381 lines
12 KiB
Python
381 lines
12 KiB
Python
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'''
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metric > -0.27 is bad registration
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'''
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import json
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import os
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# import pathlib
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import shelve
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import shutil
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import time
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import ants
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import filelock
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import matplotlib.pyplot as plt
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import numpy as np
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import SimpleITK as sitk
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# import skimage
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PATIENTS_ROOT = '/mnt/1220/Public/dataset2/M6'
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PATIENTS_ROOT = '/mnt/1220/Public/dataset2/M6_24Q3/nii/'
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OUT_ROOT = '/mnt/1220/Public/dataset2/N6'
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OUT_ROOT = '/mnt/1220/Public/dataset2/N6_24Q3.1'
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SHELVE = os.path.join(OUT_ROOT, '0shelve')
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MAX_Y = 256
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SIZE_X = 249
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SIZE_Y = 249
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SIZE_Z = 192
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# SIZE_Z = 256
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MIN_OVERLAP = 0.50
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MIN_METRIC = -0.50
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# def resize_with_crop_or_pad(image, tx = SIZE_X, ty = SIZE_Y, tz = SIZE_Z):
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def resize_with_pad(image, tx = SIZE_X, ty = SIZE_Y, tz = SIZE_Z):
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sx, sy, sz = image.GetSize()
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l = [(tx-sx)//2,
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(ty-sy)//2,
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(tz-sz)//2,]
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u = [tx-sx-l[0],
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ty-sy-l[1],
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tz-sz-l[2],
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]
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# print (l, u)
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return sitk.ConstantPad(image, l, u)
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def draw_sitk(image, d, post):
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a = sitk.GetArrayFromImage(image)
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s = a.shape
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fig, axs = plt.subplots(1, 3)
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# fig.suptitle('%dx%dx%d'%(s[2], s[1], s[0]))
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axs.flat[0].imshow(a[s[0]//2,:,:], cmap='gray')
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axs.flat[1].imshow(a[:,s[1]//2,:], cmap='gray')
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axs.flat[2].imshow(a[:,:,s[2]//2], cmap='gray')
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axs.flat[0].axis('off')
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axs.flat[1].axis('off')
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axs.flat[2].axis('off')
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axs.flat[1].invert_yaxis()
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axs.flat[2].invert_yaxis()
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plt.tight_layout()
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os.makedirs(d, exist_ok=True)
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plt.savefig(os.path.join(d, '%dx%dx%d-%s'%(s[2],s[1],s[0],post)))
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plt.close()
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# exit()
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def bbox2_3D(img):
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r = np.any(img, axis=(1, 2))
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c = np.any(img, axis=(0, 2))
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z = np.any(img, axis=(0, 1))
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if not np.any(r):
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return -1, -1, -1, -1, -1, -1
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rmin, rmax = np.where(r)[0][[0, -1]]
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cmin, cmax = np.where(c)[0][[0, -1]]
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zmin, zmax = np.where(z)[0][[0, -1]]
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return rmin, rmax, cmin, cmax, zmin, zmax
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def registration(ct0, ct1, mr):
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ct0n = ct0.numpy()
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mrn = mr.numpy()
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if np.array_equal(ct0n, mrn):
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print('EQUAL')
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return {
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'fwdtransforms': [],
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'warpedfixout': ct0,
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'warpedmovout': ct0,
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'ct': 0,
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'type': 'Identity',
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'metric': -2,
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'ratio': 1,
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}
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if ct0n.shape == mrn.shape:
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print('SAME SHAPE')
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CTS = (ct0, ct1)
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TYPES = (
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# 'Translation',
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'Rigid',
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'QuickRigid',
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'DenseRigid',
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'BOLDRigid',
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)
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else:
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print('others', mrn.shape)
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if min(mrn.shape) < 4:
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print('skip')
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return None
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CTS = (ct0, ct1)
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TYPES = (
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# 'Translation',
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'Rigid',
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'QuickRigid',
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'DenseRigid',
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'BOLDRigid',
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)
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TX = []
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start = time.time()
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for m in range(len(CTS)):
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for typ in TYPES:
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ct = CTS[m]
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print(typ)
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mytx = ants.registration(ct, mr, typ)
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ones = np.ones(mr.numpy().shape)
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mask1 = mr.new_image_like(ones)
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mytx['mask'] = ants.apply_transforms(ct0, mask1, mytx['fwdtransforms'],
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interpolator='genericLabel',
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)
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mytx['metric0M'] = ants.create_ants_metric(ct0,
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mytx['warpedmovout'],
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metric_type='MattesMutualInformation',
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moving_mask = mytx['mask'],
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).get_value()
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mytx['metric1M'] = ants.create_ants_metric(ct1,
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mytx['warpedmovout'],
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metric_type='MattesMutualInformation',
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moving_mask = mytx['mask'],
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).get_value()
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mytx['metricMM'] = ants.create_ants_metric(mr,
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mytx['warpedfixout'],
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metric_type='MattesMutualInformation',
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).get_value()
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mytx['metric'] = min([mytx['metric0M'], mytx['metric1M'], mytx['metricMM']])
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mytx['ct'] = m
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mytx['type'] = (typ, 'fwd')
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mytx['warpedout'] = mytx['warpedmovout']
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TX.append(mytx)
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print(mytx['metric'], mytx['metric0M'], mytx['metric1M'], mytx['metricMM'])
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# '''
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mytx = ants.registration(mr, ct, typ)
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ones = np.ones(mr.numpy().shape)
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mask1 = mr.new_image_like(ones)
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mytx['mask'] = ants.apply_transforms(ct0, mask1, mytx['fwdtransforms'],
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interpolator='genericLabel',
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whichtoinvert=[True],
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)
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mytx['metricMM'] = ants.create_ants_metric(mr,
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mytx['warpedmovout'],
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metric_type='MattesMutualInformation',
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).get_value()
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mytx['metric0M'] = ants.create_ants_metric(ct0,
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mytx['warpedfixout'],
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metric_type='MattesMutualInformation',
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fixed_mask = mytx['mask'],
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).get_value()
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mytx['metric1M'] = ants.create_ants_metric(ct1,
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mytx['warpedfixout'],
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metric_type='MattesMutualInformation',
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fixed_mask = mytx['mask'],
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).get_value()
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mytx['metric'] = min([mytx['metricMM'], mytx['metric0M'], mytx['metric1M']])
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mytx['ct'] = m
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mytx['type'] = (typ, 'inv')
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mytx['warpedout'] = mytx['warpedfixout']
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TX.append(mytx)
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print(mytx['metric'], mytx['metricMM'], mytx['metric0M'], mytx['metric1M'])
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if min([t['metric'] for t in TX]) < MIN_METRIC:
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break
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if min([t['metric'] for t in TX]) < MIN_METRIC:
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break
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print(time.time()-start, 'seconds')
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# exit()
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tx = {
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'metric': 0,
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}
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for t in TX:
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if t['metric'] < tx['metric']:
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tx = t
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tx['ratio'] = tx['mask'].numpy().sum() / np.prod(ct0.numpy().shape)
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return tx
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def check(epath):
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registered = 0
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for root, dirs, files in os.walk(epath):
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dirs.sort()
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RT_DIR = os.path.join(root, 'RT')
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ORGAN_DIR = os.path.join(RT_DIR, 'ORGAN')
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if not os.path.isdir(ORGAN_DIR):
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continue
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# if there is no eye, it's no a brain image
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eye = None
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organs = sorted(os.scandir(ORGAN_DIR), key=lambda e: e.name)
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for o in organs:
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if 'eye' in o.name.lower():
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eye = o
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if eye is None:
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print('no eye... skip', root)
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# exit()
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return None
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ct_image = os.path.join(RT_DIR, 'ct_image.nii.gz')
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ct0 = sitk.ReadImage(ct_image)
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ct1 = sitk.Clamp(ct0, sitk.sitkUInt8, 0, 80)
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print(ct_image, ct0.GetSize())
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outdir = os.path.join(OUT_ROOT, os.path.relpath(root, PATIENTS_ROOT))
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print(outdir)
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os.makedirs(outdir, exist_ok=True)
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ct0_nii = os.path.join(outdir, 'ct0.nii.gz')
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ct1_nii = os.path.join(outdir, 'ct1.nii.gz')
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shutil.copy(ct_image, ct0_nii)
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sitk.WriteImage(ct1, ct1_nii)
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# sitk.WriteImage(sitk.DICOMOrient(ct0), ct0_nii)
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# sitk.WriteImage(sitk.DICOMOrient(ct1), ct1_nii)
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ct0 = ants.image_read(ct0_nii, reorient=True)
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ct1 = ants.image_read(ct1_nii, reorient=True)
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for root2, dirs2, files2 in os.walk(root):
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dirs2.sort()
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skip = (root2==root) or ('RT' in root2.split('/'))
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if skip:
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continue
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if root2.endswith('CT'):
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modality = 'CT'
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# continue
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else:
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modality = 'other'
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print(skip, root2, modality)
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outdir = os.path.join(OUT_ROOT, os.path.relpath(root2, PATIENTS_ROOT))
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os.makedirs(outdir, exist_ok=True)
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for e in sorted(os.scandir(root2), key=lambda e: e.name):
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if not e.name.endswith('.nii.gz'):
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continue
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if '_RTDOSE_' in e.name:
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continue
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if '_DTI_' in e.name:
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continue
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if '_ROI1.' in e.name:
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continue
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OUT_IMG = os.path.join(outdir, e.name)
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if os.path.isfile(OUT_IMG):
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print('skip', OUT_IMG)
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continue
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print(e.name, e.path)
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fix = ants.image_read(e.path, reorient=True)
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mytx = registration(ct0, ct1, fix)
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if mytx is None:
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continue
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print(mytx['ratio'], mytx['metric'])
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registered += 1
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os.makedirs(outdir, exist_ok=True)
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OUT_WARP = OUT_IMG.replace('.nii.gz', '.warp.nii.gz')
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OUT_MSK = OUT_IMG.replace('.nii.gz', '.mask.nii.gz')
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OUT_JSON = OUT_IMG.replace('.nii.gz', '.json')
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OUT_MAT = OUT_IMG.replace('.nii.gz', '.mat')
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jj = {
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'ct' : mytx['ct'],
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'type' : mytx['type'],
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'metric': mytx['metric'],
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'ratio' : mytx['ratio'],
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}
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with open(OUT_JSON, 'w') as f:
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json.dump(jj, f, indent=1)
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if mytx['fwdtransforms']:
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shutil.copy(mytx['fwdtransforms'][0], OUT_MAT)
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ants.image_write(mytx['mask'], OUT_MSK)
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ants.image_write(mytx['warpedout'], OUT_WARP)
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metric = mytx['metric']
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metric_dir = os.path.join(OUT_ROOT, "1")
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OUT_TXT = os.path.join(metric_dir, '%f-%s'%(metric, e.name.replace('.nii.gz', '.txt')))
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jj['dir'] = outdir
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os.makedirs(metric_dir, exist_ok=True)
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with open(OUT_TXT, 'w') as f:
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json.dump(jj, f, indent=1)
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shutil.copy(e.path, OUT_IMG)
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return registered
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def main():
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# check('/mnt/1220/Public/dataset2/M6/QT6QVY34') # Lung
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# check('/mnt/1220/Public/dataset2/M6/24V62QQM') # index limit
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# check('/mnt/1220/Public/dataset2/M6/WD34XIQO') # index limit
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# check('/mnt/1220/Public/dataset2/M6/26TYQI3C') # bad registration, need DenseRigid for 1 CT only
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# check('/mnt/1220/Public/dataset2/M6/5BXKANST') # low score
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# check('/mnt/1220/Public/dataset2/M6/BQ773ST6') # bbox problem
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# check('/mnt/1220/Public/dataset2/M6/OJVMKLLO') # series naming conventions
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# check('/mnt/1220/Public/dataset2/M6/PBH6IPXE') # TOF
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# check('/mnt/1220/Public/dataset2/M6/SYPFKLU4') # strange frame, eclipse doses
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# check('/mnt/1220/Public/dataset2/M6/TCZXFBY3') # bad registration
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# exit()
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EXCLUDE = (
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# 'LLUQJUY4', #cervical
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)
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os.makedirs(OUT_ROOT, exist_ok=True)
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LOCK_DIR = os.path.join(OUT_ROOT, '0lock')
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os.makedirs(LOCK_DIR, exist_ok=True)
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||
|
|
for e in sorted(os.scandir(PATIENTS_ROOT), key=lambda e: e.name):
|
||
|
|
if e.is_dir():
|
||
|
|
d = shelve.open(SHELVE)
|
||
|
|
if e.name in d or e.name in EXCLUDE:
|
||
|
|
print('skip', e.name)
|
||
|
|
d.close()
|
||
|
|
continue
|
||
|
|
d.close()
|
||
|
|
lock_path = os.path.join(LOCK_DIR, '%s.lock'%e.name)
|
||
|
|
lock = filelock.FileLock(lock_path, timeout=1)
|
||
|
|
try:
|
||
|
|
lock.acquire()
|
||
|
|
except:
|
||
|
|
print(lock_path, 'locked')
|
||
|
|
continue
|
||
|
|
ret = check(e.path)
|
||
|
|
lock.release()
|
||
|
|
# exit()
|
||
|
|
d = shelve.open(SHELVE)
|
||
|
|
d[e.name] = ret
|
||
|
|
d.close()
|
||
|
|
|
||
|
|
if __name__ == '__main__':
|
||
|
|
main()
|