import re
from numpy import *
import cv2
import numpy as np
import os
import json
def find_matrix(rootname, name, namelist):
idx = -1
exact_match = -1
i = 0
for curname in namelist:
if rootname in curname:
idx = i
break
i += 1
i = 0
for curname in namelist:
if name == curname:
exact_match = i
i += 1
if exact_match >= 0:
return exact_match
else:
return idx
register_name = []
register_hsi = []
register_rgb = []
fregister = open('/pytorch-3dunet-master-zr_rgb_and_hsi/pytorch3dunet/datasets/data_label_company/1.txt', 'r')
flog = open('/pytorch-3dunet-master-zr_rgb_and_hsi/pytorch3dunet/datasets/data_label_company/log.txt', 'w') #raw
for eachline in fregister.readlines():
if "RGB" in eachline:
points = re.split(' ', eachline)
point1 = re.split(',', re.split(':', points[0])[1])
point2 = re.split(',', points[1])
point3 = re.split(',', points[2])
parr = np.float32(
[[np.float32(point1[0]), np.float32(point1[1])], [np.float32(point2[0]), np.float32(point2[1])], [np.float32(point3[0]), np.float32(point3[1])]])
register_rgb.append(parr)
print(len(register_rgb))
elif "HSI" in eachline:
points = re.split(' ', eachline)
point1 = re.split(',', re.split(':', points[0])[1])
point2 = re.split(',', points[0])
point3 = re.split(',', points[2])
parr = np.float32(
[[np.float64(point1[0]), np.float64(point1[1])], [np.float64(point2[0]), np.float64(point2[1])], [np.float64(point3[0]), np.float64(point3[1])]])
register_hsi.append(parr)
else:
register_name.append(eachline[:-1])
fp = open('/home/wangliuan/intern/yuxi/pytorch-3dunet-master-zr_rgb_and_hsi/pytorch3dunet/datasets/data_label_company/all.txt', 'r') #raw file
rootpath = ''
for eachline in fp.readlines():
print(eachline)
flog.write(eachline)
path, name = os.path.split(eachline)
sampleName = name[:-5]
sampleRootName = sampleName[:-5]
LNP = os.path.split(os.path.split(path)[0])[1]
idx = find_matrix(sampleRootName, sampleName, register_name)
hsi_img_path = '/pytorch-3dunet-master-zr_rgb_and_hsi/pytorch3dunet/datasets/data_label_company/' + sampleName + '.png'
rgb_img_path = '/pytorch-3dunet-master-zr_rgb_and_hsi/pytorch3dunet/datasets/data_label_company/' + sampleName + '.jpg'
hsi_img_save_path = '/pytorch-3dunet-master-zr_rgb_and_hsi/pytorch3dunet/datasets/data_label_company/' + sampleName + '_save.png'
rgb_img_save_path = '/pytorch-3dunet-master-zr_rgb_and_hsi/pytorch3dunet/datasets/data_label_company/' + sampleName + '_save.jpg'
# re_label_hsi_img_save_path = '/data1/zhourong/data/cholangiocarcinoma/processed/yuxi_label_data/labeling_data/' + LNP + '/' + sampleName + '.bmp'
# re_label_rgb_img_save_path = '/data1/zhourong/data/cholangiocarcinoma/processed/yuxi_label_data/labeling_data/' + LNP + '/' + sampleName + '.jpg'
hsi_img = cv2.imread(hsi_img_path)
rgb_img = cv2.imread(rgb_img_path)
rgb_img = np.flip(rgb_img, 0)
cv2.imwrite(hsi_img_save_path, hsi_img)
# cv2.imwrite(re_label_hsi_img_save_path, hsi_img)
# cv2.imwrite(re_label_rgb_img_save_path, rgb_img)
if idx == -1:
print("not find matrix, please label the registration !\n")
flog.write("not find matrix, please label the registration !\n")
else:
hsi_points = register_hsi[idx]
rgb_points = register_rgb[idx]
M = cv2.getAffineTransform(hsi_points, rgb_points)
dst = np.zeros([1024, 1280, 3], dtype=np.uint8)
for i in range(1024):
for j in range(1280):
new_x = int(j * M[0][0] + i * M[0][1] + M[0][2] + 0.5)
new_y = int(j * M[1][0] + i * M[1][1] + M[1][2] + 0.5)
if new_x >= 0 and new_x < 1365 and new_y >= 0 and new_y < 1024:
dst[i, j, :] = rgb_img[new_y, new_x, :]
cv2.imwrite(rgb_img_save_path, dst)
flog.close()
'''#030406-20x-roi1
pts1 = np.float32([[156, 124], [1158, 845], [1155, 26]]) #rgb
pts2 = np.float32([[85, 100], [1125, 970], [1186, 66]]) #hsi
#030406c_2-20x-roi1
pts1 = np.float32([[327, 45], [1150, 209], [219, 870]]) #rgb
pts2 = np.float32([[293, 13], [1175, 284], [85, 905]]) #hsi
#030447-20x-roi4
pts1 = np.float32([[160, 190], [1141, 108], [397, 753]]) #rgb
pts2 = np.float32([[94, 155], [1173, 172], [294, 800]]) #hsi
#test
pts1 = np.float32([[326, 601], [1151, 209], [697, 776]]) #rgb
pts2 = np.float32([[232, 624], [1174, 285], [615, 856]]) #hsi
M = cv2.getAffineTransform(pts2, pts1)
# = np.array([[0.91, -0.085, 150], [0.072, 0.91, 50]])
rootpath = "/data1/zhourong/data/cholangiocarcinoma/processed/L/img_rgb_resize_w1365h1024/"
paths = os.listdir(rootpath)
for eachline in paths:
eachline = "030406c_2-20x-roi1.jpg"
filepath = os.path.join(rootpath, eachline)
img = cv2.imread(filepath)
img = np.flip(img, 0)
savepath = "/data1/zhourong/data/cholangiocarcinoma/processed/tmp/L/" + eachline + "-.jpg"
rows,cols,ch = img.shape
dst = np.zeros([1024, 1280, 3], dtype=np.uint8)
for i in range(1024):
for j in range(1280):
new_x = int(j * M[0][0] + i * M[0][1] + M[0][2] + 0.5)
new_y = int(j * M[1][0] + i * M[1][1] + M[1][2] + 0.5)
if new_x >= 0 and new_x < 1365 and new_y >=0 and new_y < 1024:
dst[i, j, :] = img[new_y, new_x, :]
cv2.imwrite(savepath, dst)
a =0'''
'''fp = open('/data4/zhourong/workspace_pytorch/pytorch-3dunet-master-zr_rgb_and_hsi/exp/multifusion/train_2021-08-13_23-32-05.log', 'r')
op = open('/data4/zhourong/workspace_pytorch/pytorch-3dunet-master-zr_rgb_and_hsi/exp/multifusion/train_val_loss_miou.csv', 'w')
val_loss = []
val_mIou = []
train_loss = []
train_mIou = []
for eachline in fp.readlines():
if "Validation finished. Loss:" in eachline:
lines = re.split(' ', eachline)
loss = round(float(lines[9][:-1]), 4)
miou = round(float(lines[12][:-1]), 4)
val_loss.append(loss)
val_mIou.append(miou)
if "Training stats. Loss:" in eachline:
lines = re.split(' ', eachline)
loss = round(float(lines[9][:-1]), 4)
miou = round(float(lines[12][:-1]), 4)
train_loss.append(loss)
train_mIou.append(miou)
op.write("train loss:\n")
for i in train_loss:
op.write(str(i)+',')
op.write("\ntrain miou:\n")
for i in train_mIou:
op.write(str(i)+',')
op.write("\nval loss:\n")
for i in val_loss:
op.write(str(i)+',')
op.write("\nval miou:\n")
for i in val_mIou:
op.write(str(i)+',')'''
9.2 label_json
最新推荐文章于 2024-09-27 10:11:28 发布