198 lines
7.1 KiB
Python
Executable File
198 lines
7.1 KiB
Python
Executable File
import SimpleITK as sitk
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import tensorflow as tf
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from tensorflow.keras.models import load_model
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from focal_loss import BinaryFocalLoss
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import numpy as np
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import multiprocessing
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from functools import partial
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import os
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from os import path
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from tqdm import tqdm
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import argparse
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from sfransen.utils_quintin import *
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from sfransen.DWI_exp.helpers import *
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from sfransen.DWI_exp.preprocessing_function import preprocess
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from sfransen.DWI_exp.callbacks import dice_coef
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#from sfransen.FROC.blob_preprocess import *
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from sfransen.FROC.cal_froc_from_np import *
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from sfransen.load_images import load_images_parrallel
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from sfransen.DWI_exp.losses import weighted_binary_cross_entropy
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from umcglib.froc import calculate_froc, plot_froc, plot_multiple_froc, partial_auc
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from umcglib.binarize import dynamic_threshold
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from umcglib.utils import set_gpu
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set_gpu(gpu_idx=1)
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parser = argparse.ArgumentParser(
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description='Calculate the froc metrics and store in froc_metrics.yml')
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parser.add_argument('-experiment',
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help='Title of experiment')
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parser.add_argument('--series', '-s',
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metavar='[series_name]', required=True, nargs='+',
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help='List of series to include')
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parser.add_argument('-fold',
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default='',
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help='List of series to include')
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args = parser.parse_args()
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# if __name__ = '__main__':
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# bovenstaande nodig om fork probleem op te lossen (windows cs linux)
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######## CUDA ################
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os.environ["CUDA_VISIBLE_DEVICES"] = "2"
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######## constants #############
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fold = args.fold
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SERIES = args.series
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series_ = '_'.join(args.series)
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EXPERIMENT = args.experiment
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MODEL_PATH = f'./../train_output/{EXPERIMENT}_{series_}_{fold}/models/{EXPERIMENT}_{series_}_{fold}.h5'
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YAML_DIR = f'./../train_output/{EXPERIMENT}_{series_}_{fold}'
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IMAGE_DIR = f'./../train_output/{EXPERIMENT}_{series_}_{fold}'
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# MODEL_PATH = f'./../train_output/{EXPERIMENT}_{series_}/models/{EXPERIMENT}_{series_}.h5'
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# YAML_DIR = f'./../train_output/{EXPERIMENT}_{series_}'
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# IMAGE_DIR = f'./../train_output/{EXPERIMENT}_{series_}'
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DATA_DIR = "./../data/Nijmegen paths/"
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TARGET_SPACING = (0.5, 0.5, 3)
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INPUT_SHAPE = (192, 192, 24, len(SERIES))
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IMAGE_SHAPE = INPUT_SHAPE[:3]
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DATA_SPLIT_INDEX = read_yaml_to_dict(f'./../data/Nijmegen paths/train_val_test_idxs_{fold}.yml')
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# DATA_SPLIT_INDEX = read_yaml_to_dict(f'./../data/Nijmegen paths/train_val_test_idxs.yml')
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TEST_INDEX = DATA_SPLIT_INDEX['test_set0']
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N_CPUS = 12
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########## load images in parrallel ##############
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print_(f"> Loading images into RAM...")
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# # read paths from txt
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# image_paths = {}
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# for s in SERIES:
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# with open(path.join(DATA_DIR, f"{s}.txt"), 'r') as f:
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# image_paths[s] = [l.strip() for l in f.readlines()]
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# with open(path.join(DATA_DIR, f"seg.txt"), 'r') as f:
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# seg_paths = [l.strip() for l in f.readlines()]
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# num_images = len(seg_paths)
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# # create pool of workers
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# pool = multiprocessing.Pool(processes=N_CPUS)
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# partial_images = partial(load_images_parrallel,
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# seq = 'images',
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# target_shape=IMAGE_SHAPE,
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# target_space = TARGET_SPACING)
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# partial_seg = partial(load_images_parrallel,
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# seq = 'seg',
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# target_shape=IMAGE_SHAPE,
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# target_space = TARGET_SPACING)
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# #load images
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# images = []
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# for s in SERIES:
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# image_paths_seq = image_paths[s]
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# image_paths_index = np.asarray(image_paths_seq)[TEST_INDEX][:5]
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# data_list = pool.map(partial_images,image_paths_index)
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# data = np.stack(data_list, axis=0)
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# images.append(data)
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# images_list = np.transpose(images, (1, 2, 3, 4, 0))
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# print('>>>>> size image_list nmr 1:', np.shape(images_list))
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# #load segmentations
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# seg_paths_index = np.asarray(seg_paths)[TEST_INDEX][:5]
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# data_list = pool.map(partial_seg,seg_paths_index)
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# segmentations = np.stack(data_list, axis=0)
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########## test with old method #############
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image_paths = {}
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for s in SERIES:
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with open(path.join(DATA_DIR, f"{s}.txt"), 'r') as f:
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image_paths[s] = [l.strip() for l in f.readlines()]
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with open(path.join(DATA_DIR, f"seg.txt"), 'r') as f:
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seg_paths = [l.strip() for l in f.readlines()]
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num_images = len(seg_paths)
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images = []
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images_list = []
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segmentations = []
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# Read and preprocess each of the paths for each series, and the segmentations.
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for img_idx in tqdm(range(len(TEST_INDEX))): #for less images
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# print('images number',[TEST_INDEX[img_idx]])
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img_s = {f'{s}': sitk.ReadImage(image_paths[s][TEST_INDEX[img_idx]], sitk.sitkFloat32) for s in SERIES}
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seg_s = sitk.ReadImage(seg_paths[TEST_INDEX[img_idx]], sitk.sitkFloat32)
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img_n, seg_n = preprocess(img_s, seg_s,
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shape=IMAGE_SHAPE, spacing=TARGET_SPACING)
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for seq in img_n:
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images.append(img_n[f'{seq}'])
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images_list.append(images)
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images = []
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segmentations.append(seg_n)
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images_list = np.transpose(images_list, (0, 2, 3, 4, 1))
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# print('>>>>>DEBUG size image_list nmr 2:', np.shape(images_list), '. equal to: (5, 192, 192, 24, 3)?')
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########### load module ##################
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print(' >>>>>>> LOAD MODEL <<<<<<<<<')
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dependencies = {
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'dice_coef': dice_coef,
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'weighted_cross_entropy_fn':weighted_binary_cross_entropy
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}
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reconstructed_model = load_model(MODEL_PATH, custom_objects=dependencies)
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# reconstructed_model.summary(line_length=120)
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# make predictions on all TEST_INDEX
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print(' >>>>>>> START prediction <<<<<<<<<')
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predictions_blur = reconstructed_model.predict(images_list, batch_size=1)
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############# preprocess #################
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# preprocess predictions by removing the blur and making individual blobs
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print('>>>>>>>> START preprocess')
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def move_dims(arr):
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# UMCG numpy dimensions convention: dims = (batch, width, heigth, depth)
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# Joeran numpy dimensions convention: dims = (batch, depth, heigth, width)
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arr = np.moveaxis(arr, 3, 1)
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arr = np.moveaxis(arr, 3, 2)
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return arr
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# Joeran has his numpy arrays ordered differently.
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predictions_blur = move_dims(np.squeeze(predictions_blur))
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segmentations = move_dims(np.squeeze(segmentations))
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predictions = [preprocess_softmax(pred, threshold="dynamic")[0] for pred in predictions_blur]
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# Remove outer edges
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zeros = np.zeros(np.shape(predictions))
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test = np.squeeze(predictions)[:,2:-2,2:190,2:190]
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zeros[:,2:-2,2:190,2:190] = test
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predictions = zeros
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# perform Froc method joeran
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metrics = evaluate(y_true=segmentations, y_pred=predictions)
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dump_dict_to_yaml(metrics, YAML_DIR, "froc_metrics_focal_10_test", verbose=True)
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############## save image as example #################
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# save image nmr 2
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img_s = sitk.GetImageFromArray(predictions_blur[2].squeeze())
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sitk.WriteImage(img_s, f"{IMAGE_DIR}/predictions_blur_002_old.nii.gz")
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img_s = sitk.GetImageFromArray(predictions[2].squeeze())
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sitk.WriteImage(img_s, f"{IMAGE_DIR}/predictions_002_old.nii.gz")
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img_s = sitk.GetImageFromArray(segmentations[2].squeeze())
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sitk.WriteImage(img_s, f"{IMAGE_DIR}/segmentations_002_old.nii.gz")
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img_s = sitk.GetImageFromArray(np.transpose(images_list[2,:,:,:,0].squeeze()))
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sitk.WriteImage(img_s, f"{IMAGE_DIR}/t2_002_old.nii.gz")
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