added function

Author: claesnl

utils/dice_score.py

@@ -0,0 +1,68 @@
+#!/usr/bin/env python3
+
+from rhscripts.metrics import dice_similarity
+import argparse
+import nibabel as nib
+
+__scriptname__ = 'dice_similarity'
+__version__ = '0.0.1'
+
+"""
+
+VERSIONING
+  0.0.1 # Added functionality
+
+"""
+
+
+"""Calculate DICE score between two nifti files
+
+Parameters
+----------
+...
+version : boolean, optional
+    Print the version of the script
+"""
+
+""" dice_similarity 
+Author: Claes Ladefoged
+Date: 31-10-2024
+
+### Example use cases from cmd-line ###
+    
+    Get overall dice score, assuming binary input:
+        python dice_similarity.py <nii_file_1> <nii_file_2>
+    
+    Apply a threshold on the images first:
+        python dice_similarity.py <nii_file_1> <nii_file_2> --threshold <threshold>
+        
+    Use a mask to limit the threshold area:
+        python dice_similarity.py <nii_file_1> <nii_file_2> --mask <nii_file_mask>
+        
+---------------------------------------------------------------------------------------
+
+"""
+
+# INPUTS
+parser = argparse.ArgumentParser()
+parser.add_argument("nii_file_1", help='Input nii file', type=str)
+parser.add_argument("nii_file_2", help='Input nii file', type=str)
+parser.add_argument("--threshold", help='Apply a threshold to the images', type=float)
+parser.add_argument("--mask", help='Input mask file to limit the area', type=str)
+args = parser.parse_args()
+
+arr1 = nib.load(args.nii_file_1).get_fdata()
+arr2 = nib.load(args.nii_file_2).get_fdata()
+
+if args.threshold:
+    arr1 = (arr1 > args.threshold).astype(int)
+    arr2 = (arr2 > args.threshold).astype(int)
+    
+if args.mask:
+    mask = nib.load(args.mask).get_fdata()
+    arr1[mask<1] = 0
+    arr2[mask<1] = 0 
+
+dsc = dice_similarity(arr1, arr2)
+print(dsc)
+