def test_train_histogram(self):
paths = [sample['image']['path'] for sample in self.dataset]
HistogramStandardization.train(
paths,
masking_function=HistogramStandardization.mean,
output_path=(self.dir / 'landmarks.txt'),
)
HistogramStandardization.train(
paths,
mask_path=self.dataset[0]['label']['path'],
output_path=(self.dir / 'landmarks.npy'),
)
def create_normalization_file(use_controls, use_nofcd, mods):
"""
Creates t1_landmark.npy file using torchio library for brain normalizations.
"""
for j in range(1, mods + 1):
fcd_paths = sorted(glob.glob(FCD_FOLDER + f'fcd_*.{j}.nii.gz'))
nofcd_paths = sorted(glob.glob(FCD_FOLDER + f'nofcd_*.{j}.nii.gz'))
control_paths = sorted(
glob.glob(CONTROL_FOLDER + f'control_*.{j}.nii.gz'))
mri_paths = fcd_paths
if use_nofcd:
mri_paths += nofcd_paths
if use_controls:
mri_paths += control_paths
t1_landmarks_path = Path(f'./data/t1_landmarks_{j}.npy')
if t1_landmarks_path.is_file():
continue
# os.remove(f'./data/t1_landmarks_{j}.npy')
t1_landmarks = (t1_landmarks_path if t1_landmarks_path.is_file() else
HistogramStandardization.train(mri_paths))
np.save(t1_landmarks_path, t1_landmarks, allow_pickle=True)
def test_transforms(self):
landmarks_dict = dict(
t1=np.linspace(0, 100, 13),
t2=np.linspace(0, 100, 13),
)
random_transforms = (
RandomFlip(axes=(0, 1, 2), flip_probability=1),
RandomNoise(),
RandomBiasField(),
RandomElasticDeformation(proportion_to_augment=1),
RandomAffine(),
RandomMotion(proportion_to_augment=1),
)
intensity_transforms = (
Rescale(),
ZNormalization(),
HistogramStandardization(landmarks_dict=landmarks_dict),
)
for transform in random_transforms:
sample = self.get_sample()
transformed = transform(sample)
for transform in intensity_transforms:
sample = self.get_sample()
transformed = transform(sample)
def create_normalization_file(use_controls, use_nofcd):
"""
Creates t1_landmark.npy file using torchio library for brain normalizations.
"""
FCD_FOLDER = './data/fcd_brains/'
fcd_paths = sorted(list(filter(lambda x: 'nofcd' not in x, os.listdir(FCD_FOLDER))))
fcd_paths = list(map(lambda x: FCD_FOLDER + x, fcd_paths))
nofcd_paths = sorted(list(filter(lambda x: 'nofcd' in x, os.listdir(FCD_FOLDER))))
nofcd_paths = list(map(lambda x: FCD_FOLDER + x, nofcd_paths))
CONTROL_FOLDER = './data/control_brains/'
control_paths = sorted(os.listdir(CONTROL_FOLDER))
control_paths = list(map(lambda x: CONTROL_FOLDER + x, control_paths))
mri_paths = fcd_paths
if use_nofcd:
mri_paths += fcd_paths
if use_controls:
mri_paths += control_paths
t1_landmarks_path = Path('./data/t1_landmarks.npy')
if t1_landmarks_path.is_file():
os.remove('./data/t1_landmarks.npy')
t1_landmarks = (
t1_landmarks_path
if t1_landmarks_path.is_file()
else HistogramStandardization.train(mri_paths)
)
np.save(t1_landmarks_path, t1_landmarks, allow_pickle=True)
def test_with_saved_dict(self):
landmarks = np.linspace(0, 100, 13)
landmarks_dict = {'image': landmarks}
torch.save(landmarks_dict, self.dir / 'landmarks_dict.pth')
landmarks_dict = torch.load(self.dir / 'landmarks_dict.pth')
transform = HistogramStandardization(landmarks_dict)
transform(self.dataset[0])
def __init__(self,
h,
w,
nb_of_dims,
latent_dim,
use_coronal,
use_sagital,
p,
experiment_name,
parallel,
model_weights='best_model.pth',
thr=.5):
self.model = PatchModel(h, w, nb_of_dims, latent_dim, p).cuda()
if parallel:
self.model = nn.DataParallel(self.model)
self.model.load_state_dict(torch.load(model_weights))
self.model.eval()
self.h = h
self.w = w
self.best_t = thr
self.nb_of_dims = nb_of_dims
self.use_coronal = use_coronal
self.use_sagital = use_sagital
self.experiment_name = experiment_name
gray_matter_template = nib.load(
'./data/MNI152_T1_1mm_brain_gray.nii.gz')
self.gmpm = gray_matter_template.get_fdata() > 0
t1_landmarks = Path('./data/t1_landmarks.npy')
landmarks_dict = {'mri': t1_landmarks}
histogram_transform = HistogramStandardization(landmarks_dict)
znorm_transform = ZNormalization(masking_method=ZNormalization.mean)
self.transform = torchio.transforms.Compose(
[histogram_transform, znorm_transform])
def test_transforms(self):
landmarks_dict = dict(
t1=np.linspace(0, 100, 13),
t2=np.linspace(0, 100, 13),
)
transforms = (
CenterCropOrPad((9, 21, 30)),
ToCanonical(),
Resample((1, 1.1, 1.25)),
RandomFlip(axes=(0, 1, 2), flip_probability=1),
RandomMotion(proportion_to_augment=1),
RandomGhosting(proportion_to_augment=1, axes=(0, 1, 2)),
RandomSpike(),
RandomNoise(),
RandomBlur(),
RandomSwap(patch_size=2, num_iterations=5),
Lambda(lambda x: 1.5 * x, types_to_apply=INTENSITY),
RandomBiasField(),
Rescale((0, 1)),
ZNormalization(masking_method='label'),
HistogramStandardization(landmarks_dict=landmarks_dict),
RandomElasticDeformation(proportion_to_augment=1),
RandomAffine(),
Pad((1, 2, 3, 0, 5, 6)),
Crop((3, 2, 8, 0, 1, 4)),
)
transformed = self.get_sample()
for transform in transforms:
transformed = transform(transformed)
def get_hist_landmarks(img_path, lndmrk_path, names):
image_paths = list(map(lambda x: os.path.join(img_path, str(x), 'T1w',
'T1w_acpc_dc_restore_brain.nii.gz'),
names))
landmarks = HistogramStandardization.train(image_paths,
masking_function=cut_img_mask,
output_path=lndmrk_path)
return landmarks
def training_network(landmarks, dataset, subjects):
training_transform = Compose([
ToCanonical(),
Resample(4),
CropOrPad((48, 60, 48), padding_mode='reflect'),
RandomMotion(),
HistogramStandardization({'mri': landmarks}),
RandomBiasField(),
ZNormalization(masking_method=ZNormalization.mean),
RandomNoise(),
RandomFlip(axes=(0, )),
OneOf({
RandomAffine(): 0.8,
RandomElasticDeformation(): 0.2,
}),
])
validation_transform = Compose([
ToCanonical(),
Resample(4),
CropOrPad((48, 60, 48), padding_mode='reflect'),
HistogramStandardization({'mri': landmarks}),
ZNormalization(masking_method=ZNormalization.mean),
])
training_split_ratio = 0.9
num_subjects = len(dataset)
num_training_subjects = int(training_split_ratio * num_subjects)
training_subjects = subjects[:num_training_subjects]
validation_subjects = subjects[num_training_subjects:]
training_set = tio.SubjectsDataset(training_subjects,
transform=training_transform)
validation_set = tio.SubjectsDataset(validation_subjects,
transform=validation_transform)
print('Training set:', len(training_set), 'subjects')
print('Validation set:', len(validation_set), 'subjects')
return training_set, validation_set
def get_image_patches(input_img_name,
mod_nb,
gmpm=None,
use_coronal=False,
use_sagital=False,
input_mask_name=None,
augment=True,
h=16,
w=32,
coef=.2,
record_results=False,
pred_labels=None):
subject_dict = {
'mri': torchio.Image(input_img_name, torchio.INTENSITY),
}
# torchio normalization
t1_landmarks = Path(f'./data/t1_landmarks_{mod_nb}.npy')
landmarks_dict = {'mri': t1_landmarks}
histogram_transform = HistogramStandardization(landmarks_dict)
znorm_transform = ZNormalization(masking_method=ZNormalization.mean)
transform = torchio.transforms.Compose(
[histogram_transform, znorm_transform])
subject = torchio.Subject(subject_dict)
zimage = transform(subject)
target_np = zimage['mri'].data[0].numpy()
if input_mask_name is not None:
mask = nib.load(input_mask_name)
mask_np = (mask.get_fdata() > 0).astype('float')
else:
mask_np = np.zeros_like(target_np)
all_patches, all_labels, side_mask_np, mid_mask_np = get_patches_and_labels(
target_np,
gmpm,
mask_np,
use_coronal=use_coronal,
use_sagital=use_sagital,
h=h,
w=w,
coef=coef,
augment=augment,
record_results=record_results,
pred_labels=pred_labels)
if not record_results:
return all_patches, all_labels
else:
return side_mask_np, mid_mask_np
def test_train_histogram(self):
paths = [subject.image.path for subject in self.dataset]
# Use a function to mask
HistogramStandardization.train(
paths,
masking_function=HistogramStandardization.mean,
output_path=(self.dir / 'landmarks.txt'),
)
# Use a file to mask
HistogramStandardization.train(
paths,
mask_path=self.dataset[0].label.path,
output_path=(self.dir / 'landmarks.npy'),
)
# Use files to mask
masks = [subject.label.path for subject in self.dataset]
HistogramStandardization.train(
paths,
mask_path=masks,
output_path=(self.dir / 'landmarks_masks.npy'),
)
def test_with_saved_array(self):
landmarks = np.linspace(0, 100, 13)
np.save(self.dir / 'landmarks.npy', landmarks)
landmarks_dict = {'image': self.dir / 'landmarks.npy'}
transform = HistogramStandardization(landmarks_dict)
transform(self.dataset[0])
sample = dataset[0]
transform = tio.Compose([histogram_transform, znorm_transform])
znormed = transform(sample)
fig, ax = plt.subplots(dpi=100)
plot_histogram(ax, znormed.mri.data, label='Z-normed', alpha=1)
ax.set_title('Intensity values of one sample after z-normalization')
ax.set_xlabel('Intensity')
ax.grid()
training_transform = Compose([
ToCanonical(),
# Resample(4),
CropOrPad((112, 112, 48), padding_mode=0), #reflect , original 112,112,48
RandomMotion(num_transforms=6, image_interpolation='nearest', p=0.2),
HistogramStandardization({'mri': landmarks}),
RandomBiasField(p=0.2),
RandomBlur(p=0.2),
ZNormalization(masking_method=ZNormalization.mean),
RandomFlip(axes=['inferior-superior'], flip_probability=0.2),
# RandomNoise(std=0.5, p=0.2),
RandomGhosting(intensity=1.8, p=0.2),
# RandomNoise(),
# RandomFlip(axes=(0,)),
# OneOf({
# RandomAffine(): 0.8,
# RandomElasticDeformation(): 0.2,
# }),
])
validation_transform = Compose([
def test_wrong_image_key(self):
landmarks = np.linspace(0, 100, 13)
landmarks_dict = {'wrong_key': landmarks}
transform = HistogramStandardization(landmarks_dict)
with self.assertRaises(KeyError):
transform(self.dataset[0])
def test_normalize(self):
landmarks = np.linspace(0, 100, 13)
landmarks_dict = {'image': landmarks}
transform = HistogramStandardization(landmarks_dict)
transform(self.dataset[0])
import pandas as pd
import matplotlib.pyplot as plt
test = {'T1': {'csv_file':'/data/romain/HCPdata/Motion_brain_ms_train_hcp400.csv'} }
conditions = [("corr", "<", 0.98), ("|", "noise", "==", 1)]
subjects_dict, info = get_subject_list_and_csv_info_from_data_prameters(test, fpath_idx='filename', conditions=conditions,shuffle_order=True)
data_parameters = {'image': {'csv_file': '/data/romain/data_exemple/file_ms.csv', 'type': torchio.INTENSITY},
'label1': {'csv_file': '/data/romain/data_exemple/file_p1.csv', 'type': torchio.LABEL},
'label2': {'csv_file': '/data/romain/data_exemple/file_p2.csv', 'type': torchio.LABEL},
'label3': {'csv_file': '/data/romain/data_exemple/file_p3.csv', 'type': torchio.LABEL},
'sampler': {'csv_file': '/data/romain/data_exemple/file_mask.csv', 'type': torchio.SAMPLING_MAP}}
paths_dict, info = get_subject_list_and_csv_info_from_data_prameters(data_parameters) #,shuffle_order=False)
landmarks_file = '/data/romain/data_exemple/landmarks_hcp100.npy'
transforms = (HistogramStandardization(landmarks_file, mask_field_name='sampler'),)
transforms = (RandomElasticDeformation(num_control_points=8, proportion_to_augment=1, deformation_std=25, image_interpolation=Interpolation.BSPLINE),)
transforms = (RandomMotion(seed=42, degrees=0, translation=15, num_transforms=2, verbose=True,proportion_to_augment=1),)
transforms = (RandomBiasField(coefficients_range=(-0.5, 0.5),order=3), )
transform = Compose(transforms) #should be done in ImagesDataset
dataset = ImagesDataset(paths_dict, transform=transform)
dataset_not = ImagesDataset(paths_dict, transform=None)
dataload = torch.utils.data.DataLoader(dataset, num_workers=0, batch_size=1)
dataloadnot = torch.utils.data.DataLoader(dataset_not, num_workers=0, batch_size=1)
ddd = dataset[0] #next(iter(dataset))
ii = np.squeeze( ddd['image']['data'][0], axis=1)
ddno = dataset_not[0] #
def test_bad_paths_lengths(self):
with self.assertRaises(ValueError):
HistogramStandardization.train(
[1, 2],
mask_path=[1, 2, 3],
)