def vis_square(data, name_fig):
"""Take an array of shape (n, height, width) or (n, height, width, 3)
and visualize each (height, width) thing in a grid of size approx. sqrt(n) by sqrt(n)"""
# normalize data for display
data = (data - data.min()) / (data.max() - data.min())
# force the number of filters to be square
n = int(np.ceil(np.sqrt(data.shape[0])))
padding = (((0, n**2 - data.shape[0]), (0, 1),
(0, 1)) # add some space between filters
+ ((0, 0), ) * (data.ndim - 3)
) # don't pad the last dimension (if there is one)
data = np.pad(data, padding, mode='constant',
constant_values=1) # pad with ones (white)
# tile the filters into an image
data = data.reshape((n, n) + data.shape[1:]).transpose(
(0, 2, 1, 3) + tuple(range(4, data.ndim + 1)))
data = data.reshape((n * data.shape[1], n * data.shape[3]) +
data.shape[4:])
plt.imshow(data)
plt.show()
plt.imsave(name_fig, data)
return data
def crop_images(input_folder, crop_percentage):
im_files = glob.glob(os.path.join(input_folder, '*.png'))
print(im_files)
for imf in im_files:
im = plt.imread(imf)
orig_shape = np.array(im.shape[0:2])
new_shape = np.round(orig_shape * crop_percentage).astype(
'int') #crop to 60% of the image size
offset = np.round(0.5 * (orig_shape - new_shape)).astype('int')
im_out = im[offset[0]:offset[0] + new_shape[0],
offset[1]:offset[1] + new_shape[1]]
plt.imsave(imf, im_out)
def download_tiles_for_area(x_tile_min, x_tile_max,
y_tile_min, y_tile_max,
zoom, url='https://maps.wikimedia.org/osm-intl'):
"""
Download the tiles specified by the x, y and zoom values
The tileservers are accessed using the pattern {url}/{zoom}/{x_tile}/{y_tile}.png and the tiles saved as
{zoom}_{x_tile}_{y_tile}.png
:param x_tile_min: Minimum x_tile value
:param x_tile_max: Maximum x_tile value
:param y_tile_min: Minimum y_tile value
:param y_tile_max: Maximum y_tile value
:param zoom: Zoom at which to download the tiles
:param url: The url used to download the tiles.
:return: No return value
"""
# total number of tiles
tile_count = (x_tile_max-x_tile_min+1)*(y_tile_max-y_tile_min+1)
# Restrict the number of tiles that are downloaded
if tile_count > MAX_TILE_COUNT:
print('ERROR zoom value too high')
return
# download tiles
if not os.path.exists('tiles'):
os.makedirs('tiles')
i = 0
with progressbar.ProgressBar(max_value=tile_count) as bar:
for x in range(x_tile_min, x_tile_max+1):
for y in range(y_tile_min, y_tile_max+1):
tile_url = '/'.join([url, str(zoom), str(x), str(y) + '.png'])
tile_file = '_'.join(['tiles/tile', str(zoom), str(x), str(y) + '.png'])
# check if tile already downloaded
if not glob.glob(tile_file):
i += 1
bar.update(i)
if not download_tile_file(tile_url, tile_file):
tile_image = np.ones((OSM_TILE_SIZE, OSM_TILE_SIZE, 3))
plt.imsave(tile_file, tile_image)
def vis_square_seg(data, name_fig, index_lum_ker):
# Function that displays kernels of the first layer as images. kernels classified as color agnostic are surrounded by black.
# Take an array of shape (n, height, width) or (n, height, width, 3)
# and visualize each (height, width) thing in a grid of size approx. sqrt(n) by sqrt(n)"""
# normalize data for display
data = (data - data.min()) / (data.max() - data.min())
gp_top = data[0:48]
gp_bot = data[48:]
# force the number of filters to be square
n = int(np.ceil(np.sqrt(data.shape[0])))
padding = (((0, 0), (1, 2), (1, 2)) + ((0, 0), ) * (data.ndim - 3))
gp_top = np.pad(gp_top, padding, mode='constant',
constant_values=1) # pad with ones (white)
gp_bot = np.pad(gp_bot, padding, mode='constant',
constant_values=1) # pad with ones (white)
data = np.concatenate((gp_top, gp_bot), axis=0)
for i in index_lum_ker:
if i < 48:
data[i, :-1, (0, -2), :] = 0
data[i, (0, -2), :-1, :] = 0
else:
data[i, :-1, (0, -2), :] = 0
data[i, (0, -2), :-1, :] = 0
# tile the filters into an image
data = data.reshape((12, 8) + data.shape[1:]).transpose(
(0, 2, 1, 3) + tuple(range(4, data.ndim + 1)))
data = data.reshape((12 * data.shape[1], 8 * data.shape[3]) +
data.shape[4:])
data = np.insert(data, data.shape[0] / 2, np.ones((3, data.shape[1], 3)),
0)
data = data[:-1, :-1]
# print data.shape
plt.imshow(data)
plt.show()
plt.imsave(name_fig + '.png', data)
plt.imsave(name_fig + '.eps', data)
return data
def main():
#create pcd object list to save the reconstructed patch per capsule
pcd_list = []
for i in range(opt.latent_caps_size):
pcd_ = o3d.geometry.PointCloud()
pcd_list.append(pcd_)
colors = plt.cm.tab20((np.arange(20)).astype(int))
#random selected viz capsules
hight_light_caps = [
np.random.randint(0, opt.latent_caps_size) for r in range(10)
]
USE_CUDA = True
device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
capsule_net = PointCapsNet(opt.prim_caps_size, opt.prim_vec_size,
opt.latent_caps_size, opt.latent_caps_size,
opt.num_points)
if opt.model != '':
capsule_net.load_state_dict(torch.load(opt.model))
else:
print('pls set the model path')
if USE_CUDA:
print("Let's use", torch.cuda.device_count(), "GPUs!")
capsule_net = torch.nn.DataParallel(capsule_net)
capsule_net.to(device)
if opt.dataset == 'shapenet_part':
test_dataset = shapenet_part_loader.PartDataset(classification=True,
npoints=opt.num_points,
split='test')
test_dataloader = torch.utils.data.DataLoader(
test_dataset,
batch_size=opt.batch_size,
shuffle=True,
num_workers=4)
elif opt.dataset == 'shapenet_core13':
test_dataset = shapenet_core13_loader.ShapeNet(normal=False,
npoints=opt.num_points,
train=False)
test_dataloader = torch.utils.data.DataLoader(
test_dataset,
batch_size=opt.batch_size,
shuffle=True,
num_workers=4)
elif opt.dataset == 'shapenet_core55':
test_dataset = shapenet_core55_loader.Shapnet55Dataset(
batch_size=opt.batch_size,
npoints=opt.num_points,
shuffle=True,
train=False)
capsule_net.eval()
if 'test_dataloader' in locals().keys():
test_loss_sum = 0
for batch_id, data in enumerate(test_dataloader):
points, _ = data
if (points.size(0) < opt.batch_size):
break
points = Variable(points)
points = points.transpose(2, 1)
if USE_CUDA:
points = points.cuda()
latent_caps, reconstructions = capsule_net(points)
for pointset_id in range(opt.batch_size):
prc_r_all = reconstructions[pointset_id].transpose(
1, 0).contiguous().data.cpu()
prc_r_all_point = o3d.geometry.PointCloud()
prc_r_all_point.points = o3d.utility.Vector3dVector(prc_r_all)
colored_re_pointcloud = o3d.geometry.PointCloud()
jc = 0
for j in range(opt.latent_caps_size):
current_patch = torch.zeros(
int(opt.num_points / opt.latent_caps_size), 3)
for m in range(int(opt.num_points / opt.latent_caps_size)):
current_patch[m, ] = prc_r_all[
opt.latent_caps_size * m + j,
] # the reconstructed patch of the capsule m is not saved continuesly in the output reconstruction.
pcd_list[j].points = o3d.utility.Vector3dVector(
current_patch)
if (j in hight_light_caps):
pcd_list[j].paint_uniform_color(
[colors[jc, 0], colors[jc, 1], colors[jc, 2]])
jc += 1
else:
pcd_list[j].paint_uniform_color([0.8, 0.8, 0.8])
colored_re_pointcloud += pcd_list[j]
#o3d.visualization.draw_geometries([colored_re_pointcloud])
o3d.io.write_point_cloud(
f'../../output/{batch_id}_{pointset_id}.pcd',
colored_re_pointcloud)
vis = o3d.visualization.Visualizer()
vis.create_window(visible=False)
vis.add_geometry(colored_re_pointcloud)
img = vis.capture_screen_float_buffer(True)
plt.imsave(f'../../output/{batch_id}_{pointset_id}.png',
np.asarray(img))
# test process for 'shapenet_core55'
else:
test_loss_sum = 0
while test_dataset.has_next_batch():
batch_id, points_ = test_dataset.next_batch()
points = torch.from_numpy(points_)
if (points.size(0) < opt.batch_size):
break
points = Variable(points)
points = points.transpose(2, 1)
if USE_CUDA:
points = points.cuda()
latent_caps, reconstructions = capsule_net(points)
for pointset_id in range(opt.batch_size):
prc_r_all = reconstructions[pointset_id].transpose(
1, 0).contiguous().data.cpu()
prc_r_all_point = o3d.geometry.PointCloud()
prc_r_all_point.points = o3d.utility.Vector3dVector(prc_r_all)
colored_re_pointcloud = o3d.geometry.PointCloud()
jc = 0
for j in range(opt.latent_caps_size):
current_patch = torch.zeros(
int(opt.num_points / opt.latent_caps_size), 3)
for m in range(int(opt.num_points / opt.latent_caps_size)):
current_patch[m, ] = prc_r_all[
opt.latent_caps_size * m + j,
] # the reconstructed patch of the capsule m is not saved continuesly in the output reconstruction.
pcd_list[j].points = o3d.utility.Vector3dVector(
current_patch)
if (j in hight_light_caps):
pcd_list[j].paint_uniform_color(
[colors[jc, 0], colors[jc, 1], colors[jc, 2]])
jc += 1
else:
pcd_list[j].paint_uniform_color([0.8, 0.8, 0.8])
colored_re_pointcloud += pcd_list[j]
#o3d.visualization.draw_geometries([colored_re_pointcloud])
o3d.io.write_point_cloud(
f'../../output/{batch_id}_{pointset_id}.pcd',
colored_re_pointcloud)
vis = o3d.visualization.Visualizer()
vis.create_window(visible=False)
vis.add_geometry(colored_re_pointcloud)
img = vis.capture_screen_float_buffer(True)
plt.imsave(f'../../output/{batch_id}_{pointset_id}.png',
np.asarray(img))
import os
import PIL
from tensorflow.keras import layers
import time
import tensorflow as tf
def load_images_from_folder(folder):
images = []
for filename in os.listdir(folder):
bgr_img = cv2.imread(os.path.join(folder, filename))
b, g, r = cv2.split(bgr_img)
rgb_img = cv2.merge([r, g, b])
if rgb_img is not None:
images.append(rgb_img)
return images
images = load_images_from_folder(
r'C:\Users\Kevork\Documents\Histology-GAM\BACH_images')
# %%
# images=np.array(images)
image1 = images[0]
plt.imshow(image1)
plt.imsave('hist.tiff', image1)
# %%
os.mkdir('dataset/train')
os.mkdir('dataset/test')
# 10=bowl 29=dinosaur 50=mouse 63=porcupine 90=train 91=trout
classNumber = [10, 29, 50, 63, 90, 91]
for num in classNumber:
path = os.path.join('dataset/train', str(num))
os.mkdir(path)
path = os.path.join('dataset/test', str(num))
os.mkdir(path)
for i in range(50000):
if int(y_train[i]) in classNumber:
path = 'dataset/train/' + str(int(y_train[i])) + '/' + str(i) + '.png'
plt.imsave(path, x_train[i])
for i in range(10000):
if int(y_test[i]) in classNumber:
path = 'dataset/test/' + str(int(y_test[i])) + '/' + str(i) + '.png'
plt.imsave(path, x_test[i])
train_datagen = ImageDataGenerator(rescale=1. / 255)
train_generator = ImageDataGenerator().flow_from_directory(
'dataset/train/',
target_size=(32, 32),
batch_size=20,
class_mode='categorical')
test_datagen = ImageDataGenerator(rescale=1. / 255)
test_generator = ImageDataGenerator().flow_from_directory(