From 9c185d49a27c624d84840b2ad38a78df6ace2d45 Mon Sep 17 00:00:00 2001
From: Patrick McGuire <mcguirepr89@gmail.com>
Date: Wed, 29 Sep 2021 17:23:35 -0400
Subject: [PATCH] added support for a custom_species_list.txt file Added
 confidence score to extraction file

---
 scripts/birdnet_analysis.sh       | 15 +++++++++++++--
 scripts/extract_new_birdsounds.sh |  6 +++++-
 2 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/scripts/birdnet_analysis.sh b/scripts/birdnet_analysis.sh
index 04001ca..eedae8b 100755
--- a/scripts/birdnet_analysis.sh
+++ b/scripts/birdnet_analysis.sh
@@ -2,6 +2,7 @@
 # Runs BirdNET in virtual environment
 #set -x
 source /etc/birdnet/birdnet.conf
+CUSTOM_LIST="/home/pi/BirdNET-Lite/custom_species_list.txt"
 DAYS=(
 "2 days ago"
 "yesterday"
@@ -47,7 +48,7 @@ run_analysis() {
   WEEK=$(date --date="${2}" +"%U")
   cd ${HOME}/BirdNET-Lite || exit 1
   for i in "${files[@]}";do
-    if [ -f ${1}/${i} ];then
+    if [ -f ${1}/${i} ] && [ ! -f ${CUSTOM_LIST} ];then
       python3 analyze.py \
         --i "${1}/${i}" \
         --o "${1}/${i}.csv" \
@@ -56,7 +57,17 @@ run_analysis() {
         --week "${WEEK}" \
         --overlap "${OVERLAP}" \
         --min_conf "${CONFIDENCE}"
-    fi
+    elif [ -f ${1}/${i} ] && [ -f ${CUSTOM_LIST} ];then
+      python3 analyze.py \
+        --i "${1}/${i}" \
+        --o "${1}/${i}.csv" \
+        --lat "${LATITUDE}" \
+        --lon "${LONGITUDE}" \
+        --week "${WEEK}" \
+        --overlap "${OVERLAP}" \
+        --min_conf "${CONFIDENCE}" \
+	--custom_list "${CUSTOM_LIST}"
+   fi
   done
 }
 
diff --git a/scripts/extract_new_birdsounds.sh b/scripts/extract_new_birdsounds.sh
index c018d8e..d9644ca 100755
--- a/scripts/extract_new_birdsounds.sh
+++ b/scripts/extract_new_birdsounds.sh
@@ -69,7 +69,11 @@ for h in "${SCAN_DIRS[@]}";do
             | awk -F\; '!/birdnet/{print $4}')""
     SCIENTIFIC_NAME=""$(echo ${line} \
             | awk -F\; '!/birdnet/{print $3}')""
-    NEWFILE="${COMMON_NAME// /_}-${OLDFILE}"
+    CONFIDENCE=""$(echo ${line} \
+	    | awk -F\; '{print $5}' \
+	    | cut -d'.' -f2)""
+    CONFIDENCE_SCORE="${CONFIDENCE:0:2}%"
+    NEWFILE="${COMMON_NAME// /_}-${CONFIDENCE_SCORE}-${OLDFILE}"
     NEWSPECIES_BYDATE="${EXTRACTED}/By_Date/${DATE}/${COMMON_NAME// /_}"
     NEWSPECIES_BY_COMMON="${EXTRACTED}/By_Common_Name/${COMMON_NAME// /_}"
     NEWSPECIES_BY_SCIENCE="${EXTRACTED}/By_Scientific_Name/${SCIENTIFIC_NAME// /_}"