fast-mri/scripts/4.frocs.py

import SimpleITK as sitk
import tensorflow as tf
from tensorflow.keras.models import load_model
from focal_loss import BinaryFocalLoss
import numpy as np
import multiprocessing
from functools import partial
import os 

from sfransen.utils_quintin import * 
from sfransen.DWI_exp.helpers import *
from sfransen.DWI_exp.preprocessing_function import preprocess  
from sfransen.DWI_exp.callbacks import dice_coef
from sfransen.FROC.blob_preprocess import *
from sfransen.FROC.cal_froc_from_np import *
from sfransen.load_images import load_images_parrallel


parser = argparse.ArgumentParser(
    description='Calculate the froc metrics and store in froc_metrics.yml')
parser.add_argument('-experiment',
    help='Title of experiment')                
parser.add_argument('--series', '-s', 
    metavar='[series_name]', required=True, nargs='+',
    help='List of series to include')
args = parser.parse_args()

######## CUDA ################
os.environ["CUDA_VISIBLE_DEVICES"] = "2"

######## constants #############
SERIES = args.series
series_ = '_'.join(args.series)
EXPERIMENT = args.experiment

MODEL_PATH = f'./../train_output/{EXPERIMENT}_{series_}/models/{EXPERIMENT}_{series_}.h5'
YAML_DIR = f'./../train_output/{EXPERIMENT}_{series_}'
IMAGE_DIR = f'./../train_output/{EXPERIMENT}_{series_}'

DATA_DIR = "./../data/Nijmegen paths/"
TARGET_SPACING = (0.5, 0.5, 3) 
INPUT_SHAPE = (192, 192, 24, len(SERIES))
IMAGE_SHAPE = INPUT_SHAPE[:3]

DATA_SPLIT_INDEX = read_yaml_to_dict('./../data/Nijmegen paths/train_val_test_idxs.yml')
TEST_INDEX = DATA_SPLIT_INDEX['val_set0']

N_CPUS = 12


########## load images in parrallel ##############
print_(f"> Loading images into RAM...")

# read paths from txt
image_paths = {}
for s in SERIES:
    with open(path.join(DATA_DIR, f"{s}.txt"), 'r') as f:
        image_paths[s] = [l.strip() for l in f.readlines()]
with open(path.join(DATA_DIR, f"seg.txt"), 'r') as f:
    seg_paths = [l.strip() for l in f.readlines()]
num_images = len(seg_paths)

# create pool of workers
pool = multiprocessing.Pool(processes=N_CPUS)
partial_images = partial(load_images_parrallel,
                    seq = 'images',
                    target_shape=IMAGE_SHAPE,
                    target_space = TARGET_SPACING)
partial_seg = partial(load_images_parrallel,
                    seq = 'seg',
                    target_shape=IMAGE_SHAPE,
                    target_space = TARGET_SPACING)

#load images
images = []
for s in SERIES:
    image_paths_seq = image_paths[s]
    image_paths_index = np.asarray(image_paths_seq)[TEST_INDEX]
    data_list = pool.map(partial_images,image_paths_index)
    data = np.stack(data_list, axis=0)
    images.append(data)

images_list = np.transpose(images, (1, 2, 3, 4, 0))

#load segmentations
seg_paths_index = np.asarray(seg_paths)[TEST_INDEX]
data_list = pool.map(partial_seg,seg_paths_index)
segmentations = np.stack(data_list, axis=0)

########### load module ##################
print(' >>>>>>> LOAD MODEL <<<<<<<<<')

dependencies = {
    'dice_coef': dice_coef
}
reconstructed_model = load_model(MODEL_PATH, custom_objects=dependencies)
# reconstructed_model.summary(line_length=120)

# make predictions on all TEST_INDEX
print(' >>>>>>> START prediction <<<<<<<<<')
predictions_blur = reconstructed_model.predict(images_list, batch_size=1)

############# preprocess ################# 
# preprocess predictions by removing the blur and making individual blobs 
print('>>>>>>>> START preprocess')

def move_dims(arr):
    # UMCG numpy dimensions convention: dims = (batch, width, heigth, depth)
    # Joeran numpy dimensions convention: dims = (batch, depth, heigth, width)
    arr = np.moveaxis(arr, 3, 1) 
    arr = np.moveaxis(arr, 3, 2)
    return arr

# Joeran has his numpy arrays ordered differently.
predictions_blur = move_dims(np.squeeze(predictions_blur))
segmentations = move_dims(np.squeeze(segmentations))
predictions = [preprocess_softmax(pred, threshold="dynamic")[0] for pred in predictions_blur]

# Remove outer edges 
zeros = np.zeros(np.shape(predictions))
test = np.squeeze(predictions)[:,2:-2,2:190,2:190]
zeros[:,2:-2,2:190,2:190] = test
predictions = zeros

# perform Froc
metrics = evaluate(y_true=segmentations, y_pred=predictions)
dump_dict_to_yaml(metrics, YAML_DIR, "froc_metrics", verbose=True)


############## save image as example #################
# save image nmr 3
img_s = sitk.GetImageFromArray(predictions_blur[3].squeeze())
sitk.WriteImage(img_s, f"{IMAGE_DIR}/predictions_blur_001.nii.gz")

img_s = sitk.GetImageFromArray(predictions[3].squeeze())
sitk.WriteImage(img_s, f"{IMAGE_DIR}/predictions_001.nii.gz")

img_s = sitk.GetImageFromArray(segmentations[3].squeeze())
sitk.WriteImage(img_s, f"{IMAGE_DIR}/segmentations_001.nii.gz")