FIX: Tensorization script no longer worked for pngs where there is no… #566
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… ZIP_FOLDER, and could not handle it if the ZIP_FOLDER was not the first python arg
abaumann
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May 6, 2024
scripts/tensorize.sh
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| find $ZIP_FOLDER -name '*.zip' | xargs -I {} basename {} | cut -d '_' -f 1 \ | ||
| | awk -v min="$MIN_SAMPLE_ID" -v max="$MAX_SAMPLE_ID" '$1 > min && $1 < max' \ | ||
| | sort | uniq > /tmp/ml4h/sample_ids_trimmed.txt | ||
| elif [ -e "$MANIFEST" ]; then |
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is it possible for people to pass both --zip_folder and --app_csv args? If so, is it ok that this will use the zip_folder args over the manifest if that is the case?
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Thanks! You convinced me to fix this up a bit better =) I've made some changes that more explicity refer to whether a 'tensorize' or 'tensorize_pngs' job is running, so that the right data is pulled from. There are also modes to 'tensorize_ecg_pngs' and 'tensorize_partners', but Sam says no one has done that for a while and we can just have the script fail in those cases.
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… ZIP_FOLDER, and could not handle it if the ZIP_FOLDER was not the first python arg