def __init__(self, name, item_list, marked_email_list):
self.name = name
self.google_item_list = item_list
self.marked_email_list = marked_email_list
self.node_mln_list = []
self.aff_word_list = []
self.resource_dir = CONSTANT_PATH['resource']
self.input_person_list_path = os.path.join(self.resource_dir, 'input_person_list.json')
self.person_mln_dir = os.path.join(CONSTANT_PATH['mln_by_product_dir'], self.name.replace(' ', '_'))
self.grounding_file_path = os.path.join(self.person_mln_dir, 'evidence.db')
self.raw_item_file_path = os.path.join(CONSTANT_PATH['google_item_dir'], self.name + '.json')
self.processed_item_file_path = os.path.join(self.person_mln_dir, 'google_item_list.json')
self.valid_email_json_path = os.path.join(self.person_mln_dir, 'valid_email.json')
create_dir_if_not_exist(self.person_mln_dir)
self.get_aff_word_list()
self.get_node_mln_list()
def __init__(self, name, item_list, marked_email_list):
self.name = name
self.google_item_list = item_list
self.marked_email_list = marked_email_list
self.node_mln_list = []
self.aff_word_list = []
self.resource_dir = CONSTANT_PATH['resource']
self.input_person_list_path = os.path.join(self.resource_dir,
'input_person_list.json')
self.person_mln_dir = os.path.join(CONSTANT_PATH['mln_by_product_dir'],
self.name.replace(' ', '_'))
self.grounding_file_path = os.path.join(self.person_mln_dir,
'evidence.db')
self.raw_item_file_path = os.path.join(
CONSTANT_PATH['google_item_dir'], self.name + '.json')
self.processed_item_file_path = os.path.join(self.person_mln_dir,
'google_item_list.json')
self.valid_email_json_path = os.path.join(self.person_mln_dir,
'valid_email.json')
create_dir_if_not_exist(self.person_mln_dir)
self.get_aff_word_list()
self.get_node_mln_list()
def create_patch(whole_slide_dir, patch_dir, patch_size):
# Create dirs
responder_dir = patch_dir + "/1st_manual"
non_responder_dir = patch_dir
# create_dir_if_not_exist(responder_dir)
create_dir_if_not_exist(non_responder_dir)
create_dir_if_not_exist("processed")
# Iterate through files to split and group them
image_files = os.listdir(whole_slide_dir)
print(image_files)
print(len(image_files), "slide images found")
total = 0
skipped = []
for image_file in tqdm(image_files, desc="Splitting images"):
if "DS_Store" not in image_file:
image = Image.open(whole_slide_dir + "/" + image_file)
width, height = image.size
file_well_num = image_file[:image_file.rindex(".")]
save_dir = responder_dir if "1st_manual" in image_file else non_responder_dir
# Round to lowest multiple of target width and height.
# Will lead to a loss of image data around the edges, but ensures split images are all the same size.
rounded_width = patch_size * (width // patch_size)
rounded_height = patch_size * (height // patch_size)
# Split and save
xs = range(0, rounded_width, patch_size)
ys = range(0, rounded_height, patch_size)
for i_x, x in enumerate(xs):
for i_y, y in enumerate(ys):
box = (x, y, x + patch_size, y + patch_size)
cropped_data = image.crop(box)
# print(cropped_data)
cropped_image = Image.new('RGB', (patch_size, patch_size),
255)
cropped_image.paste(cropped_data)
np_data = np.array(cropped_image)
# print(np_data.shape)
# if np.mean(np_data[:, :, :1]) == 0:
# continue
# Check which dataset is being used
if 'train' in patch_dir:
processed_GT_file = os.listdir(
"test_patches/HRF128/train_GT")
elif 'valid' in patch_dir:
processed_GT_file = os.listdir(
"test_patches/HRF128/valid_GT")
else:
processed_GT_file = os.listdir(
"test_patches/HRF128/test_GT")
if "GT" in whole_slide_dir:
cropped_image.save(save_dir + "/" +
file_well_num.zfill(5) + "_x" +
str(i_x).zfill(2) + "_y" +
str(i_y).zfill(2) + ".png")
else:
naming_string = file_well_num.zfill(5) + "_x" + str(
i_x).zfill(2) + "_y" + str(i_y).zfill(2) + ".png"
if naming_string not in processed_GT_file:
continue
cropped_image.save(save_dir + "/" +
file_well_num.zfill(5) + "_x" +
str(i_x).zfill(2) + "_y" +
str(i_y).zfill(2) + ".png")
total += 1
print('Created', total, 'split images')
if skipped:
print('Labels not found for', skipped, 'so they were skipped')
import os
from util import create_dir_if_not_exist
CONSTANT_PATH = {
'google_item_dir': os.path.join('..', 'resource', 'google_items'),
'result': os.path.join('..', 'result'),
'resource': os.path.join('..', 'resource'),
'by_product_dir': os.path.join('..', 'by_product'),
'mln_by_product_dir': os.path.join('..', 'by_product', 'mln_by_product'),
'svm_by_product_dir': os.path.join('..', 'by_product', 'svm_by_product'),
'fgm_by_product_dir': os.path.join('..', 'by_product', 'fgm_by_product'),
}
for key, value in CONSTANT_PATH.items():
create_dir_if_not_exist(value)
filenames = [
os.path.join(args.data_dir, f) for f in filenames if f.endswith('.png')
]
# shuffling filneames
random.seed(SEED)
filenames.sort()
random.shuffle(filenames)
# splitting into training and validation set
split = int(TRAIN_SPLIT * len(filenames))
train_filenames = filenames[:split]
val_filenames = filenames[split:]
splited_sets = {'train': train_filenames, 'val': val_filenames}
create_dir_if_not_exist(args.output_dir)
for split in ['train', 'val']:
"""Saving to directories:
X - original images
Y - segmented images
labeled - images with converted colors from segmented images to classes
"""
output_dir_split = os.path.join(args.output_dir, '{}'.format(split))
output_dir_labeled = os.path.join(output_dir_split, 'labeled')
output_dir_X = os.path.join(output_dir_split, 'X')
output_dir_Y = os.path.join(output_dir_split, 'Y')
create_dir_if_not_exist(output_dir_split)
create_dir_if_not_exist(output_dir_labeled)
create_dir_if_not_exist(output_dir_X)
create_dir_if_not_exist(output_dir_Y)
from os.path import abspath
from util import get_ip_address
from util import create_dir_if_not_exist
reload(sys)
sys.setdefaultencoding('utf8')
sys.dont_write_bytecode = True
# server
SERVER_IP = '127.0.0.1'
# SERVER_IP = get_ip_address()
SERVER_PORT = 5000
# db
DB_DIR = join(abspath(os.path.dirname(__file__)), 'db')
create_dir_if_not_exist(DB_DIR)
class Config():
# CSRF
CSRF_ENABLED = True
SECRET_KEY = 'CSSUNB'
SECURITY_PASSWORD_SALT = 'CSSUNB23333'
# DB settings
APP_DB = 'ACE.db'
TEST_DB = 'test'
SQLALCHEMY_TRACK_MODIFICATIONS = True
SQLALCHEMY_MIGRATE_REPO = join(DB_DIR, 'db_repo')
SQLALCHEMY_DATABASE_URI = 'sqlite:///%s' % (join(DB_DIR, APP_DB))
def create_patch(image_path,
gt_path,
patch_dir,
patch_size,
patch_per_image,
inside=True):
# Create dirs
gt_dir = patch_dir + "_GT"
image_dir = patch_dir
create_dir_if_not_exist(gt_dir)
create_dir_if_not_exist(image_dir)
create_dir_if_not_exist("random")
# Iterate through files to split and group them
image_files = os.listdir(image_path)
print(len(image_files), "slide images found")
iter_tot = 0
for image_file in tqdm(image_files, desc="Splitting images"):
if "DS_Store" not in image_file:
image = Image.open(image_path + "/" + image_file)
image_np = np.asarray(image)
# print(image_np.shape)
gt = Image.open(gt_path + "/" + image_file[:-3] + 'png')
gt_np = np.asarray(gt)
# print(gt_np.shape)
gt_np = np.reshape(gt_np, (gt_np.shape[0], gt_np.shape[1], 1))
# print(gt_np.shape)
width, height = image.size
save_dir_image = image_dir
save_dir_gt = gt_dir
# Round to lowest multiple of target width and height.
# Will lead to a loss of image data around the edges, but ensures split images are all the same size.
rounded_width = patch_size * (width // patch_size)
rounded_height = patch_size * (height // patch_size)
# TODO: Added from https://github.com/QTIM-Lab/retinaunet/blob/master/lib/extract_patches.py
k = 0
patches = []
patches_gt = []
while k < patch_per_image:
x_center = randint(0 + int(patch_size / 2),
width - int(patch_size / 2))
# print "x_center " +str(x_center)
y_center = randint(0 + int(patch_size / 2),
height - int(patch_size / 2))
# print "y_center " +str(y_center)
# check whether the patch is fully contained in the FOV
# if inside == True:
# if is_patch_inside_FOV(x_center, y_center, img_w, img_h, patch_h) == False:
# continue
patch = image_np[x_center - int(patch_size / 2):x_center +
int(patch_size / 2),
y_center - int(patch_size / 2):y_center +
int(patch_size / 2), :]
patch_mask = gt_np[x_center - int(patch_size / 2):x_center +
int(patch_size / 2),
y_center - int(patch_size / 2):y_center +
int(patch_size / 2), :]
patches.append(patch)
patches_gt.append(patch_mask)
box = (x_center - int(patch_size / 2),
y_center - int(patch_size / 2),
x_center + int(patch_size / 2),
y_center + int(patch_size / 2))
cropped_data = image.crop(box)
cropped_data_gt = gt.crop(box)
cropped_image = Image.new('RGB', (patch_size, patch_size), 255)
cropped_image.paste(cropped_data)
cropped_image_gt = Image.new('RGB', (patch_size, patch_size),
255)
cropped_image_gt.paste(cropped_data_gt)
# if inside:
# if is_patch_inside_FOV(x_center, y_center, width, height, patch_size) == False:
# continue
# if np.mean(np.asarray(cropped_image_gt)) == 0:
# continue
# else:
# print(np.mean(np.asarray(cropped_image_gt)[:, :, :1]))
iter_tot += 1 # total
k += 1 # per full_img
cropped_image.save(save_dir_image + "/" +
str(iter_tot).zfill(5) + ".png")
cropped_image_gt.save(save_dir_gt + "/" +
str(iter_tot).zfill(5) + ".png")
# print(patches)
# return patches #, patches_masks
print('Created', iter_tot, 'split images')
def __init__(self, tot_data_num):
self.tot_data_num = tot_data_num
self.root_path = '../' + self.svm_name
self.data_root_path = '../' + self.svm_name + '/email/'
self.result_root_path = '../' + self.svm_name + '/result/'
self.train_dir_path = self.data_root_path + 'train/'
self.test_dir_path = self.data_root_path + 'test/'
self.model_dir_path = self.data_root_path + 'model/'
self.pred_dir_path = self.data_root_path + 'prediction/'
self.result_test_dir_path = self.result_root_path + 'test/'
self.result_compare_dir_path = self.result_root_path + 'compare/'
create_dir_if_not_exist(self.root_path)
create_dir_if_not_exist(self.data_root_path)
create_dir_if_not_exist(self.result_root_path)
create_dir_if_not_exist(self.test_dir_path)
create_dir_if_not_exist(self.train_dir_path)
create_dir_if_not_exist(self.model_dir_path)
create_dir_if_not_exist(self.pred_dir_path)
create_dir_if_not_exist(self.result_test_dir_path)
create_dir_if_not_exist(self.result_compare_dir_path)
y.unsqueeze_(0)
X = Variable(X.to(device))
outputs = model(X)
_, preds = torch.max(outputs.data, 1)
fname = os.path.basename(os.path.normpath(path))
preds, y = preds.cpu().numpy(), y.numpy()
image = plot_fast(preds, y)
imageio.imwrite('preds/' + fname, image.astype(np.uint8))
def plot_validation(model):
"""Plots predictions for whole validation set"""
test_loader = data_loader.fetch_dataloader('data/val', batch_size=8)
with torch.no_grad():
for images, y, _, fname in tqdm(test_loader):
images = images.to(device)
outputs = model(images)
_, preds = torch.max(outputs.data, 1)
preds, y = preds.cpu().numpy(), y.numpy()
for b in range(preds.shape[0]):
image = plot_fast(preds[b], y[b])
imageio.imwrite('preds/' + fname[b], image.astype(np.uint8))
if __name__ == '__main__':
model = load_model(device)
create_dir_if_not_exist('preds')
plot_validation(model)
from os.path import abspath
from util import get_ip_address
from util import create_dir_if_not_exist
reload(sys)
sys.setdefaultencoding('utf8')
sys.dont_write_bytecode = True
# server
SERVER_IP = '127.0.0.1'
# SERVER_IP = get_ip_address()
SERVER_PORT = 5000
# db
DB_DIR = join(abspath(os.path.dirname(__file__)), 'db')
create_dir_if_not_exist(DB_DIR)
class Config():
# CSRF
CSRF_ENABLED = True
SECRET_KEY = 'CSSUNB'
SECURITY_PASSWORD_SALT = 'CSSUNB23333'
# DB settings
APP_DB = 'ACE.db'
TEST_DB = 'test'
SQLALCHEMY_TRACK_MODIFICATIONS = True
SQLALCHEMY_MIGRATE_REPO = join(DB_DIR, 'db_repo')
SQLALCHEMY_DATABASE_URI = 'sqlite:///%s' % (join(DB_DIR, APP_DB))