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Changelog.md

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All notable changes to AviaNZ program will be documented in this file.

Unreleased

Added

  • New changepoint detector replaces wavelet filter as the default non-CNN recognition method (wavelet filters still work but considered deprecated)
  • Syllable-level detection: trainable filters via the new changepoint pipeline, one example filter for LSK syllables included, and parameter ranges for non-specific detectors adapted
  • New method for wind noise removal by polynomial fitting (OLS or robust options available)
  • Pre-built GPU support for CNN in compiled versions
  • Option to loop playback in both review types
  • Option to autoplay in one-by-one review
  • Non-linear frequency scale spectrograms (Mel, Bark)
  • Additional spectrogram normalization options, including PCEN

Changed

  • Training will now include subdirectories when searching for data
  • Node selection in training faster, more stable, and produces ROCs more closely consistent with testing/processing
  • Wind noise removal only available for changepoint detectors now
  • Denoising dialog will now use time-adaptive noise estimation by default
  • Filter format extended to allow setting segmenter
  • Better UI for adding species in review, search function
  • Shorter pages (5 mins) for low sampling rate files in batch mode
  • CNNs no longer redefine segment boundaries, only accept/reject
  • reduced extension length when applying CNNs to short segments
  • various changes to CNN training
  • Tab shortcut for species/calltype switch
  • different click detection process when training bat detectors
  • ground truth files no longer store resolution in the name
  • batch processing will not allow upsampling if using wind filter (only 2x or 4x "fake upsampling" which is implemented by node remapping)
  • batch review now has better feedback on input errors

Fixed

  • Faster CNN classification
  • Post-processing harmonised between batch mode, testing, testing with CNN
  • Segmenting in manual mode now only overwrites the current page segments
  • Problems when undoing segmentation in multi-page files
  • Bat BMP reading sometimes wasn't setting a parameter
  • Faster spectrogram updating in manual mode
  • Minor UI bugs in recogniser training wizard
  • Long species list now triggers button reordering in review
  • better edge case handling when adding species in review
  • ancient bugs in best basis selection for wavelet denoising
  • WAV Splitter produced bad timestamps on files starting within an hour before a DST change
  • data padding for wavelet decomposition/reconstruction was wrong length and reversed
  • Wavelet energy computation made safer and less edge-influenced
  • missing post-processing settings in batch GUI

Hidden changes (developer-mode):

  • Ridge/instantaneous freq. detection
  • Shape analysis dialog
  • Button for exporting segment sound at different speed
  • Denoising button now connected to the new denoising
  • Saving spectrogram images without axes
  • Call comparator as a separate script, clock-adjustment only

[3.2] - 2021-02-16

Added

  • Ability to undo previously deleted segments in review
  • "One-by-one" review plot size expands to dialog size
  • BatSearch-compatible output for batmode
  • National Bat Database format output for batmode
  • Segment saving feedback now shown in status bar
  • Mouse cursor indicates current mode
  • "Jump to next annotation" buttons
  • Optional frequency masking in CNN training
  • Ability to customise existing recognisers
  • Formant marking in spectrogram
  • Dialog for adjusting thresholds of stored filters
  • Ability to adjust other filter parameters for newly-trained detectors

Changed

  • Improved processing pipeline for bats
  • Improved CNN recogniser for bats
  • Extended morepork recogniser with CNN
  • "One-by-one" review (previously All Species) can now be run on single species
  • Batch Review settings separated into Advanced and Simple
  • Simpler dropdown to set review certainty bounds
  • Better spectrogram type selection UI
  • Separate UI thread to keep responsiveness when batch processing

Fixed

  • Greatly reduced CPU load for mouseover detection in spectrogram items
  • Batch settings are appropriately greyed out and provide tooltips
  • 8-bit WAV playback was not working
  • Bugs in non-specific batch processing
  • Cleaned up gap-merging algorithms, could have caused bugs in edge cases

[3.1] - 2020-10-09

Added

  • Visible frequency range in batmode defaults to full
  • Manage Recognisers deals with CNN files as well
  • ROCs during training show more information, wavelet freq. bands

Changed

  • Excel output shows absolute times of detected segments, when files have timestamps
  • Tensorflow version bumped up

Fixed

  • Graphical problems on high resolution displays
  • Safer restarting

[3.0] - 2020-09-17

Added

  • CNN training to improve precision

  • Call type annotation/correction in manual processing mode

  • Call type review in all species mode

  • Bat mode: loading, annotating and batch-processing DoC format bitmaps, with file-level annotations

  • NZ bat list and a filter to identify them (click detector and CNN)

  • Frequency guides for fast bat call annotation

  • Utilities: importing Freebird or Excel format annotations, backing up data files

  • Command line options for batch processing and testing

  • New filters for kiwi species

  • New sound and spectrogram samples

  • Recording information in the manual processing mode

  • Time axis in single species review

Changed

  • Removed user input for number of thresholds in wavelet filter training
  • Filter requirements more flexible now, to incorporate bat settings
  • Improved overview window UI
  • Better feedback, progress bars in Batch Processing and Review
  • Customizable tile size in Single species review
  • Easier access to WAV/DATA splitter
  • Better presentation of recogniser testing results
  • Wavelet training now reads clusters from calltype annotations if provided
  • Removed fund. freq. option from wavelet filter training

Fixed

  • Avoiding div by 0 in edge cases of spectrogram normalization
  • No more CTD on basic import errors in windows
  • Some minor bugfixes and safety checks

2.2 - 2020-04-28

Fixed

  • Recogniser testing summary
  • Storing zoom levels between All Species review runs
  • Better zoom and scaling in review dialogs
  • Faster and safer Excel export
  • Splitter outputs duration of existing .data files properly
  • Dialogs adapted to low screen resolutions
  • Various minor bug fixes

Added

  • CNN layer after wavelet filter in the processing pipeline to improve the precision
  • Certainty improved after CNN post-proc
  • Trained CNN models for NI brown kiwi, ready to use
  • Separate excel export in Batch Review
  • Intermittent sampling
  • Single Species review now has a frequency axis
  • All Species review now has a "Question" button to mark segments that need editing
  • File list in Manual mode now has colored icons to identify what level of annotations is present in each file

Changed

  • Human review made faster by loading the segments rather than reading whole file
  • Single Species review now displays every piece of long segments individually, rather than just showing the center
  • Lots of visual updates

2.1 - 2020-02-12

Added

  • Intermittent sampling option (under 'Action' menu)
  • Recent files
  • Split the extra long segments made by 'Any sound' mode (Batch Processing)

Changed

  • 'Skip if certainty above' default to 90 for clarity (earlier 100; Review Batch Results)

Fixed

  • .WAV case-insensitive

2.0 - 2019-11-22

Added

  • Call types (segments and wavelet filters)
  • Clustering (wavelet filter training)
  • Detailed segment information (Manual Processing)
  • Option to on/off wind detection (Batch Processing)
  • Dialog for filter (recogniser) management, export and import
  • Slow and fast playback button (Manual Processing)
  • Paging to deal with memory for large files (Batch Processing)
  • Option to run several filters in a single pass, saving time
  • Separate wizards for filter training and testing
  • "Toggle all" option (single species review)
  • WAV+DATA splitter

Changed

  • Filter format and segment format to allow call types and certainty (file_format_specification.md)
  • Windows setup as a wizard
  • Mac setup automated with a wrapper

1.5.1 - 2019-08-13

Added

  • Spectrogram zoom buttons for All Species review

Fixed

  • Various bug fixes after the workshop

1.5 - 2019-08-05

Added

  • Option to include wind masking (Batch mode)
  • Impulse masking on file read for auto detection

Changed

  • Faster filter training

Fixed

  • Minor bugs

[1.4] - 2019-06-10

Added

  • Online version of Cheat Sheet
  • Users can now train their own wavelet filters
  • New feature - spectral derivatives
  • "Quick Denoise" button

Changed

  • Wavelet packet decomposition and reconstruction rewritten entirely, allows partial (faster) and full (slower) anti-aliasing
  • Various small improvements to bird list selection and custom species input

Fixed

  • Single Species review
  • Lots of other minor bugs

[1.3] - 2018-10-24

Added

Changed

  • AviaNZ config, bird lists, and filter files to the home directory; in C: /Users/ username/ AppData/Roaming/ AviaNZ for Windows and ~/ .avianz for Mac and Linux

Fixed

  • Various bugs

[1.2] - 2018-10-24

Fixed

  • Various bugs

[1.1] - 2018-09-16 **

Added

  • Paging in the main interface
  • Volume controller
  • Option to playback only the target frequency band of a segment
  • Operator and Reviewer
  • Status bar (status updates and operator/reviewer)
  • 'Quit' to the menu
  • 'Make read only' option to avoid segments by mistake
  • Interface Settings (under the Appearance Menu) to customise the annotation colour scheme, length of the annotation overview sections, auto save frequency, page size etc.
  • 'Delete all segments'
  • Export segments to excel (Manual Segmentation)
  • Save spectrogram as image
  • Save selected sound
  • Help menu pointing to the manual
  • Batch Processing (all species/target species)
  • Review Batch Results
  • Excel summary for the batch mode

Changed

  • Start interface now has three options: Manual Segmentation, Batch Processing, and Review Batch Results
  • Assigned left/right mouse buttons for performing segmentation (one button to select and edit a segment, and the other to create a segment; user can choose which performs which action)
  • Two options to Human Review (All segments/Choose species)

Fixed

  • Various bugs

[1.0] - 2018-03-29 **

Fixed

  • Various bugs

[0.1] - 2017-06-08

Initial Release (for the Acoustic Workshop at Massey University 2017-06-09)

Added

  • Manual annotation of field recordings (with different certainty - color code)
  • Option to add segments as boxes and full-height start-end marks
  • Auto saving of the segments
  • Zooming and scrolling
  • Sound playback options
  • Overview spectrogram image
  • Fundamental frequency
  • Option to change spectrogram parameters
  • Denoise and band-pass filtering options
  • Automated segmentation (Wavelets, median clipping, fundamental frequency, etc.)
  • Find Matches (select a segment and then the program looks for others that are similar. It doesn't currently deal well with nosie)
  • Check segments (human review options)
  • Spectrogram CheatSheet (pdf format)