Merge pull request #169 from ttngu207/new_spikeglx_and_probeinterface

kabilar · web-flow · commit 3b8efe52fcc1 · 2023-09-15T20:14:31.000-05:00
New spikeglx and probeinterface
diff --git a/element_array_ephys/probe.py b/element_array_ephys/probe.py
@@ -1,10 +1,10 @@
 """
 Neuropixels Probes
 """
-from __future__ import annotations
-
 import datajoint as dj
-import numpy as np
+
+from .readers import probe_geometry
+from .readers.probe_geometry import build_electrode_layouts
 
 schema = dj.schema()
 
@@ -96,60 +96,23 @@ def create_neuropixels_probe(probe_type: str = "neuropixels 1.0 - 3A"):
 
         For electrode location, the (0, 0) is the
          bottom left corner of the probe (ignore the tip portion)
-        Electrode numbering is 1-indexing
+        Electrode numbering is 0-indexing
         """
 
-        neuropixels_probes_config = {
-            "neuropixels 1.0 - 3A": dict(
-                site_count_per_shank=960,
-                col_spacing=32,
-                row_spacing=20,
-                white_spacing=16,
-                col_count_per_shank=2,
-                shank_count=1,
-                shank_spacing=0,
-            ),
-            "neuropixels 1.0 - 3B": dict(
-                site_count_per_shank=960,
-                col_spacing=32,
-                row_spacing=20,
-                white_spacing=16,
-                col_count_per_shank=2,
-                shank_count=1,
-                shank_spacing=0,
-            ),
-            "neuropixels UHD": dict(
-                site_count_per_shank=384,
-                col_spacing=6,
-                row_spacing=6,
-                white_spacing=0,
-                col_count_per_shank=8,
-                shank_count=1,
-                shank_spacing=0,
-            ),
-            "neuropixels 2.0 - SS": dict(
-                site_count_per_shank=1280,
-                col_spacing=32,
-                row_spacing=15,
-                white_spacing=0,
-                col_count_per_shank=2,
-                shank_count=1,
-                shank_spacing=250,
-            ),
-            "neuropixels 2.0 - MS": dict(
-                site_count_per_shank=1280,
-                col_spacing=32,
-                row_spacing=15,
-                white_spacing=0,
-                col_count_per_shank=2,
-                shank_count=4,
-                shank_spacing=250,
-            ),
-        }
+        npx_probes_config = probe_geometry.M
+        npx_probes_config["neuropixels 1.0 - 3A"] = npx_probes_config["3A"]
+        npx_probes_config["neuropixels 1.0 - 3B"] = npx_probes_config["NP1010"]
+        npx_probes_config["neuropixels UHD"] = npx_probes_config["NP1100"]
+        npx_probes_config["neuropixels 2.0 - SS"] = npx_probes_config["NP2000"]
+        npx_probes_config["neuropixels 2.0 - MS"] = npx_probes_config["NP2010"]
 
         probe_type = {"probe_type": probe_type}
-        electrode_layouts = build_electrode_layouts(
-            **{**neuropixels_probes_config[probe_type["probe_type"]], **probe_type}
+        probe_params = dict(zip(
+                probe_geometry.geom_param_names,
+                npx_probes_config[probe_type["probe_type"]]
+            ))
+        electrode_layouts = probe_geometry.build_npx_probe(
+            **{**probe_params, **probe_type}
         )
         with ProbeType.connection.transaction:
             ProbeType.insert1(probe_type, skip_duplicates=True)
@@ -205,60 +168,3 @@ 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)
-        )
-    ]
diff --git a/element_array_ephys/readers/probe_geometry.py b/element_array_ephys/readers/probe_geometry.py
@@ -0,0 +1,213 @@
+from __future__ import annotations
+
+import numpy as np
+import pandas as pd
+
+"""
+Geometry definition for Neuropixels probes
+The definition here are all from Jennifer Colonell
+See:
+https://github.com/jenniferColonell/SGLXMetaToCoords/blob/main/SGLXMetaToCoords.py
+
+A better approach is to pip install and use as a package
+Unfortunately, the GitHub repo above is not yet packaged and pip installable
+
+Better yet, full integration with ProbeInterface and the probes' geometry
+ from Jennifer Colonell - this is in the making!
+
+Latest update: 07-26-2023
+"""
+
+# many part numbers have the same geometry parameters ;
+# define those sets in lists
+# [nShank, shankWidth, shankPitch, even_xOff, odd_xOff, horizPitch, vertPitch, rowsPerShank, elecPerShank]
+geom_param_names = [
+    "nShank",
+    "shankWidth",
+    "shankPitch",
+    "even_xOff",
+    "odd_xOff",
+    "horizPitch",
+    "vertPitch",
+    "rowsPerShank",
+    "elecPerShank",
+]
+
+# offset and pitch values in um
+np1_stag_70um = [1, 70, 0, 27, 11, 32, 20, 480, 960]
+nhp_lin_70um = [1, 70, 0, 27, 27, 32, 20, 480, 960]
+nhp_stag_125um_med = [1, 125, 0, 27, 11, 87, 20, 1368, 2496]
+nhp_stag_125um_long = [1, 125, 0, 27, 11, 87, 20, 2208, 4416]
+nhp_lin_125um_med = [1, 125, 0, 11, 11, 103, 20, 1368, 2496]
+nhp_lin_125um_long = [1, 125, 0, 11, 11, 103, 20, 2208, 4416]
+uhd_8col_1bank = [1, 70, 0, 14, 14, 6, 6, 48, 384]
+uhd_8col_16bank = [1, 70, 0, 14, 14, 6, 6, 768, 6144]
+np2_ss = [1, 70, 0, 27, 27, 32, 15, 640, 1280]
+np2_4s = [4, 70, 250, 27, 27, 32, 15, 640, 1280]
+NP1120 = [1, 70, 0, 6.75, 6.75, 4.5, 4.5, 192, 384]
+NP1121 = [1, 70, 0, 6.25, 6.25, 3, 3, 384, 384]
+NP1122 = [1, 70, 0, 6.75, 6.75, 4.5, 4.5, 24, 384]
+NP1123 = [1, 70, 0, 10.25, 10.25, 3, 3, 32, 384]
+NP1300 = [1, 70, 0, 11, 11, 48, 20, 480, 960]
+NP1200 = [1, 70, 0, 27, 11, 32, 20, 64, 128]
+NXT3000 = [1, 70, 0, 53, 53, 0, 15, 128, 128]
+
+"""
+Electrode coordinate system - from Bill Karsh
+(https://github.com/billkarsh/SpikeGLX/blob/master/Markdown/Metadata_30.md)
+
+The X-origin is the left edge of the shank
+The Y-origin is the center of the bottom-most elecrode row (closest to the tip) 
+"""
+
+
+M = dict(
+    [
+        ("3A", np1_stag_70um),
+        ("PRB_1_4_0480_1", np1_stag_70um),
+        ("PRB_1_4_0480_1_C", np1_stag_70um),
+        ("NP1010", np1_stag_70um),
+        ("NP1011", np1_stag_70um),
+        ("NP1012", np1_stag_70um),
+        ("NP1013", np1_stag_70um),
+        ("NP1015", nhp_lin_70um),
+        ("NP1016", nhp_lin_70um),
+        ("NP1017", nhp_lin_70um),
+        ("NP1020", nhp_stag_125um_med),
+        ("NP1021", nhp_stag_125um_med),
+        ("NP1030", nhp_stag_125um_long),
+        ("NP1031", nhp_stag_125um_long),
+        ("NP1022", nhp_lin_125um_med),
+        ("NP1032", nhp_lin_125um_long),
+        ("NP1100", uhd_8col_1bank),
+        ("NP1110", uhd_8col_16bank),
+        ("PRB2_1_4_0480_1", np2_ss),
+        ("PRB2_1_2_0640_0", np2_ss),
+        ("NP2000", np2_ss),
+        ("NP2003", np2_ss),
+        ("NP2004", np2_ss),
+        ("PRB2_4_2_0640_0", np2_4s),
+        ("PRB2_4_4_0480_1", np2_4s),
+        ("NP2010", np2_4s),
+        ("NP2013", np2_4s),
+        ("NP2014", np2_4s),
+        ("NP1120", NP1120),
+        ("NP1121", NP1121),
+        ("NP1122", NP1122),
+        ("NP1123", NP1123),
+        ("NP1300", NP1300),
+        ("NP1200", NP1200),
+        ("NXT3000", NXT3000),
+    ]
+)
+
+
+def build_npx_probe(
+    nShank: int,
+    shankWidth: float,
+    shankPitch: float,
+    even_xOff: float,
+    odd_xOff: float,
+    horizPitch: float,
+    vertPitch: float,
+    rowsPerShank: int,
+    elecPerShank: int,
+    probe_type: str = "neuropixels",
+):
+    row_offset = np.tile([even_xOff, odd_xOff], int(rowsPerShank / 2))
+
+    elec_pos_df = build_electrode_layouts(
+        probe_type=probe_type,
+        site_count_per_shank=elecPerShank,
+        col_spacing=horizPitch,
+        row_spacing=vertPitch,
+        row_offset=row_offset,
+        col_count_per_shank=int(elecPerShank / rowsPerShank),
+        shank_count=nShank,
+        shank_spacing=shankPitch,
+        y_origin="bottom",
+        as_dataframe=True,
+    )
+
+    return elec_pos_df
+
+
+def to_probeinterface(electrodes_df):
+    from probeinterface import Probe
+
+    probe_df = electrodes_df.copy()
+    probe_df.rename(
+        columns={
+            "electrode": "contact_ids",
+            "shank": "shank_ids",
+            "x_coord": "x",
+            "y_coord": "y",
+        },
+        inplace=True,
+    )
+    probe_df["contact_shapes"] = "square"
+    probe_df["width"] = 12
+
+    return Probe.from_dataframe(probe_df)
+
+
+def build_electrode_layouts(
+    probe_type: str,
+    site_count_per_shank: int,
+    col_spacing: float = None,
+    row_spacing: float = None,
+    row_offset: list = None,
+    col_count_per_shank: int = 1,
+    shank_count: int = 1,
+    shank_spacing: float = None,
+    y_origin="bottom",
+    as_dataframe=False,
+) -> 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).
+        row_offset (list): (um) per-row 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".
+        as_dataframe (bool): if True, returns as pandas DataFrame, otherwise as list of dict
+    """
+    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 row_offset is None:
+        row_offset = np.zeros_like(x_coords)
+    else:
+        assert len(row_offset) == row_count
+        row_offset = np.tile(row_offset, col_count_per_shank)
+    x_coords = x_coords + row_offset
+
+    shank_cols = np.tile(range(col_count_per_shank), row_count)
+    shank_rows = np.repeat(range(row_count), col_count_per_shank)
+
+    electrode_layout = [
+        {
+            "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)
+        )
+    ]
+
+    return pd.DataFrame(electrode_layout) if as_dataframe else electrode_layout
diff --git a/element_array_ephys/readers/spikeglx.py b/element_array_ephys/readers/spikeglx.py
