def blend(img1, img2, mask, depth=4):
gaussian1 = [img1]
for i in range(depth):
gaussian1.append(
pyramid_reduce(gaussian1[i], multichannel=True, sigma=2))
gaussian2 = [img2]
for i in range(depth):
gaussian2.append(
pyramid_reduce(gaussian2[i], multichannel=True, sigma=2))
mask = gaussian(mask, multichannel=True, sigma=20)
mask_piramid = [mask]
for i in range(depth):
mask_piramid.append(
pyramid_reduce(mask_piramid[i], multichannel=True, sigma=10))
reconstructed1 = [gaussian1[-1]]
for i in range(0, len(gaussian1) - 1):
reconstructed1.append(
pyramid_expand(reconstructed1[i], multichannel=True))
reconstructed1.reverse()
reconstructed2 = [gaussian2[-1]]
for i in range(0, len(gaussian2) - 1):
reconstructed2.append(
pyramid_expand(reconstructed2[i], multichannel=True))
reconstructed2.reverse()
laplacian1 = []
for i in range(depth + 1):
laplacian1.append(gaussian1[i] - reconstructed1[i])
laplacian2 = []
for i in range(depth + 1):
laplacian2.append(gaussian2[i] - reconstructed2[i])
assert len(gaussian1) == len(gaussian2) == len(mask_piramid) == len(
laplacian1) == len(laplacian2)
blended_piramid = []
for i in range(len(mask_piramid) - 1, -1, -1):
blended_piramid.append((laplacian1[i] * mask_piramid[i]) +
((1 - mask_piramid[i]) * laplacian2[i]))
first = (mask_piramid[-1] * reconstructed1[-1]) + (
(1 - mask_piramid[-1]) * reconstructed2[-1])
final = blended_piramid[0] + first
for i in range(1, depth + 1):
final = pyramid_expand(final, multichannel=True, sigma=2)
final = final + blended_piramid[i]
return final
def get_sample(gr, x, y, s):
img = gr.ReadAsArray(x,y,s,s)
img = img.swapaxes(0,2).swapaxes(0,1)
if s!= 256:
return (pyramid_reduce(img, downscale = s/256) * 255).astype(np.uint8)
else:
return img
def scale_images(input_folder = '../train-256', output_folder = '../train-128', pixel_size = 128.):
input_list = set([file for file in os.listdir(input_folder) if file.endswith('.jpeg')])
output_list = set([file for file in os.listdir(output_folder) if file.endswith('.jpeg')])
files_to_process = list(input_list - output_list)
for fn in files_to_process:
original_image = io.imread(input_folder + '/' + fn)
scale = original_image.shape[0] / pixel_size
if scale > 1:
output_image = transform.pyramid_reduce(original_image, downscale=scale)
elif scale < 1:
output_image = transform.pyramid_expand(original_image, upscale=1/scale)
else:
output_image = original_image
if output_image.shape != (pixel_size, pixel_size):
x = pixel_size - output_image.shape[0]
y = pixel_size - output_image.shape[1]
if x < 0:
image = output_image[:x, :]
if y < 0:
image = output_image[:, :y]
output_image = (output_image - output_image.min()) / output_image.max()
try:
io.imsave(output_folder + '/' + fn, output_image)
except ValueError:
print fn + ' not saved!'
def load_and_preprocess(filename, new_shape=None, channels="RGB",
downsample=None, crop=None):
'''
Load image and do basic preprocessing.
- resize image to a specified shape;
- subtract ImageNet mean;
- make sure output image data is 0...255 uint8.
'''
img = imread(filename) # RGB image
if downsample is not None:
img = pyramid_reduce(img)
if img.max()<=1.0:
img = img * 255.0 / img.max()
if crop is not None:
i = np.random.randint(crop//2, img.shape[0]-crop//2)
j = np.random.randint(crop//2, img.shape[1]-crop//2)
img = img[(i-crop//2):(i+crop//2),(j-crop//2):(j+crop//2)]
if new_shape is not None:
img = resize(img, new_shape, preserve_range=True)
# imagenet_mean_bgr = np.array([103.939, 116.779, 123.68])
imagenet_mean_rgb = np.array([123.68, 116.779, 103.939])
for i in range(3):
img[:,:,i] = img[:,:,i] - imagenet_mean_rgb[i]
# for VGG networks pre-trained on ImageNet, channels are BGR
# (ports from Caffe)
if channels=="BGR":
img = img[:, :, [2,1,0]] # swap channel from RGB to BGR
return img.astype(np.uint8)
def get_square(image, square_size):
height, width = image.shape
if (height > width):
differ = height
else:
differ = width
differ += 2
# square filler
mask = np.zeros((differ, differ), dtype="uint8")
x_pos = int((differ - width) / 2)
y_pos = int((differ - height) / 2)
# center image inside the square
mask[y_pos:y_pos + height, x_pos:x_pos + width] = image[0:height, 0:width]
# downscale if needed
if differ / square_size > 1:
mask = (255 * pyramid_reduce(
mask, differ / square_size, multichannel=False)).astype(np.uint8)
else:
mask = cv2.resize(mask, (square_size, square_size),
interpolation=cv2.INTER_AREA)
return mask
def get_pyramid(I, downscale=2.0, nlevel=10, min_size=16):
"""Construct image pyramid.
Parameters
----------
I : ndarray
The image to be preprocessed (Gray scale or RGB).
downscale : float
The pyramid downscale factor.
nlevel : int
The maximum number of pyramid levels.
min_size : int
The minimum size for any dimension of the pyramid levels.
Returns
-------
pyramid : list[ndarray]
The coarse to fine images pyramid.
"""
pyramid = [I]
size = min(I.shape)
count = 1
while (count < nlevel) and (size > downscale * min_size):
J = pyramid_reduce(pyramid[-1], downscale, multichannel=False)
pyramid.append(J)
size = min(J.shape)
count += 1
return pyramid[::-1]
def get_image_at_scale(self,
image,
scale,
num_scales=10,
coarsest_scale=0.1):
im = image.copy()
if num_scales > 1:
downscale = coarsest_scale**(-1.0 / (num_scales - 1))
for s in range(scale):
im = pyramid_reduce(
im, downscale,
multichannel=True) if im.ndim == 3 else pyramid_reduce(
im, downscale, multichannel=False)
if im.ndim == 3:
return np.moveaxis(im, -1, 0)
else:
return im
def _get_disk(radius: int, scale: int):
mag_radius = scale * radius
mag_disk = morphology.disk(mag_radius, dtype=np.float64)
disk = transform.pyramid_reduce(mag_disk,
downscale=scale,
order=1,
multichannel=False)
return disk
def getRandom_sample(g_raster):
x, y, s = random_loc_size(g_raster.RasterYSize, g_raster.RasterXSize)
img = g_raster.ReadAsArray(y,x,s,s)
img = img.swapaxes(0,2).swapaxes(0,1)
if s!= 256:
return (pyramid_reduce(img, downscale = s/256) * 255).astype(np.uint8)
else:
return img
def __prepare_image(image):
"""Prepare image for comparison"""
image = rgb2gray(image)
image = adjust_gamma(image)
image = pyramid_reduce(image, downscale=8)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
image = img_as_ubyte(image)
return image
def subtract_rolling_ball(image, radius):
"""Subtracts background from image using the Rolling Ball algorithm."""
subtract = SubtractBall(radius)
new_radius = subtract.ball.width
small_image = pyramid_reduce(image, downscale=subtract.ball.shrink_factor)
background = threshold_local(small_image,
new_radius,
method='generic',
param=subtract.bg)
background = resize(background, image.shape)
return image - background
def load_video(self, path, to_grey=True, downscale=2):
videodata = vread(path)
imgs = []
for img in tqdm(videodata):
if to_grey:
img = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
if downscale:
img = pyramid_reduce(img, downscale=downscale)
imgs.append(img)
imgs = np.asarray(imgs)
return imgs
def generate_GP(image_copy, gp_level):
gp_image = [image_copy]
for i in range(gp_level):
image_copy = pyramid_reduce(image_copy,
downscale=2,
multichannel=True,
sigma=3)
gp_image.append(image_copy)
return gp_image
def render(triangles, img, color_mode, fill_mode):
"""
Generates samples points for triangulation of a given image.
Parameters
----------
triangles : np.array
The delaunay triangulation of the image
img : np.array
The image to create a low-polygon approximation.
"""
t0 = time.perf_counter()
low_poly = np.empty(shape=(2 * img.shape[0], 2 * img.shape[1],
img.shape[2]),
dtype=np.uint8)
for triangle in triangles:
if fill_mode == 'wire':
rr, cc = polygon_perimeter(2 * triangle[:, 0], 2 * triangle[:, 1],
low_poly.shape)
elif fill_mode == 'solid':
rr, cc = polygon(2 * triangle[:, 0], 2 * triangle[:, 1],
low_poly.shape)
if color_mode == 'centroid':
centroid = np.mean(triangle, axis=0, dtype=np.int32)
color = img[tuple(centroid)]
elif color_mode == 'mean':
color = np.mean(img[polygon(triangle[:, 0], triangle[:, 1],
img.shape)],
axis=0)
low_poly[rr, cc] = color
t1 = time.perf_counter()
if args.time:
print(f"Render timer: {round(t1 - t0, 3)} seconds.")
fig, (ax1, ax2) = plt.subplots(nrows=1,
ncols=2,
figsize=(8, 3),
sharex=True,
sharey=True)
ax1.imshow(img)
ax1.axis('off')
low_poly = pyramid_reduce(low_poly, multichannel=True)
ax2.imshow(low_poly)
ax2.axis('off')
fig.tight_layout()
# plt.show()
if args.save:
name = args.save_name if args.save_name is not None else f"{args.img.replace('.jpg', '')}_tri.png"
imsave(name, low_poly)
def get_mask_at_scale(self,
image,
scale,
num_scales=10,
coarsest_scale=0.1,
mask_threshold=0.1):
im = image.copy()
if num_scales > 1:
downscale = coarsest_scale**(-1.0 / (num_scales - 1))
for s in range(scale):
im = pyramid_reduce(im, downscale,
multichannel=False) > mask_threshold
return im
def subsample(X):
# ndarray(seconds, channels, length/2, width/2)
# subsample(ndarray(seconds, channels, length, width)
"""
"""
seconds = X.shape[0]
channels = X.shape[1]
length = X.shape[2]
width = X.shape[3]
Xout = np.zeros((seconds,channels,length/2,width/2))
for i in range(X.shape[0]):
j = 0
while j < X.shape[1]:
Xout[i,j:j+3,:,:] = transform.pyramid_reduce(
transform.pyramid_reduce(
X[i,j:j+3,:,:].transpose(0,2,1)).transpose((0,2,1))
)
j+=3
return Xout
def one_level_laplacian(img):
# generate Gaussian pyramid for Apple
A = img.copy()
# Downsample blurred A
small_A = pyramid_reduce(A, downscale=2, multichannel=True)
# Upsample small, blurred A
# insert zeros between pixels, then apply a gaussian low pass filter
upsampled_A = pyramid_expand(small_A, upscale=2, multichannel=True)
# generate Laplacian level for A
laplace_A = A - upsampled_A
return small_A, upsampled_A, laplace_A
def downscale(self, image) -> np.ndarray:
"""Convenience method to map an image in the hi-res scale down to the original MNIST format.
Parameters
----------
image : (scale*H, scale*W) array_like
High-resolution input image.
Returns
-------
(H, W) numpy.ndarray
Low-resolution `uint8` image.
"""
image = np.asarray(image)
down_img = transform.pyramid_reduce(image, downscale=self.scale, order=3) # type: np.ndarray
return (255. * down_img).astype(np.uint8)
def test_prior_boxes_1():
voc2012 = VOC2012()
image, boxes = voc2012[random.randrange(len(voc2012))]
image, boxes = image_padding(image, boxes)
print('num boxes: {}'.format(len(boxes)))
limit = {
0: {
'min': 0,
'max': 64
},
1: {
'min': 64,
'max': 256
},
2: {
'min': 256,
'max': 512
}
}
for layer in range(3):
# switch plot
fig, ax = plt.subplots()
ax.imshow(image)
#
scale = pow(4, layer)
# loop boxes
for top, bottom, left, right, name in boxes:
height, width = bottom - top, right - left
mid_x, mid_y = (left + right) // 2, (top + bottom) // 2
if limit[layer]['min'] <= max(height, width) < limit[layer]['max']:
# prior box in current feature map
rect = patches.Rectangle((left // scale, top // scale),
width // scale,
height // scale,
edgecolor='red',
linewidth=2,
fill=False)
ax.add_patch(rect)
#
image = transform.pyramid_reduce(image, downscale=4)
plt.show()
def weight_pyramid(generator, weights=[1, 1, 1]):
nb_layers = len(weights) - 1
for batch in generator:
batch_merged = []
for img in batch:
img = img[0]
lap_pyr = []
prev = img
for i in range(nb_layers):
gauss = pyramid_reduce(prev)
lap_pyr.append(prev - pyramid_expand(gauss))
prev = gauss
merged = gauss*weights[0]
for i, lap in enumerate(reversed(lap_pyr)):
merged = pyramid_expand(merged) + weights[i+1]*lap
batch_merged.append(merged)
yield np.stack(batch_merged).reshape(batch.shape)
def spectral_cluster(inp_image,
n_clusters=int(config['SPECTRAL']['N_CLUSTERS'])):
original_shape = inp_image.shape
downsampled_img = pyramid_reduce(inp_image, 3)
shape = downsampled_img.shape
downsampled_img = downsampled_img.reshape(shape[0] * shape[1], shape[2])
sp = SpectralClustering(n_clusters=n_clusters,
eigen_solver=config['SPECTRAL']['EIGEN_SOLVER'],
affinity=config["SPECTRAL"]["AFFINITY"])
sp.fit_predict(downsampled_img)
clust = sp.labels_
clust = clust.reshape(shape[0], shape[1])
# Performimg kmeans to re generate clusters after resize, original segmentation remains intact.
clust = k_means_clustering(
n_clusters,
resize(clust,
(original_shape[:-1])).reshape((original_shape[:-1]) + (1, )))
return clust
def weight_pyramid(generator, weights=[1, 1, 1]):
nb_layers = len(weights) - 1
for batch in generator:
batch_merged = []
for img in batch:
img = img[0]
lap_pyr = []
prev = img
for i in range(nb_layers):
gauss = pyramid_reduce(prev)
lap_pyr.append(prev - pyramid_expand(gauss))
prev = gauss
merged = gauss * weights[0]
for i, lap in enumerate(reversed(lap_pyr)):
merged = pyramid_expand(merged) + weights[i + 1] * lap
batch_merged.append(merged)
yield np.stack(batch_merged).reshape(batch.shape)
def preprocess_images(input_folder = '../train', output_folder = '../train-256', pixel_size = 256.):
input_list = set([file for file in os.listdir(input_folder) if file.endswith('.jpeg')])
output_list = set([file for file in os.listdir(output_folder) if file.endswith('.jpeg')])
files_to_process = list(input_list - output_list)
for fn in files_to_process:
original_image = io.imread(input_folder + '/' + fn)
shape = original_image.shape[1] - original_image.shape[0]
if shape < 0:
shape = -shape
if shape % 2 == 0:
shape += 1
kernel = np.ones((shape, 1))
else:
if shape % 2 == 0:
shape += 1
kernel = np.ones((1, shape))
output_image = remove_padding(original_image, kernel)
grayed_image = color.rgb2gray(padded_image)
blurred_image = gaussian_filter(grayed_image,sigma=6, multichannel=False)
difference_image = equalize_hist(grayed_image - blurred_image)
scale = difference_image.shape[0] / pixel_size
if scale > 1:
output_image = transform.pyramid_reduce(difference_image, downscale=scale)
elif scale < 1:
output_image = transform.pyramid_expand(difference_image, upscale=1/scale)
else:
output_image = difference_image
if output_image.shape != (pixel_size, pixel_size):
x = pixel_size - output_image.shape[0]
y = pixel_size - output_image.shape[1]
if x < 0:
image = output_image[:x, :]
if y < 0:
image = output_image[:, :y]
output_image = (output_image - output_image.min()) / output_image.max()
try:
io.imsave(output_folder + '/' + fn, output_image)
except ValueError:
print fn + ' not saved!'
def convert_to_square(image, size, retain_aspect_ratio=False):
"""
Resizes an image while maintaing aspect ratio
image: image as numpy array
size: resize size for square
retain_aspect_ratio: if true, it will try to resize the image while maintaining it's aspect ratio.
Note: retain_aspect_ratio is not playing well with image normalization and seems to alter the original image quite a bit
"""
mask = None
if retain_aspect_ratio:
height, width = image.shape
if (height > width):
differ = height
else:
differ = width
differ += 4
# square filler
background_filler = image[0][0]
mask = np.zeros((differ, differ), dtype="uint8")
mask.fill(background_filler)
x_pos = int((differ - width) / 2)
y_pos = int((differ - height) / 2)
# center image inside the square
mask[y_pos:y_pos + height, x_pos:x_pos + width] = image[0:height,
0:width]
# downscale if needed
# note: pyramid_reduce is normalizing the image by default
if differ / size > 1:
mask = pyramid_reduce(mask, differ / size)
mask = np.round(mask, 1)
else:
mask = image
return cv2.resize(mask, (size, size), interpolation=cv2.INTER_AREA)
def downscale(self, image) -> np.ndarray:
"""Convenience method to map an image in the hi-res scale down to the original MNIST format.
Parameters
----------
image : (scale*H, scale*W) array_like
High-resolution input image.
Returns
-------
(H, W) numpy.ndarray
Low-resolution `uint8` image.
"""
image = np.asarray(image)
if self.scale > 1:
down_img = transform.pyramid_reduce(image, downscale=self.scale, order=3) # type: np.ndarray
else:
down_img = image
return (255. * down_img).astype(np.uint8)
def process(
img: Union[ndarray, str],
coloring: ColorMethod,
sampling: SampleMethod,
edging: EdgeMethod,
points: int,
blur: int,
reduce: bool,
) -> np.array:
if isinstance(img, str):
img = imread(img)
sample_points: ndarray = EdgePoints(img, points, edging).get_edge_points(
sampling=sampling, blur=blur,
)
triangulated: Delaunay = Delaunay(sample_points)
# noinspection PyUnresolvedReferences
triangles = sample_points[triangulated.simplices]
res = np.empty(
shape=(2 * img.shape[0], 2 * img.shape[1], img.shape[2]), dtype=np.uint8
)
if coloring is ColorMethod.CENTROID:
for triangle in triangles:
i, j = polygon(2 * triangle[:, 0], 2 * triangle[:, 1], res.shape)
res[i, j] = img[tuple(np.mean(triangle, axis=0, dtype=np.int32))]
elif coloring is ColorMethod.MEAN:
for triangle in triangles:
i, j = polygon(2 * triangle[:, 0], 2 * triangle[:, 1], res.shape)
res[i, j] = np.mean(
img[polygon(triangle[:, 0], triangle[:, 1], img.shape)], axis=0
)
else:
raise ValueError(
"Unexpected coloring method: {}\n"
"use {} instead: {}".format(
coloring, ColorMethod.__name__, ColorMethod.__members__
)
)
return pyramid_reduce(res, multichannel=True) if reduce else res
def get_square(image, square_size):
height, width = image.shape
if(height > width):
differ = height
else:
differ = width
differ += 4
mask = np.zeros((differ, differ), dtype = "uint8")
x_pos = int((differ - width) / 2)
y_pos = int((differ - height) / 2)
mask[y_pos: y_pos + height, x_pos: x_pos + width] = image[0: height, 0: width]
if differ / square_size > 1:
mask = pyramid_reduce(mask, differ / square_size)
else:
mask = cv2.resize(mask, (square_size, square_size), interpolation = cv2.INTER_AREA)
return mask
def resize_cyx_image(image, new_size):
"""
This function resizes a CYX image.
:param image: CYX ndarray
:param new_size: tuple of shape of desired image dimensions in CYX
:return: image with shape of new_size
"""
scaling = float(image.shape[1]) / float(new_size[1])
# get the shape of the image that is resized by the scaling factor
test_shape = np.ceil(np.divide(image.shape, [1, scaling, scaling]))
# sometimes the scaling can be rounded incorrectly and scale the image to
# one pixel too high or too low
if not np.array_equal(test_shape, new_size):
# getting the scaling from the other dimension solves this rounding problem
scaling = float(image.shape[2]) / float(new_size[2])
test_shape = np.ceil(np.divide(image.shape, [1, scaling, scaling]))
# if neither scaling factors achieve the desired shape, then the aspect ratio of the image
# is different than the aspect ratio of new_size
if not np.array_equal(test_shape, new_size):
raise ValueError(
"This image does not have the same aspect ratio as new_size")
image = image.transpose((2, 1, 0))
# im_out = t.resize(image, new_size)
if scaling < 1:
scaling = 1.0 / scaling
im_out = t.pyramid_expand(image, upscale=scaling)
elif scaling > 1:
im_out = t.pyramid_reduce(image, downscale=scaling)
else:
im_out = image
im_out = im_out.transpose((2, 1, 0))
assert im_out.shape == new_size
return im_out
def spectral_cluster(inp_image, n_clusters=2):
raise ("SPECTRAL CLUSTERING NOT WORKING!!!!")
original_shape = inp_image.shape
downsampled_img = pyramid_reduce(inp_image, 3)
shape = downsampled_img.shape
downsampled_img = downsampled_img.reshape(shape[0] * shape[1], 1)
EIGEN_SOLVER = "arpack"
AFFINITY = "nearest_neighbors"
#N_CLUSTERS=5
#WINDOW_SIZE=2
sp = SpectralClustering(n_clusters=n_clusters,
eigen_solver=EIGEN_SOLVER,
affinity=AFFINITY)
sp.fit_predict(downsampled_img)
clust = sp.labels_
clust = clust.reshape(shape[0], shape[1])
# Performimg kmeans to re generate clusters after resize, original segmentation remains intact.
clust = k_means_clustering(
resize(clust, (original_shape[-1])).reshape(shape[0], shape[1]),
n_clusters)
return computeClusterMaxoids(inp_image, clust, n_clusters)
def process_img(img):
s = img.shape
# downsample
downscale = s[1] // 100
if downscale > 1:
thumb = transform.pyramid_reduce(img, downscale=downscale)
thumb = 255 * thumb
thumb = thumb.astype('uint8')
else:
thumb = img.astype('uint8')
# slic
labels = segmentation.slic(thumb, compactness=.1, n_segments=2)
# predict tail segment
tail_mask = predict_tail2(labels)
# upsample mask
tail_mask_big = transform.resize(255 * tail_mask,
output_shape=(s[0], s[1]),
order=0,
mode='edge') #refine sizing
tail_mask_big = skimage.img_as_ubyte(tail_mask_big)
# dialate tail mask
tail_mask_big = morphology.binary_dilation(
tail_mask_big, selem=morphology.disk(radius=downscale))
# generate full res tail
alpha = np.expand_dims(255 * tail_mask_big, axis=2)
img = np.concatenate((img, alpha), axis=2)
img = skimage.img_as_ubyte(img)
# returns thumbnail, and full resolution img with alpha channels
return img
eval_list = np.loadtxt(os.path.join(base_path, 'list_eval_partition.csv'),
dtype=str,
delimiter=',',
skiprows=1)
#%%
img_sample = cv2.imread(os.path.join(img_base_path,
eval_list[0][0]))
h, w, _ = img_sample.shape
# 정사각형 이미지로 crop 해준다.
crop_sample = img_sample[int((h-w)/2):int(-(h-w)/2), :]
# 이미지를 4배만큼 축소하고 normalize 한다.
resized_sample = pyramid_reduce(crop_sample,
downscale=4,
multichannel=True) # 컬러채널 허용
pad = int((crop_sample.shape[0] - resized_sample.shape[0]) / 2)
padded_sample = cv2.copyMakeBorder(resized_sample,
top=pad,
bottom=pad,
left=pad,
right=pad,
borderType=cv2.BORDER_CONSTANT,
value=(0,0,0))
print(crop_sample.shape, padded_sample.shape)
fig, ax = plt.subplots(1,4,figsize=(12,5))
def process(self):
super(Resize, self).process()
self.resized_image.value = transform.pyramid_reduce(self.original_image.value, downscale=2)
def test_pyramid_reduce():
rows, cols, dim = image.shape
out = pyramid_reduce(image, downscale=2)
assert_array_equal(out.shape, (rows / 2, cols / 2, dim))
kernels *= diff
spread_bkg = spread_bkg_obs
comps = detector.mixture.mixture_components()
#theta = kernels.reshape((kernels.shape[0], -1))
llhs = [[] for i in xrange(detector.num_mixtures)]
print 'Iterating CAD images'
for cad_i, cad_filename in enumerate(cad_files):
cad = gv.img.load_image(cad_filename)
f = cad.shape[0]/size[0]
if f > 1:
cad = pyramid_reduce(cad, downscale=f)
elif f < 1:
cad = pyramid_expand(cad, upscale=1/f)
mixcomp = comps[cad_i]
alpha = cad[...,3]
gray_cad = gv.img.asgray(cad)
bkg_img = bkg_generator.next()
# Notice, gray_cad is not multiplied by alpha, since most files use premultiplied alpha
composite = gray_cad + bkg_img * (1 - alpha)
# Get features
X_full = descriptor.extract_features(composite, settings=dict(spread_radii=radii))
X = gv.sub.subsample(X_full, subsize)
from keras.models import Model
from keras.layers import Input, Conv2D, Activation
from keras.optimizers import Adam
from keras.losses import mean_squared_error
from keras.datasets import cifar10
import skimage.io
from skimage.transform import pyramid_reduce
import numpy as np
#Downloading dataset, downscaling, padding
(HDimages, ignore), (test_images, ignore) = cifar10.load_data()
downscaled = np.zeros((HDimages.shape[0], 16, 16, 3))
downscaled_test = np.zeros((test_images.shape[0], 16, 16, 3))
for i, image in enumerate(HDimages):
downscaled[i, :, :, :] = pyramid_reduce(image, 2)
for i, image in enumerate(test_images):
downscaled_test[i, :, :, :] = pyramid_reduce(image, 2)
pad = 3
padded = np.zeros((downscaled.shape[0], downscaled.shape[1] + 2 * pad,
downscaled.shape[2] + 2 * pad, downscaled.shape[3]))
padded_test = np.zeros(
(downscaled_test.shape[0], downscaled_test.shape[1] + 2 * pad,
downscaled_test.shape[2] + 2 * pad, downscaled_test.shape[3]))
for i, image in enumerate(downscaled):
padded[i, pad:-1 * (pad), pad:-1 * (pad), :] = image
for i, image in enumerate(downscaled_test):
padded_test[i, pad:-1 * (pad), pad:-1 * (pad), :] = image
img_path = './img2_crop.jpg'
window_size = (120, 100) #heuristically chosen for this image
img = color.rgb2gray(misc.imread(img_path))
h, w = img.shape
delta_x, delta_y = stride
x_list = range(0, w - window_size[1] + 1, delta_x)
y_list = range(0, h - window_size[0] + 1, delta_y)
lis = []
for w in x_list:
for h in y_list:
#downscale value also heurestically chosen
im = pyramid_reduce(img[h:h + window_size[0], w:w + window_size[1]],
downscale=5)
lis.append(np.array(im[2:21, :19] * 255, dtype=np.uint8))
import pickle
pickle.dump(lis, open("test-windows.pkl", "wb"))
#lis = pickle.load( open( "test-windows.pkl", "rb" ) )
##Finding-windows
k = len(lis) / 10 #no of chunks, jobs
iterator = range(0, len(lis) - k, k)
from joblib import Parallel, delayed
from parr_test import myfunc
pdb.set_trace()
results = Parallel(n_jobs=-1)(delayed(myfunc)(lis[i:i + k]) for i in iterator)
def save_2d_keypoints_and_images(video_name, video_path, npy_path,
rgb_skeleton_data, frame_time_dict):
mismatch_count = 0
## cap = cv2.VideoCapture(video_path)
## assert(cap.isOpened() == True)
container = av.open(video_path)
for k, fr in enumerate(container.decode(video=0)):
assert (k == fr.index)
## for k in frame_time_dict.keys():
nearest_idx, nearest_time = find_nearest_frameindex_from_skeleton_file(
rgb_skeleton_data[..., 0],
frame_time_dict[k]) # take column 0 (time) from rgb data
# print("k (video frame) ", k, "\t time", frame_time_dict[k], "\t nearest_idx from skeleton file", nearest_idx, "\t nearest_time", nearest_time) # print("k=>", k, nearest_idx, "<= nearest_idx")
if (abs(frame_time_dict[k] - nearest_time) >
1000000): # 100 ns ticks, so 1000000 = 0.1sec
mismatch_count += 1
continue # do not add the nearest found index if the difference is really big (>0.1sec)
else:
# print(rgb_skeleton_data[nearest_idx])
if (np.inf not in rgb_skeleton_data[nearest_idx]
): # do not add if there is np.inf in the line
## cap.set(cv2.CAP_PROP_POS_FRAMES, k)
## success, frame = cap.read() # frame is read as (h, w, c)
success = True # hard-coded for PyAV
frame = fr.to_image()
# converting PIL (<class 'PIL.Image.Image'>) to <class 'numpy.ndarray'>
img = np.asarray(frame) # h, w, c
if success:
os.makedirs(os.path.join(npy_path, video_name),
exist_ok=True)
save_dir = os.path.join(npy_path, video_name)
# 1
# save image with the original resolution
# print("kth frame =", k, frame.shape, "\n")
# cv2.imwrite(os.path.join(save_dir, video_name + "_vfr_" + str(k) + "_skfr_" + str(nearest_idx) + '.jpg'), frame)
# 2
# save downsampled image
## bgr to rgb
## img = frame[...,::-1]
img_central = img[:, 240:(1920 - 240), :]
# downsample by 4.5
img_down = pyramid_reduce(
img_central, downscale=4.5) # better than resize
# print("img_down shape (h, w, c)", img_down.shape) # height, width, channels (rgb)
skimage.io.imsave(
os.path.join(
save_dir, video_name + "_vfr_" + str(k) +
"_skfr_" + str(nearest_idx) + "_240x320.jpg"),
img_down)
# 3
# save heatmaps and pafs
sk_keypoints_with_tracking_info = rgb_skeleton_data[
nearest_idx][1:] # ignore index 0 (time)
sk_keypoints = np.delete(
sk_keypoints_with_tracking_info,
np.arange(0, sk_keypoints_with_tracking_info.size, 3)
) # this is without tracking info, by removing the tracking info
# print("sk_kp shape =", sk_keypoints.shape) # (38, )
# for 20 (actually 19 + background) heatmaps =====================================
for kpn in range(sk_keypoints.shape[0] // 2):
kpx = sk_keypoints[2 * kpn]
kpy = sk_keypoints[2 * kpn + 1] # print(kpx, kpy)
index_array = np.zeros((240 // ground_truth_factor,
320 // ground_truth_factor, 2))
for i in range(index_array.shape[0]):
for j in range(index_array.shape[1]):
index_array[i][j] = [
i, j
] # height (y), width (x) => index_array[:,:,0] = y pixel coordinate and index_array[:,:,1] = x
if kpn == 0:
heatmap = get_heatmap(
index_array, kpx_kpy_transformer([kpx, kpy])
) # /4 because image is 1080 x 1920 and so are the original pixel locations of the keypoints
else:
heatmap = np.dstack(
(heatmap,
get_heatmap(index_array,
kpx_kpy_transformer([kpx, kpy]))))
# print("heatmap.shape =", heatmap.shape)
# generate background heatmap
maxed_heatmap = np.max(
heatmap[:, :, :], axis=2
) # print("maxed_heatmap.shape = ", maxed_heatmap.shape)
heatmap = np.dstack((heatmap, 1 - maxed_heatmap))
# print("final heatmap.shape =", heatmap.shape)
np.save(
os.path.join(
save_dir, video_name + "_vfr_" + str(k) +
"_skfr_" + str(nearest_idx) + "_heatmap30x40.npy"),
heatmap)
# for 18x2 PAFs =====================================
for n, pair in enumerate(paf_pairs_indices):
# print("writing paf for index", n, pair)
index_array = np.zeros((240 // ground_truth_factor,
320 // ground_truth_factor, 2))
for i in range(index_array.shape[0]):
for j in range(index_array.shape[1]):
index_array[i][j] = [
i, j
] # height (y), width (x) => index_array[:,:,0] = y pixel coordinate and index_array[:,:,1] = x
if n == 0:
paf = get_pafx_pafy(
index_array,
kp0xy=kpx_kpy_transformer([
sk_keypoints[2 * pair[0]],
sk_keypoints[2 * pair[0] + 1]
]),
kp1xy=kpx_kpy_transformer([
sk_keypoints[2 * pair[1]],
sk_keypoints[2 * pair[1] + 1]
]))
else:
paf = np.dstack(
(paf,
get_pafx_pafy(
index_array,
kp0xy=kpx_kpy_transformer([
sk_keypoints[2 * pair[0]],
sk_keypoints[2 * pair[0] + 1]
]),
kp1xy=kpx_kpy_transformer([
sk_keypoints[2 * pair[1]],
sk_keypoints[2 * pair[1] + 1]
]))))
# print("paf.shape =", paf.shape)
# print("final paf.shape =========================", paf.shape)
np.save(
os.path.join(
save_dir, video_name + "_vfr_" + str(k) +
"_skfr_" + str(nearest_idx) + "_paf30x40.npy"),
paf)
# 4
# save the 2d keypoints of shape (38,)
# print(rgb_skeleton_data[nearest_idx])
# print(save_dir, os.path.join("", video_name + "_vfr_" + str(k) + "_skfr_" + str(nearest_idx) + '.npy'))
np.save(
os.path.join(
save_dir, video_name + "_vfr_" + str(k) +
"_skfr_" + str(nearest_idx) + '.npy'),
rgb_skeleton_data[nearest_idx][1:]
) # index 0 is time # saving all 57 values 19 * 3 (tracking, x, y)
## cap.release()
print("mismatch_count =", mismatch_count)
def _process_file(settings, bkg_stack, bkg_stack_num, fn, mixcomp):
ag.info("Processing file", fn)
seed = np.abs(hash(fn) % 123124)
descriptor_name = settings["detector"]["descriptor"]
img_size = settings["detector"]["image_size"]
part_size = settings[descriptor_name]["part_size"]
psize = settings["detector"]["subsample_size"]
# The 4 is for the edge border that falls off
# orig_sh = (img_size[0] - part_size[0] - 4 + 1, img_size[1] - part_size[1] - 4 + 1)
orig_sh = img_size
sh = gv.sub.subsample_size(np.ones(orig_sh), psize)
# We need the descriptor to generate and manipulate images
descriptor = gv.load_descriptor(settings)
counts = np.zeros(
(settings["detector"]["num_mixtures"], sh[0], sh[1], descriptor.num_parts + 1, descriptor.num_parts),
dtype=np.uint16,
)
prnds = [np.random.RandomState(seed + i) for i in xrange(5)]
# Binarize support and Extract alpha
# color_img, alpha = gv.img.load_image_binarized_alpha(fn)
color_img = gv.img.load_image(fn)
from skimage.transform import pyramid_reduce, pyramid_expand
f = color_img.shape[0] / settings["detector"]["image_size"][0]
if f > 1:
color_img = pyramid_reduce(color_img, downscale=f)
elif f < 1:
color_img = pyramid_expand(color_img, upscale=1 / f)
alpha = color_img[..., 3]
img = gv.img.asgray(color_img)
# Resize it
# TODO: This only looks at the first axis
assert img.shape == settings["detector"]["image_size"], "Target size not achieved: {0} != {1}".format(
img.shape, settings["detector"]["image_size"]
)
# Settings
bsettings = settings["edges"].copy()
radius = bsettings["radius"]
bsettings["radius"] = 0
# offsets = gv.sub.subsample_offset_shape(sh, psize)
# locations0 = xrange(offsets[0], sh[0], psize[0])
# locations1 = xrange(offsets[1], sh[1], psize[1])
locations0 = xrange(sh[0])
locations1 = xrange(sh[1])
# locations0 = xrange(10-4, 10+5)
# locations1 = xrange(10-4, 10+5)
# locations0 = xrange(10, 11)
# locations1 = xrange(10, 11)
# padded_theta = descriptor.unspread_parts_padded
# pad = 10
pad = 5
size = settings[descriptor_name]["part_size"]
X_pad_size = (size[0] + pad * 2, size[1] + pad * 2)
img_pad = ag.util.zeropad(img, pad)
alpha_pad = ag.util.zeropad(alpha, pad)
# Iterate every duplicate
dups = settings["detector"].get("duplicates", 1)
bkgs = np.empty(((descriptor.num_parts + 1) * dups,) + X_pad_size)
# cads = np.empty((descriptor.num_parts,) + X_pad_size)
# alphas = np.empty((descriptor.num_parts,) + X_pad_size, dtype=np.bool)
radii = settings["detector"]["spread_radii"]
psize = settings["detector"]["subsample_size"]
cb = settings["detector"].get("crop_border")
sett = dict(spread_radii=radii, subsample_size=psize, crop_border=cb)
plt.clf()
plt.imshow(img)
plt.savefig("output/img.png")
if 0:
# NEW{
totfeats = np.zeros(sh + (descriptor.num_parts,) * 2)
for f in xrange(descriptor.num_parts):
num = bkg_stack_num[f]
for d in xrange(dups):
feats = np.zeros(sh + (descriptor.num_parts,), dtype=np.uint8)
for i, j in itr.product(locations0, locations1):
x = i * psize[0]
y = i * psize[1]
bkg_i = prnds[4].randint(num)
bkg = bkg_stack[f, bkg_i]
selection = [slice(x, x + X_pad_size[0]), slice(y, y + X_pad_size[1])]
# X_pad = edges_pad[selection].copy()
patch = img_pad[selection]
alpha_patch = alpha_pad[selection]
# patch = np.expand_dims(patch, 0)
# alpha_patch = np.expand_dims(alpha_patch, 0)
# TODO: Which one?
# img_with_bkg = patch + bkg * (1 - alpha_patch)
img_with_bkg = patch * alpha_patch + bkg * (1 - alpha_patch)
edges_pads = ag.features.bedges(img_with_bkg, **bsettings)
X_pad_spreads = ag.features.bspread(edges_pads, spread=bsettings["spread"], radius=radius)
padding = pad - 2
X_spreads = X_pad_spreads[padding:-padding:, padding:-padding]
partprobs = ag.features.code_parts(
X_spreads,
descriptor._log_parts,
descriptor._log_invparts,
descriptor.settings["threshold"],
descriptor.settings["patch_frame"],
)
part = partprobs.argmax()
if part > 0:
feats[i, j, part - 1] = 1
# Now spread the parts
feats = ag.features.bspread(feats, spread="box", radius=2)
totfeats[:, :, f] += feats
# }
kernels = totfeats[:, :, 0].astype(np.float32) / (descriptor.num_parts * dups)
# Subsample kernels
sub_kernels = gv.sub.subsample(kernels, psize, skip_first_axis=False)
np.save("tmp2.npy", sub_kernels)
print "saved tmp2.npy"
import sys
sys.exit(0)
# ag.info("Iteration {0}/{1}".format(loop+1, num_duplicates))
# ag.info("Iteration")
for i, j in itr.product(locations0, locations1):
x = i * psize[0]
y = i * psize[1]
print "processing", i, j
selection = [slice(x, x + X_pad_size[0]), slice(y, y + X_pad_size[1])]
# X_pad = edges_pad[selection].copy()
patch = img_pad[selection]
alpha_patch = alpha_pad[selection]
patch = np.expand_dims(patch, 0)
alpha_patch = np.expand_dims(alpha_patch, 0)
for f in xrange(descriptor.num_parts + 1):
num = bkg_stack_num[f]
for d in xrange(dups):
bkg_i = prnds[4].randint(num)
bkgs[f * dups + d] = bkg_stack[f, bkg_i]
img_with_bkgs = patch * alpha_patch + bkgs * (1 - alpha_patch)
if 0:
edges_pads = ag.features.bedges(img_with_bkgs, **bsettings)
X_pad_spreads = ag.features.bspread(edges_pads, spread=bsettings["spread"], radius=radius)
padding = pad - 2
X_spreads = X_pad_spreads[:, padding:-padding:, padding:-padding]
# partprobs = ag.features.code_parts_many(X_spreads, descriptor._log_parts, descriptor._log_invparts,
# descriptor.settings['threshold'], descriptor.settings['patch_frame'])
# parts = partprobs.argmax(axis=-1)
parts = np.asarray([descriptor.extract_features(im, settings=sett)[0, 0] for im in img_with_bkgs])
for f in xrange(descriptor.num_parts + 1):
hist = np.bincount(parts[f * dups : (f + 1) * dups].ravel(), minlength=descriptor.num_parts + 1)
counts[mixcomp, i, j, f] += hist[1:]
# import pdb; pdb.set_trace()
# for f in xrange(descriptor.num_parts):
# for d in xrange(dups):
# # Code parts
# #parts = descriptor.extract_parts(X_spreads[f*dups+d].astype(np.uint8))
#
# f_plus = parts[f*dups+d]
# if f_plus > 0:
# tau = self.settings.get('tau')
# if self.settings.get('tau'):
# parts = partprobs.argmax(axis=-1)
# Accumulate and return
# counts[mixcomp,i,j,f,f_plus-1] += 1#parts[0,0]
if 0:
kernels = counts[:, :, :, 0].astype(np.float32) / (descriptor.num_parts * dups)
import pdb
pdb.set_trace()
radii = (2, 2)
aa_log = np.log(1 - kernels)
aa_log = ag.util.zeropad(aa_log, (0, radii[0], radii[1], 0))
integral_aa_log = aa_log.cumsum(1).cumsum(2)
offsets = gv.sub.subsample_offset(kernels[0], psize)
if 1:
# Fix kernels
istep = 2 * radii[0]
jstep = 2 * radii[1]
sh = kernels.shape[1:3]
for mixcomp in xrange(1):
# Note, we are going in strides of psize, given a certain offset, since
# we will be subsampling anyway, so we don't need to do the rest.
for i in xrange(offsets[0], sh[0], psize[0]):
for j in xrange(offsets[1], sh[1], psize[1]):
p = gv.img.integrate(integral_aa_log[mixcomp], i, j, i + istep, j + jstep)
kernels[mixcomp, i, j] = 1 - np.exp(p)
# Subsample kernels
sub_kernels = gv.sub.subsample(kernels, psize, skip_first_axis=True)
np.save("tmp.npy", sub_kernels)
print "saved tmp.npy"
import sys
sys.exit(0)
if 0:
for f in xrange(descriptor.num_parts):
# Pick only one background for this part and file
num = bkg_stack_num[f]
# Assumes num > 0
bkg_i = prnds[4].randint(num)
bkgmap = bkg_stack[f, bkg_i]
# Composite
img_with_bkg = gv.img.composite(patch, bkgmap, alpha_patch)
# Retrieve unspread edges (with a given background gray level)
edges_pad = ag.features.bedges(img_with_bkg, **bsettings)
# Pad the edges
# edges_pad = ag.util.zeropad(edges, (pad, pad, 0))
# Do spreading
X_pad_spread = ag.features.bspread(edges_pad, spread=bsettings["spread"], radius=radius)
# De-pad
padding = pad - 2
X_spread = X_pad_spread[padding:-padding, padding:-padding]
# Code parts
parts = descriptor.extract_parts(X_spread.astype(np.uint8))
# Accumulate and return
counts[mixcomp, i, j, f] += parts[0, 0]
# Translate counts to spread counts (since we're assuming independence of samples within one CAD image)
return counts
def montageIXM(plate_path, labelled= True, rescale_intensity=True):
""""Place into plate folder sorted by wavelength. Run. Will create a montages of
each wavelength separately and a combined RGB overlay with files ordered according
to the .HTD metadata file from the IXM which contain indicators of sites selected.
Function is set to automatically rescale image intensity unless otherwise specified."""
# Obtains the working directory of the targeted folder.
directory = plate_path
# Make a list of all subdirectories (time point folders)
subdirectories = os.walk('.').next()[1]
#print subdirectories
# Search for relevant metadata file
files_in_directory = os.listdir(directory)
#print files_in_directory
for file in files_in_directory:
htd_check = re.search('.HTD', file)
if htd_check:
metadata_file = file
if 'metadata_file' in locals():
print 'Metadata file "' + metadata_file +'" identified. Attempting to read...'
else:
print 'Error: Metadata file with .HTD extension is missing.'
return
# Reads the metadata file to a dictionary consisting of line title
# and value pairs.
with open(metadata_file, 'r') as csv_metadata:
csv_reader = csv.reader(csv_metadata)
csv_dict = dict()
# Clean up messy formatting of lines read from the proprietary
# metadata file. Removes unnecessary spaces and quotations to
# put information in readily accessible format.
for line in csv_reader:
key = line.pop(0)
#print line
line = [item.split(' ',1)[1] for item in line]
#print line
i = 0
for item in line:
line[i] = re.sub('"|"','', item)
i += 1
#print line
csv_dict.update({key:line})
key_list = csv_dict.keys()
#print key_list
print 'Metadata file read successfully.'
# Determine shape of montage based on metadata
print 'Determining the shape of your montage based on metadata...'
def list2string2int(list):
# Converts a list of a single string to an integer
list = int(re.sub("'|'",'', str(list)).replace('[','').replace(']',''))
return list
# Determine max columns and rows for sites selected
site_selection_list = []
for key in key_list:
#print key
site_selectorcheck = re.search('SiteSelection\d{1,2}', key)
if site_selectorcheck:
print site_selectorcheck.group(), ' identified!'
site_selection_list.append(csv_dict[key])
#print site_selection_list
col_selector = []
row_selector = []
for bool_list in site_selection_list:
# Identify number of columns selected
col_selection_counter = bool_list.count('TRUE')
col_selector.append(col_selection_counter)
# Identify number of rows selected
index = 0
for bool in bool_list:
if bool == 'TRUE':
row_selector.append(index)
index += 1
row_selector_counter = []
for i in row_selector:
row_selector_counter.append(row_selector.count(i))
#print row_selector_counter
columns = max(col_selector)
rows = max(row_selector_counter)
print '(columns, rows):', (columns, rows)
# Determine well setup for plate
XWells = list2string2int(csv_dict['XWells'])
YWells = list2string2int(csv_dict['YWells'])
#print XWells, YWells
grid_shape = (columns*XWells, rows*YWells)
print 'Montage grid dimensions:', grid_shape
print 'Searching for image wavelength folders...'
for subdirectory in subdirectories:
# Search file name string for site metadata
wavecheck = re.search('w\d', subdirectory)
if wavecheck:
print 'Image folder ' + str(wavecheck.group()) + ' identified.'
# Create a list of files in the current subdirectory
files = os.listdir(directory + '/' + subdirectory)
#print files
files = [subdirectory + '/' + file for file in files]
#print files
total_files = len(files)
print 'There are ' + str(total_files) + ' image files.'
###################################################################################
# METHOD 5 - NumPy binary files
# http://docs.scipy.org/doc/numpy/reference/generated/numpy.save.html#numpy.save
###################################################################################
# Issue: Works as well as (or better than!) any other method! Now add feature to correct how the montage is displayed
# Add method to create RGB composite overlay montage of DAP, FITC, and TexasRed channels
# Add text labelling functionality for verification using PIL.ImageDraw.Draw.text(xy,text,fill=None,font=None,anchor=None)?
# e.g. https://code.google.com/p/esutil/source/browse/trunk/esutil/sqlite_util.py
montage = wavecheck.group()
temp = directory + '/tmp'
# if os.path.exists(temp):
# shutil.rmtree(temp)
# os.mkdir(temp)
# Rescale intensity of images
sites_per_well = total_files/(XWells*YWells)
print 'sites_per_well: ', sites_per_well
for i in range(XWells):
row_id = 0
counter = 0
new_row = True
print 'Starting well: ', i
for j in range(sites_per_well):
# print 'counter: ', counter
# print 'new_row: ', new_row
image = Image.open(files[j+i*sites_per_well])
# print 'File:', j+i*sites_per_well
image = np.array(image, dtype=np.int16)
#print 'Converted to NumPy array.'
# To rescale the intensity of EACH image INDEPENDENTLY, uncomment the line below
# and comment the other exposure.rescale_intensity(montage_np) after the for loop ends
#image = exposure.rescale_intensity(image)
image = transform.pyramid_reduce(image, downscale=10)
#print 'Resizing image now.'
if new_row:
row_builder = image
# print 'Row initialized.'
new_row = False
else:
row_builder = np.hstack((row_builder, image))
# print 'row_builder: ' + str(row_builder.shape)
if counter == rows: # If we reached the end of a row
# print '(counter, rows):', (counter, rows)
if row_id == 0: # If the row is the first row
montage_np = row_builder
#print 'montage_np: '+ str(montage_np.shape)
else: # If the row is any other row
#print 'montage_np: '+ str(montage_np.shape)
# print 'row_builder: ', row_builder.shape
montage_np = np.vstack((montage_np,row_builder))
counter = 0
row_id += 1
new_row = True
print('Row %d complete!' % row_id)
# print row_builder.size
#test = Image.fromarray(montage_np)
#test.save(temp+'/Montage_%s_%s.tif' % (montage, row_str))
else:
counter += 1
print 'Well Montage Dimensions:', montage_np.shape
if i == 0:
well_stack = montage_np
else:
well_stack = np.hstack((well_stack, montage_np))
print 'Overall Montage Dimensions:', well_stack.shape
print('Compiling and rescaling the montage for viewing...')
# To rescale the intensity of the TOTAL MONTAGE all at once, allowing visual comparison of image intensities,
# leave the line below uncommented and comment the exposure.rescale_intensity(image) in the for loop, above
well_stack = exposure.rescale_intensity(well_stack)
img = Image.fromarray(well_stack)
print('Montage %s created.' % montage)
img.save('Montage_%s.tif' % montage)
print('Montage %s saved!' % montage)
img = color.rgb2gray(misc.imread(img_path))
h,w = img.shape
delta_x,delta_y = stride
x_list = range(0,w-window_size[1]+1,delta_x)
y_list = range(0,h-window_size[0]+1,delta_y)
lis=[]
for w in x_list:
for h in y_list:
#downscale value also heurestically chosen
im = pyramid_reduce(img[h:h+window_size[0],w:w+window_size[1]],downscale=5)
lis.append( np.array(im[2:21,:19] * 255, dtype = np.uint8) )
import pickle
pickle.dump( lis, open( "test-windows.pkl", "wb" ) )
#lis = pickle.load( open( "test-windows.pkl", "rb" ) )
##Finding-windows
k = len(lis)/10 #no of chunks, jobs
iterator = range(0,len(lis)-k,k)
from joblib import Parallel, delayed
from parr_test import myfunc
pdb.set_trace()
results = Parallel(n_jobs=-1)(delayed(myfunc)(lis[i:i+k]) for i in iterator)
