xfr/ck-preprocess
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

resample results

Browse source
This commit is contained in:
Xiao Furen 2025-02-02 14:15:48 +08:00
parent 58ecd66545
commit 81ca1a2b19
1 changed files with 15 additions and 40 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

55
src/g4synthmorph.py
View file

@ -30,7 +30,7 @@ from skimage.metrics import normalized_mutual_information
import filelock
import matplotlib.pyplot as plt
import numpy as np
import SimpleITK as sitk
# import SimpleITK as sitk
from mri_synthmorph.synthmorph import registration
# from synthmorph import registration
@ -63,40 +63,6 @@ logging.basicConfig(
logger = logging.getLogger(__name__)
# def resize_with_crop_or_pad(image, tx = SIZE_X, ty = SIZE_Y, tz = SIZE_Z):
def resize_with_pad(image, tx = SIZE_X, ty = SIZE_Y, tz = SIZE_Z):
sx, sy, sz = image.GetSize()
l = [(tx-sx)//2,
(ty-sy)//2,
(tz-sz)//2,]
u = [tx-sx-l[0],
ty-sy-l[1],
tz-sz-l[2],
]
# print (l, u)
return sitk.ConstantPad(image, l, u)
def draw_sitk(image, d, post):
a = sitk.GetArrayFromImage(image)
s = a.shape
fig, axs = plt.subplots(1, 3)
# fig.suptitle('%dx%dx%d'%(s[2], s[1], s[0]))
axs.flat[0].imshow(a[s[0]//2,:,:], cmap='gray')
axs.flat[1].imshow(a[:,s[1]//2,:], cmap='gray')
axs.flat[2].imshow(a[:,:,s[2]//2], cmap='gray')
axs.flat[0].axis('off')
axs.flat[1].axis('off')
axs.flat[2].axis('off')
axs.flat[1].invert_yaxis()
axs.flat[2].invert_yaxis()
plt.tight_layout()
os.makedirs(d, exist_ok=True)
plt.savefig(os.path.join(d, '%dx%dx%d-%s'%(s[2],s[1],s[0],post)))
plt.close()
# exit()
def bbox2_3D(img):
r = np.any(img, axis=(1, 2))
@ -132,6 +98,8 @@ def register(ct0, ct1, moving, out_root):
logger.info(' '.join((ct0, ct1, moving, str(out_root))))
orig = sf.load_volume(moving)
base = sf.load_volume(ct0)
if modality == 'CT':
clipped = out_root/'clipped.nii.gz'
@ -201,6 +169,11 @@ def register(ct0, ct1, moving, out_root):
os.environ["FREESURFER_HOME"] = FREESURFER_HOME
os.environ["XLA_FLAGS"] = '--xla_gpu_cuda_data_dir=%s'% os.environ["CONDA_PREFIX"]
fill = orig.min()
# print(fill)
# exit()
for m in MODELS:
default['model'] = m
default['out_dir'] = out_root/m
@ -231,16 +204,18 @@ def register(ct0, ct1, moving, out_root):
out = out_root/('%s.nii.gz'%m)
if m in ['affine', 'rigid']:
trans = sf.load_affine(default['out_dir']/'tra_1.lta')
prop = dict(method='linear', resample=True, fill=0)
orig.transform(trans, **prop).save(out)
prop = dict(method='linear', resample=True, fill=fill)
orig.transform(trans, **prop).resample_like(base, fill=fill).save(out)
logger.info('transformed %s'%out)
# print(prop)
# exit()
else:
# need to resample before transform in warp, too complicated, just copy it
# trans1 = default['out_dir']/'tra_1.nii.gz'
# trans = sf.load_warp(trans1)
shutil.copy(default['out_dir']/'out_1.nii.gz', out)
logger.info('copied %s'% out)
sf.load_volume(default['out_dir']/'out_1.nii.gz').resample_like(base, fill=fill).save(out)
logger.info('resampled %s'% out)
with open(out_root/'metric.txt', 'w') as f_metrics:
for m in MODELS:
@ -295,7 +270,7 @@ def check(epath):
if root2.endswith('RT'):
modality = 'RT'
logger.info('copying %s %s' %(root2, outdir))
shutil.copytree(root2, outdir)
shutil.copytree(root2, outdir, dirs_exist_ok=True)
# exit()
continue
skip = (root2==root) or ('RT' in root2.split('/'))