def __init__(self, csv_path):
"""
Pre-processing pipeline constructor.
Args:
root_dir: Root directory where all files are located.
"""
self._csv_path = csv_path
self._mean_gauge = AverageGauge()
self._std_gauge = AverageGauge()
self._dataset_mean = 0.0
def _test_s(self, S: ModelTrainer, inputs, target, metric_gauge: AverageGauge):
target_ohe = to_onehot(torch.squeeze(target, dim=1).long(), num_classes=4)
target = torch.squeeze(target, dim=1).long()
seg_pred = torch.nn.functional.softmax(S.forward(inputs), dim=1)
loss_S = S.compute_loss("DiceLoss", seg_pred, target_ohe)
S.update_test_loss("DiceLoss", loss_S.mean())
metrics = S.compute_metrics(seg_pred, target)
metric_gauge.update(np.array(metrics["Dice"]))
metrics["Dice"] = metrics["Dice"].mean()
metrics["IoU"] = metrics["IoU"].mean()
S.update_test_metrics(metrics)
return seg_pred, loss_S
def __init__(self,
model_name,
model,
criterions,
optimizer,
scheduler,
metric_computers: Dict[str, Metric],
gradient_clipping_strategy: GradientClippingStrategy = None):
super(ModelTrainer, self).__init__(model, optimizer)
self._model_name = model_name
self._criterions = criterions
self._scheduler = scheduler
self._metric_computers = metric_computers
self._gradient_clipping_strategy = gradient_clipping_strategy
self._step_train_loss = {
criterion: torch.Tensor().new_zeros((1, ))
for criterion in criterions.keys()
}
self._step_valid_loss = {
criterion: torch.Tensor().new_zeros((1, ))
for criterion in criterions.keys()
}
self._step_test_loss = {
criterion: torch.Tensor().new_zeros((1, ))
for criterion in criterions.keys()
}
self._step_train_metrics = {
metric: torch.Tensor().new_zeros((1, ))
for metric in metric_computers.keys()
}
self._step_valid_metrics = {
metric: torch.Tensor().new_zeros((1, ))
for metric in metric_computers.keys()
}
self._step_test_metrics = {
metric: torch.Tensor().new_zeros((1, ))
for metric in metric_computers.keys()
}
self._train_loss = {
criterion: AverageGauge()
for criterion in criterions.keys()
}
self._valid_loss = {
criterion: AverageGauge()
for criterion in criterions.keys()
}
self._test_loss = {
criterion: AverageGauge()
for criterion in criterions.keys()
}
self._train_metrics = {
metric_name: AverageGauge()
for metric_name in metric_computers.keys()
}
self._valid_metrics = {
metric_name: AverageGauge()
for metric_name in metric_computers.keys()
}
self._test_metrics = {
metric_name: AverageGauge()
for metric_name in metric_computers.keys()
}
self._status = Status.INITIALIZED
def __init__(self, training_config, model_trainers: List[ModelTrainer],
train_data_loader: DataLoader, valid_data_loader: DataLoader, test_data_loader: DataLoader,
reconstruction_datasets: List[Dataset],
input_reconstructor: ImageReconstructor,
segmentation_reconstructor: ImageReconstructor,
augmented_input_reconstructor: ImageReconstructor,
gt_reconstructor: ImageReconstructor,
run_config: RunConfiguration,
dataset_config: dict, save_folder: str):
super(UNetTrainer, self).__init__("UNetTrainer", train_data_loader, valid_data_loader, test_data_loader,
model_trainers, run_config)
self._training_config = training_config
self._run_config = run_config
self._dataset_configs = dataset_config
self._slicer = ImageSlicer()
self._seg_slicer = SegmentationSlicer()
self._label_mapper = LabelMapper()
self._reconstruction_datasets = reconstruction_datasets
self._input_reconstructor = input_reconstructor
self._gt_reconstructor = gt_reconstructor
self._segmentation_reconstructor = segmentation_reconstructor
self._augmented_input_reconstructor = augmented_input_reconstructor
self._num_datasets = len(list(dataset_config.keys()))
self._class_hausdorff_distance_gauge = AverageGauge()
self._mean_hausdorff_distance_gauge = AverageGauge()
self._per_dataset_hausdorff_distance_gauge = AverageGauge()
self._iSEG_dice_gauge = AverageGauge()
self._MRBrainS_dice_gauge = AverageGauge()
self._ABIDE_dice_gauge = AverageGauge()
self._iSEG_hausdorff_gauge = AverageGauge()
self._MRBrainS_hausdorff_gauge = AverageGauge()
self._ABIDE_hausdorff_gauge = AverageGauge()
self._valid_dice_gauge = AverageGauge()
self._class_dice_gauge_on_patches = AverageGauge()
self._class_dice_gauge_on_reconstructed_images = AverageGauge()
self._class_dice_gauge_on_reconstructed_iseg_images = AverageGauge()
self._class_dice_gauge_on_reconstructed_mrbrains_images = AverageGauge()
self._class_dice_gauge_on_reconstructed_abide_images = AverageGauge()
self._hausdorff_distance_gauge_on_reconstructed_iseg_images = AverageGauge()
self._hausdorff_distance_gauge_on_reconstructed_mrbrains_images = AverageGauge()
self._hausdorff_distance_gauge_on_reconstructed_abide_images = AverageGauge()
self._general_confusion_matrix_gauge = ConfusionMatrix(num_classes=4)
self._iSEG_confusion_matrix_gauge = ConfusionMatrix(num_classes=4)
self._MRBrainS_confusion_matrix_gauge = ConfusionMatrix(num_classes=4)
self._ABIDE_confusion_matrix_gauge = ConfusionMatrix(num_classes=4)
self._previous_mean_dice = 0.0
self._previous_per_dataset_table = ""
self._start_time = time.time()
self._sampler = Sampler(1.0)
self._save_folder = save_folder
self._is_sliced = True if isinstance(self._reconstruction_datasets[0], SliceDataset) else False
print("Total number of parameters: {}".format(sum(p.numel() for p in self._model_trainers[0].parameters())))
class UNetTrainer(Trainer):
def __init__(self, training_config, model_trainers: List[ModelTrainer],
train_data_loader: DataLoader, valid_data_loader: DataLoader, test_data_loader: DataLoader,
reconstruction_datasets: List[Dataset],
input_reconstructor: ImageReconstructor,
segmentation_reconstructor: ImageReconstructor,
augmented_input_reconstructor: ImageReconstructor,
gt_reconstructor: ImageReconstructor,
run_config: RunConfiguration,
dataset_config: dict, save_folder: str):
super(UNetTrainer, self).__init__("UNetTrainer", train_data_loader, valid_data_loader, test_data_loader,
model_trainers, run_config)
self._training_config = training_config
self._run_config = run_config
self._dataset_configs = dataset_config
self._slicer = ImageSlicer()
self._seg_slicer = SegmentationSlicer()
self._label_mapper = LabelMapper()
self._reconstruction_datasets = reconstruction_datasets
self._input_reconstructor = input_reconstructor
self._gt_reconstructor = gt_reconstructor
self._segmentation_reconstructor = segmentation_reconstructor
self._augmented_input_reconstructor = augmented_input_reconstructor
self._num_datasets = len(list(dataset_config.keys()))
self._class_hausdorff_distance_gauge = AverageGauge()
self._mean_hausdorff_distance_gauge = AverageGauge()
self._per_dataset_hausdorff_distance_gauge = AverageGauge()
self._iSEG_dice_gauge = AverageGauge()
self._MRBrainS_dice_gauge = AverageGauge()
self._ABIDE_dice_gauge = AverageGauge()
self._iSEG_hausdorff_gauge = AverageGauge()
self._MRBrainS_hausdorff_gauge = AverageGauge()
self._ABIDE_hausdorff_gauge = AverageGauge()
self._valid_dice_gauge = AverageGauge()
self._class_dice_gauge_on_patches = AverageGauge()
self._class_dice_gauge_on_reconstructed_images = AverageGauge()
self._class_dice_gauge_on_reconstructed_iseg_images = AverageGauge()
self._class_dice_gauge_on_reconstructed_mrbrains_images = AverageGauge()
self._class_dice_gauge_on_reconstructed_abide_images = AverageGauge()
self._hausdorff_distance_gauge_on_reconstructed_iseg_images = AverageGauge()
self._hausdorff_distance_gauge_on_reconstructed_mrbrains_images = AverageGauge()
self._hausdorff_distance_gauge_on_reconstructed_abide_images = AverageGauge()
self._general_confusion_matrix_gauge = ConfusionMatrix(num_classes=4)
self._iSEG_confusion_matrix_gauge = ConfusionMatrix(num_classes=4)
self._MRBrainS_confusion_matrix_gauge = ConfusionMatrix(num_classes=4)
self._ABIDE_confusion_matrix_gauge = ConfusionMatrix(num_classes=4)
self._previous_mean_dice = 0.0
self._previous_per_dataset_table = ""
self._start_time = time.time()
self._sampler = Sampler(1.0)
self._save_folder = save_folder
self._is_sliced = True if isinstance(self._reconstruction_datasets[0], SliceDataset) else False
print("Total number of parameters: {}".format(sum(p.numel() for p in self._model_trainers[0].parameters())))
def _train_s(self, S: ModelTrainer, inputs, target, backward=True):
S.zero_grad()
target_ohe = to_onehot(torch.squeeze(target, dim=1).long(), num_classes=4)
target = torch.squeeze(target, dim=1).long()
seg_pred = torch.nn.functional.softmax(S.forward(inputs), dim=1)
loss_S = S.compute_loss("DiceLoss", seg_pred, target_ohe)
S.update_train_loss("DiceLoss", loss_S.mean())
metrics = S.compute_metrics(seg_pred, target)
metrics["Dice"] = metrics["Dice"].mean()
metrics["IoU"] = metrics["IoU"].mean()
S.update_train_metrics(metrics)
if backward:
loss_S.mean().backward()
S.step()
return seg_pred, loss_S
def _valid_s(self, S: ModelTrainer, inputs, target):
target_ohe = to_onehot(torch.squeeze(target, dim=1).long(), num_classes=4)
target = torch.squeeze(target, dim=1).long()
seg_pred = torch.nn.functional.softmax(S.forward(inputs), dim=1)
loss_S = S.compute_loss("DiceLoss", seg_pred, target_ohe)
S.update_valid_loss("DiceLoss", loss_S.mean())
metrics = S.compute_metrics(seg_pred, target)
metrics["Dice"] = metrics["Dice"].mean()
metrics["IoU"] = metrics["IoU"].mean()
S.update_valid_metrics(metrics)
return seg_pred, loss_S
def _test_s(self, S: ModelTrainer, inputs, target, metric_gauge: AverageGauge):
target_ohe = to_onehot(torch.squeeze(target, dim=1).long(), num_classes=4)
target = torch.squeeze(target, dim=1).long()
seg_pred = torch.nn.functional.softmax(S.forward(inputs), dim=1)
loss_S = S.compute_loss("DiceLoss", seg_pred, target_ohe)
S.update_test_loss("DiceLoss", loss_S.mean())
metrics = S.compute_metrics(seg_pred, target)
metric_gauge.update(np.array(metrics["Dice"]))
metrics["Dice"] = metrics["Dice"].mean()
metrics["IoU"] = metrics["IoU"].mean()
S.update_test_metrics(metrics)
return seg_pred, loss_S
def train_step(self, inputs, target):
seg_pred, _ = self._train_s(self._model_trainers[0], inputs[AUGMENTED_INPUTS],
target[IMAGE_TARGET])
if self.current_train_step % 500 == 0:
self._update_image_plots(self.phase, inputs[AUGMENTED_INPUTS].cpu().detach(),
seg_pred.cpu().detach(),
target[IMAGE_TARGET].cpu().detach(),
target[DATASET_ID].cpu().detach())
def validate_step(self, inputs, target):
seg_pred, _ = self._valid_s(self._model_trainers[0], inputs[AUGMENTED_INPUTS],
target[IMAGE_TARGET])
if self.current_valid_step % 100 == 0:
self._update_image_plots(self.phase, inputs[AUGMENTED_INPUTS].cpu().detach(),
seg_pred.cpu().detach(),
target[IMAGE_TARGET].cpu().detach(),
target[DATASET_ID].cpu().detach())
def test_step(self, inputs, target):
inputs, target = self._sampler(inputs, target)
target = target[AUGMENTED_TARGETS]
seg_pred, _ = self._test_s(self._model_trainers[0], inputs[AUGMENTED_INPUTS], target[IMAGE_TARGET],
self._class_dice_gauge_on_patches)
if self.current_test_step % 100 == 0:
self._update_histograms(inputs[AUGMENTED_INPUTS], target)
self._update_image_plots(self.phase, inputs[AUGMENTED_INPUTS].cpu().detach(),
seg_pred.cpu().detach(),
target[IMAGE_TARGET].cpu().detach(),
target[DATASET_ID].cpu().detach())
if seg_pred[torch.where(target[DATASET_ID] == ISEG_ID)].shape[0] != 0:
self._iSEG_dice_gauge.update(np.array(self._model_trainers[0].compute_metrics(
torch.nn.functional.softmax(seg_pred[torch.where(target[DATASET_ID] == ISEG_ID)], dim=1),
torch.squeeze(target[IMAGE_TARGET][torch.where(target[DATASET_ID] == ISEG_ID)],
dim=1).long())["Dice"].numpy()))
self._iSEG_hausdorff_gauge.update(mean_hausdorff_distance(
to_onehot(
torch.argmax(
torch.nn.functional.softmax(seg_pred[torch.where(target[DATASET_ID] == ISEG_ID)], dim=1),
dim=1), num_classes=4),
to_onehot(
torch.squeeze(target[IMAGE_TARGET][torch.where(target[DATASET_ID] == ISEG_ID)], dim=1).long(),
num_classes=4))[-3:])
self._iSEG_confusion_matrix_gauge.update((
to_onehot(
torch.argmax(
torch.nn.functional.softmax(seg_pred[torch.where(target[DATASET_ID] == ISEG_ID)], dim=1),
dim=1, keepdim=False),
num_classes=4),
torch.squeeze(target[IMAGE_TARGET][torch.where(target[DATASET_ID] == ISEG_ID)].long(), dim=1)))
else:
self._iSEG_dice_gauge.update(np.zeros((3,)))
self._iSEG_hausdorff_gauge.update(np.zeros((3,)))
if seg_pred[torch.where(target[DATASET_ID] == MRBRAINS_ID)].shape[0] != 0:
self._MRBrainS_dice_gauge.update(np.array(self._model_trainers[0].compute_metrics(
torch.nn.functional.softmax(seg_pred[torch.where(target[DATASET_ID] == MRBRAINS_ID)], dim=1),
torch.squeeze(target[IMAGE_TARGET][torch.where(target[DATASET_ID] == MRBRAINS_ID)],
dim=1).long())["Dice"].numpy()))
self._MRBrainS_hausdorff_gauge.update(mean_hausdorff_distance(
to_onehot(
torch.argmax(
torch.nn.functional.softmax(seg_pred[torch.where(target[DATASET_ID] == MRBRAINS_ID)],
dim=1),
dim=1), num_classes=4),
to_onehot(
torch.squeeze(target[IMAGE_TARGET][torch.where(target[DATASET_ID] == MRBRAINS_ID)],
dim=1).long(),
num_classes=4))[-3:])
self._MRBrainS_confusion_matrix_gauge.update((
to_onehot(
torch.argmax(
torch.nn.functional.softmax(seg_pred[torch.where(target[DATASET_ID] == MRBRAINS_ID)],
dim=1),
dim=1, keepdim=False),
num_classes=4),
torch.squeeze(target[IMAGE_TARGET][torch.where(target[DATASET_ID] == MRBRAINS_ID)].long(), dim=1)))
else:
self._MRBrainS_dice_gauge.update(np.zeros((3,)))
self._MRBrainS_hausdorff_gauge.update(np.zeros((3,)))
if seg_pred[torch.where(target[DATASET_ID] == ABIDE_ID)].shape[0] != 0:
self._ABIDE_dice_gauge.update(np.array(self._model_trainers[0].compute_metrics(
torch.nn.functional.softmax(seg_pred[torch.where(target[DATASET_ID] == ABIDE_ID)], dim=1),
torch.squeeze(target[IMAGE_TARGET][torch.where(target[DATASET_ID] == ABIDE_ID)],
dim=1).long())["Dice"].numpy()))
self._ABIDE_hausdorff_gauge.update(mean_hausdorff_distance(
to_onehot(
torch.argmax(
torch.nn.functional.softmax(seg_pred[torch.where(target[DATASET_ID] == ABIDE_ID)], dim=1),
dim=1), num_classes=4),
to_onehot(
torch.squeeze(target[IMAGE_TARGET][torch.where(target[DATASET_ID] == ABIDE_ID)], dim=1).long(),
num_classes=4))[-3:])
self._ABIDE_confusion_matrix_gauge.update((
to_onehot(
torch.argmax(
torch.nn.functional.softmax(seg_pred[torch.where(target[DATASET_ID] == ABIDE_ID)], dim=1),
dim=1, keepdim=False),
num_classes=4),
torch.squeeze(target[IMAGE_TARGET][torch.where(target[DATASET_ID] == ABIDE_ID)].long(), dim=1)))
self._class_hausdorff_distance_gauge.update(
mean_hausdorff_distance(
to_onehot(torch.argmax(torch.nn.functional.softmax(seg_pred, dim=1), dim=1), num_classes=4),
to_onehot(torch.squeeze(target[IMAGE_TARGET], dim=1).long(), num_classes=4))[-3:])
self._general_confusion_matrix_gauge.update((
to_onehot(torch.argmax(torch.nn.functional.softmax(seg_pred, dim=1), dim=1, keepdim=False),
num_classes=4),
torch.squeeze(target[IMAGE_TARGET].long(), dim=1)))
def scheduler_step(self):
self._model_trainers[0].scheduler_step()
def on_epoch_begin(self):
self._class_hausdorff_distance_gauge.reset()
self._mean_hausdorff_distance_gauge.reset()
self._iSEG_dice_gauge.reset()
self._MRBrainS_dice_gauge.reset()
self._ABIDE_dice_gauge.reset()
self._iSEG_hausdorff_gauge.reset()
self._MRBrainS_hausdorff_gauge.reset()
self._ABIDE_hausdorff_gauge.reset()
self._class_dice_gauge_on_patches.reset()
self._general_confusion_matrix_gauge.reset()
self._iSEG_confusion_matrix_gauge.reset()
self._MRBrainS_confusion_matrix_gauge.reset()
self._ABIDE_confusion_matrix_gauge.reset()
def on_test_epoch_end(self):
if self.epoch % 10 == 0:
self._per_dataset_hausdorff_distance_gauge.reset()
self._class_dice_gauge_on_reconstructed_iseg_images.reset()
self._class_dice_gauge_on_reconstructed_mrbrains_images.reset()
self._class_dice_gauge_on_reconstructed_abide_images.reset()
self._hausdorff_distance_gauge_on_reconstructed_iseg_images.reset()
self._hausdorff_distance_gauge_on_reconstructed_mrbrains_images.reset()
self._hausdorff_distance_gauge_on_reconstructed_abide_images.reset()
img_input = self._input_reconstructor.reconstruct_from_patches_3d()
img_gt = self._gt_reconstructor.reconstruct_from_patches_3d()
img_seg = self._segmentation_reconstructor.reconstruct_from_patches_3d()
save_rebuilt_image(self._current_epoch, self._save_folder, self._dataset_configs.keys(), img_input,
"Input")
save_rebuilt_image(self._current_epoch, self._save_folder, self._dataset_configs.keys(), img_gt,
"Ground_Truth")
save_rebuilt_image(self._current_epoch, self._save_folder, self._dataset_configs.keys(), img_seg,
"Segmented")
if self._training_config.build_augmented_images:
img_augmented_input = self._augmented_input_reconstructor.reconstruct_from_patches_3d()
img_augmented_normalized = self._augmented_normalized_reconstructor.reconstruct_from_patches_3d()
save_augmented_rebuilt_images(self._current_epoch, self._save_folder, self._dataset_configs.keys(),
img_augmented_input, img_augmented_normalized)
mean_mhd = []
for dataset in self._dataset_configs.keys():
self.custom_variables[
"Reconstructed Segmented {} Image".format(dataset)] = self._seg_slicer.get_colored_slice(
SliceType.AXIAL, np.expand_dims(img_seg[dataset], 0), 160).squeeze(0)
self.custom_variables[
"Reconstructed Ground Truth {} Image".format(dataset)] = self._seg_slicer.get_colored_slice(
SliceType.AXIAL, np.expand_dims(img_gt[dataset], 0), 160).squeeze(0)
self.custom_variables[
"Reconstructed Input {} Image".format(dataset)] = self._slicer.get_slice(
SliceType.AXIAL, np.expand_dims(img_input[dataset], 0), 160)
if self._training_config.build_augmented_images:
self.custom_variables[
"Reconstructed Augmented Input {} Image".format(dataset)] = self._slicer.get_slice(
SliceType.AXIAL, np.expand_dims(np.expand_dims(img_augmented_input[dataset], 0), 0), 160)
self.custom_variables[
"Reconstructed Augmented {} After Normalization".format(
dataset)] = self._seg_slicer.get_colored_slice(
SliceType.AXIAL,
np.expand_dims(np.expand_dims(img_augmented_normalized[dataset], 0), 0), 160).squeeze(0)
else:
self.custom_variables["Reconstructed Augmented Input {} Image".format(
dataset)] = np.zeros((224, 192))
self.custom_variables[
"Reconstructed Initial Noise {} Image".format(
dataset)] = np.zeros((224, 192))
self.custom_variables[
"Reconstructed Augmented {} After Normalization".format(
dataset)] = np.zeros((224, 192))
mean_mhd.append(mean_hausdorff_distance(
to_onehot(torch.tensor(img_gt[dataset], dtype=torch.long), num_classes=4),
to_onehot(torch.tensor(img_seg[dataset], dtype=torch.long), num_classes=4))[-3:].mean())
metric = self._model_trainers[0].compute_metrics(
to_onehot(torch.tensor(img_seg[dataset]).unsqueeze(0).long(), num_classes=4),
torch.tensor(img_gt[dataset]).unsqueeze(0).long())
self._class_dice_gauge_on_reconstructed_images.update(np.array(metric["Dice"]))
self._per_dataset_hausdorff_distance_gauge.update(np.array(mean_mhd))
if "iSEG" in img_seg:
metric = self._model_trainers[0].compute_metrics(
to_onehot(torch.tensor(img_seg["iSEG"]).unsqueeze(0).long(), num_classes=4),
torch.tensor(img_gt["iSEG"]).unsqueeze(0).long())
self._class_dice_gauge_on_reconstructed_iseg_images.update(np.array(metric["Dice"]))
self._hausdorff_distance_gauge_on_reconstructed_iseg_images.update(mean_hausdorff_distance(
to_onehot(torch.tensor(img_gt["iSEG"], dtype=torch.long), num_classes=4),
to_onehot(torch.tensor(img_seg["iSEG"], dtype=torch.long), num_classes=4))[-3:])
else:
self._class_dice_gauge_on_reconstructed_iseg_images.update(np.array([0.0, 0.0, 0.0]))
self._hausdorff_distance_gauge_on_reconstructed_iseg_images.update(np.array([0.0, 0.0, 0.0]))
if "MRBrainS" in img_seg:
metric = self._model_trainers[0].compute_metrics(
to_onehot(torch.tensor(img_seg["MRBrainS"]).unsqueeze(0).long(), num_classes=4),
torch.tensor(img_gt["MRBrainS"]).unsqueeze(0).long())
self._class_dice_gauge_on_reconstructed_mrbrains_images.update(np.array(metric["Dice"]))
self._hausdorff_distance_gauge_on_reconstructed_mrbrains_images.update(mean_hausdorff_distance(
to_onehot(torch.tensor(img_gt["MRBrainS"], dtype=torch.long), num_classes=4),
to_onehot(torch.tensor(img_seg["MRBrainS"], dtype=torch.long), num_classes=4))[-3:])
else:
self._class_dice_gauge_on_reconstructed_mrbrains_images.update(np.array([0.0, 0.0, 0.0]))
self._hausdorff_distance_gauge_on_reconstructed_mrbrains_images.update(np.array([0.0, 0.0, 0.0]))
if "ABIDE" in img_seg:
metric = self._model_trainers[0].compute_metrics(
to_onehot(torch.tensor(img_seg["ABIDE"]).unsqueeze(0).long(), num_classes=4),
torch.tensor(img_gt["ABIDE"]).unsqueeze(0).long())
self._class_dice_gauge_on_reconstructed_abide_images.update(np.array(metric["Dice"]))
self._hausdorff_distance_gauge_on_reconstructed_abide_images.update(mean_hausdorff_distance(
to_onehot(torch.tensor(img_gt["ABIDE"], dtype=torch.long), num_classes=4),
to_onehot(torch.tensor(img_seg["ABIDE"], dtype=torch.long), num_classes=4))[-3:])
else:
self._class_dice_gauge_on_reconstructed_abide_images.update(np.array([0.0, 0.0, 0.0]))
self._hausdorff_distance_gauge_on_reconstructed_abide_images.update(np.array([0.0, 0.0, 0.0]))
if "ABIDE" not in self._dataset_configs.keys():
self.custom_variables["Reconstructed Segmented ABIDE Image"] = np.zeros((224, 192))
self.custom_variables["Reconstructed Ground Truth ABIDE Image"] = np.zeros((224, 192))
self.custom_variables["Reconstructed Input ABIDE Image"] = np.zeros((224, 192))
if "iSEG" not in self._dataset_configs.keys():
self.custom_variables["Reconstructed Segmented iSEG Image"] = np.zeros((224, 192))
self.custom_variables["Reconstructed Ground Truth iSEG Image"] = np.zeros((224, 192))
self.custom_variables["Reconstructed Input iSEG Image"] = np.zeros((224, 192))
if "MRBrainS" not in self._dataset_configs.keys():
self.custom_variables["Reconstructed Segmented MRBrainS Image"] = np.zeros((224, 192))
self.custom_variables["Reconstructed Ground Truth MRBrainS Image"] = np.zeros((224, 192))
self.custom_variables["Reconstructed Input MRBrainS Image"] = np.zeros((224, 192))
self.custom_variables["Runtime"] = to_html_time(timedelta(seconds=time.time() - self._start_time))
if self._general_confusion_matrix_gauge._num_examples != 0:
self.custom_variables["Confusion Matrix"] = np.array(
np.fliplr(self._general_confusion_matrix_gauge.compute().cpu().detach().numpy()))
else:
self.custom_variables["Confusion Matrix"] = np.zeros((4, 4))
if self._iSEG_confusion_matrix_gauge._num_examples != 0:
self.custom_variables["iSEG Confusion Matrix"] = np.array(
np.fliplr(self._iSEG_confusion_matrix_gauge.compute().cpu().detach().numpy()))
else:
self.custom_variables["iSEG Confusion Matrix"] = np.zeros((4, 4))
if self._MRBrainS_confusion_matrix_gauge._num_examples != 0:
self.custom_variables["MRBrainS Confusion Matrix"] = np.array(
np.fliplr(self._MRBrainS_confusion_matrix_gauge.compute().cpu().detach().numpy()))
else:
self.custom_variables["MRBrainS Confusion Matrix"] = np.zeros((4, 4))
if self._ABIDE_confusion_matrix_gauge._num_examples != 0:
self.custom_variables["ABIDE Confusion Matrix"] = np.array(
np.fliplr(self._ABIDE_confusion_matrix_gauge.compute().cpu().detach().numpy()))
else:
self.custom_variables["ABIDE Confusion Matrix"] = np.zeros((4, 4))
self.custom_variables["Metric Table"] = to_html(["CSF", "Grey Matter", "White Matter"],
["DSC", "HD"],
[
self._class_dice_gauge_on_patches.compute() if self._class_dice_gauge_on_patches.has_been_updated() else np.array(
[0.0, 0.0, 0.0]),
self._class_hausdorff_distance_gauge.compute() if self._class_hausdorff_distance_gauge.has_been_updated() else np.array(
[0.0, 0.0, 0.0])
])
self.custom_variables[
"Dice score per class per epoch"] = self._class_dice_gauge_on_patches.compute() if self._class_dice_gauge_on_patches.has_been_updated() else np.array(
[0.0, 0.0, 0.0])
self.custom_variables[
"Dice score per class per epoch on reconstructed image"] = self._class_dice_gauge_on_reconstructed_images.compute() if self._class_dice_gauge_on_reconstructed_images.has_been_updated() else np.array(
[0.0, 0.0, 0.0])
self.custom_variables[
"Dice score per class per epoch on reconstructed iSEG image"] = self._class_dice_gauge_on_reconstructed_iseg_images.compute() if self._class_dice_gauge_on_reconstructed_iseg_images.has_been_updated() else np.array(
[0.0, 0.0, 0.0])
self.custom_variables[
"Dice score per class per epoch on reconstructed MRBrainS image"] = self._class_dice_gauge_on_reconstructed_mrbrains_images.compute() if self._class_dice_gauge_on_reconstructed_mrbrains_images.has_been_updated() else np.array(
[0.0, 0.0, 0.0])
self.custom_variables[
"Dice score per class per epoch on reconstructed ABIDE image"] = self._class_dice_gauge_on_reconstructed_abide_images.compute() if self._class_dice_gauge_on_reconstructed_abide_images.has_been_updated() else np.array(
[0.0, 0.0, 0.0])
self.custom_variables[
"Hausdorff Distance per class per epoch on reconstructed iSEG image"] = self._hausdorff_distance_gauge_on_reconstructed_iseg_images.compute() if self._hausdorff_distance_gauge_on_reconstructed_iseg_images.has_been_updated() else np.array(
[0.0, 0.0, 0.0])
self.custom_variables[
"Hausdorff Distance per class per epoch on reconstructed MRBrainS image"] = self._hausdorff_distance_gauge_on_reconstructed_mrbrains_images.compute() if self._hausdorff_distance_gauge_on_reconstructed_mrbrains_images.has_been_updated() else np.array(
[0.0, 0.0, 0.0])
self.custom_variables[
"Hausdorff Distance per class per epoch on reconstructed ABIDE image"] = self._hausdorff_distance_gauge_on_reconstructed_abide_images.compute() if self._hausdorff_distance_gauge_on_reconstructed_abide_images.has_been_updated() else np.array(
[0.0, 0.0, 0.0])
if self._valid_dice_gauge.compute() > self._previous_mean_dice:
new_table = to_html_per_dataset(
["CSF", "Grey Matter", "White Matter"],
["DSC", "HD"],
[
[
self._iSEG_dice_gauge.compute() if self._iSEG_dice_gauge.has_been_updated() else np.array(
[0.0, 0.0, 0.0]),
self._iSEG_hausdorff_gauge.compute() if self._iSEG_hausdorff_gauge.has_been_updated() else np.array(
[0.0, 0.0, 0.0])],
[
self._MRBrainS_dice_gauge.compute() if self._MRBrainS_dice_gauge.has_been_updated() else np.array(
[0.0, 0.0, 0.0]),
self._MRBrainS_hausdorff_gauge.compute() if self._MRBrainS_hausdorff_gauge.has_been_updated() else np.array(
[0.0, 0.0, 0.0])],
[
self._ABIDE_dice_gauge.compute() if self._ABIDE_dice_gauge.has_been_updated() else np.array(
[0.0, 0.0, 0.0]),
self._ABIDE_hausdorff_gauge.compute() if self._ABIDE_hausdorff_gauge.has_been_updated() else np.array(
[0.0, 0.0, 0.0])]],
["iSEG", "MRBrainS", "ABIDE"])
self.custom_variables["Per-Dataset Metric Table"] = new_table
self._previous_mean_dice = self._valid_dice_gauge.compute()
self._previous_per_dataset_table = new_table
else:
self.custom_variables["Per-Dataset Metric Table"] = self._previous_per_dataset_table
self._valid_dice_gauge.reset()
self.custom_variables["Mean Hausdorff Distance"] = [
self._class_hausdorff_distance_gauge.compute().mean() if self._class_hausdorff_distance_gauge.has_been_updated() else np.array(
[0.0])]
self.custom_variables[
"Per Dataset Mean Hausdorff Distance"] = self._per_dataset_hausdorff_distance_gauge.compute()
def _update_image_plots(self, phase, inputs, segmenter_predictions, target, dataset_ids):
inputs = torch.nn.functional.interpolate(inputs, scale_factor=5, mode="trilinear",
align_corners=True).numpy()
segmenter_predictions = torch.nn.functional.interpolate(
torch.argmax(torch.nn.functional.softmax(segmenter_predictions, dim=1), dim=1, keepdim=True).float(),
scale_factor=5, mode="nearest").numpy()
target = torch.nn.functional.interpolate(target.float(), scale_factor=5, mode="nearest").numpy()
self.custom_variables[
"{} Input Batch Process {}".format(phase, self._run_config.local_rank)] = self._slicer.get_slice(
SliceType.AXIAL, inputs, inputs.shape[2] // 2)
self.custom_variables[
"{} Segmented Batch Process {}".format(phase,
self._run_config.local_rank)] = self._seg_slicer.get_colored_slice(
SliceType.AXIAL, segmenter_predictions, segmenter_predictions.shape[2] // 2)
self.custom_variables[
"{} Segmentation Ground Truth Batch Process {}".format(phase,
self._run_config.local_rank)] = self._seg_slicer.get_colored_slice(
SliceType.AXIAL, target, target.shape[2] // 2)
self.custom_variables[
"{} Label Map Batch Process {}".format(phase,
self._run_config.local_rank)] = self._label_mapper.get_label_map(
dataset_ids)
def _update_histograms(self, inputs, target):
self.custom_variables["Input Intensity Histogram"] = flatten(inputs.cpu().detach())
self.custom_variables["Background Input Intensity Histogram"] = inputs[
torch.where(target[IMAGE_TARGET] == 0)].cpu().detach()
self.custom_variables["CSF Input Intensity Histogram"] = inputs[
torch.where(target[IMAGE_TARGET] == 1)].cpu().detach()
self.custom_variables["GM Input Intensity Histogram"] = inputs[
torch.where(target[IMAGE_TARGET] == 2)].cpu().detach()
self.custom_variables["WM Input Intensity Histogram"] = inputs[
torch.where(target[IMAGE_TARGET] == 3)].cpu().detach()
def __init__(self, root_dirs):
"""
Pre-processing pipeline constructor.
Args:
root_dir: Root directory where all files are located.
"""
self._root_dirs = root_dirs
self._mean_gauge_iSEG = AverageGauge()
self._mean_gauge_MRBrainS = AverageGauge()
self._mean_gauge_ABIDE = AverageGauge()
self._std_gauge_iSEG = AverageGauge()
self._std_gauge_MRBrainS = AverageGauge()
self._std_gauge_ABIDE = AverageGauge()
self._dataset_mean_iSEG = 0.0
self._dataset_mean_MRBrainS = 0.0
self._dataset_mean_ABIDE = 0.0
self._dataset_std_iSEG = 0.0
self._dataset_std_MRBrainS = 0.0
self._dataset_std_ABIDE = 0.0
class MultipleDatasetPipeline(AbstractPreProcessingPipeline):
"""
An ABIDE data pre-processing pipeline. Extract necessary tissues for brain segmentation among other transformations.
"""
LOGGER = logging.getLogger("PreProcessingPipeline")
PATCH_SIZE = (1, 32, 32, 32)
STEP = (1, 4, 4, 4)
def __init__(self, root_dirs):
"""
Pre-processing pipeline constructor.
Args:
root_dir: Root directory where all files are located.
"""
self._root_dirs = root_dirs
self._mean_gauge_iSEG = AverageGauge()
self._mean_gauge_MRBrainS = AverageGauge()
self._mean_gauge_ABIDE = AverageGauge()
self._std_gauge_iSEG = AverageGauge()
self._std_gauge_MRBrainS = AverageGauge()
self._std_gauge_ABIDE = AverageGauge()
self._dataset_mean_iSEG = 0.0
self._dataset_mean_MRBrainS = 0.0
self._dataset_mean_ABIDE = 0.0
self._dataset_std_iSEG = 0.0
self._dataset_std_MRBrainS = 0.0
self._dataset_std_ABIDE = 0.0
def run(self, prefix: str = ""):
images_T1 = natural_sort(
extract_file_paths(os.path.join(self._root_dirs["iSEG"], "T1")))
labels = natural_sort(
extract_file_paths(os.path.join(self._root_dirs["iSEG"], "label")))
files = np.stack((np.array(images_T1), np.array(labels)), axis=1)
self._dataset_mean_iSEG = np.mean(
self._dispatch_jobs_in_pool(files, 5, self._get_mean_iseg))
self._dataset_std_iSEG = np.mean(
self._dispatch_jobs_in_pool(files, 5, self._get_std_iseg))
files = list()
for subject in sorted(
os.listdir(os.path.join(self._root_dirs["MRBrainS"]))):
files.append(
extract_file_paths(
os.path.join(self._root_dirs["MRBrainS"], subject)))
self._dataset_mean_MRBrainS = np.mean(
self._dispatch_jobs_in_pool(files, 5, self._get_mean_mrbrains))
self._dataset_std_MRBrainS = np.mean(
self._dispatch_jobs_in_pool(files, 5, self._get_std_mrbrains))
files = pandas.read_csv(self._root_dirs["ABIDE"])
images_T1 = np.asarray(files["T1"])
labels = np.asarray(files["labels"])
files = np.stack((np.array(images_T1), np.array(labels)), axis=1)
self._dataset_mean_ABIDE = np.mean(
self._dispatch_jobs_in_pool(files, 8, self._get_mean_abide))
self._dataset_std_ABIDE = np.mean(
self._dispatch_jobs_in_pool(files, 8, self._get_std_abide))
print("Triple Dataset mean: {}".format(
np.mean([
self._dataset_mean_iSEG, self._dataset_mean_MRBrainS,
self._dataset_mean_ABIDE
])))
print("Triple Dataset std: {}".format(
np.sqrt(
np.mean([
self._dataset_std_iSEG, self._dataset_std_MRBrainS,
self._dataset_std_ABIDE
]))))
print("Dual Dataset mean: {}".format(
np.mean([self._dataset_mean_iSEG, self._dataset_mean_MRBrainS])))
print("Dual Dataset std: {}".format(
np.sqrt(
np.mean([self._dataset_std_iSEG,
self._dataset_std_MRBrainS]))))
def _get_mean_iseg(self, files):
for file in files:
self.LOGGER.info("Processing file {}".format(file[1]))
label = self._to_numpy_array(file[1])
self.LOGGER.info("Processing file {}".format(file[0]))
t1 = self._to_numpy_array(file[0])
patches = self._extract_patches(t1, label, self.PATCH_SIZE,
self.STEP)
patches = list(map(lambda patch: patch.slice, patches))
for patch in patches:
mean = np.mean(patch)
self._mean_gauge_iSEG.update(mean)
return self._mean_gauge_iSEG.compute()
def _get_std_iseg(self, files):
for file in files:
self.LOGGER.info("Processing file {}".format(file[1]))
label = self._to_numpy_array(file[1])
self.LOGGER.info("Processing file {}".format(file[0]))
t1 = self._to_numpy_array(file[0])
patches = self._extract_patches(t1, label, self.PATCH_SIZE,
self.STEP)
patches = list(map(lambda patch: patch.slice, patches))
for patch in patches:
std = np.array(((patch - self._dataset_mean_iSEG)**2).mean())
self._std_gauge_iSEG.update(std)
return self._std_gauge_iSEG.compute()
def _get_mean_mrbrains(self, files):
for file in files:
self.LOGGER.info("Processing file {}".format(
file[LABELSFORTESTING]))
label_for_testing = MRBrainSPipeline.resample_to_template(
file[LABELSFORTESTING], file[T1_1MM], interpolation="linear")
label_for_testing = self._to_numpy_array(label_for_testing)
label_for_testing = label_for_testing.transpose((3, 0, 1, 2))
label_for_testing = np.rot90(label_for_testing, axes=(1, -2))
self.LOGGER.info("Processing file {}".format(file[T1]))
t1 = MRBrainSPipeline.resample_to_template(
file[T1], file[T1_1MM], interpolation="continuous")
t1 = self._to_numpy_array(t1)
t1 = t1.transpose((3, 0, 1, 2))
t1 = np.rot90(t1, axes=(1, -2))
t1 = MRBrainSPipeline.apply_mask(t1, label_for_testing)
patches = self._extract_patches(t1, label_for_testing,
self.PATCH_SIZE, self.STEP)
patches = list(map(lambda patch: patch.slice, patches))
for patch in patches:
mean = np.mean(patch)
self._mean_gauge_MRBrainS.update(mean)
return self._mean_gauge_MRBrainS.compute()
def _get_std_mrbrains(self, files):
for file in files:
self.LOGGER.info("Processing file {}".format(
file[LABELSFORTESTING]))
label_for_testing = MRBrainSPipeline.resample_to_template(
file[LABELSFORTESTING], file[T1_1MM], interpolation="linear")
label_for_testing = self._to_numpy_array(label_for_testing)
label_for_testing = label_for_testing.transpose((3, 0, 1, 2))
label_for_testing = np.rot90(label_for_testing, axes=(1, -2))
self.LOGGER.info("Processing file {}".format(file[T1]))
t1 = MRBrainSPipeline.resample_to_template(
file[T1], file[T1_1MM], interpolation="continuous")
t1 = self._to_numpy_array(t1)
t1 = t1.transpose((3, 0, 1, 2))
t1 = np.rot90(t1, axes=(1, -2))
t1 = MRBrainSPipeline.apply_mask(t1, label_for_testing)
patches = self._extract_patches(t1, label_for_testing,
self.PATCH_SIZE, self.STEP)
patches = list(map(lambda patch: patch.slice, patches))
for patch in patches:
std = np.array(
((patch - self._dataset_mean_MRBrainS)**2).mean())
self._std_gauge_MRBrainS.update(std)
return self._std_gauge_MRBrainS.compute()
def _get_mean_abide(self, files):
for file in files:
self.LOGGER.info("Processing file {}".format(file[1]))
label = self._to_numpy_array(file[1])
self.LOGGER.info("Processing file {}".format(file[0]))
t1 = self._to_numpy_array(file[0])
patches = self._extract_patches(t1, label, self.PATCH_SIZE,
self.STEP)
patches = list(map(lambda patch: patch.slice, patches))
for patch in patches:
mean = np.mean(patch)
self._mean_gauge_ABIDE.update(mean)
return self._mean_gauge_ABIDE.compute()
def _get_std_abide(self, files):
for file in files:
self.LOGGER.info("Processing file {}".format(file[1]))
label = self._to_numpy_array(file[1])
self.LOGGER.info("Processing file {}".format(file[0]))
t1 = self._to_numpy_array(file[0])
patches = self._extract_patches(t1, label, self.PATCH_SIZE,
self.STEP)
patches = list(map(lambda patch: patch.slice, patches))
for patch in patches:
std = np.array(((patch - self._dataset_mean_ABIDE)**2).mean())
self._std_gauge_ABIDE.update(std)
return self._std_gauge_ABIDE.compute()
def _to_numpy_array(self, file):
transform_ = transforms.Compose([ToNumpyArray()])
return transform_(file)
def _extract_patches(self, image, label, patch_size, step):
transforms_ = transforms.Compose(
[PadToPatchShape(patch_size=patch_size, step=step)])
transformed_image = transforms_(image)
transformed_label = transforms_(label)
return MultipleDatasetPipeline.get_filtered_patches(
transformed_image, transformed_label, patch_size, step)
class ABIDEPreprocessingPipeline(AbstractPreProcessingPipeline):
"""
An ABIDE data pre-processing pipeline. Extract necessary tissues for brain segmentation among other transformations.
"""
LOGGER = logging.getLogger("PreProcessingPipeline")
PATCH_SIZE = (1, 32, 32, 32)
STEP = (1, 4, 4, 4)
def __init__(self, csv_path):
"""
Pre-processing pipeline constructor.
Args:
root_dir: Root directory where all files are located.
"""
self._csv_path = csv_path
self._mean_gauge = AverageGauge()
self._std_gauge = AverageGauge()
self._dataset_mean = 0.0
def run(self, prefix: str = ""):
files = pandas.read_csv(self._csv_path)
images_T1 = np.asarray(files["T1"])
labels = np.asarray(files["labels"])
files = np.stack((np.array(images_T1), np.array(labels)), axis=1)
means = self._dispatch_jobs_in_pool(files, 8, self._find_average)
self._dataset_mean = np.mean(means)
std = self._dispatch_jobs_in_pool(files, 8, self._find_std)
std = np.sqrt(np.mean(std))
print("Dataset mean : {}".format(self._dataset_mean))
print("Dataset std : {}".format(std))
def _find_average(self, files):
for file in files:
self.LOGGER.info("Processing file {}".format(file[1]))
label = self._to_numpy_array(file[1])
self.LOGGER.info("Processing file {}".format(file[0]))
t1 = self._to_numpy_array(file[0])
patches = self._extract_patches(t1, label, self.PATCH_SIZE,
self.STEP)
patches = list(map(lambda patch: patch.slice, patches))
for patch in patches:
mean = np.mean(patch)
self._mean_gauge.update(mean)
return self._mean_gauge.compute()
def _find_std(self, files):
for file in files:
self.LOGGER.info("Processing file {}".format(file[1]))
label = self._to_numpy_array(file[1])
self.LOGGER.info("Processing file {}".format(file[0]))
t1 = self._to_numpy_array(file[0])
patches = self._extract_patches(t1, label, self.PATCH_SIZE,
self.STEP)
patches = list(map(lambda patch: patch.slice, patches))
for patch in patches:
std = np.array(((patch - self._dataset_mean)**2).mean())
self._std_gauge.update(std)
return self._std_gauge.compute()
def _do_job(self, files):
std = np.sqrt(self._std_gauge.compute())
print("Mean: {}".format(np.mean(self._mean_gauge.compute())))
print("Std: {}".format(np.mean(std)))
def _to_numpy_array(self, file):
transform_ = transforms.Compose([ToNumpyArray()])
return transform_(file)
def _extract_patches(self, image, label, patch_size, step):
transforms_ = transforms.Compose(
[PadToPatchShape(patch_size=patch_size, step=step)])
transformed_image = transforms_(image)
transformed_label = transforms_(label)
return ABIDEPreprocessingPipeline.get_filtered_patches(
transformed_image, transformed_label, patch_size, step)
class DualUNetTrainer(Trainer):
def __init__(self, training_config, model_trainers: List[ModelTrainer],
train_data_loader: DataLoader, valid_data_loader: DataLoader,
test_data_loader: DataLoader,
reconstruction_datasets: List[Dataset],
normalize_reconstructors: list, input_reconstructors: list,
segmentation_reconstructors: list,
augmented_reconstructors: list, gt_reconstructors: list,
run_config: RunConfiguration, dataset_config: dict,
save_folder: str):
super(DualUNetTrainer,
self).__init__("DualUNetTrainer", train_data_loader,
valid_data_loader, test_data_loader,
model_trainers, run_config)
self._training_config = training_config
self._run_config = run_config
self._dataset_configs = dataset_config
self._patience_segmentation = training_config.patience_segmentation
self._slicer = ImageSlicer()
self._seg_slicer = SegmentationSlicer()
self._label_mapper = LabelMapper()
self._reconstruction_datasets = reconstruction_datasets
self._normalize_reconstructors = normalize_reconstructors
self._input_reconstructors = input_reconstructors
self._gt_reconstructors = gt_reconstructors
self._segmentation_reconstructors = segmentation_reconstructors
self._augmented_reconstructors = augmented_reconstructors
self._class_hausdorff_distance_gauge = AverageGauge()
self._mean_hausdorff_distance_gauge = AverageGauge()
self._per_dataset_hausdorff_distance_gauge = AverageGauge()
self._iSEG_dice_gauge = AverageGauge()
self._MRBrainS_dice_gauge = AverageGauge()
self._ABIDE_dice_gauge = AverageGauge()
self._iSEG_hausdorff_gauge = AverageGauge()
self._MRBrainS_hausdorff_gauge = AverageGauge()
self._ABIDE_hausdorff_gauge = AverageGauge()
self._valid_dice_gauge = AverageGauge()
self._class_dice_gauge_on_patches = AverageGauge()
self._class_dice_gauge_on_reconstructed_images = AverageGauge()
self._class_dice_gauge_on_reconstructed_iseg_images = AverageGauge()
self._class_dice_gauge_on_reconstructed_mrbrains_images = AverageGauge(
)
self._class_dice_gauge_on_reconstructed_abide_images = AverageGauge()
self._hausdorff_distance_gauge_on_reconstructed_iseg_images = AverageGauge(
)
self._hausdorff_distance_gauge_on_reconstructed_mrbrains_images = AverageGauge(
)
self._hausdorff_distance_gauge_on_reconstructed_abide_images = AverageGauge(
)
self._js_div_inputs_gauge = AverageGauge()
self._js_div_gen_gauge = AverageGauge()
self._general_confusion_matrix_gauge = ConfusionMatrix(num_classes=4)
self._iSEG_confusion_matrix_gauge = ConfusionMatrix(num_classes=4)
self._MRBrainS_confusion_matrix_gauge = ConfusionMatrix(num_classes=4)
self._ABIDE_confusion_matrix_gauge = ConfusionMatrix(num_classes=4)
self._previous_mean_dice = 0.0
self._previous_per_dataset_table = ""
self._start_time = time.time()
self._save_folder = save_folder
self._sampler = Sampler(0.33)
self._is_sliced = True if isinstance(self._reconstruction_datasets[0],
SliceDataset) else False
print("Total number of parameters: {}".format(
sum(p.numel()
for p in self._model_trainers[GENERATOR].parameters()) +
sum(p.numel()
for p in self._model_trainers[SEGMENTER].parameters())))
pynvml.nvmlInit()
def _train_g(self, G: ModelTrainer, real, backward=True):
G.zero_grad()
gen_pred = torch.nn.functional.sigmoid(G.forward(real))
loss_G = G.compute_and_update_train_loss("MSELoss", gen_pred, real)
metric = G.compute_metric("MeanSquaredError", gen_pred, real)
G.update_train_metric("MeanSquaredError", metric / 32768)
if backward:
loss_G.backward()
G.step()
return gen_pred
def _valid_g(self, G: ModelTrainer, real):
gen_pred = torch.nn.functional.sigmoid(G.forward(real))
G.compute_and_update_valid_loss("MSELoss", gen_pred, real)
metric = G.compute_metric("MeanSquaredError", gen_pred, real)
G.update_valid_metric("MeanSquaredError", metric / 32768)
return gen_pred
def _test_g(self, G: ModelTrainer, real):
gen_pred = torch.nn.functional.sigmoid(G.forward(real))
G.compute_and_update_test_loss("MSELoss", gen_pred, real)
metric = G.compute_metric("MeanSquaredError", gen_pred, real)
G.update_test_metric("MeanSquaredError", metric / 32768)
return gen_pred
def _train_s(self, S: ModelTrainer, inputs, target, backward=True):
S.zero_grad()
target_ohe = to_onehot(torch.squeeze(target, dim=1).long(),
num_classes=4)
target = torch.squeeze(target, dim=1).long()
seg_pred = torch.nn.functional.softmax(S.forward(inputs), dim=1)
loss_S = S.compute_loss("DiceLoss", seg_pred, target_ohe)
S.update_train_loss("DiceLoss", loss_S.mean())
metrics = S.compute_metrics(seg_pred, target)
metrics["Dice"] = metrics["Dice"].mean()
metrics["IoU"] = metrics["IoU"].mean()
S.update_train_metrics(metrics)
if backward:
loss_S.mean().backward()
S.step()
return seg_pred, loss_S
def _valid_s(self, S: ModelTrainer, inputs, target):
target_ohe = to_onehot(torch.squeeze(target, dim=1).long(),
num_classes=4)
target = torch.squeeze(target, dim=1).long()
seg_pred = torch.nn.functional.softmax(S.forward(inputs), dim=1)
loss_S = S.compute_loss("DiceLoss", seg_pred, target_ohe)
S.update_valid_loss("DiceLoss", loss_S.mean())
metrics = S.compute_metrics(seg_pred, target)
metrics["Dice"] = metrics["Dice"].mean()
metrics["IoU"] = metrics["IoU"].mean()
S.update_valid_metrics(metrics)
return seg_pred, loss_S
def _test_s(self, S: ModelTrainer, inputs, target,
metric_gauge: AverageGauge):
target_ohe = to_onehot(torch.squeeze(target, dim=1).long(),
num_classes=4)
target = torch.squeeze(target, dim=1).long()
seg_pred = torch.nn.functional.softmax(S.forward(inputs), dim=1)
loss_S = S.compute_loss("DiceLoss", seg_pred, target_ohe)
S.update_test_loss("DiceLoss", loss_S.mean())
metrics = S.compute_metrics(seg_pred, target)
metric_gauge.update(np.array(metrics["Dice"]))
metrics["Dice"] = metrics["Dice"].mean()
metrics["IoU"] = metrics["IoU"].mean()
S.update_test_metrics(metrics)
return seg_pred, loss_S
def train_step(self, inputs, target):
inputs, target = self._sampler(inputs, target)
if self._should_activate_autoencoder():
gen_pred = self._train_g(self._model_trainers[GENERATOR],
inputs[NON_AUGMENTED_INPUTS])
seg_pred, _ = self._train_s(
self._model_trainers[SEGMENTER], inputs[NON_AUGMENTED_INPUTS],
target[NON_AUGMENTED_TARGETS][IMAGE_TARGET])
if self.current_train_step % 500 == 0:
self._update_image_plots(
self.phase, inputs[NON_AUGMENTED_INPUTS].cpu().detach(),
gen_pred.cpu().detach(),
seg_pred.cpu().detach(),
target[NON_AUGMENTED_TARGETS][IMAGE_TARGET].cpu().detach(),
target[NON_AUGMENTED_TARGETS][DATASET_ID].cpu().detach())
if self._should_activate_segmentation():
gen_pred = self._train_g(self._model_trainers[GENERATOR],
inputs[AUGMENTED_INPUTS],
backward=False)
seg_pred, loss_S = self._train_s(
self._model_trainers[SEGMENTER],
gen_pred,
target[AUGMENTED_TARGETS][IMAGE_TARGET],
backward=False)
loss_S.mean().backward()
self._model_trainers[SEGMENTER].step()
self._model_trainers[GENERATOR].step()
if self.current_train_step % 500 == 0:
self._update_image_plots(
self.phase, inputs[AUGMENTED_INPUTS].cpu().detach(),
gen_pred.cpu().detach(),
seg_pred.cpu().detach(),
target[AUGMENTED_TARGETS][IMAGE_TARGET].cpu().detach(),
target[AUGMENTED_TARGETS][DATASET_ID].cpu().detach())
def validate_step(self, inputs, target):
if self._should_activate_autoencoder():
gen_pred = self._valid_g(self._model_trainers[GENERATOR],
inputs[NON_AUGMENTED_INPUTS])
seg_pred, _ = self._valid_s(self._model_trainers[SEGMENTER],
inputs[NON_AUGMENTED_INPUTS],
target[IMAGE_TARGET])
if self._should_activate_segmentation():
gen_pred = self._valid_g(self._model_trainers[GENERATOR],
inputs[AUGMENTED_INPUTS])
seg_pred, _ = self._valid_s(self._model_trainers[SEGMENTER],
gen_pred, target[IMAGE_TARGET])
if self.current_valid_step % 100 == 0:
self._update_image_plots(
self.phase, inputs[NON_AUGMENTED_INPUTS].cpu().detach(),
gen_pred.cpu().detach(),
seg_pred.cpu().detach(), target[IMAGE_TARGET].cpu().detach(),
target[DATASET_ID].cpu().detach())
def test_step(self, inputs, target):
if self._should_activate_autoencoder():
gen_pred = self._test_g(self._model_trainers[GENERATOR],
inputs[NON_AUGMENTED_INPUTS])
seg_pred, _ = self._test_s(self._model_trainers[SEGMENTER],
inputs[NON_AUGMENTED_INPUTS],
target[IMAGE_TARGET],
self._class_dice_gauge_on_patches)
if self._should_activate_segmentation():
gen_pred = self._test_g(self._model_trainers[GENERATOR],
inputs[AUGMENTED_INPUTS])
seg_pred, loss_S = self._test_s(self._model_trainers[SEGMENTER],
gen_pred, target[IMAGE_TARGET],
self._class_dice_gauge_on_patches)
if seg_pred[torch.where(
target[DATASET_ID] == ISEG_ID)].shape[0] != 0:
self._iSEG_dice_gauge.update(
np.array(self._model_trainers[SEGMENTER].compute_metrics(
torch.nn.functional.softmax(seg_pred[torch.where(
target[DATASET_ID] == ISEG_ID)],
dim=1),
torch.squeeze(target[IMAGE_TARGET][torch.where(
target[DATASET_ID] == ISEG_ID)],
dim=1).long())["Dice"].numpy()))
self._iSEG_hausdorff_gauge.update(
mean_hausdorff_distance(
to_onehot(torch.argmax(torch.nn.functional.softmax(
seg_pred[torch.where(
target[DATASET_ID] == ISEG_ID)],
dim=1),
dim=1),
num_classes=4),
to_onehot(torch.squeeze(
target[IMAGE_TARGET][torch.where(
target[DATASET_ID] == ISEG_ID)],
dim=1).long(),
num_classes=4))[-3:])
self._iSEG_confusion_matrix_gauge.update(
(to_onehot(torch.argmax(torch.nn.functional.softmax(
seg_pred[torch.where(target[DATASET_ID] == ISEG_ID)],
dim=1),
dim=1,
keepdim=False),
num_classes=4),
torch.squeeze(target[IMAGE_TARGET][torch.where(
target[DATASET_ID] == ISEG_ID)].long(),
dim=1)))
else:
self._iSEG_dice_gauge.update(np.zeros((3, )))
self._iSEG_hausdorff_gauge.update(np.zeros((3, )))
if seg_pred[torch.where(
target[DATASET_ID] == MRBRAINS_ID)].shape[0] != 0:
self._MRBrainS_dice_gauge.update(
np.array(self._model_trainers[SEGMENTER].compute_metrics(
torch.nn.functional.softmax(seg_pred[torch.where(
target[DATASET_ID] == MRBRAINS_ID)],
dim=1),
torch.squeeze(target[IMAGE_TARGET][torch.where(
target[DATASET_ID] == MRBRAINS_ID)],
dim=1).long())["Dice"].numpy()))
self._MRBrainS_hausdorff_gauge.update(
mean_hausdorff_distance(
to_onehot(torch.argmax(torch.nn.functional.softmax(
seg_pred[torch.where(
target[DATASET_ID] == MRBRAINS_ID)],
dim=1),
dim=1),
num_classes=4),
to_onehot(torch.squeeze(
target[IMAGE_TARGET][torch.where(
target[DATASET_ID] == MRBRAINS_ID)],
dim=1).long(),
num_classes=4))[-3:])
self._MRBrainS_confusion_matrix_gauge.update(
(to_onehot(torch.argmax(torch.nn.functional.softmax(
seg_pred[torch.where(
target[DATASET_ID] == MRBRAINS_ID)],
dim=1),
dim=1,
keepdim=False),
num_classes=4),
torch.squeeze(target[IMAGE_TARGET][torch.where(
target[DATASET_ID] == MRBRAINS_ID)].long(),
dim=1)))
else:
self._MRBrainS_dice_gauge.update(np.zeros((3, )))
self._MRBrainS_hausdorff_gauge.update(np.zeros((3, )))
if seg_pred[torch.where(
target[DATASET_ID] == ABIDE_ID)].shape[0] != 0:
self._ABIDE_dice_gauge.update(
np.array(self._model_trainers[SEGMENTER].compute_metrics(
torch.nn.functional.softmax(seg_pred[torch.where(
target[DATASET_ID] == ABIDE_ID)],
dim=1),
torch.squeeze(target[IMAGE_TARGET][torch.where(
target[DATASET_ID] == ABIDE_ID)],
dim=1).long())["Dice"].numpy()))
self._ABIDE_hausdorff_gauge.update(
mean_hausdorff_distance(
to_onehot(torch.argmax(torch.nn.functional.softmax(
seg_pred[torch.where(
target[DATASET_ID] == ABIDE_ID)],
dim=1),
dim=1),
num_classes=4),
to_onehot(torch.squeeze(
target[IMAGE_TARGET][torch.where(
target[DATASET_ID] == ABIDE_ID)],
dim=1).long(),
num_classes=4))[-3:])
self._ABIDE_confusion_matrix_gauge.update(
(to_onehot(torch.argmax(torch.nn.functional.softmax(
seg_pred[torch.where(target[DATASET_ID] == ABIDE_ID)],
dim=1),
dim=1,
keepdim=False),
num_classes=4),
torch.squeeze(target[IMAGE_TARGET][torch.where(
target[DATASET_ID] == ABIDE_ID)].long(),
dim=1)))
self._class_hausdorff_distance_gauge.update(
mean_hausdorff_distance(
to_onehot(torch.argmax(torch.nn.functional.softmax(
seg_pred, dim=1),
dim=1),
num_classes=4),
to_onehot(torch.squeeze(target[IMAGE_TARGET],
dim=1).long(),
num_classes=4))[-3:])
self._general_confusion_matrix_gauge.update(
(to_onehot(torch.argmax(torch.nn.functional.softmax(seg_pred,
dim=1),
dim=1,
keepdim=False),
num_classes=4),
torch.squeeze(target[IMAGE_TARGET].long(), dim=1)))
inputs_reshaped = inputs[AUGMENTED_INPUTS].reshape(
inputs[AUGMENTED_INPUTS].shape[0],
inputs[AUGMENTED_INPUTS].shape[1] *
inputs[AUGMENTED_INPUTS].shape[2] *
inputs[AUGMENTED_INPUTS].shape[3] *
inputs[AUGMENTED_INPUTS].shape[4])
c, d, h, w = inputs[AUGMENTED_INPUTS].shape[1], inputs[AUGMENTED_INPUTS].shape[2], \
inputs[AUGMENTED_INPUTS].shape[3], inputs[AUGMENTED_INPUTS].shape[4]
hist_inputs = torch.cat([
torch.histc(inputs[AUGMENTED_INPUTS][i].view(1, c * d * h * w),
bins=256,
min=0,
max=1).unsqueeze(0)
for i in range(inputs[0].shape[0])
]).unsqueeze(0)
hist_inputs = hist_inputs / (c * d * h * w)
hist_inputs = torch.nn.Softmax(dim=2)(hist_inputs)
hist_gen = torch.cat([
torch.histc(gen_pred[i].view(1, c * d * h * w),
bins=256,
min=0,
max=1).unsqueeze(0)
for i in range(gen_pred.shape[0])
]).unsqueeze(0)
hist_gen = hist_gen / (c * d * h * w)
hist_gen = torch.nn.Softmax(dim=2)(hist_gen)
self._js_div_inputs_gauge.update(js_div(hist_inputs).item())
self._js_div_gen_gauge.update(js_div(hist_gen).item())
if self.current_test_step % 100 == 0:
self._update_histograms(inputs[NON_AUGMENTED_INPUTS], target,
gen_pred)
self._update_image_plots(
self.phase, inputs[NON_AUGMENTED_INPUTS].cpu().detach(),
gen_pred.cpu().detach(),
seg_pred.cpu().detach(), target[IMAGE_TARGET].cpu().detach(),
target[DATASET_ID].cpu().detach())
def scheduler_step(self):
self._model_trainers[GENERATOR].scheduler_step()
self._model_trainers[SEGMENTER].scheduler_step()
def on_epoch_begin(self):
self._class_hausdorff_distance_gauge.reset()
self._mean_hausdorff_distance_gauge.reset()
self._iSEG_dice_gauge.reset()
self._MRBrainS_dice_gauge.reset()
self._ABIDE_dice_gauge.reset()
self._iSEG_hausdorff_gauge.reset()
self._MRBrainS_hausdorff_gauge.reset()
self._ABIDE_hausdorff_gauge.reset()
self._class_dice_gauge_on_patches.reset()
self._js_div_inputs_gauge.reset()
self._js_div_gen_gauge.reset()
self._general_confusion_matrix_gauge.reset()
self._iSEG_confusion_matrix_gauge.reset()
self._MRBrainS_confusion_matrix_gauge.reset()
self._ABIDE_confusion_matrix_gauge.reset()
if self._current_epoch == self._training_config.patience_segmentation:
self._model_trainers[GENERATOR].optimizer_lr = 0.001
def on_test_epoch_end(self):
if self.epoch % 10 == 0:
self._per_dataset_hausdorff_distance_gauge.reset()
self._class_dice_gauge_on_reconstructed_iseg_images.reset()
self._class_dice_gauge_on_reconstructed_mrbrains_images.reset()
self._class_dice_gauge_on_reconstructed_abide_images.reset()
self._hausdorff_distance_gauge_on_reconstructed_iseg_images.reset()
self._hausdorff_distance_gauge_on_reconstructed_mrbrains_images.reset(
)
self._hausdorff_distance_gauge_on_reconstructed_abide_images.reset(
)
all_patches, ground_truth_patches = get_all_patches(
self._reconstruction_datasets, self._is_sliced)
img_input = rebuild_image(self._dataset_configs.keys(),
all_patches, self._input_reconstructors)
img_gt = rebuild_image(self._dataset_configs.keys(),
ground_truth_patches,
self._gt_reconstructors)
img_norm = rebuild_image(self._dataset_configs.keys(), all_patches,
self._normalize_reconstructors)
img_seg = rebuild_image(self._dataset_configs.keys(), all_patches,
self._segmentation_reconstructors)
save_rebuilt_image(self._current_epoch, self._save_folder,
self._dataset_configs.keys(), img_input,
"Input")
save_rebuilt_image(self._current_epoch, self._save_folder,
self._dataset_configs.keys(), img_gt,
"Ground_Truth")
save_rebuilt_image(self._current_epoch, self._save_folder,
self._dataset_configs.keys(), img_norm,
"Normalized")
save_rebuilt_image(self._current_epoch, self._save_folder,
self._dataset_configs.keys(), img_seg,
"Segmented")
if self._training_config.build_augmented_images:
img_augmented = rebuild_image(self._dataset_configs.keys(),
all_patches,
self._augmented_reconstructors)
augmented_minus_inputs, normalized_minus_inputs = rebuild_augmented_images(
img_augmented, img_input, img_gt, img_norm, img_seg)
save_augmented_rebuilt_images(self._current_epoch,
self._save_folder,
self._dataset_configs.keys(),
img_augmented,
augmented_minus_inputs,
normalized_minus_inputs)
mean_mhd = []
for dataset in self._dataset_configs.keys():
self.custom_variables[
"Reconstructed Normalized {} Image".format(
dataset)] = self._slicer.get_slice(
SliceType.AXIAL,
np.expand_dims(
np.expand_dims(img_norm[dataset], 0), 0), 160)
self.custom_variables[
"Reconstructed Segmented {} Image".format(
dataset)] = self._seg_slicer.get_colored_slice(
SliceType.AXIAL,
np.expand_dims(np.expand_dims(img_seg[dataset], 0),
0), 160).squeeze(0)
self.custom_variables[
"Reconstructed Ground Truth {} Image".format(
dataset)] = self._seg_slicer.get_colored_slice(
SliceType.AXIAL,
np.expand_dims(np.expand_dims(img_gt[dataset], 0),
0), 160).squeeze(0)
self.custom_variables["Reconstructed Input {} Image".format(
dataset)] = self._slicer.get_slice(
SliceType.AXIAL,
np.expand_dims(np.expand_dims(img_input[dataset], 0),
0), 160)
if self._training_config.build_augmented_images:
self.custom_variables[
"Reconstructed Augmented Input {} Image".format(
dataset)] = self._slicer.get_slice(
SliceType.AXIAL,
np.expand_dims(
np.expand_dims(img_augmented[dataset], 0),
0), 160)
self.custom_variables[
"Reconstructed Initial Noise {} Image".format(
dataset)] = self._seg_slicer.get_colored_slice(
SliceType.AXIAL,
np.expand_dims(
np.expand_dims(
augmented_minus_inputs[dataset], 0),
0), 160).squeeze(0)
self.custom_variables[
"Reconstructed Noise {} After Normalization".format(
dataset)] = self._seg_slicer.get_colored_slice(
SliceType.AXIAL,
np.expand_dims(
np.expand_dims(
normalized_minus_inputs[dataset], 0),
0), 160).squeeze(0)
else:
self.custom_variables[
"Reconstructed Augmented Input {} Image".format(
dataset)] = np.zeros((224, 192))
self.custom_variables[
"Reconstructed Initial Noise {} Image".format(
dataset)] = np.zeros((224, 192))
self.custom_variables[
"Reconstructed Noise {} After Normalization".format(
dataset)] = np.zeros((224, 192))
mean_mhd.append(
mean_hausdorff_distance(
to_onehot(torch.tensor(img_gt[dataset],
dtype=torch.long),
num_classes=4),
to_onehot(torch.tensor(img_seg[dataset],
dtype=torch.long),
num_classes=4))[-3:].mean())
metric = self._model_trainers[SEGMENTER].compute_metrics(
to_onehot(torch.tensor(
img_seg[dataset]).unsqueeze(0).long(),
num_classes=4),
torch.tensor(img_gt[dataset]).unsqueeze(0).long())
self._class_dice_gauge_on_reconstructed_images.update(
np.array(metric["Dice"]))
self._per_dataset_hausdorff_distance_gauge.update(
np.array(mean_mhd))
if "iSEG" in img_seg:
metric = self._model_trainers[SEGMENTER].compute_metrics(
to_onehot(torch.tensor(
img_seg["iSEG"]).unsqueeze(0).long(),
num_classes=4),
torch.tensor(img_gt["iSEG"]).unsqueeze(0).long())
self._class_dice_gauge_on_reconstructed_iseg_images.update(
np.array(metric["Dice"]))
self._hausdorff_distance_gauge_on_reconstructed_iseg_images.update(
mean_hausdorff_distance(
to_onehot(torch.tensor(img_gt["iSEG"],
dtype=torch.long),
num_classes=4),
to_onehot(torch.tensor(img_seg["iSEG"],
dtype=torch.long),
num_classes=4))[-3:])
else:
self._class_dice_gauge_on_reconstructed_iseg_images.update(
np.array([0.0, 0.0, 0.0]))
self._hausdorff_distance_gauge_on_reconstructed_iseg_images.update(
np.array([0.0, 0.0, 0.0]))
if "MRBrainS" in img_seg:
metric = self._model_trainers[SEGMENTER].compute_metrics(
to_onehot(torch.tensor(
img_seg["MRBrainS"]).unsqueeze(0).long(),
num_classes=4),
torch.tensor(img_gt["MRBrainS"]).unsqueeze(0).long())
self._class_dice_gauge_on_reconstructed_mrbrains_images.update(
np.array(metric["Dice"]))
self._hausdorff_distance_gauge_on_reconstructed_mrbrains_images.update(
mean_hausdorff_distance(
to_onehot(torch.tensor(img_gt["MRBrainS"],
dtype=torch.long),
num_classes=4),
to_onehot(torch.tensor(img_seg["MRBrainS"],
dtype=torch.long),
num_classes=4))[-3:])
else:
self._class_dice_gauge_on_reconstructed_mrbrains_images.update(
np.array([0.0, 0.0, 0.0]))
self._hausdorff_distance_gauge_on_reconstructed_mrbrains_images.update(
np.array([0.0, 0.0, 0.0]))
if "ABIDE" in img_seg:
metric = self._model_trainers[SEGMENTER].compute_metrics(
to_onehot(torch.tensor(
img_seg["ABIDE"]).unsqueeze(0).long(),
num_classes=4),
torch.tensor(img_gt["ABIDE"]).unsqueeze(0).long())
self._class_dice_gauge_on_reconstructed_abide_images.update(
np.array(metric["Dice"]))
self._hausdorff_distance_gauge_on_reconstructed_abide_images.update(
mean_hausdorff_distance(
to_onehot(torch.tensor(img_gt["ABIDE"],
dtype=torch.long),
num_classes=4),
to_onehot(torch.tensor(img_seg["ABIDE"],
dtype=torch.long),
num_classes=4))[-3:])
else:
self._class_dice_gauge_on_reconstructed_abide_images.update(
np.array([0.0, 0.0, 0.0]))
self._hausdorff_distance_gauge_on_reconstructed_abide_images.update(
np.array([0.0, 0.0, 0.0]))
if len(img_input) == 3:
self.custom_variables[
"Reconstructed Images Histograms"] = cv2.imread(
construct_triple_histrogram(
img_norm["iSEG"], img_input["iSEG"],
img_norm["MRBrainS"], img_input["MRBrainS"],
img_norm["ABIDE"], img_input["ABIDE"])).transpose(
(2, 0, 1))
elif len(img_input) == 2:
self.custom_variables[
"Reconstructed Images Histograms"] = cv2.imread(
construct_double_histrogram(
img_norm["iSEG"], img_input["iSEG"],
img_norm["MRBrainS"],
img_input["MRBrainS"])).transpose((2, 0, 1))
elif len(img_input) == 1:
self.custom_variables[
"Reconstructed Images Histograms"] = cv2.imread(
construct_single_histogram(
img_norm[list(self._dataset_configs.keys())[0]],
img_input[list(self._dataset_configs.keys())[0]],
)).transpose((2, 0, 1))
if "ABIDE" not in self._dataset_configs.keys():
self.custom_variables[
"Reconstructed Normalized ABIDE Image"] = np.zeros((224, 192))
self.custom_variables[
"Reconstructed Segmented ABIDE Image"] = np.zeros((224, 192))
self.custom_variables[
"Reconstructed Ground Truth ABIDE Image"] = np.zeros(
(224, 192))
self.custom_variables[
"Reconstructed Input ABIDE Image"] = np.zeros((224, 192))
self.custom_variables[
"Reconstructed Initial Noise ABIDE Image"] = np.zeros(
(224, 192))
self.custom_variables[
"Reconstructed Noise ABIDE After Normalization"] = np.zeros(
(224, 192))
if "iSEG" not in self._dataset_configs.keys():
self.custom_variables[
"Reconstructed Normalized iSEG Image"] = np.zeros((224, 192))
self.custom_variables[
"Reconstructed Segmented iSEG Image"] = np.zeros((224, 192))
self.custom_variables[
"Reconstructed Ground Truth iSEG Image"] = np.zeros((224, 192))
self.custom_variables["Reconstructed Input iSEG Image"] = np.zeros(
(224, 192))
self.custom_variables[
"Reconstructed Initial Noise iSEG Image"] = np.zeros(
(224, 192))
self.custom_variables[
"Reconstructed Noise iSEG After Normalization"] = np.zeros(
(224, 192))
if "MRBrainS" not in self._dataset_configs.keys():
self.custom_variables[
"Reconstructed Normalized MRBrainS Image"] = np.zeros(
(224, 192))
self.custom_variables[
"Reconstructed Segmented MRBrainS Image"] = np.zeros(
(224, 192))
self.custom_variables[
"Reconstructed Ground Truth MRBrainS Image"] = np.zeros(
(224, 192))
self.custom_variables[
"Reconstructed Input MRBrainS Image"] = np.zeros((224, 192))
self.custom_variables[
"Reconstructed Initial Noise MRBrainS Image"] = np.zeros(
(224, 192))
self.custom_variables[
"Reconstructed Noise MRBrainS After Normalization"] = np.zeros(
(224, 192))
self.custom_variables["Runtime"] = to_html_time(
timedelta(seconds=time.time() - self._start_time))
if self._general_confusion_matrix_gauge._num_examples != 0:
self.custom_variables["Confusion Matrix"] = np.array(
np.fliplr(self._general_confusion_matrix_gauge.compute().cpu().
detach().numpy()))
else:
self.custom_variables["Confusion Matrix"] = np.zeros((4, 4))
if self._iSEG_confusion_matrix_gauge._num_examples != 0:
self.custom_variables["iSEG Confusion Matrix"] = np.array(
np.fliplr(self._iSEG_confusion_matrix_gauge.compute().cpu().
detach().numpy()))
else:
self.custom_variables["iSEG Confusion Matrix"] = np.zeros((4, 4))
if self._MRBrainS_confusion_matrix_gauge._num_examples != 0:
self.custom_variables["MRBrainS Confusion Matrix"] = np.array(
np.fliplr(self._MRBrainS_confusion_matrix_gauge.compute().cpu(
).detach().numpy()))
else:
self.custom_variables["MRBrainS Confusion Matrix"] = np.zeros(
(4, 4))
if self._ABIDE_confusion_matrix_gauge._num_examples != 0:
self.custom_variables["ABIDE Confusion Matrix"] = np.array(
np.fliplr(self._ABIDE_confusion_matrix_gauge.compute().cpu().
detach().numpy()))
else:
self.custom_variables["ABIDE Confusion Matrix"] = np.zeros((4, 4))
self.custom_variables["Metric Table"] = to_html(
["CSF", "Grey Matter", "White Matter"], ["DSC", "HD"], [
self._class_dice_gauge_on_patches.compute()
if self._class_dice_gauge_on_patches.has_been_updated() else
np.array([0.0, 0.0, 0.0]),
self._class_hausdorff_distance_gauge.compute()
if self._class_hausdorff_distance_gauge.has_been_updated() else
np.array([0.0, 0.0, 0.0])
])
self.custom_variables[
"Dice score per class per epoch"] = self._class_dice_gauge_on_patches.compute(
) if self._class_dice_gauge_on_patches.has_been_updated(
) else np.array([0.0, 0.0, 0.0])
self.custom_variables[
"Dice score per class per epoch on reconstructed image"] = self._class_dice_gauge_on_reconstructed_images.compute(
) if self._class_dice_gauge_on_reconstructed_images.has_been_updated(
) else np.array([0.0, 0.0, 0.0])
self.custom_variables[
"Dice score per class per epoch on reconstructed iSEG image"] = self._class_dice_gauge_on_reconstructed_iseg_images.compute(
) if self._class_dice_gauge_on_reconstructed_iseg_images.has_been_updated(
) else np.array([0.0, 0.0, 0.0])
self.custom_variables[
"Dice score per class per epoch on reconstructed MRBrainS image"] = self._class_dice_gauge_on_reconstructed_mrbrains_images.compute(
) if self._class_dice_gauge_on_reconstructed_mrbrains_images.has_been_updated(
) else np.array([0.0, 0.0, 0.0])
self.custom_variables[
"Dice score per class per epoch on reconstructed ABIDE image"] = self._class_dice_gauge_on_reconstructed_abide_images.compute(
) if self._class_dice_gauge_on_reconstructed_abide_images.has_been_updated(
) else np.array([0.0, 0.0, 0.0])
self.custom_variables[
"Hausdorff Distance per class per epoch on reconstructed iSEG image"] = self._hausdorff_distance_gauge_on_reconstructed_iseg_images.compute(
) if self._hausdorff_distance_gauge_on_reconstructed_iseg_images.has_been_updated(
) else np.array([0.0, 0.0, 0.0])
self.custom_variables[
"Hausdorff Distance per class per epoch on reconstructed MRBrainS image"] = self._hausdorff_distance_gauge_on_reconstructed_mrbrains_images.compute(
) if self._hausdorff_distance_gauge_on_reconstructed_mrbrains_images.has_been_updated(
) else np.array([0.0, 0.0, 0.0])
self.custom_variables[
"Hausdorff Distance per class per epoch on reconstructed ABIDE image"] = self._hausdorff_distance_gauge_on_reconstructed_abide_images.compute(
) if self._hausdorff_distance_gauge_on_reconstructed_abide_images.has_been_updated(
) else np.array([0.0, 0.0, 0.0])
if self._valid_dice_gauge.compute() > self._previous_mean_dice:
new_table = to_html_per_dataset(
["CSF", "Grey Matter", "White Matter"], ["DSC", "HD"], [
[
self._iSEG_dice_gauge.compute()
if self._iSEG_dice_gauge.has_been_updated() else
np.array([0.0, 0.0, 0.0]),
self._iSEG_hausdorff_gauge.compute()
if self._iSEG_hausdorff_gauge.has_been_updated() else
np.array([0.0, 0.0, 0.0])
],
[
self._MRBrainS_dice_gauge.compute()
if self._MRBrainS_dice_gauge.has_been_updated() else
np.array([0.0, 0.0, 0.0]),
self._MRBrainS_hausdorff_gauge.compute()
if self._MRBrainS_hausdorff_gauge.has_been_updated()
else np.array([0.0, 0.0, 0.0])
],
[
self._ABIDE_dice_gauge.compute()
if self._ABIDE_dice_gauge.has_been_updated() else
np.array([0.0, 0.0, 0.0]),
self._ABIDE_hausdorff_gauge.compute()
if self._ABIDE_hausdorff_gauge.has_been_updated() else
np.array([0.0, 0.0, 0.0])
]
], ["iSEG", "MRBrainS", "ABIDE"])
self.custom_variables["Per-Dataset Metric Table"] = new_table
self._previous_mean_dice = self._valid_dice_gauge.compute()
self._previous_per_dataset_table = new_table
else:
self.custom_variables[
"Per-Dataset Metric Table"] = self._previous_per_dataset_table
self._valid_dice_gauge.reset()
self.custom_variables["Jensen-Shannon Table"] = to_html_JS(
["Input data", "Generated Data"], ["JS Divergence"], [
self._js_div_inputs_gauge.compute() if
self._js_div_gen_gauge.has_been_updated() else np.array([0.0]),
self._js_div_gen_gauge.compute() if
self._js_div_gen_gauge.has_been_updated() else np.array([0.0])
])
self.custom_variables["Jensen-Shannon Divergence"] = [
self._js_div_inputs_gauge.compute(),
self._js_div_gen_gauge.compute()
]
self.custom_variables["Mean Hausdorff Distance"] = [
self._class_hausdorff_distance_gauge.compute().mean()
if self._class_hausdorff_distance_gauge.has_been_updated() else
np.array([0.0])
]
self.custom_variables[
"Per Dataset Mean Hausdorff Distance"] = self._per_dataset_hausdorff_distance_gauge.compute(
)
def _update_image_plots(self, phase, inputs, generator_predictions,
segmenter_predictions, target, dataset_ids):
inputs = torch.nn.functional.interpolate(inputs,
scale_factor=5,
mode="trilinear",
align_corners=True).numpy()
generator_predictions = torch.nn.functional.interpolate(
generator_predictions,
scale_factor=5,
mode="trilinear",
align_corners=True).numpy()
segmenter_predictions = torch.nn.functional.interpolate(
torch.argmax(torch.nn.functional.softmax(segmenter_predictions,
dim=1),
dim=1,
keepdim=True).float(),
scale_factor=5,
mode="nearest").numpy()
target = torch.nn.functional.interpolate(target.float(),
scale_factor=5,
mode="nearest").numpy()
self.custom_variables["{} Input Batch Process {}".format(
phase, self._run_config.local_rank)] = self._slicer.get_slice(
SliceType.AXIAL, inputs, inputs.shape[2] // 2)
self.custom_variables["{} Generated Batch Process {}".format(
phase, self._run_config.local_rank)] = self._slicer.get_slice(
SliceType.AXIAL, generator_predictions,
generator_predictions.shape[2] // 2)
self.custom_variables["{} Segmented Batch Process {}".format(
phase,
self._run_config.local_rank)] = self._seg_slicer.get_colored_slice(
SliceType.AXIAL, segmenter_predictions,
segmenter_predictions.shape[2] // 2)
self.custom_variables[
"{} Segmentation Ground Truth Batch Process {}".format(
phase, self._run_config.local_rank
)] = self._seg_slicer.get_colored_slice(SliceType.AXIAL, target,
target.shape[2] // 2)
self.custom_variables["{} Label Map Batch Process {}".format(
phase,
self._run_config.local_rank)] = self._label_mapper.get_label_map(
dataset_ids)
def _should_activate_autoencoder(self):
return self._current_epoch < self._patience_segmentation
def _should_activate_segmentation(self):
return self._current_epoch >= self._patience_segmentation
def _update_histograms(self, inputs, target, gen_pred):
self.custom_variables["Generated Intensity Histogram"] = flatten(
gen_pred.cpu().detach())
self.custom_variables["Input Intensity Histogram"] = flatten(
inputs.cpu().detach())
self.custom_variables["Per-Dataset Histograms"] = cv2.imread(
construct_class_histogram(inputs, target, gen_pred)).transpose(
(2, 0, 1))
self.custom_variables[
"Background Generated Intensity Histogram"] = gen_pred[torch.where(
target[IMAGE_TARGET] == 0)].cpu().detach()
self.custom_variables["CSF Generated Intensity Histogram"] = gen_pred[
torch.where(target[IMAGE_TARGET] == 1)].cpu().detach()
self.custom_variables["GM Generated Intensity Histogram"] = gen_pred[
torch.where(target[IMAGE_TARGET] == 2)].cpu().detach()
self.custom_variables["WM Generated Intensity Histogram"] = gen_pred[
torch.where(target[IMAGE_TARGET] == 3)].cpu().detach()
self.custom_variables["Background Input Intensity Histogram"] = inputs[
torch.where(target[IMAGE_TARGET] == 0)].cpu().detach()
self.custom_variables["CSF Input Intensity Histogram"] = inputs[
torch.where(target[IMAGE_TARGET] == 1)].cpu().detach()
self.custom_variables["GM Input Intensity Histogram"] = inputs[
torch.where(target[IMAGE_TARGET] == 2)].cpu().detach()
self.custom_variables["WM Input Intensity Histogram"] = inputs[
torch.where(target[IMAGE_TARGET] == 3)].cpu().detach()
def __init__(self, training_config, model_trainers: List[ModelTrainer],
train_data_loader: DataLoader, valid_data_loader: DataLoader, test_data_loader: DataLoader,
reconstruction_datasets: List[Dataset], normalize_reconstructors: list, input_reconstructors: list,
segmentation_reconstructors: list, augmented_reconstructors: list, gt_reconstructors: list,
run_config: RunConfiguration, dataset_config: dict, save_folder: str):
super(DualUNetMultimodalTrainer, self).__init__("DualUNetMultimodalTrainer", train_data_loader, valid_data_loader,
test_data_loader, model_trainers, run_config)
self._training_config = training_config
self._run_config = run_config
self._dataset_configs = dataset_config
self._patience_segmentation = training_config.patience_segmentation
self._slicer = ImageSlicer()
self._seg_slicer = SegmentationSlicer()
self._label_mapper = LabelMapper()
self._reconstruction_datasets = reconstruction_datasets
self._normalize_reconstructors = normalize_reconstructors
self._input_reconstructors = input_reconstructors
self._gt_reconstructors = gt_reconstructors
self._segmentation_reconstructors = segmentation_reconstructors
self._augmented_reconstructors = augmented_reconstructors
self._class_hausdorff_distance_gauge = AverageGauge()
self._mean_hausdorff_distance_gauge = AverageGauge()
self._per_dataset_hausdorff_distance_gauge = AverageGauge()
self._iSEG_dice_gauge = AverageGauge()
self._MRBrainS_dice_gauge = AverageGauge()
self._ABIDE_dice_gauge = AverageGauge()
self._iSEG_hausdorff_gauge = AverageGauge()
self._MRBrainS_hausdorff_gauge = AverageGauge()
self._ABIDE_hausdorff_gauge = AverageGauge()
self._valid_dice_gauge = AverageGauge()
self._class_dice_gauge_on_patches = AverageGauge()
self._class_dice_gauge_on_reconstructed_images = AverageGauge()
self._class_dice_gauge_on_reconstructed_iseg_images = AverageGauge()
self._class_dice_gauge_on_reconstructed_mrbrains_images = AverageGauge()
self._class_dice_gauge_on_reconstructed_abide_images = AverageGauge()
self._hausdorff_distance_gauge_on_reconstructed_iseg_images = AverageGauge()
self._hausdorff_distance_gauge_on_reconstructed_mrbrains_images = AverageGauge()
self._hausdorff_distance_gauge_on_reconstructed_abide_images = AverageGauge()
self._js_div_inputs_gauge = AverageGauge()
self._js_div_gen_gauge = AverageGauge()
self._general_confusion_matrix_gauge = ConfusionMatrix(num_classes=4)
self._iSEG_confusion_matrix_gauge = ConfusionMatrix(num_classes=4)
self._MRBrainS_confusion_matrix_gauge = ConfusionMatrix(num_classes=4)
self._ABIDE_confusion_matrix_gauge = ConfusionMatrix(num_classes=4)
self._previous_mean_dice = 0.0
self._previous_per_dataset_table = ""
self._start_time = time.time()
self._save_folder = save_folder
self._sampler = Sampler(0.33)
self._is_sliced = True if isinstance(self._reconstruction_datasets[0], SliceDataset) else False
print("Total number of parameters: {}".format(
sum(p.numel() for p in self._model_trainers[GENERATOR].parameters()) +
sum(p.numel() for p in self._model_trainers[SEGMENTER].parameters())))
pynvml.nvmlInit()