def connect_extrema(im_pos, target, markers, visualize=False): ''' im_pos : XYZ positions of each point in image formation (n x m x 3) ''' height, width,_ = im_pos.shape centroid = np.array(target) im_pos = np.ascontiguousarray(im_pos.astype(np.int16)) cost_map = np.ascontiguousarray(np.zeros([height, width], dtype=np.uint16)) extrema = dgn.geodesic_map_MPI(cost_map, im_pos, np.array(centroid, dtype=np.int16), 1, 1) cost_map = extrema[-1] trails = [] for m in markers: trail = dgn.geodesic_trail(cost_map.copy()+(32000*(im_pos[:,:,2]==0)).astype(np.uint16), np.array(m, dtype=np.int16)) trails += [trail.copy()] if visualize: cost_map = deepcopy(cost_map) circ = circle(markers[0][0],markers[0][1], 5) circ = np.array([np.minimum(circ[0], height-1), np.minimum(circ[1], width-1)]) circ = np.array([np.maximum(circ[0], 0), np.maximum(circ[1], 0)]) cost_map[circ[0], circ[1]] = 0 for i,t in enumerate(trails[1:]): # embed() cost_map[t[:,0], t[:,1]] = 0 circ = circle(markers[i+1][0],markers[i+1][1], 5) circ = np.array([np.minimum(circ[0], height-1), np.minimum(circ[1], width-1)]) circ = np.array([np.maximum(circ[0], 0), np.maximum(circ[1], 0)]) cost_map[circ[0], circ[1]] = 0 return trails, cost_map else: return trails
def geodesic_extrema_MPI(im_pos,
centroid=None,
iterations=1,
visualize=False,
box=None):
'''
im : im_pos (NxMx3)
'''
if centroid == None:
try:
centroid = np.array(nd.center_of_mass(im_pos[:, :, 2]),
dtype=np.int16)
except:
return np.array([])
if box is not None:
im_pos = im_pos[box]
im_pos = np.ascontiguousarray(im_pos, dtype=np.int16)
if visualize:
cost_map = np.zeros([im_pos.shape[0], im_pos.shape[1]],
dtype=np.uint16)
extrema = dgn.geodesic_map_MPI(cost_map, im_pos,
np.array(centroid, dtype=np.int16),
iterations, 1)
cost_map = np.array(extrema[-1])
extrema = extrema[:-1]
extrema = np.array([x for x in extrema])
return extrema, cost_map
else:
extrema = np.array(
dgn.geodesic_extrema_MPI(im_pos, np.array(centroid,
dtype=np.int16),
iterations))
return extrema
def connect_extrema(im_pos, target, markers, visualize=False):
'''
im_pos : XYZ positions of each point in image formation (n x m x 3)
'''
height, width, _ = im_pos.shape
centroid = np.array(target)
im_pos = np.ascontiguousarray(im_pos.astype(np.int16))
cost_map = np.ascontiguousarray(np.zeros([height, width], dtype=np.uint16))
extrema = dgn.geodesic_map_MPI(cost_map, im_pos,
np.array(centroid, dtype=np.int16), 1, 1)
cost_map = extrema[-1]
trails = []
for m in markers:
trail = dgn.geodesic_trail(
cost_map.copy() + (32000 *
(im_pos[:, :, 2] == 0)).astype(np.uint16),
np.array(m, dtype=np.int16))
trails += [trail.copy()]
if visualize:
cost_map = deepcopy(cost_map)
circ = circle(markers[0][0], markers[0][1], 5)
circ = np.array(
[np.minimum(circ[0], height - 1),
np.minimum(circ[1], width - 1)])
circ = np.array([np.maximum(circ[0], 0), np.maximum(circ[1], 0)])
cost_map[circ[0], circ[1]] = 0
for i, t in enumerate(trails[1:]):
# embed()
cost_map[t[:, 0], t[:, 1]] = 0
circ = circle(markers[i + 1][0], markers[i + 1][1], 5)
circ = np.array([
np.minimum(circ[0], height - 1),
np.minimum(circ[1], width - 1)
])
circ = np.array([np.maximum(circ[0], 0), np.maximum(circ[1], 0)])
cost_map[circ[0], circ[1]] = 0
return trails, cost_map
else:
return trails
def geodesic_extrema_MPI(im_pos, centroid=None, iterations=1, visualize=False, box=None): ''' im : im_pos (NxMx3) ''' if centroid==None: try: centroid = np.array(nd.center_of_mass(im_pos[:,:,2]), dtype=np.int16) except: return np.array([]) if box is not None: im_pos = im_pos[box] im_pos = np.ascontiguousarray(im_pos, dtype=np.int16) if visualize: cost_map = np.zeros([im_pos.shape[0], im_pos.shape[1]], dtype=np.uint16) extrema = dgn.geodesic_map_MPI(cost_map, im_pos, np.array(centroid, dtype=np.int16), iterations, 1) cost_map = np.array(extrema[-1]) extrema = extrema[:-1] extrema = np.array([x for x in extrema]) return extrema, cost_map else: extrema = np.array(dgn.geodesic_extrema_MPI(im_pos, np.array(centroid, dtype=np.int16), iterations)) return extrema
