def init_seed(seed=None):
"""
* initialize the seed.
* Set a seed to some modules for reproducibility.
Note:
While this attempts to ensure reproducibility, it does not offer an
absolute guarantee. The results may be similar to some precision.
Also, they may be different due to an amplification to extremely
small differences.
See:
https://pytorch.org/docs/stable/notes/randomness.html
https://stackoverflow.com/questions/50744565/
how-to-handle-non-determinism-when-training-on-a-gpu
:param seed: int, a seed. Default is None: use the default seed (0).
:return:
"""
if seed is None:
seed = get_seed()
else:
os.environ["MYSEED"] = str(seed)
announce_msg("SEED: {} ".format(os.environ["MYSEED"]))
check_if_allow_multgpu_mode()
reset_seed(seed)
def __init__(self, inplans, modalities, num_classes, kmax=0.5, kmin=None,
alpha=0.6, dropout=0.0, tau=1.):
"""
:param inplans:
:param modalities:
:param num_classes:
:param kmax:
:param kmin:
:param alpha:
:param dropout:
:param tau: float > 0.
"""
announce_msg("Using Poisson hard-wired output.")
super(PoissonHead, self).__init__(
inplans=inplans, modalities=modalities, num_classes=num_classes,
kmax=kmax, kmin=kmin, alpha=alpha, dropout=dropout)
msg = "`tau` should be float. found {} ...[NOT OK]".format(
type(tau))
assert isinstance(tau, float), msg
msg = "`tau` must be in ]0., inf[. found {} ... [NOT OK]".format(tau)
assert tau > 0., msg
self.tau = tau
self.pool_to_one = nn.Sequential(
nn.Linear(num_classes, 1, bias=True),
nn.Softplus()
)
log(results_log, "\n\n ########### Results #########\n\n")
callback = None
# ==========================================================
# Data transformations: on PIL.Image.Image and torch.tensor.
# ==========================================================
train_transform_img = get_train_transforms_img(args)
transform_tensor = get_transforms_tensor(args)
# =======================================================================================================
# Datasets: create folds, load csv, preprocess files and save on disc, load datasets: train, valid, test.
# =======================================================================================================
announce_msg("SPLIT: {} \t FOLD: {}".format(args.split, args.fold))
relative_fold_path = join(args.fold_folder, args.dataset,
"split_" + str(args.split),
"fold_" + str(args.fold))
if isinstance(args.name_classes, str): # path
path_classes = join(relative_fold_path, args.name_classes)
assert os.path.isfile(
path_classes), "File {} does not exist .... [NOT OK]".format(
path_classes)
with open(path_classes, "r") as fin:
args.name_classes = yaml.load(fin)
train_csv = join(
relative_fold_path,
"train_s_" + str(args.split) + "_f_" + str(args.fold) + ".csv")
def validate(model,
dataset,
dataloader,
criterion,
device,
stats,
args,
folderout=None,
epoch=0,
log_file=None,
name_set="",
store_on_disc=False,
store_imgs=False
):
"""
Perform a validation over the validation set. Assumes a batch size of 1.
(images do not have the same size,
so we can't stack them in one tensor).
Validation samples may be large to fit all in the GPU at once.
Note: criterion is deppmil.criteria.TotalLossEval().
"""
model.eval()
metrics = Metrics(threshold=args.final_thres).to(device)
metrics.eval()
f1pos_, f1neg_, miou_, acc_ = 0., 0., 0., 0.
cnt = 0.
total_loss_ = 0.
loss_pos_ = 0.
loss_neg_ = 0.
mask_fd = None
name_fd_masks = "masks" # where to store the predictions.
name_fd_masks_bin = "masks_bin" # where to store the bin masks and al.
if folderout is not None:
mask_fd = join(folderout, name_fd_masks)
bin_masks_fd = join(folderout, name_fd_masks_bin)
if not os.path.exists(mask_fd):
os.makedirs(mask_fd)
if not os.path.exists(bin_masks_fd):
os.makedirs(bin_masks_fd)
length = len(dataloader)
t0 = dt.datetime.now()
myseed = int(os.environ["MYSEED"])
with torch.no_grad():
for i, (data, mask, label) in tqdm.tqdm(
enumerate(dataloader), ncols=80, total=length):
reproducibility.force_seed(myseed + epoch + 1)
msg = "Expected a batch size of 1. Found `{}` .... " \
"[NOT OK]".format(data.size()[0])
assert data.size()[0] == 1, msg
bsz = data.size()[0]
data = data.to(device)
labels = label.to(device)
mask = torch.tensor(mask[0])
mask_t = mask.unsqueeze(0).to(device)
assert mask_t.ndim == 4, "ndim = {} must be 4.".format(mask_t.ndim)
# In validation, we do not need reproducibility since everything
# is expected to deterministic. Plus,
# we use only one gpu since the batch size os 1.
scores_pos, scores_neg, mask_pred, sc_cl_se = model(x=data,
seed=None
)
t_loss, l_p, l_n, l_seg = criterion(scores_pos,
sc_cl_se,
labels,
mask_pred,
scores_neg
)
mask_pred = mask_pred.squeeze()
# check sizes of the mask:
_, _, h, w = mask_t.shape
hp, wp = mask_pred.shape
if (h != hp) or (w != wp): # This means that we have padded the
# input image. We crop the predicted mask in the center.
mask_pred = mask_pred[int(hp / 2) - int(h / 2): int(hp / 2) + int(h / 2) + (h % 2),
int(wp / 2) - int(w / 2): int(wp / 2) + int(w / 2) + (w % 2)]
mask_pred = mask_pred.unsqueeze(0).unsqueeze(0)
acc, dice_forg, dice_back, miou = metrics(
scores=scores_pos,
labels=labels,
masks_pred=mask_pred.contiguous().view(bsz, -1),
masks_trg=mask_t.contiguous().view(bsz, -1),
avg=False
)
# tracking
f1pos_ += dice_forg
f1neg_ += dice_back
miou_ += miou
acc_ += acc
cnt += bsz
total_loss_ += t_loss.item()
loss_pos_ += l_p.item()
loss_neg_ += l_n.item()
if (folderout is not None) and store_on_disc:
# binary mask
bin_pred_mask = metrics.get_binary_mask(mask_pred).squeeze()
bin_pred_mask = bin_pred_mask.cpu().detach().numpy().astype(np.bool)
to_save = {
"bin_pred_mask": bin_pred_mask,
"dice_forg": dice_forg,
"dice_back": dice_back,
"i": i
}
with open(join(bin_masks_fd, "{}.pkl".format(i)), "wb") as fbin:
pkl.dump(to_save, fbin, protocol=pkl.HIGHEST_PROTOCOL)
if (folderout is not None) and store_imgs and store_on_disc:
pred_label = int(scores_pos.argmax().item())
probs = softmax(scores_pos.cpu().detach().numpy())
prob = float(probs[0, pred_label])
store_pred_img(i,
dataset,
bin_pred_mask * 1.,
mask_pred.squeeze().cpu().detach().numpy(),
dice_forg,
dice_back,
prob,
pred_label,
args,
mask_fd,
)
# avg
total_loss_ /= float(cnt)
loss_pos_ /= float(cnt)
loss_neg_ /= float(cnt)
acc_ *= (100. / float(cnt))
f1pos_ *= (100. / float(cnt))
f1neg_ *= (100. / float(cnt))
miou_ *= (100. / float(cnt))
if stats is not None:
stats["total_loss"].append(total_loss_)
stats["loss_pos"].append(loss_pos_)
stats["loss_neg"].append(loss_neg_)
stats["acc"].append(acc_)
stats["f1pos"].append(f1pos_)
stats["f1neg"].append(f1neg_)
stats['miou'].append(miou_)
to_write = "EVAL ({}): TLoss: {:.2f}, L+: {:.2f}, L-: {:.2f}, " \
"F1+: {:.2f}%, F1-: {:.2f}%, MIOU: {:.2f}%, ACC: {:.2f}%, " \
"t:{}, epoch {:>2d}.".format(
name_set,
total_loss_,
loss_pos_,
loss_neg_,
f1pos_,
f1neg_,
miou_,
acc_,
dt.datetime.now() - t0,
epoch
)
print(to_write)
if log_file:
log(log_file, to_write)
if folderout is not None:
msg = "EVAL {}: \n".format(name_set)
msg += "ACC {}% \n".format(acc_)
msg += "F1+ {}% \n".format(f1pos_)
msg += "F1- {}% \n".format(f1neg_)
msg += "MIOU {}% \n".format(miou_)
announce_msg(msg)
if log_file:
log(log_file, msg)
if (folderout is not None) and store_on_disc:
pred = {
"total_loss": total_loss_,
"loss_pos": loss_pos_,
"loss_neg": loss_neg_,
"acc": acc_,
"f1pos": f1pos_,
"f1neg": f1neg_,
"miou_": miou_
}
with open(
join(folderout, "pred--{}.pkl".format(name_set)), "wb") as fout:
pkl.dump(pred, fout, protocol=pkl.HIGHEST_PROTOCOL)
# compress. delete folder.
cmdx = [
"cd {} ".format(mask_fd),
"cd .. ",
# "tar -cf {}.tar.gz {}".format(name_fd_masks, name_fd_masks),
# "rm -r {}".format(name_fd_masks)
]
cmdx += [
"cd {} ".format(bin_masks_fd),
"cd .. ",
"tar -cf {}.tar.gz {}".format(name_fd_masks_bin, name_fd_masks_bin),
"rm -r {}".format(name_fd_masks_bin)
]
cmdx = " && ".join(cmdx)
print("Running bash-cmds: \n{}".format(cmdx.replace("&& ", "\n")))
subprocess.run(cmdx, shell=True, check=True)
else:
return stats
callback = None
# ==========================================================
# Data transformations: on PIL.Image.Image and torch.tensor.
# ==========================================================
train_transform_img = get_train_transforms_img(args)
transform_tensor = get_transforms_tensor(args)
# ==========================================================================
# Datasets: create folds, load csv, preprocess files and save on disc.
# load datasets: train, valid, test.
# ==========================================================================
announce_msg("SPLIT: {} \t FOLD: {}".format(args.split, args.fold))
relative_fold_path = join(args.fold_folder, args.dataset,
"split_" + str(args.split),
"fold_" + str(args.fold))
if isinstance(args.name_classes, str): # path
path_classes = join(relative_fold_path, args.name_classes)
assert os.path.isfile(path_classes), "File {} does not exist .... " \
"[NOT OK]".format(path_classes)
with open(path_classes, "r") as fin:
args.name_classes = yaml.load(fin)
csvfiles = []
for subp in ["train_s_", "valid_s_", "test_s_"]:
csvfiles.append(
join(relative_fold_path,
subp + str(args.split) + "_f_" + str(args.fold) + ".csv"))
from deepmil.decision_pooling import WildCatPoolDecision, ClassWisePooling
thread_lock = threading.Lock() # lock for threads to protect the instruction that cause randomness and make them
# thread-safe.
import reproducibility
ACTIVATE_SYNC_BN = True
# Override ACTIVATE_SYNC_BN using variable environment in Bash:
# $ export ACTIVATE_SYNC_BN="True" ----> Activate
# $ export ACTIVATE_SYNC_BN="False" ----> Deactivate
if "ACTIVATE_SYNC_BN" in os.environ.keys():
ACTIVATE_SYNC_BN = (os.environ['ACTIVATE_SYNC_BN'] == "True")
announce_msg("ACTIVATE_SYNC_BN was set to {}".format(ACTIVATE_SYNC_BN))
if check_if_allow_multgpu_mode() and ACTIVATE_SYNC_BN: # Activate Synch-BN.
from deepmil.syncbn import nn as NN_Sync_BN
BatchNorm2d = NN_Sync_BN.BatchNorm2d
announce_msg("Synchronized BN has been activated. \n"
"MultiGPU mode has been activated. {} GPUs".format(torch.cuda.device_count()))
else:
BatchNorm2d = nn.BatchNorm2d
if check_if_allow_multgpu_mode():
announce_msg("Synchronized BN has been deactivated.\n"
"MultiGPU mode has been activated. {} GPUs".format(torch.cuda.device_count()))
else:
announce_msg("Synchronized BN has been deactivated.\n"
"MultiGPU mode has been deactivated. {} GPUs".format(torch.cuda.device_count()))
def create_k_folds_csv_bach_part_a(args):
"""
Create k folds of the dataset BACH (part A) 2018 and store the image path of each fold in a *.csv file.
1. Test set if fixed for all the splits/folds.
2. We do a k-fold over the remaining data to create train, and validation sets.
:param args: object, contain the arguments of splitting.
:return:
"""
announce_msg("Going to create the splits, and the k-folds fro BACH (PART A) 2018 .... [OK]")
rootpath = args.baseurl
if args.dataset == "bc18bch":
rootpath = join(rootpath, "ICIAR2018_BACH_Challenge/Photos")
else:
raise ValueError("Dataset name {} is unknown.".format(str(args.dataset)))
samples = glob.glob(join(rootpath, "*", "*." + args.img_extension))
# Originally, the function was written where 'samples' contains the absolute paths to the files.
# Then, we realise that using absolute path on different platforms leads to a non-deterministic folds even
# with the seed fixed. This is a result of glob.glob() that returns a list of paths more likely depending on the
# how the files are saved within the OS. Therefore, to get rid of this, we use only a short path that is constant
# across all the hosts where our dataset is saved. Then, we sort the list of paths BEFORE we go further. This
# will guarantee that whatever the OS the code is running in, the sorted list is the same.
samples = sorted([join(*sx.split(os.sep)[-4:]) for sx in samples])
classes = {key: [s for s in samples if s.split(os.sep)[-2] == key] for key in args.name_classes.keys()}
all_train = {}
test_fix = []
# Shuffle to avoid any bias.
for key in classes.keys():
for i in range(1000):
random.shuffle(classes[key])
nbr_test = int(len(classes[key]) * args.test_portion)
test_fix += classes[key][:nbr_test]
all_train[key] = classes[key][nbr_test:]
# Test set is ready. Now, we need to do k-fold over the train.
# Create the splits over the train
splits = []
for i in range(args.nbr_splits):
for t in range(1000):
for k in all_train.keys():
random.shuffle(all_train[k])
splits.append(copy.deepcopy(all_train))
readme = "csv format:\n" \
"relative path to the image file.\n" \
"Example:\n" \
"ICIAR2018_BACH_Challenge/Photos/Normal/n047.tif\n" \
"There are four classes: normal, benign, in situ, and invasive.\n" \
"The class of the sample may be infered from the parent folder of the image (in the example " \
"above:\n " \
"Normal:\n" \
"Normal: class 'normal'\n" \
"Benign: class 'benign'\n" \
"InSitu: class 'in situ'\n" \
"Invasive: class 'invasive'"
# Create k-folds for each split.
def create_folds_of_one_class(lsamps, s_tr, s_vl):
"""
Create k folds from a list of samples of the same class, each fold contains a train, and valid set with a
predefined size.
Samples need to be shuffled beforehand.
:param lsamps: list of paths to samples of the same class.
:param s_tr: int, number of samples in the train set.
:param s_vl: int, number of samples in the valid set.
:return: list_folds: list of k tuples (tr_set, vl_set, ts_set): where each element is the list (str paths)
of the samples of each set: train, valid, and test, respectively.
"""
assert len(lsamps) == s_tr + s_vl, "Something wrong with the provided sizes .... [NOT OK]"
# chunk the data into chunks of size ts (the size of the test set), so we can rotate the test set.
list_chunks = list(chunk_it(lsamps, s_vl))
list_folds = []
for i in range(len(list_chunks)):
vl_set = list_chunks[i]
right, left = [], []
if i < len(list_chunks) - 1:
right = list_chunks[i + 1:]
if i > 0:
left = list_chunks[:i]
leftoverchunks = right + left
leftoversamples = []
for e in leftoverchunks:
leftoversamples += e
tr_set = leftoversamples
list_folds.append((tr_set, vl_set))
return list_folds
# Save the folds into *.csv files.
def dump_fold_into_csv(lsamples, outpath):
"""
Write a list of RELATIVE paths into a csv file.
Relative paths allow running the code an any device.
The absolute path within the device will be determined at the running time.
csv file format: relative path to the image, relative path to the mask, class (str: benign, malignant).
:param lsamples: list of str of relative paths.
:param outpath: str, output file name.
:return:
"""
with open(outpath, 'w') as fcsv:
filewriter = csv.writer(fcsv, delimiter=',', quotechar='|', quoting=csv.QUOTE_MINIMAL)
for fname in lsamples:
filewriter.writerow([fname])
def create_one_split(split_i, test_samples, train_samples_all, nbr_folds):
"""
Create one split of k-folds.
:param split_i: int, the id of the split.
:param test_samples: dict of list, each key represents a class (test set, fixed).
:param train_samples_all: dict of list, each key represent a class (all train set).
:param nbr_folds: int, number of folds [the k value in k-folds].
:return:
"""
# Create the k-folds
list_folds_of_class = {}
for key in train_samples_all.keys():
vl_size = math.ceil(len(train_samples_all[key]) * args.folding["vl"] / 100.)
tr_size = len(train_samples_all[key]) - vl_size
list_folds_of_class[key] = create_folds_of_one_class(train_samples_all[key], tr_size, vl_size)
assert len(list_folds_of_class[key]) == nbr_folds, "We didn't get `{}` folds, but `{}` .... " \
"[NOT OK]".format(
nbr_folds, len(list_folds_of_class[key]))
print("We obtained `{}` folds for the class {}.... [OK]".format(args.nbr_folds, key))
outd = args.fold_folder
for i in range(nbr_folds):
print("Fold {}:\n\t".format(i))
out_fold = join(outd, "split_" + str(split_i) + "/fold_" + str(i))
if not os.path.exists(out_fold):
os.makedirs(out_fold)
# dump the test set
dump_fold_into_csv(test_samples, join(out_fold, "test_s_" + str(split_i) + "_f_" + str(i) + ".csv"))
train = []
valid = []
for key in list_folds_of_class.keys():
# Train
train += list_folds_of_class[key][i][0]
# Valid.
valid += list_folds_of_class[key][i][1]
# shuffle
for t in range(1000):
random.shuffle(train)
dump_fold_into_csv(train, join(out_fold, "train_s_" + str(split_i) + "_f_" + str(i) + ".csv"))
dump_fold_into_csv(valid, join(out_fold, "valid_s_" + str(split_i) + "_f_" + str(i) + ".csv"))
# dump the seed
with open(join(out_fold, "seed.txt"), 'w') as fx:
fx.write("MYSEED: " + os.environ["MYSEED"])
with open(join(out_fold, "readme.md"), 'w') as fx:
fx.write(readme)
print("BACH (PART A) 2018 splitting N° `{}` ends with success .... [OK]".format(split_i))
if not os.path.isdir(args.fold_folder):
os.makedirs(args.fold_folder)
# Creates the splits
for i in range(args.nbr_splits):
print("Split {}:\n\t".format(i))
create_one_split(i, test_fix, splits[i], args.nbr_folds)
with open(join(args.fold_folder, "readme.md"), 'w') as fx:
fx.write(readme)
print("All BACH (PART A) 2018 splitting (`{}`) ended with success .... [OK]".format(args.nbr_splits))
def validate(model,
dataset,
dataloader,
criterion,
device,
stats,
args,
folderout=None,
epoch=0,
log_file=None,
name_set="",
store_on_disc=False,
store_imgs=False,
final_mode=False,
seg_threshold=None
):
"""
Perform a validation over the validation set. Assumes a batch size of 1.
(images do not have the same size,
so we can't stack them in one tensor).
Validation samples may be large to fit all in the GPU at once.
Note: criterion is deppmil.criteria.TotalLossEval().
"""
model.eval()
fl_thres = seg_threshold if seg_threshold is not None else args.final_thres
metrics = Metrics(threshold=fl_thres).to(device)
dice_f = Dice()
iou_f = IOU()
metrics.eval()
f1pos_, f1neg_, miou_, acc_ = 0., 0., 0., 0.
l_f1pos_ = []
l_f1neg_ = []
l_miou_ = []
cnt = 0.
total_loss_ = 0.
loss_pos_ = 0.
loss_neg_ = 0.
# camelyon16
sizes_m = {
'm_pred': [], # metastatic.
'm_true': [], # metastatic
'n_pred': [], # normal
'n_true': [] # normal
}
mask_fd = None
name_fd_masks = "masks" # where to store the predictions.
name_fd_masks_bin = "masks_bin" # where to store the bin masks and al.
if folderout is not None:
mask_fd = join(folderout, name_fd_masks)
bin_masks_fd = join(folderout, name_fd_masks_bin)
if not os.path.exists(mask_fd):
os.makedirs(mask_fd)
if not os.path.exists(bin_masks_fd):
os.makedirs(bin_masks_fd)
length = len(dataloader)
t0 = dt.datetime.now()
myseed = int(os.environ["MYSEED"])
masks_sizes = []
cancer_scores = []
glabels = []
avg_forward_t = dt.timedelta(0)
with torch.no_grad():
for i, (data, mask, label) in tqdm.tqdm(
enumerate(dataloader), ncols=80, total=length):
reproducibility.force_seed(myseed + epoch + 1)
msg = "Expected a batch size of 1. Found `{}` .... " \
"[NOT OK]".format(data.size()[0])
assert data.size()[0] == 1, msg
bsz = data.size()[0]
data = data.to(device)
labels = label.to(device)
mask = mask[0].clone()
mask_t = mask.unsqueeze(0).to(device)
assert mask_t.ndim == 4, "ndim = {} must be 4.".format(mask_t.ndim)
# In validation, we do not need reproducibility since everything
# is expected to deterministic. Plus,
# we use only one gpu since the batch size os 1.
t0 = dt.datetime.now()
scores_pos, scores_neg, mask_pred, sc_cl_se, cams = model(
x=data, glabels=labels, seed=None)
delta_t = dt.datetime.now() - t0
avg_forward_t += delta_t
t_loss, l_p, l_n, l_seg = criterion(
scores_pos,
sc_cl_se,
labels,
mask_pred,
scores_neg,
cams
)
mask_pred = mask_pred.squeeze()
# check sizes of the mask:
_, _, h, w = mask_t.shape
hp, wp = mask_pred.shape
assert args.padding_size in [None, 'None', 0.0], args.padding_size
mask_pred = F.interpolate(
input=mask_pred.unsqueeze(0).unsqueeze(0),
size=(h, w),
mode='bilinear',
align_corners=True
).squeeze()
mask_pred = mask_pred.unsqueeze(0).unsqueeze(0)
if args.dataset == constants.GLAS:
cl_scores = scores_pos
acc, dice_forg, dice_back, miou = metrics(
scores=cl_scores,
labels=labels,
masks_pred=mask_pred.contiguous().view(bsz, -1),
masks_trg=mask_t.contiguous().view(bsz, -1),
avg=False
)
f1pos_ += dice_forg
f1neg_ += dice_back
miou_ += miou
elif args.dataset == constants.CAMELYON16P512:
cl_scores = sc_cl_se # sc_cl_se, scores_pos
plabels = metrics.predict_label(cl_scores)
acc = ((plabels - labels) == 0.).float().sum()
assert data.size()[0] == 1
ppixels = metrics.get_binary_mask(
mask_pred.contiguous().view(bsz, -1), metrics.threshold)
masks_trg = mask_t.contiguous().view(bsz, -1)
dice_forg = 0.
dice_back = 0.
miou = 0.
glabels.append(labels.item())
masks_sizes.append(ppixels.mean().item())
if labels.item() == 1:
sizes_m['m_pred'].append(ppixels.mean().item() * 100.)
sizes_m['m_true'].append(masks_trg.mean().item() * 100.)
elif labels.item() == 0:
sizes_m['n_pred'].append(ppixels.mean().item() * 100.)
sizes_m['n_true'].append(0.0)
else:
raise ValueError
cancer_scores.append(
torch.softmax(cl_scores, dim=1)[0, 1].item())
if masks_trg.sum() > 0:
l_f1pos_.append(dice_f(ppixels.view(bsz, -1),
masks_trg.view(bsz, -1)))
dice_forg = l_f1pos_[-1]
if (1. - masks_trg).sum() > 0:
tmp = iou_f(ppixels.view(1, -1),
masks_trg.view(1, -1))
tmp = tmp + iou_f(1. - ppixels.view(1, -1),
1. - masks_trg.view(1, -1))
l_miou_.append(tmp / 2.)
miou = l_miou_[-1]
if (1. - masks_trg).sum() > 0:
l_f1neg_.append(dice_f(1. - ppixels.view(bsz, -1),
1. - masks_trg.view(bsz, -1)))
dice_back = l_f1neg_[-1]
else:
raise NotImplementedError
acc_ += acc
cnt += bsz
total_loss_ += t_loss.item()
loss_pos_ += l_p.item()
loss_neg_ += l_n.item()
if (folderout is not None) and store_on_disc:
# binary mask
bin_pred_mask = metrics.get_binary_mask(mask_pred).squeeze()
bin_pred_mask = bin_pred_mask.cpu().detach().numpy().astype(np.bool)
if args.dataset == constants.GLAS:
to_save = {
"bin_pred_mask": bin_pred_mask,
"continuous_mask": mask_pred.cpu().detach().numpy(),
"dice_forg": dice_forg,
"dice_back": dice_back,
"i": i
}
elif args.dataset == constants.CAMELYON16P512:
to_save = {
"bin_pred_mask": bin_pred_mask,
"dice_forg": dice_forg,
"dice_back": dice_back,
"i": i
}
else:
raise NotImplementedError
with open(join(bin_masks_fd, "{}.pkl".format(i)), "wb") as fbin:
pkl.dump(to_save, fbin, protocol=pkl.HIGHEST_PROTOCOL)
if (folderout is not None) and store_imgs and store_on_disc:
pred_label = int(cl_scores.argmax().item())
probs = softmax(cl_scores.cpu().detach().numpy())
prob = float(probs[0, pred_label])
store_pred_img(i,
dataset,
bin_pred_mask * 1.,
mask_pred.squeeze().cpu().detach().numpy(),
dice_forg,
dice_back,
prob,
pred_label,
args,
mask_fd,
)
# avg
acc_ *= (100. / float(cnt))
if args.dataset == constants.CAMELYON16P512:
with open(join(folderout,
'log-cl-{}-final-{}.txt'.format(epoch,
final_mode)),
'a') as fz:
fz.write("\nClassification accuracy: {} (%)".format(acc_))
with open(join(folderout,
'log-seg-{}-final-{}.txt'.format(
epoch, final_mode)), 'a') as fz:
fz.write("\nClassification accuracy: {} (%)".format(acc_))
total_loss_ /= float(cnt)
loss_pos_ /= float(cnt)
loss_neg_ /= float(cnt)
avg_forward_t /= float(cnt)
if args.dataset == constants.GLAS:
f1pos_ *= (100. / float(cnt))
f1neg_ *= (100. / float(cnt))
miou_ *= (100. / float(cnt))
elif args.dataset == constants.CAMELYON16P512:
f1pos_ = 0.
f1neg_ = 0.
miou_ = 0.
if l_f1pos_:
f1pos_ = torch.stack(l_f1pos_).mean() * 100.
if l_f1neg_:
f1neg_ = torch.stack(l_f1neg_).mean() * 100.
if l_miou_:
miou_ = torch.stack(l_miou_).mean() * 100.
else:
raise NotImplementedError
if stats is not None:
stats["total_loss"].append(total_loss_)
stats["loss_pos"].append(loss_pos_)
stats["loss_neg"].append(loss_neg_)
stats["acc"].append(acc_)
stats["f1pos"].append(f1pos_)
stats["f1neg"].append(f1neg_)
stats['miou'].append(miou_)
to_write = "EVAL ({}): TLoss: {:.2f}, L+: {:.2f}, L-: {:.2f}, " \
"F1+: {:.2f}%, F1-: {:.2f}%, MIOU: {:.2f}%, ACC: {:.2f}%, " \
"t:{}, epoch {:>2d}.".format(
name_set,
total_loss_,
loss_pos_,
loss_neg_,
f1pos_,
f1neg_,
miou_,
acc_,
dt.datetime.now() - t0,
epoch
)
print(to_write)
if log_file:
log(log_file, to_write)
if final_mode:
assert folderout is not None
msg = "EVAL {}: \n".format(name_set)
msg += "ACC {}% \n".format(acc_)
msg += "F1+ {}% \n".format(f1pos_)
msg += "F1- {}% \n".format(f1neg_)
msg += "MIOU {}% \n".format(miou_)
announce_msg(msg)
if log_file:
log(log_file, msg)
with open(join(folderout, 'avg_forward_time.txt'), 'w') as fend:
fend.write("Model: {}. \n Average forward time (eval mode): "
" {}.".format(args.model['model_name'], avg_forward_t
))
if (folderout is not None) and store_on_disc:
pred = {
"total_loss": total_loss_,
"loss_pos": loss_pos_,
"loss_neg": loss_neg_,
"acc": acc_,
"f1pos": f1pos_,
"f1neg": f1neg_,
"miou_": miou_
}
with open(
join(folderout, "pred--{}.pkl".format(name_set)), "wb") as fout:
pkl.dump(pred, fout, protocol=pkl.HIGHEST_PROTOCOL)
# compress. delete folder.
cmdx = [
"cd {} ".format(mask_fd),
"cd .. ",
# "tar -cf {}.tar.gz {}".format(name_fd_masks, name_fd_masks),
# "rm -r {}".format(name_fd_masks)
]
cmdx += [
"cd {} ".format(bin_masks_fd),
"cd .. ",
"tar -cf {}.tar.gz {}".format(name_fd_masks_bin, name_fd_masks_bin),
"rm -r {}".format(name_fd_masks_bin)
]
cmdx = " && ".join(cmdx)
print("Running bash-cmds: \n{}".format(cmdx.replace("&& ", "\n")))
try:
subprocess.run(cmdx, shell=True, check=True)
except subprocess.SubprocessError as e:
print("Failed to run: {}. Error: {}".format(cmdx, e))
else:
return stats