def do_camelyon16_WSI_level():
"""
GlaS.
:return:
"""
# ===============
# Reproducibility
# ===============
# ===========================
reproducibility.set_seed()
# ===========================
username = getpass.getuser()
if username == "brian":
baseurl = "/media/brian/Seagate Backup Plus Drive/datasets/camelyon16"
elif username == "sbelharb":
baseurl = "/project/6004986/sbelharb/workspace/datasets/camelyon16"
else:
raise ValueError("username `{}` unknown .... [NOT OK]".format(username))
args = {"baseurl": baseurl,
"folding": {"vl": 20}, # 80 % for train, 20% for validation.
"dataset": "camelyon16",
"fold_folder": "folds/camelyon16/WSI-level",
"img_extension": "tif",
"nbr_folds": 5,
"nbr_splits": 2 # how many times to perform the k-folds over the available train samples.
}
split_valid_camelyon16_WSI_level(Dict2Obj(args))
def do_breakhis():
"""
BreakHis.
:return:
"""
# ===============
# Reproducibility
# ===============
# ===========================
reproducibility.set_seed()
# ===========================
username = getpass.getuser()
if username == "brian":
baseurl = "/media/brian/Seagate Backup Plus Drive/datasets/" \
"Breast-Cancer-Histopathological-Database-BreakHis/mkfold"
elif username == "sbelharb":
baseurl = "/project/6004986/sbelharb/workspace/datasets/" \
"Breast-Cancer-Histopathological-Database-BreakHis/mkfold"
else:
raise ValueError("username `{}` unknown .... [NOT OK]".format(username))
args = {"baseurl": baseurl,
"folding": {"vl": 20}, # 80% for train, 20% for validation.
"dataset": "breakhis",
"fold_folder": "folds/breakhis",
"img_extension": "png",
"nbr_folds": 5,
"magnification": ["40X", "100X", "200X", "400X"],
"nbr_splits": 2 # how many times to perform the k-folds over the available train samples.
}
split_valid_breakhis(Dict2Obj(args))
def do_Caltech_UCSD_Birds_200_2011():
"""
Caltech-UCSD-Birds-200-2011.
:return:
"""
# ===============
# Reproducibility
# ===============
# ===========================
reproducibility.set_seed()
# ===========================
username = getpass.getuser()
if username == "xxxx2020":
baseurl = "xxxx2020/datasets/Caltech-UCSD-Birds-200-2011"
elif username == "xxxx2020":
baseurl = "xxxx2020/datasets/Caltech-UCSD-Birds-200-2011"
else:
raise ValueError(
"Cause: anonymization of the code. username `{}` unknown. Set the absolute path to the Caltech-UCSD-Birds-200-2011 dataset. See above for an example .... [NOT OK]"
.format(username))
args = {
"baseurl": baseurl,
"folding": {
"vl": 20
}, # 80 % for train, 20% for validation.
"dataset": "Caltech-UCSD-Birds-200-2011",
"fold_folder": "folds/Caltech-UCSD-Birds-200-2011",
"img_extension": "bmp",
"nbr_splits":
2, # how many times to perform the k-folds over the available train samples.
"path_encoding":
"folds/Caltech-UCSD-Birds-200-2011/encoding-origine.yaml",
"nbr_classes":
None # Keep only 5 random classes. If you want to use the entire dataset, set this to None.
}
args["nbr_folds"] = math.ceil(100. / args["folding"]["vl"])
split_valid_Caltech_UCSD_Birds_200_2011(Dict2Obj(args))
def do_glas():
"""
GlaS.
:return:
"""
# ===============
# Reproducibility
# ===============
# ===========================
reproducibility.set_seed()
# ===========================
username = getpass.getuser()
if username == "xxxx2020":
baseurl = "xxxx2020/datasets/GlaS-2015/Warwick QU Dataset (Released 2016_07_08)"
elif username == "sbelharb":
baseurl = "xxxx2020/datasets/GlaS-2015/Warwick QU Dataset (Released 2016_07_08)"
else:
raise ValueError(
"Cause: anonymization of the code. username `{}` unknown. Set the absolute path to the Caltech-UCSD-Birds-200-2011 dataset. See above for an example .... [NOT OK]"
.format(username))
args = {
"baseurl": baseurl,
"folding": {
"vl": 20
}, # 80 % for train, 20% for validation.
"dataset": "glas",
"fold_folder": "folds/glas-test",
"img_extension": "bmp",
"nbr_splits":
2 # how many times to perform the k-folds over the available train samples.
}
args["nbr_folds"] = math.ceil(100. / args["folding"]["vl"])
split_valid_glas(Dict2Obj(args))
def do_glas():
"""
GlaS.
:return:
"""
# ===============
# Reproducibility
# ===============
# ===========================
reproducibility.set_seed()
# ===========================
warnings.warn("You are accessing an anonymized part of the code. We are going to exit. Come here and fix this "
"according to your setup. Issue: absolute path to GlaS dataset.")
sys.exit(0)
username = getpass.getuser()
if username == "XXXXXXXXXX":
baseurl = "/XXXXXXXXX/XXXXXXXXXX/XXXXXXXXXXXXXXX/datasets/GlaS-2015/Warwick QU Dataset (Released 2016_07_08)"
elif username == "XXXXXXXXXXXX":
baseurl = "/XXXXXX/XXXXXXX/XXXXXXXXXXXXXXXXX/workspace/datasets/GlaS-2015/Warwick QU Dataset (Released 2016_07_08)"
else:
raise ValueError("Cause: anonymization of the code. username `{}` unknown. Set the absolute path to the GlaS dataset. See above for an example .... [NOT OK]".format(username))
args = {"baseurl": baseurl,
"folding": {"vl": 20}, # 80 % for train, 20% for validation.
"dataset": "glas",
"fold_folder": "folds/glas-test",
"img_extension": "bmp",
"nbr_splits": 2 # how many times to perform the k-folds over the available train samples.
}
args["nbr_folds"] = math.ceil(100. / args["folding"]["vl"])
split_valid_glas(Dict2Obj(args))
def do_bach_parta_2018():
"""
BACH (PART A) 2018.
:return:
"""
# ===============
# Reproducibility
# ===============
# ===========================
reproducibility.set_seed()
# ===========================
username = getpass.getuser()
if username == "brian":
baseurl = "/media/brian/Seagate Backup Plus Drive/datasets/ICIAR-2018-BACH-Challenge"
elif username == "sbelharb":
baseurl = "/project/6004986/sbelharb/workspace/datasets/ICIAR-2018-BACH-Challenge"
else:
raise ValueError("username `{}` unknown .... [NOT OK]".format(username))
args = {"baseurl": baseurl,
"test_portion": 0.5, # percentage of samples to take from test. The left over if for train; and it will
# be divided into actual train, and validation sets.
"folding": {"vl": 20}, # vl/100 % of train set will be used for validation, while the leftover (
# 100-vl)/100% will be used for actual training.
"name_classes": {'Normal': 0, 'Benign': 1, 'InSitu': 2, 'Invasive': 3},
"dataset": "bc18bch",
"fold_folder": "folds/bach-part-a-2018",
"img_extension": "tif",
"nbr_folds": 5,
"nbr_splits": 2 # how many times to perform the k-folds over the available train samples.
}
create_k_folds_csv_bach_part_a(Dict2Obj(args))
from loader import csv_loader, PhotoDataset, default_collate, MyDataParallel
from instantiators import instantiate_models, instantiate_optimizer, instantiate_train_loss, instantiate_eval_loss
import torch
import torch.nn as nn
import reproducibility
FACTOR_MUL_WORKERS = 2 # args.num_workers * this_factor. Useful when setting set_for_eval to False, batch size =1,
# and we are in an evaluation mode (to go faster and coop with the lag between the CPU and GPU).
DEBUG_MODE = False # Can be activated only for "Caltech-UCSD-Birds-200-2011" or "Oxford-flowers-102"
# dataset to go fast. If True, we select only few samples for training, validation, and test.
PLOT_STATS = False
reproducibility.set_seed(
None) # use the default seed. Copy the see into the os.environ("MYSEED")
NBRGPUS = torch.cuda.device_count()
ALLOW_MULTIGPUS = check_if_allow_multgpu_mode()
def _init_fn(worker_id):
"""
Init. function for the worker in dataloader.
:param worker_id:
:return:
"""
pass
# np.random.seed(int(os.environ["MYSEED"]))
# random.seed(int(os.environ["MYSEED"]))
def do_Oxford_flowers_102():
"""
Oxford-flowers-102.
The train/valid/test sets are already provided.
:return:
"""
# ===============
# Reproducibility
# ===============
# ===========================
reproducibility.set_seed()
# ===========================
username = getpass.getuser()
if username == "xxxx2020":
baseurl = "xxxxx2020/datasets/Oxford-flowers-102"
elif username == "xxxx2020":
baseurl = "xxxx2020/datasets/Oxford-flowers-102"
else:
raise ValueError(
"Cause: anonymization of the code. username `{}` unknown. Set the absolute path to the Caltech-UCSD-Birds-200-2011 dataset. See above for an example .... [NOT OK]"
.format(username))
args = {
"baseurl": baseurl,
"dataset": "Oxford-flowers-102",
"fold_folder": "folds/Oxford-flowers-102",
"img_extension": "jpg",
"path_encoding": "folds/Oxford-flowers-102/encoding-origine.yaml"
}
# Convert masks into binary masks.
create_bin_mask_Oxford_flowers_102(Dict2Obj(args))
reproducibility.set_seed()
split_Oxford_flowers_102(Dict2Obj(args))
# Find min max size.
def find_stats(argsx):
"""
:param argsx:
:return:
"""
minh, maxh, minw, maxw = None, None, None, None
baseurl = argsx.baseurl
fin = find_files_pattern(join(baseurl, 'jpg'), '*.jpg')
print("Computing stats from {} dataset ...".format(argsx.dataset))
for f in tqdm.tqdm(fin, ncols=80, total=len(fin)):
w, h = Image.open(f, 'r').convert('RGB').size
if minh is None:
minh = h
maxh = h
minw = w
maxw = w
else:
minh = min(minh, h)
maxh = max(maxh, h)
minw = min(minw, w)
maxw = max(maxw, w)
print('Stats {}:\n'
'min h: {} \n'
'max h: {} \n'
'min w: {} \n'
'max w: {} \n'.format(argsx.dataset, minh, maxh, minw, maxw))
find_stats(Dict2Obj(args))
from prologues import get_eval_dataset
import torch
import reproducibility
import constants
# and we are in an evaluation mode (to go faster and coop with the lag between
# the CPU and GPU).
DEBUG_MODE = False # Can be activated only for
# "Caltech-UCSD-Birds-200-2011" or "Oxford-flowers-102"
# dataset to go fast. If True, we select only few samples for training,
# validation, and test.
PLOT_STATS = False
reproducibility.set_seed(None) # use the default seed.
# Copy the see into the os.environ("MYSEED")
NBRGPUS = torch.cuda.device_count()
ALLOW_MULTIGPUS = check_if_allow_multgpu_mode()
if __name__ == "__main__":
# =============================================
# Parse the inputs and deal with the yaml file.
# =============================================
parser = argparse.ArgumentParser()
parser.add_argument("--yaml",
type=str,
