def stack_hitology_volumes(rabbit, block_paths):
def_ablations = []
def_combineds = []
out_dir = f'/hdscratch/ucair/{rabbit}/microscopic/recons/'
if not os.path.exists(out_dir):
os.makedirs(out_dir)
for block_path in block_paths:
block = block_path.split('/')[-1]
histology_dir = f'/hdscratch/ucair/{rabbit}/microscopic/{block}/'
def_dir = f'{histology_dir}/volume/deformable/'
# Load the deformed volume
def_ablation = io.LoadITKFile(f'{def_dir}/{block}_ablation_segmentation_to_exvivo.mhd', device=device)
# def_combined = io.LoadITKFile(f'{def_dir}/{block}_ablation_and_transition_segmentation_to_invivo.mhd',
# device=device)
# Threshold the volume
def_ablation.data = (def_ablation.data >= 0.8).float()
# def_combined.data = (def_combined.data >= 0.8).float()
def_ablations.append(def_ablation)
# def_combineds.append(def_combined)
full_ablation = def_ablations[0].copy()
full_ablation = full_ablation * 0.0
for i, v in enumerate(def_ablations, 1):
if v.sum() != 0.0:
io.SaveITKFile(v, f'/home/sci/blakez/test_outs/volume{i}.nii.gz')
full_ablation = full_ablation + v
full_ablation.data = (full_ablation.data > 0.0).float()
io.SaveITKFile(full_ablation, f'{out_dir}all_ablation_segs_to_exvivo.mhd')
def stack_hitology_volumes(rabbit, block_paths, base_dir='/hdscratch/ucair/'):
def_ablations = []
def_combineds = []
out_dir = f'{base_dir}{rabbit}/microscopic/recons/'
if not os.path.exists(out_dir):
os.makedirs(out_dir)
for block_path in block_paths:
block = block_path.split('/')[-1]
histology_dir = f'{base_dir}{rabbit}/microscopic/{block}/'
def_dir = f'{histology_dir}/volume/deformable/'
# Load the deformed volume
if not os.path.exists(
f'{def_dir}/{block}_ablation_segmentation_to_invivo.mhd'):
continue
def_ablation = io.LoadITKFile(
f'{def_dir}/{block}_ablation_segmentation_to_invivo.mhd',
device=device)
def_combined = io.LoadITKFile(
f'{def_dir}/{block}_ablation_and_transition_segmentation_to_invivo.mhd',
device=device)
# Threshold the volume
def_ablation.data = (def_ablation.data >= 0.8).float()
def_combined.data = (def_combined.data >= 0.8).float()
def_ablations.append(def_ablation)
def_combineds.append(def_combined)
full_ablation = def_ablations[0].copy()
full_ablation = full_ablation * 0.0
for v in def_ablations:
full_ablation = full_ablation + v
full_ablation.data = (full_ablation.data > 0.0).float()
io.SaveITKFile(full_ablation, f'{out_dir}all_ablation_segs_to_invivo.mhd')
full_combined = def_ablations[0].copy()
full_combined = full_combined * 0.0
for v in def_combineds:
full_combined = full_combined + v
full_combined.data = (full_combined.data > 0.0).float()
io.SaveITKFile(full_combined,
f'{out_dir}all_ablation_and_transition_segs_to_invivo.mhd')
def stack_image_volumes(rabbit, block_paths, base_dir='/hdscratch/ucair/'):
def_images = []
out_dir = f'{base_dir}{rabbit}/microscopic/recons/'
if not os.path.exists(out_dir):
os.makedirs(out_dir)
for block_path in block_paths:
block = block_path.split('/')[-1]
histology_dir = f'{base_dir}{rabbit}/microscopic/{block}/'
def_dir = f'{histology_dir}/volume/deformable/'
# Load the deformed volume
if not os.path.exists(f'{def_dir}/{block}_image_volume_to_invivo.mhd'):
continue
def_image = io.LoadITKFile(
f'{def_dir}/{block}_image_volume_to_invivo.mhd', device=device)
def_images.append(def_image.copy())
full_ablation = def_images[0].copy()
full_ablation = full_ablation * 0.0
for v in def_images:
full_ablation.data = torch.stack([full_ablation.data, v.data],
dim=0).max(0)[0]
io.SaveITKFile(full_ablation, f'{out_dir}all_images_to_invivo.mhd')
def deform_histology_volumes(rabbit, block):
rerun = True
blockface_dir = f'/hdscratch/ucair/{rabbit}/blockface/{block}/'
histology_dir = f'/hdscratch/ucair/{rabbit}/microscopic/{block}/'
raw_dir = f'{histology_dir}/volume/raw/'
out_dir = f'{histology_dir}/volume/deformable/'
if not os.path.exists(out_dir):
os.makedirs(out_dir)
if os.path.exists(f'{out_dir}/{block}_ablation_segmentation_to_exvivo.mhd') and not rerun:
return
deformation = generate(rabbit, block, source_space='blockface', target_space='exvivo')
deformation.to_(device=device)
# Load the original volume
ablation_vol = io.LoadITKFile(f'{raw_dir}/{block}_ablation_segmentation.mhd', device=device)
ablation_vol.data = (ablation_vol.data >= 0.5).float()
# combined_vol = io.LoadITKFile(f'{raw_dir}/{block}_ablation_and_transition_segmentation.mhd', device=device)
def_ablation = so.ApplyGrid.Create(deformation, device=device)(ablation_vol, deformation)
# def_combined = so.ApplyGrid.Create(deformation, device=device)(combined_vol, deformation)
io.SaveITKFile(def_ablation, f'{out_dir}/{block}_ablation_segmentation_to_exvivo.mhd')
def blocks_to_exvivo(rabbit, base_dir='/hdscratch/ucair/'):
# import RabbitCommon as rc
base_path = f'{base_dir}{rabbit}/blockface/'
block_list = sorted(glob.glob(f'{base_path}block*'))
device = 'cuda:1'
rerun = True
# Deform all of the blocks
for block_path in block_list:
block = block_path.split('/')[-1]
print(f'Deforming {block} ... ', end='')
out_path = f'{base_path}{block}/'
if not os.path.exists(f'{out_path}/volumes/deformable/'):
os.makedirs(f'{out_path}/volumes/deformable/')
bf_name = f'{block_path}/volumes/raw/scatter_volume.mhd'
block_vol = io.LoadITKFile(bf_name, device=device)
# generate the deformation to the stacked block
if not os.path.exists(f'{out_path}/volumes/deformable/{block}_to_exvivo.nii.gz') or rerun:
to_exvivo = generate(rabbit, block=block, source_space='blockface', target_space='exvivo', base_dir=base_dir)
block_as_exvivo = so.ApplyGrid.Create(to_exvivo, device=device)(block_vol, to_exvivo)
io.SaveITKFile(block_as_exvivo, f'{out_path}/volumes/deformable/{block}_to_exvivo.nii.gz')
del block_as_exvivo, to_exvivo
torch.cuda.empty_cache()
print('done')
def main(rabbit, base_dir='/hdscratch/ucair/'):
device = 'cuda:1'
in_path = f'{base_dir}{rabbit}/mri/exvivo/volumes/raw/'
out_base = f'{base_dir}{rabbit}/mri/exvivo/volumes/deformable/invivo/'
if not os.path.exists(out_base):
os.makedirs(out_base)
to_invivo = generate(rabbit,
source_space='exvivo',
target_space='invivo',
base_dir=base_dir)
t2_file = sorted(glob.glob(f'{in_path}*t2*'))
t1_file = sorted(glob.glob(f'{in_path}*VIBE*'))
if len(t1_file) > 1:
t1_file = [x for x in t1_file if '0p5' in x]
exvivo_t2 = io.LoadITKFile(t2_file[0], device=device)
exvivo_t1 = io.LoadITKFile(t1_file[0], device=device)
def_t2 = so.ApplyGrid.Create(to_invivo, device=device)(exvivo_t2,
to_invivo)
def_t1 = so.ApplyGrid.Create(to_invivo, device=device)(exvivo_t1,
to_invivo)
io.SaveITKFile(def_t2,
f'{out_base}exvivo_t2_def_to_invivo_{rabbit}.nii.gz')
io.SaveITKFile(def_t1,
f'{out_base}exvivo_t1_def_to_invivo_{rabbit}.nii.gz')
# #
# to_exvivo = generate(rabbit, source_space='invivo', target_space='exvivo')
# to_exvivo_affine = generate_affine_only(rabbit, source_space='invivo', target_space='exvivo')
#
# invivo = io.LoadITKFile(sorted(glob.glob(f'/hdscratch/ucair/{rabbit}/mri/invivo/volumes/raw/*t2*'))[0], device=device)
# aff_invivo = so.ApplyGrid.Create(to_exvivo_affine, device=device)(invivo, to_exvivo_affine)
# def_invivo = so.ApplyGrid.Create(to_exvivo, device=device)(invivo, to_exvivo)
#
# io.SaveITKFile(aff_invivo, f'/home/sci/blakez/test_outs/invivo_aff_to_exvivo_npv_{rabbit}.nii.gz')
# io.SaveITKFile(def_invivo, f'/home/sci/blakez/test_outs/invivo_def_to_exvivo_npv_{rabbit}.nii.gz')
#
# io.SaveITKFile(def_exvivo, f'{out_base}/invivo/{exvivo_name}_to_invivo.nii.gz')
print('done')
def deform_image_volumes(rabbit, block, base_dir='/hdscratch/ucair/'):
histology_dir = f'{base_dir}{rabbit}/microscopic/{block}/'
raw_dir = f'{histology_dir}/volume/raw/'
out_dir = f'{histology_dir}/volume/deformable/'
if not os.path.exists(out_dir):
os.makedirs(out_dir)
deformation = generate(rabbit,
block,
source_space='blockface',
target_space='invivo',
base_dir=base_dir,
pad_mode='zeros')
def_file = f'/home/sci/blakez/ucair/longitudinal/{rabbit}/'
def_file += 'deformation_fields/Day3_non_contrast_VIBE_interday_deformation_incomp.nii.gz'
day0 = io.LoadITKFile(
f'/hdscratch/ucair/AcuteBiomarker/Data/{rabbit}/{rabbit}_day3_to_day0_phi_inv.nii.gz',
device=device)
deformation = so.ComposeGrids.Create(
device=device, padding_mode='zeros')([day0, deformation])
deformation.to_(device=device)
deformation.set_size((512, 512, 512))
# Load the original volume
image_vol = io.LoadITKFile(f'{raw_dir}/{block}_image_volume.mhd',
device=device)
def_image = so.ApplyGrid.Create(deformation, device=device)(image_vol,
deformation)
test_diff_z = np.diff(deformation.data[0, :].cpu().numpy())
test_diff_y = np.diff(deformation.data[1, :].cpu().numpy())
test_diff_x = np.diff(deformation.data[2, :].cpu().numpy())
test_diff_z_small = np.abs(test_diff_z) >= 0.5
test_diff_y_small = np.abs(test_diff_y) >= 0.5
test_diff_x_small = np.abs(test_diff_x) >= 0.5
mask = np.logical_and(np.logical_and(test_diff_x == 0, test_diff_y == 0),
test_diff_z == 0)
mask_small = np.logical_and(
np.logical_and(test_diff_x_small == 0, test_diff_y_small == 0),
test_diff_z_small == 0)
final_mask = np.logical_and(mask == False, mask_small == True)
mask = torch.zeros_like(def_image.data)[0, None]
mask[:, :, :, :-1] = torch.tensor(final_mask)
def_image.data = def_image.data * mask
io.SaveITKFile(def_image, f'{out_dir}/{block}_image_volume_to_invivo.mhd')
def process_mrti_data(rabbit, out_path):
rerun = False
if os.path.exists(f'{out_path}/{rabbit}_thermal_vol.nii.gz') and not rerun:
print(f'Processing MRTI for {rabbit} ... done')
return
print(f'Processing MRTI for {rabbit} ... ', end='')
data_dir = f'/hdscratch/ucair/AcuteBiomarker/Data/mrti/'
files = sorted(glob.glob(f'{data_dir}/*'))
mat_file = [x for x in files if rabbit in x][0]
mrti_dict = loadmat(mat_file)
cs_data = np.transpose(mrti_dict['PosDCS'][:, :, :, 0:3], (2, 1, 0, 3))
mrti_data = np.transpose(mrti_dict['temps'], (2, 1, 0, 3))
ctd_map = np.nan_to_num(np.transpose(mrti_dict['CTD_Map'], (2, 1, 0)),
nan=1.0)
ctd_map = np.log(ctd_map)
origin = np.ascontiguousarray(cs_data[0, 0, 0, ::-1])
thermal_vol = core.StructuredGrid(size=mrti_data.shape[0:3],
origin=origin,
spacing=torch.tensor([1.0, 1.0, 1.0]),
tensor=torch.tensor(mrti_data).permute(
3, 0, 1, 2),
channels=mrti_data.shape[-1])
log_ctd_map = core.StructuredGrid(
size=mrti_data.shape[0:3],
origin=origin,
spacing=torch.tensor([1.0, 1.0, 1.0]),
tensor=torch.tensor(ctd_map).unsqueeze(0),
channels=1)
io.SaveITKFile(thermal_vol, f'{out_path}/{rabbit}_thermal_vol.nii.gz')
io.SaveITKFile(log_ctd_map, f'{out_path}/{rabbit}_log_ctd_map.nii.gz')
print('done')
def generate_hist_label(rabbit, base_dir, out_path):
rerun = True
device = 'cuda:1'
# if os.path.exists(f'{out_path}/{rabbit}_hist_label.nii.gz') and not rerun:
# print(f'Processing label for {rabbit} ... done')
# return
print(f'Processing label for {rabbit} ... ', end='')
# Get the path for the
# try:
deform = io.LoadITKFile(f'{out_path}/{rabbit}_day3_to_day0_phi_inv.nii.gz',
device=device)
# except:
# def_file = f'/home/sci/blakez/ucair/longitudinal/{rabbit}/'
# def_file += 'deformation_fields/Day3_non_contrast_VIBE_interday_deformation_incomp.nii.gz'
# deform = io.LoadITKFile(def_file, device=device)
# io.SaveITKFile(deform, f'{out_path}/{rabbit}_day3_to_day0_phi_inv.nii.gz')
# Load the ablation to day3 segmentation
hist_file = f'{base_dir}/{rabbit}/microscopic/recons/all_ablation_segs_to_invivo.nrrd'
if not os.path.exists(hist_file):
hist_file = f'{base_dir}/{rabbit}/microscopic/recons/all_ablation_segs_to_invivo.mhd'
hist_seg = io.LoadITKFile(hist_file, device=device)
def_hist = so.ApplyGrid.Create(deform, device=device)(hist_seg, deform)
def_hist.to_('cpu')
def_hist.data = (def_hist.data >= 0.5).float()
def_hist_np = binary_erosion(binary_dilation(def_hist.data.squeeze(),
iterations=4),
iterations=4)
def_hist.data = torch.tensor(def_hist_np).unsqueeze(0).float()
io.SaveITKFile(def_hist, f'{out_path}/{rabbit}_hist_label.nii.gz')
print('done')
def generate_label_volume(rabbit, block):
data_dir = f'/hdscratch/ucair/{rabbit}/blockface/{block}/'
tif_files = sorted(glob.glob(f'{data_dir}volumes/raw/labels_tif/*'))
hdr = read_mhd_header(f'{data_dir}volumes/raw/difference_volume.mhd')
hdr['ElementDataFile'] = hdr['ElementDataFile'].replace(
'difference', 'segmentation')
hdr['ElementNumberOfChannels'] = 1
# Load each of the tif images and then dump it into the label dir
for tif_file in tif_files:
tif_name = tif_file.split('/')[-1].split('.')[0]
if os.path.exists(
f'{data_dir}volumes/raw/segmentation/{tif_name}.mhd'):
continue
tif = io.LoadITKFile(tif_file)
io.SaveITKFile(tif,
f'{data_dir}volumes/raw/segmentation/{tif_name}.mhd')
write_mhd_header(f'{data_dir}volumes/raw/segmentation_volume.mhd', hdr)
def data_transfer(regObj, opt):
rabbitNumber = regObj.rabbitDirectory.split('/')[-2]
# Try to read the list that comes from transferring the data
# If it isn't there, then assume we need to transfer the data
try:
dicomList = rc.ReadList(regObj.rabbitDirectory +
'/ConfigFiles/source_volume_list.txt')
except IOError:
# Use subprocess to get the list of files from RAID2
p = sp.Popen([
"ssh", "*****@*****.**",
f"find {opt.raw_dir}*{opt.rabbit[-2:]}* -type d"
],
stdout=sp.PIPE)
raidDirs, _ = p.communicate()
# There is a new line at the end which puts an empty at the end of the list
raidDirs = raidDirs.decode('utf-8').split('\n')[:-1]
dicomList = []
# Get a list of the already transferrred timepoints
transfered = sorted(glob.glob(f'{regObj.rabbitDirectory}/rawVolumes/*'))
# Get the names of the timepoints
transfered = [x.split('/')[-1] for x in transfered]
# If all of the timepoints have already been transferred then break
if all([
opt.transfer_timepoints[x] in transfered
for x in range(len(opt.transfer_timepoints))
]):
return
for timepoint in opt.transfer_timepoints:
# Use subprocess to get the list of files from RAID10
p = sp.Popen([
"ssh", "*****@*****.**",
f"find {opt.raw_dir}*{opt.rabbit[-2:]}* -type d"
],
stdout=sp.PIPE)
raidDirs, _ = p.communicate()
# There is a new line at the end which puts an empty at the end of the list
raidDirs = raidDirs.decode('utf-8').split('\n')[:-1]
dicomList = []
# Initialize an empty list
tpList = []
# Create a selector so the ablation volumes can be selected
Selector = rc.PathSelector(tk, sorted(raidDirs),
f'Choose {timepoint} Day Files to Convert')
convertFiles = Selector.get_files()
Selector.root.destroy()
tpList += convertFiles
dicomList += convertFiles
for i, path in enumerate(tpList, 1):
# Get the name of the file
filename = path.split('s0')[-1].split(' ')[-1]
# Correct the special characters in the path string so the scp command will work
path = path.replace("^", "\^").replace(" ", "\ ")
rawOutName = f'{regObj.rabbitDirectory}/rawDicoms/{timepoint}/{i:03d}_----_{filename}'
volOutName = f'{regObj.rabbitDirectory}/rawVolumes/{timepoint}/{i:03d}_----_{filename}'
rawOutName = rawOutName.replace('\\ ', '_').replace('\ ', '_')
volOutName = volOutName.replace('\\ ', '_').replace('\ ', '_')
# If the volume doesn't already exist, then copy it over
if not os.path.exists(rawOutName):
os.makedirs(rawOutName)
p = sp.Popen([
"scp", "-r", f"[email protected]:{path}/*",
rawOutName
])
os.waitpid(p.pid, 0)
if len(glob.glob(rawOutName + '/*')) == 0:
p = sp.Popen([
"scp", "-r", f"[email protected]:{path}/*",
rawOutName
])
os.waitpid(p.pid, 0)
if not os.path.exists(os.path.dirname(volOutName)):
os.makedirs(os.path.dirname(volOutName))
# Load the DICOM into a CAMP object
# if not os.path.exists(volOutName + '.nii.gz') and not os.path.exists(volOutName + '_00.nii.gz'):
rcsVolume = rc.LoadDICOM(rawOutName, opt.device)
if type(rcsVolume) == list:
for im in rcsVolume:
io.SaveITKFile(
im, volOutName + '_{0}.nii.gz'.format(
str(rcsVolume.index(im)).zfill(2)))
else:
io.SaveITKFile(rcsVolume, volOutName + '.nii.gz')
# Write out the dicom list that was transferred and reconstructed
rc.WriteList(
dicomList,
regObj.rabbitDirectory + '/ConfigFiles/source_volume_list.txt')
# Check if temperature data exists and if not, transfer it
if regObj.pipelinePhase == 'temperature':
p = sp.Popen([
"ssh", "*****@*****.**",
"find /v/raid2/sjohnson/Data/2018_RabbitData/{0}/TemperatureRecon/ForRegistration_Current/ -type f"
.format(rabbitNumber)
],
stdout=sp.PIPE)
raidDirs, _ = p.communicate()
else:
raidDirs = []
def solve_affines(block_list):
for block_path in block_list:
block = block_path.split('/')[-1]
if not os.path.exists(f'{block_path}/volumes/raw/'):
os.makedirs(f'{block_path}/volumes/raw/difference/')
os.makedirs(f'{block_path}/volumes/raw/surface/')
os.makedirs(f'{block_path}/volumes/raw/scatter/')
# elif sorted(glob.glob(f'{block_path}/volumes/raw/difference/*')):
# print('alread filtered')
# continue
image_list = sorted(glob.glob(f'{block_path}/images/filtered/*'))
if not image_list:
print(f'No filtered image files found for {block} ... skipping')
continue
print(f'Solving Affines for {block} ... ')
spacing = list(
map(float,
input(f'X,Y Spacing for {block}: ').strip().split(' ')))
# spacing = [0.0163, 0.0163]
surface_list = [x for x in image_list if 'surface' in x]
scatter_list = [x for x in image_list if 'scatter' in x]
ImScatter = io.LoadITKFile(scatter_list[0], device=device)
ImScatter.set_spacing_(spacing)
ImScatter.set_origin_(-1 * (ImScatter.size * ImScatter.spacing) / 2)
ImScatter /= ImScatter.max()
# Load the surface image
ImSurface = io.LoadITKFile(surface_list[0], device=device)
ImSurface.set_spacing_(spacing)
ImSurface.set_origin_(-1 * (ImSurface.size * ImSurface.spacing) / 2)
ImSurface /= ImSurface.max()
# Save out the first image
difference = ImScatter - ImSurface
ImDifference = core.StructuredGrid(
ImSurface.shape()[1:],
tensor=difference.data[2].unsqueeze(0),
spacing=ImSurface.spacing,
origin=ImSurface.origin,
device=device,
dtype=torch.float32,
channels=1)
io.SaveITKFile(
ImScatter, f'{block_path}/volumes/raw/scatter/IMG_001_scatter.mhd')
io.SaveITKFile(
ImSurface, f'{block_path}/volumes/raw/surface/IMG_001_surface.mhd')
io.SaveITKFile(
ImDifference,
f'{block_path}/volumes/raw/difference/IMG_001_difference.mhd')
ImPrev = ImScatter.copy()
Adict = {
'origin': ImPrev.origin.tolist(),
'spacing': ImPrev.spacing.tolist(),
scatter_list.index(scatter_list[0]): np.eye(3).tolist()
}
maxIter = 1000
for scat, surf in zip(scatter_list[1:], surface_list[1:]):
print(f'Registering {scat.split("/")[-1]} .... ')
sys.stdout.flush()
image_num = scat.split('/')[-1].split('_')[1]
# Get the number the file is from the start
dist = scatter_list.index(scat)
# Load the next image
ImScatter = io.LoadITKFile(scat, device=device)
ImScatter.set_spacing_(ImPrev.spacing)
ImScatter.set_origin_(ImPrev.origin)
ImScatter /= ImScatter.max()
ImSurface = io.LoadITKFile(surf, device=device)
ImSurface.set_spacing_(ImPrev.spacing)
ImSurface.set_origin_(ImPrev.origin)
ImSurface /= ImSurface.max()
difference = ImScatter - ImSurface
ImDifference = core.StructuredGrid(
ImSurface.shape()[1:],
tensor=difference.data[2].unsqueeze(0),
spacing=ImSurface.spacing,
origin=ImSurface.origin,
device=device,
dtype=torch.float32,
channels=1)
affine = affine_register(ImPrev.copy(),
ImSurface.copy(),
niter=maxIter,
device=device)
# Save out the images
aff_filter = so.AffineTransform.Create(affine=affine,
device=device)
aff_scatter = aff_filter(ImScatter)
aff_surface = aff_filter(ImSurface)
aff_difference = aff_filter(ImDifference)
# difference = (difference - difference.min()) / (difference.max() - difference.min())
io.SaveITKFile(
aff_scatter,
f'{block_path}/volumes/raw/scatter/IMG_{image_num}_scatter.mhd'
)
io.SaveITKFile(
aff_surface,
f'{block_path}/volumes/raw/surface/IMG_{image_num}_surface.mhd'
)
io.SaveITKFile(
aff_difference,
f'{block_path}/volumes/raw/difference/IMG_{image_num}_difference.mhd'
)
Adict[dist] = affine.detach().cpu().clone().tolist()
ImPrev = aff_scatter.copy()
with open(f'{block_path}/volumes/raw/{block}_affine_dictionary.yaml',
'w') as f:
yaml.dump(Adict, f)
_make_volumes(block_path)
def RigidMatch(regObj, opt):
# Load the points or ask where they are
try:
src_points = rc.load_slicer_points(regObj.rigid.sourcePointsFile)
tar_points = rc.load_slicer_points(regObj.rigid.targetPointsFile)
except IOError:
regObj.rigid.sourcePointsFile = _getFilePath(
'Source Points File ({0} rigid)'.format(regObj.pipelinePhase),
initialdir=regObj.rabbitDirectory)
regObj.rigid.targetPointsFile = _getFilePath(
'Target Points File ({0} rigid)'.format(regObj.pipelinePhase),
initialdir=regObj.rabbitDirectory)
src_points = rc.load_slicer_points(regObj.rigid.sourcePointsFile)
tar_points = rc.load_slicer_points(regObj.rigid.targetPointsFile)
# Use the points to find a rigid transformation
rigidMat = rc.SolveRigidAffine(src_points, tar_points)
# Change to a torch tensor to use with CAMP and inverse for camp
rigidMat = torch.tensor(rigidMat, device=opt.device,
dtype=torch.float32).inverse()
regObj.rigid.rigidMatrix = rigidMat.cpu().numpy().tolist()
regObj.rigid.outputPath = regObj.rabbitDirectory + '/rigidVolumes/' + regObj.pipelinePhase
# Create the output directory if it doesn't exist
if not os.path.exists(regObj.rigid.outputPath):
os.makedirs(regObj.rigid.outputPath)
print('Applying rigid transformation to source volumes .... ', end='')
sys.stdout.flush()
# If the pipeline phase is interday, need to check for motion corrected volumes
if regObj.pipelinePhase == 'interday':
# Do this in a try just in case there are no motion corrected files, then it will just skip
try:
# Glob the directory that would contain the motion corrected volumes
motionList = sorted(
glob.glob(regObj.rabbitDirectory +
'/elastVolumes/day3_motion/*.nii.gz'))
motionList += sorted(
glob.glob(regObj.rabbitDirectory +
'/elastVolumes/day3_motion/*.nrrd'))
origNames = [
x.split('/')[-1][:4] + '----' + x.split('/')[-1][8:]
for x in motionList
] # these names have to exist in the source files
# Create a list of paths as these original names would appear
sorcNames = [
os.path.dirname(regObj.sourceVolumes[0]) + '/' + x
for x in origNames
]
regObj.sourceVolumes = sorted(
list(set(regObj.sourceVolumes) - set(sorcNames)))
# Add on the motion list to form the complete list of the source volumes
regObj.sourceVolumes += motionList
except IOError:
pass
for volume in regObj.sourceVolumes:
# Tage the file with an 'r' to indicate rigid reg
fileName = volume.split('/')[-1]
fileName = fileName[:5] + 'r' + fileName[6:]
outName = os.path.join(regObj.rigid.outputPath, fileName)
if not os.path.exists(outName) or regObj.rigid.rerun:
src_im = io.LoadITKFile(volume, opt.device)
aff_im = rc.SolveAffineGrid(src_im,
np.array(regObj.rigid.rigidMatrix))
# Apply and save
if any(x in outName for x in ['MOCO', 'ADC']):
aff_im = so.AffineTransform.Create(affine=rigidMat,
device=opt.device,
interp_mode='nearest')(
src_im, aff_im)
else:
aff_im = so.AffineTransform.Create(affine=rigidMat,
device=opt.device)(src_im,
aff_im)
io.SaveITKFile(aff_im, outName)
print('Done')
def def_block(rabbit, block):
data_dir = f'/hdscratch/ucair/microscopic/{rabbit}/registered/{block}/'
bf_dir = f'/hdscratch/ucair/{rabbit}/blockface/{block}/'
vol_ext = '/volumes/raw/'
raw_ext = '/surfaces/raw/'
def_ext = '/volumes/deformable/'
# Load the affine
aff = np.loadtxt(f'{bf_dir}{raw_ext}{block}_rigid_tform.txt')
aff = torch.tensor(aff, device=device, dtype=torch.float32)
# Load phi_inv
phi_inv = io.LoadITKFile(f'{bf_dir}{vol_ext}{block}_phi_inv.mhd',
device=device)
phi_inv.set_size((60, 1024, 1024))
#
# # Phi_inv is in z,y,x and need x,y,z
phi_inv.data = phi_inv.data.flip(0)
# Load the volume to apply this field to
mic = io.LoadITKFile(f'{data_dir}{block}_histopathology_affine_volume.mhd',
device=device)
# seg = io.LoadITKFile(f'{data_dir}{vol_ext}segmentation_volume.mhd', device=device)
# aff_grid = core.StructuredGrid.FromGrid(phi_inv, channels=3)
# aff_grid.set_to_identity_lut_()
# aff_grid.data = aff_grid.data.flip(0)
# Apply the inverse affine to the grid
aff = aff.inverse()
a = aff[0:3, 0:3].float()
t = aff[-0:3, 3].float()
# aff_grid.data = torch.matmul(a, aff_grid.data.permute(list(range(1, 3 + 1)) + [0]).unsqueeze(-1))
# aff_grid.data = (aff_grid.data.squeeze() + t).permute([3] + list(range(0, 3)))
#
# aff_grid.data = aff_grid.data.flip(0)
#
# aff_bf = so.ApplyGrid.Create(aff_grid, device=aff_grid.device, dtype=aff_grid.dtype)(bf, out_grid=phi_inv)
phi_inv.data = torch.matmul(
a.unsqueeze(0).unsqueeze(0),
phi_inv.data.permute(list(range(1, 3 + 1)) + [0]).unsqueeze(-1))
phi_inv.data = (phi_inv.data.squeeze() + t).permute([-1] +
list(range(0, 3)))
# Flip phi_inv back to the way it was
phi_inv.data = phi_inv.data.flip(0)
# try:
# stitch_files = sorted(glob.glob(f'{data_dir}{vol_ext}{block}_phi_inv_stitch_*.mhd'))
# stitch_list = []
# for stitch_file in stitch_files:
# phi_stitch = io.LoadITKFile(stitch_file, device=device)
# phi_stitch.set_size((60, 1024, 1024))
# stitch_list += [phi_stitch.clone()]
# composer = so.ComposeGrids.Create(padding_mode='border', device=device)
# final_phi = composer([phi_inv] + stitch_list)
# phi_inv = final_phi.clone()
# except IOError:
# pass
def_mic = so.ApplyGrid.Create(phi_inv, pad_mode='zeros',
device=device)(mic, phi_inv)
# def_seg = so.ApplyGrid.Create(phi_inv, pad_mode='zeros', device=device)(seg, phi_inv)
# Save out the deformed volumes
io.SaveITKFile(def_mic,
f'{data_dir}{block}_histopathology_volume_deformable.mhd')
def compose_blocks(rabbit):
data_dir = f'/hdscratch/ucair/microscopic/{rabbit}/registered/'
bf_dir = f'/hdscratch/ucair/{rabbit}/blockface/'
old_dir = f'/home/sci/blakez/ucair/{rabbit}/rawVolumes/ExVivo*/'
def_ext = '/volumes/deformable/'
block_list = [
x.split('/')[-1] for x in sorted(glob.glob(f'{bf_dir}/block*'))
]
# Load the affine
aff = np.loadtxt(glob.glob(f'{old_dir}blocks_to_exvivo_affine.txt')[0])
aff = torch.tensor(aff, device=device, dtype=torch.float32)
# Load the deformation
phi_inv = io.LoadITKFile(glob.glob(f'{old_dir}block_phi_inv.mhd')[0],
device=device)
phi_inv.set_size((512, 512, 512))
phi_inv.data = phi_inv.data.flip(0)
# Apply the inverse affine to the grid
aff = aff.inverse()
a = aff[0:3, 0:3].float()
t = aff[-0:3, 3].float()
phi_inv.data = torch.matmul(
a.unsqueeze(0).unsqueeze(0),
phi_inv.data.permute(list(range(1, 3 + 1)) + [0]).unsqueeze(-1))
phi_inv.data = (phi_inv.data.squeeze() + t).permute([-1] +
list(range(0, 3)))
# Flip phi_inv back to the way it was
phi_inv.data = phi_inv.data.flip(0)
bf_list = []
label_list = []
for block in block_list:
print(f'Deforming {block} ... ', end='')
# if block == block_list[len(block_list) // 2]:
# bf = io.LoadITKFile(f'{data_dir}{block}/volumes/raw/difference_volume.mhd', device=device)
# # lb = io.LoadITKFile(f'{data_dir}{block}/volumes/raw/segmentation_volume.mhd', device=device)
mic = io.LoadITKFile(
f'{data_dir}{block}/{block}_histopathology_volume_deformable.mhd',
device=device)
# lb = io.LoadITKFile(f'{data_dir}{block}{def_ext}segmentation_volume_deformable.mhd', device=device)
def_bf = so.ApplyGrid.Create(phi_inv, pad_mode='zeros',
device=device)(mic, phi_inv)
# def_lb = so.ApplyGrid.Create(phi_inv, pad_mode='zeros', device=device)(lb, phi_inv)
def_bf.to_(device='cpu')
# def_lb.to_(device='cpu')
bf_list.append(def_bf.clone())
# label_list.append(def_lb.clone())
print('Done')
lb_tensor = torch.stack([x.data for x in label_list], dim=0)
lb_tensor = (lb_tensor > 0.45).float()
bf_tensor = torch.stack([x.data for x in bf_list], dim=0)
bf_sum = bf_tensor.sum(0)
lb_sum = lb_tensor.sum(0)
lb_non_zero = lb_sum.clone()
lb_non_zero[lb_non_zero == 0.0] = 1.0
bf_sum_scaled = bf_sum / lb_non_zero
bf_to_exvivo = bf_list[0].clone()
bf_to_exvivo.data = bf_sum_scaled.data.clone()
io.SaveITKFile(bf_to_exvivo, '/home/sci/blakez/TEST_STACKED.mhd')
print('Done')
def corrections(rabbit_dir, block, corr_num):
block_path = f'{rabbit_dir}{block}/'
image_list = sorted(glob.glob(f'{block_path}/images/filtered/*'))
with open(f'{block_path}/volumes/raw/{block}_affine_dictionary.yaml',
'r') as f:
Adict = yaml.load(f, Loader=yaml.FullLoader)
surface_list = [x for x in image_list if 'surface' in x]
scatter_list = [x for x in image_list if 'scatter' in x]
# Load the surface image
ImSurface_good = io.LoadITKFile(surface_list[corr_num - 1], device=device)
ImSurface_good.set_spacing_(Adict['spacing'])
ImSurface_good.set_origin_(
-1 * (ImSurface_good.size * ImSurface_good.spacing) / 2)
ImSurface_good /= 255.0
ImSurface_bad = io.LoadITKFile(surface_list[corr_num], device=device)
ImSurface_bad.set_spacing_(Adict['spacing'])
ImSurface_bad.set_origin_(-1 *
(ImSurface_bad.size * ImSurface_bad.spacing) / 2)
ImSurface_bad /= 255.0
# Apply the affines to both of the images
aff_filter = so.AffineTransform.Create(affine=torch.tensor(Adict[corr_num -
1],
device=device),
device=device)
ImSurface_good = aff_filter(ImSurface_good)
aff_filter = so.AffineTransform.Create(affine=torch.tensor(Adict[corr_num],
device=device),
device=device)
ImSurface_bad = aff_filter(ImSurface_bad)
points = torch.tensor(tools.LandmarkPicker(
[ImSurface_bad[0].squeeze().cpu(), ImSurface_good[0].squeeze().cpu()]),
dtype=torch.float32,
device=device).permute(1, 0, 2)
# Change to real coordinates
points *= torch.cat([
ImSurface_good.spacing[None, None, :], ImSurface_good.spacing[None,
None, :]
], 0)
points += torch.cat([
ImSurface_good.origin[None, None, :], ImSurface_good.origin[None,
None, :]
], 0)
aff_filter = so.AffineTransform.Create(points[1], points[0], device=device)
corr_affine = torch.eye(3, device=device, dtype=torch.float32)
corr_affine[0:2, 0:2] = aff_filter.affine
corr_affine[0:2, 2] = aff_filter.translation
ImPrev = ImSurface_good.copy()
for scat, surf in zip(scatter_list[corr_num:], surface_list[corr_num:]):
print(f'Registering {scat.split("/")[-1]} .... ')
sys.stdout.flush()
image_num = scat.split('/')[-1].split('_')[1]
# Get the number the file is from the start
dist = scatter_list.index(scat)
# Load the next image
ImScatter = io.LoadITKFile(scat, device=device)
ImScatter.set_spacing_(ImPrev.spacing)
ImScatter.set_origin_(ImPrev.origin)
ImScatter /= 255.0
ImSurface = io.LoadITKFile(surf, device=device)
ImSurface.set_spacing_(ImPrev.spacing)
ImSurface.set_origin_(ImPrev.origin)
ImSurface /= 255.0
difference = ImScatter - ImSurface
ImDifference = core.StructuredGrid(
ImSurface.shape()[1:],
tensor=difference.data[2].unsqueeze(0),
spacing=ImSurface.spacing,
origin=ImSurface.origin,
device=device,
dtype=torch.float32,
channels=1)
affine = torch.mm(corr_affine, torch.tensor(Adict[dist],
device=device))
# Save out the images
aff_filter = so.AffineTransform.Create(affine=affine, device=device)
aff_scatter = aff_filter(ImScatter)
aff_surface = aff_filter(ImSurface)
aff_difference = aff_filter(ImDifference)
# difference = (difference - difference.min()) / (difference.max() - difference.min())
io.SaveITKFile(
aff_scatter,
f'{block_path}/volumes/raw/scatter/IMG_{image_num}_scatter.mhd')
io.SaveITKFile(
aff_surface,
f'{block_path}/volumes/raw/surface/IMG_{image_num}_surface.mhd')
io.SaveITKFile(
aff_difference,
f'{block_path}/volumes/raw/difference/IMG_{image_num}_difference.mhd'
)
Adict[dist] = affine.detach().cpu().clone().tolist()
ImPrev = aff_scatter.copy()
with open(f'{block_path}/volumes/raw/{block}_affine_dictionary.yaml',
'w') as f:
yaml.dump(Adict, f)
def register(rabbit, base_dir='/hdscratch/ucair/'):
source_path = f'{base_dir}{rabbit}/mri/exvivo/surfaces/raw/'
target_path = f'{base_dir}{rabbit}/mri/invivo/surfaces/raw/'
source_file = f'{source_path}exvivo_ablation_region_decimate.obj'
target_file = f'{target_path}invivo_ablation_region_decimate.obj'
verts, faces = io.ReadOBJ(target_file)
invivo_surface = core.TriangleMesh(verts, faces)
invivo_surface.to_(device=device)
verts, faces = io.ReadOBJ(source_file)
exvivo_surface = core.TriangleMesh(verts, faces)
exvivo_surface.to_(device=device)
print('Starting Affine ... ')
# Load or create the dictionary for registration
try:
with open(f'{source_path}affine_config.yaml', 'r') as f:
params = yaml.load(f, Loader=yaml.FullLoader)
except IOError:
params = {
'spatial_sigma': [15.0],
'affine_lr': 1.0e-07,
'translation_lr': 1.0e-06,
'converge': 4.0
}
try:
aff = np.loadtxt(f'{source_path}exvivo_to_invivo_affine.txt')
aff = torch.tensor(aff, device=device)
except IOError:
aff = affine(invivo_surface.copy(),
exvivo_surface.copy(),
affine_lr=params['affine_lr'],
translation_lr=params['translation_lr'],
converge=params['converge'],
spatial_sigma=params['spatial_sigma'],
device=device)
# Save out the parameters:
with open(f'{source_path}affine_config.yaml', 'w') as f:
yaml.dump(params, f)
np.savetxt(f'{source_path}exvivo_to_invivo_affine.txt',
aff.cpu().numpy())
aff_tfrom = uo.AffineTransformSurface.Create(aff, device=device)
aff_exvivo = aff_tfrom(exvivo_surface)
if not os.path.exists(f'{source_path}../affine/'):
os.makedirs(f'{source_path}../affine/')
io.WriteOBJ(
aff_exvivo.vertices, aff_exvivo.indices,
f'{source_path}../affine/exvivo_to_invivo_{rabbit}_affine.obj')
print('Starting Deformable ... ')
try:
with open(f'{source_path}/deformable_config.yaml', 'r') as f:
params = yaml.load(f, Loader=yaml.FullLoader)
except IOError:
params = {
'currents_sigma': [5.0, 1.0],
'propagation_sigma': [8.0, 8.0, 8.0],
'deformable_lr': [2.0e-04, 1.0e-04],
'converge': 4.0,
'phi_inv_size': [32, 32, 32],
'n_iters': 500,
}
def_surface, _, phi, phi_inv = tools.deformable_register(
invivo_surface.copy(),
aff_exvivo.copy(),
src_excess=None,
deformable_lr=params['deformable_lr'],
currents_sigma=params['currents_sigma'],
prop_sigma=params['propagation_sigma'],
converge=params['converge'],
grid_size=params['phi_inv_size'],
accu_forward=True,
accu_inverse=True,
device=device,
grid_device='cuda:0',
expansion_factor=1.5,
iters=params['n_iters'])
# Save out the parameters:
with open(f'{source_path}deformable_config.yaml', 'w') as f:
yaml.dump(params, f)
if not os.path.exists(f'{source_path}../../volumes/raw//'):
os.makedirs(f'{source_path}../../volumes/raw//')
if not os.path.exists(f'{source_path}../deformable/'):
os.makedirs(f'{source_path}../deformable/')
io.SaveITKFile(
phi_inv,
f'{source_path}../../volumes/raw/exvivo_to_invivo_phi_inv.mhd')
io.SaveITKFile(phi,
f'{source_path}../../volumes/raw/exvivo_to_invivo_phi.mhd')
io.WriteOBJ(def_surface.vertices, def_surface.indices,
f'{source_path}../deformable/exvivo_to_invivo_deformable.obj')
def stitch_surfaces(rabbit):
rabbit_dir = f'/hdscratch/ucair/{rabbit}/blockface/'
raw_ext = '/surfaces/raw/'
vol_ext = '/volumes/raw/'
# Get a list of the blocks
block_list = sorted(glob.glob(f'{rabbit_dir}block*'))
# complete = ['block08']
complete = ['block06', 'block09']
for i, block_path in enumerate(block_list):
block = block_path.split('/')[-1]
stitching_dir = f'{rabbit_dir}{block}{raw_ext}/stitching/'
if block in complete:
continue
if not os.path.exists(stitching_dir):
print(f'No stitching surfaces found for {block}.')
continue
target_surface_path = f'{stitching_dir}/raw/{block}_target_faces.obj'
source_surface_path = f'{stitching_dir}/raw/{block}_source_faces.obj'
# Load the target surface
try:
verts, faces = io.ReadOBJ(target_surface_path)
tar_surface = core.TriangleMesh(verts, faces)
tar_surface.to_(device)
except IOError:
print(
f'The target stitching surface for {block} was not found ... skipping'
)
continue
try:
verts, faces = io.ReadOBJ(source_surface_path)
src_surface = core.TriangleMesh(verts, faces)
src_surface.to_(device)
src_surface.flip_normals_()
except IOError:
print(
f'The source stitching surface for {block} was not found ... skipping'
)
continue
# Need to load the exterior to drag along
try:
verts, faces = io.ReadOBJ(
f'{rabbit_dir}/{block}/{raw_ext}/{block}_decimate.obj')
surface_ext = core.TriangleMesh(verts, faces)
surface_ext.to_(device)
except IOError:
print(
f'The source stitching surface for {block} was not found ... skipping'
)
continue
# Determine the surface half way between the source and the target
try:
with open(
f'{stitching_dir}/raw/{block}_middle_surface_config.yaml',
'r') as f:
params = yaml.load(f, Loader=yaml.FullLoader)
except IOError:
params = {
'currents_sigma': [5.0, 0.25, 0.05],
'propagation_sigma': [1.0, 1.0, 1.0],
'deformable_lr': [0.0008, 0.01, 0.01],
'converge': 0.05,
'mid_offset': 0.5
}
# Do the deformable registration
def_src_surface, def_ext = tools.deformable_register(
tar_surface.copy(),
src_surface.copy(),
src_excess=None,
deformable_lr=params['deformable_lr'],
currents_sigma=params['currents_sigma'],
prop_sigma=params['propagation_sigma'],
grid_size=None,
converge=params['converge'],
accu_forward=False,
accu_inverse=False,
device=device,
)
new_verts = src_surface.vertices.clone() + (
(def_src_surface.vertices - src_surface.vertices) *
params['mid_offset'])
mid_surface = src_surface.copy()
mid_surface.vertices = new_verts.clone()
mid_surface.calc_normals()
mid_surface.calc_centers()
io.WriteOBJ(
def_src_surface.vertices, def_src_surface.indices,
f'{stitching_dir}/deformable_pieces/{block}_source_faces.obj')
io.WriteOBJ(
mid_surface.vertices, mid_surface.indices,
f'{stitching_dir}/deformable_pieces/{block}_source_middle.obj')
with open(f'{stitching_dir}/raw/{block}_middle_surface_config.yaml',
'w') as f:
yaml.dump(params, f)
# Load the binary volume for the block
mask = io.LoadITKFile(
f'{rabbit_dir}/{block}/{vol_ext}/segmentation_volume.mhd',
device='cuda:0')
# Load the other surfaces to drag along
extras_paths = [
f'{rabbit_dir}{block}{raw_ext}{block}_decimate.obj',
f'{rabbit_dir}{block}{raw_ext}{block}_ext.obj'
]
if os.path.exists(f'{rabbit_dir}{block}{raw_ext}{block}_head.obj'):
extras_paths += [f'{rabbit_dir}{block}{raw_ext}{block}_head.obj']
if os.path.exists(f'{rabbit_dir}{block}{raw_ext}{block}_foot.obj'):
extras_paths += [f'{rabbit_dir}{block}{raw_ext}{block}_foot.obj']
if os.path.exists(
f'{rabbit_dir}{block}{raw_ext}{block}_head_support.obj'):
extras_paths += [
f'{rabbit_dir}{block}{raw_ext}{block}_head_support.obj'
]
if os.path.exists(
f'{rabbit_dir}{block}{raw_ext}{block}_foot_support.obj'):
extras_paths += [
f'{rabbit_dir}{block}{raw_ext}{block}_foot_support.obj'
]
extra_surfaces = []
for path in extras_paths:
try:
verts, faces = io.ReadOBJ(path)
except IOError:
extra_name = path.split('/')[-1]
print(
f'{extra_name} not found as an extra ... removing from list'
)
_ = extras_paths.pop(extras_paths.index(path))
continue
extra_surfaces += [core.TriangleMesh(verts, faces)]
extra_surfaces[-1].to_(device)
# Define the diffusion parameters for the registration
try:
with open(f'{stitching_dir}/raw/{block}_diffusion_config.yaml',
'r') as f:
diff_params = yaml.load(f, Loader=yaml.FullLoader)
except IOError:
diff_params = {
'z_diff_c': 5.0,
'y_diff_c': 200.0,
'x_diff_c': 30.0,
'background_c': 0.5,
'niter': 10000,
'gamma': 0.0005,
'propegation_sigma': [0.2, 0.2, 0.2],
'grad_amp': 300.0
}
try:
with open(
f'{stitching_dir}/raw/{block}_stitch_surface_config.yaml',
'r') as f:
params = yaml.load(f, Loader=yaml.FullLoader)
except IOError:
params = {
'currents_sigma': [2.0, 1.0],
'smoothing_sigma': [2.0, 2.0, 2.0],
'deformable_lr': [0.0001, 0.001],
'grid_size': [40, 256, 256],
'converge': 0.05,
'grid_device': 'cpu',
'niters': 25
}
# Do the deformable registration with the source to the mid
def_src_surface, def_tar_surface, def_extra_surfaces, phi, phi_inv = deformable_register(
tar_surface.copy(),
src_surface.copy(),
mid_surface.copy(),
src_excess=extra_surfaces,
deformable_lr=params['deformable_lr'],
currents_sigma=params['currents_sigma'],
prop_sigma=params['smoothing_sigma'],
grid_size=params['grid_size'],
converge=params['converge'],
accu_forward=True,
accu_inverse=True,
grid_device=params['grid_device'],
device=device,
mask=mask,
diff_params=diff_params,
iters=params['niters'])
with open(f'{stitching_dir}/raw/{block}_stitch_surface_config.yaml',
'w') as f:
yaml.dump(params, f)
with open(f'{stitching_dir}/raw/{block}_diffusion_config.yaml',
'w') as f:
yaml.dump(diff_params, f)
io.WriteOBJ(
def_src_surface.vertices, def_src_surface.indices,
f'{stitching_dir}/deformable/{block}_whole_stitched_decimate.obj')
io.SaveITKFile(phi,
f'{stitching_dir}/deformable/{block}_stitch_phi.mhd')
io.SaveITKFile(
phi_inv, f'{stitching_dir}/deformable/{block}_stitch_phi_inv.mhd')
out_path = f'{stitching_dir}/deformable/'
for extra_path, extra_surface in zip(extras_paths, def_extra_surfaces):
name = extra_path.split('/')[-1]
io.WriteOBJ(extra_surface.vertices, extra_surface.indices,
f'{out_path}{name}')
vol = io.LoadITKFile(
'/hdscratch/ucair/18_047/blockface/block08/volumes/raw/difference_volume.mhd',
device='cuda:0')
# phi_inv.set_size((60, 1024, 1024))
# phi.set_size((60, 1024, 1024))
# resampled_stitched = so.ApplyGrid.Create(phi_inv, device='cuda:0')(vol, phi_inv)
# resampled_unstitched = so.ApplyGrid.Create(phi, device='cuda:0')(resampled_stitched, phi)
# io.SaveITKFile(resampled_stitched, '/home/sci/blakez/stitched_block08.mhd')
# io.SaveITKFile(resampled_unstitched, '/home/sci/blakez/unstitched_block08.mhd')
print(f'Done stitching {block} ... ')
def mr_to_block(block_path, rabbit):
day0_dir = f'/hdscratch/ucair/{rabbit}/mri/day0/'
day3_dir = f'/hdscratch/ucair/{rabbit}/mri/invivo/'
stacked_blocks_dir = f'/hdscratch/ucair/{rabbit}/blockface/recons/'
block = block_path.split('/')[-1]
# exvivo_out = f'/hdscratch/ucair/18_047/mri/exvivo/volumes/deformable/{block}/'
invivo_out = f'/hdscratch/ucair/18_062/mri/day0/volumes/deformable/{block}/'
if not os.path.exists(invivo_out):
os.makedirs(invivo_out)
deformations = []
# # Get the transformation from day0 to day3
# day0_to_day3 = get_day0_to_day3(day0_dir)
# deformations.append(day0_to_day3)
in_path = f'/hdscratch/ucair/{rabbit}/'
# Need to load and deform the day 0 NPV volume
day0_files = sorted(glob.glob(f'/scratch/rabbit_data/{rabbit}/rawVolumes/Ablation*/*'))
# day3_files = sorted(glob.glob(f'{in_path}/mri/invivo/volumes/raw/*'))
# hist_file = f'{in_path}/microscopic/recons/all_ablation_segs_to_invivo.nrrd'
# if not os.path.exists(hist_file):
# hist_file = f'{in_path}/microscopic/recons/all_ablation_segs_to_invivo.mhd'
interday_file = sorted(glob.glob(f'{in_path}/mri/day0/volumes/raw/*'))
log_ctd = '/hdscratch/ucair/AcuteBiomarker/Data/18_062/18_062_log_ctd_map.nii.gz'
t1_nc_file = '/home/sci/blakez/ucair/longitudinal/18_062/Day0_non_contrast_VIBE.nii.gz'
day0_npv_file = [x for x in day0_files if 'npv' in x or 'NPV' in x and '.nrrd' in x][0]
day0_t1_file = [x for x in day0_files if '0.5x' in x][-1]
# day3_npv_file = [x for x in day3_files if 'npv' in x or 'NPV' in x and '.nrrd' in x][0]
interday = [x for x in interday_file if 'phi' in x and '.mhd' in x][0]
day0_npv = io.LoadITKFile(day0_npv_file, device)
day0_t1 = io.LoadITKFile(day0_t1_file, device)
deform = io.LoadITKFile(interday, device)
log_ctd = io.LoadITKFile(log_ctd, device)
day0_nc_t1 = io.LoadITKFile(t1_nc_file, device)
def_day0 = so.ApplyGrid.Create(deform, device=device)(day0_npv, deform)
def_day0_t1 = so.ApplyGrid.Create(deform, device=device)(day0_t1, deform)
def_log_ctd = so.ApplyGrid.Create(deform, device=device)(log_ctd, deform)
def_nc_t1 = so.ApplyGrid.Create(deform, device=device)(day0_nc_t1, deform)
to_block = gd.generate(rabbit, block=block, source_space='invivo', target_space='blockface')
# Get the transformation with the affine included from invivo to exvivo
# invivo_to_exvivo = mr_to_exvivo(day3_dir)
# deformations.append(invivo_to_exvivo)
# Get the transformation with the affine included from exvivo to the stacked blocks
# exvivo_to_stacked = exvivo_to_blocks(stacked_blocks_dir)
# deformations.append(exvivo_to_stacked)
#
# # Load the transformation from the stacked blocks to the block of interest
# stacked_to_block = stacked_blocks_to_block(block_path)
# deformations.append(stacked_to_block)
# # Load the transformation for stitching if there is one
# if os.path.exists(f'{block_path}/volumes/raw/{block}_phi_stitch.mhd'):
# block_stitching = block_stitch(block_path)
# deformations.append(block_stitching)
# Load the Day3 MR file to be deformed
# t2_motion = io.LoadITKFile(
# '/home/sci/blakez/ucair/18_047/rawVolumes/Ablation_2018-06-28/089_----_t2_spc_1mm_iso_cor_post20min.nii.gz',
# device=device
# )
#
# ce_t1 = io.LoadITKFile(
# '/home/sci/blakez/ucair/18_047/rawVolumes/Ablation_2018-06-28/102_----_3D_VIBE_1mmIso_NoGrappa_1avg_fatsat_cor_00.nii.gz',
# device=device
# )
# npv = io.LoadITKFile(
# '/hdscratch/ucair/18_062/mri/invivo/volumes/raw/028_----_Day3_lr_NPV_Segmentation_062.nrrd',
# device=device
# )
# ctd = io.LoadITKFile(
# '/home/sci/blakez/ucair/18_047/rawVolumes/Ablation_2018-06-28/CTD_map.nrrd',
# device=device
# )
# ctd.data[ctd.data < 240] = 0.0
# ctd.data[ctd.data > 0.0] = 1.0
torch.cuda.empty_cache()
# t2_to_block = so.ApplyGrid.Create(invivo_to_block, device=device, pad_mode='zeros')(t2_motion, invivo_to_block)
# io.SaveITKFile(t2_to_block, f'{invivo_out}day0_t2_to_{block}.mhd')
#
# t1_to_block = so.ApplyGrid.Create(invivo_to_block, device=device, pad_mode='zeros')(ce_t1, invivo_to_block)
# io.SaveITKFile(t1_to_block, f'{invivo_out}day0_ce_t1_to_{block}.mhd')
npv_to_block = so.ApplyGrid.Create(to_block, device=device, pad_mode='zeros')(def_day0, to_block)
io.SaveITKFile(npv_to_block, f'{invivo_out}day0_npv_to_{block}.mhd')
t1_to_block = so.ApplyGrid.Create(to_block, device=device, pad_mode='zeros')(def_day0_t1, to_block)
io.SaveITKFile(t1_to_block, f'{invivo_out}day0_t1_to_{block}.mhd')
log_ctd_block = so.ApplyGrid.Create(to_block, device=device, pad_mode='zeros')(def_log_ctd, to_block)
io.SaveITKFile(log_ctd_block, f'{invivo_out}day0_log_ctd_to_{block}.mhd')
def_nc_t1 = so.ApplyGrid.Create(to_block, device=device, pad_mode='zeros')(def_nc_t1, to_block)
io.SaveITKFile(def_nc_t1, f'{invivo_out}day0_t1_nc_to_{block}.mhd')
# ctd_to_block = so.ApplyGrid.Create(invivo_to_block, device=device, pad_mode='zeros')(ctd, invivo_to_block)
# io.SaveITKFile(ctd_to_block, f'{invivo_out}day0_ctd_to_{block}.mhd')
print(f'Done with {block}')
def TPS(regObj, opt):
import matplotlib
matplotlib.use('qt5agg')
import matplotlib.pyplot as plt
plt.ion()
# Load the points or ask where they are
if not os.path.exists(f'{regObj.tps.outputPath}/tps_deformation.nii.gz'
) or regObj.tps.rerun:
regObj.tps.outputPath = regObj.rabbitDirectory + '/tpsVolumes/' + regObj.pipelinePhase
if not os.path.exists(regObj.tps.outputPath):
os.makedirs(regObj.tps.outputPath)
try:
src_points = rc.load_slicer_points(regObj.tps.sourcePointsDir)
tar_points = rc.load_slicer_points(regObj.tps.targetPointsDir)
except IOError:
regObj.tps.sourcePointsDir = _getFilePath(
'Source Points File ({0} TPS)'.format(regObj.pipelinePhase),
initialdir=regObj.rabbitDirectory)
regObj.tps.targetPointsDir = _getFilePath(
'Target Points File ({0} TPS)'.format(regObj.pipelinePhase),
initialdir=regObj.rabbitDirectory)
src_points = rc.load_slicer_points(regObj.tps.sourcePointsDir)
tar_points = rc.load_slicer_points(regObj.tps.targetPointsDir)
try:
source_image = io.LoadITKFile(regObj.tps.source_image, opt.device)
target_image = io.LoadITKFile(regObj.tps.target_image, opt.device)
except RuntimeError:
regObj.tps.source_image = _getFilePath(
'Source Image File (TPS)', initialdir=regObj.rabbitDirectory)
regObj.tps.target_image = _getFilePath(
'Target Image File (TPS)', initialdir=regObj.rabbitDirectory)
source_image = io.LoadITKFile(regObj.tps.source_image, opt.device)
target_image = io.LoadITKFile(regObj.tps.target_image, opt.device)
rbf_filter = so.RadialBasis.Create(tar_points,
src_points,
sigma=1.0,
device=opt.device)
# Solve for the rigid transform for determining the grid to sample onto
rigidMat = rc.SolveRigidAffine(np.array(src_points),
np.array(tar_points))
# Solve for the radial basis funtion deformation
if regObj.tps.incompressible:
rbf_source, rbf_grid = rbf_filter.filter_incompressible(
in_grid=source_image,
out_grid=target_image,
t_step=10000,
conv=0.8,
step=0.03)
else:
rbf_source, rbf_grid = rbf_filter(in_grid=source_image,
out_grid=target_image)
io.SaveITKFile(rbf_grid,
f'{regObj.tps.outputPath}/tps_deformation.nii.gz')
else:
rbf_grid = io.LoadITKFile(
f'{regObj.tps.outputPath}/tps_deformation.nii.gz',
device=opt.device)
# Check if there are rigid volumes, if not, get them from the source
volumes = sorted(glob.glob(regObj.rigid.outputPath + '/*'))
if volumes == []:
volumes = regObj.sourceVolumes
print('Applying TPS transformation to source volumes .... ', end='')
sys.stdout.flush()
for volume in volumes:
# Tag the file with 't' to indicate it had thin plate splines applied
fileName = volume.split('/')[-1]
fileName = fileName[:6] + 't' + fileName[7:]
outName = os.path.join(regObj.tps.outputPath, fileName)
if not os.path.exists(outName) or regObj.tps.rerun:
# Load the source image
src_im = io.LoadITKFile(volume, device=opt.device)
aff_im = rc.SolveAffineGrid(src_im, np.array(rigidMat))
# Determine the subvol onto which the image needs to be resampled
try:
h_resample = so.ResampleWorld.Create(
aff_im, device=opt.device)(rbf_grid)
except RuntimeError:
h_resample = so.ResampleWorld.Create(
target_image, device=opt.device)(rbf_grid)
# Apply and save
if any(x in outName for x in ['MOCO', 'ADC', 't1_map']):
def_im = so.ApplyGrid.Create(h_resample,
device=opt.device,
interp_mode='nearest')(src_im,
h_resample)
else:
def_im = so.ApplyGrid.Create(h_resample,
device=opt.device)(src_im,
h_resample)
io.SaveITKFile(def_im, outName)
print('Done')
def generate_segmentation_volume(rabbit, block, base_dir='/hdscratch/ucair/'):
blockface_dir = f'{base_dir}{rabbit}/blockface/{block}/'
histology_dir = f'{base_dir}{rabbit}/microscopic/{block}/'
def_dir = f'{histology_dir}deformations/'
out_dir = f'{histology_dir}/volume/raw/'
if not os.path.exists(out_dir):
os.makedirs(out_dir)
raw_images = glob.glob(f'{histology_dir}/raw/*_image.tif')
if not raw_images:
raw_images += sorted(raw_images +
glob.glob(f'{histology_dir}/raw/*_image.jpg'))
image_nums = sorted(
[int(x.split('/')[-1].split('_')[1]) for x in raw_images])
deformed_ablation_segs = []
deformed_combined_segs = []
deformed_images = []
for im in image_nums:
print(f'Loading and deforming image {im} ... ', end='')
# Load the healthy segmentation as a reference
healthy = io.LoadITKFile(
f'{histology_dir}segmentations/IMG_{im:03d}/img_{im:03d}_healthy_tissue.nrrd',
device=device)
# Load the affine
aff = np.loadtxt(
glob.glob(f'{def_dir}img_{im:03d}_affine_to_blockface.txt')[0])
aff = torch.tensor(aff, device=device, dtype=torch.float32)
# Load the deformation
deformation_data = io.LoadITKFile(
f'{def_dir}/img_{im:03d}_deformation_to_blockface.mhd',
device=device)
deformation = core.StructuredGrid(
size=deformation_data.size[0:2],
spacing=deformation_data.spacing[1:3],
origin=deformation_data.origin[1:3],
device=deformation_data.device,
tensor=deformation_data.data.squeeze().permute(2, 0, 1),
channels=2)
# Apply the inverse affine to the grid
aff = aff.inverse()
a = aff[0:2, 0:2].float()
t = aff[-0:2, 2].float()
deformation.data = torch.matmul(
a.unsqueeze(0).unsqueeze(0),
deformation.data.permute(list(range(1, 2 + 1)) +
[0]).unsqueeze(-1))
deformation.data = (deformation.data.squeeze() +
t).permute([-1] + list(range(0, 2)))
try:
ablation = io.LoadITKFile(
f'{histology_dir}segmentations/IMG_{im:03d}/img_{im:03d}_ablated_region.nrrd',
device=device)
except RuntimeError:
ablation = (healthy * 0.0).copy()
try:
transition = io.LoadITKFile(
f'{histology_dir}segmentations/IMG_{im:03d}/img_{im:03d}_uncertain_region.nrrd',
device=device)
except RuntimeError:
transition = (healthy * 0.0).copy()
# Load the actual image
#### Apply the affine to the image
mic_file = f'{histology_dir}hdf5/{block}_img{im:03d}_image.hdf5'
meta_dict = {}
with h5py.File(mic_file, 'r') as f:
mic = f['RawImage/ImageData'][:, ::10, ::10]
for key in f['RawImage'].attrs:
meta_dict[key] = f['RawImage'].attrs[key]
mic = core.StructuredGrid(mic.shape[1:],
tensor=torch.tensor(mic,
dtype=torch.float32,
device=device),
spacing=torch.tensor([10.0, 10.0],
dtype=torch.float32,
device=device),
device=device,
dtype=torch.float32,
channels=3)
mic = (mic - mic.min()) / (mic.max() - mic.min())
if not os.path.exists(
f'{histology_dir}deformable/img_{im:03d}_to_blockface/'):
os.makedirs(
f'{histology_dir}deformable/img_{im:03d}_to_blockface/')
def_mic = so.ApplyGrid.Create(deformation, device=device)(mic,
deformation)
# Need to put the mic image in the right slice
z_or = (im - 1) * 0.05
def_mic = core.StructuredGrid(
[2] + list(def_mic.shape()[1:]),
tensor=def_mic.data.unsqueeze(1).repeat(1, 2, 1, 1),
spacing=torch.tensor(
[0.05, def_mic.spacing[0], def_mic.spacing[1]],
dtype=torch.float32,
device=device),
origin=torch.tensor([z_or, def_mic.origin[0], def_mic.origin[1]],
dtype=torch.float32,
device=device),
device=device,
dtype=torch.float32,
channels=3)
io.SaveITKFile(
def_mic,
f'{histology_dir}deformable/img_{im:03d}_to_blockface/img_{im:03d}_to_blockface.mhd'
)
combined = ablation + transition
combined.data = (combined.data >= 0.5).float()
def_ablation = so.ApplyGrid.Create(deformation,
device=device)(ablation,
deformation)
def_combined = so.ApplyGrid.Create(deformation,
device=device)(combined,
deformation)
deformed_ablation_segs.append(def_ablation.copy())
deformed_combined_segs.append(def_combined.copy())
deformed_images.append(def_mic.copy())
del def_ablation, def_combined, def_mic, combined, mic, deformation
torch.cuda.empty_cache()
print('done')
# Now need to load the blockface volume
block_vol = io.LoadITKFile(
f'{blockface_dir}volumes/raw/difference_volume.mhd', device='cpu')
image_vol = core.StructuredGrid(size=block_vol.size,
spacing=block_vol.spacing,
origin=block_vol.origin,
device=block_vol.device,
channels=3)
for ii, im in enumerate(image_nums):
image_vol.data[:, im - 1] = deformed_images[ii].data[:,
0].clone().cpu()
io.SaveITKFile(image_vol, f'{out_dir}/{block}_image_volume.mhd')
del image_vol, deformed_images
torch.cuda.empty_cache()
single_vol = core.StructuredGrid(size=block_vol.size,
spacing=block_vol.spacing,
origin=block_vol.origin,
device=block_vol.device,
channels=1)
for ii, im in enumerate(image_nums):
single_vol.data[:, im -
1] = deformed_ablation_segs[ii].data[:].clone().cpu()
io.SaveITKFile(single_vol,
f'{out_dir}/{block}_ablation_segmentation_no_interp.mhd')
del single_vol
torch.cuda.empty_cache()
# Now need to load the blockface volume
ablation_vol = core.StructuredGrid(size=block_vol.size,
spacing=block_vol.spacing,
origin=block_vol.origin,
device=device,
channels=1)
for ii, im in enumerate(image_nums):
if ii == len(image_nums) - 1:
continue
next_slice = image_nums[ii + 1]
for s, slice in enumerate(range(im, next_slice + 1)):
step = 1.0 / (next_slice - im)
cur_alpha = 1.0 - (s * step)
next_alpa = 0.0 + (s * step)
ablation_vol.data[:, slice] = (
deformed_ablation_segs[ii].data *
cur_alpha) + (deformed_ablation_segs[ii + 1].data * next_alpa)
gauus_ablation = so.Gaussian.Create(1,
10, [0.1, 2, 2],
dim=3,
device=device)(ablation_vol)
io.SaveITKFile(gauus_ablation,
f'{out_dir}/{block}_ablation_segmentation.mhd')
del gauus_ablation, deformed_ablation_segs
torch.cuda.empty_cache()
combined_vol = core.StructuredGrid(size=block_vol.size,
spacing=block_vol.spacing,
origin=block_vol.origin,
device=block_vol.device,
channels=1)
for ii, im in enumerate(image_nums):
if ii == len(image_nums) - 1:
continue
next_slice = image_nums[ii + 1]
for s, slice in enumerate(range(im, next_slice + 1)):
step = 1.0 / (next_slice - im)
cur_alpha = 1.0 - (s * step)
next_alpa = 0.0 + (s * step)
combined_vol.data[:, slice] = (
deformed_combined_segs[ii].data *
cur_alpha) + (deformed_combined_segs[ii + 1].data * next_alpa)
# gauus_ablation = so.Gaussian.Create(1, 10, [0.1, 2, 2], dim=3, device=device)(ablation_vol)
io.SaveITKFile(
combined_vol,
f'{out_dir}/{block}_ablation_and_transition_segmentation.mhd')
del block_vol
del combined_vol
torch.cuda.empty_cache()
def generate_image_volume(rabbit, block, base_dir='/hdscratch/ucair/'):
blockface_dir = f'{base_dir}{rabbit}/blockface/{block}/'
histology_dir = f'{base_dir}{rabbit}/microscopic/{block}/'
def_dir = f'{histology_dir}deformations/'
out_dir = f'{histology_dir}/volume/raw/'
if not os.path.exists(out_dir):
os.makedirs(out_dir)
raw_images = glob.glob(f'{histology_dir}/raw/*_image.tif')
if not raw_images:
raw_images += sorted(raw_images +
glob.glob(f'{histology_dir}/raw/*_image.jpg'))
image_nums = sorted(
[int(x.split('/')[-1].split('_')[1]) for x in raw_images])
deformed_images = []
for im in image_nums:
print(f'Loading and deforming image {im} ... ', end='')
# Load the healthy segmentation as a reference
healthy = io.LoadITKFile(
f'{histology_dir}segmentations/IMG_{im:03d}/img_{im:03d}_healthy_tissue.nrrd',
device=device)
try:
ablation = io.LoadITKFile(
f'{histology_dir}segmentations/IMG_{im:03d}/img_{im:03d}_ablated_region.nrrd',
device=device)
except RuntimeError:
ablation = (healthy * 0.0).copy()
try:
transition = io.LoadITKFile(
f'{histology_dir}segmentations/IMG_{im:03d}/img_{im:03d}_uncertain_region.nrrd',
device=device)
except RuntimeError:
transition = (healthy * 0.0).copy()
combined = ablation + transition + healthy
combined.data = (combined.data >= 0.5).float()
# Load the affine
aff = np.loadtxt(
glob.glob(f'{def_dir}img_{im:03d}_affine_to_blockface.txt')[0])
aff = torch.tensor(aff, device=device, dtype=torch.float32)
# Load the deformation
deformation_data = io.LoadITKFile(
f'{def_dir}/img_{im:03d}_deformation_to_blockface.mhd',
device=device)
deformation = core.StructuredGrid(
size=deformation_data.size[0:2],
spacing=deformation_data.spacing[1:3],
origin=deformation_data.origin[1:3],
device=deformation_data.device,
tensor=deformation_data.data.squeeze().permute(2, 0, 1),
channels=2)
# Apply the inverse affine to the grid
aff = aff.inverse()
a = aff[0:2, 0:2].float()
t = aff[-0:2, 2].float()
deformation.data = torch.matmul(
a.unsqueeze(0).unsqueeze(0),
deformation.data.permute(list(range(1, 2 + 1)) +
[0]).unsqueeze(-1))
deformation.data = (deformation.data.squeeze() +
t).permute([-1] + list(range(0, 2)))
# Load the actual image
#### Apply the affine to the image
mic_file = f'{histology_dir}hdf5/{block}_img{im:03d}_image.hdf5'
meta_dict = {}
with h5py.File(mic_file, 'r') as f:
mic = f['RawImage/ImageData'][:, ::10, ::10]
for key in f['RawImage'].attrs:
meta_dict[key] = f['RawImage'].attrs[key]
mic = core.StructuredGrid(mic.shape[1:],
tensor=torch.tensor(mic,
dtype=torch.float32,
device=device),
spacing=torch.tensor([10.0, 10.0],
dtype=torch.float32,
device=device),
device=device,
dtype=torch.float32,
channels=3)
mic = (mic - mic.min()) / (mic.max() - mic.min())
mic.data = mic.data * combined.data
def_mic = so.ApplyGrid.Create(deformation, device=device)(mic,
deformation)
# Need to put the mic image in the right slice
z_or = (im - 1) * 0.05
def_mic = core.StructuredGrid(
[2] + list(def_mic.shape()[1:]),
tensor=def_mic.data.unsqueeze(1).repeat(1, 2, 1, 1),
spacing=torch.tensor(
[0.05, def_mic.spacing[0], def_mic.spacing[1]],
dtype=torch.float32,
device=device),
origin=torch.tensor([z_or, def_mic.origin[0], def_mic.origin[1]],
dtype=torch.float32,
device=device),
device=device,
dtype=torch.float32,
channels=3)
deformed_images.append(def_mic.copy())
del def_mic, mic, deformation
torch.cuda.empty_cache()
print('done')
# Now need to load the blockface volume
block_vol = io.LoadITKFile(
f'{blockface_dir}volumes/raw/difference_volume.mhd', device='cpu')
# image_vol = core.StructuredGrid(
# size=block_vol.size,
# spacing=block_vol.spacing,
# origin=block_vol.origin,
# device=block_vol.device,
# channels=3
# )
image_z_spacing = np.diff(np.array(image_nums)).mean() * 0.05
image_z_origin = image_nums[0] * 0.05
image_vol = core.StructuredGrid(
size=[len(image_nums)] + list(block_vol.size[-2:].numpy()),
spacing=[image_z_spacing] + list(block_vol.spacing[-2:].numpy()),
origin=[image_z_origin] + list(block_vol.origin[-2:].numpy()),
device=block_vol.device,
channels=3)
for ii, im in enumerate(image_nums):
image_vol.data[:, ii] = deformed_images[ii].data[:, 0].clone().cpu()
io.SaveITKFile(image_vol, f'{out_dir}/{block}_image_volume.mhd')
del image_vol, deformed_images, block_vol
torch.cuda.empty_cache()
def block_stacking(rabbit):
rabbit_dir = f'/hdscratch2/{rabbit}/blockface/'
raw_ext = '/surfaces/raw/'
rigid_ext = '/surfaces/rigid/'
deform_ext = '/surfaces/deformable/'
vol_ext = '/volumes/raw/'
stitch_ext = '/surfaces/raw/stitching/deformable/'
# Get a list of the blocks
block_list = sorted(glob.glob(f'{rabbit_dir}block*'))
# for block_path in block_list:
# block = block_path.split('/')[-1]
# with open(f'{rabbit_dir}{block}{raw_ext}{block}_deformable_config.yaml', 'r') as f:
# params = yaml.load(f, Loader=yaml.FullLoader)
# params['propagation_sigma'] = [8.0, 8.0, 3.0]
# params['currents_sigma'] = [3.0, 1.5]
# with open(f'{rabbit_dir}{block}{raw_ext}{block}_deformable_config.yaml', 'w') as f:
# yaml.dump(params, f)
# Determine the middle block
# middle_block = block_list[9]
middle_block = block_list[5]
foot_blocks = block_list[block_list.index(middle_block):]
head_blocks = block_list[:block_list.index(middle_block) + 1][::-1]
rerun = True
rigid = False
# skip_blocks = ['block01', 'block02', 'block03', 'block04', 'block05', 'block06', 'block07', 'block08']
skip_blocks = []
# Go ahead and just delete any deformable surfaces to make sure that everything resets
# for block_path in block_list:
# filelist = glob.glob(f'{block_path}/surfaces/deformable/*')
# for f in filelist:
# os.remove(f)
if rerun or not os.path.exists(
f'{middle_block}{vol_ext}{middle_block.split("/")[-1]}_phi_stacking.mhd'
):
mid_block = middle_block.split('/')[-1]
# middle = io.LoadITKFile(f'{middle_block}{vol_ext}difference_volume.mhd')
middle = io.LoadITKFile(
f'{middle_block}{vol_ext}difference_volume.nii.gz')
# middle = io.LoadITKFile(f'{middle_block}{vol_ext}{mid_block}_volume.nrrd')
middle.set_size((60, 1024, 1024))
deformation = core.StructuredGrid.FromGrid(middle, channels=3)
deformation.set_to_identity_lut_()
io.SaveITKFile(
deformation,
f'{middle_block}{vol_ext}{middle_block.split("/")[-1]}_phi_inv_stacking.mhd'
)
io.SaveITKFile(
deformation,
f'{middle_block}{vol_ext}{middle_block.split("/")[-1]}_phi_stacking.mhd'
)
affine_tform = torch.eye(4)
np.savetxt(
f'{rabbit_dir}{mid_block}{raw_ext}{mid_block}_rigid_tform.txt',
affine_tform.numpy())
np.savetxt(
f'{rabbit_dir}{mid_block}{vol_ext}{mid_block}_rigid_tform.txt',
affine_tform.numpy())
# Copy the files from raw to deformable for the middle surface
# if os.path.exists(f'{rabbit_dir}{mid_block}{stitch_ext}'):
# mid_path = f'{mid_block}{stitch_ext}'
# else:
mid_path = f'{mid_block}{raw_ext}'
files = [
f'{rabbit_dir}{mid_path}{mid_block}_decimate.obj',
f'{rabbit_dir}{mid_path}{mid_block}_ext.obj',
]
if os.path.exists(f'{rabbit_dir}{mid_path}{mid_block}_foot.obj'):
files += [f'{rabbit_dir}{mid_path}{mid_block}_foot.obj']
if os.path.exists(f'{rabbit_dir}{mid_path}{mid_block}_head.obj'):
files += [f'{rabbit_dir}{mid_path}{mid_block}_head.obj']
if os.path.exists(
f'{rabbit_dir}{mid_path}{mid_block}_foot_support.obj'):
files += [f'{rabbit_dir}{mid_path}{mid_block}_foot_support.obj']
if os.path.exists(
f'{rabbit_dir}{mid_path}{mid_block}_head_support.obj'):
files += [f'{rabbit_dir}{mid_path}{mid_block}_head_support.obj']
out_names = []
out_path = f'{rabbit_dir}{mid_block}{deform_ext}{mid_block}'
for path in files:
name = path.split('/')[-1].split(f'{mid_block}')[-1].replace(
'.', '_deformable.')
out_names += [f'{out_path}{name}']
if not os.path.exists(out_path):
os.makedirs(out_path)
for in_file, out_file in zip(files, out_names):
shutil.copy(in_file, out_file)
# Loop over the foot blocks
for i, block_path in enumerate(foot_blocks, 1):
if i == len(foot_blocks):
break
target_block = block_path.split('/')[-1]
source_block = foot_blocks[i].split('/')[-1]
if source_block in skip_blocks:
continue
# if os.path.exists(f'{rabbit_dir}{source_block}{stitch_ext}'):
# mid_path = f'{source_block}{stitch_ext}'
# else:
mid_path = f'{source_block}{raw_ext}'
target_surface_path = f'{rabbit_dir}{target_block}{deform_ext}{target_block}_foot_deformable.obj'
source_surface_path = f'{rabbit_dir}{mid_path}{source_block}_head.obj'
# if os.path.exists(f'{rabbit_dir}{mid_path}{source_block}_head_stitched.obj'):
# source_surface_path = f'{rabbit_dir}{source_block}{raw_ext}{source_block}_head_stitched.obj'
extras_paths = [
f'{rabbit_dir}{mid_path}{source_block}_decimate.obj',
f'{rabbit_dir}{mid_path}{source_block}_ext.obj',
]
if i < len(foot_blocks) - 1:
extras_paths += [f'{rabbit_dir}{mid_path}{source_block}_foot.obj']
if os.path.exists(
f'{rabbit_dir}{mid_path}{source_block}_foot_support.obj'):
extras_paths += [
f'{rabbit_dir}{mid_path}{source_block}_foot_support.obj'
]
if os.path.exists(
f'{rabbit_dir}{source_block}{deform_ext}{source_block}_head_deformable.obj'
) and not rerun:
print(
f'The deformed surface for {source_block} already exists ... Next block'
)
continue
try:
verts, faces = io.ReadOBJ(target_surface_path)
tar_surface = core.TriangleMesh(verts, faces)
tar_surface.to_(device)
except IOError:
print(
f'The deformed foot surface for {target_block} was not found ... Next block'
)
continue
# Need to see if the target needs any support
support_block = block_list[block_list.index(block_path) -
1].split('/')[-1]
if os.path.exists(
f'{rabbit_dir}{support_block}{deform_ext}{support_block}_foot_support_deformable.obj'
):
verts, faces = io.ReadOBJ(
f'{rabbit_dir}{support_block}{deform_ext}{support_block}_foot_support_deformable.obj'
)
tar_surface.add_surface_(verts.to(device=device),
faces.to(device=device))
try:
verts, faces = io.ReadOBJ(source_surface_path)
src_surface = core.TriangleMesh(verts, faces)
src_surface.to_(device)
src_surface.flip_normals_()
except IOError:
print(
f'The raw head surface for {source_block} was not found ... Next block'
)
continue
extra_surfaces = []
for path in extras_paths:
try:
verts, faces = io.ReadOBJ(path)
except IOError:
extra_name = path.split('/')[-1]
print(
f'{extra_name} not found as an extra ... removing from list'
)
_ = extras_paths.pop(extras_paths.index(path))
continue
extra_surfaces += [core.TriangleMesh(verts, faces)]
extra_surfaces[-1].to_(device)
# Load or create the dictionary for registration
try:
if rerun:
raise IOError
with open(
f'{rabbit_dir}{source_block}{raw_ext}{source_block}_affine_config.yaml',
'r') as f:
params = yaml.load(f, Loader=yaml.FullLoader)
except IOError:
params = {
'spatial_sigma': [2.0, 0.5],
'affine_lr': 1.0e-08,
'translation_lr': 1.0e-05,
'converge': 1.0,
'rigid_transform': True
}
print(f'Registering {source_block} to {target_block}:')
affine_tform = tools.affine_register(
tar_surface.copy(),
src_surface.copy(),
spatial_sigma=params['spatial_sigma'],
affine_lr=params['affine_lr'],
translation_lr=params['translation_lr'],
rigid=params['rigid_transform'],
converge=params['converge'],
device=device)
# Apply the affine to the source element and the excess
aff_tformer = uo.AffineTransformSurface.Create(affine_tform,
device=device)
aff_src_surface = aff_tformer(src_surface)
aff_extra_surface = []
for surface in extra_surfaces:
aff_extra_surface += [aff_tformer(surface)]
out_path = f'{rabbit_dir}{source_block}{rigid_ext}{source_block}'
if not os.path.exists(out_path):
os.makedirs(out_path)
for extra_path, extra_surface in zip(extras_paths, aff_extra_surface):
name = extra_path.split('/')[-1].split(
f'{source_block}')[-1].replace('.', '_rigid.')
# if '_stitched' in name:
# name = name.replace('_stitched', '')
if not os.path.exists(f'{out_path}{name}') or rerun:
io.WriteOBJ(extra_surface.vertices, extra_surface.indices,
f'{out_path}{name}')
if rigid:
continue
# Save out the parameters:
with open(
f'{rabbit_dir}{source_block}{raw_ext}{source_block}_affine_config.yaml',
'w') as f:
yaml.dump(params, f)
# Save out all of the affine transformed surfaces and the transformation
out_path = f'{rabbit_dir}{source_block}{rigid_ext}{source_block}'
# Save the affine in the volumes and in the surfaces location
np.savetxt(
f'{rabbit_dir}{source_block}{raw_ext}{source_block}_rigid_tform.txt',
affine_tform.numpy())
np.savetxt(
f'{rabbit_dir}{source_block}{vol_ext}{source_block}_rigid_tform.txt',
affine_tform.numpy())
if not os.path.exists(f'{out_path}_head_rigid.obj') or rerun:
io.WriteOBJ(aff_src_surface.vertices, aff_src_surface.indices,
f'{out_path}_head_rigid.obj')
for extra_path, extra_surface in zip(extras_paths, aff_extra_surface):
name = extra_path.split('/')[-1].split(
f'{source_block}')[-1].replace('.', '_rigid.')
if not os.path.exists(f'{out_path}{name}') or rerun:
io.WriteOBJ(extra_surface.vertices, extra_surface.indices,
f'{out_path}{name}')
try:
if rerun:
raise IOError
with open(
f'{rabbit_dir}{source_block}{raw_ext}{source_block}_deformable_config.yaml',
'r') as f:
params = yaml.load(f, Loader=yaml.FullLoader)
except IOError:
params = {
'currents_sigma': [3.0, 0.5],
'propagation_sigma': [6.0, 6.0, 3.0],
'deformable_lr': [1.0e-04, 0.5e-04],
'converge': 1.0,
'grid_size': [20, 100, 100],
'niter': 500
}
# params = {
# 'currents_sigma': [3.0, 1.5],
# 'propagation_sigma': [6.0, 6.0, 3.0],
# 'deformable_lr': [2.0e-04, 1.0e-04],
# 'converge': 1.0,
# 'grid_size': [20, 100, 100],
# 'niter': 500
# }
# Account for some old parameter names - can be deleted later
if 'spatial_sigma' in params.keys():
params['currents_sigma'] = params['spatial_sigma']
del params['spatial_sigma']
if 'phi_inv_size' in params.keys():
params['grid_size'] = params['phi_inv_size']
del params['phi_inv_size']
if 'rigid_transform' in params.keys():
del params['rigid_transform']
if 'smoothing_sigma' in params.keys():
params['propagation_sigma'] = params['smoothing_sigma']
del params['smoothing_sigma']
if type(params['deformable_lr']) is not list:
params['deformable_lr'] = [params['deformable_lr']] * len(
params['spatial_sigma'])
# Do the deformable registration
def_surface, def_extras, phi, phi_inv = tools.deformable_register(
tar_surface.copy(),
aff_src_surface.copy(),
currents_sigma=params['currents_sigma'],
prop_sigma=params['propagation_sigma'],
deformable_lr=params['deformable_lr'],
converge=params['converge'],
grid_size=params['grid_size'],
src_excess=aff_extra_surface,
accu_forward=True,
accu_inverse=True,
device=device,
grid_device='cuda:1',
iters=params['niter'])
# Save out the parameters:
with open(
f'{rabbit_dir}{source_block}{raw_ext}{source_block}_deformable_config.yaml',
'w') as f:
yaml.dump(params, f)
# Save out all of the deformable transformed surfaces and phi inv
io.SaveITKFile(
phi_inv,
f'{rabbit_dir}{source_block}{vol_ext}{source_block}_phi_inv_stacking.mhd'
)
io.SaveITKFile(
phi,
f'{rabbit_dir}{source_block}{vol_ext}{source_block}_phi_stacking.mhd'
)
out_path = f'{rabbit_dir}{source_block}{deform_ext}{source_block}'
if not os.path.exists(out_path):
os.makedirs(out_path)
if not os.path.exists(f'{out_path}_head_deformable.obj') or rerun:
io.WriteOBJ(def_surface.vertices, def_surface.indices,
f'{out_path}_head_deformable.obj')
for extra_path, extra_surface in zip(extras_paths, def_extras):
name = extra_path.split('/')[-1].split(
f'{source_block}')[-1].replace('.', '_deformable.')
# if '_stitched' in name:
# name = name.replace('_stitched', '')
if not os.path.exists(f'{out_path}{name}') or rerun:
io.WriteOBJ(extra_surface.vertices, extra_surface.indices,
f'{out_path}{name}')
print('Done registering foots blocks to middle block.')
# Loop over the head blocks
for i, block_path in enumerate(head_blocks, 1):
if i == len(head_blocks):
break
target_block = block_path.split('/')[-1]
source_block = head_blocks[i].split('/')[-1]
if source_block in skip_blocks:
continue
if os.path.exists(f'{rabbit_dir}{source_block}{stitch_ext}'):
mid_path = f'{source_block}{stitch_ext}'
else:
mid_path = f'{source_block}{raw_ext}'
target_surface_path = f'{rabbit_dir}{target_block}{deform_ext}{target_block}_head_deformable.obj'
source_surface_path = f'{rabbit_dir}{mid_path}{source_block}_foot.obj'
if os.path.exists(
f'{rabbit_dir}{mid_path}{source_block}_foot_stitched.obj'):
source_surface_path = f'{rabbit_dir}{mid_path}{source_block}_foot_stitched.obj'
extras_paths = [
f'{rabbit_dir}{mid_path}{source_block}_decimate.obj',
f'{rabbit_dir}{mid_path}{source_block}_ext.obj'
]
if i < len(head_blocks) - 1:
extras_paths += [f'{rabbit_dir}{mid_path}{source_block}_head.obj']
if os.path.exists(
f'{rabbit_dir}{mid_path}{source_block}_head_support.obj'):
extras_paths += [
f'{rabbit_dir}{mid_path}{source_block}_head_support.obj'
]
if os.path.exists(
f'{rabbit_dir}{source_block}{deform_ext}{source_block}_foot_deformable.obj'
) and not rerun:
print(
f'The deformed surface for {source_block} already exists ... Next block'
)
continue
try:
verts, faces = io.ReadOBJ(target_surface_path)
tar_surface = core.TriangleMesh(verts, faces)
tar_surface.to_(device)
except IOError:
print(
f'The deformed foot surface for {target_block} was not found ... Next block'
)
continue
# Need to see if the target needs any support
support_block = block_list[block_list.index(block_path) +
1].split('/')[-1]
if os.path.exists(
f'{rabbit_dir}{support_block}{deform_ext}{support_block}_head_support_deformable.obj'
):
verts, faces = io.ReadOBJ(
f'{rabbit_dir}{support_block}{deform_ext}{support_block}_head_support_deformable.obj'
)
tar_surface.add_surface_(verts.to(device=device),
faces.to(device=device))
try:
verts, faces = io.ReadOBJ(source_surface_path)
src_surface = core.TriangleMesh(verts, faces)
src_surface.to_(device)
src_surface.flip_normals_()
except IOError:
print(
f'The raw foot surface for {source_block} was not found ... Next block'
)
continue
extra_surfaces = []
for path in extras_paths:
try:
verts, faces = io.ReadOBJ(path)
except IOError:
extra_name = path.split('/')[-1]
print(
f'{extra_name} not found as an extra ... removing from list'
)
_ = extras_paths.pop(extras_paths.index(path))
continue
extra_surfaces += [core.TriangleMesh(verts, faces)]
extra_surfaces[-1].to_(device)
# Load or create the dictionary for registration
try:
if rerun:
raise IOError
with open(
f'{rabbit_dir}{source_block}{raw_ext}{source_block}_affine_config.yaml',
'r') as f:
params = yaml.load(f, Loader=yaml.FullLoader)
except IOError:
params = {
'spatial_sigma': [2.0, 0.5],
'affine_lr': 1.0e-08,
'translation_lr': 1.0e-05,
'converge': 1.0,
'rigid_transform': True
}
print(f'Registering {source_block} to {target_block}:')
affine_tform = tools.affine_register(
tar_surface.copy(),
src_surface.copy(),
spatial_sigma=params['spatial_sigma'],
affine_lr=params['affine_lr'],
translation_lr=params['translation_lr'],
rigid=params['rigid_transform'],
converge=params['converge'],
device=device)
# Apply the affine to the source element and the excess
aff_tformer = uo.AffineTransformSurface.Create(affine_tform,
device=device)
aff_src_surface = aff_tformer(src_surface)
aff_extra_surface = []
for surface in extra_surfaces:
aff_extra_surface += [aff_tformer(surface)]
out_path = f'{rabbit_dir}{source_block}{rigid_ext}{source_block}'
if not os.path.exists(out_path):
os.makedirs(out_path)
for extra_path, extra_surface in zip(extras_paths, aff_extra_surface):
name = extra_path.split('/')[-1].split(
f'{source_block}')[-1].replace('.', '_rigid.')
if '_stitched' in name:
name = name.replace('_stitched', '')
if not os.path.exists(f'{out_path}{name}') or rerun:
io.WriteOBJ(extra_surface.vertices, extra_surface.indices,
f'{out_path}{name}')
if rigid:
continue
# Save out the parameters:
with open(
f'{rabbit_dir}{source_block}{raw_ext}{source_block}_affine_config.yaml',
'w') as f:
yaml.dump(params, f)
# Save out all of the affine transformed surfaces and the transformation
out_path = f'{rabbit_dir}{source_block}{rigid_ext}{source_block}'
# Save the affine in the volumes and in the surfaces location
np.savetxt(
f'{rabbit_dir}{source_block}{raw_ext}{source_block}_rigid_tform.txt',
affine_tform.numpy())
np.savetxt(
f'{rabbit_dir}{source_block}{vol_ext}{source_block}_rigid_tform.txt',
affine_tform.numpy())
if not os.path.exists(f'{out_path}_foot_rigid.obj') or rerun:
io.WriteOBJ(aff_src_surface.vertices, aff_src_surface.indices,
f'{out_path}_foot_rigid.obj')
for extra_path, extra_surface in zip(extras_paths, aff_extra_surface):
name = extra_path.split('/')[-1].split(
f'{source_block}')[-1].replace('.', '_rigid.')
if not os.path.exists(f'{out_path}{name}') or rerun:
io.WriteOBJ(extra_surface.vertices, extra_surface.indices,
f'{out_path}{name}')
try:
if rerun:
raise IOError
with open(
f'{rabbit_dir}{source_block}{raw_ext}{source_block}_deformable_config.yaml',
'r') as f:
params = yaml.load(f, Loader=yaml.FullLoader)
except IOError:
params = {
'currents_sigma': [3.0, 0.5],
'propagation_sigma': [6.0, 6.0, 3.0],
'deformable_lr': [1.0e-04, 0.5e-04],
'converge': 1.0,
'grid_size': [20, 100, 100],
'niter': 500
}
# if 'spatial_sigma' in params.keys():
# params['currents_sigma'] = params['spatial_sigma']
# del params['spatial_sigma']
# if 'phi_inv_size' in params.keys():
# params['grid_size'] = params['phi_inv_size']
# del params['phi_inv_size']
# if 'rigid_transform' in params.keys():
# del params['rigid_transform']
# if 'smoothing_sigma' in params.keys():
# params['propagation_sigma'] = params['smoothing_sigma']
# del params['smoothing_sigma']
#
# if type(params['deformable_lr']) is not list:
# params['deformable_lr'] = [params['deformable_lr']] * len(params['spatial_sigma'])
# Do the deformable registration
def_surface, def_extras, phi, phi_inv = tools.deformable_register(
tar_surface.copy(),
aff_src_surface.copy(),
currents_sigma=params['currents_sigma'],
prop_sigma=params['propagation_sigma'],
deformable_lr=params['deformable_lr'],
converge=params['converge'],
grid_size=params['grid_size'],
src_excess=aff_extra_surface,
accu_forward=True,
accu_inverse=True,
device=device,
grid_device='cuda:1',
iters=params['niter'])
# Save out the parameters:
with open(
f'{rabbit_dir}{source_block}{raw_ext}{source_block}_deformable_config.yaml',
'w') as f:
yaml.dump(params, f)
# Save out all of the deformable transformed surfaces and phi inv
io.SaveITKFile(
phi_inv,
f'{rabbit_dir}{source_block}{vol_ext}{source_block}_phi_inv_stacking.mhd'
)
io.SaveITKFile(
phi,
f'{rabbit_dir}{source_block}{vol_ext}{source_block}_phi_stacking.mhd'
)
out_path = f'{rabbit_dir}{source_block}{deform_ext}{source_block}'
if not os.path.exists(out_path):
os.makedirs(out_path)
if not os.path.exists(f'{out_path}_foot_deformable.obj') or rerun:
io.WriteOBJ(def_surface.vertices, def_surface.indices,
f'{out_path}_foot_deformable.obj')
for extra_path, extra_surface in zip(extras_paths, def_extras):
name = extra_path.split('/')[-1].split(
f'{source_block}')[-1].replace('.', '_deformable.')
# if '_stitched' in name:
# name = name.replace('_stitched', '')
if not os.path.exists(f'{out_path}{name}') or rerun:
io.WriteOBJ(extra_surface.vertices, extra_surface.indices,
f'{out_path}{name}')
print('Done registering head blocks to middle block.')
def _convert_mat_files(Obj):
rabbitNumber = Obj.rabbitDirectory.split('/')[-1]
matList = sorted(glob.glob(f'{Obj.rabbitDirectory}/externalRecons/AblationImaging/*'))
# Do some string comparison to make sure that this file is a sonication file
matList = [x for x in matList if 'Son' in x]
# Have to keep track of the MIN and MAX of each transfor so we can know the bounding box to resample to
size = []
orgn = []
if not os.path.exists(os.path.join(Obj.rabbitDirectory + '/rawVolumes/TemperatureRecon/RegVols/')):
os.makedirs(os.path.join(Obj.rabbitDirectory + '/rawVolumes/TemperatureRecon/RegVols/'))
for tempFile in matList:
# Create the output folder for all of the timepoint images
outDir = os.path.splitext(tempFile)[0]
outName = outDir.split('/')[-1]
dirOutName = os.path.join(Obj.rabbitDirectory + '/rawVolumes/TemperatureRecon/', outName)
if not os.path.exists(dirOutName):
os.makedirs(dirOutName)
# Have to add mroe logic here because there are varying lengths of numbers FUN
preLength = len(outName.split('_')[0])
outName = outName[:preLength] + '_----' + outName[preLength:]
struct = spi.loadmat(tempFile)
imData = struct['ims']
# Could put some logic here to make sure that they all have a 4th dimension
timePts = np.shape(imData)[-1]
# Get transformation and solve for the affine
# tform = struct['PosDCS']
# print('min: {0} .... '.format(np.min(np.min(np.min(tform, 0), 0), 0).tolist()))
# print('max: {0} .... '.format(np.max(np.max(np.max(tform, 0), 0), 0).tolist()))
# dim = np.shape(tform)[0:3]
# dim = [x - 1 for x in dim]
# print('shape: {0} .... '.format(dim))
# Pull points from the transformation to solve for the affine
# landmarks = []
# landmarks.append([[0, 0, 0], tform[0, 0, 0].tolist()])
# landmarks.append([[dim[0], 0, 0], tform[dim[0], 0, 0].tolist()])
# landmarks.append([[0, dim[1], 0], tform[0, dim[1], 0].tolist()])
# landmarks.append([[dim[0], dim[1], 0], tform[dim[0], dim[1], 0].tolist()])
# landmarks.append([[0, 0, dim[2]], tform[0, 0, dim[2]].tolist()])
# landmarks.append([[dim[0], 0, dim[2]], tform[dim[0], 0, dim[2]].tolist()])
# landmarks.append([[0, dim[1], dim[2]], tform[0, dim[1], dim[2]].tolist()])
# landmarks.append([[dim[0], dim[1], dim[2]], tform[dim[0], dim[1], dim[2]].tolist()])
# Solve for the affine
# affine = apps.SolveAffine(landmarks)
affine = struct['geomInfo'][0,0]['AffineDCS']
temp = core.StructuredGrid(
[imData.shape[0], imData.shape[1], imData.shape[2]],
tensor=torch.tensor(np.real(imData)).permute(-1, 0, 1, 2),
origin= [0, 0, 0],
channels=imData.shape[-1]
)
# temp = ca.Image3D(cc.MakeGrid(np.shape(tform)[0:3], ca.MEM_DEVICE), ca.MEM_DEVICE)
# temp.setOrigin(ca.Vec3Df(0, 0, 0))
# temp.setSpacing(ca.Vec3Df(1, 1, 1))
affGrid = rc.SolveAffineGrid(temp, affine)
size.append(affGrid.size.tolist())
orgn.append(affGrid.origin.tolist())
print('Converting files for {0} time series images .... '.format(timePts), end='')
sys.stdout.flush()
for time in range(0, timePts):
magIm_np = np.real(imData[:, :, :, time])
phsIm_np = np.imag(imData[:, :, :, time])
magIm = core.StructuredGrid(
[magIm_np.shape[0], magIm_np.shape[1], magIm_np.shape[2]],
tensor=torch.tensor(magIm_np).unsqueeze(0).float(),
origin=[0, 0, 0],
channels=1
)
phsIm = core.StructuredGrid(
[phsIm_np.shape[0], phsIm_np.shape[1], phsIm_np.shape[2]],
tensor=torch.tensor(phsIm_np).unsqueeze(0).float(),
origin=[0, 0, 0],
channels=1
)
affFilt = so.AffineTransform.Create(affine=torch.tensor(affine).float())
affMagIm = affFilt(magIm, out_grid=affGrid)
affPhsIm = affFilt(phsIm, out_grid=affGrid)
io.SaveITKFile(affMagIm, dirOutName + '/' + outName + '_real_{0}.nii.gz'.format(str(time).zfill(2)))
io.SaveITKFile(affPhsIm, dirOutName + '/' + outName + '_imag_{0}.nii.gz'.format(str(time).zfill(2)))
if time == 0:
# We need to have the magnitude image for registration
regIm_np = np.abs(imData[:, :, :, time])
regIm = core.StructuredGrid(
[regIm_np.shape[0], regIm_np.shape[1], regIm_np.shape[2]],
tensor=torch.tensor(regIm_np).unsqueeze(0).float(),
origin=[0, 0, 0],
channels=1
)
affRegIm = affFilt(regIm, out_grid=affGrid)
io.SaveITKFile(affRegIm, dirOutName + '/../RegVols/' + outName[0:5] + '.nii.gz')
# print('size: {0} .... '.format(magIm_np.shape), end='')
print('Done')
return size, orgn
def register_histopathology_to_blockface(rabbit, block, img_num, bf_slice):
blockface_dir = f'/hdscratch/ucair/{rabbit}/blockface/{block}/'
histology_dir = f'/hdscratch/ucair/{rabbit}/microscopic/{block}/'
out_dir = f'{histology_dir}deformations/'
if not os.path.exists(out_dir):
os.makedirs(out_dir)
# if os.path.exists(f'{out_dir}/img_{img_num}_deformation_to_blockface.mhd'):
# return
# Load and make the histopathology segmentation
segs = []
segs += [
io.LoadITKFile(
f'{histology_dir}segmentations/IMG_{img_num}/img_{img_num}_healthy_tissue.nrrd',
device=device)
]
if os.path.exists(
f'{histology_dir}segmentations/IMG_{img_num}/img_{img_num}_ablated_region.nrrd'
):
segs += [
io.LoadITKFile(
f'{histology_dir}segmentations/IMG_{img_num}/img_{img_num}_ablated_region.nrrd',
device=device)
]
if os.path.exists(
f'{histology_dir}segmentations/IMG_{img_num}/img_{img_num}_uncertain_region.nrrd'
):
segs += [
io.LoadITKFile(
f'{histology_dir}segmentations/IMG_{img_num}/img_{img_num}_uncertain_region.nrrd',
device=device)
]
histology_seg = core.StructuredGrid.FromGrid(segs[0], channels=1)
for seg in segs:
histology_seg += seg
try:
blockface_seg = io.LoadITKFile(
f'{blockface_dir}volumes/raw/hd_labels/{block}_hdlabel_volume.nrrd',
device=device)
except:
blockface_seg = io.LoadITKFile(
f'{blockface_dir}volumes/raw/segmentation_volume.nrrd',
device=device)
# # Load the surface slice and get the difference
# blockface_surf = io.LoadITKFile(f'{blockface_dir}volumes/raw/surface/IMG_{bf_slice:03d}_surface.mhd',
# device=device)
#
# blockface_surf_p1 = io.LoadITKFile(f'{blockface_dir}volumes/raw/surface/IMG_{bf_slice + 1:03d}_surface.mhd',
# device=device)
#
# diff = (blockface_surf - blockface_surf_p1).data[2]
#
# diff = (diff - diff.min()) / (diff.max() - diff.min())
# Extract the slice
blockface_seg = blockface_seg.extract_slice(bf_slice - 1, dim=0)
aff_seg, affine = solve_affine(histology_seg,
blockface_seg,
img_num,
out_dir=out_dir,
device=device)
np.savetxt(f'{out_dir}/img_{img_num}_affine_to_blockface.txt',
affine.cpu().numpy())
#### Apply the affine to the image
mic_file = f'{histology_dir}hdf5/{block}_img{img_num}_image.hdf5'
meta_dict = {}
with h5py.File(mic_file, 'r') as f:
mic = f['RawImage/ImageData'][:, ::10, ::10]
for key in f['RawImage'].attrs:
meta_dict[key] = f['RawImage'].attrs[key]
mic = core.StructuredGrid(mic.shape[1:],
tensor=torch.tensor(mic,
dtype=torch.float32,
device=device),
spacing=torch.tensor([10.0, 10.0],
dtype=torch.float32,
device=device),
origin=histology_seg.origin,
device=device,
dtype=torch.float32,
channels=3)
mic = (mic - mic.min()) / (mic.max() - mic.min())
aff_mic = so.AffineTransform.Create(affine=affine)(mic, blockface_seg)
# plt.figure()
# plt.imshow(aff_mic.data.permute(1,2,0).cpu())
# plt.axis('off')
# plt.gca().invert_yaxis()
# plt.savefig(f'/home/sci/blakez/ucair/Animations/Scrolls/Mic/Images/{blockface_slice}_image.png', dpi=500, bbox_inches='tight', pad_inches=0)
def_histology, deformation = deformable_histology_to_blockface(
aff_seg,
blockface_seg,
steps=[0.01, 0.005],
scales=[4, 1],
gauss=True,
mic=aff_mic)
# Save out the deformation
io.SaveITKFile(deformation,
f'{out_dir}/img_{img_num}_deformation_to_blockface.mhd')
def tempRecon(Obj, opt):
if not os.path.exists(f'{Obj.rabbitDirectory}/rawVolumes/TemperatureRecon/'):
os.makedirs(f'{Obj.rabbitDirectory}/rawVolumes/TemperatureRecon/')
size, orgn = _convert_mat_files(Obj)
unionOrigin = np.min(orgn, 0).tolist()
adj = np.abs(np.max(orgn, 0) - np.min(orgn, 0))
unionSize = (np.max(size, 0) + adj).tolist()
unionSize = [int(x) for x in unionSize]
# We are going to create a config file for each registration
sonicationList = natural_sort(glob.glob(Obj.rabbitDirectory + '/rawVolumes/TemperatureRecon/*'))
# Need to remove the resample from the list
sonicationList = [x for x in sonicationList if '_resample' not in x]
sonicationList = [x for x in sonicationList if 'RegVols' not in x]
lastName = sonicationList[-1].split('/')[-1]
preLength = len(lastName.split('_')[0])
lastName = lastName[:preLength] + '_----' + lastName[preLength:]
# Set up the Config directory
if not os.path.exists(Obj.rabbitDirectory + '/ConfigFiles/temperatureConfigs/'):
os.makedirs(Obj.rabbitDirectory + '/ConfigFiles/temperatureConfigs/')
# Construct teh common Grid: at this point assuming isotropic spacing of 1
if 'unionSize' in locals():
unionSpacing = [1.0, 1.0, 1.0]
unionIm = core.StructuredGrid(
size=unionSize,
origin=unionOrigin,
spacing=unionSpacing,
channels=1,
device=device
)
def_im = unionIm.clone()
else:
configList = glob.glob(Obj.rabbitDirectory + '/ConfigFiles/temperatureConfigs/*')
tmpObj = Config.Load(TempConfigSpec, configList[0])
unionSize = tmpObj.unionSize
unionOrigin = tmpObj.unionOrigin
unionSpacing = tmpObj.unionSpacing
unionIm = core.StructuredGrid(
size=unionSize,
origin=unionOrigin,
spacing=unionSpacing,
channels=1,
device=device
)
def_im = unionIm.clone()
# We need to register the last image to the VIBE
son = sonicationList[-1]
try:
regObj = Config.Load(TempConfigSpec,
Obj.rabbitDirectory + '/ConfigFiles/temperatureConfigs/{0}_config.yaml'.format(
son.split('/')[-1]))
except IOError:
regObj = Config.SpecToConfig(TempConfigSpec)
regObj.Niter = [40]
regObj.gaussSigma = [0.1]
regObj.gaussKernel = [3]
regObj.regWeight = [2.0]
regObj.stepSize = [0.004]
regObj.I0 = 'None'
regObj.I1 = 'None'
regObj.unionSize = unionSize
regObj.unionSpacing = unionSpacing
regObj.unionOrigin = unionOrigin
# Need to get the name of the volume
outName = son.split('/')[-1]
preLength = len(outName.split('_')[0])
outName = outName[:preLength] + '_----' + outName[preLength:]
regObj.outputPath = Obj.rabbitDirectory + '/elastVolumes/TemperatureRecon/' + son.split('/')[-1]
if not os.path.exists(regObj.outputPath):
os.makedirs(regObj.outputPath)
plt.close('all')
# Get the deformation field that takes the first of the sonication images to the final
h_post = ER.MultiscaleElast(regObj, opt)
io.SaveITKFile(h_post, regObj.outputPath + '/final_deformation_Is_to_It.mha')
rc.WriteConfig(TempConfigSpec, regObj,
Obj.rabbitDirectory + '/ConfigFiles/temperatureConfigs/{0}_config.yaml'.format(son.split('/')[-1]))
print('Applying elast transformation to {0} volumes .... '.format(son.split('/')[-1]), end='')
sys.stdout.flush()
for image in glob.glob('{0}/rawVolumes/TemperatureRecon/'.format(Obj.rabbitDirectory) + son.split('/')[-1] + '/*'):
# Update the name
outName = image.split('/')[-1]
outName = outName[:preLength + 4] + 'e' + outName[preLength + 5:]
im = io.LoadITKFile(image, device=device)
temp = so.ResampleWorld.Create(unionIm, device=device)(im)
def_im = so.ApplyGrid.Create(h_post, device=device)(temp)
io.SaveITKFile(def_im, regObj.outputPath + '/' + outName)
# common.DebugHere()
# # Need to resample the final image onto the new grid
# for image in glob.glob('{0}/rawVolumes/TemperatureRecon/'.format(Obj.rabbitDirectory) + sonicationList[-1].split('/')[-1] + '/*'):
# outputPath = Obj.rabbitDirectory + '/rawVolumes/TemperatureRecon/' + sonicationList[-1].split('/')[-1] + '_resample'
# if not os.path.exists(outputPath):
# os.makedirs(outputPath)
# outName = image.split('/')[-1]
# im = common.LoadITKImage(image, ca.MEM_DEVICE)
# cc.ResampleWorld(unionIm, im, bg=3)
# common.SaveITKImage(unionIm, outputPath + '/' + outName)
for son in sonicationList[:-1]:
# Create the registration object for elastic
try:
regObj = Config.Load(TempConfigSpec,
Obj.rabbitDirectory + '/ConfigFiles/temperatureConfigs/{0}_config.yaml'.format(
son.split('/')[-1]))
except IOError:
regObj = Config.SpecToConfig(TempConfigSpec)
# Need to get the name of the volume
outName = son.split('/')[-1]
preLength = len(outName.split('_')[0])
outName = outName[:preLength] + '_----' + outName[preLength:]
# Always set the target image to the last file - have to get the first mag image!
regObj.I0 = son + '/../RegVols/' + outName[0:5] + '.nii.gz'
# Do we have to get the file that has been registered to the vibe??
regObj.I1 = sonicationList[-1] + '/../RegVols/' + lastName[0:5] + '.nii.gz'
# Set the grid parameters of the unionFOV
regObj.unionSize = unionSize
regObj.unionSpacing = unionSpacing
regObj.unionOrigin = unionOrigin
# if sonicationList.index(son) < 8:
# regObj.stepSize = [0.000]
# else:
# regObj.stepSize = [0.004]
regObj.outputPath = Obj.rabbitDirectory + '/elastVolumes/TemperatureRecon/' + son.split('/')[-1]
if not os.path.exists(regObj.outputPath):
os.makedirs(regObj.outputPath)
plt.close('all')
# Get the deformation field that takes the first of the sonication images to the final
h = ER.MultiscaleElast(regObj, opt)
# Need to compose the h field to get the full deformation
h_comp = so.ComposeGrids.Create(device=device)([h, h_post])
io.SaveITKFile(h_comp, regObj.outputPath + '/final_deformation_Is_to_It.mha')
# Write out the config file
if not os.path.exists(Obj.rabbitDirectory + '/ConfigFiles/temperatureConfigs'):
os.makedirs(Obj.rabbitDirectory + '/ConfigFiles/temperatureConfigs')
rc.WriteConfig(TempConfigSpec, regObj,
Obj.rabbitDirectory + '/ConfigFiles/temperatureConfigs/{0}_config.yaml'.format(
son.split('/')[-1]))
# Need to itterate through all the mag and phase images and apply the deformation
print('Applying elast transformation to {0} volumes .... '.format(son.split('/')[-1]), end='')
sys.stdout.flush()
for image in glob.glob(
'{0}/rawVolumes/TemperatureRecon/'.format(Obj.rabbitDirectory) + son.split('/')[-1] + '/*'):
# Update the name
outName = image.split('/')[-1]
outName = outName[:preLength + 4] + 'e' + outName[preLength + 5:]
im = io.LoadITKFile(image, device=device)
temp = so.ResampleWorld.Create(unionIm, device=device)(im)
def_im = so.ApplyGrid.Create(h_post, device=device)(temp)
io.SaveITKFile(def_im, regObj.outputPath + '/' + outName)
def process_mic(rabbit):
raw_mic_dir = f'/hdscratch/ucair/{rabbit}/microscopic/'
bf_dir = f'/hdscratch/ucair/{rabbit}/blockface/'
raw_bf_dir = f'/hdscratch/ucair/blockface/{rabbit}/'
block_list = sorted(glob.glob(f'{raw_mic_dir}/*'))
# for block_path in block_list:
# block = block_path.split('/')[-1]
#
# mic_list = sorted(glob.glob(f'{block_path}/raw/*_image.tif'))
#
# img_nums = [x.split('/')[-1].split('_')[1] for x in mic_list]
#
# # Load the image
# for img in img_nums:
# print(f'Processing {block}, {img} ... ', end='')
# mic_file = f'{raw_mic_dir}{block}/hdf5/{block}_img{img}_image.hdf5'
#
# mic = io.LoadITKFile(f'{raw_mic_dir}{block}/raw/IMG_{img}_histopathology_image.tif')
#
# with h5py.File(mic_file, 'w') as f:
# g = f.create_group('RawImage')
# g.create_dataset('ImageData', data=mic.data.numpy())
#
# print('Done')
for block_path in block_list:
block = block_path.split('/')[-1]
mic_list = sorted(glob.glob(f'{block_path}/raw/*_image.tif'))
img_nums = [x.split('/')[-1].split('_')[1] for x in mic_list]
for img in img_nums:
mic_file = f'{raw_mic_dir}{block}/hdf5/{block}_img{img}_image.hdf5'
mic_seg = f'{raw_mic_dir}{block}/hdf5/{block}_img{img}_label.hdf5'
blockface_image = f'{bf_dir}{block}/volumes/raw/difference/IMG_{img}_difference.mhd'
blockface_label = f'{bf_dir}{block}/volumes/raw/segmentation/IMG_{img}_segmentation.mhd'
meta_dict = {}
with h5py.File(mic_file, 'r') as f:
for key in f['RawImage'].attrs:
meta_dict[key] = f['RawImage'].attrs[key]
if 'Affine' in meta_dict.keys():
continue
blockface = io.LoadITKFile(blockface_image, device=device)
label_data = io.LoadITKFile(blockface_label, device=device)
blockface = (blockface - blockface.min()) / (blockface.max() -
blockface.min())
label = blockface.clone()
label.data = label_data.data.clone()
print(f'Affine Registering ... ')
aff_mic, aff_mic_seg, affine = tools.process_mic(mic_file,
mic_seg,
blockface,
label,
device=device)
print(f'Done')
aff_mic *= aff_mic_seg
blockface *= label
blockface_s = core.StructuredGrid.FromGrid(
blockface, tensor=blockface[0].unsqueeze(0), channels=1)
aff_mic = (aff_mic - aff_mic.min()) / (aff_mic.max() -
aff_mic.min())
print(f'Deformable Registering Labels ... ')
def_label, label_deformation = match_bf_mic(aff_mic_seg,
label,
steps=[0.01, 0.005],
scales=[4, 1],
gauss=True)
print(f'Done')
label_def_mic = so.ApplyGrid(label_deformation,
device=device)(aff_mic,
label_deformation)
print(f'Deformable Registering Images ... ')
def_image, image_deformation = match_bf_mic(
label_def_mic,
blockface_s,
steps=[0.01, 0.01],
scales=[2, 1],
)
print(f'Done')
composer = so.ComposeGrids(device=device,
dtype=torch.float32,
padding_mode='border')
deformation = composer([image_deformation, label_deformation])
def_mic = so.ApplyGrid(deformation, device=device)(aff_mic,
deformation)
try:
with h5py.File(mic_file, 'r') as f:
mic = f['ImageData'][:]
except KeyError:
with h5py.File(mic_file, 'r') as f:
mic = f['RawImage/ImageData'][:]
mic = core.StructuredGrid(mic.shape[1:],
tensor=torch.tensor(mic,
dtype=torch.float32,
device=device),
device=device,
dtype=torch.float32,
channels=3)
print('Saving ... ')
with h5py.File(mic_file, 'w') as f:
g = f.create_group('RawImage')
d = f.create_group('Deformation')
g.create_dataset('ImageData', data=mic.data.cpu().numpy())
d.create_dataset('Phi', data=deformation.data.cpu().numpy())
g.attrs['Shape'] = list(mic.shape())
g.attrs['Spacing'] = mic.spacing.tolist()
g.attrs['Origin'] = mic.origin.tolist()
g.attrs['Affine'] = affine.tolist()
d.attrs['Shape'] = list(deformation.shape())
d.attrs['Spacing'] = deformation.spacing.tolist()
d.attrs['Origin'] = deformation.origin.tolist()
io.SaveITKFile(
def_mic,
f'{raw_mic_dir}{block}/volume/images/IMG_{img}_def_histopathology.mhd'
)
print('Done')
plt.close('all')
print('All Done')
def ExternalRecon(regObj, opt):
rerun = False
# If the path doesn't exists, we can make it and try to transfer the files
if not os.path.exists(f'{regObj.rabbitDirectory}/externalRecons/'):
for timepoint in opt.transfer_timepoints:
# Use subprocess to get the list of files from RAID10
p = sp.Popen([
"ssh", "*****@*****.**",
f"find {opt.raw_dir}*{opt.rabbit[-2:]}* -type d"
],
stdout=sp.PIPE)
raidDirs, _ = p.communicate()
# There is a new line at the end which puts an empty at the end of the list
raidDirs = raidDirs.decode('utf-8').split('\n')[:-1]
# Sort out the offline recon directories
offlineDirs = [x for x in raidDirs if 'OfflineRecon' in x]
offlineFiles = []
for offDir in offlineDirs:
# Use subprocess to get the list of files from RAID10
p = sp.Popen([
"ssh", "*****@*****.**",
f"find {offDir.split(' ')[0]}*/OfflineRecon/"
],
stdout=sp.PIPE)
offline_files, _ = p.communicate()
# There is a new line at the end which puts an empty at the end of the list
offline_files = offline_files.decode('utf-8').split('\n')[:-1]
offlineFiles += offline_files
tpList = []
# Create a selector so the ablation volumes can be selected
Selector = rc.PathSelector(
tk, sorted(offlineFiles),
f'Choose {timepoint} Day Offline Files to Transfer')
convertFiles = Selector.get_files()
Selector.root.destroy()
tpList += convertFiles
for i, path in enumerate(tpList, 1):
# Get the name of the file
filename = path.split('OfflineRecon/')[-1]
# Correct the special characters in the path string so the scp command will work
path = path.replace("^", "\^").replace(" ", "\ ")
rawOutName = f'{regObj.rabbitDirectory}/externalRecons/{timepoint}/{filename}'
rawOutName = rawOutName.replace('\\ ', '_').replace('\ ', '_')
# Check if the folder exists or not
if not os.path.exists(os.path.dirname(rawOutName)):
os.makedirs(os.path.dirname(rawOutName))
# If the volume doesn't already exist, then copy it over
if not os.path.exists(rawOutName):
p = sp.Popen([
"scp", "-r", f"[email protected]:{path}",
rawOutName
])
os.waitpid(p.pid, 0)
# print('No external files to recon ... skipping')
# return
print('Reconning External Files ... ', end='')
# Get a list of the files
ablation_files = sorted(
glob.glob(
f'{regObj.rabbitDirectory}/externalRecons/AblationImaging/*'))
pre_files = sorted(
[x for x in ablation_files if 'Pre' in x and 'STIR' in x])[::-1]
post_files = sorted(
[x for x in ablation_files if 'Post' in x and 'STIR' in x])[::-1]
pre_dicts = [loadmat(x) for x in pre_files]
post_dicts = [loadmat(x) for x in post_files]
pre_vol = _get_stir_vol(pre_dicts)
post_vol = _get_stir_vol(post_dicts)
# Get a list of the volumes in the ablation imaging already so we can assign the right number.
files = glob.glob(f'{regObj.rabbitDirectory}/rawVolumes/AblationImaging/*')
start_num = len(files)
out_dir = f'{regObj.rabbitDirectory}/rawVolumes/AblationImaging/'
pre_name = '_----_pre_ablation_t1_map.nii.gz'
post_name = '_----_post_ablation_t1_map.nii.gz'
if not any([pre_name in x for x in files]) or rerun:
io.SaveITKFile(pre_vol, f'{out_dir}{start_num + 1:03d}{pre_name}')
if not any([post_name in x for x in files]) or rerun:
io.SaveITKFile(post_vol, f'{out_dir}{start_num + 2:03d}{post_name}')
long_files = sorted(
glob.glob(f'{regObj.rabbitDirectory}/externalRecons/PostImaging/*'))
long_files = [x for x in long_files if 'STIR' in x]
long_dicts = [loadmat(x) for x in long_files]
long_vol = _get_stir_vol(long_dicts)
files = glob.glob(f'{regObj.rabbitDirectory}/rawVolumes/PostImaging/*')
start_num = len(files)
out_dir = f'{regObj.rabbitDirectory}/rawVolumes/PostImaging/'
long_name = '_----_t1_map.nii.gz'
if not any([long_name in x for x in files]) or rerun:
io.SaveITKFile(long_vol, f'{out_dir}{start_num + 1:03d}{long_name}')
print('Done')
#### TO DO ####
# Make it so that this recon doesn't run every time
def def_block(rabbit, block):
data_dir = f'/hdscratch/ucair/{rabbit}/blockface/{block}/'
vol_ext = '/volumes/raw/'
raw_ext = '/surfaces/raw/'
def_ext = '/volumes/deformable/'
# Load the affine
aff = np.loadtxt(f'{data_dir}{raw_ext}{block}_rigid_tform.txt')
aff = torch.tensor(aff, device=device, dtype=torch.float32)
# Load phi_inv
phi_inv = io.LoadITKFile(f'{data_dir}{vol_ext}{block}_phi_inv.mhd',
device=device)
phi_inv.set_size((60, 1024, 1024))
#
# # Phi_inv is in z,y,x and need x,y,z
phi_inv.data = phi_inv.data.flip(0)
# Load the volume to apply this field to
bf = io.LoadITKFile(f'{data_dir}{vol_ext}scatter_volume.mhd',
device=device)
seg = io.LoadITKFile(f'{data_dir}{vol_ext}segmentation_volume.mhd',
device=device)
# aff_grid = core.StructuredGrid.FromGrid(phi_inv, channels=3)
# aff_grid.set_to_identity_lut_()
# aff_grid.data = aff_grid.data.flip(0)
# Apply the inverse affine to the grid
aff = aff.inverse()
a = aff[0:3, 0:3].float()
t = aff[-0:3, 3].float()
# aff_grid.data = torch.matmul(a, aff_grid.data.permute(list(range(1, 3 + 1)) + [0]).unsqueeze(-1))
# aff_grid.data = (aff_grid.data.squeeze() + t).permute([3] + list(range(0, 3)))
#
# aff_grid.data = aff_grid.data.flip(0)
#
# aff_bf = so.ApplyGrid.Create(aff_grid, device=aff_grid.device, dtype=aff_grid.dtype)(bf, out_grid=phi_inv)
phi_inv.data = torch.matmul(
a.unsqueeze(0).unsqueeze(0),
phi_inv.data.permute(list(range(1, 3 + 1)) + [0]).unsqueeze(-1))
phi_inv.data = (phi_inv.data.squeeze() + t).permute([-1] +
list(range(0, 3)))
# Flip phi_inv back to the way it was
phi_inv.data = phi_inv.data.flip(0)
try:
stitch_files = sorted(
glob.glob(f'{data_dir}{vol_ext}{block}_phi_inv_stitch_*.mhd'))
stitch_list = []
for stitch_file in stitch_files:
phi_stitch = io.LoadITKFile(stitch_file, device=device)
phi_stitch.set_size((60, 1024, 1024))
stitch_list += [phi_stitch.clone()]
composer = so.ComposeGrids.Create(padding_mode='border', device=device)
final_phi = composer([phi_inv] + stitch_list)
phi_inv = final_phi.clone()
except IOError:
pass
test = so.ApplyGrid.Create(stitch_list[0], pad_mode='zeros',
device=device)(bf, stitch_list[0])
io.SaveITKFile(test, '/home/sci/blakez/HOPEFUL.mhd')
# unstitch_files = sorted(glob.glob(f'{data_dir}{vol_ext}{block}_phi_stitch_*.mhd'))
# phi_unstitch = io.LoadITKFile(unstitch_files[0], device=device)
# phi_unstitch.set_size((60, 1024, 1024))
# test_undone = so.ApplyGrid.Create(phi_unstitch, pad_mode='zeros', device=device)(test, phi_unstitch)
# io.SaveITKFile(test_undone, '/home/sci/blakez/HOPEFUL_undone.mhd')
def_bf = so.ApplyGrid.Create(phi_inv, pad_mode='zeros',
device=device)(bf, phi_inv)
def_seg = so.ApplyGrid.Create(phi_inv, pad_mode='zeros',
device=device)(seg, phi_inv)
# Save out the deformed volumes
io.SaveITKFile(def_bf,
f'{data_dir}{def_ext}difference_volume_deformable.mhd')
io.SaveITKFile(def_seg,
f'{data_dir}{def_ext}segmentation_volume_deformable.mhd')
def mr_to_block(block_path,
rabbit,
t1_vol,
npv_vol=None,
t2_vol=None,
ext_vols=[]):
day3_dir = f'/hdscratch/ucair/{rabbit}/mri/invivo/'
stacked_blocks_dir = f'/hdscratch/ucair/{rabbit}/blockface/recons/'
block = block_path.split('/')[-1]
exvivo_out = f'/hdscratch/ucair/{rabbit}/mri/exvivo/volumes/deformable/{block}/'
invivo_out = f'/hdscratch/ucair/{rabbit}/mri/invivo/volumes/deformable/{block}/'
if not os.path.exists(invivo_out):
os.makedirs(invivo_out)
# deformations = []
# # Get the transformation with the affine included from invivo to exvivo
# invivo_to_exvivo = mr_to_exvivo(day3_dir)
# deformations.append(invivo_to_exvivo)
#
# # Get the transformation with the affine included from exvivo to the stacked blocks
# exvivo_to_stacked = exvivo_to_blocks(stacked_blocks_dir)
# deformations.append(exvivo_to_stacked)
#
# # Load the transformation from the stacked blocks to the block of interest
# stacked_to_block = stacked_blocks_to_block(block_path)
# deformations.append(stacked_to_block)
# # Load the transformation for stitching if there is one
# if os.path.exists(f'{block_path}/volumes/raw/{block}_phi_stitch.mhd'):
# block_stitching = block_stitch(block_path)
# deformations.append(block_stitching)
# Genereate the deformation for the block
to_block = gd.generate(rabbit,
block=block,
source_space='invivo',
target_space='blockface')
# Load the Day3 MR file to be deformed
# t2_motion = io.LoadITKFile(t2_vol, device=device)
ce_t1 = io.LoadITKFile(t1_vol, device=device)
# adc = io.LoadITKFile(ext_vols[0], device=device)
npv = io.LoadITKFile(npv_vol, device=device)
torch.cuda.empty_cache()
# t2_to_block = so.ApplyGrid.Create(to_block, device=device, pad_mode='zeros')(t2_motion, to_block)
# io.SaveITKFile(t2_to_block, f'{invivo_out}invivo_t2_to_{block}.mhd')
t1_to_block = so.ApplyGrid.Create(to_block,
device=device,
pad_mode='zeros')(ce_t1, to_block)
io.SaveITKFile(t1_to_block, f'{invivo_out}invivo_ce_t1_to_{block}.mhd')
# adc_to_block = so.ApplyGrid.Create(to_block, device=device, pad_mode='zeros')(adc, to_block)
# io.SaveITKFile(adc_to_block, f'{invivo_out}invivo_adc_to_{block}.mhd')
#
npv_to_block = so.ApplyGrid.Create(to_block,
device=device,
pad_mode='zeros')(npv, to_block)
io.SaveITKFile(npv_to_block, f'{invivo_out}invivo_npv_to_{block}.mhd')
# # Load the exvivo
# ex_ce_t1 = io.LoadITKFile(
# '/home/sci/blakez/ucair/18_047/rawVolumes/ExVivo_2018-07-26/011_----_3D_VIBE_0p5iso_cor_3ave.nii.gz',
# device=device
# )
#
# ex_t2 = io.LoadITKFile(
# '/home/sci/blakez/ucair/18_047/rawVolumes/ExVivo_2018-07-26/015_----_t2_spc_0p5x0p5x1mm_iso_satBand_3p5ave'
# '.nii.gz',
# device=device
# )
# exvivo_to_block = so.ComposeGrids.Create(device=device)(deformations[1:][::-1])
# t1_ex_to_block = so.ApplyGrid.Create(exvivo_to_block, device=device, pad_mode='zeros')(ex_ce_t1, exvivo_to_block)
# io.SaveITKFile(t1_ex_to_block, f'{exvivo_out}exvivo_ce_t1_to_{block}.mhd')
#
# t2_ex_to_block = so.ApplyGrid.Create(exvivo_to_block, device=device, pad_mode='zeros')(ex_t2, exvivo_to_block)
# io.SaveITKFile(t2_ex_to_block, f'{exvivo_out}exvivo_t2_to_{block}.mhd')
print(f'Done with {block}')