def test_squeeze_end_dims(self):
with tempfile.TemporaryDirectory() as tempdir:
for squeeze_end_dims in [False, True]:
saver = NiftiSaver(
output_dir=tempdir,
output_postfix="",
output_ext=".nii.gz",
dtype=np.float32,
squeeze_end_dims=squeeze_end_dims,
)
fname = "testfile_squeeze"
meta_data = {"filename_or_obj": fname}
# 2d image w channel
saver.save(torch.randint(0, 255, (1, 2, 2)), meta_data)
im = LoadImage(image_only=True)(os.path.join(
tempdir, fname, fname + ".nii.gz"))
self.assertTrue(im.ndim == 2 if squeeze_end_dims else 4)
def run_inference(self, model, data_loader):
logger = self.logger
logger.info('Running inference...')
model.eval() # activate evaluation mode of model
dice_scores = np.zeros(len(data_loader))
if self.model == "UNet2d5_spvPA":
model_segmentation = lambda *args, **kwargs: model(
*args, **kwargs)[0]
else:
model_segmentation = model
with torch.no_grad(
): # turns off PyTorch's auto grad for better performance
for i, data in enumerate(data_loader):
logger.info("starting image {}".format(i))
outputs = sliding_window_inference(
inputs=data["image"].to(self.device),
roi_size=self.sliding_window_inferer_roi_size,
sw_batch_size=1,
predictor=model_segmentation,
mode="gaussian",
)
dice_score = self.compute_dice_score(
outputs, data["label"].to(self.device))
dice_scores[i] = dice_score.item()
logger.info(f"dice_score = {dice_score.item()}")
# export to nifti
if self.export_inferred_segmentations:
logger.info(f"export to nifti...")
nifti_data_matrix = np.squeeze(
torch.argmax(outputs, dim=1, keepdim=True))[None, :]
data['label_meta_dict']['filename_or_obj'] = data[
'label_meta_dict']['filename_or_obj'][0]
data['label_meta_dict']['affine'] = np.squeeze(
data['label_meta_dict']['affine'])
data['label_meta_dict']['original_affine'] = np.squeeze(
data['label_meta_dict']['original_affine'])
folder_name = os.path.basename(
os.path.dirname(
data['label_meta_dict']['filename_or_obj']))
saver = NiftiSaver(output_dir=os.path.join(
self.results_folder_path,
'inferred_segmentations_nifti', folder_name),
output_postfix='')
saver.save(nifti_data_matrix,
meta_data=data['label_meta_dict'])
# plot centre of mass slice of label
label = torch.squeeze(data["label"][0, 0, :, :, :])
slice_idx = self.get_center_of_mass_slice(
label
) # choose slice of selected validation set image volume for the figure
plt.figure("check", (18, 6))
plt.clf()
plt.subplot(1, 3, 1)
plt.title("image " + str(i) + ", slice = " + str(slice_idx))
plt.imshow(data["image"][0, 0, :, :, slice_idx],
cmap="gray",
interpolation="none")
plt.subplot(1, 3, 2)
plt.title("label " + str(i))
plt.imshow(data["label"][0, 0, :, :, slice_idx],
interpolation="none")
plt.subplot(1, 3, 3)
plt.title("output " + str(i) +
f", dice = {dice_score.item():.4}")
plt.imshow(torch.argmax(outputs,
dim=1).detach().cpu()[0, :, :,
slice_idx],
interpolation="none")
plt.savefig(
os.path.join(self.figures_path,
"best_model_output_val" + str(i) + ".png"))
plt.figure("dice score histogram")
plt.hist(dice_scores, bins=np.arange(0, 1.01, 0.01))
plt.savefig(
os.path.join(self.figures_path,
"best_model_output_dice_score_histogram.png"))
logger.info(f"all_dice_scores = {dice_scores}")
logger.info(
f"mean_dice_score = {dice_scores.mean()} +- {dice_scores.std()}")