def generate_train_batch(self):
subjects = self._data[0]
subject_idx = int(random.uniform(0, len(subjects)))
data, seg = load_training_data(self.Config, subjects[subject_idx])
# Convert peaks to tensors if tensor model
if self.Config.NR_OF_GRADIENTS == 18*self.Config.NR_SLICES:
data = peak_utils.peaks_to_tensors(data)
slice_direction = data_utils.slice_dir_to_int(self.Config.TRAINING_SLICE_DIRECTION)
if data.shape[slice_direction] <= self.batch_size:
print("INFO: Batch size bigger than nr of slices. Therefore sampling with replacement.")
slice_idxs = np.random.choice(data.shape[slice_direction], self.batch_size, True, None)
else:
slice_idxs = np.random.choice(data.shape[slice_direction], self.batch_size, False, None)
if self.Config.NR_SLICES > 1:
x, y = data_utils.sample_Xslices(data, seg, slice_idxs, slice_direction=slice_direction,
labels_type=self.Config.LABELS_TYPE, slice_window=self.Config.NR_SLICES)
else:
x, y = data_utils.sample_slices(data, seg, slice_idxs, slice_direction=slice_direction,
labels_type=self.Config.LABELS_TYPE)
# Can be replaced by crop
# x = pad_nd_image(x, self.Config.INPUT_DIM, mode='constant', kwargs={'constant_values': 0})
# y = pad_nd_image(y, self.Config.INPUT_DIM, mode='constant', kwargs={'constant_values': 0})
# x = center_crop_2D_image_batched(x, self.Config.INPUT_DIM)
# y = center_crop_2D_image_batched(y, self.Config.INPUT_DIM)
# If want to convert e.g. 1.25mm (HCP) image to 2mm image (bb)
# x, y = self._zoom_x_and_y(x, y, 0.67) # very slow -> try spatial_transform, should be fast
if self.Config.PAD_TO_SQUARE:
#Crop and pad to input size
x, y = crop(x, y, crop_size=self.Config.INPUT_DIM) # does not work with img with batches and channels
else:
# Works -> results as good?
# Will pad each axis to be multiple of 16. (Each sample can end up having different dimensions. Also x and y
# can be different)
# This is needed for Schizo dataset
x = pad_nd_image(x, shape_must_be_divisible_by=(16, 16), mode='constant', kwargs={'constant_values': 0})
y = pad_nd_image(y, shape_must_be_divisible_by=(16, 16), mode='constant', kwargs={'constant_values': 0})
# Does not make it slower
x = x.astype(np.float32)
y = y.astype(np.float32)
# possible optimization: sample slices from different patients and pad all to same size (size of biggest)
data_dict = {"data": x, # (batch_size, channels, x, y, [z])
"seg": y,
"slice_dir": slice_direction} # (batch_size, channels, x, y, [z])
return data_dict
def process_bundle(idx):
print("idx: {}".format(idx))
dirs_per_bundle = []
for jdx in range(3): # 3 orientations
peak = img[:, :, :, idx * 3:idx * 3 + 3, jdx]
tensor = peak_utils.peaks_to_tensors(peak)
dirs_per_bundle.append(tensor)
merged_tensor = np.array(dirs_per_bundle).mean(axis=0)
merged_peak = peak_utils.tensors_to_peaks(merged_tensor)
return merged_peak
def get_batch_generator(self, batch_size=1):
if self.data is not None:
exp_utils.print_verbose(
self.Config.VERBOSE,
"Loading data from PREDICT_IMG input file")
data = np.nan_to_num(self.data)
# Use dummy mask in case we only want to predict on some data (where we do not have ground truth))
seg = np.zeros(
(self.Config.INPUT_DIM[0], self.Config.INPUT_DIM[0],
self.Config.INPUT_DIM[0],
self.Config.NR_OF_CLASSES)).astype(self.Config.LABELS_TYPE)
elif self.subject is not None:
if self.Config.TYPE == "combined":
# Load from npy file for Fusion
data = np.load(join(C.DATA_PATH, self.Config.DATASET_FOLDER,
self.subject,
self.Config.FEATURES_FILENAME + ".npy"),
mmap_mode="r")
seg = np.load(join(C.DATA_PATH, self.Config.DATASET_FOLDER,
self.subject,
self.Config.LABELS_FILENAME + ".npy"),
mmap_mode="r")
data = np.nan_to_num(data)
seg = np.nan_to_num(seg)
data = np.reshape(data,
(data.shape[0], data.shape[1], data.shape[2],
data.shape[3] * data.shape[4]))
else:
from tractseg.data.data_loader_training import load_training_data
data, seg = load_training_data(self.Config, self.subject)
# Convert peaks to tensors if tensor model
if self.Config.NR_OF_GRADIENTS == 18 * self.Config.NR_SLICES:
data = peak_utils.peaks_to_tensors(data)
data, transformation = data_utils.pad_and_scale_img_to_square_img(
data, target_size=self.Config.INPUT_DIM[0], nr_cpus=1)
seg, transformation = data_utils.pad_and_scale_img_to_square_img(
seg, target_size=self.Config.INPUT_DIM[0], nr_cpus=1)
else:
raise ValueError("Neither 'data' nor 'subject' set.")
if self.Config.DIM == "2D":
batch_gen = BatchGenerator2D_data_ordered_standalone(
(data, seg), batch_size=batch_size)
else:
batch_gen = BatchGenerator3D_data_ordered_standalone(
(data, seg), batch_size=batch_size)
batch_gen.Config = self.Config
batch_gen = self._augment_data(batch_gen, type=type)
return batch_gen
def generate_train_batch(self):
# np.random.seed(1234)
subjects = self._data[0]
subject_idx = int(random.uniform(0, len(subjects))) # len(subjects)-1 not needed because int always rounds to floor
data, seg = load_training_data(self.Config, subjects[subject_idx])
#Convert peaks to tensors if tensor model
if self.Config.NR_OF_GRADIENTS == 18*self.Config.NR_SLICES:
data = peak_utils.peaks_to_tensors(data)
slice_direction = data_utils.slice_dir_to_int(self.Config.TRAINING_SLICE_DIRECTION)
slice_idxs = np.random.choice(data.shape[slice_direction], self.batch_size, False, None)
if self.Config.NR_SLICES > 1:
x, y = data_utils.sample_Xslices(data, seg, slice_idxs, slice_direction=slice_direction,
labels_type=self.Config.LABELS_TYPE, slice_window=self.Config.NR_SLICES)
else:
x, y = data_utils.sample_slices(data, seg, slice_idxs, slice_direction=slice_direction,
labels_type=self.Config.LABELS_TYPE)
# Can be replaced by crop
# x = pad_nd_image(x, self.Config.INPUT_DIM, mode='constant', kwargs={'constant_values': 0})
# y = pad_nd_image(y, self.Config.INPUT_DIM, mode='constant', kwargs={'constant_values': 0})
# x = center_crop_2D_image_batched(x, self.Config.INPUT_DIM)
# y = center_crop_2D_image_batched(y, self.Config.INPUT_DIM)
#Crop and pad to input size
x, y = crop(x, y, crop_size=self.Config.INPUT_DIM) # does not work with img with batches and channels
# Works -> results as good? -> todo: make the same way for inference!
# This is needed for Schizo dataset
# x = pad_nd_image(x, shape_must_be_divisible_by=(16, 16), mode='constant', kwargs={'constant_values': 0})
# y = pad_nd_image(y, shape_must_be_divisible_by=(16, 16), mode='constant', kwargs={'constant_values': 0})
# Does not make it slower
x = x.astype(np.float32)
y = y.astype(np.float32) # if not doing this: during validation: ConnectionResetError: [Errno 104] Connection
# reset by peer
#possible optimization: sample slices from different patients and pad all to same size (size of biggest)
data_dict = {"data": x, # (batch_size, channels, x, y, [z])
"seg": y,
"slice_dir": slice_direction} # (batch_size, channels, x, y, [z])
return data_dict
