substantial development.. syncs EEG and ET of all Q1K tasks except NSP, FSP and VS.

Author: jadesjardins

q1k_eeg_et_sync.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -16,12 +16,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
-    "subject_id = '0006'\n",
-    "task = 'ssvep'\n",
+    "#subject_id = '0008'\n",
+    "#task = 'ssvep'\n",
     "bids_root = '.'"
    ]
   },
@@ -32,14 +32,35 @@
    "outputs": [],
    "source": [
     "#read EEG mff data\n",
-    "eeg_raw = mne.io.read_raw_egi('sourcedata/s06/eeg/s06/s06_ssvep_20230313_113128.mff/',preload=True)\n",
+    "eeg_raw = mne.io.read_raw_egi('sourcedata/s06/eeg/s06/s06_plr_20230313_115649.mff/',preload=True)\n",
     "eeg_raw_df = eeg_raw.to_data_frame()\n",
     "\n",
     "#get the EEG events from the stim stim channel\n",
-    "eeg_events = mne.find_events(eeg_raw, stim_channel='STI 014')\n",
+    "#eeg_events = mne.find_events(eeg_raw, stim_channel='STI 014', shortest_event = 1)\n",
+    "eeg_events = mne.find_events(eeg_raw, shortest_event = 1)\n",
     "\n",
+    "#create the event dictionary..\n",
+    "eeg_event_dict = qst.get_event_dict(eeg_raw,eeg_events)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "#handle task specific EEG event interpretation..\n",
-    "eeg_events, eeg_stims, eeg_iti, eeg_event_dict = qst.eeg_event_test(eeg_events,task_name='ssvep')"
+    "eeg_events, eeg_stims, eeg_iti, eeg_event_dict = qst.eeg_event_test(eeg_events,eeg_event_dict,task_name='plr')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fig=px.scatter(x=eeg_events[:,0],y=eeg_events[:,2])\n",
+    "fig.show()"
    ]
   },
   {
@@ -49,11 +70,29 @@
    "outputs": [],
    "source": [
     "#read the asc eye tracking data and convert it to a dataframe\n",
-    "et_raw = mne.io.read_raw_eyelink ('sourcedata/s06/eyetracking/s06ssvep.asc')\n",
+    "et_raw = mne.io.read_raw_eyelink ('sourcedata/s06/eyetracking/s06plr.asc')\n",
     "et_raw_df = et_raw.to_data_frame()\n",
     "\n",
+    "#get the events from the annotation structure\n",
+    "et_annot_events, et_annot_event_dict = mne.events_from_annotations(et_raw)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Number of eye-tracking stimulus onset DIN events: 32\n"
+     ]
+    }
+   ],
+   "source": [
     "#handle task specific ET event interpretation..\n",
-    "et_events, et_stims, et_iti = qst.et_event_test(et_raw_df,task_name='ssvep')"
+    "et_event_raw_df, et_events, et_stims, et_iti = qst.et_event_test(et_raw_df,task_name='plr')"
    ]
   },
   {
@@ -62,7 +101,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "eeg_et_raw = qst.eeg_et_combine(eeg_raw, et_raw, eeg_stims, et_stims)"
+    "fig=px.scatter(x=et_events['index'],y=et_events['DIN_diff'])\n",
+    "fig.show()"
    ]
   },
   {
@@ -71,8 +111,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "scalings=dict(eyegaze=1e1)\n",
-    "eeg_et_raw.plot(events=eeg_events,scalings=scalings)"
+    "qst.show_sync_offsets(eeg_stims,et_stims)"
    ]
   },
   {
@@ -81,17 +120,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "bids_path = mne_bids.BIDSPath(subject=subject_id, task=task, root=bids_root)\n",
-    "mne_bids.write_raw_bids(eeg_raw, bids_path, events=eeg_events, event_id=eeg_event_dict, overwrite=True, allow_preload=True, format='EDF')"
+    "eeg_et_raw = qst.eeg_et_combine(eeg_raw, et_raw, eeg_stims, et_stims)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 18,
    "metadata": {},
    "outputs": [],
    "source": [
-    "qst.show_sync_offsets(eeg_stims,et_stims)"
+    "eeg_et_raw_df = eeg_et_raw.to_data_frame()"
    ]
   },
   {
@@ -100,8 +138,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#plot the event latencies\n",
-    "fig = px.scatter(x=eeg_events[:,0],y=eeg_events[:,2])\n",
+    "fig=px.line(x=eeg_et_raw_df['time'],y=eeg_et_raw_df['pupil_right'])\n",
     "fig.show()"
    ]
   },
@@ -111,9 +148,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#show the stimulus DIN event inter-trial intervals... this should be replicated in the eye-tracking recording..\n",
-    "fig = px.line(y=eeg_iti)\n",
-    "fig.show()"
+    "scalings=dict(eyegaze=1e2)\n",
+    "eeg_et_raw.plot(events=eeg_events,duration=4,scalings=scalings)\n",
+    "#eeg_et_raw.plot(scalings=scalings)"
    ]
   },
   {
@@ -122,7 +159,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig = px.scatter(x=et_events['index'],y=et_events['DIN'])\n",
+    "fig=px.scatter(x=et_events['index'],y=et_events['DIN_diff'])\n",
     "fig.show()"
    ]
   },
@@ -132,7 +169,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig = px.scatter(x=et_events['index'],y=et_events['DIN_diff'])\n",
+    "fig=px.scatter(x=et_events['time'],y=et_events['index'].diff())\n",
     "fig.show()"
    ]
   },
@@ -142,7 +179,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig = px.scatter(x=et_events['index'],y=et_events['index'].diff())\n",
+    "fig=px.line(x=et_raw_df['time'],y=et_raw_df['DIN'])\n",
     "fig.show()"
    ]
   },
@@ -152,7 +189,29 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig = px.line(y=et_iti)\n",
+    "scalings=dict(eyegaze=1e5)\n",
+    "eeg_et_raw.plot(events=eeg_events,duration=4,scalings=scalings)\n",
+    "#eeg_et_raw.plot(scalings=scalings)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "bids_path = mne_bids.BIDSPath(subject=subject_id, task=task, root=bids_root)\n",
+    "mne_bids.write_raw_bids(eeg_raw, bids_path, events=eeg_events, event_id=eeg_event_dict, overwrite=True, allow_preload=True, format='EDF')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#plot the event latencies\n",
+    "fig = px.scatter(x=eeg_events[:,0],y=eeg_events[:,2])\n",
     "fig.show()"
    ]
   },
@@ -162,7 +221,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig = px.scatter(y=eeg_et_offset)\n",
+    "#show the stimulus DIN event inter-trial intervals... this should be replicated in the eye-tracking recording..\n",
+    "fig = px.line(y=eeg_iti)\n",
     "fig.show()"
    ]
   }
@@ -185,7 +245,12 @@
    "pygments_lexer": "ipython3",
    "version": "3.8.10"
   },
-  "orig_nbformat": 4
+  "orig_nbformat": 4,
+  "vscode": {
+   "interpreter": {
+    "hash": "4d51abd469969a131aa91b4c30bbe09eccdda015d2c1385281ae2bb665bb8f08"
+   }
+  }
  },
  "nbformat": 4,
  "nbformat_minor": 2