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

RobinNet/allModelsCreatePredNpys.py

@@ -238,13 +238,13 @@ def main():
                         os.makedirs(npy_savepath)
                     np.save(npy_savepath + "_pred3D", y_pred3d)
 
-                    output_volume = np.squeeze(y_pred3d)
+                    output_volume = np.squeeze(X_test)
                     output_nifty = nib.Nifti1Image(output_volume, np.eye(4))
 
                     fname = npy_savepath+'_Scan.nii.gz'
                     nib.save(output_nifty, fname)
 
-                    output_label = np.argmax(output_volume, axis=-1)
+                    output_label = np.argmax(y_pred3d, axis=-1)
                     output_label = output_label.astype(np.uint8)
                     output_label_nifty = nib.Nifti1Image(output_label, np.eye(4))
 

RobinNet/dice_gt_seg.py

@@ -18,7 +18,7 @@ from nets.Unet import dice_loss
 
 
 def main():
-    mr = True
+    mr = False
     if mr:
         file_path = "data/npy_thresh/"
         gt_types = ['ctseg', 'ctthresh', 'unetpred']
@@ -190,6 +190,10 @@ def main():
                     all3dhdds.append(hdd3d)
                 except:
                     pass
+                    
+                dice_Score16.append(np.mean(patient_dsc))
+                print("Dice Score for patient", patientnumber, np.mean(patient_dsc))
+                
             print("All 3d-HDDs for", gt_type, ": ", all3dhdds)
             #print("Dice-Score mean: ", np.mean(dice_Score16))
             #print("Dice-Score std: ", np.std(dice_Score16))
@@ -425,4 +429,4 @@ def show_loss_plot(slice, loss_list):
 
 
 if __name__ == "__main__":
-    main()
\ No newline at end of file
+    main()

necro_to_nifty.py

+import numpy as np
+import os
+import nibabel as nib
+from os import listdir
+from os.path import isfile, join
+import SimpleITK as sitk
+
+src_path = "../hueftdaten/"
+
+folders = ["T1/", "T2/"]
+for folder in folders:
+    for i in range(1, 40):
+        patient_folder = 'P'+str(i).zfill(2)
+        if os.path.exists(os.path.join(src_path+folder, patient_folder)):
+            reader = sitk.ImageFileReader()
+            for f in listdir(os.path.join(src_path, patient_folder)):
+                cur_file_path = join(src_path, patient_folder, f)
+                print(f)
+                if isfile(cur_file_path):
+                    if '.gipl' in f:
+                        # cur_file_path_dst = join(dst_path, f)
+                        reader.SetFileName(cur_file_path)
+                        pimgs = reader.Execute()
+                        pimgs_array = sitk.GetArrayFromImage(pimgs)
+
+                        if "seg" in cur_file_path:
+                            output_label = np.argmax(pimgs_array, axis=-1)
+                            output_label = output_label.astype(np.uint8)
+                            output_label_nifty = nib.Nifti1Image(output_label, np.eye(4))
+
+                            fname = cur_file_path+'.nii.gz'
+                            nib.save(output_label_nifty, fname)
+                        elif "necro" in cur_file_path or "kopf" in cur_file_path:
+                            output_volume = np.squeeze(pimgs_array)
+                            output_nifty = nib.Nifti1Image(output_volume, np.eye(4))
+
+                            fname = cur_file_path+'.nii.gz'
+                            nib.save(output_nifty, fname)
+
+