Merge pull request #210 from kushalbakshi/main

Fix(spikeglx): robust IMAX value detection from IMEC file

Author: ttngu207

CHANGELOG.md

@@ -1,5 +1,11 @@
 # CHANGELOG
 
+## v0.3.7 (2024-11-01)
+
+### Fix
+
+* Fix(spikeglx): robust IMAX value detection from IMEC file (metadata 3.0)
+
 ## v0.3.6 (2024-10-01)
 
 ### Chore

element_array_ephys/ephys_acute.py

@@ -126,7 +126,7 @@ class AcquisitionSoftware(dj.Lookup):
         acq_software ( varchar(24) ): Acquisition software, e.g,. SpikeGLX, OpenEphys
     """
 
-    definition = """  # Software used for recording of neuropixels probes
+    definition = """  # Name of software used for recording of neuropixels probes - SpikeGLX or Open Ephys
     acq_software: varchar(24)
     """
     contents = zip(["SpikeGLX", "Open Ephys"])
@@ -533,7 +533,6 @@ def make(self, key):
                 - 1 : 0 : -self._skip_channel_counts
             ]
 
-            # (sample x channel)
             lfp = oe_probe.lfp_timeseries[:, lfp_channel_ind]
             lfp = (
                 lfp * np.array(oe_probe.lfp_meta["channels_gains"])[lfp_channel_ind]

element_array_ephys/ephys_no_curation.py

@@ -58,7 +58,6 @@ def activate(
     global _linking_module
     _linking_module = linking_module
 
-    # activate
     probe.activate(
         probe_schema_name, create_schema=create_schema, create_tables=create_tables
     )
@@ -315,8 +314,9 @@ def make(self, key):
                 break
         else:
             raise FileNotFoundError(
-                "Ephys recording data not found!"
-                " Neither SpikeGLX nor Open Ephys recording files found"
+                f"Ephys recording data not found!"
+                f" Neither SpikeGLX nor Open Ephys recording files found"
+                f" in {session_dir}"
             )
 
         supported_probe_types = probe.ProbeType.fetch("probe_type")

element_array_ephys/readers/spikeglx.py

@@ -96,15 +96,15 @@ def get_channel_bit_volts(self, band="ap"):
                 dataVolts = dataInt * Vmax / Imax / gain
         """
         vmax = float(self.apmeta.meta["imAiRangeMax"])
+        imax = self.apmeta.meta.get("imMaxInt")
+        imax = float(imax) if imax else IMAX[self.apmeta.probe_model]
 
         if band == "ap":
-            imax = IMAX[self.apmeta.probe_model]
             imroTbl_data = self.apmeta.imroTbl["data"]
             imroTbl_idx = 3
             chn_ind = self.apmeta.get_recording_channels_indices(exclude_sync=True)
 
         elif band == "lf":
-            imax = IMAX[self.lfmeta.probe_model]
             imroTbl_data = self.lfmeta.imroTbl["data"]
             imroTbl_idx = 4
             chn_ind = self.lfmeta.get_recording_channels_indices(exclude_sync=True)

element_array_ephys/version.py

@@ -1,3 +1,3 @@
 """Package metadata."""
 
-__version__ = "0.3.6"
+__version__ = "0.3.7"