def get_polygon_centline(contours,
world_coords=[],
segmentize_maxlen=8,
max_points=3000,
simplification=0.05,
smooth_sigma=5):
if not isinstance(contours, list):
contours = [contours]
results = []
for contour in contours:
try:
polygon = Polygon(contour)
# print(polygon)
centerlines = get_centerline(polygon,
segmentize_maxlen=segmentize_maxlen,
max_points=max_points,
simplification=simplification,
smooth_sigma=smooth_sigma)
# print(centerline1)
results.append(centerlines)
except Exception as e:
print("Error in get_polygon_centline():", e)
results.append(0)
continue
if len(world_coords) > 0:
# coords =
# centerlines = [np.c_[cont, np.ones((len(cont),))] for cont in contours]
results = [
shapely.affinity.affine_transform(cont, world_coords)
for cont in results
]
print(results)
return results
def main():
#-- Read the system arguments listed after the program
if len(sys.argv) == 1:
sys.exit('No input file given')
else:
input_list = sys.argv[1:]
for INPUT in input_list:
#-- read shapefile
gdf = gpd.read_file(INPUT)
out_gdf = gdf.copy()
#-- remove 'err' from ID
out_gdf['ID'][0] = gdf['ID'][0].replace('err', '')
#-- check if this is a pinning point
if gdf['Class'][0] == 'Pinning Contour':
#-- pinning point. Just get perimeter of polygon
out_gdf['Class'][0] = 'Pinning Point'
else:
#-- convert to polygon
p = Polygon(gdf['geometry'][0])
dis = p.length / 10
mx = p.length / 80
out_gdf['geometry'][0] = get_centerline(p,
segmentize_maxlen=dis,
max_points=mx)
out_gdf['Class'][0] = 'Grounding Line'
#-- save centerline to file
gl_file = INPUT.replace('_ERR', '')
out_gdf.to_file(gl_file)
def _feature_worker(feature, segmentize_maxlen, max_points, simplification,
smooth):
try:
start = time.time()
centerline = get_centerline(shape(feature["geometry"]),
segmentize_maxlen, max_points,
simplification, smooth)
except CenterlineError:
return [(dict(properties=feature["properties"]),
round(time.time() - start, 3))]
finally:
elapsed = round(time.time() - start, 3)
if centerline.geom_type == "LineString":
return [(dict(feature, geometry=mapping(centerline)), elapsed)]
elif centerline.geom_type == "MultiLineString":
return [(dict(feature, geometry=mapping(subgeom)), elapsed)
for subgeom in centerline]
return result
fig, ax = plt.subplots(1)
for poly in match:
# try:
# line = get_centerline(poly, segmentize_maxlen=0.5, max_points=8000, simplification=5, smooth_sigma=0.5)
# x, y = line.xy
# ax.plot(x, y, 'y.')
# except Exception:
# pass
try:
centerline = get_centerline(poly,
segmentize_maxlen=10,
max_points=8000,
simplification=5,
smooth_sigma=0.5)
x, y = centerline.xy
ax.plot(x, y, 'r')
patch1 = PolygonPatch(centerline.buffer(10),
fc='yellow',
ec='yellow',
alpha=0.5,
zorder=2)
ax.add_patch(patch1)
except CenterlineError:
pass
x, y = track1.xy
ax.plot(x, y, 'b')
def main():
#-- Read the system arguments listed after the program
long_options=['INPUT=','FILTER=']
optlist,arglist = getopt.getopt(sys.argv[1:],'I:F',long_options)
#-- Set default settings
INPUT = os.path.join(os.path.expanduser('~'),'GL_learning_data','geocoded_v1',\
'stitched.dir','atrous_32init_drop0.2_customLossR727.dir',\
'gl_007_180518-180524-180530-180605_021954-011058-022129-011233_T050854_T050855.tif')
FILTER = 0.
flt_str = ''
for opt, arg in optlist:
if opt in ("-I","--INPUT"):
INPUT = arg
elif opt in ("-F","--FILTER"):
if arg not in ['NONE','none','None','N','n',0]:
FILTER = float(arg)
flt_str = '_%.1fkm'%(FILTER/1000)
#-- threshold for getting contours and centerlines
eps = 0.3
#-- read file
raster = rasterio.open(INPUT,'r')
im = raster.read(1)
#-- get transformation matrix
trans = raster.transform
#-- also read the corresponding mask file
mask_file = INPUT.replace('.tif','_mask.tif')
print(mask_file)
mask_raster = rasterio.open(mask_file,'r')
mask = mask_raster.read(1)
mask_raster.close()
#-- get contours of prediction
#-- close contour ends to make polygons
im[np.nonzero(im[:,0] > eps),0] = eps
im[np.nonzero(im[:,-1] > eps),-1] = eps
im[0,np.nonzero(im[0,:] > eps)] = eps
im[-1,np.nonzero(im[-1,:] > eps)] = eps
contours = find_contours(im, eps)
#-- make contours into closed polyons to find pinning points
#-- also apply noise filter and append to noise list
x = {}
y = {}
noise = []
pols = [None]*len(contours)
pol_type = [None]*len(contours)
for n,contour in enumerate(contours):
#-- convert to coordinates
x[n],y[n] = rasterio.transform.xy(trans, contour[:,0], contour[:,1])
pols[n] = Polygon(zip(x[n],y[n]))
#-- get elements of mask the contour is on
submask = mask[np.round(contour[:, 0]).astype('int'), np.round(contour[:, 1]).astype('int')]
#-- if more than half of the elements are from test tile, count contour as test type
if np.count_nonzero(submask) > submask.size/2.:
pol_type[n] = 'Test'
else:
pol_type[n] = 'Train'
#-- loop through and apply noise filter
for n in range(len(contours)):
#-- apply filter
if (n not in ignore_list) and (len(x[n]) < 2 or LineString(zip(x[n],y[n])).length <= FILTER):
noise.append(n)
#-- loop through remaining polygons and determine which ones are
#-- pinning points based on the width and length of the bounding box
pin_list = []
box_ll = [None]*len(contours)
box_ww = [None]*len(contours)
for n in range(len(pols)):
box_ll[n] = pols[n].length
box_ww[n] = pols[n].area/box_ll[n]
if (n not in noise):
#-- if the with is larger than 1/25 of the length, it's a pinning point
if box_ww[n] > box_ll[n]/25:
pin_list.append(n)
#-- Loop through all the polygons and take any overlapping areas out
#-- of the enclosing polygon and ignore the inside polygon
ignore_list = []
for i in range(len(pols)):
for j in range(len(pols)):
if (i != j) and pols[i].contains(pols[j]):
# pols[i] = pols[i].difference(pols[j])
if (i in pin_list) and (j in pin_list):
#-- if it's a pinning point, ignore outer loop
ignore_list.append(i)
else:
#-- if not, add inner loop to ignore list
ignore_list.append(j)
#-- find overlap between ignore list nad noise list
if len(list(set(noise) & set(ignore_list))) != 0:
sys.exit('Overlap not empty: ', list(set(noise) & set(ignore_list)))
#-- initialize list of contour linestrings
er = [None]*len(contours)
cn = []
n = 0 # total center line counter
pc = 1 # pinning point counter
lc = 1 # line counter
er_type = [None]*len(er)
cn_type = []
er_class = [None]*len(er)
cn_class = []
er_lbl = [None]*len(er)
cn_lbl = []
#-- loop through polygons, get centerlines, and save
for idx,p in enumerate(pols):
er[idx] = [list(a) for a in zip(x[idx],y[idx])]
er_type[idx] = pol_type[idx]
if idx in noise:
er_class[idx] = 'Noise'
elif idx in ignore_list:
er_class[idx] = 'Ignored Contour'
else:
if idx in pin_list:
#-- pinning point. Just get perimeter of polygon
xc,yc = pols[idx].exterior.coords.xy
cn.append([list(a) for a in zip(xc,yc)])
cn_class.append('Pinning Point')
cn_type.append(pol_type[idx])
#-- set label
cn_lbl.append('pin%i'%pc)
pc += 1 #- incremenet pinning point counter
else:
dis = pols[idx].length/10
mx = pols[idx].length/80
merged_lines = get_centerline(p,segmentize_maxlen=dis,max_points=mx)
#-- save coordinates of linestring
xc,yc = merged_lines.coords.xy
cn.append([list(a) for a in zip(xc,yc)])
cn_class.append('Grounding Line')
cn_lbl.append('line%i'%lc)
cn_type.append(pol_type[idx])
er_class[idx] = 'GL Uncertainty'
#-- set label
er_lbl[idx] = 'err%i'%lc
lc += 1 #- incremenet line counter
#-- save all linestrings to file
output_dir = os.path.join(os.path.dirname(INPUT),'shapefiles.dir')
if (not os.path.isdir(output_dir)):
os.mkdir(output_dir)
filename = os.path.basename(INPUT)
#-- make separate files for centerlines and errors
# 1) GL file
gl_file = os.path.join(output_dir,filename.replace('.tif','%s.shp'%flt_str))
w = shapefile.Writer(gl_file)
w.field('ID', 'C')
w.field('Type','C')
w.field('Class','C')
#-- loop over contour centerlines
for n in range(len(cn)):
w.line([cn[n]])
w.record(cn_lbl[n], cn_type[n], cn_class[n])
w.close()
# create the .prj file
prj = open(gl_file.replace('.shp','.prj'), "w")
prj.write(raster.crs.to_wkt())
prj.close()
# 2) Err File
er_file = os.path.join(output_dir,filename.replace('.tif','%s_ERR.shp'%flt_str))
w = shapefile.Writer(er_file)
w.field('ID', 'C')
w.field('Type','C')
w.field('Class','C')
w.field('Length','C')
w.field('Width','C')
#-- loop over contours and write them
for n in range(len(er)):
w.line([er[n]])
w.record(er_lbl[n] , er_type[n], er_class[n], box_ll[n], box_ww[n])
w.close()
# create the .prj file
prj = open(er_file.replace('.shp','.prj'), "w")
prj.write(raster.crs.to_wkt())
prj.close()
#-- close input file
raster.close()
lineThickness = 1
# for line in centerline1:
# # print(list(line.coords)[0])
# coords = list(line.coords)
# start = (int(coords[0][0]), int(coords[0][1]))
# end = (int(coords[1][0]), int(coords[1][1]))
# cv2.line(t, start, end, (0, 0, 255), lineThickness)
for cont in contours:
contour = np.squeeze(cont)
polygon = Polygon(contour)
print(polygon)
centerline1 = get_centerline(polygon,
segmentize_maxlen=8,
max_points=3000,
simplification=0.05,
smooth_sigma=5)
print(centerline1)
line = centerline1
# print(list(line.coords)[0])
coords = list(line.coords)
print(len(coords), coords)
for idx, coord in enumerate(coords[:-1]):
# print(idx, )
start = (int(coords[idx][0]), int(coords[idx][1]))
end = (int(coords[idx + 1][0]), int(coords[idx + 1][1]))
cv2.line(t, start, end, (0, 0, 255), lineThickness)
cv2.imshow('closed', t)
if cv2.waitKey(0) == ord('q'):
def test_centerline(alps_shape):
cl = get_centerline(alps_shape)
assert cl.is_valid
assert cl.geom_type == "LineString"
