def run():
parser = argparse.ArgumentParser()
parser.add_argument("--weights-path", type=str)
parser.add_argument("--input-images", type=str, default="")
parser.add_argument("--output-path", type=str, default="")
parser.add_argument("--input-size", type=int, default=713)
parser.add_argument("--model-name", type=str, default="standard")
parser.add_argument("--save-imgs", type=bool, default=True)
args = parser.parse_args()
model_name = args.model_name
images_path = args.input_images
input_size = args.input_size
save_imgs = args.save_imgs
model_choices = {
'densenet': build_densenet,
'unet': build_unet,
'unet-old': build_unet_old
}
model_choice = model_choices[model_name]
model = model_choice((input_size, input_size), 1)
gpus = get_number_of_gpus()
if gpus > 1:
model = ModelMGPU(model, gpus)
model.compile(optimizer=Adam(lr=1e-4),
loss=binary_soft_jaccard_loss,
metrics=['acc', binary_jaccard_distance_rounded])
model.load_weights(args.weights_path)
probs = []
for i, filename in enumerate(tqdm(os.listdir(images_path))):
imgpath = os.path.join(images_path, filename)
if not os.path.isfile(imgpath):
continue
img = np.array(Image.open(imgpath))
if not img.shape[0] == img.shape[1]:
continue
img = np.expand_dims(img, axis=0)
prob = model.predict(img, verbose=1)
probs.append(prob)
probs = np.round(probs)
if not save_imgs:
return
for i, prob in enumerate(probs):
prob = (prob[:, :, 0] * 255.).astype(np.uint8)
pred_name = "pred-{}.tif".format(i)
pred_save_path = "{}/{}".format(args.output_path, pred_name)
cv2.imwrite(pred_save_path, prob)
def lrtest_densenet(data_dir, logdir, weights_dir, weights_name, input_size,
nb_classes, batch_size, config, initial_epoch,
pre_trained_weight, augment):
session_config()
model = build_densenet(input_size, nb_classes, config=config)
gpus = get_number_of_gpus()
print('Found {} gpus'.format(gpus))
if gpus > 1:
model = ModelMGPU(model, gpus)
binary = nb_classes == 1
if binary:
loss = binary_soft_jaccard_loss
else:
loss = soft_jaccard_loss
model.compile(optimizer=Adam(lr=1e-3),
loss=loss,
metrics=['acc', binary_jaccard_distance_rounded])
train_generator, num_samples = create_generator(os.path.join(
data_dir, 'train'),
input_size,
batch_size,
nb_classes,
rescale_masks=False,
binary=binary,
augment=augment)
steps_per_epoch = num_samples // batch_size
if augment:
steps_per_epoch = steps_per_epoch * 4
steps_per_epoch = 1000
clr = CyclicLR(base_lr=0,
max_lr=1e-1,
step_size=10 * steps_per_epoch,
mode='triangular')
model.fit_generator(generator=train_generator,
steps_per_epoch=steps_per_epoch,
epochs=10,
verbose=True,
workers=8,
callbacks=[clr])
h = clr.history
lr = h['lr']
acc = h['acc']
print(lr)
print()
print(acc)
def run():
parser = argparse.ArgumentParser()
parser.add_argument("--weights-path", type=str)
parser.add_argument("--test-image", type=str, default="")
parser.add_argument("--sample-images", type=str, default="")
parser.add_argument("--output-path", type=str, default="")
parser.add_argument("--input-size", type=int, default=713)
parser.add_argument("--model-name", type=str, default="")
parser.add_argument("--name", type=str, default="")
args = parser.parse_args()
model_name = args.model_name
image_path = args.test_image
input_size = args.input_size
output_path = args.output_path
output_name = args.name
model_choices = {
'unet': build_unet,
'densenet': build_densenet
}
model_choice = model_choices[model_name]
model = model_choice((input_size, input_size), 1)
gpus = get_number_of_gpus()
print('Fund {} gpus'.format(gpus))
if gpus > 1:
model = ModelMGPU(model, gpus)
model.compile(
optimizer=Adam(lr=1e-4),
loss=binary_soft_jaccard_loss,
metrics=['acc', binary_jaccard_distance_rounded])
model.load_weights(args.weights_path)
generator = get_generator()
# load the image
image = Image.open(image_path)
size = image.size[0]
factor = input_size / 512
image = image.resize((int(size*factor), int(size*factor)))
image = np.array(image)
pred = predict_img_with_smooth_windowing(
image,
window_size=input_size,
subdivisions=2, # Minimal amount of overlap for windowing. Must be an even number.
nb_classes=1,
pred_func=(
lambda img_batch_subdiv: model.predict(
image_to_neural_input(img_batch_subdiv, generator), verbose=True
)
)
)
pred = np.round(pred)
pred = (pred[:, :, 0] * 255.).astype(np.uint8)
pred = Image.fromarray(pred, 'L')
pred = pred.resize((size, size))
pred = np.array(pred)
out_path = os.path.join(output_path, output_name)
print(cv2.imwrite(out_path, pred))
cheap = cheap_tiling_prediction(image, window_size=input_size, nb_classes=1, pred_func=(
lambda img_batch_subdiv: model.predict(
image_to_neural_input(np.array(img_batch_subdiv), generator), verbose=True
)
))
cheap = np.round(cheap)
cheap = (cheap[:, :, 0] * 255.).astype(np.uint8)
cheap = Image.fromarray(cheap, 'L')
cheap = cheap.resize((size, size))
cheap = np.array(cheap)
out_path = os.path.join(output_path, '{}-cheap.tif'.format(output_name))
print(cv2.imwrite(out_path, cheap))
def run():
np.random.seed(2)
tf.set_random_seed(2)
data_dir = '/data/{}/'
weights_dir = 'weights_train'
for i, run in enumerate(runs):
base_lr = run['base_lr']
max_lr = run['max_lr']
input_size = (run['input_size'], run['input_size'])
weights_name = run['name']
logs_dir = 'logs/{}'.format(run['name'])
batch_size = run['batch_size']
print("Running for config {}".format(run))
for j, dataset in enumerate(run['datasets']):
binary = True if dataset != 'multiclass' else False
nb_classes = 1 if binary else 5
print('Running training for {}'.format(dataset))
train_generator, num_samples = create_generator(
os.path.join(data_dir.format(dataset), 'train'),
input_size,
batch_size,
nb_classes=nb_classes,
rescale_masks=run['rescale_masks'],
binary=binary,
augment=False,
mean=np.array([[[0.36654497, 0.35386439, 0.30782658]]]),
std=np.array([[[0.19212837, 0.19031791, 0.18903286]]]))
val_generator, val_samples = create_generator(
os.path.join(data_dir.format(dataset), 'val'),
input_size,
batch_size,
nb_classes=nb_classes,
rescale_masks=run['rescale_masks'],
binary=binary,
augment=False,
mean=np.array([[[0.36654497, 0.35386439, 0.30782658]]]),
std=np.array([[[0.19212837, 0.19031791, 0.18903286]]]))
if run['network'] == 'unet':
model = build_unet(input_size, nb_classes=nb_classes)
else:
model = build_densenet(input_size, nb_classes, 67)
model.summary()
gpus = get_number_of_gpus()
print('Fund {} gpus'.format(gpus))
if gpus > 1:
model = ModelMGPU(model, gpus)
if binary:
loss = binary_soft_jaccard_loss
else:
loss = soft_jaccard_loss
model.compile(optimizer=Adam(),
loss=loss,
metrics=['acc', binary_jaccard_distance_rounded])
if run['pre_weights_name']:
pre_weights_name = run['pre_weights_name'].format(dataset)
weight = 'weights_train/weights.{}.h5'.format(pre_weights_name)
print('Loading weights: {}'.format(weight))
model.load_weights(weight)
steps_per_epoch = num_samples // batch_size
cyclic = 'triangular2'
cb = [
ValidationCallback(
val_samples // batch_size, val_generator, binary=binary)
] + callbacks(logs_dir.format(dataset),
filename=weights_name.format(dataset),
weightsdir=weights_dir,
monitor_val='mIOU',
base_lr=base_lr,
max_lr=max_lr,
steps_per_epoch=steps_per_epoch,
cyclic=cyclic)
model.fit_generator(generator=train_generator,
steps_per_epoch=steps_per_epoch,
epochs=100,
verbose=True,
workers=8,
callbacks=cb)
K.clear_session()
def build_unet16(input_shape, nb_classes, lr=1e-4):
"""
Build a Unet16 with a VGG16 encoder pretrained on the imagenet dataset
"""
base_model = VGG16(weights='imagenet', include_top=False)
inputs = layers.Input((input_shape[0], input_shape[1], 3))
# Block 1
x = base_model.get_layer('block1_conv1')(inputs)
x = BatchNormalization(axis=-1)(x)
x = base_model.get_layer('block1_conv2')(x)
x1 = BatchNormalization(axis=-1)(x)
x = MaxPooling2D(pool_size=(2, 2), data_format="channels_last")(x1)
# Block 2
x = base_model.get_layer('block2_conv1')(x)
x = BatchNormalization(axis=-1)(x)
x = base_model.get_layer('block2_conv2')(x)
x2 = BatchNormalization(axis=-1)(x)
x = MaxPooling2D(pool_size=(2, 2), data_format="channels_last")(x2)
# Block 3
x = base_model.get_layer('block3_conv1')(x)
x = BatchNormalization(axis=-1)(x)
x = base_model.get_layer('block3_conv2')(x)
x = BatchNormalization(axis=-1)(x)
x = base_model.get_layer('block3_conv3')(x)
x3 = BatchNormalization(axis=-1)(x)
x = MaxPooling2D(pool_size=(2, 2), data_format="channels_last")(x3)
# Block 4
x = base_model.get_layer('block4_conv1')(x)
x = BatchNormalization(axis=-1)(x)
x = base_model.get_layer('block4_conv2')(x)
x = BatchNormalization(axis=-1)(x)
x = base_model.get_layer('block4_conv3')(x)
x4 = BatchNormalization(axis=-1)(x)
x = MaxPooling2D(pool_size=(2, 2), data_format="channels_last")(x4)
# Block 5
x = base_model.get_layer('block5_conv1')(x)
x = BatchNormalization(axis=-1)(x)
x = base_model.get_layer('block5_conv2')(x)
x = BatchNormalization(axis=-1)(x)
x = base_model.get_layer('block5_conv3')(x)
x5 = BatchNormalization(axis=-1)(x)
x = MaxPooling2D(pool_size=(2, 2), data_format="channels_last")(x5)
# Bottleneck
x = down_block(x, 1024, bottleneck=True)
x = up_block(x, x5, 512)
x = up_block(x, x4, 512)
x = up_block(x, x3, 256)
x = up_block(x, x2, 128)
x = up_block(x, x1, 64)
x = layers.Conv2D(nb_classes, (1, 1))(x)
if nb_classes == 1:
activation = 'sigmoid'
else:
activation = 'softmax'
act = Activation(activation)(x)
model = Model(inputs=inputs, outputs=act)
gpus = get_number_of_gpus()
if gpus > 1:
model = ModelMGPU(model, gpus)
return model
def build_unet_old(input_shape, nb_classes, lr=1e-4):
concat_axis = 3
inputs = layers.Input((input_shape[0], input_shape[1], 3))
conv1 = Conv2D(32, (3, 3), padding="same", name="conv1_1", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(inputs)
conv1 = BatchNormalization(axis=-1)(conv1)
conv1 = Conv2D(32, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(conv1)
conv1 = BatchNormalization(axis=-1)(conv1)
pool1 = MaxPooling2D(pool_size=(2, 2), data_format="channels_last")(conv1)
conv2 = Conv2D(64, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(pool1)
conv2 = BatchNormalization(axis=-1)(conv2)
conv2 = Conv2D(64, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(conv2)
conv2 = BatchNormalization(axis=-1)(conv2)
pool2 = MaxPooling2D(pool_size=(2, 2), data_format="channels_last")(conv2)
conv3 = Conv2D(128, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(pool2)
conv3 = BatchNormalization(axis=-1)(conv3)
conv3 = Conv2D(128, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(conv3)
conv3 = BatchNormalization(axis=-1)(conv3)
pool3 = MaxPooling2D(pool_size=(2, 2), data_format="channels_last")(conv3)
conv4 = Conv2D(256, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(pool3)
conv4 = BatchNormalization(axis=-1)(conv4)
conv4 = Conv2D(256, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(conv4)
conv4 = BatchNormalization(axis=-1)(conv4)
pool4 = MaxPooling2D(pool_size=(2, 2), data_format="channels_last")(conv4)
conv5 = Conv2D(512, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(pool4)
conv5 = BatchNormalization(axis=-1)(conv5)
conv5 = Conv2D(512, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(conv5)
conv5 = BatchNormalization(axis=-1)(conv5)
pool5 = MaxPooling2D(pool_size=(2, 2), data_format="channels_last")(conv5)
convbott = Conv2D(1024, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(pool5)
convbott = BatchNormalization(axis=-1)(convbott)
convbott = Conv2D(1024, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(convbott)
convbott = BatchNormalization(axis=-1)(convbott)
up_convbott = UpSampling2D(size=(2, 2), data_format="channels_last")(convbott)
ch, cw = get_crop_shape(conv5, up_convbott)
crop_conv5 = Cropping2D(cropping=(ch, cw), data_format="channels_last")(conv5)
upbott = concatenate([up_convbott, crop_conv5], axis=concat_axis)
convbott1 = Dropout(0.2)(upbott)
convbott1 = Conv2D(512, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(convbott1)
convbott1 = Conv2D(512, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(convbott1)
up_convbott1 = UpSampling2D(size=(2, 2), data_format="channels_last")(convbott1)
ch, cw = get_crop_shape(conv4, up_convbott1)
crop_conv4 = Cropping2D(cropping=(ch, cw), data_format="channels_last")(conv4)
up6 = concatenate([up_convbott1, crop_conv4], axis=concat_axis)
conv6 = Dropout(0.2)(up6)
conv6 = Conv2D(256, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(conv6)
conv6 = Conv2D(256, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(conv6)
up_conv6 = UpSampling2D(size=(2, 2), data_format="channels_last")(conv6)
ch, cw = get_crop_shape(conv3, up_conv6)
crop_conv3 = Cropping2D(cropping=(ch, cw), data_format="channels_last")(conv3)
up7 = concatenate([up_conv6, crop_conv3], axis=concat_axis)
conv7 = Dropout(0.2)(up7)
conv7 = Conv2D(128, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(conv7)
conv7 = Conv2D(128, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(conv7)
up_conv7 = UpSampling2D(size=(2, 2), data_format="channels_last")(conv7)
ch, cw = get_crop_shape(conv2, up_conv7)
crop_conv2 = Cropping2D(cropping=(ch, cw), data_format="channels_last")(conv2)
up8 = concatenate([up_conv7, crop_conv2], axis=concat_axis)
conv8 = Dropout(0.2)(up8)
conv8 = Conv2D(64, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(conv8)
conv8 = Conv2D(64, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(conv8)
up_conv8 = UpSampling2D(size=(2, 2), data_format="channels_last")(conv8)
ch, cw = get_crop_shape(conv1, up_conv8)
crop_conv1 = Cropping2D(cropping=(ch, cw), data_format="channels_last")(conv1)
up9 = concatenate([up_conv8, crop_conv1], axis=concat_axis)
conv9 = Dropout(0.2)(up9)
conv9 = Conv2D(32, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(conv9)
conv9 = Conv2D(32, (3, 3), padding="same", activation="relu", data_format="channels_last",
kernel_initializer='he_uniform')(conv9)
ch, cw = get_crop_shape(inputs, conv9)
conv9 = layers.ZeroPadding2D(padding=((ch[0], ch[1]), (cw[0], cw[1])))(conv9)
conv10 = layers.Conv2D(nb_classes, (1, 1))(conv9)
activation = 'softmax'
if nb_classes == 1:
activation = 'sigmoid'
act = Activation(activation)(conv10)
model = Model(inputs=inputs, outputs=act)
gpus = get_number_of_gpus()
if gpus > 1:
model = ModelMGPU(model, gpus)
return model
def pred():
image_path = '/data/{}/test'
for dataset in datasets:
im_path = image_path.format(dataset['name'])
for model in models:
input_size = model['input_size']
generator, _ = create_generator(
im_path,
(input_size, input_size),
dataset['size'],
1,
rescale_masks=True,
with_file_names=True,
binary=True,
mean=np.array([[[0.36654497, 0.35386439, 0.30782658]]]),
std=np.array([[[0.19212837, 0.19031791, 0.18903286]]])
)
images, masks, file_names = next(generator)
m = model['method']((input_size, input_size), 1)
gpus = get_number_of_gpus()
if gpus > 1:
m = ModelMGPU(m, gpus)
m.compile(
optimizer=Adam(lr=1e-4),
loss=binary_soft_jaccard_loss,
metrics=['acc', binary_jaccard_distance_rounded])
weights_path = 'weights_train/weights.{}-{}-final-finetune.h5'.format(model['name'], dataset['name'])
m.load_weights(weights_path)
probs = m.predict(images, verbose=1)
probs = np.round(probs)
iou = batch_general_jaccard(masks, probs)
f1 = f1_score(masks, probs)
print('Mean IOU for {} on {}: {}'.format(model['name'], dataset['name'], np.mean(iou)))
print('F1 score for {} on {}: {}'.format(model['name'], dataset['name'], f1))
# wow such hack
from keras_utils.prediction import get_real_image, get_geo_frame, geo_reference_raster
for i, (prob, mask) in enumerate(zip(probs, masks)):
if i > 200:
break
raster = get_real_image(im_path, file_names[i], use_gdal=True)
R = raster.GetRasterBand(1).ReadAsArray()
G = raster.GetRasterBand(2).ReadAsArray()
B = raster.GetRasterBand(3).ReadAsArray()
img = np.zeros((512, 512, 3))
img[:, :, 0] = B
img[:, :, 1] = G
img[:, :, 2] = R
prob = np.round(prob)
prob = (prob[:, :, 0] * 255.).astype(np.uint8)
mask = (mask[:, :, 0] * 255.).astype(np.uint8)
pred_name = "pred-{}.tif".format(i)
out_path = '/data/finalpreds/{}/{}'.format(model['name'], dataset['name'])
pred_save_path = "{}/{}".format(out_path, pred_name)
cv2.imwrite(pred_save_path, prob)
cv2.imwrite("{}/image-{}.tif".format(out_path, i), img)
cv2.imwrite("{}/mask-{}.tif".format(out_path, i), mask)
try:
# Get coordinates for corresponding image
ulx, scalex, skewx, uly, skewy, scaley = get_geo_frame(raster)
# Geo reference newly created raster
geo_reference_raster(
pred_save_path,
[ulx, scalex, skewx, uly, skewy, scaley]
)
except ValueError as e:
print("Was not able to reference image at path: {}".format(pred_save_path))
K.clear_session()
def run():
parser = argparse.ArgumentParser()
parser.add_argument("--weights-path", type=str)
parser.add_argument("--epoch-number", type=int, default=5)
parser.add_argument("--test-images", type=str, default="")
parser.add_argument("--output-path", type=str, default="")
parser.add_argument("--input-size", type=int, default=713)
parser.add_argument("--batch-size", type=int, default=713)
parser.add_argument("--model-name", type=str, default="standard")
parser.add_argument("--save-imgs", type=bool, default=True)
args = parser.parse_args()
model_name = args.model_name
images_path = args.test_images
input_size = args.input_size
batch_size = args.batch_size
save_imgs = args.save_imgs
all_probs = {}
model_choices = {
'densenet': build_densenet,
'unet': build_unet
}
model_choice = model_choices[model_name]
generator, _ = create_generator(
images_path,
(input_size, input_size),
batch_size,
5,
rescale_masks=True,
with_file_names=True,
binary=False,
mean=np.array([[[0.36654497, 0.35386439, 0.30782658]]]),
std=np.array([[[0.19212837, 0.19031791, 0.18903286]]])
)
images, masks, file_names = next(generator)
for dataset in datasets:
model = model_choice((input_size, input_size), 1)
gpus = get_number_of_gpus()
print('Fund {} gpus'.format(gpus))
if gpus > 1:
model = ModelMGPU(model, gpus)
model.compile(
optimizer=Adam(lr=1e-4),
loss=binary_soft_jaccard_loss,
metrics=['acc', binary_jaccard_distance_rounded])
model.load_weights(args.weights_path.format(dataset))
probs = model.predict(images, verbose=1)
probs = np.round(probs)
# iou = batch_general_jaccard(masks, probs, binary=True)
# f1 = K.eval(f1_score(K.variable(masks), K.variable(probs)))
# print('Mean IOU for {}: {}'.format(dataset, np.mean(iou)))
# print('F1 score for {}: {}'.format(dataset, f1))
all_probs[dataset] = probs
final_prob = None
for i, key in enumerate(all_probs):
prob = all_probs[key]
prob[prob == 1] = scores[key]
if i == 0: # First iteration
final_prob = prob
continue
final_prob = np.maximum.reduce([final_prob, prob])
masks = np.argmax(masks, axis=2)
iou = batch_general_jaccard(masks, final_prob)
f1 = K.eval(f1_score(K.variable(masks), K.variable(final_prob)))
print('Mean IOU for {}: {}'.format('multiclass', np.mean(iou)))
print('F1 score for {}: {}'.format('multiclass', f1))
if not save_imgs:
return
# wow such hack
from keras_utils.prediction import get_real_image, get_geo_frame, geo_reference_raster
for i, prob in enumerate(final_prob):
mask = np.argmax(masks[i], axis=2)
raster = get_real_image(os.path.join(images_path, 'multiclass', 'test'), file_names[i], use_gdal=True)
R = raster.GetRasterBand(1).ReadAsArray()
G = raster.GetRasterBand(2).ReadAsArray()
B = raster.GetRasterBand(3).ReadAsArray()
img = np.zeros((512, 512, 3))
img[:, :, 0] = B
img[:, :, 1] = G
img[:, :, 2] = R
seg_pred = np.zeros((input_size, input_size, 3))
seg_mask = np.zeros((input_size, input_size, 3))
for c in range(5):
seg_pred[:, :, 0] += ((prob[:, :, 0] == c) * (class_color_map[c][2])).astype('uint8')
seg_pred[:, :, 1] += ((prob[:, :, 0] == c) * (class_color_map[c][1])).astype('uint8')
seg_pred[:, :, 2] += ((prob[:, :, 0] == c) * (class_color_map[c][0])).astype('uint8')
seg_mask[:, :, 0] += ((mask[:, :] == c) * (class_color_map[c][2])).astype('uint8')
seg_mask[:, :, 1] += ((mask[:, :] == c) * (class_color_map[c][1])).astype('uint8')
seg_mask[:, :, 2] += ((mask[:, :] == c) * (class_color_map[c][0])).astype('uint8')
pred_name = "pred-{}.tif".format(i)
pred_save_path = "{}/{}".format(args.output_path, pred_name)
cv2.imwrite(pred_save_path, seg_pred)
cv2.imwrite("{}/mask-{}.tif".format(args.output_path, i), seg_mask)
cv2.imwrite("{}/image-{}.tif".format(args.output_path, i), img)
try:
# Get coordinates for corresponding image
ulx, scalex, skewx, uly, skewy, scaley = get_geo_frame(raster)
# Geo reference newly created raster
geo_reference_raster(
pred_save_path,
[ulx, scalex, skewx, uly, skewy, scaley]
)
except ValueError as e:
print("Was not able to reference image at path: {}".format(pred_save_path))
def run():
parser = argparse.ArgumentParser()
parser.add_argument("--weights-path", type=str)
parser.add_argument("--test-image", type=str, default="")
parser.add_argument("--sample-images", type=str, default="")
parser.add_argument("--output-path", type=str, default="")
parser.add_argument("--input-size", type=int, default=713)
parser.add_argument("--model-name", type=str, default="")
parser.add_argument("--name", type=str, default="")
parser.add_argument("--mask", type=str, default="")
args = parser.parse_args()
model_name = args.model_name
image_path = args.test_image
input_size = args.input_size
output_path = args.output_path
file_name = args.name
mask_path = args.mask
nb_classes = 5
model_choices = {'unet': build_unet, 'densenet': build_densenet}
model_choice = model_choices[model_name]
model = model_choice((input_size, input_size), nb_classes)
gpus = get_number_of_gpus()
print('Fund {} gpus'.format(gpus))
if gpus > 1:
model = ModelMGPU(model, gpus)
model.compile(optimizer=Adam(lr=1e-4),
loss=binary_soft_jaccard_loss,
metrics=['acc', binary_jaccard_distance_rounded])
model.load_weights(args.weights_path)
generator = get_generator()
# load the image
image = Image.open(image_path)
size = image.size[0]
factor = input_size / 512
image = image.resize((int(size * factor), int(size * factor)))
image = np.array(image)
pred = predict_img_with_smooth_windowing(
image,
window_size=input_size,
subdivisions=
2, # Minimal amount of overlap for windowing. Must be an even number.
nb_classes=nb_classes,
pred_func=(lambda img_batch_subdiv: model.predict(
image_to_neural_input(img_batch_subdiv, generator), verbose=True)))
pred = np.argmax(pred, axis=2)
pred_color = np.zeros((pred.shape[0], pred.shape[0], 3))
if mask_path:
mask = Image.open(mask_path).convert('L')
mask = mask.resize((pred.shape[0], pred.shape[0]))
mask = np.array(mask)
mask = np.reshape(mask, (1, mask.shape[0], mask.shape[1]))
p = np.reshape(pred, (1, pred.shape[0], pred.shape[1]))
print('mIOU:', batch_general_jaccard(mask, p))
print('F1:', batch_classwise_f1_score(mask, p))
class_color_map = {
0: [237, 237, 237], # Empty
1: [254, 241, 179], # Roads
2: [116, 173, 209], # Water
3: [193, 235, 176], # Grass
4: [170, 170, 170] # Buildings
}
for c in range(nb_classes):
pred_color[:, :, 0] += ((pred[:, :] == c) *
(class_color_map[c][2])).astype('uint8')
pred_color[:, :, 1] += ((pred[:, :] == c) *
(class_color_map[c][1])).astype('uint8')
pred_color[:, :, 2] += ((pred[:, :] == c) *
(class_color_map[c][0])).astype('uint8')
out_path = os.path.join(output_path, file_name)
print(cv2.imwrite(out_path, pred_color))
cheap = cheap_tiling_prediction(
image,
window_size=input_size,
nb_classes=nb_classes,
pred_func=(lambda img_batch_subdiv: model.predict(
image_to_neural_input(np.array(img_batch_subdiv), generator),
verbose=True)))
cheap = np.argmax(cheap, axis=2)
cheap_color = np.zeros((cheap.shape[0], cheap.shape[1], 3))
if mask_path:
mask = Image.open(mask_path).convert('L')
mask = mask.resize((cheap.shape[0], cheap.shape[0]))
mask = np.array(mask)
mask = np.reshape(mask, (1, mask.shape[0], mask.shape[1]))
p = np.reshape(cheap, (1, cheap.shape[0], cheap.shape[1]))
print('mIOU:', batch_general_jaccard(mask, p))
print('F1:', batch_classwise_f1_score(mask, p))
for c in range(nb_classes):
cheap_color[:, :, 0] += ((cheap[:, :] == c) *
(class_color_map[c][2])).astype('uint8')
cheap_color[:, :, 1] += ((cheap[:, :] == c) *
(class_color_map[c][1])).astype('uint8')
cheap_color[:, :, 2] += ((cheap[:, :] == c) *
(class_color_map[c][0])).astype('uint8')
out_path = os.path.join(output_path, 'cheap-{}'.format(file_name))
print(cv2.imwrite(out_path, cheap_color))
def train_densenet(data_dir, logdir, weights_dir, weights_name, input_size,
nb_classes, batch_size, config, initial_epoch,
pre_trained_weight, augment):
session_config()
model = build_densenet(input_size, nb_classes, config=config)
model.summary()
gpus = get_number_of_gpus()
print('Found {} gpus'.format(gpus))
if gpus > 1:
model = ModelMGPU(model, gpus)
is_binary = nb_classes == 1
if is_binary:
loss = binary_soft_jaccard_loss
else:
loss = soft_jaccard_loss
model.compile(optimizer=Adam(lr=1e-3),
loss=loss,
metrics=['acc', binary_jaccard_distance_rounded])
train_generator, num_samples = create_generator(
os.path.join(data_dir, 'train'),
input_size,
batch_size,
nb_classes,
rescale_masks=True,
binary=is_binary,
augment=False,
mean=np.array([[[0.42800662, 0.40565866, 0.3564895]]]),
std=np.array([[[0.19446792, 0.1984272, 0.19501258]]]))
val_generator, val_samples = create_generator(
os.path.join(data_dir, 'val'),
input_size,
batch_size,
nb_classes,
rescale_masks=True,
binary=is_binary,
augment=False,
mean=np.array([[[0.42800662, 0.40565866, 0.3564895]]]),
std=np.array([[[0.19446792, 0.1984272, 0.19501258]]]))
if pre_trained_weight:
print('Loading weights: {}'.format(pre_trained_weight))
model.load_weights(pre_trained_weight)
steps_per_epoch = num_samples // batch_size
if augment:
steps_per_epoch = steps_per_epoch * 4
base_lr = 0.00002
max_lr = 0.00055
cb = [
ValidationCallback(val_samples // batch_size, val_generator, is_binary)
] + callbacks(logdir,
filename=weights_name,
weightsdir=weights_dir,
monitor_val='mIOU',
base_lr=base_lr,
max_lr=max_lr,
steps_per_epoch=steps_per_epoch,
cyclic='triangular2')
model.fit_generator(generator=train_generator,
steps_per_epoch=steps_per_epoch,
epochs=100,
verbose=True,
workers=8,
callbacks=cb,
initial_epoch=initial_epoch)
def run(args):
n_classes = args.classes
model_name = args.model_name
images_path = args.test_images
input_size = args.input_size
batch_size = args.batch_size
no_save_imgs = args.no_save_imgs
model_choices = {
'unet': build_unet,
'densenet': build_densenet,
'pspnet': build_pspnet
}
model_choice = model_choices[model_name]
model = model_choice((input_size, input_size), n_classes)
gpus = get_number_of_gpus()
print('Fund {} gpus'.format(gpus))
if gpus > 1:
model = ModelMGPU(model, gpus)
model.compile(optimizer=Adam(lr=1e-4),
loss=binary_soft_jaccard_loss,
metrics=['acc', binary_jaccard_distance_rounded])
model.load_weights(args.weights_path)
binary = n_classes == 1
generator, samples = create_generator(
images_path, (input_size, input_size),
batch_size,
nb_classes=n_classes,
rescale_masks=False,
with_file_names=True,
binary=binary,
augment=False,
mean=np.array([[[0.36654497, 0.35386439, 0.30782658]]]),
std=np.array([[[0.19212837, 0.19031791, 0.18903286]]]))
steps = samples // batch_size
f1s = []
ious = []
for i in range(steps):
images, masks, file_names = next(generator)
probs = model.predict(images, verbose=1)
probs = np.argmax(probs, axis=3)
masks = np.argmax(masks, axis=3)
iou = batch_general_jaccard(masks, probs)
f1 = batch_classwise_f1_score(masks, probs)
ious.append(iou)
f1s.append(f1)
if no_save_imgs:
continue
for i, prob in enumerate(probs):
result = prob
mask_result = masks[i]
# img = get_real_image(images_path, file_names[i])
raster = get_real_image(images_path, file_names[i], use_gdal=True)
R = raster.GetRasterBand(1).ReadAsArray()
G = raster.GetRasterBand(2).ReadAsArray()
B = raster.GetRasterBand(3).ReadAsArray()
img = np.zeros((512, 512, 3))
img[:, :, 0] = B
img[:, :, 1] = G
img[:, :, 2] = R
seg_img = np.zeros((input_size, input_size, 3))
seg_mask = np.zeros((input_size, input_size, 3))
for c in range(n_classes):
seg_img[:, :, 0] += ((result[:, :] == c) *
(class_color_map[c][2])).astype('uint8')
seg_img[:, :, 1] += ((result[:, :] == c) *
(class_color_map[c][1])).astype('uint8')
seg_img[:, :, 2] += ((result[:, :] == c) *
(class_color_map[c][0])).astype('uint8')
seg_mask[:, :, 0] += ((mask_result[:, :] == c) *
(class_color_map[c][2])).astype('uint8')
seg_mask[:, :, 1] += ((mask_result[:, :] == c) *
(class_color_map[c][1])).astype('uint8')
seg_mask[:, :, 2] += ((mask_result[:, :] == c) *
(class_color_map[c][0])).astype('uint8')
pred_name = "pred-{}.tif".format(i)
pred_save_path = "{}/{}".format(args.output_path, pred_name)
cv2.imwrite(pred_save_path, seg_img)
cv2.imwrite("{}/mask-{}.tif".format(args.output_path, i), seg_mask)
cv2.imwrite("{}/image-{}.tif".format(args.output_path, i), img)
try:
# Get coordinates for corresponding image
ulx, scalex, skewx, uly, skewy, scaley = get_geo_frame(raster)
# Geo reference newly created raster
geo_reference_raster(pred_save_path,
[ulx, scalex, skewx, uly, skewy, scaley])
except ValueError as e:
print("Was not able to reference image at path: {}".format(
pred_save_path))
print('Mean IOU: {}'.format(np.mean(ious)))
print('F1 score: {}'.format(np.mean(f1s)))