Merge pull request #44 from bendichter/convert_to_nwb

Convert to nwb

Author: kabilar

element_array_ephys/__init__.py

@@ -1 +1,2 @@
+# ephys_acute as default
 import element_array_ephys.ephys_acute as ephys

element_array_ephys/ephys_acute.py

@@ -301,7 +301,6 @@ def make(self, key):
                 shank, shank_col, shank_row, _ = spikeglx_recording.apmeta.shankmap['data'][recorded_site]
                 electrode_keys.append(probe_electrodes[(shank, shank_col, shank_row)])
         elif acq_software == 'Open Ephys':
-            
             session_dir = find_full_path(get_ephys_root_data_dir(), 
                                          get_session_directory(key))
 

element_array_ephys/export/__init__.py

@@ -0,0 +1,55 @@
+# Exporting data to NWB
+
+The `export/nwb/nwb.py` module maps from the element-array-ephys data structure to NWB.
+The main function is `ecephys_session_to_nwb`, which contains flags to control calling the following functions, 
+which can be called independently:
+
+1. `session.export.nwb.session_to_nwb`: Gathers session-level metadata
+
+
+2. `add_electrodes_to_nwb`: Add electrodes table to NWBFile. This is needed for any ElectricalSeries, including
+   raw source data and LFP.
+
+   
+    ephys.InsertionLocation -> ElectrodeGroup.location
+
+    probe.Probe::probe -> device.name
+    probe.Probe::probe_comment -> device.description
+    probe.Probe::probe_type -> device.manufacturer
+
+    probe.ProbeType.Electrode::electrode -> electrodes["id_in_probe"]
+    probe.ProbeType.Electrode::y_coord -> electrodes["rel_y"]
+    probe.ProbeType.Electrode::x_coord -> electrodes["rel_x"]
+    probe.ProbeType.Electrode::shank -> electrodes["shank"]
+    probe.ProbeType.Electrode::shank_col -> electrodes["shank_col"]
+    probe.ProbeType.Electrode::shank_row -> electrodes["shank_row"]
+
+3. `add_ephys_recording_to_nwb`: Read voltage data directly from source files and iteratively transfer them to the 
+   NWB file. Automatically applies lossless compression to the data, so the final file might be smaller than the original, but there is no
+   data loss. Currently supports Neuropixels data acquired with SpikeGLX or Open Ephys, and relies on SpikeInterface to read the data.
+
+
+    source data -> acquisition["ElectricalSeries"]
+
+4. `add_ephys_units_to_nwb`: Add spiking data from CuratedClustering to NWBFile.
+
+
+    ephys.CuratedClustering.Unit::unit -> units.id
+    ephys.CuratedClustering.Unit::spike_times -> units["spike_times"]
+    ephys.CuratedClustering.Unit::spike_depths -> units["spike_depths"]
+    ephys.CuratedClustering.Unit::cluster_quality_label -> units["cluster_quality_label"]
+
+    ephys.WaveformSet.PeakWaveform::peak_electrode_waveform -> units["waveform_mean"]
+
+5. `add_ephys_lfp_from_dj_to_nwb`: Read LFP data from the data in element-array-ephys and convert to NWB.
+
+
+    ephys.LFP.Electrode::lfp -> processing["ecephys"].lfp.electrical_series["ElectricalSeries{insertion_number}"].data
+    ephys.LFP::lfp_time_stamps -> processing["ecephys"].lfp.electrical_series["ElectricalSeries{insertion_number}"].timestamps
+
+6. `add_ephys_lfp_from_source_to_nwb`: Read the LFP data directly from the source file. Currently, only works for 
+   SpikeGLX data. Can be used instead of `add_ephys_lfp_from_dj_to_nwb`.
+
+
+    source data -> processing["ecephys"].lfp.electrical_series["ElectricalSeries{insertion_number}"].data
+    source data -> processing["ecephys"].lfp.electrical_series["ElectricalSeries{insertion_number}"].timestamps

element_array_ephys/export/nwb/README.md

@@ -0,0 +1 @@
+from .nwb import ecephys_session_to_nwb, write_nwb