Code for processing TLAE dataset

bayes_ca/data/tlae-embeddings.py

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+import json
+from pathlib import Path
+
+import click
+import whisper
+import numpy as np
+from sentence_transformers import SentenceTransformer
+
+
+@click.command()
+@click.option("--file")
+@click.option("--datadir")
+@click.option("--outdir")
+def main(file, datadir, outdir):
+    """
+    This script assumes you have access to the copyrighted stimuli
+    and that you are running in an environment with SBert (i.e.,
+    sentence-transformers) and OpenAI's Whisper installed.
+
+    Params
+    ------
+    file : str
+        Stimulus file to transcribe and generate embedding
+    datadir : str
+        Local path to the stimuli files
+    outdir : str
+        Local path to store transcriptions and embeddings
+    """
+    model = whisper.load_model("medium.en")
+    result = model.transcribe(str(Path(datadir, file)))
+
+    whisper_outname = "whisper-" + str(Path(file).with_suffix(".json"))
+    with open(Path(outdir, whisper_outname), "w") as outfile:
+        json.dump(result, outfile, indent=4)
+
+    sentences = result["text"].split(". ")
+    model = SentenceTransformer("all-mpnet-base-v2")
+
+    embeddings = model.encode(sentences)
+    sbert_outname = Path(outdir, f"sbert-{whisper_outname}")
+    np.save(sbert_outname, embeddings, allow_pickle=False)
+
+    return
+
+
+if __name__ == "__main__":
+    main()

bayes_ca/data/tlae-fmriprep.sh

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+#!/bin/bash
+#
+#SBATCH --job-name=tlae_fMRIPrep
+#SBATCH --output=tlae_fmriprep.%j.out
+#SBATCH --time=1-00:00
+#SBATCH --cpus-per-task=16
+#SBATCH --mem-per-cpu=8GB
+#SBATCH --array=0-25
+#SBATCH -p russpold,owners
+
+# Define directories
+
+DATADIR=$OAK/users/emdupre/think-like-an-expert/ds003233
+OUTDIR=$SCRATCH/think-like-an-expert
+SIFDIR=$OAK/users/emdupre/think-like-an-expert/
+LICENSE=$HOME/submission_scripts
+
+# Begin work section
+subj_list=(`find $DATADIR -maxdepth 1 -type d -name 'sub-s*' -printf '%f\n' | sort -n -ts -k2.1`)
+sub="${subj_list[$SLURM_ARRAY_TASK_ID]}"
+echo "SUBJECT_ID: " $sub
+
+singularity run --cleanenv -B ${DATADIR}:/data:ro \
+	-B ${OUTDIR}:/out \
+	-B ${LICENSE}/license.txt:/license/license.txt:ro \
+	${SIFDIR}/fmriprep-23-2-0.sif \
+	/data /out participant \
+    --participant-label ${sub} \
+	--output-space fsaverage5 MNI152NLin2009cAsym:res-2 \
+	-w /out/workdir \
+	--notrack \
+    --fs-license-file /license/license.txt