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Improve run.sh script #44

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Jan 24, 2025
Merged

Improve run.sh script #44

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19 changes: 9 additions & 10 deletions run.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -6,9 +6,9 @@
docker pull [image_id]

1.a.1. If use a GPU:
docker run -it --gpus device=0 -v [repo path]:/codabench [image_id] /bin/bash
docker run -it --gpus device=0 -v [repo_path]:/codabench [image_id] /bin/bash
1.a.2. If only use CPU:
docker run -it -v [repo path]:/codabench [image_id] /bin/bash
docker run -it -v [repo_path]:/codabench [image_id] /bin/bash

cd codabench

Expand All @@ -34,12 +34,12 @@ export baseline_model="bioclip"
export task_folder="${data_split}_${baseline_model}"


## create folder structure
# Create folder structure
if [[ "$task_type" == *"folder"* ]]; then
mkdir -p sample_result_submission/$task_folder/ref
mkdir -p sample_result_submission/$task_folder/res
export ref_path="/home/wu.5686/imageo/challenge/reference_data/ref_$data_split.csv"
cp $ref_path sample_result_submission/$task_folder/ref
export ref_path="[the path of folder you put the simulated ground truth csv file]/ref_$data_split.csv"
cp $ref_path sample_result_submission/$task_folder/ref # Put the simulated ground truth csv file in the ref folder.
fi

: <<'END_COMMENT'
Expand All @@ -51,11 +51,10 @@ sample_result_submission
-- res
END_COMMENT

## get the predictions
# Get the predictions
if [[ "$task_type" == *"predict"* ]]; then
export input_dir="input_data/$data_split"
# export input_dir="/local/scratch/wu.5686/anomaly_challenge/input_data/$data_split"
export output_dir="sample_result_submission/$task_folder/res"
export input_dir="input_data/$data_split" # This is the directory you put the images in.
export output_dir="sample_result_submission/$task_folder/res" # The prediction file will output to this directory.
export program_dir="ingestion_program"
if [ "$baseline_model" == "bioclip" ]; then
export submission_dir="baselines/BioCLIP_code_submission"
Expand All @@ -69,7 +68,7 @@ if [[ "$task_type" == *"predict"* ]]; then
python3 ingestion_program/ingestion.py $input_dir $output_dir $program_dir $submission_dir
fi

## score the predictions
# Score the predictions
if [[ "$task_type" == *"evaluate"* ]]; then
export input_dir="sample_result_submission/$task_folder"
export output_dir="sample_result_submission/$task_folder"
Expand Down