def predict(self, src):
stride = self.options["stride"]
sharpen = self.options["sharpen"]
shrink = self.options["shrink"]
p_size = self.options["p_size"]
g_size = self.options["g_size"]
n_cell = self.options["n_cell"]
n_tree_eval = self.options["n_tree_eval"]
nms = self.options["nms"] if "nms" in self.options else False
thrs = self.model["thrs"]
fids = self.model["fids"]
cids = self.model["cids"]
edge_bnds = self.model["edge_bnds"]
edge_pts = self.model["edge_pts"]
n_seg = self.model["n_seg"]
segs = self.model["segs"]
p_rad = p_size / 2
g_rad = g_size / 2
pad = cv2.copyMakeBorder(src,
p_rad,
p_rad,
p_rad,
p_rad,
borderType=cv2.BORDER_REFLECT)
reg_ch, ss_ch = self.get_shrunk_channels(pad)
if sharpen != 0:
pad = conv_tri(pad, 1)
dst = predict_core(pad, reg_ch, ss_ch, shrink, p_size, g_size, n_cell,
stride, sharpen, n_tree_eval, thrs, fids, cids,
n_seg, segs, edge_bnds, edge_pts)
if sharpen == 0:
alpha = 2.1 * stride**2 / g_size**2 / n_tree_eval
elif sharpen == 1:
alpha = 1.8 * stride**2 / g_size**2 / n_tree_eval
else:
alpha = 1.65 * stride**2 / g_size**2 / n_tree_eval
dst = N.minimum(dst * alpha, 1.0)
dst = conv_tri(dst, 1)[g_rad:src.shape[0] + g_rad,
g_rad:src.shape[1] + g_rad]
if nms:
dy, dx = N.gradient(conv_tri(dst, 4))
_, dxx = N.gradient(dx)
dyy, dxy = N.gradient(dy)
orientation = N.arctan2(dyy * N.sign(-dxy) + 1e-5, dxx)
orientation[orientation < 0] += N.pi
dst = non_maximum_supr(dst, orientation, 1, 5, 1.02)
return dst
def predict(self, src):
stride = self.options["stride"]
sharpen = self.options["sharpen"]
shrink = self.options["shrink"]
p_size = self.options["p_size"]
g_size = self.options["g_size"]
n_cell = self.options["n_cell"]
n_tree_eval = self.options["n_tree_eval"]
nms = self.options["nms"] if "nms" in self.options else False
thrs = self.model["thrs"]
fids = self.model["fids"]
cids = self.model["cids"]
edge_bnds = self.model["edge_bnds"]
edge_pts = self.model["edge_pts"]
n_seg = self.model["n_seg"]
segs = self.model["segs"]
p_rad = p_size / 2
g_rad = g_size / 2
pad = cv2.copyMakeBorder(src, p_rad, p_rad, p_rad, p_rad,
borderType=cv2.BORDER_REFLECT)
reg_ch, ss_ch = self.get_shrunk_channels(pad)
if sharpen != 0:
pad = conv_tri(pad, 1)
dst = predict_core(pad, reg_ch, ss_ch, shrink, p_size, g_size, n_cell,
stride, sharpen, n_tree_eval, thrs, fids, cids,
n_seg, segs, edge_bnds, edge_pts)
if sharpen == 0:
alpha = 2.1 * stride ** 2 / g_size ** 2 / n_tree_eval
elif sharpen == 1:
alpha = 1.8 * stride ** 2 / g_size ** 2 / n_tree_eval
else:
alpha = 1.65 * stride ** 2 / g_size ** 2 / n_tree_eval
dst = N.minimum(dst * alpha, 1.0)
dst = conv_tri(dst, 1)[g_rad: src.shape[0] + g_rad,
g_rad: src.shape[1] + g_rad]
if nms:
dy, dx = N.gradient(conv_tri(dst, 4))
_, dxx = N.gradient(dx)
dyy, dxy = N.gradient(dy)
orientation = N.arctan2(dyy * N.sign(-dxy) + 1e-5, dxx)
orientation[orientation < 0] += N.pi
dst = non_maximum_supr(dst, orientation, 1, 5, 1.02)
return dst
def get_shrunk_channels(self, src):
shrink = self.options["shrink"]
n_orient = self.options["n_orient"]
grd_smooth_rad = self.options["grd_smooth_rad"]
grd_norm_rad = self.options["grd_norm_rad"]
luv = rgb2luv(src)
size = (luv.shape[0] / shrink, luv.shape[1] / shrink)
channels = [resize(luv, size)]
for scale in [1.0, 0.5]:
img = resize(luv, (luv.shape[0] * scale, luv.shape[1] * scale))
img = conv_tri(img, grd_smooth_rad)
magnitude, orientation = gradient(img, grd_norm_rad)
downscale = max(1, int(shrink * scale))
hist = histogram(magnitude, orientation, downscale, n_orient)
channels.append(resize(magnitude, size)[:, :, None])
channels.append(resize(hist, size))
channels = N.concatenate(channels, axis=2)
reg_smooth_rad = self.options["reg_smooth_rad"] / float(shrink)
ss_smooth_rad = self.options["ss_smooth_rad"] / float(shrink)
if reg_smooth_rad > 1.0:
reg_ch = conv_tri(channels, int(round(reg_smooth_rad)))
else:
reg_ch = conv_tri(channels, reg_smooth_rad)
if ss_smooth_rad > 1.0:
ss_ch = conv_tri(channels, int(round(ss_smooth_rad)))
else:
ss_ch = conv_tri(channels, ss_smooth_rad)
return reg_ch, ss_ch
def merge_trees(self):
"""
Accumulate trees and merge into final model
"""
n_tree = self.options["n_tree"]
g_size = self.options["g_size"]
if not os.path.exists(self.forest_dir):
os.makedirs(self.forest_dir)
forest_path = os.path.join(self.forest_dir, self.forest_name)
if os.path.exists(forest_path):
print "Found model, reusing..."
return
trees = []
for i in xrange(n_tree):
tree_file = self.tree_prefix + str(i + 1) + ".h5"
tree_path = os.path.join(self.tree_dir, tree_file)
with tables.open_file(tree_path, filters=self.comp_filt) as mfile:
tree = {"fids": mfile.get_node("/fids")[:],
"thrs": mfile.get_node("/thrs")[:],
"cids": mfile.get_node("/cids")[:],
"segs": mfile.get_node("/segs")[:]}
trees.append(tree)
max_n_node = 0
for i in xrange(n_tree):
max_n_node = max(max_n_node, trees[i]["fids"].shape[0])
# merge all fields of all trees
thrs = N.zeros((n_tree, max_n_node), dtype=N.float64)
fids = N.zeros((n_tree, max_n_node), dtype=N.int32)
cids = N.zeros((n_tree, max_n_node), dtype=N.int32)
segs = N.zeros((n_tree, max_n_node, g_size, g_size), dtype=N.int32)
for i in xrange(n_tree):
tree = trees[i]
n_node = tree["fids"].shape[0]
thrs[i, :n_node] = tree["thrs"].flatten()
fids[i, :n_node] = tree["fids"].flatten()
cids[i, :n_node] = tree["cids"].flatten()
segs[i, :n_node] = tree["segs"]
# remove very small segments (<=5 pixels)
n_seg = N.max(segs.reshape((n_tree, max_n_node, g_size ** 2)), axis=2) + 1
for i in xrange(n_tree):
for j in xrange(max_n_node):
m = n_seg[i, j]
if m <= 1:
continue
S = segs[i, j]
remove = False
for k in xrange(m):
Sk = (S == k)
if N.count_nonzero(Sk) > 5:
continue
S[Sk] = N.median(S[conv_tri(Sk.astype(N.float64), 1) > 0])
remove = True
if remove:
S = N.unique(S, return_inverse=True)[1]
segs[i, j] = S.reshape((g_size, g_size))
n_seg[i, j] = N.max(S) + 1
# store compact representations of sparse binary edge patches
n_bnd = self.options["sharpen"] + 1
edge_pts = []
edge_bnds = N.zeros((n_tree, max_n_node, n_bnd), dtype=N.int32)
for i in xrange(n_tree):
for j in xrange(max_n_node):
if cids[i, j] != 0 or n_seg[i, j] <= 1:
continue
E = gradient(segs[i, j].astype(N.float64))[0] > 0.01
E0 = 0
for k in xrange(n_bnd):
r, c = N.nonzero(E & (~ E0))
edge_pts += [r[m] * g_size + c[m] for m in xrange(len(r))]
edge_bnds[i, j, k] = len(r)
E0 = E
E = conv_tri(E.astype(N.float64), 1) > 0.01
segs = segs.reshape((-1, segs.shape[-2], segs.shape[-1]))
edge_pts = N.asarray(edge_pts, dtype=N.int32)
edge_bnds = N.hstack(([0], N.cumsum(edge_bnds.flatten()))).astype(N.int32)
with tables.open_file(forest_path, "w", filters=self.comp_filt) as mfile:
mfile.create_carray("/", "thrs", obj=thrs)
mfile.create_carray("/", "fids", obj=fids)
mfile.create_carray("/", "cids", obj=cids)
mfile.create_carray("/", "edge_bnds", obj=edge_bnds)
mfile.create_carray("/", "edge_pts", obj=edge_pts)
mfile.create_carray("/", "n_seg", obj=n_seg)
mfile.create_carray("/", "segs", obj=segs)
mfile.close()
def merge_trees(self):
"""
Accumulate trees and merge into final model
"""
n_tree = self.options["n_tree"]
g_size = self.options["g_size"]
if not os.path.exists(self.forest_dir):
os.makedirs(self.forest_dir)
forest_path = os.path.join(self.forest_dir, self.forest_name)
if os.path.exists(forest_path):
print("Found model, reusing...")
return
trees = []
for i in xrange(n_tree):
tree_file = self.tree_prefix + str(i + 1) + ".h5"
tree_path = os.path.join(self.tree_dir, tree_file)
with tables.open_file(tree_path, filters=self.comp_filt) as mfile:
tree = {"fids": mfile.get_node("/fids")[:],
"thrs": mfile.get_node("/thrs")[:],
"cids": mfile.get_node("/cids")[:],
"segs": mfile.get_node("/segs")[:]}
trees.append(tree)
max_n_node = 0
for i in xrange(n_tree):
max_n_node = max(max_n_node, trees[i]["fids"].shape[0])
# merge all fields of all trees
thrs = N.zeros((n_tree, max_n_node), dtype=N.float64)
fids = N.zeros((n_tree, max_n_node), dtype=N.int32)
cids = N.zeros((n_tree, max_n_node), dtype=N.int32)
segs = N.zeros((n_tree, max_n_node, g_size, g_size), dtype=N.int32)
for i in xrange(n_tree):
tree = trees[i]
n_node = tree["fids"].shape[0]
thrs[i, :n_node] = tree["thrs"].flatten()
fids[i, :n_node] = tree["fids"].flatten()
cids[i, :n_node] = tree["cids"].flatten()
segs[i, :n_node] = tree["segs"]
# remove very small segments (<=5 pixels)
n_seg = N.max(segs.reshape((n_tree, max_n_node, g_size ** 2)), axis=2) + 1
for i in xrange(n_tree):
for j in xrange(max_n_node):
m = n_seg[i, j]
if m <= 1:
continue
S = segs[i, j]
remove = False
for k in xrange(m):
Sk = (S == k)
if N.count_nonzero(Sk) > 5:
continue
S[Sk] = N.median(S[conv_tri(Sk.astype(N.float64), 1) > 0])
remove = True
if remove:
S = N.unique(S, return_inverse=True)[1]
segs[i, j] = S.reshape((g_size, g_size))
n_seg[i, j] = N.max(S) + 1
# store compact representations of sparse binary edge patches
n_bnd = self.options["sharpen"] + 1
edge_pts = []
edge_bnds = N.zeros((n_tree, max_n_node, n_bnd), dtype=N.int32)
for i in xrange(n_tree):
for j in xrange(max_n_node):
if cids[i, j] != 0 or n_seg[i, j] <= 1:
continue
E = gradient(segs[i, j].astype(N.float64))[0] > 0.01
E0 = 0
for k in xrange(n_bnd):
r, c = N.nonzero(E & (~ E0))
edge_pts += [r[m] * g_size + c[m] for m in xrange(len(r))]
edge_bnds[i, j, k] = len(r)
E0 = E
E = conv_tri(E.astype(N.float64), 1) > 0.01
segs = segs.reshape((-1, segs.shape[-2], segs.shape[-1]))
edge_pts = N.asarray(edge_pts, dtype=N.int32)
edge_bnds = N.hstack(([0], N.cumsum(edge_bnds.flatten()))).astype(N.int32)
with tables.open_file(forest_path, "w", filters=self.comp_filt) as mfile:
mfile.create_carray("/", "thrs", obj=thrs)
mfile.create_carray("/", "fids", obj=fids)
mfile.create_carray("/", "cids", obj=cids)
mfile.create_carray("/", "edge_bnds", obj=edge_bnds)
mfile.create_carray("/", "edge_pts", obj=edge_pts)
mfile.create_carray("/", "n_seg", obj=n_seg)
mfile.create_carray("/", "segs", obj=segs)
mfile.close()