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Merge pull request #169 from ttngu207/new_spikeglx_and_probeinterface
New spikeglx and probeinterface
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| from __future__ import annotations | ||
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| import numpy as np | ||
| import pandas as pd | ||
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| """ | ||
| 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 | ||
| """ | ||
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| # 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", | ||
| ] | ||
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| # 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] | ||
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| """ | ||
| 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) | ||
| """ | ||
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| 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), | ||
| ] | ||
| ) | ||
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| 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)) | ||
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| 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, | ||
| ) | ||
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| return elec_pos_df | ||
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| def to_probeinterface(electrodes_df): | ||
| from probeinterface import Probe | ||
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| 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 | ||
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| return Probe.from_dataframe(probe_df) | ||
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| 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) | ||
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| 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 | ||
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| shank_cols = np.tile(range(col_count_per_shank), row_count) | ||
| shank_rows = np.repeat(range(row_count), col_count_per_shank) | ||
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| 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) | ||
| ) | ||
| ] | ||
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| return pd.DataFrame(electrode_layout) if as_dataframe else electrode_layout |
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