ignore invalid minecraft mission (#533)

* ignore invalid minecraft mission

* Update readme

human_experiments/synchronize_signal_task/README.md

@@ -1,3 +1,72 @@
 # Synchronize signal task
 
-This project is for synchronizing EEG and fNIRS signals with task data.
+This project is for synchronizing EEG, EKG, GSR, and fNIRS signals with task data.
+
+## Install dependencies
+
+This project requires Python 3.11.
+
+### Install dependencies with Conda
+
+Ensure that Conda is already installed, then run the following command to install dependencies into a new conda environment
+
+```
+conda conda create -n tomcat-synchronize python=3.11
+conda activate tomcat-synchronize
+pip install -r requirements.txt
+```
+
+### Install dependcies with Pip
+
+You can install the packages using Pip3 in a base environment or an environment created for this project, then run the follow command to install dependencies
+
+```
+pip3 install -r requirements.txt
+```
+
+### Install dependencies manually
+
+If you want to set up environment and install dependencies manually, then you need the following packages
+
+```
+numpy
+scipy
+pandas
+scikit-learn
+mne
+tqdm
+python-dotenv
+python-dateutil
+```
+
+## Set up project
+
+Ensure that you downloaded the ToMCAT raw data [here](tomcat.ivilab.org)
+
+Set the following variables in the `config.py` file:
+
+- `DB_PATH` is the full path to the ToMCAT data you downloaded.
+- `EEG_FILTERED_PATH` is the full path to the ToMCAT filtered EEG data.
+- `FNIRS_FILTERED_PATH` is the full path to the ToMCAT filtered fNIRS data.
+- `NUM_PROCESSES` number of processes you can use to run the data processing in parallel.
+- `OUTPUT_DIR` the full path to where the output will be located.
+
+## Run project
+
+After setting up the `config.py` file, you can launch the program (make sure that you are in the python environment with required dependencies installed):
+
+### Synchronize fNIRS with each task at 10 Hz
+
+```
+python3 process_nirs_10hz.py
+```
+
+### Synchronize EEG-EKG-GSR with each task at 500 Hz
+
+```
+python3 process_eeg_500hz.py
+```
+
+## Output
+
+The program will output synchronized data to the path specified in `output_dir` in `config.py`.

human_experiments/synchronize_signal_task/config.py

@@ -5,7 +5,14 @@
 EEG_FILTERED_PATH = f"/space/{USER}/eeg_filtered"
 FNIRS_FILTERED_PATH = f"/space/{USER}/fnirs_filtered"
 NUM_PROCESSES = 40
-OUTPUT_DIR = "/tomcat/data/derived/drafts/release_2023_08_19_17"
+OUTPUT_DIR = "/tomcat/data/derived/drafts/release_2023_08_20_19"
+
+MINECRAFT_MISSION_BLACKLIST = [
+    "560d4c45-dc45-4e19-bdb3-e4e15021728a",
+    "a48f475f-40b0-46b9-8284-0db267dddb67",
+    "171a8713-a554-4d8e-a4b1-3ec1b728d0a2",
+    "9cde1985-1179-4aac-8b67-1fc60ed65243",
+]
 
 EXPERIMENT_SESSIONS = [
     "exp_2022_09_30_10", "exp_2022_11_01_10", "exp_2022_12_02_15", "exp_2023_02_21_14",

human_experiments/synchronize_signal_task/process_eeg_500hz.py

@@ -37,4 +37,4 @@
     synchronized_task_signals = synchronize_task_signal_all(task_synchronization_info)
 
     output_dir = os.path.join(OUTPUT_DIR, f"eeg_{desired_freq}hz")
-    write_csv_all(synchronized_task_signals, OUTPUT_DIR, NUM_PROCESSES)
+    write_csv_all(synchronized_task_signals, output_dir, NUM_PROCESSES)

human_experiments/synchronize_signal_task/read_data/tasks/minecraft.py

@@ -1,5 +1,6 @@
 import json
 import sqlite3
+from config import MINECRAFT_MISSION_BLACKLIST
 
 import pandas as pd
 
@@ -16,11 +17,22 @@ def _get_testbed_messages(db_path: str, experiment: str, mission: str) -> pd.Dat
     if mission_id is None:
         return None
 
-    mission_id_result = mission_id.fetchone()
+    mission_id_result = mission_id.fetchall()
     if mission_id_result is None or len(mission_id_result) == 0:
         return None
 
-    mission_id = mission_id_result[0]
+    mission_found = False
+    for mission_id_considering in mission_id_result:
+        if mission_id_considering[0] not in MINECRAFT_MISSION_BLACKLIST:
+            mission_id = mission_id_considering[0]
+            mission_found = True
+            break
+
+    if not mission_found:
+        return None
+
+    if len(mission_id) != 36:
+        raise ValueError("Incorrect mission ID length")
 
     query = f"""
             SELECT *