Merge branch 'master' of https://fsstud.is.uni-due.de:8090/sjromuel/Masterarbeit

RobinNet/13unet_mrt_threshgt.py

@@ -124,7 +124,7 @@ def main():
     continue_training = False
     e               = 0
     gt_type         = "_mr_ctunetpred"
-    modelname       = "mr_unet_cv_ctthresh"
+    modelname       = "mr_unet_cv_unetpred"
 
     ###############################
 

RobinNet/nets/BaseNetwork.py

@@ -442,7 +442,7 @@ class BaseNetwork:
             self.log.write('Loading Training Data ...'+"\r")
 
         ### initializing weights ###
-        weights = init_weights(manual_seed=np.sum(self.test_patients)*7)
+        weights = init_weights(manual_seed=np.sum(self.test_patients))
 
         filter_multiplier = int(self.newSize[0] / 128)
 

RobinNet/saveImgs_run_trained_model.py

@@ -21,7 +21,7 @@ def main():
 
     root = tk.Tk()
     root.withdraw()
-    file_path = filedialog.askopenfilename(initialdir="finalResults/complete_segmr/mr_unet_cv_ctthresh")
+    file_path = filedialog.askopenfilename(initialdir="saves/mr_unet_cv_unetpred")
     file_path = file_path[:-9]
     print(file_path)
 
@@ -61,7 +61,7 @@ def main():
         print('GT Type:', gt_type)
 
         ### Load test patient
-        if gt_type == "thresh" or gt_type == "ctthresh_gt":
+        if gt_type == "thresh" or gt_type == "ctthresh_gt" or gt_type == "_mr_ctunetpred":
             img_path = "data/npy_thresh/"
         else:
             img_path = "data/npy/"
@@ -88,6 +88,7 @@ def main():
                     if gt_type == "ctthresh_gt":
                         ytrue_img_list.append(elem)
                         ytrue_img_list.append(elem)
+            
 
         else:
             for elem in full_list:
@@ -105,6 +106,8 @@ def main():
                     if gt_type == "thresh":
                         ytrue_img_list.append(elem)
                         ytrue_img_list.append(elem)
+        #if gt_type =="_mr_ctunetpred":
+         #       X_img_list.remove("P17_mr_T1.gipl.npy")
         list.sort(X_img_list)
         list.sort(GT_img_list)
         list.sort(ytrue_img_list)
@@ -442,4 +445,4 @@ def show_loss_plot(slice, loss_list):
 
 
 if __name__ == "__main__":
-    main()
\ No newline at end of file
+    main()

RobinNet/threshunetpred_gts.py

@@ -180,8 +180,10 @@ def main():
             if npys3d:
                 filename = "P" + str(TP_num).zfill(2)
                 y_pred3d = cut_mr_ctunetpred(filename, y_pred3d)
+                ythresh3d = np.flip(cut_mr_ctunetpred(filename, GT_test))
                 #np.save(img_savepath + "P" + str(TP_num).zfill(2) + "_pred3D", y_pred3d)
-                np.save("data/npy_thresh/" + "P" + str(TP_num).zfill(2) + "_mr_ctunetpred.gipl", y_pred3d)
+                print(np.shape(ythresh3d[:,:,:,0]))
+                np.save("data/npy_thresh/" + "P" + str(TP_num).zfill(2) + "_mr_ctunetpred.gipl", ythresh3d[:,:,:,0])
                 print("ypred shape: ", np.shape(y_pred3d))
             #plt.show()
             #print(test_loss)
@@ -351,4 +353,4 @@ def show_loss_plot(slice, loss_list):
 
 
 if __name__ == "__main__":
-    main()
\ No newline at end of file
+    main()

RobinNet/tryOut.py

@@ -10,12 +10,32 @@ from scipy import ndimage
 from datetime import datetime
 
 
-img = np.load("data/npy_thresh/P01_250_thresh.gipl.npy")
-print(np.shape(img))
+inputimg = np.load("data/npy_thresh/P01_mr_T1.gipl.npy")
+gt = np.load("data/npy_thresh/P01_mr_ctunetpred.gipl.npy")
+ytrue = np.load("data/npy_thresh/P01_segmr.gipl.npy")
+
+print(np.shape(inputimg))
+print(np.shape(gt))
+print(np.shape(ytrue))
+
+for i in range(25):
+    fig = plt.figure()
+    fig.add_subplot(2, 3, 1)
+    plt.imshow(inputimg[i, :, :], cmap=plt.cm.bone)
+    plt.title('Input')
+    fig.add_subplot(2, 3, 2)
+    plt.imshow(gt[i,:,:], cmap=plt.cm.bone)
+    plt.title('gt')
+    fig.add_subplot(2, 3, 3)
+    plt.imshow(ytrue[i,:,:], cmap=plt.cm.bone)
+    plt.title('True')
+    plt.show()
+    
+'''print(np.shape(img))
 img = np.flip(img)
 #for i in range(np.shape(img)[0]):
 plt.imshow(np.flipud(img[1,:, :]), cmap=plt.cm.bone)
-plt.show()
+plt.show()'''
 
 '''mr_img = np.load("data/npy/P03_mr_T1.gipl.npy")
 ct_img = np.load("data/npy/P03_mr_ctseg_gt.gipl.npy")
@@ -82,4 +102,4 @@ val_pat_images = np.load(file_path)
 for slice in val_pat_images:
     plt.imshow(slice[:,:,0], cmap=plt.cm.bone)
 plt.show()
-'''
\ No newline at end of file
+'''