Initial draft of generic recogniser guide

Closes #406 This is a combination of 22 commits. Create DIY_CallRecognizersUsingAP.md Start of manual for DIY call recognizers Update toc.yml for DIY call recognizers Delete index.md Remove index.md Trying to set up call recognizer manual Trying to set up call recognizer manual Settoing up manual Issue #406 Update DIY_CallRecognizersUsingAP.md Issue#406 edit manual FUrther progress with writing manual for DIY Recognizer. Issue #406 Added text and images Update DIY_CallRecognizersUsingAP.md Issue #406 More work on the manual. Have almost finished scoping out the manual. Now need to polish the contents. Update DIY_CallRecognizersUsingAP.md Issue #406 Update DIY_CallRecognizersUsingAP.md Issue #406 continue editing. Issue #406 Continue editing manual for DIY recognizer. Update DIY_CallRecognizersUsingAP.md More work on manual. Update DIY_CallRecognizersUsingAP.md Issue #406 Work on description of Profiles. Update DIY_CallRecognizersUsingAP.md Issue #406 More work on describing the content of the configuration file Update DIY_CallRecognizersUsingAP.md Issue #406. Finish up to Section 8. Only sections 9 and 10 remaining. Update DIY_CallRecognizersUsingAP.md Issue #406 I have completed the basic text for all 10 sections of the manual. It now remains to include diagrams and complete the TODO sections. Update DIY_CallRecognizersUsingAP.md Issue #406 Add in description of parameters for harmonics and oscillations. Update DIY_CallRecognizersUsingAP.md Issue #406 More work on oscillation and harmonic events. Update DIY_CallRecognizersUsingAP.md Issue #406 Work on the Oscillation and Harmonics event description Update DIY_CallRecognizersUsingAP.md Issue #406 Fixed a few errors. Add in 5 diagrams to the guide. Issue #406 Fix up details conerning sideband filter Issue #406
QutEcoacoustics · Feb 1, 2021 · 29032ea · 29032ea
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diff --git a/docs/guides/DIY_CallRecognizersUsingAP.md b/docs/guides/DIY_CallRecognizersUsingAP.md
diff --git a/...figFiles/Towsey.BotaurusPoiciloptilus.yml → docs/guides/Ecosounds.NinoxBoobook.yml b/...figFiles/Towsey.BotaurusPoiciloptilus.yml → docs/guides/Ecosounds.NinoxBoobook.yml
@@ -1,13 +1,8 @@
 ---
 
-# Australasian Bittern = Botaurus poiciloptilus
-#NOTE: The parameter values in this config file were optimised on a data set supplied by Elizabeth Znidersic.
-#      It consisted of 14 consecutive hours of recording from Medeas Cove, St. Helens, Tasmania.
-#      The recordings contain 55 Bittern calls.
-#      Latest test (Oct 2020) on this dataset achieved: Recall = 87%. Precision = 76%.
-
+# Boobook Owl = Towsey.NinoxBoobook
 # Resample rate must be 2 X the desired Nyquist
-ResampleRate: 8000
+#ResampleRate: 22050
 # SegmentDuration: units=seconds;    
 SegmentDuration: 60
 # SegmentOverlap: units=seconds;
@@ -16,23 +11,24 @@ SegmentOverlap: 0
 # Each of these profiles will be analyzed
 # This profile is required for the species-specific recogniser and must have the current name.
 Profiles:
-    BitternSyllable: !OnebinTrackParameters
-        ComponentName: Whistle 
-        SpeciesName: BotaurusPoiciloptilus
-        FrameSize: 512
+    BoobookSyllable: !ForwardTrackParameters
+        ComponentName: RidgeTrack 
+        SpeciesName: NinoxBoobook
+        FrameSize: 1024
         FrameStep: 256
         WindowFunction: HANNING
+
         # min and max of the freq band to search
-        MinHertz: 90          
-        MaxHertz: 210
-        MinDuration: 0.2
-        MaxDuration: 0.8
-        # Scan the freq band using these thresholds.
+        MinHertz: 400          
+        MaxHertz: 1100
+        MinDuration: 0.17
+        MaxDuration: 1.2
+        # Scan the frequency band at these thresholds
         DecibelThresholds:
-            - 3.0
             - 6.0
             - 9.0
-
+            - 12.0
+
 #################### POST-PROCESSING of EVENTS ###################
 
 PostProcessing:
@@ -48,33 +44,33 @@ PostProcessing:
     # 2: Combine possible syllable sequences
     SyllableSequence:
         CombinePossibleSyllableSequence: true
-        SyllableStartDifference: 3.0
-        SyllableHertzGap: 40
+        SyllableStartDifference: 0.6
+        SyllableHertzGap: 350
         FilterSyllableSequence: true
-        SyllableMaxCount: 7
-        ExpectedPeriod: 2.5
+        SyllableMaxCount: 2
+        ExpectedPeriod: 0.4
 
     # 3: Remove events whose duration lies outside 3 SDs of an expected value.
     #Duration:
         ExpectedDuration: 0.14
         DurationStandardDeviation: 0.01        
 
     # 4: Remove events whose bandwidth lies outside 3 SDs of an expected value.
-    Bandwidth:
-        ExpectedBandwidth: 100
-        BandwidthStandardDeviation: 15
+ #   Bandwidth:
+        ExpectedBandwidth: 280
+        BandwidthStandardDeviation: 40
 
     # 5: Filter the events for excess activity in their sidebands, i.e. upper and lower buffer zones
     SidebandActivity:
         LowerHertzBuffer: 150
-        UpperHertzBuffer: 200
-        MaxAverageSidebandDecibels: 6.0
+        UpperHertzBuffer: 400
+        MaxAverageSidebandDecibels: 3.0
 
 # Options to save results files
 # 1: 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: True
-#SaveSonogramImages: WhenEventsDetected
+SaveSonogramImages: WhenEventsDetected
 
 # 2: Available options for saving data files (case-sensitive): [False/Never | True/Always | WhenEventsDetected]
 SaveIntermediateWavFiles: Never
@@ -86,3 +82,5 @@ DisplayCsvImage: false
 
 # Other config files to reference
 HighResolutionIndicesConfig: "../Towsey.Acoustic.HiResIndicesForRecognisers.yml"
+
+...
diff --git a/docs/guides/Images/DCTparameters.jpg b/docs/guides/Images/DCTparameters.jpg
diff --git a/docs/guides/Images/Fig2EventParameters.png b/docs/guides/Images/Fig2EventParameters.png
diff --git a/docs/guides/Images/ParametersForSteps1-3.png b/docs/guides/Images/ParametersForSteps1-3.png
diff --git a/docs/guides/Images/SevenKindsAcousticEvent.jpg b/docs/guides/Images/SevenKindsAcousticEvent.jpg
diff --git a/docs/guides/index.md b/docs/guides/index.md
@@ -9,4 +9,4 @@ contentsTitle: Available Guides
 Guides are short focused examples on how to achieve something. They'll require
 some adaption to work for your use case.
 
-See the tutorials section for long form working examples that use real data.
+See the tutorials section for long form working examples that use real data.
diff --git a/docs/guides/toc.yml b/docs/guides/toc.yml
@@ -3,5 +3,9 @@
 
 - name: Scripting AP.exe
   href: scripting.md
+
 - name: Scripting AP.exe with R
   href: using_r.md
+
+- name: DIY Call Recognizer
+  href: DIY_CallRecognizersUsingAP.md