2024-02-22 updates (#566)

This PR:

- Updates the documentation for the tomcat.ivilab.org to describe the addition of the new sync and vocalic feature tables, updates to the existing tables, fixing of a couple of minor timestamp issues, and acknowledging the new ARL grant.
-  Updates the entity-relationship diagram for the database.
- Updates the `docker-compose.prod.yml`to use `inspect-data.json` instead of `inspect_file.json`
- Updates a couple of scripts to point to Paulo's subdirectory in `/space` instead of the users
- Updates the copy_screenshots_to_server script, and adds a .sh extension

human_experiments/datasette_interface/bin/launch_dev

@@ -3,7 +3,7 @@
 
 set -euo pipefail
 datasette \
-    /space/${USER}/tomcat/tomcat.db \
+    /space/paulosoares/tomcat/tomcat.db \
     --metadata metadata.yml \
     --reload \
     --template-dir=templates \

human_experiments/datasette_interface/bin/update_inspect_file

@@ -1,4 +1,4 @@
 #!/usr/bin/env bash
 
 # Update inspect-data.json
-time datasette inspect /space/$USER/tomcat/tomcat.db > inspect-data.json
+time datasette inspect /space/paulosoares/tomcat/tomcat.db > inspect-data.json

human_experiments/datasette_interface/docker-compose.prod.yml

@@ -17,7 +17,7 @@ services:
         --metadata /repo/metadata.yml
         --template-dir /repo/templates
         --plugins-dir /repo/plugins
-        --inspect-file /repo/inspect_file.json
+        --inspect-file /repo/inspect-data.json
         --static assets:/repo/static
         --setting sql_time_limit_ms 10000
         --setting facet_time_limit_ms 10000

human_experiments/datasette_interface/inspect-data.json

@@ -0,0 +1,78 @@
+{
+  "tomcat": {
+    "hash": "e658dd324b33f88e17a02a77b45a7e16f0807b719ddeba440b552968efb54eae",
+    "size": 460870664192,
+    "file": "/space/paulosoares/tomcat/tomcat.db",
+    "tables": {
+      "task": {
+        "count": 9
+      },
+      "modality": {
+        "count": 3
+      },
+      "group_session": {
+        "count": 40
+      },
+      "participant": {
+        "count": 114
+      },
+      "station": {
+        "count": 4
+      },
+      "rest_state_task": {
+        "count": 40
+      },
+      "ping_pong_competitive_task_observation": {
+        "count": 647242
+      },
+      "eeg_device": {
+        "count": 120
+      },
+      "affective_task_event": {
+        "count": 14586
+      },
+      "eeg_raw": {
+        "count": 320700934
+      },
+      "ping_pong_cooperative_task_observation": {
+        "count": 323806
+      },
+      "finger_tapping_task_observation": {
+        "count": 99875
+      },
+      "data_validity": {
+        "count": 3060
+      },
+      "gaze_raw": {
+        "count": 129554477
+      },
+      "minecraft_mission": {
+        "count": 100
+      },
+      "minecraft_testbed_message": {
+        "count": 6370941
+      },
+      "screen_capture": {
+        "count": 4100470
+      },
+      "audio_vocalics": {
+        "count": 33049497
+      },
+      "eeg_sync": {
+        "count": 124351398
+      },
+      "fnirs_raw": {
+        "count": 6849295
+      },
+      "fnirs_sync": {
+        "count": 125359661
+      },
+      "gsr_sync": {
+        "count": 124351398
+      },
+      "ekg_sync": {
+        "count": 97446792
+      }
+    }
+  }
+}

human_experiments/datasette_interface/templates/base.html

@@ -50,6 +50,7 @@
 
                         <ul class="dropdown-menu" aria-labelledby="navbarDropdownMenuLink">
                             <li><a class="dropdown-item" href="/updates">All updates</a></li>
+                            <li><a class="dropdown-item" href="/updates/2024-02-22">2024-02-22</a></li>
                             <li><a class="dropdown-item" href="/updates/2023-07-19">2023-07-19</a></li>
                             <li><a class="dropdown-item" href="/updates/2023-07-17">2023-07-17</a></li>
                         </ul>

human_experiments/datasette_interface/templates/index.html

@@ -57,9 +57,13 @@ <h2 style="padding-left: 10px; border-left: 10px solid #{{ database.color }}">
 {{ render_markdown("""
 ## Funding Acknowledgment
 
-The creation of this dataset was funded by the Army Research Office and was
+- The creation of this dataset was funded by the Army Research Office and was
 accomplished under Grant Number W911NF-20-1-0002. The grant was awarded through
-the Defense Advanced Research Projects Agency (DARPA). We would also like to
-acknowledge intramural seed funding from the University of Arizona's SensorLab.
+the Defense Advanced Research Projects Agency (DARPA).
+- We would also like to acknowledge intramural seed funding from the University
+of Arizona's SensorLab.
+- Continued support (documentation updates, replying to questions from dataset
+users, etc.) is supported by Army Research Office (ARO) Award Number
+W911NF-24-2-0034.
 """) }}
 {% endblock %}

human_experiments/datasette_interface/templates/pages/updates.html

@@ -12,7 +12,10 @@
 
 ## List of updates
 
-- [2023-07-19](/updates/2023-07-19): This update adds the following:
+- [2024-02-22](/updates/2024-02-22): Added new tables with vocalic data,
+synchronized data, fixed a couple of data issues.
+- [2023-07-19](/updates/2023-07-19): This update adds the following (see
+[here](/updates/2023-07-19) for details):
     - [Data Products document](http://ivilab.cs.arizona.edu/data/tomcat/data_products.pdf),
     which contains descriptions of both the raw
     data (this is primarily meant for internal documentation purposes) and the

human_experiments/datasette_interface/templates/pages/updates/2024-02-22.html

@@ -0,0 +1,90 @@
+{% extends "base.html" %}
+
+{% block body_class %}index{% endblock %}
+
+{% block content %}
+{{ render_markdown(
+"""
+# 2024-02-22 update
+
+## 1. New data
+
+### 1.1 Synchronized physio data tables
+
+Added new tables (`fnirs_sync`, `gsr_sync`, `eeg_sync`, and `ekg_sync`)
+to store preprocessed signals synchronized to a main clock for four modalities
+(fNIRS, GSR, EEG, and EKG) across experiments, with filtering for artifact
+removal. For each experiment, a main clock was defined with start time at 5
+seconds before the beginning of the first task (rest state), end time at 5
+seconds after the end of last task (Minecraft), and frequency at 200 Hz.
+
+The changes are introduced in this PR:
+https://github.com/ml4ai/tomcat/pull/558.
+
+### 1.2 Vocalic features table
+
+Added a table called `audio_vocalics` that contains vocalic features extracted
+using [OpenSMILE](https://github.com/audeering/opensmile/releases/tag/v3.0.0).
+
+### 1.3 Updated `fnirs_raw` table
+
+Expanded fNIRS data by adding raw signals for 760 nm and 850 nm wavelengths to
+the `fnirs_raw` table, in case users wish to transform those into HbO and HbR
+themselves.
+
+### 1.4 Added advisor information
+
+Added a column to the `group_session` table containing information about which
+advisor was present during the trials.
+
+## 2. Timestamp corrections
+
+### 2.1 Timestamp corrections for exp_2023_01_31_14
+
+**Summary**: Corrected Minecraft start/end timestamps for exp_2023_01_31_14
+which had inconsistent dates in the future.
+
+**Explanation**: `exp_2023_01_31_14` had dates for trial start/stop and mission
+stop (same as trial stop due to the absence of a mission stop message in the
+corresponding `.metadata` file) in the past due to inconsistency.  We noticed
+that the code was not taking the most recent trial dates into consideration in
+case of multiple trial start/stop.  We fixed the data processing code and
+updated the dates manually.  The wrong dates were causing the main clock not to
+have any ticks because rest state (with correct timestamp) had timestamp after
+the Minecraft task which is used to compute the final timestamp of the main
+clock when synchronizing signals.
+
+### 2.2 Timestamps for rest state task in exp_2022_12_05_12.
+
+**Summary**: Added start and end timestamps for the rest state task in
+`exp_2022_12_05_12`.
+
+**Explanation**: If there are no start and end timestamps saved in the raw data
+file for the rest state task (prior to 2023-04, the timestamps for the rest
+state task were being saved in a CSV file), we use the file modification date
+as an approximation to the start timestamp when it started and add 300 seconds
+to the start timestamp to obtain the end timestamp. The file is created when
+the task start so the offset should be minimal. So far, only experiment
+`exp_2022_12_05_12` has this issue. We use the start time of the rest state
+when defining the main clock, so having that information is important for us
+not to lose any data.
+
+## 3. Fixed swapped signals for EKG and GSR for some experiments.
+
+Addressed an issue where EKG and GSR signals were swapped in specific
+experiments:
+
+- `exp_2022_09_30_10`
+- `exp_2022_10_04_09` for the `lion` station
+- `exp_2022_10_04_09` for the `tiger` station) by updating the raw EEG data
+processing processing to swap the signals for these specific instances.
+
+## Other updates
+
+- Updated funding acknowledgment section on the landing page to include new
+grant from ARO.
+- Updated entity-relationship diagram.
+
+""")
+}}
+{% endblock %}