Merge branch 'main' of https://github.com/sidhulyalkar/element-array-ephys

Author: sidhulyalkar

CHANGELOG.md

@@ -1,20 +1,48 @@
 # Changelog
 
-Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
+Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
+ [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.1.4] - 2022-07-11
+
++ Bugfix - Handle case where `spike_depths` data is present.
+
+## [0.1.3] - 2022-06-16
+
++ Update - Allow for the `precluster_output_dir` attribute to be nullable when no pre-clustering is performed.
+
+## [0.1.2] - 2022-06-09
+
++ Bugfix - Handle case where `pc_features.npy` does not exist.
+
+## [0.1.1] - 2022-06-01
+
++ Add - Secondary attributes to `PreClusterParamSteps` table
+
+## [0.1.0] - 2022-05-26
+
++ Update - Rename module for acute probe insertions from `ephys.py` to `ephys_acute.py`.
++ Add - Module for pre-clustering steps (`ephys_precluster.py`), which is built off of `ephys_acute.py`.
++ Add - Module for chronic probe insertions (`ephys_chronic.py`).  
++ Bugfix - Missing `fileTimeSecs` key in SpikeGLX meta file.
++ Update - Move common functions to `element-interface` package.
++ Add - NWB export function
 
 ## [0.1.0b0] - 2021-05-07
-### Added
-+ First beta release
 
++ Update - First beta release
 
 ## [0.1.0a5] - 2021-05-05
-### Added 
-+ Added GitHub Action release process
-+ `probe` and `ephys` elements
-+ Readers for: `SpikeGLX`, `Open Ephys`, `Kilosort`
-+ Probe table supporting: Neuropixels probes 1.0 - 3A, 1.0 - 3B, 2.0 - SS, 2.0 - MS
 
++ Add - GitHub Action release process
++ Add - `probe` and `ephys` elements
++ Add - Readers for: `SpikeGLX`, `Open Ephys`, `Kilosort`
++ Add - Probe table supporting: Neuropixels probes 1.0 - 3A, 1.0 - 3B, 2.0 - SS, 2.0 - MS
 
-[0.1.0b0]: https://github.com/datajoint/element-array-ephys/compare/0.1.0a5...0.1.0b0
+[0.1.4]: https://github.com/datajoint/element-array-ephys/releases/tag/0.1.4
+[0.1.3]: https://github.com/datajoint/element-array-ephys/releases/tag/0.1.3
+[0.1.2]: https://github.com/datajoint/element-array-ephys/releases/tag/0.1.2
+[0.1.1]: https://github.com/datajoint/element-array-ephys/releases/tag/0.1.1
+[0.1.0]: https://github.com/datajoint/element-array-ephys/compare/0.1.0b0...0.1.0
+[0.1.0b0]: https://github.com/datajoint/element-array-ephys/releases/tag/0.1.0b0
 [0.1.0a5]: https://github.com/datajoint/element-array-ephys/releases/tag/0.1.0a5

README.md

@@ -16,7 +16,30 @@ ephys pipeline.
 
 ## Element architecture
 
-![element-array-ephys diagram](images/attached_array_ephys_element.svg)
+`element-array-ephys` is comprised of two schemas, `probe` and `ephys`.  To handle 
+several use cases of this pipeline, we have designed several `ephys` schemas, including 
+`ephys_acute`, `ephys_chronic`, and `ephys_precluster`.
+
++ `ephys_acute` - A probe(s) is inserted into a new location during each session.
+
++ `ephys_chronic` - A probe(s) is inserted once and used to record across multiple 
+sessions.
+
++ `ephys_precluster` - A probe(s) is inserted into a new location during each session.  
+And pre-clustering steps (e.g. CatGT) are performed on the data from each probe prior 
+to Kilosort analysis.
+
+### `ephys_acute` module
+![element-array-ephys acute diagram](images/attached_array_ephys_element_acute.svg)
+
+
+### `ephys_chronic` module
+![element-array-ephys chronic diagram](images/attached_array_ephys_element_chronic.svg)
+
+### `ephys_precluster` module
+![element-array-ephys precluster diagram](
+    images/attached_array_ephys_element_precluster.svg)
+
 
 As the diagram depicts, the array ephys element starts immediately downstream from `Session`, 
 and also requires some notion of `Location` as a dependency for `InsertionLocation`. We 

element_array_ephys/ephys_acute.py

@@ -503,7 +503,7 @@ class Unit(dj.Part):
         spike_count: int         # how many spikes in this recording for this unit
         spike_times: longblob    # (s) spike times of this unit, relative to the start of the EphysRecording
         spike_sites : longblob   # array of electrode associated with each spike
-        spike_depths : longblob  # (um) array of depths associated with each spike, relative to the (0, 0) of the probe    
+        spike_depths=null : longblob  # (um) array of depths associated with each spike, relative to the (0, 0) of the probe    
         """
 
     def make(self, key):
@@ -551,7 +551,7 @@ def make(self, key):
                     'spike_times': unit_spike_times,
                     'spike_count': spike_count,
                     'spike_sites': spike_sites[kilosort_dataset.data['spike_clusters'] == unit],
-                    'spike_depths': spike_depths[kilosort_dataset.data['spike_clusters'] == unit]})
+                    'spike_depths': spike_depths[kilosort_dataset.data['spike_clusters'] == unit] if spike_depths is not None else None})
 
         self.insert1(key)
         self.Unit.insert([{**key, **u} for u in units])

element_array_ephys/ephys_chronic.py

@@ -502,7 +502,7 @@ class Unit(dj.Part):
         spike_count: int         # how many spikes in this recording for this unit
         spike_times: longblob    # (s) spike times of this unit, relative to the start of the EphysRecording
         spike_sites : longblob   # array of electrode associated with each spike
-        spike_depths : longblob  # (um) array of depths associated with each spike, relative to the (0, 0) of the probe    
+        spike_depths=null : longblob  # (um) array of depths associated with each spike, relative to the (0, 0) of the probe    
         """
 
     def make(self, key):
@@ -550,7 +550,7 @@ def make(self, key):
                     'spike_times': unit_spike_times,
                     'spike_count': spike_count,
                     'spike_sites': spike_sites[kilosort_dataset.data['spike_clusters'] == unit],
-                    'spike_depths': spike_depths[kilosort_dataset.data['spike_clusters'] == unit]})
+                    'spike_depths': spike_depths[kilosort_dataset.data['spike_clusters'] == unit] if spike_depths is not None else None})
 
         self.insert1(key)
         self.Unit.insert([{**key, **u} for u in units])