opschonen van 2.froc.py
This commit is contained in:
parent
be5b392456
commit
02d5b371d6
|
@ -1,63 +1,56 @@
|
|||
import sys
|
||||
from os import path
|
||||
import SimpleITK as sitk
|
||||
import tensorflow as tf
|
||||
from tensorflow.keras.models import load_model
|
||||
from focal_loss import BinaryFocalLoss
|
||||
import json
|
||||
import matplotlib.pyplot as plt
|
||||
import numpy as np
|
||||
import multiprocessing
|
||||
from functools import partial
|
||||
import os
|
||||
|
||||
sys.path.append('./../code')
|
||||
from utils_quintin import *
|
||||
|
||||
sys.path.append('./../code/DWI_exp')
|
||||
from helpers import *
|
||||
from preprocessing_function import preprocess
|
||||
from callbacks import dice_coef
|
||||
|
||||
sys.path.append('./../code/FROC')
|
||||
from blob_preprocess import *
|
||||
from cal_froc_from_np import *
|
||||
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='Train a U-Net model for segmentation/detection tasks.' +
|
||||
'using cross-validation.')
|
||||
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, must correspond with' +
|
||||
"path files in ./data/")
|
||||
help='List of series to include')
|
||||
args = parser.parse_args()
|
||||
|
||||
######## parsed inputs #############
|
||||
# SERIES = ['b50', 'b400', 'b800'] #can be parsed
|
||||
######## CUDA ################
|
||||
os.environ["CUDA_VISIBLE_DEVICES"] = "2"
|
||||
|
||||
######## constants #############
|
||||
SERIES = args.series
|
||||
series_ = '_'.join(args.series)
|
||||
# Import model
|
||||
# MODEL_PATH = f'./../train_output/train_10h_{series_}/models/train_10h_{series_}.h5'
|
||||
# YAML_DIR = f'./../train_output/train_10h_{series_}'
|
||||
MODEL_PATH = f'./../train_output/train_n0.001_{series_}/models/train_n0.001_{series_}.h5'
|
||||
print(MODEL_PATH)
|
||||
YAML_DIR = f'./../train_output/train_n0.001_{series_}'
|
||||
################ constants ############
|
||||
EXPERIMENT = args.experiment
|
||||
|
||||
MODEL_PATH = f'./../train_output/{EXPERIMENT}_{series_}/models/{EXPERIMENT}_{series_}.h5'
|
||||
YAML_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]
|
||||
|
||||
# import val_indx
|
||||
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 ##############
|
||||
images, image_paths = {s: [] for s in SERIES}, {}
|
||||
segmentations = []
|
||||
########## 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()]
|
||||
|
@ -65,90 +58,33 @@ 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)
|
||||
|
||||
# Read and preprocess each of the paths for each SERIES, and the segmentations.
|
||||
|
||||
from typing import List
|
||||
|
||||
|
||||
def load_images(
|
||||
image_paths: str,
|
||||
seq: str,
|
||||
target_shape: List[int],
|
||||
target_space = List[float]):
|
||||
|
||||
img_s = sitk.ReadImage(image_paths, sitk.sitkFloat32)
|
||||
|
||||
#resample
|
||||
mri_tra_s = resample(img_s,
|
||||
min_shape=target_shape,
|
||||
method=sitk.sitkNearestNeighbor,
|
||||
new_spacing=target_space)
|
||||
|
||||
#center crop
|
||||
mri_tra_s = center_crop(mri_tra_s, shape=target_shape)
|
||||
#normalize
|
||||
if seq != 'seg':
|
||||
filter = sitk.NormalizeImageFilter()
|
||||
mri_tra_s = filter.Execute(mri_tra_s)
|
||||
else:
|
||||
filter = sitk.BinaryThresholdImageFilter()
|
||||
filter.SetLowerThreshold(1.0)
|
||||
mri_tra_s = filter.Execute(mri_tra_s)
|
||||
|
||||
return sitk.GetArrayFromImage(mri_tra_s).T
|
||||
|
||||
N_CPUS = 12
|
||||
# create pool of workers
|
||||
pool = multiprocessing.Pool(processes=N_CPUS)
|
||||
partial_f = partial(load_images,
|
||||
partial_images = partial(load_images_parrallel,
|
||||
seq = 'images',
|
||||
target_shape=IMAGE_SHAPE,
|
||||
target_space = TARGET_SPACING)
|
||||
|
||||
images_2 = []
|
||||
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_f,image_paths_index)
|
||||
data = np.stack(data_list, axis=0)
|
||||
images_2.append(data)
|
||||
# print(s)
|
||||
# print(np.shape(data))
|
||||
print(np.shape(images_2))
|
||||
|
||||
partial_f = partial(load_images,
|
||||
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_f,seg_paths_index)
|
||||
data_list = pool.map(partial_seg,seg_paths_index)
|
||||
segmentations = np.stack(data_list, axis=0)
|
||||
|
||||
# print("segmentations pool",np.shape(segmentations_2))
|
||||
|
||||
# for img_idx in TEST_INDEX: #for less images
|
||||
# img_s = {s: sitk.ReadImage(image_paths[s][img_idx], sitk.sitkFloat32)
|
||||
# for s in SERIES}
|
||||
# seg_s = sitk.ReadImage(seg_paths[img_idx], sitk.sitkFloat32)
|
||||
# img_n, seg_n = preprocess(img_s, seg_s,
|
||||
# shape=IMAGE_SHAPE, spacing=TARGET_SPACING)
|
||||
# for seq in img_n:
|
||||
# images[seq].append(img_n[seq])
|
||||
# segmentations.append(seg_n)
|
||||
|
||||
# print("segmentations old",np.shape(segmentations))
|
||||
|
||||
# # from dict to list
|
||||
# # images_list = [img nmbr, [INPUT_SHAPE]]
|
||||
# images_list = [images[s] for s in images.keys()]
|
||||
# images_list = np.transpose(images_list, (1, 2, 3, 4, 0))
|
||||
images_list = np.transpose(images_2, (1, 2, 3, 4, 0))
|
||||
|
||||
print("images size ",np.shape(images_list))
|
||||
print("size segmentation",np.shape(segmentations))
|
||||
# print("images size pool",np.shape(images_list_2))
|
||||
|
||||
import os
|
||||
os.environ["CUDA_VISIBLE_DEVICES"] = "2"
|
||||
########### load module ##################
|
||||
print(' >>>>>>> LOAD MODEL <<<<<<<<<')
|
||||
|
||||
|
@ -158,21 +94,18 @@ dependencies = {
|
|||
reconstructed_model = load_model(MODEL_PATH, custom_objects=dependencies)
|
||||
# reconstructed_model.summary(line_length=120)
|
||||
|
||||
# make predictions on all val_indx
|
||||
# make predictions on all TEST_INDEX
|
||||
print(' >>>>>>> START prediction <<<<<<<<<')
|
||||
predictions_blur = reconstructed_model.predict(images_list, batch_size=1)
|
||||
|
||||
# print("The shape of the predictions list is: ",np.shape(predictions_blur))
|
||||
# print(type(predictions))
|
||||
# np.save('predictions',predictions)
|
||||
|
||||
############# 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) # Joeran has his numpy arrays ordered differently.
|
||||
arr = np.moveaxis(arr, 3, 1)
|
||||
arr = np.moveaxis(arr, 3, 2)
|
||||
return arr
|
||||
|
||||
|
@ -192,8 +125,8 @@ metrics = evaluate(y_true=segmentations, y_pred=predictions)
|
|||
dump_dict_to_yaml(metrics, YAML_DIR, "froc_metrics", verbose=True)
|
||||
|
||||
|
||||
|
||||
# save one image
|
||||
############## save image as example #################
|
||||
# save image nmr 3
|
||||
IMAGE_DIR = f'./../train_output/train_10h_{series_}'
|
||||
img_s = sitk.GetImageFromArray(predictions_blur[3].squeeze())
|
||||
sitk.WriteImage(img_s, f"{IMAGE_DIR}/predictions_blur_001.nii.gz")
|
||||
|
@ -202,16 +135,4 @@ 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")
|
||||
|
||||
|
||||
|
||||
|
||||
# create plot
|
||||
# json_path = './../scripts/metrics.json'
|
||||
# f = open(json_path)
|
||||
# data = json.load(f)
|
||||
# x = data['fpr']
|
||||
# y = data['tpr']
|
||||
# auroc = data['auroc']
|
||||
# plt.plot(x,y)
|
||||
sitk.WriteImage(img_s, f"{IMAGE_DIR}/segmentations_001.nii.gz")
|
|
@ -11,24 +11,16 @@ import numpy as np
|
|||
|
||||
from sfransen.Saliency.base import *
|
||||
from sfransen.Saliency.integrated_gradients import *
|
||||
# from tensorflow.keras.vis.visualization import visualize_saliency
|
||||
|
||||
sys.path.append('./../code')
|
||||
from utils_quintin import *
|
||||
|
||||
sys.path.append('./../code/DWI_exp')
|
||||
# from preprocessing_function import preprocess
|
||||
from sfransen.utils_quintin import *
|
||||
from sfransen.DWI_exp import preprocess
|
||||
print("done step 1")
|
||||
from sfransen.DWI_exp.helpers import *
|
||||
# from helpers import *
|
||||
from callbacks import dice_coef
|
||||
from sfransen.DWI_exp.callbacks import dice_coef
|
||||
from sfransen.FROC.blob_preprocess import *
|
||||
from sfransen.FROC.cal_froc_from_np import *
|
||||
|
||||
|
||||
|
||||
sys.path.append('./../code/FROC')
|
||||
from blob_preprocess import *
|
||||
from cal_froc_from_np import *
|
||||
|
||||
quit()
|
||||
# train_10h_t2_b50_b400_b800_b1400_adc
|
||||
SERIES = ['t2','b50','b400','b800','b1400','adc']
|
||||
MODEL_PATH = f'./../train_output/train_10h_t2_b50_b400_b800_b1400_adc/models/train_10h_t2_b50_b400_b800_b1400_adc.h5'
|
||||
|
@ -46,7 +38,7 @@ IMAGE_SHAPE = INPUT_SHAPE[:3]
|
|||
experiment_path = f'./../train_output/train_10h_t2_b50_b400_b800_b1400_adc/froc_metrics.yml'
|
||||
experiment_metrics = read_yaml_to_dict(experiment_path)
|
||||
DATA_SPLIT_INDEX = read_yaml_to_dict('./../data/Nijmegen paths/train_val_test_idxs.yml')
|
||||
TEST_INDEX = DATA_SPLIT_INDEX['val_set0']
|
||||
TEST_INDEX = DATA_SPLIT_INDEX['test_set0']
|
||||
|
||||
top_10_idx = np.argsort(experiment_metrics['roc_pred'])[-10:]
|
||||
TEST_INDEX = [TEST_INDEX[i] for i in top_10_idx]
|
||||
|
@ -90,7 +82,6 @@ print('START prediction')
|
|||
ig = IntegratedGradients(reconstructed_model)
|
||||
saliency_map = []
|
||||
for img_idx in range(len(images_list)):
|
||||
# input_img = np.resize(images_list[img_idx],(1,48,48,8,8))
|
||||
input_img = np.resize(images_list[img_idx],(1,192,192,24,len(SERIES)))
|
||||
saliency_map.append(ig.get_mask(input_img).numpy())
|
||||
print("size saliency map is:",np.shape(saliency_map))
|
||||
|
|
Loading…
Reference in New Issue