run_prepro_pipeline.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from SI_sorting import run_prepro\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",
    "######################################################################################################\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 already preprocessed recording objects\n",
    "#       if FALSE it will check whether preprocessed and motion_iterpolated recordings exist \n",
    "#           if those exist, it will skip the preprocessing\n",
    "rewrite_prepro = False"
   ]
  },
  {
   "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 = 4\n",
    "sessionDay = 1\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-C1-257' \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 = None\n"
   ]
  },
  {
   "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",
    "###########################################################\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",
    "}\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run_prepro(parentRecordingFolder, parentPreproFolder,\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",
    "    )\n",
    "\n",
    "clear_SItempdir()"
   ]
  }
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