def main(config):
num = 100000
palette_path = config['palette_dir']
with open(palette_path) as f:
palette = f.readlines()
palette = list(
np.asarray([[int(p) for p in pal[0:-1].split(' ')]
for pal in palette]).reshape(768))
n_shots = config['task']['n_shots']
n_ways = config['task']['n_ways']
set_seed(config['seed'])
cudnn.enabled = True
cudnn.benchmark = True
torch.cuda.set_device(device=config['gpu_id'])
torch.set_num_threads(1)
model = FewShotSeg(cfg=config['model'])
model = nn.DataParallel(model.cuda(), device_ids=[
config['gpu_id'],
])
if config['train']:
model.load_state_dict(
torch.load(config['snapshots'], map_location='cpu'))
model.eval()
data_name = config['dataset']
if data_name == 'davis':
make_data = davis2017_test
else:
raise ValueError('Wrong config for dataset!')
labels = CLASS_LABELS[data_name]['val']
list_label = []
for i in labels:
list_label.append(i)
list_label = sorted(list_label)
transforms = [Resize(size=config['input_size'])]
transforms = Compose(transforms)
with torch.no_grad():
for run in range(config['n_runs']):
set_seed(config['seed'] + run)
dataset = make_data(base_dir=config['path'][data_name]['data_dir'],
split=config['path'][data_name]['data_split'],
transforms=transforms,
to_tensor=ToTensorNormalize(),
labels=labels)
testloader = DataLoader(dataset,
batch_size=config['batch_size'],
shuffle=False,
num_workers=1,
pin_memory=True,
drop_last=False)
for iteration, batch in enumerate(testloader):
class_name = batch[2]
if not os.path.exists(f'./result/{num}/{class_name[0]}'):
os.makedirs(f'./result/{num}/{class_name[0]}')
num_frame = batch[1]
all_class_data = batch[0]
class_ids = all_class_data[0]['obj_ids']
support_images = [[
all_class_data[0]['image'].cuda() for _ in range(n_shots)
] for _ in range(n_ways)]
support_mask = all_class_data[0]['label'][
list_label[iteration]]
support_fg_mask = [[
get_fg_mask(support_mask, class_ids[way])
for shot in range(n_shots)
] for way in range(len(class_ids))]
support_bg_mask = [[
get_bg_mask(support_mask, class_ids)
for _ in range(n_shots)
] for _ in range(n_ways)]
s_fg_mask = [[shot['fg_mask'].float().cuda() for shot in way]
for way in support_fg_mask]
s_bg_mask = [[shot['bg_mask'].float().cuda() for shot in way]
for way in support_bg_mask]
# print(f'fg_mask {s_bg_mask[0][0].shape}')
# print(f'bg_mask {s_bg_mask[0][0].shape}')
# print(support_mask.shape)
for idx, data in enumerate(all_class_data):
query_images = [
all_class_data[idx]['image'].cuda()
for i in range(n_ways)
]
query_labels = torch.cat([
query_label.cuda() for query_label in [
all_class_data[idx]['label'][
list_label[iteration]],
]
])
# print(f'query_image{query_images[0].shape}')
if idx > 0:
pre_mask = [
pred_mask,
]
elif idx == 0:
pre_mask = [
support_mask.float().cuda(),
]
query_pred, _ = model(support_images, s_fg_mask, s_bg_mask,
query_images, pre_mask)
pred = query_pred.argmax(dim=1, keepdim=True)
pred = pred.data.cpu().numpy()
img = pred[0, 0]
img_e = Image.fromarray(img.astype('float32')).convert('P')
pred_mask = tr_F.resize(img_e,
config['input_size'],
interpolation=Image.NEAREST)
pred_mask = torch.Tensor(np.array(pred_mask))
pred_mask = torch.unsqueeze(pred_mask, dim=0)
pred_mask = pred_mask.float().cuda()
img_e.putpalette(palette)
# print(os.path.join(f'./result/{class_name[0]}/', '{:05d}.png'.format(idx)))
# print(batch[3][idx])
img_e.save(
os.path.join(f'./result/{num}/{class_name[0]}/',
'{:05d}.png'.format(idx)))
def main(_run, _config, _log):
for source_file, _ in _run.experiment_info['sources']:
os.makedirs(os.path.dirname(f'{_run.observers[0].dir}/source/{source_file}'),
exist_ok=True)
_run.observers[0].save_file(source_file, f'source/{source_file}')
shutil.rmtree(f'{_run.observers[0].basedir}/_sources')
set_seed(_config['seed'])
cudnn.enabled = True
cudnn.benchmark = True
torch.cuda.set_device(device=_config['gpu_id'])
torch.set_num_threads(1)
_log.info('###### Create model ######')
model = FewShotSeg(pretrained_path=_config['path']['init_path'], cfg=_config['model'])
model = nn.DataParallel(model.cuda(), device_ids=[_config['gpu_id'],])
if not _config['notrain']:
model.load_state_dict(torch.load(_config['snapshot'], map_location='cpu'))
model.eval()
_log.info('###### Prepare data ######')
data_name = _config['dataset']
if data_name == 'VOC':
make_data = voc_fewshot
max_label = 20
elif data_name == 'COCO':
make_data = coco_fewshot
max_label = 6
else:
raise ValueError('Wrong config for dataset!')
labels = CLASS_LABELS[data_name]['all'] - CLASS_LABELS[data_name][_config['label_sets']]
transforms = [Resize(size=_config['input_size'])]
if _config['scribble_dilation'] > 0:
transforms.append(DilateScribble(size=_config['scribble_dilation']))
transforms = Compose(transforms)
_log.info('###### Testing begins ######')
metric = Metric(max_label=max_label, n_runs=_config['n_runs'])
with torch.no_grad():
for run in range(_config['n_runs']):
_log.info(f'### Run {run + 1} ###')
set_seed(_config['seed'] + run)
_log.info(f'### Load data ###')
dataset = make_data(
base_dir=_config['path'][data_name]['data_dir'],
split=_config['path'][data_name]['data_split'],
transforms=transforms,
to_tensor=ToTensorNormalize(),
labels=labels,
max_iters=_config['n_steps'] * _config['batch_size'],
n_ways=_config['task']['n_ways'],
n_shots=_config['task']['n_shots'],
n_queries=_config['task']['n_queries']
)
if _config['dataset'] == 'COCO':
coco_cls_ids = dataset.datasets[0].dataset.coco.getCatIds()
testloader = DataLoader(dataset, batch_size=_config['batch_size'], shuffle=False,
num_workers=1, pin_memory=True, drop_last=False)
_log.info(f"Total # of Data: {len(dataset)}")
for sample_batched in tqdm.tqdm(testloader):
if _config['dataset'] == 'COCO':
label_ids = [coco_cls_ids.index(x) + 1 for x in sample_batched['class_ids']]
else:
label_ids = list(sample_batched['class_ids'])
support_images = [[shot.cuda() for shot in way]
for way in sample_batched['support_images']]
suffix = 'scribble' if _config['scribble'] else 'mask'
if _config['bbox']:
support_fg_mask = []
support_bg_mask = []
for i, way in enumerate(sample_batched['support_mask']):
fg_masks = []
bg_masks = []
for j, shot in enumerate(way):
fg_mask, bg_mask = get_bbox(shot['fg_mask'],
sample_batched['support_inst'][i][j])
fg_masks.append(fg_mask.float().cuda())
bg_masks.append(bg_mask.float().cuda())
support_fg_mask.append(fg_masks)
support_bg_mask.append(bg_masks)
else:
support_fg_mask = [[shot[f'fg_{suffix}'].float().cuda() for shot in way]
for way in sample_batched['support_mask']]
support_bg_mask = [[shot[f'bg_{suffix}'].float().cuda() for shot in way]
for way in sample_batched['support_mask']]
query_images = [query_image.cuda()
for query_image in sample_batched['query_images']]
query_labels = torch.cat(
[query_label.cuda()for query_label in sample_batched['query_labels']], dim=0)
query_pred, _ = model(support_images, support_fg_mask, support_bg_mask,
query_images)
# # visual
# mean = [0.485, 0.456, 0.406]
# std = [0.229, 0.224, 0.225]
# pred = np.array(query_pred.argmax(dim=1)[0].cpu())
# prediction = pred.transpose()
# q_img = query_images[0].cpu()[0]
# qu_img = np.array(q_img.permute(2, 1, 0))
# # qu_img = np.array(torch.transpose(q_img, 0, 2))
# que_img = (qu_img * std + mean) * 255
# que_img = que_img.reshape(512, 512, 3).astype(np.uint8)
# # plt.imshow(que_img)
# # plt.show()
# blend_image_label = color_map.blend_img_colorlabel(que_img, prediction)
# blend = np.asarray(blend_image_label)
# cv2.namedWindow("Zhanfen", 0)
# cv2.resizeWindow("Zhanfen", 512, 512)
# cv2.imshow("Zhanfen", blend)
# cv2.waitKey(0)
metric.record(np.array(query_pred.argmax(dim=1)[0].cpu()),
np.array(query_labels[0].cpu()),
labels=label_ids, n_run=run)
classIoU, meanIoU = metric.get_mIoU(labels=sorted(labels), n_run=run)
classIoU_binary, meanIoU_binary = metric.get_mIoU_binary(n_run=run)
_run.log_scalar('classIoU', classIoU.tolist())
_run.log_scalar('meanIoU', meanIoU.tolist())
_run.log_scalar('classIoU_binary', classIoU_binary.tolist())
_run.log_scalar('meanIoU_binary', meanIoU_binary.tolist())
_log.info(f'classIoU: {classIoU}')
_log.info(f'meanIoU: {meanIoU}')
_log.info(f'classIoU_binary: {classIoU_binary}')
_log.info(f'meanIoU_binary: {meanIoU_binary}')
classIoU, classIoU_std, meanIoU, meanIoU_std = metric.get_mIoU(labels=sorted(labels))
classIoU_binary, classIoU_std_binary, meanIoU_binary, meanIoU_std_binary = metric.get_mIoU_binary()
_log.info('----- Final Result -----')
_run.log_scalar('final_classIoU', classIoU.tolist())
_run.log_scalar('final_classIoU_std', classIoU_std.tolist())
_run.log_scalar('final_meanIoU', meanIoU.tolist())
_run.log_scalar('final_meanIoU_std', meanIoU_std.tolist())
_run.log_scalar('final_classIoU_binary', classIoU_binary.tolist())
_run.log_scalar('final_classIoU_std_binary', classIoU_std_binary.tolist())
_run.log_scalar('final_meanIoU_binary', meanIoU_binary.tolist())
_run.log_scalar('final_meanIoU_std_binary', meanIoU_std_binary.tolist())
_log.info(f'classIoU mean: {classIoU}')
_log.info(f'classIoU std: {classIoU_std}')
_log.info(f'meanIoU mean: {meanIoU}')
_log.info(f'meanIoU std: {meanIoU_std}')
_log.info(f'classIoU_binary mean: {classIoU_binary}')
_log.info(f'classIoU_binary std: {classIoU_std_binary}')
_log.info(f'meanIoU_binary mean: {meanIoU_binary}')
_log.info(f'meanIoU_binary std: {meanIoU_std_binary}')
def main(_run, _config, _log):
for source_file, _ in _run.experiment_info['sources']:
os.makedirs(
os.path.dirname(f'{_run.observers[0].dir}/source/{source_file}'),
exist_ok=True)
_run.observers[0].save_file(source_file, f'source/{source_file}')
shutil.rmtree(f'{_run.observers[0].basedir}/_sources')
set_seed(_config['seed'])
cudnn.enabled = True
cudnn.benchmark = True
torch.cuda.set_device(device=_config['gpu_id'])
torch.set_num_threads(1)
_log.info('###### Create model ######')
model = FewShotSeg(pretrained_path=_config['path']['init_path'],
cfg=_config['model'])
model = nn.DataParallel(model.cuda(), device_ids=[
_config['gpu_id'],
])
if not _config['notrain']:
model.load_state_dict(
torch.load(_config['snapshot'], map_location='cpu'))
print("Snapshotttt")
print(_config['snapshot'])
model.eval()
# u2_model_dir = '/content/gdrive/My Drive/Research/U-2-Net/saved_models/'+ 'u2net' + '/' + 'u2net_bce_itr_3168_train_1.523160_tar_0.203136.pth'
# u2_net = U2NET(3,1)
# u2_net.load_state_dict(torch.load(u2_model_dir))
# if torch.cuda.is_available():
# u2_net.cuda()
_log.info('###### Prepare data ######')
data_name = _config['dataset']
if data_name == 'VOC':
make_data = voc_fewshot
max_label = 20
elif data_name == 'COCO':
make_data = coco_fewshot
max_label = 80
else:
raise ValueError('Wrong config for dataset!')
labels = CLASS_LABELS[data_name]['all'] - CLASS_LABELS[data_name][
_config['label_sets']]
transforms = [Resize(size=_config['input_size'])]
if _config['scribble_dilation'] > 0:
transforms.append(DilateScribble(size=_config['scribble_dilation']))
transforms = Compose(transforms)
_log.info('###### Testing begins ######')
metric = Metric(max_label=max_label, n_runs=_config['n_runs'])
with torch.no_grad():
for run in range(_config['n_runs']):
_log.info(f'### Run {run + 1} ###')
set_seed(_config['seed'] + run)
_log.info(f'### Load data ###')
dataset = make_data(
base_dir=_config['path'][data_name]['data_dir'],
split=_config['path'][data_name]['data_split'],
transforms=transforms,
to_tensor=ToTensorNormalize(),
labels=labels,
max_iters=_config['n_steps'] * _config['batch_size'],
n_ways=_config['task']['n_ways'],
n_shots=_config['task']['n_shots'],
n_queries=_config['task']['n_queries'])
if _config['dataset'] == 'COCO':
coco_cls_ids = dataset.datasets[0].dataset.coco.getCatIds()
testloader = DataLoader(dataset,
batch_size=_config['batch_size'],
shuffle=False,
num_workers=1,
pin_memory=True,
drop_last=False)
_log.info(f"Total # of Data: {len(dataset)}")
for sample_batched in tqdm.tqdm(testloader):
if _config['dataset'] == 'COCO':
label_ids = [
coco_cls_ids.index(x) + 1
for x in sample_batched['class_ids']
]
else:
label_ids = list(sample_batched['class_ids'])
support_images = [[shot.cuda() for shot in way]
for way in sample_batched['support_images']]
suffix = 'scribble' if _config['scribble'] else 'mask'
if _config['bbox']:
support_fg_mask = []
support_bg_mask = []
for i, way in enumerate(sample_batched['support_mask']):
fg_masks = []
bg_masks = []
for j, shot in enumerate(way):
fg_mask, bg_mask = get_bbox(
shot['fg_mask'],
sample_batched['support_inst'][i][j])
fg_masks.append(fg_mask.float().cuda())
bg_masks.append(bg_mask.float().cuda())
support_fg_mask.append(fg_masks)
support_bg_mask.append(bg_masks)
else:
support_fg_mask = [[
shot[f'fg_{suffix}'].float().cuda() for shot in way
] for way in sample_batched['support_mask']]
support_bg_mask = [[
shot[f'bg_{suffix}'].float().cuda() for shot in way
] for way in sample_batched['support_mask']]
query_images = [
query_image.cuda()
for query_image in sample_batched['query_images']
]
query_labels = torch.cat([
query_label.cuda()
for query_label in sample_batched['query_labels']
],
dim=0)
# u2net
inputs = query_images[0].type(torch.FloatTensor)
labels_v = query_labels.type(torch.FloatTensor)
if torch.cuda.is_available():
inputs_v, labels_v = Variable(
inputs.cuda(),
requires_grad=False), Variable(labels_v.cuda(),
requires_grad=False)
else:
inputs_v, labels_v = Variable(
inputs,
requires_grad=False), Variable(labels_v,
requires_grad=False)
#d1,d2,d3,d4,d5,d6,d7= u2_net(inputs_v)
# normalization
# pred = d1[:,0,:,:]
# pred = normPRED(pred)
pred = []
query_pred, _, _ = model(support_images, support_fg_mask,
support_bg_mask, query_images, pred)
metric.record(np.array(query_pred.argmax(dim=1)[0].cpu()),
np.array(query_labels[0].cpu()),
labels=label_ids,
n_run=run)
classIoU, meanIoU = metric.get_mIoU(labels=sorted(labels),
n_run=run)
classIoU_binary, meanIoU_binary = metric.get_mIoU_binary(n_run=run)
_run.log_scalar('classIoU', classIoU.tolist())
_run.log_scalar('meanIoU', meanIoU.tolist())
_run.log_scalar('classIoU_binary', classIoU_binary.tolist())
_run.log_scalar('meanIoU_binary', meanIoU_binary.tolist())
_log.info(f'classIoU: {classIoU}')
_log.info(f'meanIoU: {meanIoU}')
_log.info(f'classIoU_binary: {classIoU_binary}')
_log.info(f'meanIoU_binary: {meanIoU_binary}')
classIoU, classIoU_std, meanIoU, meanIoU_std = metric.get_mIoU(
labels=sorted(labels))
classIoU_binary, classIoU_std_binary, meanIoU_binary, meanIoU_std_binary = metric.get_mIoU_binary(
)
_log.info('----- Final Result -----')
_run.log_scalar('final_classIoU', classIoU.tolist())
_run.log_scalar('final_classIoU_std', classIoU_std.tolist())
_run.log_scalar('final_meanIoU', meanIoU.tolist())
_run.log_scalar('final_meanIoU_std', meanIoU_std.tolist())
_run.log_scalar('final_classIoU_binary', classIoU_binary.tolist())
_run.log_scalar('final_classIoU_std_binary', classIoU_std_binary.tolist())
_run.log_scalar('final_meanIoU_binary', meanIoU_binary.tolist())
_run.log_scalar('final_meanIoU_std_binary', meanIoU_std_binary.tolist())
_log.info(f'classIoU mean: {classIoU}')
_log.info(f'classIoU std: {classIoU_std}')
_log.info(f'meanIoU mean: {meanIoU}')
_log.info(f'meanIoU std: {meanIoU_std}')
_log.info(f'classIoU_binary mean: {classIoU_binary}')
_log.info(f'classIoU_binary std: {classIoU_std_binary}')
_log.info(f'meanIoU_binary mean: {meanIoU_binary}')
_log.info(f'meanIoU_binary std: {meanIoU_std_binary}')
def main(_run, _config, _log):
os.makedirs(f'{_run.observers[0].dir}/features', exist_ok=True)
for source_file, _ in _run.experiment_info['sources']:
os.makedirs(os.path.dirname(f'{_run.observers[0].dir}/source/{source_file}'),
exist_ok=True)
_run.observers[0].save_file(source_file, f'source/{source_file}')
shutil.rmtree(f'{_run.observers[0].basedir}/_sources')
set_seed(_config['seed'])
cudnn.enabled = True
cudnn.benchmark = True
torch.cuda.set_device(device=_config['gpu_id'])
torch.set_num_threads(1)
_log.info('###### Create model ######')
model = FewShotSeg(pretrained_path=_config['path']['init_path'], cfg=_config['model'], task=_config['task'])
model = nn.DataParallel(model.cuda(), device_ids=[_config['gpu_id'],])
if not _config['notrain']:
model.load_state_dict(torch.load(_config['snapshot'], map_location='cpu'))
model.eval()
_log.info('###### Prepare data ######')
data_name = _config['dataset']
if data_name == 'VOC':
make_data = voc_fewshot
max_label = 20
elif data_name == 'COCO':
make_data = coco_fewshot
max_label = 80
else:
raise ValueError('Wrong config for dataset!')
labels = CLASS_LABELS[data_name]['all'] - CLASS_LABELS[data_name][_config['label_sets']]
transforms = [Resize(size=_config['input_size'])]
transforms = Compose(transforms)
_log.info('###### Testing begins ######')
metric = Metric(max_label=max_label, n_runs=_config['n_runs'])
with torch.no_grad():
for run in range(_config['n_runs']):
_log.info(f'### Run {run + 1} ###')
set_seed(_config['seed'] + run)
features_dfs = []
_log.info(f'### Load data ###')
dataset = make_data(
base_dir=_config['path'][data_name]['data_dir'],
split=_config['path'][data_name]['data_split'],
transforms=transforms,
to_tensor=ToTensorNormalize(),
labels=labels,
max_iters=_config['n_steps'] * _config['batch_size'],
n_ways=_config['task']['n_ways'],
n_shots=_config['task']['n_shots'],
n_queries=_config['task']['n_queries']
)
if _config['dataset'] == 'COCO':
coco_cls_ids = dataset.datasets[0].dataset.coco.getCatIds()
testloader = DataLoader(dataset, batch_size=_config['batch_size'], shuffle=False,
num_workers=1, pin_memory=True, drop_last=False)
_log.info(f"Total # of Data: {len(dataset)}")
for sample_batched in tqdm.tqdm(testloader):
if _config['dataset'] == 'COCO':
label_ids = [coco_cls_ids.index(x) + 1 for x in sample_batched['class_ids']]
else:
label_ids = list(sample_batched['class_ids'])
support_ids = [[sample_batched['support_ids'][way*_config['task']['n_shots'] + shot][0]
for shot in range(_config['task']['n_shots'])]
for way in range(_config['task']['n_ways'])]
support_images = [[shot.cuda() for shot in way]
for way in sample_batched['support_images']]
support_fg_mask = [[shot[f'fg_mask'].float().cuda() for shot in way]
for way in sample_batched['support_mask']]
support_bg_mask = [[shot[f'bg_mask'].float().cuda() for shot in way]
for way in sample_batched['support_mask']]
query_images = [query_image.cuda()
for query_image in sample_batched['query_images']]
query_labels = torch.cat(
[query_label.cuda()for query_label in sample_batched['query_labels']], dim=0)
query_pred, _, supp_fts = model(support_images, support_fg_mask, support_bg_mask,
query_images)
metric.record(np.array(query_pred.argmax(dim=1)[0].cpu()),
np.array(query_labels[0].cpu()),
labels=label_ids, n_run=run)
# Save features row
for i, label_id in enumerate(label_ids):
lbl_df = pd.DataFrame(torch.cat(supp_fts[i]).cpu().numpy())
lbl_df['label'] = label_id.item()
lbl_df['id'] = pd.Series(support_ids[i])
features_dfs.append(lbl_df)
classIoU, meanIoU = metric.get_mIoU(labels=sorted(labels), n_run=run)
classIoU_binary, meanIoU_binary = metric.get_mIoU_binary(n_run=run)
_run.log_scalar('classIoU', classIoU.tolist())
_run.log_scalar('meanIoU', meanIoU.tolist())
_run.log_scalar('classIoU_binary', classIoU_binary.tolist())
_run.log_scalar('meanIoU_binary', meanIoU_binary.tolist())
_log.info(f'classIoU: {classIoU}')
_log.info(f'meanIoU: {meanIoU}')
_log.info(f'classIoU_binary: {classIoU_binary}')
_log.info(f'meanIoU_binary: {meanIoU_binary}')
_log.info('### Exporting features CSV')
features_df = pd.concat(features_dfs)
features_df = features_df.drop_duplicates(subset=['id'])
cols = list(features_df)
cols = [cols[-1], cols[-2]] + cols[:-2]
features_df = features_df[cols]
features_df.to_csv(f'{_run.observers[0].dir}/features/features_run_{run+1}.csv', index=False)
classIoU, classIoU_std, meanIoU, meanIoU_std = metric.get_mIoU(labels=sorted(labels))
classIoU_binary, classIoU_std_binary, meanIoU_binary, meanIoU_std_binary = metric.get_mIoU_binary()
_log.info('###### Saving features visualization ######')
all_fts = pd.concat([pd.read_csv(f'{_run.observers[0].dir}/features/features_run_{run+1}.csv') for run in range(_config['n_runs'])])
all_fts = all_fts.drop_duplicates(subset=['id'])
_log.info('### Obtaining Umap visualization ###')
plot_umap(all_fts, f'{_run.observers[0].dir}/features/Umap_fts.png')
_log.info('### Obtaining TSNE visualization ###')
plot_tsne(all_fts, f'{_run.observers[0].dir}/features/TSNE_fts.png')
_log.info('----- Final Result -----')
_run.log_scalar('final_classIoU', classIoU.tolist())
_run.log_scalar('final_classIoU_std', classIoU_std.tolist())
_run.log_scalar('final_meanIoU', meanIoU.tolist())
_run.log_scalar('final_meanIoU_std', meanIoU_std.tolist())
_run.log_scalar('final_classIoU_binary', classIoU_binary.tolist())
_run.log_scalar('final_classIoU_std_binary', classIoU_std_binary.tolist())
_run.log_scalar('final_meanIoU_binary', meanIoU_binary.tolist())
_run.log_scalar('final_meanIoU_std_binary', meanIoU_std_binary.tolist())
_log.info(f'classIoU mean: {classIoU}')
_log.info(f'classIoU std: {classIoU_std}')
_log.info(f'meanIoU mean: {meanIoU}')
_log.info(f'meanIoU std: {meanIoU_std}')
_log.info(f'classIoU_binary mean: {classIoU_binary}')
_log.info(f'classIoU_binary std: {classIoU_std_binary}')
_log.info(f'meanIoU_binary mean: {meanIoU_binary}')
_log.info(f'meanIoU_binary std: {meanIoU_std_binary}')
def main(_run, _config, _log):
for source_file, _ in _run.experiment_info['sources']:
os.makedirs(
os.path.dirname(f'{_run.observers[0].dir}/source/{source_file}'),
exist_ok=True)
_run.observers[0].save_file(source_file, f'source/{source_file}')
shutil.rmtree(f'{_run.observers[0].basedir}/_sources')
set_seed(_config['seed'])
cudnn.enabled = True
cudnn.benchmark = True
torch.cuda.set_device(device=_config['gpu_id'])
torch.set_num_threads(1)
_log.info('###### Create model ######')
model = FewShotSeg(pretrained_path=_config['path']['init_path'],
cfg=_config['model'])
model = nn.DataParallel(model.cuda(), device_ids=[
_config['gpu_id'],
])
if not _config['notrain']:
model.load_state_dict(
torch.load(_config['snapshot'], map_location='cpu'))
model.eval()
_log.info('###### Load data ######')
data_name = _config['dataset']
make_data = meta_data
max_label = 1
tr_dataset, val_dataset, ts_dataset = make_data(_config)
testloader = DataLoader(
dataset=ts_dataset,
batch_size=1,
shuffle=False,
# num_workers=_config['n_work'],
pin_memory=False, # True
drop_last=False)
if _config['record']:
_log.info('###### define tensorboard writer #####')
board_name = f'board/test_{_config["board"]}_{date()}'
writer = SummaryWriter(board_name)
_log.info('###### Testing begins ######')
# metric = Metric(max_label=max_label, n_runs=_config['n_runs'])
img_cnt = 0
# length = len(all_samples)
length = len(testloader)
img_lists = []
pred_lists = []
label_lists = []
saves = {}
for subj_idx in range(len(ts_dataset.get_cnts())):
saves[subj_idx] = []
with torch.no_grad():
loss_valid = 0
batch_i = 0 # use only 1 batch size for testing
for i, sample_test in enumerate(
testloader): # even for upward, down for downward
subj_idx, idx = ts_dataset.get_test_subj_idx(i)
img_list = []
pred_list = []
label_list = []
preds = []
fnames = sample_test['q_fname']
s_x_orig = sample_test['s_x'].cuda(
) # [B, Support, slice_num=1, 1, 256, 256]
s_x = s_x_orig.squeeze(2) # [B, Support, 1, 256, 256]
s_y_fg_orig = sample_test['s_y'].cuda(
) # [B, Support, slice_num, 1, 256, 256]
s_y_fg = s_y_fg_orig.squeeze(2) # [B, Support, 1, 256, 256]
s_y_fg = s_y_fg.squeeze(2) # [B, Support, 256, 256]
s_y_bg = torch.ones_like(s_y_fg) - s_y_fg
q_x_orig = sample_test['q_x'].cuda() # [B, slice_num, 1, 256, 256]
q_x = q_x_orig.squeeze(1) # [B, 1, 256, 256]
q_y_orig = sample_test['q_y'].cuda() # [B, slice_num, 1, 256, 256]
q_y = q_y_orig.squeeze(1) # [B, 1, 256, 256]
q_y = q_y.squeeze(1).long() # [B, 256, 256]
s_xs = [[s_x[:, shot, ...] for shot in range(_config["n_shot"])]]
s_y_fgs = [[
s_y_fg[:, shot, ...] for shot in range(_config["n_shot"])
]]
s_y_bgs = [[
s_y_bg[:, shot, ...] for shot in range(_config["n_shot"])
]]
q_xs = [q_x]
q_yhat, align_loss = model(s_xs, s_y_fgs, s_y_bgs, q_xs)
# q_yhat = q_yhat[:,1:2, ...]
q_yhat = q_yhat.argmax(dim=1)
q_yhat = q_yhat.unsqueeze(1)
preds.append(q_yhat)
img_list.append(q_x_orig[batch_i, 0].cpu().numpy())
pred_list.append(q_yhat[batch_i].cpu().numpy())
label_list.append(q_y_orig[batch_i, 0].cpu().numpy())
saves[subj_idx].append(
[subj_idx, idx, img_list, pred_list, label_list, fnames])
print(f"test, iter:{i}/{length} - {subj_idx}/{idx} \t\t", end='\r')
img_lists.append(img_list)
pred_lists.append(pred_list)
label_lists.append(label_list)
print("start computing dice similarities ... total ", len(saves))
dice_similarities = []
for subj_idx in range(len(saves)):
imgs, preds, labels = [], [], []
save_subj = saves[subj_idx]
for i in range(len(save_subj)):
# print(len(save_subj), len(save_subj)-q_slice_n+1, q_slice_n, i)
subj_idx, idx, img_list, pred_list, label_list, fnames = save_subj[
i]
# print(subj_idx, idx, is_reverse, len(img_list))
# print(i, is_reverse, is_reverse_next, is_flip)
for j in range(len(img_list)):
imgs.append(img_list[j])
preds.append(pred_list[j])
labels.append(label_list[j])
# pdb.set_trace()
img_arr = np.concatenate(imgs, axis=0)
pred_arr = np.concatenate(preds, axis=0)
label_arr = np.concatenate(labels, axis=0)
# pdb.set_trace()
# print(ts_dataset.slice_cnts[subj_idx] , len(imgs))
# pdb.set_trace()
dice = np.sum([label_arr * pred_arr
]) * 2.0 / (np.sum(pred_arr) + np.sum(label_arr))
dice_similarities.append(dice)
print(f"computing dice scores {subj_idx}/{10}", end='\n')
if _config['record']:
frames = []
for frame_id in range(0, len(save_subj)):
frames += overlay_color(torch.tensor(imgs[frame_id]),
torch.tensor(preds[frame_id]).float(),
torch.tensor(labels[frame_id]))
visual = make_grid(frames, normalize=True, nrow=5)
writer.add_image(f"test/{subj_idx}", visual, i)
writer.add_scalar(f'dice_score/{i}', dice)
if _config['save_sample']:
## only for internal test (BCV - MICCAI2015)
sup_idx = _config['s_idx']
target = _config['target']
save_name = _config['save_name']
dirs = ["gt", "pred", "input"]
save_dir = f"../sample/panet_organ{target}_sup{sup_idx}_{save_name}"
for dir in dirs:
try:
os.makedirs(os.path.join(save_dir, dir))
except:
pass
subj_name = fnames[0][0].split("/")[-2]
if target == 14:
src_dir = "/user/home2/soopil/Datasets/MICCAI2015challenge/Cervix/RawData/Training/img"
orig_fname = f"{src_dir}/{subj_name}-Image.nii.gz"
pass
else:
src_dir = "/user/home2/soopil/Datasets/MICCAI2015challenge/Abdomen/RawData/Training/img"
orig_fname = f"{src_dir}/img{subj_name}.nii.gz"
itk = sitk.ReadImage(orig_fname)
orig_spacing = itk.GetSpacing()
label_arr = label_arr * 2.0
# label_arr = np.concatenate([np.zeros([1,256,256]), label_arr,np.zeros([1,256,256])])
# pred_arr = np.concatenate([np.zeros([1,256,256]), pred_arr,np.zeros([1,256,256])])
# img_arr = np.concatenate([np.zeros([1,256,256]), img_arr,np.zeros([1,256,256])])
itk = sitk.GetImageFromArray(label_arr)
itk.SetSpacing(orig_spacing)
sitk.WriteImage(itk, f"{save_dir}/gt/{subj_idx}.nii.gz")
itk = sitk.GetImageFromArray(pred_arr.astype(float))
itk.SetSpacing(orig_spacing)
sitk.WriteImage(itk, f"{save_dir}/pred/{subj_idx}.nii.gz")
itk = sitk.GetImageFromArray(img_arr)
itk.SetSpacing(orig_spacing)
sitk.WriteImage(itk, f"{save_dir}/input/{subj_idx}.nii.gz")
print(f"test result \n n : {len(dice_similarities)}, mean dice score : \
{np.mean(dice_similarities)} \n dice similarities : {dice_similarities}")
if _config['record']:
writer.add_scalar(f'dice_score/mean', np.mean(dice_similarities))