adding include_list and exclude_list to analyze.py and

birdnet_analysis.sh

analyze.py

@@ -17,10 +17,8 @@ import math
 import time
 from decimal import Decimal
 import json
-###############################################################################    
 import requests
 import mysql.connector
-###############################################################################
 import datetime
 import pytz
 from tzlocal import get_localzone
@@ -185,14 +183,15 @@ def writeResultsToFile(detections, min_conf, path):
         rfile.write('Start (s);End (s);Scientific name;Common name;Confidence\n')
         for d in detections:
             for entry in detections[d]:
-                if entry[1] >= min_conf and (entry[0] in WHITE_LIST or len(WHITE_LIST) == 0):
+                if entry[1] >= min_conf and ((entry[0] in INCLUDE_LIST or len(INCLUDE_LIST) == 0) and (entry[0] not in EXCLUDE_LIST or len(EXCLUDE_LIST) == 0) ):
                     rfile.write(d + ';' + entry[0].replace('_', ';') + ';' + str(entry[1]) + '\n')
                     rcnt += 1
     print('DONE! WROTE', rcnt, 'RESULTS.')
 
 def main():
 
-    global WHITE_LIST
+    global INCLUDE_LIST
+    global EXCLUDE_LIST
 
     # Parse passed arguments
     parser = argparse.ArgumentParser()
@@ -204,7 +203,8 @@ def main():
     parser.add_argument('--overlap', type=float, default=0.0, help='Overlap in seconds between extracted spectrograms. Values in [0.0, 2.9]. Defaults tp 0.0.')
     parser.add_argument('--sensitivity', type=float, default=1.0, help='Detection sensitivity; Higher values result in higher sensitivity. Values in [0.5, 1.5]. Defaults to 1.0.')
     parser.add_argument('--min_conf', type=float, default=0.1, help='Minimum confidence threshold. Values in [0.01, 0.99]. Defaults to 0.1.')   
-    parser.add_argument('--custom_list', default='', help='Path to text file containing a list of species. Not used if not provided.')
+    parser.add_argument('--include_list', default='', help='Path to text file containing a list of included species. Not used if not provided.')
+    parser.add_argument('--exclude_list', default='', help='Path to text file containing a list of excluded species. Not used if not provided.')
     parser.add_argument('--birdweather_id', default='99999', help='Private Station ID for BirdWeather.')    
 
     args = parser.parse_args()
@@ -212,11 +212,16 @@ def main():
     # Load model
     interpreter = loadModel()
  
-    # Load custom species list
+    # Load custom species lists - INCLUDED and EXCLUDED
-    if not args.custom_list == '':
+    if not args.include_list == '':
-        WHITE_LIST = loadCustomSpeciesList(args.custom_list)
+        INCLUDE_LIST = loadCustomSpeciesList(args.include_list)
     else:
-        WHITE_LIST = []
+        INCLUDE_LIST = []
+    
+    if not args.exclude_list == '':
+        EXCLUDE_LIST = loadCustomSpeciesList(args.exclude_list)
+    else:
+        EXCLUDE_LIST = []
 
     birdweather_id = args.birdweather_id
 
@@ -246,7 +251,6 @@ def main():
 
     # Process audio data and get detections
     detections = analyzeAudioData(audioData, args.lat, args.lon, week, sensitivity, args.overlap, interpreter)
-
     # Write detections to output file
     min_conf = max(0.01, min(args.min_conf, 0.99))
     writeResultsToFile(detections, min_conf, args.o)
@@ -351,3 +355,4 @@ if __name__ == '__main__':
     # Example calls
     # python3 analyze.py --i 'example/XC558716 - Soundscape.mp3' --lat 35.4244 --lon -120.7463 --week 18
     # python3 analyze.py --i 'example/XC563936 - Soundscape.mp3' --lat 47.6766 --lon -122.294 --week 11 --overlap 1.5 --min_conf 0.25 --sensitivity 1.25 --custom_list 'example/custom_species_list.txt'
+

scripts/birdnet_analysis.sh

@@ -27,7 +27,8 @@ if ! diff ${LAST_RUN} ${THIS_RUN};then
   done
 fi
 
-CUSTOM_LIST="/home/pi/BirdNET-Pi/custom_species_list.txt"
+INCLUDE_LIST="/home/pi/BirdNET-Pi/include_species_list.txt"
+EXCLUDE_LIST="/home/pi/BirdNET-Pi/exclude_species_list.txt"
 
 # Create an array of the audio files
 # Takes one argument:
@@ -103,7 +104,7 @@ run_analysis() {
       done
     fi
 
-    if [ -f ${1}/${i} ] && [ ! -f ${CUSTOM_LIST} ] && [ -z $BIRDWEATHER_ID ];then
+    if [ -f ${1}/${i} ] && [ ! -f ${INCLUDE_LIST} ] && [ ! -f ${EXCLUDE_LIST} ] && [ -z $BIRDWEATHER_ID ];then
       echo "python3 analyze.py \
 --i "${1}/${i}" \
 --o "${1}/${i}.csv" \
@@ -122,7 +123,7 @@ run_analysis() {
         --overlap "${OVERLAP}" \
         --sensitivity "${SENSITIVITY}" \
         --min_conf "${CONFIDENCE}"
-    elif [ -f ${1}/${i} ] && [ -f ${CUSTOM_LIST} ] && [ -z $BIRDWEATHER_ID ];then
+    elif [ -f ${1}/${i} ] && [ -f ${INCLUDELIST} ] && [ ! -f ${EXCLUDE_LIST} ] && [ -z $BIRDWEATHER_ID ];then
       echo "python3 analyze.py \
 --i "${1}/${i}" \
 --o "${1}/${i}.csv" \
@@ -132,7 +133,7 @@ run_analysis() {
 --overlap "${OVERLAP}" \
 --sensitivity "${SENSITIVITY}" \
 --min_conf "${CONFIDENCE}" \
---custom_list "${CUSTOM_LIST}""
+--include_list "${INCLUDE_LIST}""
       "${VENV}"/bin/python analyze.py \
         --i "${1}/${i}" \
         --o "${1}/${i}.csv" \
@@ -142,8 +143,8 @@ run_analysis() {
         --overlap "${OVERLAP}" \
 	--sensitivity "${SENSITIVITY}" \
         --min_conf "${CONFIDENCE}" \
-	      --custom_list "${CUSTOM_LIST}"
+	--include_list "${INCLUDE_LIST}"
-    elif [ -f ${1}/${i} ] && [ ! -f ${CUSTOM_LIST} ] && [ ! -z $BIRDWEATHER_ID ];then
+    elif [ -f ${1}/${i} ] && [ ! -f ${INCLUDE_LIST} ] && [ -f ${EXCLUDE_LIST} ] && [ -z $BIRDWEATHER_ID ];then
       echo "python3 analyze.py \
 --i "${1}/${i}" \
 --o "${1}/${i}.csv" \
@@ -153,7 +154,51 @@ run_analysis() {
 --overlap "${OVERLAP}" \
 --sensitivity "${SENSITIVITY}" \
 --min_conf "${CONFIDENCE}" \
---birdweather_id IN_USE" 
+--exclude_list "${EXCLUDE_LIST}"
+      "${VENV}"/bin/python analyze.py \
+        --i "${1}/${i}" \
+        --o "${1}/${i}.csv" \
+        --lat "${LATITUDE}" \
+        --lon "${LONGITUDE}" \
+        --week "${WEEK}" \
+        --overlap "${OVERLAP}" \
+	--sensitivity "${SENSITIVITY}" \
+        --min_conf "${CONFIDENCE}" \
+	--exclude_list "${EXCLUDE_LIST}"
+    elif [ -f ${1}/${i} ] && [ -f ${INCLUDE_LIST} ] && [ -f ${EXCLUDE_LIST} ] && [ -z $BIRDWEATHER_ID ];then
+      echo "python3 analyze.py \
+--i "${1}/${i}" \
+--o "${1}/${i}.csv" \
+--lat "${LATITUDE}" \
+--lon "${LONGITUDE}" \
+--week "${WEEK}" \
+--overlap "${OVERLAP}" \
+--sensitivity "${SENSITIVITY}" \
+--min_conf "${CONFIDENCE}" \
+--include_list "${INCLUDE_LIST}" \
+--exclude_list "${EXCLUDE_LIST}"
+      "${VENV}"/bin/python analyze.py \
+        --i "${1}/${i}" \
+        --o "${1}/${i}.csv" \
+        --lat "${LATITUDE}" \
+        --lon "${LONGITUDE}" \
+        --week "${WEEK}" \
+        --overlap "${OVERLAP}" \
+	--sensitivity "${SENSITIVITY}" \
+        --min_conf "${CONFIDENCE}" \
+        --include_list "${INCLUDE_LIST}" \
+        --exclude_list "${EXCLUDE_LIST}" 
+    elif [ -f ${1}/${i} ] && [ ! -f ${INCLUDE_LIST} ] && [ ! -f ${EXCLUDE_LIST} ] && [ ! -z $BIRDWEATHER_ID ];then
+      echo "python3 analyze.py \
+--i "${1}/${i}" \
+--o "${1}/${i}.csv" \
+--lat "${LATITUDE}" \
+--lon "${LONGITUDE}" \
+--week "${WEEK}" \
+--overlap "${OVERLAP}" \
+--sensitivity "${SENSITIVITY}" \
+--min_conf "${CONFIDENCE}" \
+--birdweather_id "${BIRDWEATHER_ID}"
       "${VENV}"/bin/python analyze.py \
         --i "${1}/${i}" \
         --o "${1}/${i}.csv" \
@@ -164,7 +209,7 @@ run_analysis() {
 	--sensitivity "${SENSITIVITY}" \
         --min_conf "${CONFIDENCE}" \
         --birdweather_id "${BIRDWEATHER_ID}" 
-    elif [ -f ${1}/${i} ] && [ -f ${CUSTOM_LIST} ] && [ ! -z $BIRDWEATHER_ID ];then
+    elif [ -f ${1}/${i} ] && [ -f ${INCLUDE_LIST} ] && [ ! -f ${EXCLUDE_LIST} ] && [ ! -z $BIRDWEATHER_ID ];then
       echo "python3 analyze.py \
 --i "${1}/${i}" \
 --o "${1}/${i}.csv" \
@@ -174,8 +219,8 @@ run_analysis() {
 --overlap "${OVERLAP}" \
 --sensitivity "${SENSITIVITY}" \
 --min_conf "${CONFIDENCE}" \
---custom_list "${CUSTOM_LIST}" \
+--include_list "${INCLUDE_LIST}" \
---birdweather_id IN_USE" 
+--birdweather_id "${BIRDWEATHER_ID}"
       "${VENV}"/bin/python analyze.py \
         --i "${1}/${i}" \
         --o "${1}/${i}.csv" \
@@ -185,7 +230,55 @@ run_analysis() {
         --overlap "${OVERLAP}" \
 	--sensitivity "${SENSITIVITY}" \
         --min_conf "${CONFIDENCE}" \
-        --custom_list "${CUSTOM_LIST}" \
+        --include_list "${INCLUDE_LIST}" \
+        --birdweather_id "${BIRDWEATHER_ID}" 
+    elif [ -f ${1}/${i} ] && [ ! -f ${INCLUDE_LIST} ] && [ -f ${EXCLUDE_LIST} ] && [ ! -z $BIRDWEATHER_ID ];then
+      echo "python3 analyze.py \
+--i "${1}/${i}" \
+--o "${1}/${i}.csv" \
+--lat "${LATITUDE}" \
+--lon "${LONGITUDE}" \
+--week "${WEEK}" \
+--overlap "${OVERLAP}" \
+--sensitivity "${SENSITIVITY}" \
+--min_conf "${CONFIDENCE}" \
+--exclude_list "${EXCLUDE_LIST}" \
+--birdweather_id "${BIRDWEATHER_ID}"
+      "${VENV}"/bin/python analyze.py \
+        --i "${1}/${i}" \
+        --o "${1}/${i}.csv" \
+        --lat "${LATITUDE}" \
+        --lon "${LONGITUDE}" \
+        --week "${WEEK}" \
+        --overlap "${OVERLAP}" \
+	--sensitivity "${SENSITIVITY}" \
+        --min_conf "${CONFIDENCE}" \
+        --exclude_list "${EXCLUDE_LIST}" \
+        --birdweather_id "${BIRDWEATHER_ID}" 
+    elif [ -f ${1}/${i} ] && [ -f ${INCLUDE_LIST} ] && [ -f ${EXCLUDE_LIST} ] && [ ! -z $BIRDWEATHER_ID ];then
+      echo "python3 analyze.py \
+--i "${1}/${i}" \
+--o "${1}/${i}.csv" \
+--lat "${LATITUDE}" \
+--lon "${LONGITUDE}" \
+--week "${WEEK}" \
+--overlap "${OVERLAP}" \
+--sensitivity "${SENSITIVITY}" \
+--min_conf "${CONFIDENCE}" \
+--include_list "${INCLUDE_LIST}" \
+--exclude_list "${EXCLUDE_LIST}" \
+--birdweather_id "${BIRDWEATHER_ID}"
+      "${VENV}"/bin/python analyze.py \
+        --i "${1}/${i}" \
+        --o "${1}/${i}.csv" \
+        --lat "${LATITUDE}" \
+        --lon "${LONGITUDE}" \
+        --week "${WEEK}" \
+        --overlap "${OVERLAP}" \
+	    --sensitivity "${SENSITIVITY}" \
+        --min_conf "${CONFIDENCE}" \
+        --include_list "${INCLUDE_LIST}" \
+        --exclude_list "${EXCLUDE_LIST}" \
         --birdweather_id "${BIRDWEATHER_ID}" 
     fi
   done