def setUp(self):
# We create an artificial lf
imgs = np.zeros((50,100,150), dtype=np.uint8)
for i in range(50):
for j in range(2):
rr, cc = line(0, 10+j+i, 99, 10+j+i)
imgs[i, rr, cc] = 75
for j in range(5):
rr, cc = line(0, 12+j+i, 99, 12+j+i)
imgs[i, rr, cc] = 125
for j in range(2):
rr, cc = line(0, 17+j+i, 99, 17+j+i)
imgs[i, rr, cc] = 75
for j in range(5):
rr, cc = line(0, 20+j+2*i, 99, 20+j+2*i)
imgs[i, rr, cc] = 175
for j in range(10):
rr, cc = line(0, 35+j+2*i, 99, 35+j+2*i)
imgs[i, rr, cc] = 250
#ski.io.imsave("img_{i}.png".format(i=i), imgs[i])
# We create epis out of it
self.epis = np.zeros((100,50,150), dtype=np.uint8)
for i in range(100):
self.epis[i] = np.reshape(imgs[:,i], (50,150))
#ski.io.imsave("epi_{i}.png".format(i=i), epis[i])
self.epi = self.epis[25]
def add_rectangle(img, y0, x0, y1, x1, color="r", width=1):
"""Colors: 'r', 'g', 'b', 'w', 'k'"""
im = np.copy(img)
if im.ndim == 2:
im = gray2rgb(im)
max_val = 1
if np.max(img) > 1:
max_val = 255
channel = 3 # Bogus value when color = 'w' or 'k'
if color == "r":
channel = 0
if color == "g":
channel = 1
if color == "b":
channel = 2
for i in range(width):
yy0 = y0 + i
xx0 = x0 + i
yy1 = y1 - i
xx1 = x1 - i
rr, cc = line(yy0, xx0, yy1, xx0) # left
im = paint_line(im, rr, cc, color, channel, max_val)
rr, cc = line(yy1, xx0, yy1, xx1) # bottom
im = paint_line(im, rr, cc, color, channel, max_val)
rr, cc = line(yy1, xx1, yy0, xx1) # right
im = paint_line(im, rr, cc, color, channel, max_val)
rr, cc = line(yy0, xx1, yy0, xx0) # top
im = paint_line(im, rr, cc, color, channel, max_val)
return im
def drawBounds(img, boxes):
outimg = np.zeros((img.shape[0], img.shape[1], 3))
outimg[:,:]=[255,255,255]
outimg[~img]=[0,0,0]
for box in boxes:
if abs(box.x1-box.x2) < 10 or abs(box.y1-box.y2) < 15:
continue
rr,cc = line(box.x1, box.y1, box.x1, box.y2)
try:
outimg[cc,rr]=[255,0,0]
except IndexError:
pass
rr,cc = line(box.x1, box.y1, box.x2, box.y1)
try:
outimg[cc,rr]=[255,0,0]
except IndexError:
pass
rr,cc = line(box.x1, box.y2, box.x2, box.y2)
try:
outimg[cc,rr]=[255,0,0]
except IndexError:
pass
rr,cc = line(box.x2, box.y1, box.x2, box.y2)
try:
outimg[cc,rr]=[255,0,0]
except IndexError:
pass
return outimg
def test_skeletonize_num_neighbours():
# an empty image
image = np.zeros((300, 300))
# foreground object 1
image[10:-10, 10:100] = 1
image[-100:-10, 10:-10] = 1
image[10:-10, -100:-10] = 1
# foreground object 2
rs, cs = draw.line(250, 150, 10, 280)
for i in range(10):
image[rs + i, cs] = 1
rs, cs = draw.line(10, 150, 250, 280)
for i in range(20):
image[rs + i, cs] = 1
# foreground object 3
ir, ic = np.indices(image.shape)
circle1 = (ic - 135)**2 + (ir - 150)**2 < 30**2
circle2 = (ic - 135)**2 + (ir - 150)**2 < 20**2
image[circle1] = 1
image[circle2] = 0
result = skeletonize_3d(image)
# there should never be a 2x2 block of foreground pixels in a skeleton
mask = np.array([[1, 1],
[1, 1]], np.uint8)
blocks = ndi.correlate(result, mask, mode='constant')
assert_(not np.any(blocks == 4))
def houghLines(img):
w,h = img.shape
acc=[]
for i in range(h):
rr,cc = line(0, i, w-1, h-i-1)
acc.append(np.sum(img[rr, cc]))
#print acc[i]
mi = np.argmax(acc)
ret = np.zeros(img.shape, dtype=np.bool)
rr,cc = line(0, mi, w-1, h-mi-1)
ret[rr,cc]=True
return ret
def display_triangle(im, tr, col):
rows, cols = im.shape
rr, cc = line(*map(int, tr[0]), *map(int, tr[1]))
ind = logical_and.reduce((rr >= 0, rr < rows, cc >= 0, cc < cols))
rr, cc = rr[ind], cc[ind]
im[rr, cc] = col
rr, cc = line(*map(int, tr[1]), *map(int, tr[2]))
ind = logical_and.reduce((rr >= 0, rr < rows, cc >= 0, cc < cols))
rr, cc = rr[ind], cc[ind]
im[rr, cc] = col
rr, cc = line(*map(int, tr[2]), *map(int, tr[0]))
ind = logical_and.reduce((rr >= 0, rr < rows, cc >= 0, cc < cols))
rr, cc = rr[ind], cc[ind]
im[rr, cc] = col
def draw_hough_line(image, dist, theta, color=0):
"""
Draws a line described by the hough transform to an image
:param image: Image to draw on
:param dist: Hough transform distance
:param theta: Hough transform angle
:param color: intensity to draw line
"""
rows, cols = image.shape
if abs(theta) < pi/4:
# Find the x (col) intercepts
x0 = int_(dist/cos(theta))
x1 = int_(x0 - rows * sin(theta))
intercepts = (0, x0, rows, x1)
else:
# Find the y (row) intercepts
y0 = int_(dist/sin(theta))
y1 = int_(y0 + cols * cos(theta))
intercepts = (y0, 0, y1, cols)
r, c = line(*intercepts)
# Check to make sure each point stays in the image bounds and draw it
for n in range(r.size):
if r[n] >= 0 and c[n] >= 0:
if r[n] < rows and c[n] < cols:
image[r[n], c[n]] = color
def display_edges(image, g, threshold):
"""Draw edges of a RAG on its image
Returns a modified image with the edges drawn.Edges are drawn in green
and nodes are drawn in yellow.
Parameters
----------
image : ndarray
The image to be drawn on.
g : RAG
The Region Adjacency Graph.
threshold : float
Only edges in `g` below `threshold` are drawn.
Returns:
out: ndarray
Image with the edges drawn.
"""
image = image.copy()
for edge in g.edges_iter():
n1, n2 = edge
r1, c1 = map(int, rag.node[n1]['centroid'])
r2, c2 = map(int, rag.node[n2]['centroid'])
line = draw.line(r1, c1, r2, c2)
circle = draw.circle(r1,c1,2)
if g[n1][n2]['weight'] < threshold :
image[line] = 0,1,0
image[circle] = 1,1,0
return image
def line_image(shape, lines):
image = np.zeros(shape, dtype=bool)
for end_points in lines:
# hough lines returns (x, y) points, draw.line wants (row, columns)
end_points = np.asarray(end_points)[:, ::-1]
image[draw.line(*np.ravel(end_points))] = 1
return image
def removeChessboard(img):
# Get the major lines in the image
edges, dilatedEdges, (h, theta, d) = findLines(img)
# Create image with ones to fill inn lines
lines = np.ones(img.shape[:2])
# Add lines to image as zeroes
for _, angle, dist in zip(*hough_line_peaks(h, theta, d)):
y0 = (dist - 0 * np.cos(angle)) / np.sin(angle)
y1 = (dist - img.shape[1] * np.cos(angle)) / np.sin(angle)
x, y = line(int(y1), 0, int(y0), img.shape[1] - 1)
x = np.clip(x, 0, img.shape[0] - 1)
y = np.clip(y, 0, img.shape[1] - 1)
lines[x, y] = 0
# Remove border edges from image with all edges
w = 4
edges = np.pad(edges[w:img.shape[0] - w, w:img.shape[1] - w], w, mode='constant')
# Erode the lines bigger, such that they cover the original lines
lines = erosion(lines, square(13))
# Remove major lines and close shape paths
removedChessboard = closing(edges * lines, square(8))
return removedChessboard
def polygon_perimeter(polygon, img_side=28):
"""
Generate the perimeter of a polygon including the vertices.
"""
# Create empty image
img_shape = [img_side, img_side]
img = np.zeros(img_shape, dtype=np.float32)
prev_idx, cur_idx = -1, 0
poly_len = len(polygon)
while cur_idx < poly_len:
# Get vertices
prev_vertex = polygon[prev_idx]
cur_vertex = polygon[cur_idx]
# Get line pixels
prev_rr, prev_cc = draw.line(
prev_vertex[1], prev_vertex[0],
cur_vertex[1], cur_vertex[0]
)
# Draw lines
img[prev_rr, prev_cc] = 1.
# Increment prev_idx and cur_idx
prev_idx += 1
cur_idx += 1
return img
def getRandomMotionBlurMask(extent):
X = makeRandomWalkCurve(40, 20, 2)
Y = smoothCurve(X, 20)
Y = Y - np.mean(Y, 0)[None, :]
Y = Y/np.max(Y, 0)
Y = Y*extent
theta = np.random.rand()*2*np.pi
Y[:, 0] = Y[:, 0] + np.cos(theta)*np.linspace(0, extent, Y.shape[0])
Y[:, 1] = Y[:, 1] + np.sin(theta)*np.linspace(0, extent, Y.shape[0])
D = np.sum(Y**2, 1)[:, None]
D = D + D.T - 2*Y.dot(Y.T)
D[D < 0] = 0
D = 0.5*(D + D.T)
D = np.sqrt(D)
Y = Y*extent/np.max(D)
Y = Y - np.mean(Y, 0)[None, :]
Y = Y - np.min(Y)
I = np.zeros((extent, extent))
for i in range(Y.shape[0]-1):
c = [Y[i, 0], Y[i, 1], Y[i+1, 0], Y[i+1, 1]]
c = [int(np.round(cc)) for cc in c]
rr, cc = line(c[0], c[1], c[2], c[3])
rr = [min(max(rrr, 0), extent-1) for rrr in rr]
cc = [min(max(ccc, 0), extent-1) for ccc in cc]
I[rr, cc] += 1.0
I = I/np.sum(I)
return (Y, I)
def draw_tile_layout(image, tiles, color=1):
"""
Draw the tile edges on a copy of image. Make a dot at each tile center.
This is a utility for inspecting a tile layout, not a necessary step in
the mosaic-building process.
Parameters
----------
image : array
tiles : list
list of pairs of slices, as generated by :func:`partition`
color : int or array
value to "draw" onto ``image`` at tile boundaries
Returns
-------
annotated_image : array
"""
annotated_image = copy.deepcopy(image)
for y, x in tqdm(tiles):
edges = (
(y.start, x.start, y.stop - 1, x.start),
(y.stop - 1, x.start, y.stop - 1, x.stop - 1),
(y.stop - 1, x.stop - 1, y.start, x.stop - 1),
(y.start, x.stop - 1, y.start, x.start),
)
for edge in edges:
rr, cc = draw.line(*edge)
annotated_image[rr, cc] = color # tile edges
annotated_image[_tile_center((y, x))] = color # dot at center
return annotated_image
def draw_keypoints(img, keypoints, draw_prob):
"""Draws for each keypoint a circle (roughly matching the sigma of the scale)
with a line for the orientation.
Args:
img The image to which to add the keypoints (gets copied)
keypoints The keypoints to draw
draw_prob Probability of drawing a keypoint (the lower the less keypoints are drawn)
Returns:
Image with keypoints"""
height, width = img.shape
img = np.copy(img)
# convert from grayscale image to RGB so that keypoints can be drawn in red
img = img[:, :, np.newaxis]
img = np.repeat(img, 3, axis=2)
for (y, x), orientation, scale_idx, scale_size, kp_type in keypoints:
if draw_prob < 1.0 and random.random() <= draw_prob:
# draw the circle
radius = int(scale_size)
rr, cc = draw.circle_perimeter(y, x, radius, shape=img.shape)
img[rr, cc, 0] = 1.0
img[rr, cc, 1:] = 0
# draw orientation
orientation = util.quantize(orientation, [-135, -90, -45, 0, 45, 90, 135, 180])
x_start = x
y_start = y
if orientation == 0:
x_end = x + radius
y_end = y
elif orientation == 45:
x_end = x + radius*(1/math.sqrt(2))
y_end = y + radius*(1/math.sqrt(2))
elif orientation == 90:
x_end = x
y_end = y + radius
elif orientation == 135:
x_end = x - radius*(1/math.sqrt(2))
y_end = y - radius*(1/math.sqrt(2))
elif orientation == 180:
x_end = x - radius
y_end = y
elif orientation == -135:
x_end = x - radius*(1/math.sqrt(2))
y_end = y - radius*(1/math.sqrt(2))
elif orientation == -90:
x_end = x
y_end = y - radius
elif orientation == -45:
x_end = x + radius*(1/math.sqrt(2))
y_end = y - radius*(1/math.sqrt(2))
x_end = np.clip(x_end, 0, width-1)
y_end = np.clip(y_end, 0, height-1)
rr, cc = draw.line(int(y_start), int(x_start), int(y_end), int(x_end))
img[rr, cc, 0] = 1.0
img[rr, cc, 1:] = 0
img = np.clip(img, 0, 1.0)
return img
def footprint_fitness_error(self, points): temp_footprint = np.zeros(self.FOOTPRINT_added_boundary.shape, dtype=np.uint8) len_points = len(points) for idx1 in xrange(0, len_points): rr,cc = line(points[idx1][0], points[idx1][1], points[idx1-1][0],points[idx1-1][1]) temp_footprint[rr,cc] = 1 temp_footprint = ndimage.binary_fill_holes(temp_footprint) temp_footprint = temp_footprint * 1 rr,cc = np.nonzero(temp_footprint) #RATIO OF ZEROS AND ONES SA LOOB zero_counter = 0.0 nonzero_counter = 0.0 for point in zip(rr,cc): if self.FOOTPRINT_added_boundary[point[0]][point[1]] == 0: zero_counter += 1.0 else: nonzero_counter += 1.0 footprint_copy = copy.deepcopy(self.FOOTPRINT_added_boundary) footprint_copy[rr,cc] = 0 nonzero = len(footprint_copy[footprint_copy != 0]) total = (len(footprint_copy[footprint_copy == 0]) + nonzero) * 1.0 return (nonzero / total) + (zero_counter / (nonzero_counter + zero_counter))
def remove_deep_points(self, CIRCLE_RADIUS = 5, MINIMUM_BOUNDARY = 70): for point in self.POINTS_initial: segments = [] circle_x, circle_y = circle_perimeter(point[0],point[1],CIRCLE_RADIUS) circle_points = np.array(list(sorted(set(zip(circle_x,circle_y))))) sortedpoints = np.empty([len(circle_points), 2], dtype=int) test1 = circle_points[circle_points[:,0] == point[0] - CIRCLE_RADIUS] start = len(test1) end = len_cpoints = len(sortedpoints) sortedpoints[0:start] = test1 for x in xrange(point[0] - CIRCLE_RADIUS + 1, point[0] + CIRCLE_RADIUS): test1 = circle_points[circle_points[:,0] == x] testlen = len(test1) if x <= point[0]: sortedpoints[start:start+testlen/2] = test1[testlen/2:] sortedpoints[end-testlen/2:end] = test1[:testlen/2] else: sortedpoints[start:start+testlen/2] = test1[testlen/2:][::-1] sortedpoints[end-testlen/2:end] = test1[:testlen/2][::-1] start += testlen/2 end -= testlen/2 test1 = circle_points[circle_points[:,0] == point[0] + CIRCLE_RADIUS] sortedpoints[start:start + len(test1)] = test1[::-1] for c_perimeter in sortedpoints: segments.append(True) line_x, line_y = line(point[0], point[1], c_perimeter[0], c_perimeter[1]) for line_points in zip(line_x,line_y)[1:]: # if original_image[line_points[0]][line_points[1]] != 0: if self.FOOTPRINT_cleaned_opening[line_points[0]][line_points[1]] != 0: segments[-1] = False break min_boundpoints = (MINIMUM_BOUNDARY / 360.0) * len_cpoints seg_sizes = [] new_segment = True for segment in segments: if segment: if new_segment: seg_sizes.append(1) new_segment = False else: seg_sizes[-1] += 1 else: new_segment = True if segments[0] == True and segments[-1] == True and len(seg_sizes) > 1: seg_sizes[0] = seg_sizes[0] + seg_sizes[-1] seg_sizes.pop() if(len(seg_sizes) == 0 or max(seg_sizes) < min_boundpoints): # boundary_image[point[0]][point[1]] = 0 #TAMA BANG TANGGALIN? if (point[0],point[1]) in self.POINTS_ordered: ## IDENTIFY KUNG BAKIT NAGKA-ERRROR, EXAMPLE pt000120_merged4.py obj 1301 self.POINTS_ordered.remove((point[0],point[1]))
def lines(end_points, shape):
"""
Parameters
----------
end_points : iterable
coordinates of the starting point and the ending point of each
line: e.g., [(start_x, start_y, end_x, end_y), (x1, y1, x2, y2)]
shape : tuple
Image shape which is used to determine the maximum extent of output
pixel coordinates. Order is (rr, cc).
Returns
-------
label_array : array
Elements not inside any ROI are zero; elements inside each
ROI are 1, 2, 3, corresponding to the order they are specified
in coords. Order is (rr, cc).
"""
label_array = np.zeros(shape, dtype=np.int64)
label = 0
for points in end_points:
if len(points) != 4:
raise ValueError("end points should have four number of"
" elements, giving starting co-ordinates,"
" ending co-ordinates for each line")
rr, cc = line(np.max([points[0], 0]), np.max([points[1], 0]),
np.min([points[2], shape[0]-1]),
np.min([points[3], shape[1]-1]))
label += 1
label_array[rr, cc] = label
return label_array
def output(self):
"""Return the drawn line and the resulting scan.
Returns
-------
line_image : (M, N) uint8 array, same shape as image
An array of 0s with the scanned line set to 255.
If the linewidth of the line tool is greater than 1,
sets the values within the profiled polygon to 128.
scan : (P,) or (P, 3) array of int or float
The line scan values across the image.
"""
end_points = self.line_tool.end_points
line_image = np.zeros(self.image_viewer.image.shape[:2],
np.uint8)
width = self.line_tool.linewidth
if width > 1:
rp, cp = measure.profile._line_profile_coordinates(
*end_points[:, ::-1], linewidth=width)
# the points are aliased, so create a polygon using the corners
yp = np.rint(rp[[0, 0, -1, -1],[0, -1, -1, 0]]).astype(int)
xp = np.rint(cp[[0, 0, -1, -1],[0, -1, -1, 0]]).astype(int)
rp, cp = draw.polygon(yp, xp, line_image.shape)
line_image[rp, cp] = 128
(x1, y1), (x2, y2) = end_points.astype(int)
rr, cc = draw.line(y1, x1, y2, x2)
line_image[rr, cc] = 255
return line_image, self.scan_data
def p7(img, hough_img, hough_threshold):
hough_img[hough_img < hough_threshold] = 0
img_height, img_width = thresholded_edge_img.shape
theta_ind = np.linspace(-pi/2, pi/2, AMOUNT_OF_BINS_THETA)
ro_ind, step = np.linspace(0, np.sqrt(img_height**2 + img_width**2), AMOUNT_OF_BINS_RO, retstep=True)
theta_ar, ro_ar = hough_img.nonzero()
plt.imshow(thresholded_edge_img)
plt.autoscale(False)
for line_num in xrange(len(theta_ar)):
theta = theta_ind[theta_ar[line_num]]
ro = ro_ind[ro_ar[line_num]]
tang = sin(theta) / cos(theta)
b = ro / cos(theta)
y_pos = img_width*tang + b
y_neg = b
try:
coords_one, coords_two = line(0, int(y_neg), img_width, int(y_pos))
except:
continue
pairs = zip(coords_two, coords_one)
line_started = False
for r, c in pairs:
#print line_started
smaller_check = r >= 0 and c >= 0
bigger_check = r < img_height and c < img_width
if not (smaller_check and bigger_check):
continue
if thresholded_edge_img[r, c] and (not line_started):
line_started = True
thresholded_edge_img[r, c] = 10000
plt.plot(c, r, 'ro')
continue
if (not thresholded_edge_img[r, c]) and line_started:
line_started = False
thresholded_edge_img[r, c] = 10000
plt.plot(c, r, 'ro')
continue
plt.plot([0, img_width], [y_neg, y_pos], color='r', linestyle='-', linewidth=1)
plt.show()
def _calculate_spacing(self, im):
h, w, d = im.shape
# cw, ch = 600, 600
cw, ch = 300, 300
cx = (w - cw) / 2
cy = (h - ch) / 2
im = crop(im, cx, cy, cw, ch)
# d = self.test_image.plotdata.get_data('imagedata000')
d = grayspace(im)
# d /= 255.
# edges = filter.canny(d, sigma=3,
# # low_threshold=0,
# # high_threshold=
# )
# edges = edges.astype('uint8')
# edges = vsobel(d)
edges = sobel(d)
nim = zeros_like(edges)
nim[edges > 0.1] = 255
edges = nim
self.test_image.set_image(edges)
hspace, angles, dists = hough_line(edges)
self.test_image.set_image(hspace, 1)
_hspace, angles, dists = hough_peaks(hspace, angles, dists,
)
nim = zeros_like(edges)
h, w, d = im.shape
xs = []
for ti, di in zip(angles, dists):
ai = math.degrees(ti) + 180
di = abs(int(round(di)))
aa = abs(ai - 90) < 1
bb = abs(ai - 270) < 1
if aa or bb :
adi = abs(di)
coords = line(0, adi, h - 1, adi)
nim[coords] = 200
xs.append(di)
self.test_image.set_image(nim, 2)
xs.sort()
# compute difference between each pair
dxs = diff(xs)
print dxs
dd = sorted(dxs)[1:]
print dd
while len(dd):
if std(dd) < 3:
print dd
return mean(dd) * 4 # each bar =0.25mm
else:
dd = dd[:-1]
def draw(self,img, color=red):
line = draw.line(self.y1, self.x1, self.y2, self.x2)
draw.set_color(img, line, color)
if self.cx and self.cy:
centre = draw.circle(self.cy, self.cx, 3)
draw.set_color(img, centre, color)
def outline(py,px):
"""Pixels contained in polygon edge"""
oy, ox = [], []
for y0,x0,y1,x1 in zip(py,px,np.roll(py,1),np.roll(px,1)):
ly,lx = line(y0,x0,y1,x1)
oy += list(ly)
ox += list(lx)
return (np.array(oy,int), np.array(ox,int))
def window(image_path): img = io.imread(image_path) h = img.shape[0] w = img.shape[1] step_size=32 for i in range(0, h, step_size): for j in range(0, w, step_size): img1 = img.copy() if i+step_size<h and j+step_size<w: rr,cc = draw.line(i,j, i,j+step_size) img1[rr,cc] = 1 rr,cc = draw.line(i,j, i+step_size,j) img1[rr,cc] = 1 rr,cc = draw.line(i+step_size,j, i+step_size,j+step_size) img1[rr,cc] = 1 rr,cc = draw.line(i,j+step_size, i+step_size,j+step_size) img1[rr,cc] = 1 ImageViewer(img1).show()
def getMask(self):
from skimage.draw import line
x=np.array([p[0] for p in self.pts], dtype=int)
y=np.array([p[1] for p in self.pts], dtype=int)
xx, yy = line(x[0],y[0],x[1],y[1])
idx_to_keep = np.logical_not( (xx>=self.window.mx) | (xx<0) | (yy>=self.window.my) | (yy<0))
xx = xx[idx_to_keep]
yy = yy[idx_to_keep]
return xx, yy
def test_ellipse_perimeter_flat_zeroangle():
# flat ellipse
img = np.zeros((20, 18), 'uint8')
img_ = np.zeros((20, 18), 'uint8')
rr, cc = ellipse_perimeter(6, 7, 0, 5, 0)
img[rr, cc] = 1
rr, cc = line(6, 2, 6, 12)
img_[rr, cc] = 1
assert_array_equal(img, img_)
def test_line_diag():
img = np.zeros((5, 5))
rr, cc = line(0, 0, 4, 4)
img[rr, cc] = 1
img_ = np.eye(5)
assert_array_equal(img, img_)
def test_line_reverse():
img = np.zeros((10, 10))
rr, cc = line(0, 9, 0, 0)
img[rr, cc] = 1
img_ = np.zeros((10, 10))
img_[0, :] = 1
assert_array_equal(img, img_)
def test_line_horizontal():
img = np.zeros((10, 10))
rr, cc = line(0, 0, 0, 9)
img[rr, cc] = 1
img_ = np.zeros((10, 10))
img_[0, :] = 1
assert_array_equal(img, img_)
def test_line_vertical():
img = np.zeros((10, 10))
rr, cc = line(0, 0, 9, 0)
img[rr, cc] = 1
img_ = np.zeros((10, 10))
img_[:, 0] = 1
assert_array_equal(img, img_)
def test_set_color():
img = np.zeros((10, 10))
rr, cc = line(0, 0, 0, 30)
set_color(img, (rr, cc), 1)
img_ = np.zeros((10, 10))
img_[0, :] = 1
assert_array_equal(img, img_)
def get_bresenham_paths(self, paths):
self.bresenham_path_list = []
for path in paths:
points = path['points']
bresenham_points = [None, None, None]
for idx, point in enumerate(points):
if idx == 0:
prev_point = point
else:
current_point = point
xx, yy = line(int(prev_point[0]), int(prev_point[1]),
int(current_point[0]), int(current_point[1]))
if bresenham_points[0] is None:
bresenham_points[0] = xx
else:
bresenham_points[0] = np.hstack(
(bresenham_points[0], xx))
if bresenham_points[1] is None:
bresenham_points[1] = yy
else:
bresenham_points[1] = np.hstack(
(bresenham_points[1], yy))
# angle calculation
angle_deg = self.calc_angle(prev_point, current_point)
if (idx < len(points) - 1):
next_point = points[idx + 1]
next_angle_deg = self.calc_angle(
current_point, next_point)
if np.abs(next_angle_deg - angle_deg) < 180:
aa = np.arange(
len(xx)) * (next_angle_deg -
angle_deg) / len(xx) + angle_deg
else:
if (next_angle_deg - angle_deg) < 0:
aa = np.arange(
len(xx)) * (next_angle_deg - angle_deg +
360) / len(xx) + angle_deg
else:
aa = np.arange(
len(xx)) * (next_angle_deg - angle_deg -
360) / len(xx) + angle_deg
else:
aa = np.ones((len(xx))) * angle_deg
if bresenham_points[2] is None:
bresenham_points[2] = aa
else:
bresenham_points[2] = np.hstack(
(bresenham_points[2], aa))
prev_point = current_point
self.bresenham_path_list.append(bresenham_points)
return self.bresenham_path_list
def mouse_move(self, ips, x, y, btn, **key):
if self.status == None and ips.mark != None:
ips.mark = None
ips.update()
if not self.status in [
'local_pen', 'local_brush', 'local_sketch', 'local_in',
'local_out', 'move'
]:
return
img, color = ips.img, ColorManager.get_front()
x = int(round(min(max(x, 0), img.shape[1])))
y = int(round(min(max(y, 0), img.shape[0])))
if self.status == 'move':
x, y = key['canvas'].to_panel_coor(x, y)
key['canvas'].move(x - self.oldp[0], y - self.oldp[1])
self.oldp = x, y
ips.update()
print('move')
return
rs, cs = line(*[int(round(i)) for i in self.oldp + (y, x)])
np.clip(rs, 0, img.shape[0] - 1, out=rs)
np.clip(cs, 0, img.shape[1] - 1, out=cs)
color = (np.mean(color), color)[img.ndim == 3]
for r, c in zip(rs, cs):
start = time()
w = self.para['win']
sr = (max(0, r - w), min(img.shape[0], r + w))
sc = (max(0, c - w), min(img.shape[1], c + w))
r, c = min(r, w), min(c, w)
backclip = imgclip = img[slice(*sr), slice(*sc)]
if not ips.back is None:
backclip = ips.back.img[slice(*sr), slice(*sc)]
if self.status == 'local_pen':
local_pen(imgclip, r, c, self.para['r'], color)
if self.status == 'local_brush':
if (imgclip[r, c] - color).sum() == 0: continue
local_brush(imgclip, backclip, r, c, color, 0, self.para['ms'])
if self.status == 'local_in':
local_in_fill(imgclip, r, c, self.para['r'], self.pickcolor,
color)
if self.status == 'local_sketch':
local_sketch(imgclip, r, c, self.para['r'], self.pickcolor,
color)
if self.status == 'local_out':
local_out_fill(imgclip, r, c, self.para['r'], self.pickcolor,
color)
ips.mark = self.make_mark(x, y)
self.oldp = (y, x)
ips.update()
def prepare_deform_slice(slice_shape, deformation_strength, iterations,
randomseed):
# grow slice shape by 2 x deformation strength
np.random.seed(randomseed)
grow_by = 2 * deformation_strength
#print ('sliceshape: '+str(slice_shape[0])+' growby: '+str(grow_by)+ ' strength: '+str(deformation_strength))
shape = (slice_shape[0] + grow_by, slice_shape[1] + grow_by)
# randomly choose fixed x or fixed y with p = 1/2
fixed_x = np.random.random() < .5
if fixed_x:
x0, y0 = 0, np.random.randint(1, shape[1] - 2)
x1, y1 = shape[0] - 1, np.random.randint(1, shape[1] - 2)
else:
x0, y0 = np.random.randint(1, shape[0] - 2), 0
x1, y1 = np.random.randint(1, shape[0] - 2), shape[1] - 1
## generate the mask of the line that should be blacked out
#print (shape)
line_mask = np.zeros(shape, dtype='bool')
rr, cc = line(x0, y0, x1, y1)
line_mask[rr, cc] = 1
# generate vectorfield pointing towards the line to compress the image
# first we get the unit vector representing the line
line_vector = np.array([x1 - x0, y1 - y0], dtype='float32')
line_vector /= np.linalg.norm(line_vector)
# next, we generate the normal to the line
normal_vector = np.zeros_like(line_vector)
normal_vector[0] = -line_vector[1]
normal_vector[1] = line_vector[0]
# make meshgrid
x, y = np.meshgrid(np.arange(shape[1]), np.arange(shape[0]))
# generate the vector field
flow_x, flow_y = np.zeros(shape), np.zeros(shape)
# find the 2 components where coordinates are bigger / smaller than the line
# to apply normal vector in the correct direction
components, n_components = label(np.logical_not(line_mask).view('uint8'))
assert n_components == 2, "%i" % n_components
neg_val = components[0, 0] if fixed_x else components[-1, -1]
pos_val = components[-1, -1] if fixed_x else components[0, 0]
flow_x[components == pos_val] = deformation_strength * normal_vector[1]
flow_y[components == pos_val] = deformation_strength * normal_vector[0]
flow_x[components == neg_val] = -deformation_strength * normal_vector[1]
flow_y[components == neg_val] = -deformation_strength * normal_vector[0]
# generate the flow fields
flow_x, flow_y = (x + flow_x).reshape(-1, 1), (y + flow_y).reshape(-1, 1)
# dilate the line mask
line_mask = binary_dilation(line_mask, iterations=iterations) # default=10
return flow_x, flow_y, line_mask
def plot_deformed_lattice_on_image_with_affinity_label(lattice_pos,
ori_image,
adjacent,
save_path,
pairs,
affinity,
grid_pos,
thresh,
mask=None):
plt.gca().invert_yaxis()
image = ori_image.copy()
#for edges
for idx, p in enumerate(pairs):
x1, y1 = grid_pos[p[0]]
x2, y2 = grid_pos[p[1]]
x1, y1, x2, y2 = int(x1), int(y1), int(x2), int(y2)
#line = draw.line(x1, y1, x2, y2)
line = draw.line(y1, x1, y2, x2)
pred = affinity[idx]
if pred > thresh:
image[line] = 0, 1, 0
else:
image[line] = 1, 1, 0
fig, ax = plt.subplots(figsize=(image.shape[1] // 30,
image.shape[0] // 30))
ax.imshow(image)
#plot control points
x, y = np.where(adjacent != 0)
conn = zip(x, y)
if not mask is None:
color = ['r' if i == 1 else 'g' for i in mask]
size = [4 if i == 1 else 1 for i in mask]
else:
color = ['r' for i in range(lattice_pos.shape[0])]
size = [1 for i in range(lattice_pos.shape[0])]
graph = nx.Graph()
#adding nodes/connections in the graph
for node in range(lattice_pos.shape[0]):
graph.add_node(node)
graph.add_edges_from(conn)
nx.draw(graph, [(x, y) for x, y in lattice_pos],
node_size=size,
ax=ax,
node_color=color)
plt.savefig(save_path)
plt.close()
def hough(img, nb_lines):
"""Applies the Hough Transformation to an image.
Args:
img The image
nb_lines The number of lines to search for.
Returns:
Accumulator image,
Local maxima in accumulator image,
image with detected lines"""
height, width = img.shape
magnitude = grad_magnitude(img)
mag_avg = np.average(magnitude)
max_d = math.sqrt(height**2 + width**2)
min_d = -max_d
alphas = np.linspace(0, np.pi, NB_QUANTIZATION_STEPS)
distances = np.linspace(min_d, max_d, NB_QUANTIZATION_STEPS)
accumulator = np.zeros((NB_QUANTIZATION_STEPS, NB_QUANTIZATION_STEPS))
for y in range(1, height - 1):
for x in range(1, width - 1):
if magnitude[y, x] > mag_avg:
for alpha_idx, alpha in enumerate(alphas):
distance = x * math.cos(alpha) + y * math.sin(alpha)
distance_idx = util.quantize_idx(distance, distances)
accumulator[alpha_idx, distance_idx] += 1
img_hough = np.zeros((height, width, 3))
img_hough[:, :, 0] = np.copy(img)
img_hough[:, :, 1] = np.copy(img)
img_hough[:, :, 2] = np.copy(img)
local_maxima = find_local_maxima(accumulator)
peaks_idx = get_peak_indices(local_maxima, nb_lines)
for value, (alpha_idx, distance_idx) in peaks_idx:
peak_alpha_rad = alphas[alpha_idx]
peak_distance = distances[distance_idx]
x0 = 0
x1 = width - 1
y0 = (peak_distance -
0 * np.cos(peak_alpha_rad)) / (np.sin(peak_alpha_rad) + 1e-8)
y1 = (peak_distance -
(width - 1) * np.cos(peak_alpha_rad)) / (np.sin(peak_alpha_rad) +
1e-8)
y0 = np.clip(y0, 0, height - 1)
y1 = np.clip(y1, 0, height - 1)
rr, cc = draw.line(int(y0), int(x0), int(y1), int(x1))
img_hough[rr, cc, 0] = 1
img_hough[rr, cc, 1] = 0
img_hough[rr, cc, 2] = 0
return accumulator, local_maxima, img_hough
def draw_line(line_params):
x1 = int(line_params['X1'])
y1 = int(line_params['Y1'])
x2 = int(line_params['X2'])
y2 = int(line_params['Y2'])
rr, cc = line(x1, y1, x2, y2)
return rr, cc
def test_transpose_image():
image = np.zeros((10, 10))
rr, cc = line(4, 0, 4, 2)
image[rr, cc] = 1
rr, cc = line(3, 2, 3, 5)
image[rr, cc] = 1
rr, cc = line(1, 2, 8, 2)
image[rr, cc] = 1
rr, cc = line(1, 0, 1, 8)
image[rr, cc] = 1
skeleton1 = csr.Skeleton(image)
skeleton2 = csr.Skeleton(image.T)
assert (skeleton1.n_paths == skeleton2.n_paths)
np.testing.assert_allclose(
np.sort(skeleton1.path_lengths()),
np.sort(skeleton2.path_lengths()),
)
def _shape(self, init_state, state):
init_canvas, init_position = init_state
canvas, position = state
drawn_canvas = np.copy(init_canvas)
for i, vertex in enumerate(vertices[1:], start=1):
rr, cc = line(vertices[i - 1][0], vertices[i - 1][1],
vertex[0], vertex[1])
drawn_canvas[rr, cc] = 0
return np.equal(drawn_canvas, canvas) and np.equal(
position, init_position)
def X_marksTspot(I, S_hit, S_miss):
#make a color image and insert the binary image in one channel.
I2 = Normalize(I)
Iout = np.dstack([I2, I2, I2])
#get hits from hit or miss
hits = binary_hit_or_miss(
I, structure1=S_hit,
structure2=S_miss) #, origin1 = (n//2, m//2), origin2 = (n//2, m//2))
loc = np.array(np.where(hits == True))
#draw x in red at locations for hits
for i in range(loc.shape[1]):
x, y = loc[:, i]
rr, cc = line(x - 10, y - 8, x + 10, y + 8)
Iout[rr, cc, :] = [1, 0, 0]
rr, cc = line(x + 10, y - 8, x - 10, y + 8)
Iout[rr, cc, :] = [1, 0, 0]
return (Iout)
def fitness_min_risk(grid, grid_max, path):
# This also handles obstacle collisions as they are encoded as np.inf in the grid,
# therefore summing with them gives np.inf as well
risk = 0
enc = path.enc_path
for idx, n0 in enumerate(enc[:-1]):
n1 = enc[idx + 1]
l = line(n0[0], n0[1], n1[0], n1[1])
risk += grid[l[0], l[1]].sum()
return risk / grid_max
def draw_lines(image, x, y, radius, n):
tetha_step = 2 * np.pi / n
for i in range(0, n):
tetha = i * tetha_step
line_len = int(radius * 0.7)
x1 = int(x + line_len * np.sin(tetha))
j1 = int(y + line_len * np.cos(tetha))
rr, cc = line(x, y, x1, j1)
if x1 >= image.shape[0] or j1 >= image.shape[1]:
continue
image[rr, cc] = 1
def make_data(has_spaceship: bool = None,
noise_level: float = 0.8,
no_lines: int = 6,
image_size: int = 200,
classification=False) -> Tuple[np.ndarray, np.ndarray]:
""" Data generator
Args:
has_spaceship (bool, optional): Whether a spaceship is included. Defaults to None (randomly sampled).
noise_level (float, optional): Level of the background noise. Defaults to 0.8.
no_lines (int, optional): No. of lines for line noise. Defaults to 6.
image_size (int, optional): Size of generated image. Defaults to 200.
Returns:
Tuple[np.ndarray, np.ndarray]: Generated Image and the corresponding label
The label parameters are x, y, yaw, x size, and y size respectively
An empty array is returned when a spaceship is not included.
"""
if has_spaceship is None:
has_spaceship = np.random.choice([True, False], p=(0.8, 0.2))
img = np.zeros(shape=(image_size, image_size))
if classification:
label = 0
else:
label = np.full(5, np.nan)
# draw ship
if has_spaceship:
params = (_get_pos(image_size), _get_yaw(), _get_size(), _get_l2w(),
_get_t2l())
pts, label = _make_spaceship(*params)
if classification:
label = 1
rr, cc = polygon_perimeter(pts[:, 0], pts[:, 1])
valid = (rr >= 0) & (rr < image_size) & (cc >= 0) & (cc < image_size)
img[rr[valid], cc[valid]] = np.random.rand(np.sum(valid))
# noise lines
line_noise = np.zeros(shape=(image_size, image_size))
for _ in range(no_lines):
rr, cc = line(*np.random.randint(0, 200, size=4))
line_noise[rr, cc] = np.random.rand(rr.size)
# combined noise
noise = noise_level * np.random.rand(image_size, image_size)
img = np.stack([img, noise, line_noise], axis=0).max(axis=0)
img = img.T # ensure image space matches with coordinate space
return img, label
def integral_over_line(image, line: LineString):
assert line.is_valid, "LineString is invalid"
try:
for pt0, pt1 in pairwise(line.coords):
r0, c0, r1, c1 = np.array(list(pt0) + list(pt1)).astype(int)
rr, cc = draw.line(r0, c0, r1, c1)
ss = np.sum(image[rr, cc])
return ss
except Exception:
logger.warning('integral_over_line measured incorrectly')
return np.nan
def test_bezier_segment_straight():
image = np.zeros((200, 200), dtype=int)
r0, r1, r2 = 50, 150, 150
c0, c1, c2 = 50, 50, 150
rr, cc = _bezier_segment(r0, c0, r1, c1, r2, c2, 0)
image[rr, cc] = 1
image2 = np.zeros((200, 200), dtype=int)
rr, cc = line(r0, c0, r2, c2)
image2[rr, cc] = 1
assert_array_equal(image, image2)
def displayVelocities(left, right, shape=(200, 200)):
# NOTE: For display purposes only! To use as a distribution, call np.flipud
# on the output
r = shape[0]
c = shape[1]
# draw a circle representing the robot shape
rr1, cc1 = circle(r / 2, c / 2, r / 10, shape)
# draw lines representing the robot left wheel
rr2, cc2 = line(r / 2, c / 4, r / 2 + int(left * 100), c / 4)
rr3, cc3 = line(r / 2, c * 3 / 4, r / 2 + int(right * 100), c * 3 / 4)
diff = (right - left) * 100
avg = (right + left / 2) * 100
rr4, cc4 = line(r / 2, c / 2, r / 2 + int(avg), c / 2 + int(diff))
# push the drawings onto a color image
img = np.zeros((r, c, 3), dtype=np.uint8)
img[rr1, cc1, :2] = 255
img[rr2, cc2, 1:] = 255
img[rr3, cc3, 1:] = 255
img[rr4, cc3, 1] = 255
return np.flipud(img)
def test_line_aa_diagonal():
img = np.zeros((10, 10))
rr, cc, val = line_aa(0, 0, 9, 6)
img[rr, cc] = 1
# Check that each pixel belonging to line,
# also belongs to line_aa
r, c = line(0, 0, 9, 6)
for r_i, c_i in zip(r, c):
assert_equal(img[r_i, c_i], 1)
def draw_models(self, labels, data=None, correct=None):
'''
Draw circles for a batch of images.
labels -- circle parameters, array shape (Nx3) where
N is the number of images in the batch
3 is the number of circles parameters (center x, center y, radius)
data -- batch of images to draw to, if empty a new batch wil be created according to the shape of labels
and circles will be green, circles will be blue otherwise
correct -- array of shape (N) indicating whether a circle estimate is correct
'''
n = labels.shape[0]
if data is None:
data = np.zeros((n, self.imgH, self.imgW, 3), dtype=np.float32)
data.fill(self.bg_clr)
clr = (0, 1, 0)
else:
clr = (0, 0, 1)
for i in range(0, n):
self.draw_circle(data[i], labels[i, 0], labels[i, 1], labels[i, 2],
clr)
if correct is not None:
# draw border green if estiamte is correct, red otherwise
if correct[i]: borderclr = (0, 1, 0)
else: borderclr = (1, 0, 0)
set_color(data[i], line(0, 0, 0, self.imgW - 1), borderclr)
set_color(data[i], line(0, 0, self.imgH - 1, 0), borderclr)
set_color(data[i],
line(self.imgH - 1, 0, self.imgH - 1, self.imgW - 1),
borderclr)
set_color(data[i],
line(0, self.imgW - 1, self.imgH - 1, self.imgW - 1),
borderclr)
return data
def draw_models(self, labels, data=None, correct=None):
'''
Draw lines for a batch of images.
labels -- line parameters, array shape (Nx2) where
N is the number of images in the batch
2 is the number of line parameters (intercept, slope)
data -- batch of images to draw to, if empty a new batch wil be created according to the shape of labels
and lines will be green, lines will be blue otherwise
correct -- array of shape (N) indicating whether a line estimate is correct
'''
n = labels.shape[0]
if data is None:
data = np.zeros((n, self.imgH, self.imgW, 3), dtype=np.float32)
data.fill(self.bg_clr)
clr = (0, 1, 0)
else:
clr = (0, 0, 1)
for i in range(0, n):
lY1 = int(labels[i, 0] * self.imgH)
lY2 = int(labels[i, 1] * self.imgW + labels[i, 0] * self.imgH)
self.draw_line(data[i], 0, lY1, self.imgW, lY2, clr)
if correct is not None:
# draw border green if estiamte is correct, red otherwise
if correct[i]: borderclr = (0, 1, 0)
else: borderclr = (1, 0, 0)
set_color(data[i], line(0, 0, 0, self.imgW - 1), borderclr)
set_color(data[i], line(0, 0, self.imgH - 1, 0), borderclr)
set_color(data[i],
line(self.imgH - 1, 0, self.imgH - 1, self.imgW - 1),
borderclr)
set_color(data[i],
line(0, self.imgW - 1, self.imgH - 1, self.imgW - 1),
borderclr)
return data
def draw_line(self, x0y0, x1y1, color=(255, 0, 255)):
# because Bresenham's line algorithm only works for integers we cast to int
x0y0 = x0y0.astype(int)
x1y1 = x1y1.astype(int)
out = line(
x0y0[0],
x0y0[1],
x1y1[0],
x1y1[1]
)
# wrap around out toroidal world
self.data[out[0] % (self.res[0] - 1), out[1] % (self.res[1] - 1)] = color
def create_pos(input_size, noise=False):
global count
img = np.zeros(input_size)
coord = [2,2,2,5]
img[draw.line(*coord)] = 255.
coord = [2,5,5,5]
img[draw.line(*coord)] = 255.
coord = [5,5,5,2]
img[draw.line(*coord)] = 255.
coord = [5,2,2,2]
img[draw.line(*coord)] = 255.
if noise:
a = np.zeros([5,5])
b = np.zeros([5,5])
for m, n in product(range(5), range(5)):
a[m,n] = np.sum(idxs[count:count+10] == [m,n])*5.
b[m,n] = np.sum(idxsn[count:count+10] == [m,n])*5.
count+=10
img[3:8,3:8]-=a
img[1:6,2:7]+=b
return img[:,:,None]
def create_random_square(self, image_size, size_min, size_max):
image = np.zeros((image_size, image_size), dtype=np.float64)
size = np.random.randint(size_min, size_max)
x = np.random.randint(0, image_size - size + 1)
y = np.random.randint(0, image_size - size + 1)
for i in range(0, size):
rr, cr = draw.line(y, x + i, y + size - 1, x + i)
image[rr, cr] = 1
image = np.reshape(image, (image_size, image_size, 1))
return image
def get_min_radius_to_edge(dist_img, start_pos, end_pos, dist_threshold=0.01):
# get lines coordinates
line = np.transpose(
np.array(draw.line(start_pos[0], start_pos[1], end_pos[0],
end_pos[1])))
# get dist values overlapping the line
data = dist_img[line[:, 1], line[:, 0]]
# find first index below threshold
radius = np.argmax(data < dist_threshold)
return radius
def _line(self, init_state, state):
init_canvas, init_position = init_state
canvas, position = state
drawn_canvas = np.copy(init_canvas)
rr, cc = line(init_position[0], init_position[1],
init_position[0] + direction[0],
init_position[1] + direction[1])
drawn_canvas[rr, cc] = 0
return np.equal(drawn_canvas, canvas) and np.equal(
position, init_position + direction)
def drawStuff(self, nLines):
patch = numpy.zeros((self.shapeSize, self.shapeSize))
for n in range(nLines):
(r1, c1, r2, c2) = numpy.random.randint(self.shapeSize, size=4)
rr, cc = draw.line(r1, c1, r2, c2)
patch[rr, cc] = random.uniform(1 - random_pixels,
1 + random_pixels)
return patch
def draw_female(self,
color=(255, 0, 0),
thickness=2,
show_head_location=True):
"""Draws an ellipse perimeter around a female.
Parameters
----------
color : 3-tuple
Color of ellipse outline.
thickness : int
Thickness of ellipse outline.
show_head_location : bool (optional, default=True)
If true, will draw an arrow from female's rear->head.
Returns
-------
image : 3D np.ndarray of shape [arena.background_image.shape]
Background image with female surrounded by ellipse.
"""
image = self.arena.background_image.copy()
# convert to color
image = gray2rgb(image)
assert image.dtype == np.uint8, "image is not of type uint8"
if self.maj_ax_rad <= 1:
return image
rr, cc = ellipse_perimeter(
self.center[0],
self.center[1],
self.min_ax_rad,
self.maj_ax_rad,
orientation=(self.orientation * np.pi /
180), # Negating this value
# gives good results in test_trk_female.py
# but leads to improperly oriented ellipse in
# the gui display.
shape=self.arena.background_image.shape)
ellipse_outline_mask = np.zeros_like(self.arena.background_image)
ellipse_outline_mask[rr, cc] = 1
dilated_ellipse_outline = dilation(ellipse_outline_mask,
disk(thickness))
rr, cc = np.where(dilated_ellipse_outline)
image[rr, cc, :] = color
if show_head_location:
rr, cc = line(self.center[0], self.center[1], self.head[0],
self.head[1])
image[rr, cc] = color
return image
def draw_a_line_on_image(inputs):
current_x = int(round(inputs['current_mouse']['repr']['xdata']))
current_y = int(round(inputs['current_mouse']['repr']['ydata']))
previous_x = int(round(inputs['previous_mouse']['repr']['xdata']))
previous_y = int(round(inputs['previous_mouse']['repr']['ydata']))
if current_x >= 0 and current_y >= 0 and previous_x >= 0 and previous_y >= 0:
rr, cc = line(previous_x, previous_y, current_x, current_y)
dd = np.zeros(len(rr), dtype=np.int64)
#print(rr.dtype, cc.dtype, dd.dtype)
# NEED TO EITHER COPY THIS IMAGE, OR ASSUME NON-SHARING (CURRENTLY THIS HOLDS)
inputs['accum']['repr'][cc, rr, dd] = 1.0 # 255
return {'current_image_mouse': inputs['accum']}
def test_hough_line_peaks():
img = np.zeros((100, 150), dtype=int)
rr, cc = line(60, 130, 80, 10)
img[rr, cc] = 1
out, angles, d = tf.hough_line(img)
out, theta, dist = tf.hough_line_peaks(out, angles, d)
assert_equal(len(dist), 1)
assert_almost_equal(dist[0], 80.723, 1)
assert_almost_equal(theta[0], 1.41, 1)
def draw_network(network, label_image, index=1):
nodes_coord = get_node_coord_array(network)
label_image[nodes_coord[:, 0], nodes_coord[:, 1]] = index
for edge in list(network.edges):
start = list(network.nodes[edge[1]]['xy'])
end = list(network.nodes[edge[0]]['xy'])
line = draw.line(*(start + end))
label_image[line] = index
return label_image
def draw(self, action):
action = np.clip(action, -1, 1)
a = scale(action[0:3], -1, 1, 0, 1)
b = scale(action[3:13], -1, 1, 0, config['STATE_DIM'][0] - 1)
c = scale(action[13:14], -1, 1, 0, 4)
action = np.concatenate([a, b, c]).reshape(config['ACTION_DIM'], )
# Parameter Validation and noises
action_category = np.argmax(action[0:3])
if self.stroke_count == 0:
axis = np.asarray(action[3:13], dtype=np.uint8) + np.int_(
np.random.normal(0, 2, action[3:13].shape[0]))
c_p = action[13] + np.random.normal(0, 1)
else:
axis = np.asarray(action[3:13], dtype=np.uint8)
c_p = action[13]
for i in range(axis.shape[0]):
if axis[i] < 2:
axis[i] = 2
elif axis[i] >= self.dim[0] - 2:
axis[i] = self.dim[0] - 2
if action_category == 1:
self.stroke_count += 1
# Draw line
rr, cc = line(axis[0], axis[1], axis[2], axis[3])
self.canvas[rr, cc] = 1
if action_category == 2:
self.stroke_count += 1
# Draw Curve
try:
rr, cc = bezier_curve(axis[4], axis[5], axis[6], axis[7],
axis[8], axis[9], c_p)
except MemoryError:
while True:
try:
_x1, _y1 = move_point(axis[4], axis[5])
_x2, _y2 = move_point(axis[6], axis[7])
_x3, _y3 = move_point(axis[8], axis[9])
rr, cc = bezier_curve(_x1, _y1, _x2, _y2, _x3, _y3,
c_p)
break
except MemoryError:
continue
try:
self.canvas[rr, cc] = 1
except IndexError:
rr = np.clip(rr, 0, config['STATE_DIM'][0] - 1)
cc = np.clip(cc, 0, config['STATE_DIM'][1] - 1)
self.canvas[rr, cc] = 1
def __init__(self, point_1, point_2, point_3):
self.line_bg_mem = line(point_1[0], point_1[1], point_2[0], point_2[1])
self.line_cyt_sept = line(point_2[0], point_2[1], point_3[0],
point_3[1])
self.background = None
self.membrane = None
self.septum = None
self.fr = None
self.image = None
x_points = []
x_points.extend(self.line_bg_mem[0])
x_points.extend(self.line_cyt_sept[0])
y_points = []
y_points.extend(self.line_bg_mem[1])
y_points.extend(self.line_cyt_sept[1])
self.box = min(x_points) - 10, min(y_points) - \
10, max(x_points) + 10, max(y_points) + 10