def __init__(self, Generator, Discriminator, opt):
self.Generator = Generator
self.Discriminator = Discriminator
self.opt = opt
### Set parameters for the training of the 0th layer
self.Gs = [] # Generator list for each scale
self.Zs = [] # Optimal noise list for each scale [z*, 0, 0, ..., 0]
self.NoiseAmp = [
] # Ratio of noise when merging with the output of the previous layer for each scale
self.in_s = 0 # 0 Tensor with the downsampled dimensions of the input image for scale 0
### TrainedModel Directory
dir2save = generate_dir2save(self.opt)
if (os.path.exists(dir2save)):
print(
"Would you look at that, the TrainedModel directory already exists!"
)
else:
try:
os.makedirs(dir2save)
except OSError:
print("Making the directory really didn't work out, hyelp")
# In case we're not training, load existing model
if self.opt.mode != 'train':
self.Gs, self.Zs, _, _, self.NoiseAmp = load_trained_pyramid(
self.opt)
# We might wish to replace content or style images
if self.opt.test_content is not None:
self.opt.content = self.opt.test_content
if self.opt.test_style is not None:
self.opt.style = self.opt.test_style
### Content image pyramid
self.real_ = read_image(self.opt)
self.style_ = read_image(self.opt, style=True)
if self.style_.shape != self.real_.shape:
self.style_ = imresize_to_shape(
self.style_, [self.real_.shape[2], self.real_.shape[3]], opt)
self.style_ = self.style_[:, :, :self.real_.shape[2], :self.real_.
shape[3]]
# "adjust_scales2image" also arranges network parameters according to input dimensions
assert self.real_.shape == self.style_.shape
self.real = adjust_scales2image(self.real_, self.opt)
self.reals = create_reals_pyramid(self.real, self.opt)
self.style = imresize(self.style_, self.opt.scale1, self.opt)
self.styles = create_reals_pyramid(self.style, self.opt)
def crop_images_according_to_annotations(dir_annotations, dir_images, dir_out):
list_files = utilities.get_list_of_files(dir_annotations)
utilities.check_output_dir(dir_out)
print("Cropping and saving {} images.".format(len(list_files)))
for i in range(0, len(list_files)):
imagename = list_files[i].replace(".txt", ".png")
image = utilities.read_image(dir_images, imagename)
annotation = utilities.read_anno(dir_annotations, list_files[i])
cropped_image = image[int(annotation[1]):int(annotation[3]),
int(annotation[0]):int(annotation[2])]
utilities.save_image(dir_out, imagename, cropped_image)
def __init__(self, image_modality, image_path_or_object):
"""
image_modality: one of the statics fields defined within the class
image_path_or_object: An ITK image object or the dicom/image path.
"""
if self.check_modality(image_modality):
self.image_modality = image_modality
else:
print('Incorrect image Modality ' + image_modality +
". Specify one from " + self.modalities_list)
return None
self.itk_image = read_image(image_path_or_object)
self.label_mask = None
self.label_mask_array = None
self.resample_image = None
self.resample_image_array = None
def select_obj_frame(filename):
"""
This method reads the image and displays user each block. Then user choses
a block with higher objects of interest and enters that block number to
use the interactive segmentation method.
:param filename: full filepath of the image
:type filename: str
:return: None
"""
global img_list, base_mean, break_flag
def close_event(evt):
global break_flag
print("Closed figure")
break_flag = True
block_size = (1024, 1024)
img = read_image(filename)
print("FILE: {}".format(filename))
img_list, _ = split_image(img, block_size)
frame_no = 0
fig = plt.figure()
fig.canvas.mpl_connect('close_event', close_event)
for img in img_list:
rgb_image = cv2.cvtColor(img, cv2.COLOR_BGR2RGB)
try:
plt.imshow(rgb_image)
plt.title('Frame No %s' % frame_no)
frame_no += 1
plt.show()
plt.grid(b=False)
plt.waitforbuttonpress(.5)
except:
break_flag = True
break
if break_flag:
break
inp = get_input("Enter Frame number : ")
if len(inp) != 0:
frame_no = int(inp)
if 0 <= frame_no < len(img_list):
get_obj_color(img_list[frame_no])
print(Style.RESET_ALL)
images = files.get_images(root_path) # Note line below resets the blue
print(Style.RESET_ALL + Fore.GREEN +
"Number of images in the path: {:d}".format(len(images)))
# Create the image matrix here
height, width = 30, 30
img_matrix = np.zeros((len(images), height * width)) # (num_imgs x dim)
# Going through all the images and polutating the img_matrix
size = 20 # Length of the loading bar in chars
for i, img_path in enumerate(images):
# Open each image
img = ut.read_image(img_path, "BGR2GRAY")
resized = cv2.resize(img, (height, width), cv2.INTER_AREA)
reshaped = resized.reshape(width * height) # So we have it as a vector
# populate the matrix
img_matrix[i, :] = reshaped
# Progress bar stuff
perc = (i + 1) / len(images)
bar = int(np.round(perc * size))
line = "Opening images ["
line += "=" * bar + " " * (size - bar)
line += "] {:d}%".format(int(np.round(perc * 100)))
ut.update_line(line) # This func will use carriage return
print("\nFinding the principal components.")
# Print the resizing settings
print("Resizing set to {0}{1}{2}.".format(Fore.GREEN, resize, Fore.BLUE))
if resize:
print("Width: {0}{1}px{2}".format(Fore.WHITE, width, Fore.BLUE))
print("Height: {0}{1}px{2}".format(Fore.WHITE, height, Fore.BLUE))
# Reset colour
print(Style.RESET_ALL)
images = files.get_images(root_path) # Note line below resets the blue
print(Style.RESET_ALL + Fore.GREEN + "Number of images in the path: {:d}".format(len(images)))
size = 20 # Length of the loading bar in chars
for i, img_path in enumerate(images):
image = ut.read_image(img_path, "BGR2RGB") #grayscale
# Do the image cropping and save to the output
rect = an.get_rect(image) # Ruple with bounding rect coords
cropped = image[rect[1]:rect[3],rect[0]:rect[2]] # Simple cropping
# This is the resizing stuff. Here I am assuming we
# will be decimating the image (reducing size), hence
# the interpolation used is the AREA relation.
if resize:
inter = cv2.INTER_AREA # OpenCV const for such interpolation
cropped = cv2.resize(cropped, (width, height), interpolation=inter)
# Saving the processed file
name = files.get_filename(img_path) + ".jpg"
Dist = Xs*Xs + Ys*Ys mask = Dist < r**2 ############################################################# # Params for fitting the curve to the image and displaying it max_weight = 5 # Max weights of points (0-max) Xs = np.linspace(0, 450, 2000) # The linspace X for drawing line # The hypothesis function def func(x, a, b, c): # So we can fit a parabola return a*x**2 + b*x + c # Loading all the images in the path and detecting the OD in them for i, img_path in enumerate(images): if i > 129 : original_image = ut.read_image(img_path, "BGR2GRAY") original_size = original_image.shape[0:2] # Stores the original size for later S = 450 # the square size of the image # Resize the image (with dims (450,450)) img_resized = cv2.resize(original_image, (S,S), cv2.INTER_AREA) masked_img = img_resized*mask # Sliding algorithm (y,x is the center pixel) offset = np.max([width, height])//2 + 2 # The offset from the boarders for y in range(offset, N-offset, 5): for x in range(offset, N-offset, 5): # Tuples to represent the window box starts = np.array([y-height/2, x-width/2], dtype=int) stops = np.array([starts[0]+height, starts[1]+width], dtype=int)
def set_label_mask(self, labels_mask_image):
self.label_mask_image = read_image(
labels_mask_image
) if labels_mask_image is not None else self.get_labels_mask()
"""
File to carry out the Fourier Transform on images and produce a magnitude image to be analyised and altered.
The inverse Fourier Transform can be applied to the altered magnitude image to recreate the original image but sharper.
"""
import numpy as np
import utilities
# Load image and convert to grayscale
img = utilities.read_image("osc.jpg", "BGR2GRAY")
size = img.shape
# Fourier Transform
# CURRENTLY FOR ONLY ONE PIXEL takes a lot of time to cycle through for all the pixels in an image
def fourier(u, v, size):
# get dimensions
N = size[0] # rows
M = size[1] # columns
f = 0
for x in range(M):
for y in range(N):
f += np.sum(img[x,y] * exp(j*2*pi * ((u*x)/N + (v*y)/M)))
# get the magnitude from the value of F
# MAGNITUDE(F) = SQRT( REAL(F)^2+IMAGINARY(F)^2 )
magnitude = np.absolute(f)
return magnitude
def main():
#print(f'datetime.datetime={str(datetime.datetime)}, datetime.date={str(datetime.date)}, strftime():{datetime.datetime.now().strftime("%Y%d%H%M%S")}')
thrash = True
print('tf version:{0}'.format(tf.VERSION))
print('tf.keras version:{0}'.format(tf.keras.__version__))
start_time = datetime.datetime.now().strftime("%Y%d%H%M%S")
flags, unparsed = ut.parseArgs()
print(flags)
SAMPLE_FILE = flags.train_data_path + flags.sample + '.' + flags.img_file_extension
img = ut.read_image(filename=SAMPLE_FILE, show=False)
img = np.array(img)
if thrash == True:
img = ut.thrash_img(img)
IMG_SHAPE=img.shape
(x_train, y_train), (x_test, y_test)=ut.load_data(numclasses=flags.numclasses, train_path=flags.train_data_path, test_path=flags.test_data_path, onehot=True, extension=flags.img_file_extension)
print('IMG_SHAPE:{0}, y_train shape:{1}'.format(IMG_SHAPE,y_train[0].shape))
if flags.load_model:
model = ut.load_stored_model(name=flags.model_dir + flags.model_name)
elif flags.model == 'dense':
model = ut.make_dense_model(flags=flags)
elif flags.model == 'conv2d':
model = ut.make_convnet_model(flags=flags, shape=IMG_SHAPE)
else:
print('No model, no hope. Quitting...')
return
if flags.load_data:
model = ut.load_stored_data(model=model, date_file_name=flags.data_dir + flags.data_name)
print('Saving in {0}'.format(flags.tb_dir + start_time))
tensorboard = TensorBoard(log_dir=flags.tb_dir + '{0}'.format(start_time))
adam=tf.keras.optimizers.Adam(lr=flags.learning_rate)
model.compile(optimizer=adam,
loss=flags.loss,
metrics=[flags.metric]
)
if flags.train == True:
print('Training...')
scores = []
for epoch in range(flags.epochs):
print('Epoch:{0} of {1}'.format(epoch+1, flags.epochs))
n = len(x_train)
for batch in range(0,len(x_train), flags.batch_size):
print('Batch {0} of {1}, epoch {2} of {3}.'.format(batch+1,n+1, epoch+1, flags.epochs))
bunch_x, bunch_y = x_train[batch:batch+flags.batch_size], y_train[batch:batch+flags.batch_size]
if len(bunch_x) < flags.batch_size: # skip partial batches
print('Skipping {0} samples..'.format(len(bunch_x)))
continue
xs = []
ys = []
print("Iterating {0} samples".format(len(bunch_x)))
for datum in range(len(bunch_x)):
file = bunch_x[datum]
img = ut.read_image(filename=flags.train_data_path+file, show=False)
img=np.array(img)
if thrash == True:
img = ut.thrash_img(img)
xs.append(img)
ys.append(bunch_y[datum])
X= np.stack(xs, axis=0)
Y= np.stack(ys, axis=0)
score_before = model.evaluate(x=X,y=Y, batch_size=flags.batch_size)
_ = model.fit(x=X, y=Y, shuffle=flags.shuffle, callbacks=[tensorboard])
score_after = model.evaluate(x=X,y=Y, batch_size=flags.batch_size)
if score_before == score_after:
print("Scores before and after training are identical")
scores.append(score_after)
if epoch == 0 and batch == 0:
model.summary()
print('Score:{0}'.format(score_after))
loss,acc = np.array([s[0] for s in scores]), np.array([s[1] for s in scores])
print("Average loss:{0} Average accuracy:{1}%".format(np.mean(loss), 100*np.mean(acc)))
if flags.save_model:
model_name = flags.model_name if flags.model_name != None else start_time
ut.save_model(model, flags.model_dir+model_name)
print('Saved model to disk, json in {0}'.format(flags.model_dir + model_name + ".json"))
if flags.save_data:
data_name = flags.data_name if flags.data_name != None else start_time
model.save_weights(flags.data_dir + data_name + ".h5")
print('Saved data to disk in {0}'.format(flags.model_dir + data_name + ".h5"))
test_scores = []
predictions = []
if flags.evaluate or flags.predict:
n = len(x_test)
nTotal = 0
sums_array = None
for batch in range(0, len(x_test), flags.batch_size):
print('Batch {0} of {1}.'.format(batch+1, n+1))
bunch_x, bunch_y = x_test[batch:batch + flags.batch_size], y_test[batch:batch + flags.batch_size]
if len(bunch_x) < flags.batch_size: # skip partial batches
print('Skipping {0} samples..'.format(len(bunch_x)))
continue
xs = []
ys = []
for d in range(len(bunch_x)):
file = bunch_x[d]
img = ut.read_image(filename=flags.test_data_path + file, show=False)
img = np.array(img)
if thrash == True:
img = ut.thrash_img(img)
xs.append(img)
ys.append(bunch_y[d])
X = np.stack(xs, axis=0)
Y = np.stack(ys, axis=0)
if flags.evaluate:
score = model.evaluate(x=X, y=Y, batch_size=flags.batch_size)
test_scores.append(score)
print('Test score:{0}'.format(score))
if flags.predict:
prediction = model.predict(X, verbose=2)
processed_predictions = ut.process_predictions(prediction, Y)
for pp in processed_predictions:
if sums_array is None:
sums_array = np.zeros_like(pp)
sums_array = np.add(sums_array, pp)
nTotal = nTotal+1
pass
if flags.predict:
sums_array /= nTotal
if predictions != None:
pass
print('Average score:{0},{1}'.format(np.mean([test_scores[i][0] for i in range(len(test_scores))]),np.mean([test_scores[i][1] for i in range(len(test_scores))])))
if flags.show_results:
y_axis = np.arange(0, 1.0, 1.0/float(len(sums_array)))
plt.plot(y_axis,sums_array)
plt.show()
pass
images = files.get_images(root_path) # Note line below resets the blue
print(Style.RESET_ALL + Fore.GREEN +
"Number of images in the path: {:d}".format(len(images)))
# CALCULATE THE QUALITIES OF THE IMAGES
hist_size = 256
histograms = np.zeros(
(len(images), hist_size)) # Define matrix for storing histograms
stats = np.zeros(
(len(images),
2)) # Define matrix for storing laplacian variance and ERR
size = 20 # Length of the loading bar in chars
for i, img_path in enumerate(images):
image_gray = ut.read_image(img_path, "BGR2GRAY") #grayscale
lp = an.get_laplacian(image_gray) # Laplacian
err = an.get_err(image_gray) # Err
# Fill the matrices (Log domain)
histograms[i, :] = an.get_histogram(image_gray).ravel()
stats[i, 0] = np.log(np.var(lp))
stats[i, 1] = np.log(err)
# Progress bar stuff
perc = (i + 1) / len(images)
bar = int(np.round(perc * size))
line = "Processing ["
line += "=" * bar + " " * (size - bar)
line += "] {:d}%".format(int(np.round(perc * 100)))
ut.update_line(line) # Thins func will use carriage return
