Needed to make copy of project file

extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py

@@ -203,7 +203,7 @@ def compare_object_maps(truth: GenericImageDataAccessor, inferred: GenericImageD
 if __name__ == '__main__':
     root =  Path('c:/Users/rhodes/projects/proj0011-plankton-seg/')
     template_ilp = root / 'exp0014/template_obj.ilp'
-    where_patch_stack = root / 'exp0009/output/labeled_patches-20231018-0000'
+    where_patch_stack = root / 'exp0009/output/labeled_patches-20231018-0001'
 
     # auto-populate an object classifier
     new_ilp = generate_ilastik_object_classifier(
@@ -212,11 +212,11 @@ if __name__ == '__main__':
         stack_name='train'
     )
 
-    def infer_and_compare(suffix):
+    def infer_and_compare(ilp, suffix):
         # infer object labels from the same data used to train the classifier
         train_zstack_raw = generate_file_accessor(where_patch_stack / 'zstack_train_raw.tif')
         train_zstack_mask = generate_file_accessor(where_patch_stack / 'zstack_train_mask.tif')
-        mod = PatchStackObjectClassifier({'project_file': where_patch_stack / new_ilp})
+        mod = PatchStackObjectClassifier({'project_file': where_patch_stack / ilp})
         result_acc, _ = mod.infer(train_zstack_raw, train_zstack_mask)
         write_accessor_data_to_file(where_patch_stack / f'zstack_train_result_{suffix}.tif', result_acc)
 
@@ -229,17 +229,22 @@ if __name__ == '__main__':
             ),
             index=False
         )
+        print(f'Generated ilastik project {ilp}')
         print('Truth and inferred labels match?')
         print(pd.value_counts(df_comp['truth_label'] == df_comp['inferred_label']))
 
     # infer object labels from the same data used to train the classifier
-    infer_and_compare('before')
+    infer_and_compare(new_ilp, 'before')
 
-    # prompt user input when ilastik file has been modified in-app
-    print(f'Press enter when project file {new_ilp} has been updated in ilastik')
+    # copy project and prompt user input once ilastik file has been modified in-app
+    mod_ilp = shutil.copy(
+        new_ilp,
+        where_patch_stack / autonumber_new_file(where_patch_stack, 'auto-obj', 'ilp')
+    )
+    print(f'Press enter when project file {mod_ilp} has been updated in ilastik')
     input()
 
-    # repeat inference with the same project file, but a fresh model handle
-    infer_and_compare('after')
+    # repeat inference with the modified project file
+    infer_and_compare(mod_ilp, 'after')