Final tweaks to NSW DPI recognisers

Had to fix a few given recent changes to post-processing.

docs/basics/config_files.md

@@ -74,7 +74,7 @@ Here are some **invalid** examples:
    _AP_ looks for an analysis called `Towsey.Acousticmarine` which doesn't exist. It should be `Towsey.Acoustic.marine.yml`
 
 If you find a config file that does not match this format, it will likely produce an error.
-If your config file must be named in a different format the `--analysis-name` (or the short form `-a`) argument can be used to
+If your config file must be named in a different format the `--analysis-identifier` (or the short form `-a`) argument can be used to
 disambiguate the analysis type you want to use.
 
 Please note this rule does not apply to other config files not directly used by `audio2csv`. For example,

docs/guides/generic_recognizers.md

@@ -252,7 +252,7 @@ the names of the algorithms (used to find those events) describe how the algorit
 | Whistle        | `OnebinTrack`     | `!OnebinTrackParameters`     |
 | Chirp          | `ForwardTrack`    | `!ForwardTrackParameters`    |
 | Whip           | `UpwardTrack`     | `!UpwardTrackParameters`     |
-| Click          | `VerticalTrack`   | `!VerticalTrackParameters`   |
+| Click          | `VerticalTrack`   | `!OneframeTrackParameters`   |
 | Oscillation    | `Oscillation`     | `!OscillationParameters`     |
 | Harmonic       | `Harmonic`        | `!HarmonicParameters`        |
 

src/AnalysisConfigFiles/RecognizerConfigFiles/Towsey.NinoxStrenua.yml

@@ -11,7 +11,7 @@
 
 # Resample rate must be 2 X the desired Nyquist
 #ResampleRate: 22050
-# SegmentDuration: units=seconds;    
+# SegmentDuration: units=seconds;
 SegmentDuration: 60
 # SegmentOverlap: units=seconds;
 SegmentOverlap: 0
@@ -20,14 +20,14 @@ SegmentOverlap: 0
 # This profile is required for the species-specific recogniser and must have the current name.
 Profiles:
     StrenuaSyllable: !ForwardTrackParameters
-        ComponentName: RidgeTrack 
+        ComponentName: RidgeTrack
         SpeciesName: NinoxStrenua
         FrameSize: 1024
         FrameStep: 256
         WindowFunction: HANNING
-        
+
         # min and max of the freq band to search
-        MinHertz: 300          
+        MinHertz: 300
         MaxHertz: 600
         MinDuration: 0.3
         MaxDuration: 0.6
@@ -38,7 +38,7 @@ Profiles:
             - 24.0
             - 30.0
             - 36.0
-         
+
 #################### POST-PROCESSING of EVENTS ###################
 
 PostProcessing:
@@ -63,7 +63,7 @@ PostProcessing:
     # 3: Remove events whose duration lies outside 3 SDs of an expected value.
     #Duration:
     #    ExpectedDuration: 0.14
-    #    DurationStandardDeviation: 0.01        
+    #    DurationStandardDeviation: 0.01
 
     # 4: Remove events whose bandwidth lies outside 3 SDs of an expected value.
     Bandwidth:
@@ -77,7 +77,7 @@ PostProcessing:
         MaxBackgroundDecibels: null
         MaxActivityDecibels: null
 
-    # 6: In the case of sets of nested/enclosed events, filter/remove all but the outermost event. 
+    # 6: In the case of sets of nested/enclosed events, filter/remove all but the outermost event.
     RemoveEnclosedEvents: true
 
 

src/AnalysisConfigFiles/RecognizerConfigFiles/Towsey.Pteropus.V2.yml

@@ -0,0 +1,65 @@
+---
+# Second version adapted to generic recognizer format by Anthony Truskinger
+SpeciesName: Pteropus
+CommonName: Flying Fox
+
+# Proposed Approach:
+#    Typically the lowest harmonic will lie between 1200 Hz and 3000 Hz and the higher ones evenly spaced.
+#    This is the tricky bit due to variability but may work to use spectrum auto-correlation.
+
+ResampleRate: 22050
+SegmentDuration: 60
+SegmentOverlap: 0
+
+CommonParameters: &common_parameters
+    SpeciesName: Pteropus
+    FrameSize: 512
+    FrameStep: 256
+    WindowFunction: HANNING
+    NoiseReductionType: Standard
+    BgNoiseThreshold: 3
+    # Scan the frequency band at these thresholds
+    DecibelThresholds:
+        - 6.0
+
+
+# Each of these profiles will be analyzed
+Profiles:
+  Territorial: !HarmonicParameters
+    <<: *common_parameters
+
+    # min and max of the freq band to search
+    MinHertz: 800
+    MaxHertz: 8000
+    MinDuration: 0.15
+    MaxDuration: 0.8
+    MinFormantGap: 150
+    MaxFormantGap: 7200
+    DctThreshold: 0.15
+  Wingbeats: !OscillationParameters
+    <<: *common_parameters
+
+    MinHertz: 200
+    MaxHertz: 2000
+    DecibelThreshold: 6.0
+    # duration of DCT in seconds
+    DctDuration: 0.5
+    # minimum acceptable value of a DCT coefficient
+    DctThreshold: 0.5
+    # ignore oscillation rates below the min & above the max threshold
+    # A sample of four wingbeats yielded an average of 5.1 +/-0.5 beats/s.
+    # 95% confidence interval (2 SDs) is therefore approx 4-6 beats/s.
+    # OSCILLATIONS PER SECOND
+    MinOscillationFrequency: 4
+    MaxOscillationFrequency: 6
+    # Minimum and maximum duration for the length of a true call.
+    MinDuration: 1.0
+    MaxDuration: 10.0
+    # Event threshold - use this to determine FP / FN trade-off for events.
+    EventThreshold: 0.5
+
+
+SaveIntermediateWavFiles: Never
+SaveIntermediateCsvFiles: false
+SaveSonogramImages: WhenEventsDetected
+...

src/AnalysisConfigFiles/RecognizerConfigFiles/Towsey.PteropusSpecies.yml

@@ -20,7 +20,7 @@ AbbreviatedSpeciesName: PteropusSp
 # Resample rate must be 2 X the desired Nyquist
 ResampleRate: 22050
 
-# SegmentDuration: units=seconds;    
+# SegmentDuration: units=seconds;
 SegmentDuration: 60
 # SegmentOverlap: units=seconds;
 SegmentOverlap: 0
@@ -34,24 +34,24 @@ Profiles:
   #EventThreshold: 0.2
   Territorial:
     # min and max of the freq band to search
-    MinHz: 800          
+    MinHz: 800
     MaxHz: 8000
     MinDuration: 0.15
     MaxDuration: 0.8
-    DecibelThreshold: 9.0
+    DecibelThresholds: 9.0
   Wingbeats:
-    MinHz: 200          
+    MinHz: 200
     MaxHz: 2000
     DecibelThreshold: 6.0
-    # duration of DCT in seconds 
+    # duration of DCT in seconds
     DctDuration: 0.5
     # minimum acceptable value of a DCT coefficient
     DctThreshold: 0.5
     # ignore oscillation rates below the min & above the max threshold
     # A sample of four wingbeats yielded an average of 5.1 +/-0.5 beats/s.
-    # 95% confidence interval (2 SDs) is therefore approx 4-6 beats/s.    
+    # 95% confidence interval (2 SDs) is therefore approx 4-6 beats/s.
     # OSCILLATIONS PER SECOND
-    MinOscilFreq: 4        
+    MinOscilFreq: 4
     MaxOscilFreq: 6
     # Minimum and maximum duration for the length of a true call.
     MinDuration: 1.0

src/AnalysisConfigFiles/RecognizerConfigFiles/Truskinger.AtrichornisRufescens.yml

@@ -14,10 +14,11 @@ CommonParameters: &common_parameters
       FrameStep: 512
       WindowFunction: HAMMING
       NoiseReductionType: Modal
-      BgNoiseThreshold: 0.2
+      BgNoiseThreshold: 0.1
 
       # Scan the frequency band at these thresholds
       DecibelThresholds:
+          - 2
           - 3
           - 6
           - 9

src/AnalysisConfigFiles/RecognizerConfigFiles/Truskinger.PetaurusAustralis.yml

@@ -8,89 +8,87 @@ SegmentDuration: 60
 # SegmentOverlap: units=seconds;
 SegmentOverlap: 0
 
+CommonParameters: &common_parameters
+    SpeciesName: Petaurus australis
+    FrameSize: 512
+    FrameStep: 512
+    WindowFunction: HANNING
+    NoiseReductionType: Modal
+    BgNoiseThreshold: 0.0
+
+
 # Each of these profiles will be analyzed
 # This profile is required for the species-specific recognizer and must have the current name.
 Profiles:
-    YellowBelliedGlider_FirstShriek: !BlobParameters
-        SpeciesName: Petaurus australis
-        FrameSize: 1024
-        FrameStep: 256
-        WindowFunction: HANNING
+    FirstShriek: !BlobParameters
+        <<: *common_parameters
 
         # min and max of the freq band to search
-        MinHertz: 1200
-        MaxHertz: 2100
-        BottomHertzBuffer: 100
-        TopHertzBuffer: 100
-        MinDuration: 0.4
+        MinHertz: 270
+        MaxHertz: 3300
+        BottomHertzBuffer: 0
+        TopHertzBuffer: 0
+        MinDuration: 0.1
         MaxDuration: 0.6
         # Scan the frequency band at these thresholds
         DecibelThresholds:
-            - 1.0
-            - 3.0
+            - 3
             - 6.0
-    YellowBelliedGlider2_SecondShriek: !BlobParameters
-        SpeciesName: Petaurus australis
-        FrameSize: 1024
-        FrameStep: 256
-        WindowFunction: HANNING
+            - 9.0
+    SecondShriek: !BlobParameters
+        <<: *common_parameters
 
         # min and max of the freq band to search
-        MinHertz: 2200
-        MaxHertz: 3550
+        MinHertz: 2000
+        MaxHertz: 6500
         BottomHertzBuffer: 100
         TopHertzBuffer: 50
-        MinDuration: 0.6
-        MaxDuration: 0.8
+        MinDuration: 0.5
+        MaxDuration: 1.5
         # Scan the frequency band at these thresholds
         DecibelThresholds:
-            - 1.0
             - 3.0
             - 6.0
-    YellowBelliedGlider3_TrailingShriek: !BlobParameters
-        SpeciesName: Petaurus australis
-        FrameSize: 1024
-        FrameStep: 256
-        WindowFunction: HANNING
+    TrailingShriek: !BlobParameters
+        <<: *common_parameters
 
         # min and max of the freq band to search
-        MinHertz: 1200
-        MaxHertz: 2100
+        MinHertz: 200
+        MaxHertz: 5400
         BottomHertzBuffer: 100
         TopHertzBuffer: 100
-        MinDuration: 0.6
+        MinDuration: 0.15
         MaxDuration: 2.0
         # Scan the frequency band at these thresholds
         DecibelThresholds:
-            - 1.0
             - 3.0
             - 6.0
 
 #################### POST-PROCESSING of EVENTS ###################
 
 PostProcessing:
+    PostProcessInDecibelGroups: false
 # # The following generic post-processing steps are determined by config settings.
 # # Step 1: Combine overlapping events - events derived from all profiles.
 # # Step 2: Combine possible syllable sequences and filter on excess syllable count.
 # # Step 3: Remove events whose bandwidth is too small or large.
 # # Step 4: Remove events that have excessive noise in their side-bands.
 
 #     # 1: Combine overlapping events
-#     CombineOverlappingEvents: true
+    CombineOverlappingEvents: false
 
     # 2: Combine possible syllable sequences
     SyllableSequence:
-        CombinePossibleSyllableSequence: true
-        SyllableStartDifference: 0.6
+        SyllableStartDifference: 1.2
         SyllableHertzGap: 2400
-        FilterSyllableSequence: true
-        SyllableMaxCount: 3
-        ExpectedPeriod: 0.1
+        # FilterSyllableSequence: true
+        # SyllableMaxCount: 3
+        # ExpectedPeriod: 0.1
 
-#     # 3: Remove events whose duration lies outside 3 SDs of an expected value.
-#     #Duration:
-#         ExpectedDuration: 0.14
-#         DurationStandardDeviation: 0.01
+# #     # 3: Remove events whose duration lies outside 3 SDs of an expected value.
+    Duration:
+        ExpectedDuration: 2.5
+        DurationStandardDeviation: 0.6
 
 #     # 4: Remove events whose bandwidth lies outside 3 SDs of an expected value.
 #  #   Bandwidth:
@@ -102,11 +100,12 @@ PostProcessing:
 #         LowerHertzBuffer: 150
 #         UpperHertzBuffer: 400
 #         MaxAverageSidebandDecibels: 3.0
+    RemoveEnclosedEvents: false
 
 # Options to save results files
 # Available options for saving spectrograms (case-sensitive): [False/Never | True/Always | WhenEventsDetected]
 # "True" is useful when debugging but "WhenEventsDetected" is required for operational use.
-SaveSonogramImages: WhenEventsDetected
+SaveSonogramImages: Always
 
 # Available options for saving data files (case-sensitive): [False/Never | True/Always | WhenEventsDetected]
 SaveIntermediateWavFiles: Never