transform geom map to shank map

Thinh Nguyen · Thinh Nguyen · commit 9857aef544eb · 2023-07-26T15:08:10.000-05:00
diff --git a/element_array_ephys/readers/spikeglx.py b/element_array_ephys/readers/spikeglx.py
@@ -318,6 +318,9 @@ def __init__(self, meta_filepath):
             else None
         )
 
+        if self.shankmap is None and self.geommap is not None:
+            self.shankmap = self._transform_geom_to_shank()
+
         # Channels being recorded, exclude Sync channels - basically a 1-1 mapping to shankmap
         self.recording_channels = np.arange(len(self.imroTbl["data"]))[
             self.get_recording_channels_indices(exclude_sync=True)

Original file line number	Diff line number	Diff line change
`@@ -318,6 +318,9 @@ def __init__(self, meta_filepath):`
`318`	`318`	`else None`
`319`	`319`	`)`
`320`	`320`
	`321`	`+ if self.shankmap is None and self.geommap is not None:`
	`322`	`+ self.shankmap = self._transform_geom_to_shank()`
	`323`	`+`
`321`	`324`	`# Channels being recorded, exclude Sync channels - basically a 1-1 mapping to shankmap`
`322`	`325`	`self.recording_channels = np.arange(len(self.imroTbl["data"]))[`
`323`	`326`	`self.get_recording_channels_indices(exclude_sync=True)`