updating references to old repo to new repo

2021-09-28 14:48:25 -04:00
parent 7d31737f03
commit bc2d3df898
42 changed files with 3078 additions and 217 deletions
@@ -0,0 +1,158 @@
+#!/usr/bin/env bash
+# Exit when any command fails
+#set -x
+set -e
+# Keep track of the last executed command
+trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG
+# Echo an error message before exiting
+trap 'echo "\"${last_command}\" command exited with code $?."' EXIT
+# Remove temporary file
+trap 'rm -f $TMPFILE' EXIT
+
+source /etc/birdnet/birdnet.conf
+
+# Set Variables
+TMPFILE=$(mktemp)
+# SCAN_DIRS are all directories marked "Analyzed"
+SCAN_DIRS=($(find ${ANALYZED} -type d | sort ))
+
+# This sets our while loop integer iterator 'a' -- it first checks whether
+# there are any extractions, and if so, this instance of the extraction will
+# start the 'a' value where the most recent instance left off.
+# Ex: If the last extraction file is 189-%date%species.wav, 'a' will be 190.
+# Else, 'a' starts at 1
+if [ "$(find ${EXTRACTED} -name '*.wav' | wc -l)" -ge 1 ];then
+  a=$(( $( find "${EXTRACTED}" -name '*.wav' \
+    | awk -F "/" '{print $NF}' \
+    | cut -d'-' -f1 \
+    | sort -n \
+    | tail -n1 ) + 1 ))
+else
+  a=1
+fi
+
+echo "Starting numbering at ${a}"
+
+for h in "${SCAN_DIRS[@]}";do
+  echo "Creating the TMPFILE"
+  # The TMPFILE is created from each "Selection" txt file BirdNET creates
+  # within each "Analyzed" directory
+  #  Field 1: Original WAVE file name
+  #  Field 2: Extraction start time in seconds
+  #  Field 3: Extraction end time in seconds
+  #  Field 4: New WAVE file name to use
+  #  Field 5: The species name
+  # Iterates over each "Analyzed" directory
+  for i in $(find ${h} -name '*txt' | sort );do 
+    # Iterates over each '.txt' file found in each "Analyzed" directory
+    # to create the TMPFILE
+    sort -k 6n "$i" \
+    | awk '/Spect/ {print}' \
+    >> $TMPFILE
+  done
+
+  # The extraction reads each line of the TMPFILE and sets the variables ffmpeg
+  # will use.
+  while read -r line;do
+    a=$a
+    DATE="$(echo "${line}" \
+	   | awk '{print $5}' \
+	   | awk -F- '{print $1"-"$2"-"$3}')"
+    OLDFILE="$(echo "${line}" | awk '{print $5}')" 
+    START="$(echo "${line}" | awk '{print $6}')" 
+    END="$(echo "${line}" | awk '{print $7}')" 
+    SPECIES=""$(echo ${line//\'} \
+	      | awk '{for(i=11;i<=NF;++i)printf $i""FS ; print ""}' \
+	      | cut -d'0' -f1 \
+	      | xargs)""
+    NEWFILE="${SPECIES// /_}-${OLDFILE}" 
+    NEWSPECIES_BYDATE="${EXTRACTED}/By_Date/${DATE}/${SPECIES// /_}"
+    NEWSPECIES_BYSPEC="${EXTRACTED}/By_Species/${SPECIES// /_}"
+
+    # If the extracted file already exists, increment the 'a' variable once
+    # but move onto the next line of the TMPFILE for extraction.
+    if [[ -f "${NEWSPECIES_BYDATE}/${a}-${NEWFILE}" ]];then
+      echo "Extraction exists. Moving on"
+      a=$((a+1))
+      continue
+    fi
+
+
+    echo "Checking for ${h}/${OLDFILE}"
+    # Before extracting the "Selection," the script checks to be sure the
+    # original WAVE file still exists.
+    [[ -f "${h}/${OLDFILE}" ]] || continue
+
+
+    echo "Checking for ${NEWSPECIES_BYDATE}"
+    # If a directory does not already exist for the species (by date),
+    # it is created
+    [[ -d "${NEWSPECIES_BYDATE}" ]] || mkdir -p "${NEWSPECIES_BYDATE}"
+
+
+    echo "Checking for ${NEWSPECIES_BYSPEC}"
+    # If a directory does not already exist for the species (by-species),
+    # it is created.
+    [[ -d "${NEWSPECIES_BYSPEC}" ]] || mkdir -p "${NEWSPECIES_BYSPEC}"
+
+
+    # If there are already 20 extracted entries for a given species
+    # for today, remove the oldest file and create the new one.
+    if [[ "$(find ${NEWSPECIES_BYDATE} | wc -l)" -ge 21 ]];then
+      echo "20 ${SPECIES}s, already! Removing the oldest by-date and making a new one"
+      cd ${NEWSPECIES_BYDATE} || exit 1
+      ls -1t . | tail -n +21 | xargs -r rm -vv
+    fi   
+
+    echo "Extracting audio . . . "
+    # If the above tests have passed, then the extraction happens.
+    # After creating the extracted files by-date, and a directory tree 
+    # structured by-species, symbolic links are made to populate the new 
+    # directory.
+
+    ffmpeg -hide_banner -loglevel error -nostdin -i "${h}/${OLDFILE}" \
+      -acodec copy -ss "${START}" -to "${END}"\
+        "${NEWSPECIES_BYDATE}/${a}-${NEWFILE}"
+    if [[ "$(find ${NEWSPECIES_BYSPEC} | wc -l)" -ge 21 ]];then
+      echo "20 ${SPECIES}s, already! Removing the oldest by-species and making a new one"
+      cd ${NEWSPECIES_BYSPEC} || exit 1
+      ls -1t . | tail -n +21 | xargs -r rm -vv
+      ln -fs "${NEWSPECIES_BYDATE}/${a}-${NEWFILE}"\
+        "${NEWSPECIES_BYSPEC}/${a}-${NEWFILE}"
+      echo "Success! New extraction for ${SPECIES}"
+    else
+      ln -fs "${NEWSPECIES_BYDATE}/${a}-${NEWFILE}"\
+        "${NEWSPECIES_BYSPEC}/${a}-${NEWFILE}"
+    fi   
+
+
+    # Finally, 'a' is incremented by one to allow multiple extractions per
+    # species per minute.
+    a=$((a + 1))
+
+  done < "${TMPFILE}"
+  
+  echo -e "\n\n\nFINISHED!!! Processed extractions for ${h}"
+  # Once each line of the TMPFILE has been processed, the TMPFILE is emptied
+  # for the next iteration of the for loop.
+  >"${TMPFILE}"
+
+  # Rename files that have been processed so that they are not processed on the
+  # next extraction.
+  [[ -d "${PROCESSED}" ]] || mkdir "${PROCESSED}"
+  echo "Moving processed files to ${PROCESSED}"
+  mv -v ${h}/* ${PROCESSED} || continue
+done
+
+echo "Linking Processed files to "${EXTRACTED}/Processed" web directory"
+# After all audio extractions have taken place, a directory is created to house
+# the original WAVE and .txt files used for this extraction processs.
+if [[ ! -L ${EXTRACTED}/Processed ]] || [[ ! -e ${EXTRACTED}/Processed ]];then
+  ln -sf ${PROCESSED} ${EXTRACTED}/Processed
+fi
+  
+
+
+# That's all!
+echo "Finished -- the extracted sections are in:
+$(find -L ${EXTRACTED} -maxdepth 1)"