def get_disc_batch(
self,
X,
y,
generator,
batch_counter,
patch_size,
label_smoothing=False,
label_flipping=0):
'''
Get the discriminator batch data
Generator predict the sample
'''
generator.train_on_batch(X, y)
y_disc = np.zeros((X.shape[0], 2), dtype=np.uint8)
if batch_counter % 2 == 0:
X_disc = generator.predict(X)
y_disc[:, 0] = 1
else:
X_disc = y
if label_smoothing:
y_disc[:, 1] = np.random.uniform(
low=0.9, high=1, size=y_disc.shape[0])
else:
y_disc[:, 1] = 1
if label_flipping > 0:
p = np.random.binomial(1, label_flipping)
if p > 0:
y_disc[:, [0, 1]] = y_disc[:, [1, 0]]
X_disc = extract_patches(X_disc, patch_size)
return X_disc, y_disc
def predict(img, patch_size, patch_step, nb_filters, nb_conv, batch_size, dim_img, wpath):
"""
the cnn model for image transformation
Parameters
----------
img : array
The image need to be calculated
patch_size : (int, int)
The patches dimension
dim_img : int
The input image dimension
Returns
-------
img_rec
Description.
"""
# img = nor_data(img)
img_y, img_x = img.shape
x_img = extract_patches(img, patch_size, patch_step)
x_img = np.reshape(x_img, (len(x_img), 1, dim_img, dim_img))
mdl = mirror_model(dim_img, nb_filters, nb_conv)
mdl.load_weights(wpath)
y_img = mdl.predict(x_img, batch_size=batch_size)
del x_img
y_img = np.reshape(y_img, (len(y_img), dim_img, dim_img))
img_rec = reconstruct_patches(y_img, (img_y, img_x), patch_step)
return img_rec
def train(img_x, img_y, patch_size, patch_step, dim_img, nb_filters, nb_conv, batch_size, nb_epoch, x_test, y_test):
"""
Function description.
Parameters
----------
parameter_01 : type
Description.
parameter_02 : type
Description.
parameter_03 : type
Description.
Returns
-------
return_01
Description.
"""
# img_x = nor_data(img_x)
img_y = nor_data(img_y)
img_input = extract_patches(img_x, patch_size, 1)
img_output = extract_patches(img_y, patch_size, 1)
img_input = np.reshape(img_input, (len(img_input), 1, dim_img, dim_img))
img_output = np.reshape(img_output, (len(img_input), 1, dim_img, dim_img))
# test_x = nor_data(x_test)
test_y = nor_data(y_test)
test_x = extract_patches(x_test, patch_size, 1)
test_y = extract_patches(test_y, patch_size, 1)
test_x = np.reshape(test_x, (len(test_x), 1, dim_img, dim_img))
test_y = np.reshape(test_y, (len(test_y), 1, dim_img, dim_img))
mdl = mirror_model(dim_img, nb_filters, nb_conv)
print(mdl.summary())
mdl.fit(img_input, img_output, batch_size=batch_size, nb_epoch=nb_epoch, validation_data=(test_x,test_y))
return mdl
def dataset(dataset_train_path,batch_size,scale_factor):
assert(os.path.exists(dataset_train_path))
data = []
for file in os.listdir(dataset_train_path):
if file.endswith('.bmp'):
filepath = os.path.join(dataset_train_path,file)
img = imageio.imread(filepath).dot([0.299, 0.587, 0.114])
patches = extract_patches(img,(36,36),0.166)
data += [patches[idx] for idx in range(patches.shape[0])]
mod_data = [from_numpy(np.expand_dims(blur(upscale(patch,scale_factor),scale_factor),0)).float() for patch in data]
data = [from_numpy(np.expand_dims(upscale(patch,scale_factor),0)).float() for patch in data]
l = len(data)
for idx in range(0,l,batch_size):
yield stack(mod_data[idx:min(idx+batch_size,l)]),stack(data[idx:min(idx+batch_size,l)])
im_train_x = np.array(
Image.open(os.path.join(topdir, '2idd_0034_P_crop62x62_top.tif')))
im_train_y = np.array(
Image.open(os.path.join(topdir, '2idd_0043_P_fine310x310_top.tif')))
im_test_x = np.array(
Image.open(os.path.join(bottomdir, '2idd_0034_P_crop62x62_bottom.tif')))
im_test_y = np.array(
Image.open(os.path.join(bottomdir, '2idd_0043_P_fine310x310_bottom.tif')))
patch_size = [15, 30]
patch_step = 1
pxH, pyH = patch_size
pxh, pyh = np.multiply(5, patch_size)
nxH, nyH = im_train_x.shape
nxh, nyh = im_train_y.shape
train_x = extract_patches(im_train_x, patch_size, patch_step)
train_y = extract_patches(im_train_y, [pxh, pyh], patch_step * 5)
X_train = np.reshape(train_x, (len(train_x), pxH, pyH))
Y_train = np.reshape(train_y, (len(train_y), pxh, pyh))
X_test = extract_patches(im_test_x, patch_size, patch_step)
X_test = np.reshape(X_test, (len(X_test), pxH, pyH))
Y_test = extract_patches(im_test_y, [pxh, pyh], patch_step * 5)
Y_test = np.reshape(Y_test, (len(Y_test), pxh, pyh))
model = []
model = Sequential()
model.add(Dense(pxh * pyh, input_dim=pxH * pyH))
model.add(Dense(pxh * pyh, input_dim=pxH * pyH))
model.add(Dense(pxh * pyh, input_dim=pxH * pyH))
model.compile(loss='categorical_crossentropy',
bsp_out_dir = sys.argv[arg_index + 1]
# Check whether the --asp_out_dir command line parameter was
# provided.
asp_out_dir = None
if '--asp_out_dir' in sys.argv:
# Get the command line parameter value.
arg_index = sys.argv.index('--asp_out_dir')
asp_out_dir = sys.argv[arg_index + 1]
if bsp_columns_file is None and asp_columns_file is None:
sys.exit('One or both of the --bsp_columns_file'
' --asp_columns_file must be provided.')
images, _ = load_images(imgs_dir, extensions=('.jpg',),
img_shape=(256, 256))
patches = extract_patches(images, (16, 16), images.shape[0]*256,
randomize=False)
if asp_columns_file is not None:
with open(asp_columns_file, 'rb') as fp:
asp_columns = pickle.load(fp)
asp_activations =\
reconstruct_images(alg='asp', images=patches, columns=asp_columns,
connect_threshold=0.2,
desired_activity_mult=0.05, min_overlap=3,
img_shape=(256, 256), out_dir=asp_out_dir)
calculate_print_stats(asp_activations, alg='ASP')
save_activations(asp_activations, asp_columns_file)
if bsp_columns_file is not None:
with open(bsp_columns_file, 'rb') as fp:
bsp_columns = pickle.load(fp)
def predict_one_img(img,
weights_path,
inception_model,
model,
labels = {'Benign': 0, 'InSitu': 1, 'Invasive': 2, 'Normal': 3}
):
#predicts the class label of one 2048*1536 img
#labels is a the class labels dict
#return the label 0,1,2 or 3
label_vals = list(labels.values())
print('label_vals',label_vals)
#list to hold predicted labels and confidence scores of the patches
patch_pred_labels = []
patch_pred_confs = []
for patch,index in extract_patches(img,512):
#print('[INFO]....Processing patch no. '+str(index))
#model = InceptionModel()
label,confidence = inception_model.predict(patch,model,weights_path)
patch_pred_labels.append(label)
patch_pred_confs.append(confidence)
#print('patch_pred_labels,patch_pred_confs',patch_pred_labels,patch_pred_confs)
#Majority Voting Decision over all the patches
#to predict class label of entire image
#predict label with max occurences in patch_pred_labels
#if tie, choose label with max total confidence
#if tie again , choose any of those labels at random
patches_pred_label_freqs = {}
for label in label_vals:
label_freq = patch_pred_labels.count(label)
#print('label '+str(label)+' has a freq of ',label_freq)
patches_pred_label_freqs[str(label)] = label_freq
#print('patches_pred_label_freqs',patches_pred_label_freqs)
#print(patches_pred_label_freqs)
max_freq = max(patches_pred_label_freqs.values())
#print('max_freq',max_freq)
#list of labels with max_freq
argmax_freqs = [int(k) for k, v in patches_pred_label_freqs.items() if v == max_freq]
#print('list of labels with max_freq',argmax_freqs)
if (len(argmax_freqs) == 1):
print('Only one class majority')
print('Predicted Label : ',argmax_freqs[0])
return argmax_freqs[0]
elif (len(argmax_freqs) > 1):
#if tie, choose label with max total confidence
print('Multiple classes with same majority')
argmax_confs_dict = {}
for argmax_freq in argmax_freqs:
total_confidence = 0
total_instances = 0
#print('Current label',argmax_freq)
for label,confidence in zip(patch_pred_labels,patch_pred_confs):
#print('label',label)
if (label == argmax_freq):
total_confidence += confidence
total_instances += 1
#print('total_confidence',total_confidence)
#print('total_instances',total_instances)
mean_confidence = total_confidence/max_freq
#print('mean_confidence',mean_confidence)
argmax_confs_dict[str(argmax_freq)] = mean_confidence
#print('argmax_confs_dict',argmax_confs_dict)
max_conf = max(argmax_confs_dict.values())
#print('max_conf',max_conf)
#list of labels with max_conf
argmax_confs = [int(k) for k, v in argmax_confs_dict.items() if v == max_conf]
#print('argmax_confs',argmax_confs)
if (len(argmax_confs) == 1):
print('Predicted Label : ',argmax_confs[0])
return argmax_confs[0]
elif (len(argmax_confs) > 1):
#if tie again,choose any of those labels at random
op_label = random.choice(argmax_confs)
print('Predicted Label : ',op_label)
return op_label
if patches_file is not None:
# If the patches_file command line parameter was provided,
# read it from disk.
pprint("Reading patches file ...")
with open(patches_file, 'rb') as fp:
patches = pickle.load(fp)
else:
# If the patches_file command line parameter was not provided,
# load the images from disk, ...
pprint("Loading images ...")
images, image_files = load_images(images_path, extensions=['.png'],
img_shape=(256, 256))
if create_patches:
# and if the --create_patches was provided generate the patches.
pprint("Extracting patches ...")
patches = extract_patches(images, patch_shape=(16, 16))
if patches_file is not None:
pprint("Saving patches to disk ...")
with open(patches_file, 'wb') as fp:
pickle.dump(patches, fp)
else:
# or, if the --create_patches was not provided, use the images
# themselves as the patches.
patches = images
# Finally, start the learning procedure.
pprint("Starting training ...")
columns = spatial_pooler(patches, shape=(16, 16, 16, 16), p_connect=0.1,
connect_threshold=0.2, p_inc=0.0005, p_dec=0.0025,
b_inc=0.005, p_mult=0.01,
min_activity_threshold=0.01,
import numpy as np
import matplotlib.pyplot as plt
import utils
DATASET_PATH = "./dataset/van_hateren/"
mode = "l4"
p = int(5e5) # number of samples
n = 256 # data dimension
num_steps = 1000
# process data
print("processing data")
img_arr = utils.read_raw_imgs(DATASET_PATH)
img_arr = utils.normalize_imgs(img_arr)
img_arr = utils.extract_patches(img_arr, p)
img_arr, wtn_mat = utils.whiten_imgs(img_arr)
# initialize model
Y = img_arr.reshape(p, n).T
A = np.linalg.qr(np.random.rand(n, n))[0]
# train model
if mode == "l4":
for t in range(num_steps):
dA = 4 * np.power(A @ Y, 3) @ Y.T
U, _, V = np.linalg.svd(dA, compute_uv=True)
A = U @ V
#
loss = np.sum(np.power(A @ Y, 4))
print(f'step: {t}\tloss: {loss}')
interpolation=cv2.INTER_LINEAR) for label in amsr_labels
]
# Replacing invalid data with NaNs
no_data = np.logical_or(np.isnan(HH), np.isnan(HH_nersc))
CT[no_data] = np.nan
DST[no_data] = np.nan
INC[no_data] = np.nan
HH_nersc[no_data] = np.nan
HV_nersc[no_data] = np.nan
for AMSR_channel in AMSR:
AMSR_channel[no_data] = np.nan
# Extract all patches (shape=patch_shape) from HH and return indices of all patches without NaN values
HH_patches, non_nan_idxs = utils.extract_patches(HH,
patch_shape=PATCH_SHAPE,
return_non_nan_idxs=True,
overlap=OVERLAP)
if not len(non_nan_idxs) == 0: # if valid non-NaN patches in scene
HH_patches = HH_patches[non_nan_idxs]
del HH
HV_patches = utils.extract_patches(HV,
patch_shape=PATCH_SHAPE,
overlap=OVERLAP)[non_nan_idxs]
del HV
HH_nersc_patches = utils.extract_patches(HH_nersc,
patch_shape=PATCH_SHAPE,
overlap=OVERLAP)[non_nan_idxs]
del HH_nersc
HV_nersc_patches = utils.extract_patches(HV_nersc,
patch_shape=PATCH_SHAPE,
overlap=OVERLAP)[non_nan_idxs]