Rename actual_x to confirmed_x

catalystneuro · Jun 29, 2024 · 055e9f5 · 055e9f5
1 parent a9bc351
commit 055e9f5
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Showing 4 changed files with 19 additions and 19 deletions.
diff --git a/spec/ndx-extracellular-channels.extensions.yaml b/spec/ndx-extracellular-channels.extensions.yaml
@@ -206,7 +206,7 @@ groups:
     dtype: text
     doc: The brain area of the estimated contact position, e.g., 'CA1'.
     quantity: '?'
-  - name: actual_position_in_mm
+  - name: confirmed_position_in_mm
     neurodata_type_inc: VectorData
     dtype:
     - name: ap
@@ -229,7 +229,7 @@ groups:
       doc: Reference point for the position coordinates. e.g., "bregma at the cortical
         surface".
       required: false
-  - name: actual_brain_area
+  - name: confirmed_brain_area
     neurodata_type_inc: VectorData
     dtype: text
     doc: The brain area of the actual contact position, e.g., 'CA1'.

diff --git a/src/pynwb/tests/test_classes.py b/src/pynwb/tests/test_classes.py
@@ -426,8 +426,8 @@ def test_constructor_add_row(self):
             filter="High-pass at 300 Hz",
             estimated_position_in_mm=[-1.5, 2.5, -2.5],
             estimated_brain_area="CA3",
-            actual_position_in_mm=[-1.5, 2.4, -2.4],
-            actual_brain_area="CA3",
+            confirmed_position_in_mm=[-1.5, 2.4, -2.4],
+            confirmed_brain_area="CA3",
         )
 
         ct.add_row(
@@ -436,14 +436,14 @@ def test_constructor_add_row(self):
             filter="High-pass at 300 Hz",
             estimated_position_in_mm=[-1.5, 2.5, -2.4],
             estimated_brain_area="CA3",
-            actual_position_in_mm=[-1.5, 2.4, -2.3],
-            actual_brain_area="CA3",
+            confirmed_position_in_mm=[-1.5, 2.4, -2.3],
+            confirmed_brain_area="CA3",
         )
 
         # TODO might be nice to put this on the constructor of ContactsTable as position__reference
         # without using a custom mapper
         ct["estimated_position_in_mm"].reference = "Bregma at the cortical surface"
-        ct["actual_position_in_mm"].reference = "Bregma at the cortical surface"
+        ct["confirmed_position_in_mm"].reference = "Bregma at the cortical surface"
 
         # TODO
         assert ct.name == "Neuropixels1ChannelsTable"
@@ -484,8 +484,8 @@ def addContainer(self):
             filter="High-pass at 300 Hz",
             estimated_position_in_mm=[-1.5, 2.5, -2.5],
             estimated_brain_area="CA3",
-            actual_position_in_mm=[-1.5, 2.4, -2.4],
-            actual_brain_area="CA3",
+            confirmed_position_in_mm=[-1.5, 2.4, -2.4],
+            confirmed_brain_area="CA3",
         )
 
         ct.add_row(
@@ -494,15 +494,15 @@ def addContainer(self):
             filter="High-pass at 300 Hz",
             estimated_position_in_mm=[-1.5, 2.5, -2.4],
             estimated_brain_area="CA3",
-            actual_position_in_mm=[-1.5, 2.4, -2.3],
-            actual_brain_area="CA3",
+            confirmed_position_in_mm=[-1.5, 2.4, -2.3],
+            confirmed_brain_area="CA3",
         )
 
         # TODO might be nice to put this on the constructor of ContactsTable as position__reference
         # without using a custom mapper
         # TODO does matching this happen in the container equals roundtrip test?
         ct["estimated_position_in_mm"].reference = "Bregma at the cortical surface"
-        ct["actual_position_in_mm"].reference = "Bregma at the cortical surface"
+        ct["confirmed_position_in_mm"].reference = "Bregma at the cortical surface"
 
         # put this in nwbfile.acquisition for testing
         self.nwbfile.add_acquisition(ct)

diff --git a/src/pynwb/tests/test_example_usage_all.py b/src/pynwb/tests/test_example_usage_all.py
@@ -98,20 +98,20 @@
     filter="High-pass at 300 Hz",
     estimated_position_in_mm=[-1.5, 2.5, -2.5],
     estimated_brain_area="CA3",
-    actual_position_in_mm=[-1.5, 2.4, -2.4],
-    actual_brain_area="CA3",
+    confirmed_position_in_mm=[-1.5, 2.4, -2.4],
+    confirmed_brain_area="CA3",
 )
 channels_table.add_row(
     contact=1,
     reference_contact=2,
     filter="High-pass at 300 Hz",
     estimated_position_in_mm=[-1.5, 2.5, -2.4],
     estimated_brain_area="CA3",
-    actual_position_in_mm=[-1.5, 2.4, -2.3],
-    actual_brain_area="CA3",
+    confirmed_position_in_mm=[-1.5, 2.4, -2.3],
+    confirmed_brain_area="CA3",
 )
 channels_table["estimated_position_in_mm"].reference = "Bregma at the cortical surface"
-channels_table["actual_position_in_mm"].reference = "Bregma at the cortical surface"
+channels_table["confirmed_position_in_mm"].reference = "Bregma at the cortical surface"
 
 # put this in nwbfile.acquisition for testing
 nwbfile.add_acquisition(channels_table)

diff --git a/src/spec/create_extension_spec.py b/src/spec/create_extension_spec.py
@@ -377,7 +377,7 @@ def main():
                 quantity="?",
             ),
             NWBDatasetSpec(
-                name="actual_position_in_mm",
+                name="confirmed_position_in_mm",
                 neurodata_type_inc="VectorData",
                 doc=(
                     "Stereotactic coordinates (AP, ML, DV) of the the verified actual contact position, such as from "
@@ -415,7 +415,7 @@ def main():
                 ],
             ),
             NWBDatasetSpec(
-                name="actual_brain_area",
+                name="confirmed_brain_area",
                 neurodata_type_inc="VectorData",
                 dtype="text",
                 doc=("The brain area of the actual contact position, e.g., 'CA1'."),