Merge pull request #226 from arayabrain/feature/fix-nwbfile

fix nwbfile data inheritance
arayabrain · Dec 7, 2023 · 86a47c6 · 86a47c6
2 parents 40ae189 + 12ae917
commit 86a47c6
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Showing 2 changed files with 22 additions and 5 deletions.
diff --git a/studio/app/common/core/rules/runner.py b/studio/app/common/core/rules/runner.py
@@ -72,10 +72,11 @@ def run(cls, __rule: Rule, last_output):
             gc.collect()
 
         except Exception as e:
-            PickleWriter.write(
-                __rule.output,
-                list(traceback.TracebackException.from_exception(e).format())[-2:],
-            )
+            err_msg = list(traceback.TracebackException.from_exception(e).format())
+            # show full trace to console
+            print(*err_msg, sep="\n")
+            # save msg for GUI
+            PickleWriter.write(__rule.output, err_msg)
 
     @classmethod
     def set_func_start_timestamp(cls, output_dirpath):
@@ -142,9 +143,25 @@ def read_input_info(cls, input_files):
         input_info = {}
         for filepath in input_files:
             load_data = PickleReader.read(filepath)
+            merged_nwb = cls.deep_merge(
+                load_data.pop("nwbfile", {}), input_info.pop("nwbfile", {})
+            )
             input_info = dict(list(load_data.items()) + list(input_info.items()))
+            input_info["nwbfile"] = merged_nwb
         return input_info
 
+    @classmethod
+    def deep_merge(cls, dict1, dict2):
+        if not isinstance(dict1, dict) or not isinstance(dict2, dict):
+            return dict2
+        merged = dict1.copy()
+        for k, v in dict2.items():
+            if k in merged and isinstance(merged[k], dict):
+                merged[k] = cls.deep_merge(merged[k], v)
+            else:
+                merged[k] = v
+        return merged
+
     @classmethod
     def dict2leaf(cls, root_dict: dict, path_list):
         path = path_list.pop(0)

diff --git a/studio/app/optinist/core/nwb/nwb_creater.py b/studio/app/optinist/core/nwb/nwb_creater.py
@@ -182,8 +182,8 @@ def motion_correction(cls, nwbfile, function_id, mc_data, xy_trans_data):
 
     @classmethod
     def roi(cls, nwbfile, function_id, roi_list):
-        image_seg = nwbfile.processing["ophys"].data_interfaces["ImageSegmentation"]
         nwbfile = cls.add_plane_segmentation(nwbfile, function_id)
+        image_seg = nwbfile.processing["ophys"].data_interfaces["ImageSegmentation"]
         plane_seg = image_seg.plane_segmentations[function_id]
 
         if roi_list: