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Issue500 koala recognizer3 #521

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ae34d1c
Update HarmonicAlgorithmTests.cs
towsey Jun 23, 2021
6272d90
Change name of config file previously prepared.
towsey Jun 24, 2021
a6af0ca
Set up recognizer and unit test for Koala recognizer
towsey Jun 24, 2021
b117b5a
Changed signature of the Oscllation2012 method
towsey Jun 25, 2021
c2c05f0
Changed signature of Oscillations2012.Execute()
towsey Jun 28, 2021
84c6ea2
Update Plot.cs
towsey Jun 28, 2021
0b46e3b
Two other methods impacted by change to method signature of Oscillati…
towsey Jun 28, 2021
943ac26
Shift two properties from DctParameters to OscillParameters
towsey Jun 28, 2021
c720320
Update OscillationEvent.cs
towsey Jun 28, 2021
840fae2
Update GenericRecognizer.cs
towsey Jun 28, 2021
b15f22f
Set up new Koala mark3 call recognizer.
towsey Jun 28, 2021
53a723f
Update Image_MultiTrack.cs
towsey Jun 29, 2021
9521508
Make two Oscillation algorithms available
towsey Jun 29, 2021
86fb4f9
Move method ConvertOscillationScores2Events()
towsey Jun 29, 2021
26ec9fb
Update Towsey.PhascolarctosCinereusMark3.yml
towsey Jun 29, 2021
6b90e4f
Update PteropusSpTests.cs
towsey Jun 29, 2021
4fc5bdc
Create new class to contain DCT methods
towsey Jun 30, 2021
f28f54e
Update Oscillations2010.cs
towsey Jun 30, 2021
8163d1d
Update OscillationEvent.cs
towsey Jul 1, 2021
94b9aaf
Add extensive summary notes on the two oscillation alorithms, Oscilla…
towsey Jul 1, 2021
ccc8f31
Experiment with best test parameters.
towsey Jul 1, 2021
ae8cc1a
Remove the Oscillations2010 class
towsey Jul 2, 2021
3ba8d88
Remove EPR.cs
towsey Jul 5, 2021
4b50171
Add comments re oscillation algorithms
towsey Jul 5, 2021
7ce09b2
Work on unit tests.
towsey Jul 5, 2021
e00c812
Update HarmonicParameters.cs
towsey Jul 21, 2021
83e7886
Update OscillationEvent.cs
towsey Sep 7, 2021
d69208f
Update MatrixTools.cs
towsey Sep 7, 2021
6056087
Update InitialiseIndexProperties.cs
towsey Sep 7, 2021
e938042
Update GenericRecognizer.cs
towsey Sep 7, 2021
19bef80
Refactor methods for calculation of event statistics.
towsey Sep 8, 2021
350a2f9
Update SpectrogramTools.cs
towsey Nov 1, 2021
72286c2
Update PhascolarctosCinereusMark3.cs
towsey Nov 1, 2021
26a3b2d
Add more debug messages
towsey Nov 2, 2021
7021502
Update PhascolarctosCinereusMark3.cs
towsey Nov 3, 2021
4756338
Set up new unit test for Koala calls
towsey Nov 3, 2021
90a0ddb
Update OscillationParameters.cs
towsey Nov 3, 2021
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Original file line number Diff line number Diff line change
@@ -0,0 +1,108 @@
---

# Male Koala: Phascolarctos cinereus version 3.
# Resample rate must be 2 X the desired Nyquist
ResampleRate: 22050
# SegmentDuration: units=seconds;
SegmentDuration: 60
# SegmentOverlap: units=seconds;
SegmentOverlap: 0

CommonParameters: &common_parameters
SpeciesName: PhascolarctosCinereus
WindowFunction: HANNING
NoiseReductionType: Standard
BgNoiseThreshold: 0.0


# Each of these profiles will be analyzed
Profiles:
# This profile detections oscillation in the inhale.
KoalaOsc: !OscillationParameters
<<: *common_parameters
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The YAML referencing trick is really only useful when you have to reuse blocks in multiple profile definitions


Algorithm: Standard
#Algorithm: MultiBin
ComponentName: Oscillation
FrameSize: 256
FrameStep: 110
# min and max of the freq band to search
MinHertz: 170
MaxHertz: 800
# Min and max durations for the length of a true event (seconds).
MinDuration: 0.2
MaxDuration: 3.5
# duration of DCT in seconds
# this cannot be too long because the oscillations are not constant.
#DctDuration: 0.30
DctDuration: 0.2
# minimum acceptable amplitude of a DCT coefficient
DctThreshold: 0.5
# OSCILLATIONS PER SECOND: ignore oscillation rates below the min & above the max threshold
MinOscillationFrequency: 15
MaxOscillationFrequency: 60
# Event threshold - Determines FP / FN trade-off for events.
EventThreshold: 0.4
DecibelThresholds:
- 3.0

#################### 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: false

# 2: Combine possible syllable sequences
SyllableSequence:
SyllableStartDifference: 3.5
SyllableHertzGap: 200
#FilterSyllableSequence: false
# SyllableMaxCount: 3
# ExpectedPeriod: 0.1

# 3: Remove events whose duration lies outside 3 SDs of an expected value.
# Koala calls can last for 90 seconds or more.
# The following has the effect of removing events shorter than 3 seconds & longer than 93 sec.
Duration:
ExpectedDuration: 48.0
DurationStandardDeviation: 15.0

# # 4: Remove events whose bandwidth lies outside 3 SDs of an expected value.
# # Bandwidth:
# ExpectedBandwidth: 280
# BandwidthStandardDeviation: 40

# # 5: Filter the events for excess activity in their sidebands, i.e. upper and lower buffer zones
# THis will not work for koala calls.
# SidebandActivity:
# 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: Always
#SaveSonogramImages: WhenEventsDetected

# Save intermediate file options (case-sensitive): [False/Never | True/Always | WhenEventsDetected]
SaveIntermediateWavFiles: Never
SaveIntermediateCsvFiles: false

# DisplayCsvImage is obsolete - ensure it remains set to: false
DisplayCsvImage: false

# Other config files to reference
IndexPropertiesConfig: ".\\IndexPropertiesConfig.yml"
...
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