a b/scripts/pull_n_chop_glom.sh 

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#!/bin/bash





  
  

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#cell#





  
  

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# COPY the data to local disk





  
  

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# sudo chown -R dlituiev /home/dlituiev/.gsutil/tracker-files





  
  

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TMPDIR=/tmp/kidney





  
  

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XMLFILELIST=../tables/deidentified_glom_xmls.list





  
  

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mkdir -p $TMPDIR 





  
  

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LINE=2





  
  

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for LINE in `seq 1 83`





  
  

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do





  
  

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    # PREV_SLIDEID=$(head  /home/dlituiev/metadata/xmlfiles.list | sed -n -e $((${LINE}-1))p | sed 's/\.xml//' )





  
  

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    # rm "$HOME/tmpdata/${PREV_SLIDEID}.svs"





  
  

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    SLIDEID=$(cat  $XMLFILELIST | sed -n -e ${LINE}p | sed 's/\.xml//' ) || exit 1





  
  

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    echo -e "SLIDE ID:\t$SLIDEID"





  
  

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    SVS="$TMPDIR/${SLIDEID}.svs"





  
  

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    XML="$TMPDIR/${SLIDEID}.xml"





  
  

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    if [ -a "$SVS" ] ; then





  
  

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        echo -e "${SVS}\talready exists"





  
  

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    else





  
  

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        gsutil cp gs://kidney-rejection/${SLIDEID}.xml $TMPDIR  && \





  
  

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        gsutil cp gs://kidney-rejection/${SLIDEID}.svs $TMPDIR





  
  

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    fi





  
  

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    python3 $PWD/sample_from_slide.py --data-root "../data/glom" $XML && rm $SVS





  
  

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done





  
  

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# exit 1





  
  

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#rm -rf $TMPDIR





  
  

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# LINK images for binary classification (inflammation / normal)