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from light_training.preprocessing.preprocessors.default_preprocessor_liver_2017 import DefaultPreprocessor
import numpy as np
import pickle
import json
def process_train():
# fullres spacing is [0.5 0.70410156 0.70410156]
# median_shape is [602.5 516.5 516.5]
base_dir = "/home/xingzhaohu/data/Liver_2017"
preprocessor = DefaultPreprocessor(base_dir=base_dir)
out_spacing = [1.0, 0.76757812, 0.76757812]
output_dir = "./data/fullres/train/"
with open("./data_analysis_result.txt", "r") as f:
content = f.read().strip("\n")
print(content)
content = eval(content)
foreground_intensity_properties_per_channel = content["intensity_statistics_per_channel"]
preprocessor.run(output_spacing=out_spacing,
output_dir=output_dir,
all_labels=[1, 2],
num_processes=16,
foreground_intensity_properties_per_channel=foreground_intensity_properties_per_channel)
def process_val():
# fullres spacing is [0.5 0.70410156 0.70410156]
# median_shape is [602.5 516.5 516.5]
base_dir = "./data/raw_data/Val"
image_dir = "img"
preprocessor = DefaultPreprocessor(base_dir=base_dir,
image_dir=image_dir,
label_dir=None,
)
out_spacing = [0.5, 0.70410156, 0.70410156]
with open("./data_analysis_result.txt", "r") as f:
content = f.read().strip("\n")
print(content)
content = eval(content)
foreground_intensity_properties_per_channel = content["intensity_statistics_per_channel"]
output_dir = "./data/fullres/val_test/"
preprocessor.run(output_spacing=out_spacing,
output_dir=output_dir,
all_labels=[1, ],
foreground_intensity_properties_per_channel=foreground_intensity_properties_per_channel,
num_processes=16)
def process_val_semi():
# fullres spacing is [0.5 0.70410156 0.70410156]
# median_shape is [602.5 516.5 516.5]
base_dir = "./data/raw_data/Val_semi_postprocess"
image_dir = "img"
preprocessor = DefaultPreprocessor(base_dir=base_dir,
image_dir=image_dir,
label_dir="gt",
)
out_spacing = [0.5, 0.70410156, 0.70410156]
with open("./data_analysis_result.txt", "r") as f:
content = f.read().strip("\n")
print(content)
content = eval(content)
foreground_intensity_properties_per_channel = content["intensity_statistics_per_channel"]
output_dir = "./data/fullres/val_semi_postprocess/"
preprocessor.run(output_spacing=out_spacing,
output_dir=output_dir,
all_labels=[1, ],
foreground_intensity_properties_per_channel=foreground_intensity_properties_per_channel)
def plan():
base_dir = "/home/xingzhaohu/data/Liver_2017"
preprocessor = DefaultPreprocessor(base_dir=base_dir,
)
preprocessor.run_plan()
if __name__ == "__main__":
# plan()
process_train()
# import time
# s = time.time()
# process_val()
# e = time.time()
# print(f"preprocessing time is {e - s}")
# process_val_semi()
#
# preprocessor.run(output_spacing=[3, 0.9765625, 0.9765625], output_dir=output_dir)
# data = np.load("/home/xingzhaohu/sharefs/datasets/AIIB23_nnunet/train/AIIB23_96.npz")
# image = data["data"]
# label = data["seg"]
# print(image.shape)
# print(label.shape)
# import matplotlib.pyplot as plt
# for i in range(20):
# plt.imshow(image[0, i], cmap="gray")
# plt.show()
# df = open("/home/xingzhaohu/sharefs/datasets/AIIB23_nnunet/train/AIIB23_96.pkl", "rb")
# info = pickle.load(df)
# print(info) |