Trace landsat using an arbitrary cutoff """
# get a complex test image (landsat)
geoimg = download_image(self.test_url)
geoimg.set_nodata(0)
lines = vectorize.potrace(geoimg[0] > 9500, close=0)
self.assertEqual(len(lines), 16551)
fout = os.path.splitext(os.path.join(os.path.dirname(__file__), os.path.basename(self.test_url)))[0] + '.geojson'
vectorize.save_geojson(lines, fout)
print('\nPerform visual inspection on %s' % fout)
def _test_trace_line(self):
""" Trace image of line """
geoimg = self.create_image_with_line()
geojson = vectorize.potrace(geoimg[0], geoloc=False)
# check returned geometry
coords = geojson['features'][0]['geometry']['coordinates']
self.assertEqual(len(coords), len(self.truth_coords))
for c in coords:
self.assertTrue(c in self.truth_coords)
def test_potrace_only_nodata(self):
""" Trace image that has only nodata """
geoimg = create_image(empty=True)
arr = geoimg.read()
# make a nodata region
arr[0:5, 0:5] = geoimg[0].nodata()
geoimg[0].write(arr)
lines = vectorize.potrace(geoimg[0], geoloc=False)
self.assertEqual(len(lines), 0)
geoj = vectorize.to_geojson(lines)
self.assertEqual(len(geoj['features']), 0)
def test_save_geojson(self):
""" Validate geojson returned from trace """
geoimg = create_image()
lines = vectorize.potrace(geoimg[0])
fout = os.path.join(os.path.dirname(__file__), 'test.geojson')
vectorize.save_geojson(lines, fout, source='test')
with open(fout, 'r') as f:
geojson = json.loads(f.read())
self.assertTrue('type' in geojson.keys())
self.assertEqual(geojson['type'], 'FeatureCollection')
self.assertTrue('features' in geojson.keys())
self.assertEqual(len(geojson['features']), 0)
os.remove(fout)
def test_potrace_nodata(self):
""" Trace image with nodata present """
geoimg = self.create_image_with_box()
arr = geoimg.read()
# make a nodata region
arr[0:10, 0:10] = geoimg[0].nodata()
geoimg[0].write(arr)
lines = vectorize.potrace(geoimg[0], latlon=False)
self.assertEqual(len(lines), 1)
self.assertEqual(len(lines[0]), 7)
self.assertEqual(
lines[0], [[0.65, 0.8], [0.8, 0.8], [0.8, 0.5],
[0.8, 0.19999999999999996], [0.5, 0.19999999999999996],
[0.2, 0.19999999999999996], [0.2, 0.35]])
def test_simplify(self):
""" Simplify GeoJSON geometries """
geoimg = download_image(self.test_url)
geoimg.set_nodata(0)
lines = vectorize.potrace(geoimg[0] > 9500, close=0)
fout = os.path.join(os.path.dirname(__file__), 'test.geojson')
vectorize.save_geojson(lines, fout)
# check file
df = ogr.Open(fout)
layer = df.GetLayer()
self.assertEqual(layer.GetFeatureCount(), len(lines))
geom = json.loads(layer.GetNextFeature().ExportToJson())
self.assertEqual(len(geom['geometry']['coordinates']), len(lines[0]))
df = None
# simplify and check file
vectorize.simplify(fout, tolerance=0.001)
df = ogr.Open(fout)
layer = df.GetLayer()
geom = json.loads(layer.GetNextFeature().ExportToJson())
self.assertEqual(len(geom['geometry']['coordinates']), 22)
def process(geoimg,
coastmask=defaults['coastmask'],
minsize=defaults['minsize'],
close=defaults['close'],
simple=defaults['simple'],
smooth=defaults['smooth'],
outdir='',
bname=None):
""" Process data from indir to outdir """
if bname is None:
bname = geoimg.basename()
if outdir is None:
outdir = tempfile.mkdtemp()
prefix = os.path.join(outdir, bname)
# calculate NWDI
fout = prefix + '_ndwi.tif'
logger.info('Saving NDWI to file %s' % fout,
action='Save file',
actee=fout,
actor=__name__)
imgout = alg.indices(geoimg, ['ndwi'], filename=fout)
# mask with coastline
if coastmask:
# open coastline vector
fname = os.path.join(os.path.dirname(__file__), 'coastmask.shp')
fout_coast = prefix + '_coastmask.tif'
try:
imgout = bfmask.mask_with_vector(imgout, (fname, ''),
filename=fout_coast)
except Exception as e:
if str(e) == 'No features after masking':
logger.warning(
'Image does not intersect coastal mask. Generating empty geojson file. Error: %s/'
% str(e))
geojson = {'type': 'FeatureCollection', 'features': []}
fout = prefix + '.geojson'
logger.info('Saving GeoJSON to file %s' % fout,
action='Save file',
actee=fout,
actor=__name__)
with open(fout, 'w') as f:
f.write(json.dumps(geojson))
return geojson
if str(e) == "'NoneType' object has no attribute 'ExportToJson'":
logger.warning(
'Image does not intersect coastal mask. Generating empty geojson file. Error: %s/'
% str(e))
geojson = {'type': 'FeatureCollection', 'features': []}
fout = prefix + '.geojson'
logger.info('Saving GeoJSON to file %s' % fout,
action='Save file',
actee=fout,
actor=__name__)
with open(fout, 'w') as f:
f.write(json.dumps(geojson))
return geojson
else:
logger.warning('Error encountered during masking. Error : %s' %
str(e))
raise RuntimeError(e)
# calculate optimal threshold
threshold = bfproc.otsu_threshold(imgout[0])
logger.debug("Otsu's threshold = %s" % threshold)
#import pdb; pdb.set_trace()
# save thresholded image
#if False: #logger.level <= logging.DEBUG:
fout = prefix + '_thresh.tif'
logger.debug('Saving thresholded image as %s' % fout)
logger.info('Saving threshold image to file %s' % fout,
action='Save file',
actee=fout,
actor=__name__)
imgout2 = gippy.GeoImage.create_from(imgout, filename=fout, dtype='byte')
imgout2.set_nodata(255)
#pdb.set_trace()
(imgout[0] > threshold).save(imgout2[0])
imgout = imgout2
# vectorize threshdolded (ie now binary) image
coastline = bfvec.potrace(imgout[0],
minsize=minsize,
close=close,
alphamax=smooth)
# convert coordinates to GeoJSON
geojson = bfvec.to_geojson(coastline, source=geoimg.basename())
# write geojson output file
fout = prefix + '.geojson'
logger.info('Saving GeoJSON to file %s' % fout,
action='Save file',
actee=fout,
actor=__name__)
with open(fout, 'w') as f:
f.write(json.dumps(geojson))
if simple is not None:
fout = bfvec.simplify(fout, tolerance=simple)
return geojson
def test_close_line_strings(self):
""" Close line strings """
geoimg = self.create_image_with_box()
lines = vectorize.potrace(geoimg[0], geoloc=True, close=6)
self.assertEqual(len(lines[0]), 9)
