def read_image_and_map_and_apply_map(image_filename,map_filename):
"""
Reads an image and a map and applies the map to an image
:param image_filename: input image filename
:param map_filename: input map filename
:return: the warped image and its image header as a tupe (im,hdr)
"""
im_warped = None
map,map_hdr = fileio.MapIO().read(map_filename)
im,hdr,_,_ = fileio.ImageIO().read_to_map_compatible_format(image_filename,map)
spacing = hdr['spacing']
#TODO: check that the spacing is compatible with the map
if (im is not None) and (map is not None):
# make pytorch arrays for subsequent processing
im_t = AdaptVal(torch.from_numpy(im))
map_t = AdaptVal(torch.from_numpy(map))
im_warped = utils.t2np( utils.compute_warped_image_multiNC(im_t,map_t,spacing) )
return im_warped,hdr
else:
print('Could not read map or image')
return None,None
def createImage(self, ex_len=64):
example_img_len = ex_len
dim = 2
szEx = np.tile(example_img_len,
dim) # size of the desired images: (sz)^dim
I0, I1, self.spacing = eg.CreateSquares(dim).create_image_pair(
szEx,
self.params) # create a default image size with two sample squares
self.sz = np.array(I0.shape)
# create the source and target image as pyTorch variables
self.ISource = AdaptVal(torch.from_numpy(I0.copy()))
self.ITarget = AdaptVal(torch.from_numpy(I1))
# smooth both a little bit
self.params[('image_smoothing', {}, 'image smoothing settings')]
self.params['image_smoothing'][(
'smooth_images', True,
'[True|False]; smoothes the images before registration')]
self.params['image_smoothing'][('smoother', {},
'settings for the image smoothing')]
self.params['image_smoothing']['smoother'][(
'gaussian_std', 0.05, 'how much smoothing is done')]
self.params['image_smoothing']['smoother'][(
'type', 'gaussian', "['gaussianSpatial'|'gaussian'|'diffusion']")]
cparams = self.params['image_smoothing']
s = SF.SmootherFactory(self.sz[2::],
self.spacing).create_smoother(cparams)
self.ISource = s.smooth(self.ISource)
self.ITarget = s.smooth(self.ITarget)
def invert_map(map, spacing):
"""
Inverts the map and returns its inverse. Assumes standard map parameterization [-1,1]^d
:param map: Input map to be inverted
:return: inverted map
"""
# make pytorch arrays for subsequent processing
map_t = AdaptVal(torch.from_numpy(map))
# identity map
id = utils.identity_map_multiN(map_t.data.shape, spacing)
id_t = AdaptVal(torch.from_numpy(id))
# parameter to store the inverse map
invmap_t = AdaptVal(Parameter(torch.from_numpy(id.copy())))
# some optimizer settings, probably too strict
nr_of_iterations = 1000
rel_ftol = 1e-6
optimizer = CO.LBFGS_LS([invmap_t],
lr=1.0,
max_iter=1,
tolerance_grad=rel_ftol * 10,
tolerance_change=rel_ftol,
max_eval=5,
history_size=5,
line_search_fn='backtracking')
#optimizer = torch.optim.SGD([invmap_t], lr=0.001, momentum=0.9, dampening=0, weight_decay=0,nesterov=True)
def compute_loss():
# warps map_t with inv_map, if it is the inverse should result in the identity map
wmap = utils.compute_warped_image_multiNC(map_t, invmap_t, spacing)
current_loss = ((wmap - id_t)**2).sum()
return current_loss
def _closure():
optimizer.zero_grad()
loss = compute_loss()
loss.backward()
return loss
last_loss = utils.t2np(compute_loss())
for iter in range(nr_of_iterations):
optimizer.step(_closure)
current_loss = utils.t2np(compute_loss())
print('Iter = ' + str(iter) + '; E = ' + str(current_loss))
if (current_loss >= last_loss):
break
else:
last_loss = current_loss
return utils.t2np(invmap_t)
def compute_average_image(images):
im_io = FIO.ImageIO()
Iavg = None
for nr, im_name in enumerate(images):
Ic, hdrc, spacing, _ = im_io.read_to_nc_format(filename=im_name)
if nr == 0:
Iavg = AdaptVal(torch.from_numpy(Ic))
else:
Iavg += AdaptVal(torch.from_numpy(Ic))
Iavg = Iavg / len(images)
return Iavg, spacing
def add_texture_on_img(im_orig,
texture_gaussian_smoothness=0.1,
texture_magnitude=0.3):
# do this separately for each integer intensity level
levels = np.unique((np.floor(im_orig)).astype('int'))
im = np.zeros_like(im_orig)
for current_level in levels:
sz = im_orig.shape
rand_noise = np.random.random(sz[2:]).astype('float32') - 0.5
rand_noise = rand_noise.view().reshape(sz)
r_params = pars.ParameterDict()
r_params['smoother']['type'] = 'gaussian'
r_params['smoother']['gaussian_std'] = texture_gaussian_smoothness
spacing = 1.0 / (np.array(sz[2:]).astype('float32') - 1)
s_r = sf.SmootherFactory(sz[2::], spacing).create_smoother(r_params)
rand_noise_smoothed = s_r.smooth(AdaptVal(
torch.from_numpy(rand_noise))).detach().cpu().numpy()
rand_noise_smoothed /= rand_noise_smoothed.max()
rand_noise_smoothed *= texture_magnitude
c_indx = (im_orig >= current_level - 0.5)
im[c_indx] = im_orig[c_indx] + rand_noise_smoothed[c_indx]
return torch.Tensor(im)
def get_labeled_image(img_pair):
s_path, t_path = img_pair
moving = torch.load(s_path)
target = torch.load(t_path)
moving_np = moving.cpu().numpy()
target_np = target.cpu().numpy()
ind_value_list = np.unique(moving_np)
ind_value_list_target = np.unique(target_np)
assert len(set(ind_value_list) - set(ind_value_list_target)) == 0
lmoving = torch.zeros_like(moving)
ltarget = torch.zeros_like(target)
ind_value_list.sort()
for i, value in enumerate(ind_value_list):
lmoving[moving == value] = i
ltarget[target == value] = i
return AdaptVal(lmoving), AdaptVal(ltarget)
def __init__(self):
dx = AdaptVal(
torch.Tensor([[[-1., -3., -1.], [-3., -6., -3.], [-1., -3., -1.]],
[[0., 0., 0.], [0., 0, 0.], [0., 0., 0.]],
[[1., 3., 1.], [3., 6., 3.],
[1., 3., 1.]]])).view(1, 1, 3, 3, 3)
dy = AdaptVal(
torch.Tensor([[[1., 3., 1.], [0., 0., 0.], [-1., -3., -1.]],
[[3., 6., 3.], [0., 0, 0.], [-3., -6., -3.]],
[[1., 3., 1.], [0., 0., 0.],
[-1., -3., -1.]]])).view(1, 1, 3, 3, 3)
dz = AdaptVal(
torch.Tensor([[[-1., 0., 1.], [-3., 0., 3.], [-1., 0., 1.]],
[[-3., 0., 3.], [-6., 0, 6.], [-3., 0., 3.]],
[[-1., 0., 1.], [-3., 0., 3.],
[-1., 0., 1.]]])).view(1, 1, 3, 3, 3)
self.spatial_filter = torch.cat((dx, dy, dz), 0)
self.spatial_filter = self.spatial_filter.repeat(1, 1, 1, 1, 1)
def __get_smoothed_target(self, I0):
ITarget = AdaptVal(torch.from_numpy(I0.copy()))
# cparams = pars.ParameterDict()
# cparams[('smoother', {})]
# cparams['smoother']['type'] = 'gaussianSpatial'
# cparams['smoother']['gaussianStd'] = 0.005
# s = SF.SmootherFactory(sz[2::], spacing).create_smoother(cparams)
# ITarget = s.smooth(ITarget).detach()
ITarget = self.fourier_smoother(ITarget).detach()
return ITarget
def upsample_to_compatible_size_single_image(gt_weight,
weight,
interpolation_order=1):
# upsample the weights if needed
if gt_weight.shape == weight.shape:
return weight
else:
sampler = IS.ResampleImage()
weight_sz = weight.shape
weight_reshaped = AdaptVal(
torch.from_numpy(weight.view().reshape([1, 1] +
list(weight_sz))).float())
spacing = np.array([1., 1.])
desired_size = gt_weight.shape
weight_upsampled_t, _ = sampler.upsample_image_to_size(
weight_reshaped, spacing, desired_size, interpolation_order)
weight_upsampled = weight_upsampled_t.detach().cpu().numpy()
return weight_upsampled
def downsample_to_compatible_size_single_image(gt_weight,
weight,
interpolation_order=3):
# downsample the ground truth weights if needed
if gt_weight.shape == weight.shape:
return gt_weight
else:
sampler = IS.ResampleImage()
gt_weight_sz = gt_weight.shape
gt_weight_reshaped = AdaptVal(
torch.from_numpy(
gt_weight.view().reshape([1, 1] + list(gt_weight_sz))).float())
spacing = np.array([1., 1.])
desired_size = weight.shape
gt_weight_downsampled_t, _ = sampler.downsample_image_to_size(
gt_weight_reshaped, spacing, desired_size, interpolation_order)
gt_weight_downsampled = gt_weight_downsampled_t.detach().cpu().numpy()
return gt_weight_downsampled
def resample_image(I,
spacing,
desiredSize,
spline_order=1,
zero_boundary=False,
identity_map=None):
"""
Resample an image to a given desired size
:param I: Input image (expected to be of BxCxXxYxZ format)
:param spacing: array describing the spatial spacing
:param desiredSize: array for the desired size (excluding B and C, i.e, 1 entry for 1D, 2 for 2D, and 3 for 3D)
:return: returns a tuple: the downsampled image, the new spacing after downsampling
"""
desiredSize = desiredSize[2:]
sz = np.array(list(I.size()))
# check that the batch size and the number of channels is the same
nrOfI = sz[0]
nrOfC = sz[1]
desiredSizeNC = np.array([nrOfI, nrOfC] + list(desiredSize))
newspacing = spacing * ((sz[2::].astype('float') - 1.) /
(desiredSizeNC[2::].astype('float') - 1.)
) ###########################################
if identity_map is not None:
idDes = identity_map
else:
idDes = AdaptVal(
torch.from_numpy(
py_utils.identity_map_multiN(desiredSizeNC, newspacing)))
# now use this map for resampling
ID = py_utils.compute_warped_image_multiNC(I, idDes, newspacing,
spline_order, zero_boundary)
return ID, newspacing
def compare_det_of_jac_from_map(map,
gt_map,
label_image,
visualize=False,
print_output_directory=None,
clean_publication_directory=None,
pair_nr=None):
sz = np.array(map.shape[2:])
# synthetic spacing
spacing = np.array(1. / (sz - 1))
map_torch = AdaptVal(torch.from_numpy(map).float())
gt_map_torch = AdaptVal(torch.from_numpy(gt_map).float())
det_est = eu.compute_determinant_of_jacobian(map_torch, spacing)
det_gt = eu.compute_determinant_of_jacobian(gt_map_torch, spacing)
n = det_est - det_gt
if visualize:
if clean_publication_directory is None:
plt.clf()
plt.subplot(131)
plt.imshow(det_gt)
plt.colorbar()
plt.title('det_gt')
plt.subplot(132)
plt.imshow(det_est)
plt.colorbar()
plt.title('det_est')
plt.subplot(133)
plt.imshow(n)
plt.colorbar()
plt.title('det_est - det_gt')
if print_output_directory is None:
plt.show()
else:
plt.savefig(
os.path.join(
print_output_directory,
'{:0>3d}'.format(pair_nr) + '_det_jac_validation.pdf'))
if clean_publication_directory is not None:
plt.clf()
plt.imshow(det_gt)
plt.colorbar()
plt.axis('image')
plt.axis('off')
plt.savefig(os.path.join(
clean_publication_directory,
'det_gt_{:0>3d}'.format(pair_nr) + '_det_jac_validation.pdf'),
bbox_inches='tight',
pad_inches=0)
plt.clf()
plt.imshow(det_est)
plt.colorbar()
plt.axis('image')
plt.axis('off')
plt.savefig(os.path.join(
clean_publication_directory,
'det_est_{:0>3d}'.format(pair_nr) + '_det_jac_validation.pdf'),
bbox_inches='tight',
pad_inches=0)
plt.clf()
plt.imshow(n)
plt.colorbar()
plt.axis('image')
plt.axis('off')
plt.savefig(os.path.join(
clean_publication_directory,
'det_est_m_det_gt_{:0>3d}'.format(pair_nr) +
'_det_jac_validation.pdf'),
bbox_inches='tight',
pad_inches=0)
ds = compute_image_stats(n, label_image)
return ds
def build_atlas(images, nr_of_cycles, warped_images, temp_folder, visualize):
si = SI.RegisterImagePair()
im_io = FIO.ImageIO()
# compute first average image
Iavg, sp = compute_average_image(images)
Iavg = Iavg.data
if visualize:
plt.imshow(AdaptVal(Iavg[0, 0, ...]).detach().cpu().numpy(),
cmap='gray')
plt.title('Initial average based on ' + str(len(images)) + ' images')
plt.colorbar()
plt.show()
# initialize list to save model parameters in between cycles
mp = []
# register all images to the average image and while doing so compute a new average image
for c in range(nr_of_cycles):
print('Starting cycle ' + str(c + 1) + '/' + str(nr_of_cycles))
for i, im_name in enumerate(images):
print('Registering image ' + str(i) + '/' + str(len(images)))
Ic, hdrc, spacing, _ = im_io.read_to_nc_format(filename=im_name)
# set former model parameters if available
if c != 0:
si.set_model_parameters(mp[i])
# register current image to average image
si.register_images(Ic,
AdaptVal(Iavg).detach().cpu().numpy(),
spacing,
model_name='svf_scalar_momentum_map',
map_low_res_factor=0.5,
nr_of_iterations=5,
visualize_step=None,
similarity_measure_sigma=0.5)
wi = si.get_warped_image()
# save current model parametrs for the next circle
if c == 0:
mp.append(si.get_model_parameters())
elif c != nr_of_cycles - 1:
mp[i] = si.get_model_parameters()
if c == nr_of_cycles - 1: # last time this is run, so let's save the image
current_filename = warped_images + '/atlas_reg_Image' + str(
i + 1).zfill(4) + '.nrrd'
print("writing image " + str(i + 1))
im_io.write(current_filename, wi, hdrc)
if i == 0:
newAvg = wi.data
else:
newAvg += wi.data
Iavg = newAvg / len(images)
if visualize:
plt.imshow(AdaptVal(Iavg[0, 0, ...]).detach().cpu().numpy(),
cmap='gray')
plt.title('Average ' + str(c + 1) + '/' + str(nr_of_cycles))
plt.colorbar()
plt.show()
return Iavg
def warp_data(data_list):
return [AdaptVal(data) for data in data_list]
import mermaid.smoother_factory as SF
import matplotlib.pyplot as plt
params = MP.ParameterDict()
dim = 2
szEx = np.tile(64, dim)
I0, I1, spacing = eg.CreateSquares(dim).create_image_pair(
szEx, params) # create a default image size with two sample squares
sz = np.array(I0.shape)
# create the source and target image as pyTorch variables
ISource = AdaptVal(torch.from_numpy(I0.copy()))
smoother = SF.MySingleGaussianFourierSmoother(sz[2:], spacing, params)
g_std = smoother.get_gaussian_std()
ISmooth = smoother.smooth_scalar_field(ISource)
ISmooth.backward(torch.ones_like(ISmooth))
#ISmooth.backward(torch.zeros_like(ISmooth))
print('g_std.grad')
print(g_std.grad)
plt.subplot(121)
plt.imshow(utils.t2np(ISource[0, 0, ...]))
params['square_example_images'] = ({},
'Settings for example image generation')
params['square_example_images']['len_s'] = int(szEx.min() // 6)
params['square_example_images']['len_l'] = int(szEx.max() // 4)
# create a default image size with two sample squares
I0, I1, spacing = eg.CreateSquares(ds.dim).create_image_pair(szEx, params)
sz = np.array(I0.shape)
assert (len(sz) == ds.dim + 2)
print('Spacing = ' + str(spacing))
# create the source and target image as pyTorch variables
ISource = AdaptVal(torch.from_numpy(I0.copy()))
ITarget = AdaptVal(torch.from_numpy(I1))
# if desired we smooth them a little bit
if ds.smooth_images:
# smooth both a little bit
params['image_smoothing'] = ds.par_algconf['image_smoothing']
cparams = params['image_smoothing']
s = SF.SmootherFactory(sz[2::], spacing).create_smoother(cparams)
ISource = s.smooth(ISource)
ITarget = s.smooth(ITarget)
##############################3
# Setting up the optimizer
# ^^^^^^^^^^^^^^^^^^^^^^^^
#
def do_registration( I0_name, I1_name, visualize, visualize_step, use_multi_scale, normalize_spacing, normalize_intensities, squeeze_image, par_algconf ):
from mermaid.data_wrapper import AdaptVal
import mermaid.smoother_factory as SF
import mermaid.multiscale_optimizer as MO
from mermaid.config_parser import nr_of_threads
params = pars.ParameterDict()
par_image_smoothing = par_algconf['algconf']['image_smoothing']
par_model = par_algconf['algconf']['model']
par_optimizer = par_algconf['algconf']['optimizer']
use_map = par_model['deformation']['use_map']
map_low_res_factor = par_model['deformation']['map_low_res_factor']
model_name = par_model['deformation']['name']
if use_map:
model_name = model_name + '_map'
else:
model_name = model_name + '_image'
# general parameters
params['model']['registration_model'] = par_algconf['algconf']['model']['registration_model']
torch.set_num_threads( nr_of_threads )
print('Number of pytorch threads set to: ' + str(torch.get_num_threads()))
I0, I1, spacing, md_I0, md_I1 = read_images( I0_name, I1_name, normalize_spacing, normalize_intensities,squeeze_image )
sz = I0.shape
# create the source and target image as pyTorch variables
ISource = AdaptVal(torch.from_numpy(I0.copy()))
ITarget = AdaptVal(torch.from_numpy(I1))
smooth_images = par_image_smoothing['smooth_images']
if smooth_images:
# smooth both a little bit
params['image_smoothing'] = par_algconf['algconf']['image_smoothing']
cparams = params['image_smoothing']
s = SF.SmootherFactory(sz[2::], spacing).create_smoother(cparams)
ISource = s.smooth_scalar_field(ISource)
ITarget = s.smooth_scalar_field(ITarget)
if not use_multi_scale:
# create multi-scale settings for single-scale solution
multi_scale_scale_factors = [1.0]
multi_scale_iterations_per_scale = [par_optimizer['single_scale']['nr_of_iterations']]
else:
multi_scale_scale_factors = par_optimizer['multi_scale']['scale_factors']
multi_scale_iterations_per_scale = par_optimizer['multi_scale']['scale_iterations']
mo = MO.MultiScaleRegistrationOptimizer(sz, spacing, use_map, map_low_res_factor, params)
optimizer_name = par_optimizer['name']
mo.set_optimizer_by_name(optimizer_name)
mo.set_visualization(visualize)
mo.set_visualize_step(visualize_step)
mo.set_model(model_name)
mo.set_source_image(ISource)
mo.set_target_image(ITarget)
mo.set_scale_factors(multi_scale_scale_factors)
mo.set_number_of_iterations_per_scale(multi_scale_iterations_per_scale)
# and now do the optimization
mo.optimize()
optimized_energy = mo.get_energy()
warped_image = mo.get_warped_image()
optimized_map = mo.get_map()
optimized_reg_parameters = mo.get_model_parameters()
return warped_image, optimized_map, optimized_reg_parameters, optimized_energy, params, md_I0