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cremi_reverse.py
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######## IMPORTS & Helpful Functions ########
import numpy as np
import imageio
import math
import gc, argparse, sys, os, errno
import h5py
import warnings
warnings.filterwarnings('ignore')
import scipy
from scipy.ndimage.measurements import label
from skimage.measure import regionprops
import cv2
from shutil import copyfile
def readh5(filename, datasetname=None):
import h5py
fid = h5py.File(filename,'r')
if datasetname is None:
if sys.version[0]=='2': # py2
datasetname = fid.keys()
else: # py3
datasetname = list(fid)
if len(datasetname) == 1:
datasetname = datasetname[0]
if isinstance(datasetname, (list,)):
out=[None]*len(datasetname)
for di,d in enumerate(datasetname):
out[di] = np.array(fid[d])
return out
else:
return np.array(fid[datasetname])
def writeh5(filename, dtarray, datasetname='main'):
import h5py
fid=h5py.File(filename,'w')
if isinstance(datasetname, (list,)):
for i,dd in enumerate(datasetname):
ds = fid.create_dataset(dd, dtarray[i].shape, compression="gzip", dtype=dtarray[i].dtype)
ds[:] = dtarray[i]
else:
ds = fid.create_dataset(datasetname, dtarray.shape, compression="gzip", dtype=dtarray.dtype)
ds[:] = dtarray
fid.close()
def get_roi(image,anotherimage):
img = np.copy(image)
img_ = np.copy(image)
labels = label(image)
img[np.where(labels[0]==1)] =0
img_[np.where(labels[0]==2)] =0
anoimg = np.copy(anotherimage)
anoimg_ = np.copy(anotherimage)
anoimg[np.where(labels[0]==1)] =0
anoimg_[np.where(labels[0]==2)] =0
return anoimg,anoimg_
def convert_to_uint8(filepath):
with h5py.File(filepath) as f:
data = f['main'][:].astype('uint8')
os.system('rm '+filepath)
with h5py.File(filepath) as f:
f.create_dataset('main',data=data)
######## Input Properties ########
crack_path = 'crack/'# output path of the images with crack (no need to change)
trial = 'result04/' # working directory
num_channels = 1 # Default channels
# Sanity Check
if not os.path.exists('prediction/'+trial):
os.makedirs('prediction/'+trial)
if not os.path.exists('reverse/'+trial):
os.makedirs('reverse/'+trial)
#Paths of Vol's to be reversed
pred_file_path = 'prediction/'+trial
pred_A = 'im_A+_v2_200_nocrack_pred.h5'
pred_B = 'im_B+_v2_200_pred.h5'
pred_C = 'im_C+_v2_200_pred.h5'
######## Vol A resolve ########
def deal_with_crack():
"""Uses SIFT and Affine Transforms to fit 15th and 48th prediction"""
ind = [15,48]
vid = 0
for i in ind:
for j in range(1, 3):
im_path = 'crack/tmp/im0' + str(i) + '_prediction' + str(j) + '.png'
im = imageio.imread(im_path)
sz = im.shape
#print("Size of image: ", sz)
vol_path = 'crack/align_' + str(vid) + '_' + str(i) + '_' + str(j) + '.hdf'
tmp = readh5(vol_path)
tmpp = tmp[1, :, :]
tmpp_inv = np.linalg.inv(tmpp)
trans_matrix = tmpp_inv[:2, :]
if j == 1:
B = cv2.warpAffine(im, trans_matrix, dsize = (1912, 1741), flags = cv2.INTER_LINEAR)
else:
B = B + cv2.warpAffine(im, trans_matrix, dsize = (1912, 1741), flags = cv2.INTER_LINEAR)
save_path = 'crack/tmp/im_0' + str(i)+ '_reverse0.png'
imageio.imwrite(save_path, B)
def crack_fix(path_A):
vol = readh5(path_A)
# Extract 14th and 47th slice
prediction_14 = vol[0, 14, :, :]
prediction_47 = vol[0, 47, :, :]
# Extract ROI and save as PNG
## Sanity Check
if os.path.exists(crack_path+'tmp'):
os.system('rm -rf '+crack_path+'tmp')
os.mkdir(crack_path+'tmp')
else:
os.mkdir(crack_path+'tmp')
imageio.imwrite(crack_path+'tmp/im015_prediction1.png',get_roi(imageio.imread(crack_path+'im015_warp0.png'),prediction_14.T)[1])
imageio.imwrite(crack_path+'tmp/im015_prediction2.png',get_roi(imageio.imread(crack_path+'im015_warp0.png'),prediction_14.T)[0])
imageio.imwrite(crack_path+'tmp/im048_prediction1.png',get_roi(imageio.imread(crack_path+'im048_warp0.png'),prediction_47.T)[1])
imageio.imwrite(crack_path+'tmp/im048_prediction2.png',get_roi(imageio.imread(crack_path+'im048_warp0.png'),prediction_47.T)[0])
deal_with_crack()
with h5py.File(pred_file_path+pred_A) as f:
resultsA_reverse1 = f['main'][:]
resultsA_reverse1[0, 14, :, :] = imageio.imread(crack_path+'tmp/im_015_reverse0.png').T
resultsA_reverse1[0, 47, :, :] = imageio.imread(crack_path+'tmp/im_048_reverse0.png').T
writeh5(pred_file_path+'im_A+_v2_200_pred.h5', resultsA_reverse1)
#with h5py.File(pred_file_path+'im_A+_v2_200_pred.h5') as f:
#f.create_dataset('main',data=resultsA_reverse1)
def bad_slices_fix(vol_idx, channel_num):
"""Fixes wrong 15th and 79th slice in Vol A+ and Vol B+"""
for i in vol_idx:
if i == 0:
vol_name = "A+"
elif i == 1:
vol_name = "B+"
elif i == 2:
continue
vol_path = 'reverse/result04/results_new_' + vol_name + '_v2_200_' + str(channel_num) + '.h5'
print("Fixing bad slices in: ", vol_path)
vol = readh5(vol_path, 'main')
_14_slice = vol[14, :, :].copy()
old_15_slice = vol[15, :, :].copy()
vol[15, :, :] = _14_slice
new_15_slice = vol[15, :, :]
_78_slice = vol[78, :, :].copy()
old_79_slice = vol[79, :, :].copy()
vol[79, :, :] = _78_slice
new_79_slice = vol[79, :, :]
if np.array_equal(new_15_slice, old_15_slice):
print("14->15 done incorrectly")
else:
print("14 -> 15 Swap done right!")
if np.array_equal(new_79_slice, old_79_slice):
print("78->79 done incorrectly")
else:
print("78 -> 79 Swap done right!")
writeh5(vol_path, vol)
def threshold_vol(vol_idx, channel_num, thres):
for i in vol_idx:
if i == 0:
vol_name = "A+"
elif i == 1:
vol_name = "B+"
elif i == 2:
vol_name = "C+"
vol_path = 'reverse/result04/results_new_' + vol_name + '_v2_200_' + str(channel_num) + '.h5'
vol = readh5(vol_path)
threshold_limit = thres*255
vol_mod = (vol>threshold_limit).astype(np.uint8)
writeh5(vol_path, vol_mod)
def reverse_all(vol_idx, channel_num):
# volume names
nn=['A','B','C','A+','B+','C+']
# bad slices
bb=[[143],[1,29,30,58,59,91],[28,88,100],[65,93,94,122,123,125],[1,29,30,58,59,91],[28,88,100]]
# to be replaced
gg=[[142],[0,28,31,57,60,90],[27,87,99],[64,92,95,121,124,126],[0,28,31,57,60,90],[27,87,99]]
# newly-aligned image size
sz=[[1727,1842],[2069,1748],[1986,2036],[1741,1912],[2898,1937],[1914,1983]]
# CREMI: 125,1250,1250
# _v2_200: 200 margin from manual label
suf='v2_200'
vol_idx_new = [x+3 for x in vol_idx]
#print("Vol Idx New: ", vol_idx_new)
for nid in vol_idx_new:
trial = 'result04/'
vol = nn[nid]
sn='05'
if len(vol)==2:
sn = "06"
pw=0
ph=0
if vol == 'B+':
ph=700
syn_warp = readh5('prediction/' + trial + 'im_'+ vol + '_v2_200_pred.h5','/main')
syn_warp = syn_warp[channel_num, :, :, :]
sz_r = syn_warp.shape #Shape of the vol
sz_r = tuple((sz_r))
new_size = sz[nid]
new_size = np.array(new_size)
n_size = np.flipud(new_size)
modified_vol_shape = n_size - 400
#print('modified vol shape: ', modified_vol_shape)
temp = np.insert(modified_vol_shape, 0, 125, axis=0)
sz_bad = sz_r - temp
sz_bad = sz_bad//2
#print('sz_bad: ', sz_bad)
#print('syn_warp old shape: ', syn_warp.shape)
syn_warp = syn_warp[sz_bad[0]: -sz_bad[0], sz_bad[1]: -sz_bad[1], sz_bad[2]: -sz_bad[2]]
#print('syn_warp new shape: ', syn_warp.shape)
pp=np.loadtxt('align/trans_' + vol + '_v2.txt', delimiter = ',')
pp = np.cumsum(pp, 0)
_77thElement = pp[76, :]
pp = pp - _77thElement
pp = -pp #Since it's -bsxfun()
max1, max2 = pp.max(axis = 0)
min1, min2 = pp.min(axis = 0)
max1 = math.ceil(max1)
max2 = math.ceil(max2)
min1 = math.ceil(-min1)
min2 = math.ceil(-min2)
ww = np.array([max1, max2, min1, min2])
result_o = np.zeros((125,1250,1250),dtype = np.int16)
for i in range(0, 125):
pd = np.round(pp[14+i])
tmp = np.zeros((3072, 3072))
tmp2 = np.pad(tmp, pad_width = ((0, 0), (ph, ph)), mode = 'symmetric')
x_start = int(911 + pd[0] - ww[0] + ph)
x_end = int(911 + pd[0] + 1250 + ww[2] + ph)
y_start = int(911 + pd[1] - ww[1] + pw)
y_end = int(911 + pd[1] + 1250 + ww[3] + pw)
tmp2[y_start:y_end, x_start:x_end] = syn_warp[i, :, :]
result_o[i, :, : ] = tmp2[pw + 911 : pw + 911 + 1250, ph + 911 : ph + 911 + 1250]
writeh5('reverse/' + trial + 'results_new_' + vol + '_' + suf + '_' + str(channel_num) + '.h5',result_o, 'main')
def type_conversion(vol_idx, channel_num):
for i in vol_idx:
if i == 0:
vol_name = "A+"
elif i == 1:
vol_name = "B+"
elif i == 2:
vol_name = "C+"
vol_path = 'reverse/result04/results_new_' + vol_name + '_v2_200_' + str(channel_num) + '.h5'
convert_to_uint8(vol_path)
def parse_arguments():
parser = argparse.ArgumentParser(description='CREMI Reverse Script')
parser.add_argument('-a', '--pathA', help='Filepath for VolA', default='.', type=str)
parser.add_argument('-b', '--pathB', help='Filepath for VolB', default='.', type=str)
parser.add_argument('-c', '--pathC', help='Filepath for VolC', default='.', type=str)
parser.add_argument('-thres', '--threshold', help='Threshold for volume generation', default=None, type=float)
args = parser.parse_args()
return args
def file_copy(filePath, volIdx):
if volIdx == 0: #volA
copyfile(filePath, pred_file_path + 'im_A+_v2_200_nocrack_pred.h5')
if volIdx == 1: #volB
copyfile(filePath, pred_file_path + 'im_B+_v2_200_pred.h5')
if volIdx == 2:
copyfile(filePath, pred_file_path + 'im_C+_v2_200_pred.h5')
def get_num_channels(file_path):
vol = readh5(file_path)
num_channels = vol.shape[0]
return num_channels
if __name__ == "__main__":
#0/1/2 corresponding to vols
args = parse_arguments()
vol_idx = []
if args.pathA != ".":
vol_idx.append(0)
file_copy(args.pathA, 0)
if args.pathB != ".":
vol_idx.append(1)
file_copy(args.pathB, 1)
if args.pathC != ".":
vol_idx.append(2)
file_copy(args.pathC, 2)
# Fix cracks in first channel of volA. This Assumes First channel contains probability map
if 0 in vol_idx:
print("Dealing with Cracks in Vol A")
crack_fix(pred_file_path+pred_A)
# Calculate number of channels
num_channels = get_num_channels(args.pathA)
print("Number of channels: ", num_channels)
for channel in range(num_channels):
print('\n')
print(f"Dealing with channel: {channel}")
print("#"*40)
print("Reversing Volumes Now....")
reverse_all(vol_idx, channel)
print("Converting to np.uint8....")
type_conversion(vol_idx, channel)
print("Bad slices are being fixed...")
bad_slices_fix(vol_idx, channel)
if args.threshold != None and args.threshold < 1 and args.threshold > 0:
print("Thresholding for final submission...")
threshold_vol(vol_idx, channel, args.threshold)
print("Done!")
print("Reversed volumes available at reverse/result04/")