def test_segment_volume_2d():
model = imed_models.Unet(in_channel=1,
out_channel=1,
depth=2,
drop_rate=DROPOUT,
bn_momentum=BN)
# temporary folder that will be deleted at the end of the test
if not os.path.exists(PATH_MODEL):
os.mkdir(PATH_MODEL)
torch.save(model, os.path.join(PATH_MODEL, "model_test.pt"))
config = {
"loader_parameters": {
"slice_filter_params": {
"filter_empty_mask": False,
"filter_empty_input": False
},
"roi_params": {
"suffix": None,
"slice_filter_roi": 10
},
"slice_axis": "axial"
},
"transformation": {
"Resample": {
"wspace": 0.75,
"hspace": 0.75
},
"ROICrop": {
"size": [48, 48]
},
"RandomTranslation": {
"translate": [0.03, 0.03],
"applied_to": ["im", "gt"],
"dataset_type": ["training"]
},
"NumpyToTensor": {},
"NormalizeInstance": {
"applied_to": ["im"]
}
},
"postprocessing": {},
"training_parameters": {
"batch_size": BATCH_SIZE
}
}
PATH_CONFIG = os.path.join(PATH_MODEL, 'model_test.json')
with open(PATH_CONFIG, 'w') as fp:
json.dump(config, fp)
nib_lst, _ = imed_inference.segment_volume(PATH_MODEL, [IMAGE_PATH],
ROI_PATH)
nib_img = nib_lst[0]
assert np.squeeze(nib_img.get_fdata()).shape == nib.load(IMAGE_PATH).shape
assert (nib_img.dataobj.max() <= 1.0) and (nib_img.dataobj.min() >= 0.0)
assert nib_img.dataobj.dtype == 'float32'
shutil.rmtree(PATH_MODEL)
def test_segment_volume_2d(download_functional_test_files):
model = imed_models.Unet(in_channel=1,
out_channel=1,
depth=2,
dropout_rate=DROPOUT,
bn_momentum=BN)
if not PATH_MODEL.exists():
PATH_MODEL.mkdir(parents=True, exist_ok=True)
torch.save(model, Path(PATH_MODEL, "model_test.pt"))
config = {
"loader_parameters": {
"slice_filter_params": {
"filter_empty_mask": False,
"filter_empty_input": False
},
"roi_params": {
"suffix": "_seg-manual",
"slice_filter_roi": 10
},
"slice_axis": "axial"
},
"transformation": {
"Resample": {
"wspace": 0.75,
"hspace": 0.75
},
"ROICrop": {
"size": [48, 48]
},
"RandomTranslation": {
"translate": [0.03, 0.03],
"applied_to": ["im", "gt"],
"dataset_type": ["training"]
},
"NormalizeInstance": {
"applied_to": ["im"]
}
},
"postprocessing": {},
"training_parameters": {
"batch_size": BATCH_SIZE
}
}
PATH_CONFIG = Path(PATH_MODEL, 'model_test.json')
with PATH_CONFIG.open(mode='w') as fp:
json.dump(config, fp)
nib_lst, _ = imed_inference.segment_volume(
str(PATH_MODEL), [str(PATH_IMAGE)],
options={'fname_prior': str(PATH_ROI)})
nib_img = nib_lst[0]
assert np.squeeze(nib_img.get_fdata()).shape == nib.load(PATH_IMAGE).shape
assert (nib_img.dataobj.max() <= 1.0) and (nib_img.dataobj.min() >= 0.0)
assert nib_img.dataobj.dtype == 'float32'
shutil.rmtree(PATH_MODEL)
def test_segment_volume_2d_no_prepro_transform(download_functional_test_files):
model = imed_models.Unet(in_channel=1,
out_channel=1,
depth=2,
dropout_rate=DROPOUT,
bn_momentum=BN)
if not PATH_MODEL.exists():
PATH_MODEL.mkdir()
torch.save(model, Path(PATH_MODEL, "model_test.pt"))
config = {
"loader_parameters": {
"slice_filter_params": {
"filter_empty_mask": False,
"filter_empty_input": False
},
"roi_params": {
"suffix": None,
"slice_filter_roi": None
},
"slice_axis": "axial"
},
"transformation": {
"NormalizeInstance": {
"applied_to": ["im"]
}
},
"postprocessing": {},
"training_parameters": {
"batch_size": BATCH_SIZE
}
}
PATH_CONFIG = Path(PATH_MODEL, 'model_test.json')
with PATH_CONFIG.open(mode='w') as fp:
json.dump(config, fp)
nib_lst, _ = imed_inference.segment_volume(str(PATH_MODEL),
[str(PATH_IMAGE)])
nib_img = nib_lst[0]
assert np.squeeze(nib_img.get_fdata()).shape == nib.load(PATH_IMAGE).shape
assert (nib_img.dataobj.max() <= 1.0) and (nib_img.dataobj.min() >= 0.0)
assert nib_img.dataobj.dtype == 'float32'
shutil.rmtree(PATH_MODEL)
def test_inference(transforms_dict, test_lst, target_lst, roi_params, testing_params):
cuda_available, device = imed_utils.define_device(GPU_ID)
model_params = {"name": "Unet", "is_2d": True}
loader_params = {
"transforms_params": transforms_dict,
"data_list": test_lst,
"dataset_type": "testing",
"requires_undo": True,
"contrast_params": {"contrast_lst": ['T2w'], "balance": {}},
"path_data": [__data_testing_dir__],
"target_suffix": target_lst,
"roi_params": roi_params,
"slice_filter_params": {
"filter_empty_mask": False,
"filter_empty_input": True
},
"slice_axis": SLICE_AXIS,
"multichannel": False
}
loader_params.update({"model_params": model_params})
# Get Testing dataset
ds_test = imed_loader.load_dataset(**loader_params)
test_loader = DataLoader(ds_test, batch_size=BATCH_SIZE,
shuffle=False, pin_memory=True,
collate_fn=imed_loader_utils.imed_collate,
num_workers=0)
# Undo transform
val_undo_transform = imed_transforms.UndoCompose(imed_transforms.Compose(transforms_dict))
# Update testing_params
testing_params.update({
"slice_axis": loader_params["slice_axis"],
"target_suffix": loader_params["target_suffix"],
"undo_transforms": val_undo_transform
})
# Model
model = imed_models.Unet()
if cuda_available:
model.cuda()
model.eval()
metric_fns = [imed_metrics.dice_score,
imed_metrics.hausdorff_score,
imed_metrics.precision_score,
imed_metrics.recall_score,
imed_metrics.specificity_score,
imed_metrics.intersection_over_union,
imed_metrics.accuracy_score]
metric_mgr = imed_metrics.MetricManager(metric_fns)
if not os.path.isdir(__output_dir__):
os.makedirs(__output_dir__)
preds_npy, gt_npy = imed_testing.run_inference(test_loader=test_loader,
model=model,
model_params=model_params,
testing_params=testing_params,
ofolder=__output_dir__,
cuda_available=cuda_available)
metric_mgr(preds_npy, gt_npy)
metrics_dict = metric_mgr.get_results()
metric_mgr.reset()
print(metrics_dict)
def test_inference_target_suffix(download_data_testing_test_files, transforms_dict, test_lst, target_lst, roi_params,
testing_params):
"""
This test checks if the filename(s) of the prediction(s) saved as NifTI file(s) in the pred_masks
dir conform to the target_suffix or not. Thus, independent of underscore(s) in the target_suffix. As a result,
_seg-axon-manual or _seg-axon_manual should yield the same filename(s).
(c.f: https://github.com/ivadomed/ivadomed/issues/1135)
"""
cuda_available, device = imed_utils.define_device(GPU_ID)
model_params = {"name": "Unet", "is_2d": True, "out_channel": 3}
loader_params = {
"transforms_params": transforms_dict,
"data_list": test_lst,
"dataset_type": "testing",
"requires_undo": True,
"contrast_params": {"contrast_lst": ['SEM'], "balance": {}},
"path_data": [str(Path(__data_testing_dir__, "microscopy_png"))],
"bids_config": f"{path_repo_root}/ivadomed/config/config_bids.json",
"target_suffix": target_lst,
"extensions": [".png"],
"roi_params": roi_params,
"slice_filter_params": {"filter_empty_mask": False, "filter_empty_input": True},
"patch_filter_params": {"filter_empty_mask": False, "filter_empty_input": False},
"slice_axis": SLICE_AXIS,
"multichannel": False
}
loader_params.update({"model_params": model_params})
# restructuring the dataset
gt_path = f'{loader_params["path_data"][0]}/derivatives/labels/'
for file_path in Path(gt_path).rglob('*.png'):
src_filename = file_path.resolve()
dst_filename = '_'.join(str(src_filename).rsplit('-', 1))
src_filename.rename(Path(dst_filename))
bids_df = BidsDataframe(loader_params, __tmp_dir__, derivatives=True)
ds_test = imed_loader.load_dataset(bids_df, **loader_params)
test_loader = DataLoader(ds_test, batch_size=BATCH_SIZE,
shuffle=False, pin_memory=True,
collate_fn=imed_loader_utils.imed_collate,
num_workers=0)
# Undo transform
val_undo_transform = imed_transforms.UndoCompose(imed_transforms.Compose(transforms_dict))
# Update testing_params
testing_params.update({
"slice_axis": loader_params["slice_axis"],
"target_suffix": loader_params["target_suffix"],
"undo_transforms": val_undo_transform
})
# Model
model = imed_models.Unet(out_channel=model_params['out_channel'])
if cuda_available:
model.cuda()
model.eval()
if not __output_dir__.is_dir():
__output_dir__.mkdir(parents=True, exist_ok=True)
preds_npy, gt_npy = imed_testing.run_inference(test_loader=test_loader,
model=model,
model_params=model_params,
testing_params=testing_params,
ofolder=str(__output_dir__),
cuda_available=cuda_available)
for x in __output_dir__.iterdir():
if x.name.endswith('_pred.nii.gz'):
assert x.name.rsplit('_', 1)[0].endswith(loader_params['contrast_params']['contrast_lst'][-1]), (
'Incompatible filename(s) of the prediction(s) saved as NifTI file(s)!'
)
def test_inference_2d_microscopy(download_data_testing_test_files, transforms_dict, test_lst, target_lst, roi_params,
testing_params):
"""
This test checks if the number of NifTI predictions equals the number of test subjects on 2d microscopy data.
Used to catch a bug where the last slice of the last volume wasn't appended to the prediction
(see: https://github.com/ivadomed/ivadomed/issues/823)
Also tests the conversions to PNG predictions when source files are not Nifti and checks if the number of PNG
predictions is 2x the number of test subjects (2-class model, outputs 1 PNG per class per subject).
"""
cuda_available, device = imed_utils.define_device(GPU_ID)
model_params = {"name": "Unet", "is_2d": True, "out_channel": 3}
loader_params = {
"transforms_params": transforms_dict,
"data_list": test_lst,
"dataset_type": "testing",
"requires_undo": True,
"contrast_params": {"contrast_lst": ['SEM'], "balance": {}},
"path_data": [str(Path(__data_testing_dir__, "microscopy_png"))],
"bids_config": f"{path_repo_root}/ivadomed/config/config_bids.json",
"target_suffix": target_lst,
"extensions": [".png"],
"roi_params": roi_params,
"slice_filter_params": {"filter_empty_mask": False, "filter_empty_input": True},
"patch_filter_params": {"filter_empty_mask": False, "filter_empty_input": False},
"slice_axis": SLICE_AXIS,
"multichannel": False
}
loader_params.update({"model_params": model_params})
bids_df = BidsDataframe(loader_params, __tmp_dir__, derivatives=True)
# Get Testing dataset
ds_test = imed_loader.load_dataset(bids_df, **loader_params)
test_loader = DataLoader(ds_test, batch_size=BATCH_SIZE,
shuffle=False, pin_memory=True,
collate_fn=imed_loader_utils.imed_collate,
num_workers=0)
# Undo transform
val_undo_transform = imed_transforms.UndoCompose(imed_transforms.Compose(transforms_dict))
# Update testing_params
testing_params.update({
"slice_axis": loader_params["slice_axis"],
"target_suffix": loader_params["target_suffix"],
"undo_transforms": val_undo_transform
})
# Model
model = imed_models.Unet(out_channel=model_params['out_channel'])
if cuda_available:
model.cuda()
model.eval()
if not __output_dir__.is_dir():
__output_dir__.mkdir(parents=True, exist_ok=True)
preds_npy, gt_npy = imed_testing.run_inference(test_loader=test_loader,
model=model,
model_params=model_params,
testing_params=testing_params,
ofolder=str(__output_dir__),
cuda_available=cuda_available)
assert len([x for x in __output_dir__.iterdir() if x.name.endswith(".nii.gz")]) == len(test_lst)
assert len([x for x in __output_dir__.iterdir() if x.name.endswith(".png")]) == 2*len(test_lst)
def test_model_creation():
# creating basic model for test
model = imed_models.Unet()
torch.save(model, "testing_data/model_unet_test.pt")
assert os.path.isfile("testing_data/model_unet_test.pt")
