fast-mri/scripts/test3.py

from glob import glob
from os.path import normpath, basename
import SimpleITK as sitk
import numpy as np
import os 
from os import path
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
from sfransen.DWI_exp.losses import weighted_binary_cross_entropy
from umcglib.froc import *
from umcglib.binarize import dynamic_threshold
from tensorflow.keras.models import load_model


def get_paths(main_dir):
    all_niftis = glob(main_dir, recursive=True)

    dwis_b800 = [i for i in all_niftis if ("diff" in i.lower() or "dwi" in i.lower()) and ("b-800" in i.lower() or "b800" in i.lower())] 
    dwis_b400 = [i for i in all_niftis if ("diff" in i.lower() or "dwi" in i.lower()) and ("b-400" in i.lower() or "b400" in i.lower())] 

    return dwis_b800, dwis_b400


def get_paths_seg(main_dir):
    seg = glob(main_dir, recursive=True)
    return seg

def get_paths_train(dir,SERIES,pat_id):
    image_path = {}
    for s in SERIES:
        with open(path.join(dir, f"{s}.txt"), 'r') as f:
            image_paths = [l.strip() for l in f.readlines()]
        image_path[s] = [i for i in image_paths if pat_id in i]

    return image_path

pat_numbers_worst = ['pat0132','pat0091','pat0352','pat0844','pat1006','pat0406','pat0128','pat0153','pat0062','pat0758','pat0932','pat0248','pat0129','pat0429','pat0181','pat0063','pat0674','pat0176','pat0366','pat0082']
pat_numbers_best =  ['pat0651','pat0889','pat0448','pat1022','pat0887','pat0194','pat0603','pat0742','pat0811','pat0489','pat0622','pat0582','pat0105','pat0084','pat0643','pat0529','pat0476','pat0514','pat0506','pat0567']
pat_numbers_worst = ['pat0132', 'pat0091','pat0352','pat0844','pat1006','pat0636','pat1009','pat0584','pat0588','pat0198']
load_path = '../../datasets/radboud_new/{pat_number}/2016/**/*.nii.gz'

for idx, pat_number in enumerate(pat_numbers_worst):
    print(pat_number)
    dwis_b800,dwis_b400 = get_paths(f'../../datasets/radboud_new/{pat_number}/2016/**/*.nii.gz')
    seg_path = get_paths_seg(f'/data/pca-rad/datasets/radboud_lesions_2022/{pat_number}*.nii.gz')

    # load 
    dwi_b800 = sitk.ReadImage(dwis_b800, sitk.sitkFloat32)
    dwi_b400 = sitk.ReadImage(dwis_b400, sitk.sitkFloat32)
    seg = sitk.ReadImage(seg_path, sitk.sitkFloat32)
    seg = sitk.GetArrayFromImage(seg)
    print('count:', np.sum(np.clip(seg,0,1)))
    # write 
    output_path_b800 = f'../temp/lowest_pred_exp/worst/{idx}_{pat_number}_b800.nii.gz'
    output_path_b400 = f'../temp/lowest_pred_exp/worst/{idx}_{pat_number}_b400.nii.gz'
    sitk.WriteImage(dwi_b800, output_path_b800)
    sitk.WriteImage(dwi_b400, output_path_b400)


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