fix_nbc.sh

#!/bin/bash
testing=true
#This script will fix the filenames of any image files generated by the stainer_ui that had a failed barcode reading
#The desired filenames look like [projectName]_[dateAndTimeOfImageCapture]_[indexInSeriesOfAutomaticCaptures]_[sectionID]_section.png, for example, vnc1_1513740272_c36_2243_section.png
#Bad file names will look like vnc1_1513740272_c36_nbc_section.png

#Step 1: Check if projectNames are properly set -- this is important because strings are split by the _ character, and so if some files have projectName 'vnc1' and others have projectName 'no_project_name_set', there will be different numbers of _ characters in different file names, and this will cause problems. This could be coded around, but I provide a simple rename command to fix this
if grep -q no_project_name_set <<< `ls $1`
then
   echo Go fix your project names first with a rename command along the lines of:
   echo rename \'s/no_project_name_set/yourSamplesName/\' yourSampleFolder/*
   exit
fi

#Step 2: Get a list of section.png files, and determine how many _ characters are in the file name of the first image. The script assumes that all filenames will have that many _ characters in them. This should probably be explicitly checked, or changed to be more flexible

sectionList=`ls $1/*section.png`
sectionArr=($sectionList)

#Find which column has the section number
onlyDividers=$(tr -dc '_' <<< ${sectionArr[0]})
columnWithSectNum=${#onlyDividers}

#Code version 2: Slightly less generalizable, definitely easier to see that it's doing the right thing for the vnc1 images
for i in ${!sectionArr[@]}; do
   sectNum=$(cut -d'_' -f $columnWithSectNum <<< ${sectionArr[$i]})
   echo $i $(($sectNum+$i)) $(($sectNum-$i)) ${sectionArr[$i]}
   if [[ $(($sectNum+$i)) -ne 4443 ]]; then
      read -rsn1 -p "Press y to change this sectNum to $((4443-$i))" userInput
      echo ""
      if [[ $userInput != 'y' ]]; then continue; fi
      echo Changing
      perlSubstitutionExpression=s/${sectNum}_section.png/$((4443-$i))_section.png/
      if $testing; then
         echo cp ${sectionArr[$i]} ${sectionArr[$i]}.old
         echo rename $perlSubstitutionExpression ${sectionArr[$i]}
      else
         cp ${sectionArr[$i]} ${sectionArr[$i]}.old
         rename $perlSubstitutionExpression ${sectionArr[$i]}
      fi
   fi
done


if [[ 1 -eq 0 ]]; then

#Step 4: Find filenames with 'nbc' in them, and rename them 
difference=''
for i in ${!sectionArr[@]}; do
   echo $i ${sectionArr[$i]}
   if [[ $i -lt 2 ]]; then continue; fi
   sectionNumPreviousImage=$(cut -d'_' -f $columnWithSectNum <<< ${sectionArr[$(($i-1))]})
   sectionNumTwoImagesBack=$(cut -d'_' -f $columnWithSectNum <<< ${sectionArr[$(($i-2))]})
   currentDifference=$(($sectionNumPreviousImage-$sectionNumTwoImagesBack))
   if [[ $currentDifference -ne 1 ]] && [[ $currentDifference -ne -1 ]]; then
      echo Non-sequential images found at ${sectionArr[$(($i-1))]}, skipping;
      continue
   fi
   if [[ $(cut -d'_' -f $columnWithSectNum <<< ${sectionArr[$i]}) = nbc ]]; then
      if [[ -z ${difference:+x} ]]; then
         difference=$currentDifference
         for fn in ${sectionArr[@]:$(($i-2)):5}; do echo $fn; done
         #ls $1/*section.png | head
         if [[ $difference -eq 1 ]]; then
            read -rsn1 -p "The section IDs seem to be counting up. Press y to confirm or any other key to quit" pressedKey
            echo
            if [[ $pressedKey != 'y' ]]; then break; fi
         fi
         if [[ $difference -eq -1 ]]; then
            read -rsn1 -p "The section IDs seem to be counting down. Press y to confirm or any other key to quit" pressedKey
            echo
            if [[ $pressedKey != 'y' ]]; then break; fi
         fi
      fi
      if [[ $currentDifference -ne $difference ]]; then
         echo Something seems wrong around files ${sectionArr[$(($i-1))]}. Did the section indexing switch directions for some reason? Please go fix it by hand. Aborting.
         break
      fi
      echo $sectionNumTwoImagesBack $sectionNumPreviousImage $currentDifference $difference
      perlSubstitutionExpression=s/nbc_section.png/$(($sectionNumPreviousImage+$difference))_section.png/

      if $testing; then
         echo cp ${sectionArr[$i]} ${sectionArr[$i]}.old
         echo rename $perlSubstitutionExpression ${sectionArr[$i]}
      else
         cp ${sectionArr[$i]} ${sectionArr[$i]}.old
         rename $perlSubstitutionExpression ${sectionArr[$i]}
      fi

      #Refresh the sectionList and sectionArr, so that the just-renamed file can be used to rename the next file
      sectionList=`ls $1/*section.png`
      sectionArr=($sectionList)
   fi
done
fi