rerunModels.py 11.9 KB
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import numpy as np
import tensorflow as tf
import matplotlib.pyplot as plt
import tkinter as tk
import os
import matplotlib
from tkinter import filedialog
from skimage import transform
import SimpleITK as sitk
import argparse
#import os
#import pydot
#from graphviz import Digraph
#import shutil
#from tensorflow.keras import layers, models
#from utils.dataLoader import *
from utils.other_functions import *
from nets.Unet import *

def main():
    models = ["12", "34", "56", "78", "910", "1112", "1314", "1516"]
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    folder_path = "finalResults/complete_segmr/mr_unet_cv_unetpred/"
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    #modeltype = "Cluster_"
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    #modeltype = "Class_"
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    #modeltype = "Cluster_class_"
    modeltype = "Unet_"
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    all3dhdds = []
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    ##################### U-Net #####################
    for fold in models:

        file_path = folder_path+"TPs"+fold+modeltype

        ### read out files ###
        weights = np.load(file_path+"model.npy", allow_pickle=True)
        [test_patients,
         val_patients,
         number_patients,
         img_path,
         shrink_data,
         newSize,
         lr,
         batch_size,
         num_epochs,
         e,
         augment,
         save_path,
         gt_type,
         filter_multiplier] = np.load(file_path+"params.npy", allow_pickle=True)
        #  autoencoder_model__e100_switchclass1024_nohiddenclusternet needs to comment out gt_type and val_patients
        print('Training Parameters:')
        print('-----------------')
        print('Number of Patients: ', number_patients)
        print('Number of epochs: ', num_epochs)
        print('Test Patient number: ', test_patients)
        print('Image Size: ', newSize)
        print('Filter Multiplier: ', filter_multiplier)
        print('Data Augmentation: ', augment)
        print('Learning rate: ', lr)
        print('Image Path: ', img_path)
        print('Save Path: ', save_path)
        print('GT Type:', gt_type)

        ### Load test patient
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        if gt_type == "thresh" or gt_type == "ctthresh_gt" or gt_type == "_mr_ctunetpred":
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            img_path = "data/npy_thresh/"
        else:
            img_path = "data/npy/"
        full_list = os.listdir(img_path)
        seg_list = os.listdir("data/npy/")

        X_img_list = []
        GT_img_list = []
        ytrue_img_list = []
        # thresh_img_list = []
        if "mr" in save_path:
            for elem in full_list:
                if elem.endswith("T1.gipl.npy") and (elem.startswith('P' + str(test_patients[0]).zfill(2)) or elem.startswith('P' + str(test_patients[1]).zfill(2))):
                    X_img_list.append(elem)
                    if gt_type == "ctthresh_gt":
                        X_img_list.append(elem)
                        X_img_list.append(elem)

                elif elem.endswith(gt_type + ".gipl.npy") and (elem.startswith('P' + str(test_patients[0]).zfill(2)) or elem.startswith('P' + str(test_patients[1]).zfill(2))):
                    GT_img_list.append(elem)
            for elem in seg_list:
                if elem.endswith("segmr.gipl.npy") and (elem.startswith('P' + str(test_patients[0]).zfill(2)) or elem.startswith('P' + str(test_patients[1]).zfill(2))):
                    ytrue_img_list.append(elem)
                    if gt_type == "ctthresh_gt":
                        ytrue_img_list.append(elem)
                        ytrue_img_list.append(elem)

        else:
            for elem in full_list:
                if elem.endswith("ct.gipl.npy") and (elem.startswith('P' + str(test_patients[0]).zfill(2)) or elem.startswith('P' + str(test_patients[1]).zfill(2))):
                    X_img_list.append(elem)
                    if gt_type == "thresh":
                        X_img_list.append(elem)
                        X_img_list.append(elem)

                elif elem.endswith(gt_type+".gipl.npy") and (elem.startswith('P' + str(test_patients[0]).zfill(2)) or elem.startswith('P' + str(test_patients[1]).zfill(2))):
                    GT_img_list.append(elem)
            for elem in seg_list:
                if elem.endswith("seg.gipl.npy") and (elem.startswith('P' + str(test_patients[0]).zfill(2)) or elem.startswith('P' + str(test_patients[1]).zfill(2))):
                    ytrue_img_list.append(elem)
                    if gt_type == "thresh":
                        ytrue_img_list.append(elem)
                        ytrue_img_list.append(elem)
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        #if gt_type =="_mr_ctunetpred":
            #X_img_list.remove("P17_mr_T1.gipl.npy")
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        list.sort(X_img_list)
        list.sort(GT_img_list)
        list.sort(ytrue_img_list)
        print("Input Image List", X_img_list)
        print("GT Image List", GT_img_list)
        print("True Segmentation Image List", ytrue_img_list)


        for j in range(2):
            if gt_type == "thresh" or gt_type == "ctthresh_gt":
                X_img_npys = np.load(img_path + X_img_list[j*3])
                GT_img_npys = np.load(img_path + GT_img_list[j*3])
                ytrue_img_npys = np.load(img_path + ytrue_img_list[j*3])
                print(GT_img_list[j*3])
                print(GT_img_list[j * 3+1])
                print(GT_img_list[j * 3+2])

                X_img_npys = np.append(X_img_npys, np.load(img_path + X_img_list[j * 3+1]), axis=0)
                GT_img_npys = np.append(GT_img_npys, np.load(img_path + GT_img_list[j * 3+1]), axis=0)
                ytrue_img_npys = np.append(ytrue_img_npys, np.load(img_path + ytrue_img_list[j * 3+1]), axis=0)

                X_img_npys = np.append(X_img_npys, np.load(img_path + X_img_list[j * 3+2]), axis=0)
                GT_img_npys = np.append(GT_img_npys, np.load(img_path + GT_img_list[j * 3+2]), axis=0)
                ytrue_img_npys = np.append(ytrue_img_npys, np.load(img_path + ytrue_img_list[j * 3+2]), axis=0)

                print("Input shape: ", np.shape(X_img_npys))
                print("GT shape: ", np.shape(GT_img_npys))
                print("True Segm shape: ", np.shape(ytrue_img_npys))

            else:
                X_img_npys = np.load(img_path + X_img_list[j])
                GT_img_npys = np.load(img_path + GT_img_list[j])
                ytrue_img_npys = np.load(img_path + ytrue_img_list[j])

                print("Input shape: ", np.shape(X_img_npys))
                print("GT shape: ", np.shape(GT_img_npys))
                print("True Segm shape: ", np.shape(ytrue_img_npys))



            X_img_npys = transform.resize(X_img_npys, (X_img_npys.shape[0], newSize[0], newSize[1]), order=0,
                                          preserve_range=True, mode='constant', anti_aliasing=False,
                                          anti_aliasing_sigma=None)
            GT_img_npys = transform.resize(GT_img_npys, (GT_img_npys.shape[0], newSize[0], newSize[1]), order=0,
                                           preserve_range=True, mode='constant', anti_aliasing=False,
                                           anti_aliasing_sigma=None)
            ytrue_img_npys = transform.resize(ytrue_img_npys, (ytrue_img_npys.shape[0], newSize[0], newSize[1]),
                                              order=0,
                                              preserve_range=True, mode='constant', anti_aliasing=False,
                                              anti_aliasing_sigma=None)
            X_test = np.reshape(X_img_npys, (X_img_npys.shape[0], X_img_npys.shape[1], X_img_npys.shape[2], 1))
            GT_test = np.reshape(GT_img_npys, (GT_img_npys.shape[0], GT_img_npys.shape[1], GT_img_npys.shape[2], 1))
            ytrue = np.reshape(ytrue_img_npys,
                               (ytrue_img_npys.shape[0], ytrue_img_npys.shape[1], ytrue_img_npys.shape[2], 1))


            test_dataset = tf.data.Dataset.from_tensor_slices((X_test, ytrue))
            test_dataset = test_dataset.batch(batch_size=1)
            print(test_patients)
            TP_num = test_patients[j]

            ###################################################################################

            detailed_images = False
            npys3d          = True

            ###################################################################################



            test_loss = []
            test_loss_hdd = []
            test_loss_hdd2 = []
            y_pred3d = []
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            y_true3d = []
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            for features in test_dataset:
                image, y_true = features
                y_true = onehotencode(y_true)
                y_pred = Unet(image, weights, filter_multiplier, training=False)
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                '''if y_pred3d == []:
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                        y_pred3d = y_pred[:,:,:,0].numpy()
                else:
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                    y_pred3d =  np.append(y_pred[:,:,:,0].numpy(), y_pred3d, axis=0)'''
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                loss = dice_loss(y_pred, y_true)
                loss = tf.make_ndarray(tf.make_tensor_proto(loss))
                test_loss.append(loss)
                #print(test_loss)
                try:
                    y_true_np = np.squeeze(y_true[0, :, :, 0].numpy() > 0.5)
                    y_true_np = y_true_np.astype(np.float_)
                    pred_np = np.squeeze(y_pred[0, :, :, 0].numpy() > 0.5)
                    pred_np = pred_np.astype(np.float_)
                    hausdorff_distance_filter = sitk.HausdorffDistanceImageFilter()
                    hausdorff_distance_filter.Execute(sitk.GetImageFromArray(y_true_np), sitk.GetImageFromArray(pred_np))
                    test_loss_hdd.append(hausdorff_distance_filter.GetHausdorffDistance())

                    hausdorff_distance_filter2 = sitk.HausdorffDistanceImageFilter()
                    hausdorff_distance_filter2.Execute(sitk.GetImageFromArray(pred_np), sitk.GetImageFromArray(y_true_np))
                    test_loss_hdd2.append(hausdorff_distance_filter2.GetHausdorffDistance())
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                    '''if y_pred3d ==[]:
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                        y_pred3d = pred_np
                        y_true3d = y_true_np
                    else:
                        y_pred3d = np.append(pred_np, y_pred3d, axis=0)
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                        y_true3d = np.append(y_true_np, y_true3d, axis=0)'''
                    if y_pred3d == []:
                        y_pred3d = np.reshape(pred_np, newshape=(1, 512, 512))
                        y_true3d = np.reshape(y_true_np, newshape=(1, 512, 512))
                    else:
                        y_pred3d = np.append(np.reshape(pred_np, newshape=(1, 512, 512)), y_pred3d, axis=0)
                        y_true3d = np.append(np.reshape(y_true_np, newshape=(1, 512, 512)), y_true3d, axis=0)
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                except:
                    pass

            #plt.show()
            #print(test_loss)
            print("TestLoss Mean for P", test_patients[j], ": ", np.mean(test_loss))

            #print(test_loss_hdd)
            print("Hausdorff-Distance for P", test_patients[j],":", np.mean(test_loss_hdd))
            print("Hausdorff-Distance2 for P", test_patients[j], ":", np.mean(test_loss_hdd2))
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            #### Hausdorff 3D: 
            
            '''ytrue = tf.convert_to_tensor(ytrue)
            y_pred3d = tf.convert_to_tensor(y_pred3d)

            print(tf.shape(ytrue))
            y_true3d = np.squeeze(ytrue[:,:,:,0].numpy() > 0.5)
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            y_true3d = np.float_(y_true)
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            print(np.shape(y_true3d))
            print(type(y_true3d))
            print(type(y_pred3d))
            pred3d = np.squeeze(y_pred3d[:,:,:].numpy() > 0.5)
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            pred3d = np.float(pred3d)
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            print(np.shape(pred3d))
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            print(type(pred3d))'''
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            try:
                hausdorff_distance_filter = sitk.HausdorffDistanceImageFilter()
                hausdorff_distance_filter.Execute(sitk.GetImageFromArray(y_true3d), sitk.GetImageFromArray(y_pred3d))
                hdd3d = hausdorff_distance_filter.GetHausdorffDistance()
                print("3D HDD for patient", test_patients[j], ":", hdd3d)
                all3dhdds.append(hdd3d)
            except:
                pass
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    print("All 3d-HDDs: ", all3dhdds)
    print(folder_path)
    print(modeltype)
           
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      #####

if __name__ == "__main__":
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    main()