plot_rawvsclean.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['c:\\\\Users\\\\jz421\\\\Desktop\\\\GlobalLocal', 'C:\\\\Users\\\\jz421\\\\Desktop\\\\GlobalLocal\\\\IEEG_Pipelines', 'c:\\\\Users\\\\jz421\\\\AppData\\\\Local\\\\anaconda3\\\\envs\\\\ieeg\\\\python311.zip', 'c:\\\\Users\\\\jz421\\\\AppData\\\\Local\\\\anaconda3\\\\envs\\\\ieeg\\\\DLLs', 'c:\\\\Users\\\\jz421\\\\AppData\\\\Local\\\\anaconda3\\\\envs\\\\ieeg\\\\Lib', 'c:\\\\Users\\\\jz421\\\\AppData\\\\Local\\\\anaconda3\\\\envs\\\\ieeg', '', 'C:\\\\Users\\\\jz421\\\\AppData\\\\Roaming\\\\Python\\\\Python311\\\\site-packages', 'C:\\\\Users\\\\jz421\\\\AppData\\\\Roaming\\\\Python\\\\Python311\\\\site-packages\\\\win32', 'C:\\\\Users\\\\jz421\\\\AppData\\\\Roaming\\\\Python\\\\Python311\\\\site-packages\\\\win32\\\\lib', 'C:\\\\Users\\\\jz421\\\\AppData\\\\Roaming\\\\Python\\\\Python311\\\\site-packages\\\\Pythonwin', 'c:\\\\Users\\\\jz421\\\\AppData\\\\Local\\\\anaconda3\\\\envs\\\\ieeg\\\\Lib\\\\site-packages', 'c:\\\\Users\\\\jz421\\\\AppData\\\\Local\\\\anaconda3\\\\envs\\\\ieeg\\\\Lib\\\\site-packages\\\\win32', 'c:\\\\Users\\\\jz421\\\\AppData\\\\Local\\\\anaconda3\\\\envs\\\\ieeg\\\\Lib\\\\site-packages\\\\win32\\\\lib', 'c:\\\\Users\\\\jz421\\\\AppData\\\\Local\\\\anaconda3\\\\envs\\\\ieeg\\\\Lib\\\\site-packages\\\\Pythonwin']\n"
     ]
    }
   ],
   "source": [
    "import sys\n",
    "print(sys.path)\n",
    "sys.path.append(\"C:/Users/jz421/Desktop/GlobalLocal/IEEG_Pipelines/\") #need to do this cuz otherwise ieeg isn't added to path...\n",
    "\n",
    "import mne\n",
    "import os\n",
    "from ieeg.mt_filter import line_filter\n",
    "from ieeg.io import get_data, raw_from_layout, save_derivative, update\n",
    "from ieeg import viz\n",
    "from bids import BIDSLayout\n",
    "from ieeg.viz.utils import figure_compare\n",
    "from ieeg.navigate import trial_ieeg, channel_outlier_marker, crop_empty_data, outliers_to_nan\n",
    "import pandas as pd\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['D0057', 'D0059', 'D0063', 'D0065', 'D0069', 'D0071', 'D0077', 'D0090', 'D0094', 'D0100', 'D0102', 'D0103']\n"
     ]
    }
   ],
   "source": [
    "HOME = os.path.expanduser(\"~\")\n",
    "if 'SLURM_ARRAY_TASK_ID' in os.environ.keys():\n",
    "    LAB_root = os.path.join(HOME, \"workspace\", \"CoganLab\")\n",
    "    subject = int(os.environ['SLURM_ARRAY_TASK_ID'])\n",
    "else:  # if not then set box directory\n",
    "    LAB_root = os.path.join(HOME, \"Box\", \"CoganLab\")\n",
    "    subject = 57\n",
    "\n",
    "    \"\"\"\n",
    "Line noise filtering script\n",
    "===================================\n",
    "\n",
    "Filters the 60Hz line noise from the data, as well as the harmonics. Includes\n",
    "environment checks for SLURM jobs for convenience\n",
    "\"\"\"\n",
    "\n",
    "import mne\n",
    "import os\n",
    "from ieeg.io import save_derivative, raw_from_layout\n",
    "from ieeg.mt_filter import line_filter\n",
    "from ieeg.viz.utils import figure_compare\n",
    "from bids import BIDSLayout\n",
    "\n",
    "# %%\n",
    "# Set up paths\n",
    "# ------------\n",
    "HOME = os.path.expanduser(\"~\")\n",
    "\n",
    "# get box directory depending on OS\n",
    "if os.name == 'nt': # windows\n",
    "    LAB_root = os.path.join(HOME, \"Box\", \"CoganLab\")\n",
    "else: # mac\n",
    "    LAB_root = os.path.join(HOME, \"Library\", \"CloudStorage\", \"Box-Box\", \"CoganLab\")\n",
    "\n",
    "\n",
    "## Load Data\n",
    "layout = get_data(\"GlobalLocal\", LAB_root)\n",
    "subjects = layout.get_subjects()\n",
    "subjects.sort()\n",
    "print(subjects)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Extracting EDF parameters from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-01_ieeg.edf...\n",
      "EDF file detected\n",
      "Setting channel info structure...\n",
      "Creating raw.info structure...\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Reading events from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-01_events.tsv.\n",
      "Reading channel info from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_channels.tsv.\n",
      "Reading electrode coords from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_space-ACPC_electrodes.tsv.\n",
      "Extracting EDF parameters from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-02_ieeg.edf...\n",
      "EDF file detected\n",
      "Setting channel info structure...\n",
      "Creating raw.info structure...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: The number of channels in the channels.tsv sidecar file (230) does not match the number of channels in the raw data file (248). Will not try to set channel names.\n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n",
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: Cannot set channel type for the following channels, as they are missing in the raw data: \n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n",
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: DigMontage is only a subset of info. There are 23 channel positions not present in the DigMontage. The channels missing from the montage are:\n",
      "\n",
      "['FZ', 'CZ', 'PZ', 'F7', 'F8', 'LEMG', 'A1', 'A2', 'T5', 'T6', 'REMG', 'FP1', 'FP2', 'F3', 'F4', 'C3', 'C4', 'P3', 'P4', 'O1', 'O2', 'T3', 'T4'].\n",
      "\n",
      "Consider using inst.rename_channels to match the montage nomenclature, or inst.set_channel_types if these are not EEG channels, or use the on_missing parameter if the channel positions are allowed to be unknown in your analyses.\n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n",
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: participants.tsv file not found for C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-01_ieeg.edf\n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Reading events from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-02_events.tsv.\n",
      "Reading channel info from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_channels.tsv.\n",
      "Reading electrode coords from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_space-ACPC_electrodes.tsv.\n",
      "Extracting EDF parameters from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-03_ieeg.edf...\n",
      "EDF file detected\n",
      "Setting channel info structure...\n",
      "Creating raw.info structure...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: The number of channels in the channels.tsv sidecar file (230) does not match the number of channels in the raw data file (248). Will not try to set channel names.\n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n",
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: Cannot set channel type for the following channels, as they are missing in the raw data: \n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n",
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: DigMontage is only a subset of info. There are 23 channel positions not present in the DigMontage. The channels missing from the montage are:\n",
      "\n",
      "['FZ', 'CZ', 'PZ', 'F7', 'F8', 'LEMG', 'A1', 'A2', 'T5', 'T6', 'REMG', 'FP1', 'FP2', 'F3', 'F4', 'C3', 'C4', 'P3', 'P4', 'O1', 'O2', 'T3', 'T4'].\n",
      "\n",
      "Consider using inst.rename_channels to match the montage nomenclature, or inst.set_channel_types if these are not EEG channels, or use the on_missing parameter if the channel positions are allowed to be unknown in your analyses.\n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n",
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: participants.tsv file not found for C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-02_ieeg.edf\n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Reading events from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-03_events.tsv.\n",
      "Reading channel info from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_channels.tsv.\n",
      "Reading electrode coords from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_space-ACPC_electrodes.tsv.\n",
      "Extracting EDF parameters from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-04_ieeg.edf...\n",
      "EDF file detected\n",
      "Setting channel info structure...\n",
      "Creating raw.info structure...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: The number of channels in the channels.tsv sidecar file (230) does not match the number of channels in the raw data file (248). Will not try to set channel names.\n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n",
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: Cannot set channel type for the following channels, as they are missing in the raw data: \n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n",
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: DigMontage is only a subset of info. There are 23 channel positions not present in the DigMontage. The channels missing from the montage are:\n",
      "\n",
      "['FZ', 'CZ', 'PZ', 'F7', 'F8', 'LEMG', 'A1', 'A2', 'T5', 'T6', 'REMG', 'FP1', 'FP2', 'F3', 'F4', 'C3', 'C4', 'P3', 'P4', 'O1', 'O2', 'T3', 'T4'].\n",
      "\n",
      "Consider using inst.rename_channels to match the montage nomenclature, or inst.set_channel_types if these are not EEG channels, or use the on_missing parameter if the channel positions are allowed to be unknown in your analyses.\n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n",
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: participants.tsv file not found for C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-03_ieeg.edf\n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Reading events from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-04_events.tsv.\n",
      "Reading channel info from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_channels.tsv.\n",
      "Reading electrode coords from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_space-ACPC_electrodes.tsv.\n",
      "Reading 0 ... 7448575  =      0.000 ...  3637.000 secs...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: The number of channels in the channels.tsv sidecar file (230) does not match the number of channels in the raw data file (248). Will not try to set channel names.\n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n",
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: Cannot set channel type for the following channels, as they are missing in the raw data: \n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n",
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: DigMontage is only a subset of info. There are 23 channel positions not present in the DigMontage. The channels missing from the montage are:\n",
      "\n",
      "['FZ', 'CZ', 'PZ', 'F7', 'F8', 'LEMG', 'A1', 'A2', 'T5', 'T6', 'REMG', 'FP1', 'FP2', 'F3', 'F4', 'C3', 'C4', 'P3', 'P4', 'O1', 'O2', 'T3', 'T4'].\n",
      "\n",
      "Consider using inst.rename_channels to match the montage nomenclature, or inst.set_channel_types if these are not EEG channels, or use the on_missing parameter if the channel positions are allowed to be unknown in your analyses.\n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n",
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: participants.tsv file not found for C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-04_ieeg.edf\n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Extracting EDF parameters from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\derivatives\\clean\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-01_desc-clean_ieeg.edf...\n",
      "EDF file detected\n",
      "Setting channel info structure...\n",
      "Creating raw.info structure...\n",
      "Reading events from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\derivatives\\clean\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-01_desc-clean_events.tsv.\n",
      "Reading channel info from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\derivatives\\clean\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-01_desc-clean_channels.tsv.\n",
      "Reading electrode coords from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\derivatives\\clean\\sub-D0103\\ieeg\\sub-D0103_acq-01_space-ACPC_electrodes.tsv.\n",
      "Not fully anonymizing info - keeping his_id, sex, and hand info\n",
      "Extracting EDF parameters from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\derivatives\\clean\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-02_desc-clean_ieeg.edf...\n",
      "EDF file detected\n",
      "Setting channel info structure...\n",
      "Creating raw.info structure...\n",
      "Reading events from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\derivatives\\clean\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-02_desc-clean_events.tsv.\n",
      "Reading channel info from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\derivatives\\clean\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-02_desc-clean_channels.tsv.\n",
      "Reading electrode coords from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\derivatives\\clean\\sub-D0103\\ieeg\\sub-D0103_acq-01_space-ACPC_electrodes.tsv.\n",
      "Not fully anonymizing info - keeping his_id, sex, and hand info\n",
      "Extracting EDF parameters from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\derivatives\\clean\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-03_desc-clean_ieeg.edf...\n",
      "EDF file detected\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: Omitted 226 annotation(s) that were outside data range.\n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting channel info structure...\n",
      "Creating raw.info structure...\n",
      "Reading events from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\derivatives\\clean\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-03_desc-clean_events.tsv.\n",
      "Reading channel info from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\derivatives\\clean\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-03_desc-clean_channels.tsv.\n",
      "Reading electrode coords from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\derivatives\\clean\\sub-D0103\\ieeg\\sub-D0103_acq-01_space-ACPC_electrodes.tsv.\n",
      "Not fully anonymizing info - keeping his_id, sex, and hand info\n",
      "Extracting EDF parameters from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\derivatives\\clean\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-04_desc-clean_ieeg.edf...\n",
      "EDF file detected\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: Omitted 228 annotation(s) that were outside data range.\n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting channel info structure...\n",
      "Creating raw.info structure...\n",
      "Reading events from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\derivatives\\clean\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-04_desc-clean_events.tsv.\n",
      "Reading channel info from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\derivatives\\clean\\sub-D0103\\ieeg\\sub-D0103_task-GlobalLocal_acq-01_run-04_desc-clean_channels.tsv.\n",
      "Reading electrode coords from C:\\Users\\jz421\\Box\\CoganLab\\BIDS-1.1_GlobalLocal\\BIDS\\derivatives\\clean\\sub-D0103\\ieeg\\sub-D0103_acq-01_space-ACPC_electrodes.tsv.\n",
      "Not fully anonymizing info - keeping his_id, sex, and hand info\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\io.py:113: RuntimeWarning: Omitted 226 annotation(s) that were outside data range.\n",
      "  new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)\n"
     ]
    }
   ],
   "source": [
    "sub = 'D0103'\n",
    "raw = raw_from_layout(layout, subject=sub, extension=\".edf\", desc=None, preload=True)\n",
    "filt = raw_from_layout(layout.derivatives['derivatives/clean'], subject=sub,\n",
    "                            extension='.edf', desc='clean', preload=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "No projector specified for this dataset. Please consider the method self.add_proj.\n",
      "Effective window size : 1.000 (s)\n",
      "Spectogram using 2048-point FFT on 2048 samples with 0 overlap and hamming window\n",
      "Got 6 parallel jobs after requesting 6\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[Parallel(n_jobs=6)]: Using backend LokyBackend with 6 concurrent workers.\n",
      "[Parallel(n_jobs=6)]: Done   3 out of   6 | elapsed:   40.7s remaining:   40.7s\n",
      "[Parallel(n_jobs=6)]: Done   6 out of   6 | elapsed:   55.2s finished\n",
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\viz\\utils.py:42: UserWarning: This figure was using a layout engine that is incompatible with subplots_adjust and/or tight_layout; not calling subplots_adjust.\n",
      "  fig.subplots_adjust(top=0.85)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "No projector specified for this dataset. Please consider the method self.add_proj.\n",
      "Effective window size : 1.000 (s)\n",
      "Spectogram using 2048-point FFT on 2048 samples with 0 overlap and hamming window\n",
      "Got 6 parallel jobs after requesting 6\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[Parallel(n_jobs=6)]: Using backend LokyBackend with 6 concurrent workers.\n",
      "[Parallel(n_jobs=6)]: Done   3 out of   6 | elapsed:   27.7s remaining:   27.7s\n",
      "[Parallel(n_jobs=6)]: Done   6 out of   6 | elapsed:   39.7s finished\n",
      "C:\\Users\\jz421\\Desktop\\GlobalLocal\\IEEG_Pipelines\\ieeg\\viz\\utils.py:42: UserWarning: This figure was using a layout engine that is incompatible with subplots_adjust and/or tight_layout; not calling subplots_adjust.\n",
      "  fig.subplots_adjust(top=0.85)\n"
     ]
    },
    {
     "ename": "",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31mThe Kernel crashed while executing code in the current cell or a previous cell. \n",
      "\u001b[1;31mPlease review the code in the cell(s) to identify a possible cause of the failure. \n",
      "\u001b[1;31mClick <a href='https://aka.ms/vscodeJupyterKernelCrash'>here</a> for more info. \n",
      "\u001b[1;31mView Jupyter <a href='command:jupyter.viewOutput'>log</a> for further details."
     ]
    }
   ],
   "source": [
    "figure_compare([raw, filt],\n",
    "            labels=[\"Un\", \"\"],\n",
    "            avg=True,\n",
    "            n_jobs=6,\n",
    "            verbose=10,\n",
    "            proj=True,\n",
    "            fmax=250)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "ieeg",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
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   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
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