run_prepro_and_sorting_pipeline.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from SI_sorting import run_prepro_and_sorting\n",
    "from SI_tools import clear_SItempdir\n",
    "\n",
    "############################################################################################################################################################################################################\n",
    "#                                                          Set the Parent Directories\n",
    "############################################################################################################################################################################################################\n",
    "\n",
    "#########################################################################################################################\n",
    "# \"parentRecordingFolder\"\n",
    "#   Folder from where to read NWB (read from server, unless you copied the files into the local machine)\n",
    "parentRecordingFolder = 'Y:\\Data_Albus\\Albus_NeuralData\\Albus-S1'\n",
    "\n",
    "#########################################################################################################################\n",
    "# \"parentPreproFolder\":\n",
    "#   Folder to save all the Plots & recording objects from the preprocessing (server is recommended to keep record of the sorting process)\n",
    "parentPreproFolder = 'Y:\\Data_Albus\\Albus_NeuralData\\Albus-S1-Prepro' \n",
    "\n",
    "#########################################################################################################################\n",
    "# \"parentSortingFolder\" \n",
    "# Folder to save \"recording\" (binalry) & \"sorting_analyzer\"\n",
    "# if \"parentSortingFolder\" is not provided, then:\n",
    "#       if exporting \"sorting_analyzer\" to phy is True, both objects will be created temporary and deleted at the end\n",
    "#       if exporting \"sorting_analyzer\" to phy is False, both objects will be created in the same parentPreproFolder\n",
    "parentSortingFolder = None\n",
    "\n",
    "#########################################################################################################################\n",
    "# \"parentPhyFolder\":\n",
    "# Folder to save the results from sorting into phy format.\n",
    "# If None, it will use the same path as the \"parentPreproFolder\"\n",
    "parentPhyFolder = None \n",
    "\n",
    "######################################################################################################\n",
    "# \"localProcess_NWB\" : \n",
    "#       if TRUE, it will copy NWB files into a temporary directory in the same disk as this script and it will deleted the NWB files at the end\n",
    "#                it will not create recording objects due to the lost of path links after deleting the temprary files\n",
    "#       if FALSE it will read files from original location and it will create recording objects with paths linked to the original NWB locations.\n",
    "localProcess_NWB = False\n",
    "\n",
    "# \"rewrite_prepro\" : \n",
    "#       if TRUE it will run all the preprocessing regardless of finding the previous recording objects\n",
    "#       if FALSE it will check whether preprocessed and motion_iterpolated recordings exist \n",
    "#           if those exists, it will be reloaded and pass it to the sorter\n",
    "#           if those not exists then it will re run the preprocessing and pass it to the sorter\n",
    "rewrite_prepro = False\n",
    "\n",
    "# \"export2phy\"\n",
    "#       if FALSE it will save the sorter analyzer and the binary recording folder (see \"parentSortingFolder\")\n",
    "#       if TRUE it will export the sorter analyzer to phy with the binary recording. The sorter analyzer might be deleted depending on the value of \"parentSortingFolder\"\n",
    "export2phy = True"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "############################################################################################################################################################################################################\n",
    "#                                               SELECT EXPERIMENT DAY AND SESSIONS (listID or None)\n",
    "############################################################################################################################################################################################################\n",
    "\n",
    "#########################################################################################################################\n",
    "# Experiment Day : YEAR, MONTH, DAY\n",
    "sessionYear = 2024\n",
    "sessionMonth = 2\n",
    "sessionDay = 23\n",
    "\n",
    "#########################################################################################################################\n",
    "# ElectrodeGroupe Name (based on NWBfile naming schema) \n",
    "# Note: if there were different coordinates within the same day, you need to add '-sub1', '-sub2', etc. \n",
    "# It is recommended to run \"SI_run_prepro\" first, it will create folder for all the unique electrode groups from that day.\n",
    "# In case you want to explore how many electrodeGroup-subX exists, run:\n",
    "#       from SI_tools import print_recordingInfo\n",
    "#       print_recordingInfo(parentRecordingFolder, sessionYear, sessionMonth, sessionDay)\n",
    "###########################################################################################################################\n",
    "electrodeGroup_Name = 'raw-B1-129-160' \n",
    "\n",
    "#########################################################################################################################\n",
    "# Session index is based on the dateTime. Zero is the first session of the day from the selected electrodeGroup\n",
    "# If None, it will use all sessions from this electrodeGroup in this experiment Day\n",
    "session_index = [0, 1] "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "############################################################################################################################################################################################################\n",
    "#                                                                   SET GENERAL PARAMETERS FOR PREPROCESSING\n",
    "############################################################################################################################################################################################################\n",
    "\n",
    "######################################################################################################\n",
    "# PARAMETER FOR \"LOCAL REFERENCING\"\n",
    "exclude_radius_chans = 1 # Number of neighbor channels to exclude because are too close to the reference channel\n",
    "include_radius_chans = 4 # Number of neighbor channels delineates the outer boundary of the annulus whose role is to exclude channels that are too far away\n",
    "\n",
    "######################################################################################################\n",
    "# NOISY FREQUENCY TO BE REMOVED (i.e., \"spre.notch_filter\")\n",
    "noisy_freq = None\n",
    "\n",
    "# TODO: bandpass filter\n",
    "###########################################################\n",
    "# DETECT PEAKS: \n",
    "peak_detect_threshold = 5 #  MAD: Median Amplitude Deviations\n",
    "peak_sign = 'both' # (“neg” | “pos” | “both”)\n",
    "nearest_chans = 3 # Number of neighbor channels to search for events that occurred at the same time\n",
    "\n",
    "######################################################################################################\n",
    "# GENERAL PARAMETER FOR \"PEAKS LOCATIONS\"\n",
    "ms_before = 0.6\n",
    "ms_after = 1.5\n",
    "\n",
    "######################################################################################################\n",
    "# MOTION ESTIMATION\n",
    "do_motion = True # if TRUE it will do motion estimation and interpolation\n",
    "\n",
    "# OPTIONS to run : monopolar triangulation + non-rigid + decentralized + kriging\n",
    "motion_rigid = False\n",
    "motion_options = {\n",
    "    'method': 'dredge_ap', # Paninski Lab\n",
    "    'method_kwargs' : {} \n",
    "}\n",
    "interpolate_options = {\n",
    "    'method': 'kriging', # Kilosort-like\n",
    "    'border_mode': 'remove_channels' # ('remove_channels' | 'force_extrapolate' | 'force_zeros')\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "############################################################################################################################################################################################################\n",
    "#                                                                   SET GENERAL PARAMETERS FOR SORTING\n",
    "############################################################################################################################################################################################################\n",
    "\n",
    "# If False, it will only run preprocessing (If you changed some preprocessing params, set \"rewrite_prepro\" to True)\n",
    "run_sorting = True\n",
    "\n",
    "######################################################################################################\n",
    "# SORTER NAME (options: mountainsort5 & kilosort4)\n",
    "sorterName = 'kilosort4'\n",
    "\n",
    "# mountainsort5: ZCA-Whitening units (default = 5.5) [you can try with values as low as 2.5]\n",
    "# kilosort4: STD units from whithening traces (default = 3) [you can try values as low as 1.5]\n",
    "# If None, it will use default values according to each sorting\n",
    "sorter_detect_threshold = 3\n",
    "\n",
    "# Number of neighbor channels to search for the same waveform during sorting & sorting_analyzer\n",
    "# \"nearest_chans = 0\" will perform similar to sorting single channels. \n",
    "# If set to None, it will use the \"nearest_chans\" value from peaks locations\n",
    "sorter_nearest_chans = 2 "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run_prepro_and_sorting(\n",
    "    parentRecordingFolder = parentRecordingFolder, \n",
    "    parentPreproFolder = parentPreproFolder, \n",
    "    parentSortingFolder = parentSortingFolder, \n",
    "    parentPhyFolder = parentPhyFolder, \n",
    "    sessionYear = sessionYear, \n",
    "    sessionMonth = sessionMonth, \n",
    "    sessionDay = sessionDay, \n",
    "    electrodeGroup_Name = electrodeGroup_Name, \n",
    "    session_index = session_index,\n",
    "    local_radius_chans = (exclude_radius_chans, include_radius_chans), \n",
    "    noisy_freq = noisy_freq, \n",
    "    ms_before = ms_before, \n",
    "    ms_after = ms_after, \n",
    "    peak_sign = peak_sign,\n",
    "    nearest_chans = nearest_chans, \n",
    "    peak_detect_threshold = peak_detect_threshold, \n",
    "    do_motion = do_motion,\n",
    "    motion_rigid = motion_rigid, \n",
    "    motion_options = motion_options, \n",
    "    interpolate_options = interpolate_options,\n",
    "    localProcess_NWB = localProcess_NWB,\n",
    "    rewrite_prepro = rewrite_prepro,\n",
    "    run_sorting = run_sorting,\n",
    "    sorterName = sorterName, \n",
    "    sorter_detect_threshold = sorter_detect_threshold,\n",
    "    sorter_nearest_chans = sorter_nearest_chans,\n",
    "    export2phy = export2phy\n",
    ")\n",
    "\n",
    "clear_SItempdir()"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "SIenv",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.11.9"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}