def __init__(self, args, image_size, eval_iteration=0):
self._args = args
self._image_size = image_size
self._viz = vis.Visdom(port=args.port)
self._device = th.device("cuda:" + str(args.gpu_ids[0]))
self._grid = compute_grid([image_size[0], image_size[1]], device=self._device)
if args.image_loss_eval == "MSE":
self._image_loss = il.MSE()
else:
print("Image loss is not suported")
self._eval_iterations = eval_iteration
self._min_global_evaluation_error = 1e10
th.manual_seed(args.seed)
self._patients = sorted(os.listdir(args.eval_path))
# compute mean image of all data
self._mean_image_filenames = []
for patient in self._patients:
examinations = sorted(os.listdir(os.path.join(args.eval_path, patient)))
for exa in examinations:
slices = sorted(os.listdir(os.path.join(args.eval_path, patient, exa)))
for image_slice in slices:
slice_path = os.path.join(args.eval_path, patient, exa, image_slice)
images = sorted(os.listdir(slice_path))
self._mean_image_filenames.append(get_fixe_image_filename(slice_path, images))
self._out_path_image_data = os.path.join(args.o, "image_data")
if not os.path.exists(self._out_path_image_data):
os.makedirs(self._out_path_image_data)
self._win = None
def reg(args, state, fix_image_filename, moving_image_filename, iterations):
args_state = state['args']
image_size = [256, 256]
gpu_id = args.gpu_id
device = th.device("cuda:" + str(gpu_id))
if gpu_id >= 0:
th.cuda.set_device(gpu_id)
if args_state.model == "R2NN":
model = gru.GRU_Registration(image_size, 2, args=args_state, device=device)
else:
raise ValueError('model type {0} is not known'.format(args_state.model))
model.eval()
model.load_state_dict(state['model'])
print("model loaded")
if gpu_id >= 0:
with th.cuda.device(gpu_id):
model.cuda()
if args_state.image_loss == "MSE":
image_loss = il.MSE()
else:
print("Image loss is not suported")
grid = compute_grid([image_size[0], image_size[1]], device=device)
if not os.path.exists(args.o):
os.makedirs(args.o)
fixed_image = sitk.ReadImage(fix_image_filename, sitk.sitkFloat32)
fixed_image = th.tensor(sitk.GetArrayFromImage(fixed_image)).squeeze().unsqueeze_(0).unsqueeze_(0)
fixed_image = fixed_image.to(device=device)
fixed_image = fixed_image - th.mean(fixed_image)
fixed_image = fixed_image / th.std(fixed_image)
fixed_image.clamp_(-2, 2)
moving_image = sitk.ReadImage(moving_image_filename, sitk.sitkFloat32)
moving_image = th.tensor(sitk.GetArrayFromImage(moving_image)).squeeze().unsqueeze_(0).unsqueeze_(0)
moving_image = moving_image.to(device=device)
moving_image = moving_image - th.mean(moving_image)
moving_image = moving_image / th.std(moving_image)
moving_image.clamp_(-2, 2)
image_loss_f, warped_image, displacement, displacement_param, displacement_pixel, single_displacement, warped_local_image = eval_rnn(iterations,
model,
fixed_image,
moving_image,
image_loss, grid)
show_text = False
for idx, param in enumerate(displacement_param):
sigma = 2 * param[0].squeeze().cpu().numpy() * 255
pos = ((param[2].squeeze().cpu().numpy() + 1) / 2) * 255
angle = -(param[3].cpu().numpy() * 180.0) / np.pi
displacement_sum = th.sqrt(displacement_pixel[idx][0, 0, ...].pow(2) + displacement_pixel[idx][0, 1, ...].pow(2))
fig = plt.imshow(displacement_sum.cpu().squeeze().numpy(), cmap='jet', vmax=0.08, vmin=0)
ax = plt.gca()
ax.add_patch(Ellipse(pos, width=sigma[0], height=sigma[1],
angle=angle,
edgecolor='white',
facecolor='none',
linewidth=2))
fig.axes.get_xaxis().set_visible(False)
fig.axes.get_yaxis().set_visible(False)
plt.axis('off')
if show_text:
plt.text(8, 250, r"transformation sum: $t=" + str(idx) + "$", {'color': 'w', 'fontsize': 18})
plt.savefig(os.path.join(args.o, "displacement_sum_" + str(idx) + ".png"), bbox_inches='tight', pad_inches=0)
plt.close()
##############################################################################################################
displacement_local = th.sqrt(single_displacement[idx][0, 0, ...].pow(2) + single_displacement[idx][0, 1, ...].pow(2))
fig = plt.imshow(displacement_local.cpu().squeeze().numpy(), cmap='jet',vmax=0.03, vmin=0)
fig.axes.get_xaxis().set_visible(False)
fig.axes.get_yaxis().set_visible(False)
plt.axis('off')
if show_text:
plt.text(32, 15, r"network output: $t=" + str(idx) + "$", {'color': 'w', 'fontsize': 18})
plt.text(8, 250, r"transformation local: $t=" + str(idx) + "$", {'color': 'w', 'fontsize': 18})
# plt.show()
plt.savefig(os.path.join(args.o, "displacement_local_" + str(idx) + ".png"), bbox_inches='tight', pad_inches=0)
plt.close()
##############################################################################################################
fig = plt.imshow(warped_local_image[idx].cpu().squeeze().numpy(), cmap='gray')
fig.axes.get_xaxis().set_visible(False)
fig.axes.get_yaxis().set_visible(False)
plt.axis('off')
plt.axis('off')
if show_text:
if idx == 0:
plt.text(16, 250, r"moving image", {'color': 'r', 'fontsize': 18})
else:
plt.text(16, 250, r"warped image: $t=" + str(idx - 1) + "$", {'color': 'r', 'fontsize': 18})
plt.text(3, 15, r"input: $t=" + str(idx) + "$", {'color': 'r', 'fontsize': 18})
plt.savefig(os.path.join(args.o, "warped_loacl_input_" + str(idx) + ".png"), bbox_inches='tight', pad_inches=0)
plt.close()
##############################################################################################################
fig = plt.imshow(warped_local_image[idx + 1].cpu().squeeze().numpy(), cmap='gray')
ax = plt.gca()
ax.add_patch(Ellipse(pos, width=sigma[0], height=sigma[1],
angle=angle,
edgecolor='white',
facecolor='none',
linewidth=2))
fig.axes.get_xaxis().set_visible(False)
fig.axes.get_yaxis().set_visible(False)
plt.axis('off')
plt.axis('off')
if show_text:
plt.text(16, 250, r"warped image: $t=" + str(idx) + "$", {'color': 'r', 'fontsize': 18})
plt.savefig(os.path.join(args.o, "warped_loacl_output_" + str(idx) + ".png"), bbox_inches='tight', pad_inches=0)
plt.close()
##############################################################################################################
diff_image = warped_local_image[idx].cpu().squeeze().data.fill_(1).numpy()
fig = plt.imshow(diff_image, cmap='gray')
fig.axes.get_xaxis().set_visible(False)
fig.axes.get_yaxis().set_visible(False)
plt.axis('off')
if show_text:
plt.text(128, 150, "Recurrent Registration\n" "Neural Networks for\n" "Deformable Image\n""Registration",
{'color': 'w', 'fontsize': 18}, ha='center', wrap=True, )
plt.savefig(os.path.join(args.o, "diff_image_" + str(idx) + ".png"), bbox_inches='tight', pad_inches=0)
plt.close()
fig = plt.imshow(fixed_image.cpu().squeeze().numpy(), cmap='gray')
fig.axes.get_xaxis().set_visible(False)
fig.axes.get_yaxis().set_visible(False)
plt.axis('off')
if show_text:
plt.text(64, 250, r"fixed image", {'color': 'r', 'fontsize': 18})
plt.text(180, 15, r"network ", {'color': 'r', 'fontsize': 18})
plt.savefig(os.path.join(args.o, "fixed_image.png"), bbox_inches='tight', pad_inches=0)
def reg(args, state, fix_image_filename, moving_image_filename, iterations):
args_state = state['args']
image_size = [256, 256]
gpu_id = args.gpu_id
device = th.device("cuda:" + str(gpu_id))
if gpu_id >= 0:
th.cuda.set_device(gpu_id)
if args_state.model == "R2NN":
model = gru.GRU_Registration(image_size,
2,
args=args_state,
device=device)
else:
raise ValueError('model type {0} is not known'.format(
args_state.model))
model.eval()
model.load_state_dict(state['model'])
print("model loaded")
if gpu_id >= 0:
with th.cuda.device(gpu_id):
model.cuda()
if args_state.image_loss == "MSE":
image_loss = il.MSE()
else:
print("Image loss is not suported")
grid = compute_grid([image_size[0], image_size[1]], device=device)
if not os.path.exists(args.o):
os.makedirs(args.o)
fixed_image = sitk.ReadImage(fix_image_filename, sitk.sitkFloat32)
fixed_image = th.tensor(sitk.GetArrayFromImage(
fixed_image)).squeeze().unsqueeze_(0).unsqueeze_(0)
fixed_image = fixed_image.to(device=device)
fixed_image = fixed_image - th.mean(fixed_image)
fixed_image = fixed_image / th.std(fixed_image)
fixed_image.clamp_(-2, 2)
moving_image = sitk.ReadImage(moving_image_filename, sitk.sitkFloat32)
moving_image = th.tensor(sitk.GetArrayFromImage(
moving_image)).squeeze().unsqueeze_(0).unsqueeze_(0)
moving_image = moving_image.to(device=device)
moving_image = moving_image - th.mean(moving_image)
moving_image = moving_image / th.std(moving_image)
moving_image.clamp_(-2, 2)
image_loss_f, warped_image, displacement, displacement_param, displacement_pixel, single_displacement, warped_local_image = eval_rnn(
iterations, model, fixed_image, moving_image, image_loss, grid)
weight_x = []
weight_y = []
shape_x = []
shape_y = []
angle = []
for idx, param in enumerate(displacement_param):
shape_x.append(param[0][0].cpu().numpy())
shape_y.append(param[0][1].cpu().numpy())
weight_x.append(param[1][0].cpu().numpy())
weight_y.append(param[1][1].cpu().numpy())
angle.append(-(param[3].cpu().numpy() * 180.0) / np.pi)
plt.plot(shape_y, label='shape size $\sigma_x$')
plt.plot(shape_x, label='shape size $\sigma_y$')
plt.xlabel("Time steps $t$")
plt.ylabel("Shape size $\sigma_t$ of the local transformation")
plt.legend(bbox_to_anchor=(0.5, 0.9), loc=2, borderaxespad=0.)
matplotlib2tikz.save("/tmp/shape.tex")
plt.show()
plt.plot(weight_x, label='weight $v_x$')
plt.plot(weight_y, label='weight $v_y$')
plt.xlabel("Time steps $t$")
plt.ylabel("Weights $v_t$ of the local transformations ")
plt.legend(bbox_to_anchor=(0.5, 0.9), loc=2, borderaxespad=0.)
matplotlib2tikz.save("/tmp/weight.tex")
plt.show()
plt.plot(angle)
plt.xlabel("Time steps $t$")
plt.ylabel("Time steps $t$")
plt.grid(True)
plt.show()
matplotlib2tikz.save("/tmp/test.tex")
def reg(args, state, fix_image_filename, moving_image_filename, iterations):
args_state = state['args']
image_size = [256, 256]
gpu_id = args.gpu_id
device = th.device("cuda:" + str(gpu_id))
if gpu_id >= 0:
th.cuda.set_device(gpu_id)
if args_state.model == "R2NN":
model = gru.GRU_Registration(image_size,
2,
args=args_state,
device=device)
else:
raise ValueError('model type {0} is not known'.format(
args_state.model))
model.eval()
model.load_state_dict(state['model'])
print("model loaded")
if gpu_id >= 0:
with th.cuda.device(gpu_id):
model.cuda()
if args_state.image_loss == "MSE":
image_loss = il.MSE()
else:
print("Image loss is not suported")
grid = compute_grid([image_size[0], image_size[1]], device=device)
if not os.path.exists(args.o):
os.makedirs(args.o)
fixed_image = sitk.ReadImage(fix_image_filename, sitk.sitkFloat32)
fixed_image = th.tensor(sitk.GetArrayFromImage(
fixed_image)).squeeze().unsqueeze_(0).unsqueeze_(0)
fixed_image = fixed_image.to(device=device)
fixed_image = fixed_image - th.mean(fixed_image)
fixed_image = fixed_image / th.std(fixed_image)
fixed_image.clamp_(-2, 2)
moving_image = sitk.ReadImage(moving_image_filename, sitk.sitkFloat32)
moving_image = th.tensor(sitk.GetArrayFromImage(
moving_image)).squeeze().unsqueeze_(0).unsqueeze_(0)
moving_image = moving_image.to(device=device)
moving_image = moving_image - th.mean(moving_image)
moving_image = moving_image / th.std(moving_image)
moving_image.clamp_(-2, 2)
image_loss_f, warped_image, displacement, displacement_param, displacement_pixel = eval_rnn(
iterations, model, fixed_image, moving_image, image_loss, grid)
displacement_mag = th.sqrt(displacement_pixel[1][0, 0, ...].pow(2) +
displacement_pixel[1][0, 1, ...].pow(2))
fig = plt.imshow(displacement_mag.cpu().squeeze().numpy(),
cmap='jet',
vmax=0.08,
vmin=0)
for idx, param in enumerate(displacement_param):
if idx < 2:
sigma = 2 * param[0].squeeze().cpu().numpy() * 255
pos = ((param[2].squeeze().cpu().numpy() + 1) / 2) * 255
angle = -(param[3].cpu().numpy() * 180.0) / np.pi
ax = plt.gca()
ax.add_patch(
Ellipse(pos,
width=sigma[0],
height=sigma[1],
angle=angle,
edgecolor='white',
facecolor='none',
linewidth=2))
fig.axes.get_xaxis().set_visible(False)
fig.axes.get_yaxis().set_visible(False)
plt.axis('off')
plt.savefig(os.path.join(args.o, "disp_2.png"),
bbox_inches='tight',
pad_inches=0)
plt.close()
displacement_mag = th.sqrt(displacement_pixel[3][0, 0, ...].pow(2) +
displacement_pixel[3][0, 1, ...].pow(2))
fig = plt.imshow(displacement_mag.cpu().squeeze().numpy(),
cmap='jet',
vmax=0.08,
vmin=0)
for idx, param in enumerate(displacement_param):
if idx < 4:
sigma = 2 * param[0].squeeze().cpu().numpy() * 255
pos = ((param[2].squeeze().cpu().numpy() + 1) / 2) * 255
angle = -(param[3].cpu().numpy() * 180.0) / np.pi
ax = plt.gca()
ax.add_patch(
Ellipse(pos,
width=sigma[0],
height=sigma[1],
angle=angle,
edgecolor='white',
facecolor='none',
linewidth=2))
fig.axes.get_xaxis().set_visible(False)
fig.axes.get_yaxis().set_visible(False)
plt.axis('off')
plt.savefig(os.path.join(args.o, "disp_4.png"),
bbox_inches='tight',
pad_inches=0)
plt.close()
displacement_mag = th.sqrt(displacement_pixel[7][0, 0, ...].pow(2) +
displacement_pixel[7][0, 1, ...].pow(2))
fig = plt.imshow(displacement_mag.cpu().squeeze().numpy(),
cmap='jet',
vmax=0.08,
vmin=0)
for idx, param in enumerate(displacement_param):
if idx < 8:
sigma = 2 * param[0].squeeze().cpu().numpy() * 255
pos = ((param[2].squeeze().cpu().numpy() + 1) / 2) * 255
angle = -(param[3].cpu().numpy() * 180.0) / np.pi
ax = plt.gca()
ax.add_patch(
Ellipse(pos,
width=sigma[0],
height=sigma[1],
angle=angle,
edgecolor='white',
facecolor='none',
linewidth=2))
fig.axes.get_xaxis().set_visible(False)
fig.axes.get_yaxis().set_visible(False)
plt.axis('off')
plt.savefig(os.path.join(args.o, "disp_8.png"),
bbox_inches='tight',
pad_inches=0)
plt.close()
displacement_mag = th.sqrt(displacement[0, 0, ...].pow(2) +
displacement[0, 1, ...].pow(2))
fig = plt.imshow(displacement_mag.cpu().squeeze().numpy(),
cmap='jet',
vmax=0.08,
vmin=0)
for idx, param in enumerate(displacement_param):
sigma = 2 * param[0].squeeze().cpu().numpy() * 255
pos = ((param[2].squeeze().cpu().numpy() + 1) / 2) * 255
angle = -(param[3].cpu().numpy() * 180.0) / np.pi
ax = plt.gca()
ax.add_patch(
Ellipse(pos,
width=sigma[0],
height=sigma[1],
angle=angle,
edgecolor='white',
facecolor='none',
linewidth=2))
fig.axes.get_xaxis().set_visible(False)
fig.axes.get_yaxis().set_visible(False)
plt.axis('off')
plt.savefig(os.path.join(args.o, "disp_25.png"),
bbox_inches='tight',
pad_inches=0)
plt.close()
fig = plt.imshow(fixed_image.cpu().squeeze().numpy(), cmap='gray')
fig.axes.get_xaxis().set_visible(False)
fig.axes.get_yaxis().set_visible(False)
plt.axis('off')
plt.savefig(os.path.join(args.o, "fixed_image.png"),
bbox_inches='tight',
pad_inches=0)
plt.close()
fig = plt.imshow(moving_image.cpu().squeeze().numpy(), cmap='gray')
fig.axes.get_xaxis().set_visible(False)
fig.axes.get_yaxis().set_visible(False)
plt.axis('off')
plt.savefig(os.path.join(args.o, "moving_image.png"),
bbox_inches='tight',
pad_inches=0)
plt.close()
fig = plt.imshow(warped_image.cpu().squeeze().numpy(), cmap='gray')
fig.axes.get_xaxis().set_visible(False)
fig.axes.get_yaxis().set_visible(False)
plt.axis('off')
plt.savefig(os.path.join(args.o, "warped_image.png"),
bbox_inches='tight',
pad_inches=0)
plt.close()
fig = plt.imshow(displacement_mag.cpu().squeeze().numpy(),
cmap='jet',
vmax=0.08,
vmin=0)
fig.axes.get_xaxis().set_visible(False)
fig.axes.get_yaxis().set_visible(False)
plt.axis('off')
plt.savefig(os.path.join(args.o, "displacement.png"),
bbox_inches='tight',
pad_inches=0)
plt.close()
def test(args, state, image_size=[256, 256]):
args_state = state['args']
gpu_id = args.gpu_id
device = th.device("cuda:" + str(gpu_id))
if gpu_id >= 0:
th.cuda.set_device(gpu_id)
patients = sorted(os.listdir(args.test_path))
# compute mean image of all data
mean_image_filenames = []
for patient in patients:
examinations = sorted(os.listdir(os.path.join(args.test_path, patient)))
for exa in examinations:
slices = sorted(os.listdir(os.path.join(args.test_path, patient, exa)))
for image_slice in slices:
slice_path = os.path.join(args.test_path, patient, exa, image_slice)
images = sorted(os.listdir(slice_path))
images = [f for f in images if os.path.isfile(os.path.join(os.path.join(args.test_path, patient, exa, image_slice, f)))]
mean_image_filenames.append(get_fixe_image_filename(slice_path, images))
print(len(mean_image_filenames))
print(mean_image_filenames)
if args_state.model == "R2NN":
model = gru.GRU_Registration(image_size, 2, args=args_state, device=device)
else:
raise ValueError('model type {0} is not known'.format(args_state.model))
model.eval()
model.load_state_dict(state['model'])
print("model loaded")
if gpu_id >= 0:
with th.cuda.device(gpu_id):
model.cuda()
if args_state.image_loss == "MSE":
image_loss = il.MSE()
else:
print("Image loss is not suported")
grid = compute_grid([image_size[0], image_size[1]], device=device)
if args_state.model == "R2NN":
evaluate_net = eval_rnn
elif args_state.model == "UNET":
evaluate_net = eval_feed_forward
if not os.path.exists(args.o):
os.makedirs(args.o)
out_path_image_data = os.path.join(args.o, "image_data")
if not os.path.exists(out_path_image_data):
os.makedirs(out_path_image_data)
slice_index_global = 0
gloabl_eval_error = []
for patient in patients:
if os.path.exists(os.path.join(args.o, "error_" + patient + ".csv")):
os.remove(os.path.join(args.o, "error_" + patient + ".csv"))
if os.path.exists(os.path.join(args.o, "tre_" + patient + ".csv")):
os.remove(os.path.join(args.o, "tre_" + patient + ".csv"))
for patient in patients:
examinations = sorted(os.listdir(os.path.join(args.test_path, patient)))
image_loss_examination = 0
for exa in examinations:
slices = sorted(os.listdir(os.path.join(args.test_path, patient, exa)))
image_loss_slices = 0
for image_slice in slices:
slice_path = os.path.join(args.test_path, patient, exa, image_slice)
image_filenames = sorted(os.listdir(slice_path))
image_filenames = [f for f in image_filenames if f.endswith(".dcm")]
output_path = os.path.join(out_path_image_data, patient, exa, image_slice)
if not os.path.exists(output_path):
os.makedirs(output_path)
fix_image_filename = os.path.join(slice_path, mean_image_filenames[slice_index_global])
fixed_image = sitk.ReadImage(os.path.join(slice_path, fix_image_filename), sitk.sitkFloat32)
# load fixed image landmarks
fix_landmarks_filenames = os.path.join(slice_path, "landmarks", "landmarks_" + mean_image_filenames[slice_index_global][:-4] + ".vtk")
fixed_image_points = Points.read(fix_landmarks_filenames)
fixed_image = th.tensor(sitk.GetArrayFromImage(fixed_image)).squeeze().unsqueeze_(0).unsqueeze_(0)
fixed_image = fixed_image.to(device=device)
fixed_image = fixed_image - th.mean(fixed_image)
fixed_image = fixed_image / th.std(fixed_image)
fixed_image.clamp_(-2, 2)
sitk.WriteImage(sitk.GetImageFromArray(fixed_image.detach().cpu().squeeze().numpy()),
os.path.join(output_path, "fixed_"
+ mean_image_filenames[slice_index_global][:-4] + ".vtk"))
image_loss_images = 0
image_loss_images_csv = []
tre_slice = []
tre_slice.append(image_slice)
tre_slice.append(fix_image_filename)
image_loss_images_csv.append(image_slice)
image_loss_images_csv.append(fix_image_filename)
for image_filename in image_filenames:
moving_image = sitk.ReadImage(os.path.join(slice_path, image_filename), sitk.sitkFloat32)
# get image properties
image_spacing = [1, 1]
image_origin = [0, 0]
moving_image = th.tensor(sitk.GetArrayFromImage(moving_image)).squeeze().unsqueeze_(0) \
.unsqueeze_(0)
moving_image = moving_image.to(device=device)
moving_image = moving_image - th.mean(moving_image)
moving_image = moving_image / th.std(moving_image)
moving_image.clamp_(-2, 2)
# load moving image landmarks
moving_landmarks_filenames = os.path.join(slice_path, "landmarks", "landmarks_" + image_filename[:-4] + ".vtk")
moving_image_points = Points.read(moving_landmarks_filenames)
start = time.time()
image_loss_f, warped_image, displacement = evaluate_net(args_state, model, fixed_image,
moving_image, image_loss, grid)
stop = time.time()
displacement = displacement.flip(2)
displacement = displacement.transpose(1, 2).transpose(2, 3)
displacement = displacement.squeeze().to(dtype=th.float64, device='cpu')
# transform to itk displacement
for dim in range(displacement.shape[-1]):
tmp = float(displacement.shape[-dim - 2] - 1)
displacement[..., dim] = float(displacement.shape[-dim - 2] - 1) * displacement[..., dim] / 2.0
itk_displacement = sitk.GetImageFromArray(displacement.numpy(), isVector=True)
itk_displacement.SetSpacing(image_spacing)
itk_displacement.SetOrigin(image_origin)
#
# displacement_al = Displacement(displacement, image_size=[256, 256], image_spacing=image_spacing,
# image_origin=image_origin)
# displacement_al.image = displacement_al.image*image_spacing[0]
moving_points_transformed = Points.transform(moving_image_points, itk_displacement)
tre = Points.TRE(moving_points_transformed, fixed_image_points)
tre_slice.append(tre)
print("Time", stop-start)
image_loss_images_csv.append(image_loss_f)
Points.write(os.path.join(output_path, "warped_points_" + image_filename[:-4] + ".vtk"), moving_points_transformed)
Points.write(os.path.join(output_path, "moving_points_" + image_filename[:-4] + ".vtk"), moving_image_points)
Points.write(os.path.join(output_path, "fixed_points_" + image_filename[:-4] + ".vtk"), fixed_image_points)
image_loss_images += image_loss_f
sitk.WriteImage(sitk.GetImageFromArray(warped_image.detach().cpu().squeeze().numpy()),
os.path.join(output_path, "warped_" + image_filename[:-4] + ".vtk"))
sitk.WriteImage(sitk.GetImageFromArray(moving_image.detach().cpu().squeeze().numpy()),
os.path.join(output_path, "moving_" + image_filename[:-4] + ".vtk"))
sitk.WriteImage(sitk.GetImageFromArray(
displacement.detach().cpu().squeeze().numpy(), isVector=True),
os.path.join(output_path, "displacement_" + image_filename[:-4] + ".vtk"))
slice_index_global += 1
with open(os.path.join(args.o, "error_" + patient + ".csv"), 'a') as csvFile:
writer = csv.writer(csvFile, delimiter=',')
writer.writerow(image_loss_images_csv)
with open(os.path.join(args.o, "tre_" + patient + ".csv"), 'a') as csvFile:
writer = csv.writer(csvFile, delimiter=',')
writer.writerow(tre_slice)
image_loss_images /= len(image_filenames)
image_loss_slices += image_loss_images
image_loss_slices /= len(slices)
image_loss_examination += image_loss_slices
image_loss_examination /= len(examinations)
gloabl_eval_error.append(image_loss_examination)
with open(os.path.join(args.o, "error_all_patients.csv"), 'a') as csvFile:
writer = csv.writer(csvFile, delimiter=',')
writer.writerow([patient, examinations, image_loss_examination])
def train_sync(args):
continue_optimization = False
eval_iteration = 0
if args.model_state != "":
state = th.load(args.model_state, map_location='cpu')
continue_optimization = True
eval_iteration = state['eval_counter']
gpu_id = args.gpu_ids[0]
th.manual_seed(args.seed)
np.random.seed(args.seed)
device = th.device("cuda:" + str(gpu_id))
viz = vis.Visdom(port=args.port)
data_manager = dm.DataManager(args.training_path,
normalize_std=args.normalize_std,
random_sampling=args.random_img_pair)
image_size = data_manager.image_size()
# Parameters
params = {
'batch_size': args.batch_size,
'shuffle': True,
'num_workers': args.nb_workers,
'pin_memory': True
}
training_generator = data.DataLoader(data_manager, **params)
model = gru.GRU_Registration(image_size, 2, device=device, args=args)
if continue_optimization:
model.load_state_dict(state['model'])
model.train()
model_parameters = filter(lambda p: p.requires_grad, model.parameters())
params = sum([np.prod(p.size()) for p in model_parameters])
print("number of parameters model", params)
evaluater = Evaluater(args, image_size, eval_iteration=eval_iteration)
if gpu_id >= 0:
with th.cuda.device(gpu_id):
model.cuda()
if gpu_id >= 0:
th.cuda.manual_seed(args.seed)
th.cuda.set_device(gpu_id)
if args.optimizer == 'RMSprop':
optimizer = th.optim.RMSprop(model.parameters(), lr=args.lr)
elif args.optimizer == 'Adam':
optimizer = th.optim.Adam(model.parameters(),
lr=args.lr,
amsgrad=args.amsgrad)
elif args.optimizer == 'Rprop':
optimizer = th.optim.Rprop(model.parameters(), lr=args.lr)
if continue_optimization:
optimizer.load_state_dict = state['optimizer']
if args.image_loss == "MSE":
image_loss = il.MSE()
else:
print("Image loss is not suported")
regulariser = dl.IsotropicTVRegulariser([1.0, 1.0])
grid = compute_grid([image_size[0], image_size[1]]).cuda()
train_counter = 0
if continue_optimization:
train_counter = state['train_counter']
loss_plot = None
print("start optimization")
scale = 1
if args.use_diff_loss:
scale = -1
while True:
for fixed_image, moving_image in training_generator:
fixed_image = fixed_image.cuda()
moving_image = moving_image.cuda()
if train_counter % args.eval_interval == 0:
print("Start evaluation")
evaluater.evaluation(model)
image_loss_epoch = 0
model.reset()
model.zero_grad()
warped_image = moving_image
displacement = th.zeros(args.batch_size,
2,
image_size[0],
image_size[1],
device=fixed_image.device,
dtype=fixed_image.dtype)
displacement_trans = displacement.transpose(1, 2).transpose(
2, 3) + grid
if args.entropy_regularizer_weight > 0:
shapes = th.zeros(1,
1,
image_size[0],
image_size[1],
device=fixed_image.device,
dtype=fixed_image.dtype)
single_entropy = 0
loss_start, _ = image_loss(displacement_trans, fixed_image,
warped_image)
if args.early_stopping > 0:
if loss_start.item() < args.early_stopping:
continue
start = time.time()
for j in range(args.rnn_iter):
net_input = th.cat((fixed_image, warped_image), dim=1)
net_ouput = model(net_input)
displacement = displacement + net_ouput[0]
if args.entropy_regularizer_weight > 0:
f_x = net_ouput[1] / (th.sum(net_ouput[1]) + 1e-5) + 1e-5
shapes = shapes + f_x
single_entropy = single_entropy + compute_entropy(f_x)
displacement_trans = displacement.transpose(1, 2).transpose(
2, 3) + grid
warped_image = F.grid_sample(moving_image, displacement_trans)
loss_, _ = image_loss(displacement_trans, fixed_image,
warped_image)
if args.use_diff_loss:
image_loss_epoch = image_loss_epoch + (loss_start - loss_)
loss_start = loss_
else:
image_loss_epoch = image_loss_epoch + loss_
if args.early_stopping > 0:
if loss_.item() < args.early_stopping:
break
if args.stop_on_reverse:
if loss_.item() <= loss_start.item():
loss_start = loss_
else:
break
j = j + 1
displacement_loss = args.reg_weight * regulariser(displacement)
loss = scale * image_loss_epoch / j + displacement_loss
if args.entropy_regularizer_weight > 0:
entropy_loss = (compute_entropy(shapes / j) + single_entropy /
j) * args.entropy_regularizer_weight
loss = loss - entropy_loss
entropy_loss_value = entropy_loss.data.item()
else:
entropy_loss_value = 0
optimizer.zero_grad()
loss.backward()
if args.clip_gradients:
th.nn.utils.clip_grad_norm_(model.parameters(), 1)
optimizer.step()
end = time.time()
if train_counter % args.save_model == 0:
state = {
'train_counter': train_counter,
'eval_counter': evaluater.eval_iterations,
'args': args,
'agent_id': -1,
'optimizer': optimizer.state_dict(),
'model': model.state_dict()
}
path = os.path.join(args.o, "state_agent_sync.pt")
th.save(state, path)
print("iter ", train_counter, "image loss ",
image_loss_epoch.item() / j, "displacement loss ",
displacement_loss.item(), "loss ", loss.item(), "time",
end - start)
if loss_plot is None:
opts = dict(title=("loss_value"),
width=1000,
height=500,
showlegend=True)
loss_value_ = np.column_stack(
np.array([
image_loss_epoch.data.item() / j,
displacement_loss.data.item(), entropy_loss_value
]))
loss_plot = viz.line(X=np.column_stack(
np.ones(3) * train_counter),
Y=loss_value_,
opts=opts)
else:
loss_value_ = np.column_stack(
np.array([
image_loss_epoch.data.item() / j,
displacement_loss.data.item(), entropy_loss_value
]))
loss_plot = viz.line(X=np.column_stack(
np.ones(3) * train_counter),
Y=loss_value_,
win=loss_plot,
update='append')
if train_counter % 250 == 0:
fixed_image_vis = imfilter.normalize_image(
fixed_image[0, ...]).cpu().unsqueeze(0)
moving_image_vis = imfilter.normalize_image(
moving_image[0, ...]).cpu().unsqueeze(0)
displacement_vis = imfilter.normalize_image(
displacement[0, ...]).cpu().unsqueeze(0).detach()
warped_image_vis = imfilter.normalize_image(
warped_image[0, ...]).cpu().unsqueeze(0).detach()
checkerboard_image = sitk.GetArrayFromImage(
sitk.CheckerBoard(
sitk.GetImageFromArray(
moving_image_vis.squeeze().numpy()),
sitk.GetImageFromArray(
fixed_image_vis.squeeze().numpy()), [20, 20]))
checkerboard_image_vis_nor_reg = th.Tensor(
checkerboard_image).unsqueeze(0).unsqueeze(0)
checkerboard_image = sitk.GetArrayFromImage(
sitk.CheckerBoard(
sitk.GetImageFromArray(
warped_image_vis.squeeze().numpy()),
sitk.GetImageFromArray(
fixed_image_vis.squeeze().numpy()), [20, 20]))
checkerboard_image_vis = th.Tensor(
checkerboard_image).unsqueeze(0).unsqueeze(0)
image_stack = th.cat(
(fixed_image_vis, moving_image_vis,
displacement_vis[:, 0, ...].unsqueeze(1),
displacement_vis[:, 1,
...].unsqueeze(1), warped_image_vis,
checkerboard_image_vis, checkerboard_image_vis_nor_reg),
dim=0)
opts = dict(title="results")
viz.images(image_stack, opts=opts, win=2)
train_counter += 1