Merge pull request #116 from JaerongA/ephys_test

modify build_electrodes function

Author: CBroz1

CHANGELOG.md

@@ -3,17 +3,17 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
  [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
-## [0.2.1] - Unreleased
+## [0.2.1] - 2022-01-06
 
++ Add - `build_electrode_layouts` function in `probe.py` to compute the electrode layout for all types of probes.
 + Update - parameterize run_CatGT step from parameters retrieved from `ClusteringParamSet` table
 + Update - clustering step, update duration for "median_subtraction" step
 + Bugfix - handles single probe recording in "Neuropix-PXI" format
 + Update - safeguard in creating/inserting probe types upon probe activation
 + Add - quality control metric dashboard
 + Update & fix docstrings
 + Update - `ephys_report.UnitLevelReport` to add `ephys.ClusterQualityLabel` as a foreign key reference
-+ Add `.pre-commit-config.yaml`
-
++ Add - `.pre-commit-config.yaml`
 
 ## [0.2.0] - 2022-10-28
 

element_array_ephys/ephys_acute.py

@@ -680,7 +680,7 @@ class ClusterQualityLabel(dj.Lookup):
 
     Attributes:
         cluster_quality_label (foreign key, varchar(100) ): Cluster quality type.
-        cluster_quality_description (varchar(4000) ): Description of the cluster quality type.
+        cluster_quality_description ( varchar(4000) ): Description of the cluster quality type.
     """
 
     definition = """
@@ -704,7 +704,7 @@ class ClusteringTask(dj.Manual):
     Attributes:
         EphysRecording (foreign key): EphysRecording primary key.
         ClusteringParamSet (foreign key): ClusteringParamSet primary key.
-        clustering_outdir_dir (varchar (255) ): Relative path to output clustering results.
+        clustering_output_dir ( varchar (255) ): Relative path to output clustering results.
         task_mode (enum): `Trigger` computes clustering or and `load` imports existing data.
     """
 
@@ -793,7 +793,7 @@ class Clustering(dj.Imported):
     Attributes:
         ClusteringTask (foreign key): ClusteringTask primary key.
         clustering_time (datetime): Time when clustering results are generated.
-        package_version (varchar(16) ): Package version used for a clustering analysis.
+        package_version ( varchar(16) ): Package version used for a clustering analysis.
     """
 
     definition = """
@@ -918,10 +918,10 @@ class Curation(dj.Manual):
         Clustering (foreign key): Clustering primary key.
         curation_id (foreign key, int): Unique curation ID.
         curation_time (datetime): Time when curation results are generated.
-        curation_output_dir (varchar(255) ): Output directory of the curated results.
+        curation_output_dir ( varchar(255) ): Output directory of the curated results.
         quality_control (bool): If True, this clustering result has undergone quality control.
         manual_curation (bool): If True, manual curation has been performed on this clustering result.
-        curation_note (varchar(2000) ): Notes about the curation task.
+        curation_note ( varchar(2000) ): Notes about the curation task.
     """
 
     definition = """

element_array_ephys/ephys_no_curation.py

@@ -11,7 +11,6 @@
 from element_interface.utils import dict_to_uuid, find_full_path, find_root_directory
 
 from . import ephys_report, get_logger, probe
-
 from .readers import kilosort, openephys, spikeglx
 
 log = get_logger(__name__)

element_array_ephys/probe.py

@@ -78,9 +78,9 @@ class Electrode(dj.Part):
         ---
         shank: int           # shank index, starts at 0, advance left to right
         shank_col: int       # column index, starts at 0, advance left to right
-        shank_row: int       # row index, starts at 0, advance tip to tail
-        x_coord=NULL: float  # (um) x coordinate of the electrode within the probe, (0, 0) is the bottom left corner of the probe
-        y_coord=NULL: float  # (um) y coordinate of the electrode within the probe, (0, 0) is the bottom left corner of the probe
+        shank_row: int       # row index, starts at 0.
+        x_coord=NULL: float  # (um) x coordinate of the electrode within the probe.
+        y_coord=NULL: float  # (um) y coordinate of the electrode within the probe.
         """
 
     @staticmethod
@@ -100,114 +100,59 @@ def create_neuropixels_probe(probe_type: str = "neuropixels 1.0 - 3A"):
 
         neuropixels_probes_config = {
             "neuropixels 1.0 - 3A": dict(
-                site_count=960,
+                site_count_per_shank=960,
                 col_spacing=32,
                 row_spacing=20,
                 white_spacing=16,
-                col_count=2,
+                col_count_per_shank=2,
                 shank_count=1,
                 shank_spacing=0,
             ),
             "neuropixels 1.0 - 3B": dict(
-                site_count=960,
+                site_count_per_shank=960,
                 col_spacing=32,
                 row_spacing=20,
                 white_spacing=16,
-                col_count=2,
+                col_count_per_shank=2,
                 shank_count=1,
                 shank_spacing=0,
             ),
             "neuropixels UHD": dict(
-                site_count=384,
+                site_count_per_shank=384,
                 col_spacing=6,
                 row_spacing=6,
                 white_spacing=0,
-                col_count=8,
+                col_count_per_shank=8,
                 shank_count=1,
                 shank_spacing=0,
             ),
             "neuropixels 2.0 - SS": dict(
-                site_count=1280,
+                site_count_per_shank=1280,
                 col_spacing=32,
                 row_spacing=15,
                 white_spacing=0,
-                col_count=2,
+                col_count_per_shank=2,
                 shank_count=1,
                 shank_spacing=250,
             ),
             "neuropixels 2.0 - MS": dict(
-                site_count=1280,
+                site_count_per_shank=1280,
                 col_spacing=32,
                 row_spacing=15,
                 white_spacing=0,
-                col_count=2,
+                col_count_per_shank=2,
                 shank_count=4,
                 shank_spacing=250,
             ),
         }
 
-        def build_electrodes(
-            site_count: int,
-            col_spacing: float,
-            row_spacing: float,
-            white_spacing: float,
-            col_count: int,
-            shank_count: int,
-            shank_spacing: float,
-        ) -> dict:
-            """Builds electrode layouts.
-
-            Args:
-                site_count (int): site count per shank
-                col_spacing (float): (um) horizontal spacing between sites
-                row_spacing (float): (um) vertical spacing between columns
-                white_spacing (float): (um) offset spacing
-                col_count (int): number of column per shank
-                shank_count (int): number of shank
-                shank_spacing (float): spacing between shanks
-            """
-            row_count = int(site_count / col_count)
-            x_coords = np.tile(
-                np.arange(0, col_spacing * col_count, col_spacing), row_count
-            )
-            y_coords = np.repeat(np.arange(row_count) * row_spacing, col_count)
-
-            if white_spacing:
-                x_white_spaces = np.tile(
-                    [white_spacing, white_spacing, 0, 0], int(row_count / 2)
-                )
-                x_coords = x_coords + x_white_spaces
-
-            shank_cols = np.tile(range(col_count), row_count)
-            shank_rows = np.repeat(range(row_count), col_count)
-
-            npx_electrodes = []
-            for shank_no in range(shank_count):
-                npx_electrodes.extend(
-                    [
-                        {
-                            "electrode": (site_count * shank_no) + e_id,
-                            "shank": shank_no,
-                            "shank_col": c_id,
-                            "shank_row": r_id,
-                            "x_coord": x + (shank_no * shank_spacing),
-                            "y_coord": y,
-                        }
-                        for e_id, (c_id, r_id, x, y) in enumerate(
-                            zip(shank_cols, shank_rows, x_coords, y_coords)
-                        )
-                    ]
-                )
-
-            return npx_electrodes
-
-        electrodes = build_electrodes(**neuropixels_probes_config[probe_type])
         probe_type = {"probe_type": probe_type}
+        electrode_layouts = build_electrode_layouts(
+            **{**neuropixels_probes_config[probe_type["probe_type"]], **probe_type}
+        )
         with ProbeType.connection.transaction:
             ProbeType.insert1(probe_type, skip_duplicates=True)
-            ProbeType.Electrode.insert(
-                [{**probe_type, **e} for e in electrodes], skip_duplicates=True
-            )
+            ProbeType.Electrode.insert(electrode_layouts, skip_duplicates=True)
 
 
 @schema
@@ -217,7 +162,7 @@ class Probe(dj.Lookup):
     Attributes:
         probe (foreign key, varchar(32) ): Unique ID for this model of the probe.
         ProbeType (dict): ProbeType entry.
-        probe_comment (varchar(1000) ): Comment about this model of probe.
+        probe_comment ( varchar(1000) ): Comment about this model of probe.
     """
 
     definition = """
@@ -236,7 +181,7 @@ class ElectrodeConfig(dj.Lookup):
     Attributes:
         electrode_config_hash (foreign key, uuid): unique index for electrode configuration.
         ProbeType (dict): ProbeType entry.
-        electrode_config_name (varchar(4000) ): User-friendly name for this electrode configuration.
+        electrode_config_name ( varchar(4000) ): User-friendly name for this electrode configuration.
     """
 
     definition = """
@@ -259,3 +204,61 @@ class Electrode(dj.Part):
         -> master
         -> ProbeType.Electrode
         """
+
+
+def build_electrode_layouts(
+    probe_type: str,
+    site_count_per_shank: int,
+    col_spacing: float = None,
+    row_spacing: float = None,
+    white_spacing: float = None,
+    col_count_per_shank: int = 1,
+    shank_count: int = 1,
+    shank_spacing: float = None,
+    y_origin="bottom",
+) -> list[dict]:
+
+    """Builds electrode layouts.
+
+    Args:
+        probe_type (str): probe type (e.g., "neuropixels 1.0 - 3A").
+        site_count_per_shank (int): site count per shank.
+        col_spacing (float): (um) horizontal spacing between sites. Defaults to None (single column).
+        row_spacing (float): (um) vertical spacing between columns. Defaults to None (single row).
+        white_spacing (float): (um) offset spacing. Defaults to None.
+        col_count_per_shank (int): number of column per shank. Defaults to 1 (single column).
+        shank_count (int): number of shank. Defaults to 1 (single shank).
+        shank_spacing (float): (um) spacing between shanks. Defaults to None (single shank).
+        y_origin (str): {"bottom", "top"}. y value decrements if "top". Defaults to "bottom".
+    """
+    row_count = int(site_count_per_shank / col_count_per_shank)
+    x_coords = np.tile(
+        np.arange(0, (col_spacing or 1) * col_count_per_shank, (col_spacing or 1)),
+        row_count,
+    )
+    y_coords = np.repeat(np.arange(row_count) * (row_spacing or 1), col_count_per_shank)
+
+    if white_spacing:
+        x_white_spaces = np.tile(
+            [white_spacing, white_spacing, 0, 0], int(row_count / 2)
+        )
+        x_coords = x_coords + x_white_spaces
+
+    shank_cols = np.tile(range(col_count_per_shank), row_count)
+    shank_rows = np.repeat(range(row_count), col_count_per_shank)
+
+    return [
+        {
+            "probe_type": probe_type,
+            "electrode": (site_count_per_shank * shank_no) + e_id,
+            "shank": shank_no,
+            "shank_col": c_id,
+            "shank_row": r_id,
+            "x_coord": x + (shank_no * (shank_spacing or 1)),
+            "y_coord": {"top": -y, "bottom": y}[y_origin],
+        }
+        for shank_no in range(shank_count)
+        for e_id, (c_id, r_id, x, y) in enumerate(
+            zip(shank_cols, shank_rows, x_coords, y_coords)
+        )
+    ]

setup.py

@@ -16,7 +16,7 @@
 
 setup(
     name=pkg_name.replace("_", "-"),
-    version=__version__, # noqa F821
+    version=__version__,  # noqa F821
     description="DataJoint Element for Extracellular Array Electrophysiology",
     long_description=long_description,
     long_description_content_type="text/markdown",