import SimpleITK as sitk
from shubow_tools import imreadseq_multithread, imsaveseq
import os
import re
import shutil
wkdir = r"/home/blue/SITK_registered_image_14um/3rd batch tibia"
dst = r"/home/blue/SITK_registered_image_14um/Flipped"
os.chdir(wkdir)
with open("failed.txt", "r") as f:
retry_file = f.readlines()
retry_list = [i[:-1] for i in retry_file]
for fd in retry_list:
if not 'right' in fd:
continue
print(fd)
output = os.path.join(dst, fd)
if os.path.exists(output):
shutil.rmtree(output)
os.mkdir(output)
image = imreadseq_multithread(os.path.join(wkdir, fd))
image = image[::-1, :, :]
imsaveseq(image, os.path.join(dst, fd), fd)
print('Next!')
wkdir = r'D:/MicroCT data/Yoda1 11.13.2019/Tibia Femur fully seg'
masterdir = os.path.join(wkdir, 'week 3 tibia')
masteroutput = os.path.join(wkdir, 'Registered tibia week 3')
refdir = os.path.join(wkdir, 'Registered tibia week 0')
format = "%(asctime)s: %(message)s"
logging.basicConfig(format=format, level=logging.INFO, datefmt="%H:%M:%S")
for file in sorted(os.listdir(masterdir)):
if re.search(r'(410.*left)', file):
#if re.search(r'\d{3} week \d (left|right) tibia',file):
imgtitle = file
logging.info('Loading image of {} ...'.format(imgtitle))
reftitle = file.replace('week 3', 'week 0') + ' registered'
ref_img = imreadseq_multithread(os.path.join(refdir, reftitle))
tar_img = imreadseq_multithread(os.path.join(masterdir, file),
sitkimg=False,
rmbckgrd=60,
z_range=[0, 840])
tar_img = sitk.GetImageFromArray(
auto_crop(Rotate_by_Euler_angles(tar_img)))
ini_transform = cent_transform(ref_img, tar_img)
metric_values = []
multires_iterations = []
suboutput = os.path.join(masteroutput, imgtitle + " registered")
if not os.path.exists(suboutput):
os.mkdir(suboutput)
logging.info('Registration of {} is in process...'.format(imgtitle))
masterdir = r"F:\Shubo MicroCT data\CTimages for plotting\3rd batch loading"
pattern = re.compile(
r"(\d{3}.week.\d).(left|right|runner|nonrunner).*composite")
#pattern = re.compile(r"(320 week 4) (right) w0w4composite")
format = "%(asctime)s: %(message)s"
logging.basicConfig(format=format, level=logging.INFO, datefmt="%H:%M:%S")
for folder in sorted(os.listdir(masterdir)):
pattern.search(folder)
sampleID = pattern.search(folder)
if sampleID:
separator = "_"
logging.info("Processing {}".format(sampleID.group(0)))
try:
trab_imseq = os.path.join(masterdir, folder, "Trab-ROI-wx")
trab = imreadseq_multithread(trab_imseq)
trab_nii = os.path.join(
masterdir,
separator.join(
[sampleID.group(1),
sampleID.group(2), "Trab.nii"]))
sitk.WriteImage(trab, trab_nii)
logging.info("Trabecular bone saved!")
except Exception as ex:
logging.info("Trabecular bone failed! {}".format(ex))
pass
try:
cort_imseq = os.path.join(masterdir, folder, "Cort-ROI-wx")
cort = imreadseq_multithread(cort_imseq)
cort_nii = os.path.join(
masterdir = os.path.join(wkdir, 'Registered femur week 3')
masteroutput = os.path.join(wkdir,
'VOI450-590_Registered femur week 3_thred75')
refdir = os.path.join(wkdir, 'Registered femur week 0')
format = "%(asctime)s: %(message)s"
logging.basicConfig(format=format, level=logging.INFO, datefmt="%H:%M:%S")
for file in sorted(os.listdir(masterdir)):
#if re.search(r'416.*left femur',file):
if re.search(r'\d{3} week \d (left|right) femur', file):
imgtitle = file[0:-11]
logging.info('Loading image of {} ...'.format(imgtitle))
reftitle = imgtitle.replace('week 3', 'week 0') + ' registered'
ref_img = imreadseq_multithread(os.path.join(refdir, reftitle),
z_range=[450, 590],
rmbckgrd=80)
tar_img = imreadseq_multithread(os.path.join(masterdir, file),
sitkimg=False,
z_range=[410, 630],
rmbckgrd=75)
tar_img = sitk.GetImageFromArray(
auto_crop(Rotate_by_Euler_angles(tar_img))) # femur
ini_transform = cent_transform(ref_img, tar_img)
metric_values = []
multires_iterations = []
suboutput = os.path.join(masteroutput, imgtitle + " registered")
logging.info('Registration of {} is in process...'.format(imgtitle))
#! /home/spl/ml/sitk/bin/python
# -*- coding: utf-8 -*-
import SimpleITK as sitk
import os
import sys
from pathlib import Path
import re
from shubow_tools import imreadseq_multithread
import glob
src = r'/media/spl/D/MicroCT_data/Machine learning/SITK_reg_7um'
dst = r'/run/user/1000/gvfs/smb-share:server=lywanglab.local,share=micro_ct_data/Deep learning project/7_um_data'
os.chdir(src)
for fd in glob.glob('*registered'):
print('reading: ' + fd)
s = re.search(r'(\d{3}) week (\d) (left|right)', fd)
name = '{}{}T_w{}'.format(s.group(1),s.group(3)[0].upper(), s.group(2))
img = imreadseq_multithread(fd, z_range=[-300,None])
sitk.WriteImage(img, os.path.join(dst,name+'.nii.gz'))
print(name + '.nii.gz saved')
masterdir = r"E:\Yoda1-tumor-loading 2.26.2021\Tibia & femur week 3"
masteroutput = r"E:\Yoda1-tumor-loading 2.26.2021\Registration week 3"
refdir = r"E:\Yoda1-tumor-loading 2.26.2021\Registration week 0"
BASELINE_REGISTRATION = True
if not os.path.exists(masteroutput):
os.mkdir(masteroutput)
format = "%(asctime)s: %(message)s"
logging.basicConfig(format = format, level = logging.INFO,
datefmt="%H:%M:%S")
if not BASELINE_REGISTRATION:
logging.info('Loading reference image...')
ref_img = imreadseq_multithread(refdir,thread = 2, sitkimg=True, z_range=[-355,-5])
#ref_img = down_scale(ref_img, down_scale_factor=1.0)
failed_list = []
'''with open("failed.txt", "r") as f :
retry_file = f.readlines()
retry_list = [i[:-3] for i in retry_file]
read_range_list = [i[-2] for i in retry_file]'''
for file in sorted(os.listdir(masterdir)):
if re.search(r"\d{3}.(week.\d) (left|right) tibia", file):
imgtitle = file
if BASELINE_REGISTRATION:
import shutil
import numpy as np
wkdir = r"/media/spl/D/MicroCT_data/Machine learning/1st batch tibia registration"
os.chdir(wkdir)
masterdir = r"/media/spl/D/MicroCT_data/Machine learning/Jul 2018 1st batch L & R tibia/L & R tibia 7.9"
masteroutput = r"/media/spl/D/MicroCT_data/Machine learning/1st batch tibia registration"
refdir = r"/media/spl/D/MicroCT_data/MicroCT registration ref/6w F WT tibia"
format = "%(asctime)s: %(message)s"
logging.basicConfig(format = format, level = logging.INFO,
datefmt="%H:%M:%S")
logging.info('Loading reference image...')
ref_img = imreadseq_multithread(refdir,thread = 2, sitkimg=True, rmbckgrd=75, z_range=[-756,None])
ref_img = down_scale(ref_img, down_scale_factor=2.0)
failed_list = []
'''
with open("failed2.txt", "r") as f :
retry = f.readlines()
retry = [i[:-1] for i in retry]
'''
for file in sorted(os.listdir(masterdir))[:]:
if re.search(r"\d{3} (week \d) (left|right) tibia", file): #and file in retry:
imgtitle = file
logging.info('Loading image {} ...'.format(imgtitle))
if 'right' in file: