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Open Source Checklist #140

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31 tasks done
atruskie opened this issue Dec 5, 2017 · 2 comments
Closed
31 tasks done

Open Source Checklist #140

atruskie opened this issue Dec 5, 2017 · 2 comments
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@atruskie
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atruskie commented Dec 5, 2017

We intend for this project to be released as an open source project.
There are a few things we have to complete before this becomes a reality:

  • Basic approval
    • ✔️ Paul has said we can do this
  • Intellectual property
    • Clear open sourcing with QUT Bluebox
    • Check IP of any student code
    • Choose an open source lisence
      • Dual licence - code before open source commit should have a restricted licence
  • Code removal and cleanup
  • Other
@atruskie
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atruskie commented Jan 16, 2018

From @towsey (https://github.com/QutBioacoustics/Ecoacoustics/issues/197):

Removal of obsolete classes from the AudioAnalysis solution.

The following classes have the potential to be removed from AnalysisPrograms. There may be unintended consequences that require, for example, the moving of single methods to another class etc.
There may be other classes that could be removed - I have only indicated those which I have worked on.

  • CanetoadOld_OBSOLETE.cs
  • Crow.cs
  • Dong.Felt.Main.cs
  • DrawEasyImage.cs
  • EPR.cs
  • FeltTemplate_Create.cs
  • FeltTemplate_Edit.cs
  • FeltTemplates_Use.cs
  • FrogRibit_OBSOLETE.cs
  • Frogs_OBSOLETE.cs
  • GratingDetection_OBSOLETE.cs
  • HerveGlotinCollaboration.cs
  • Human1.cs
  • LewinsRail3OBSOLETE.cs
  • LimnodynastesConvex_OBSOLETE.cs
  • LitoriaFallax_OBSOLETE.cs
  • PlanesTrainsAndAutomobiles.cs
  • Rain_OBSOLETE.cs
  • RheobatrachusSilus.cs
  • SPR_OBSOLETE.cs
  • SURFAnalysis.cs
  • XiesAnalysis.cs

Some classes in other folders that can likely be removed.

  • /Recognizers/CriniaTinnula_OBSOLETE.cs
  • /AnalysisConfigFiles/Towsey.MultiAnalyser.OBSOLETE.yml
  • /AudioAnalysisTools/BirdClefExperiment1.cs
  • /AudioAnalysisTools/FrommoltProject.cs
  • /AudioAnalysisTools/SURFFeatures.cs
  • /AudioAnalysisTools/DSP/AudioSegmentationOBSOLETE.cs
  • /AudioAnalysis/Dong.Felt
  • /AudioAnalysis/TowseyLibrary/Gratings.cs

atruskie pushed a commit that referenced this issue Jan 27, 2018
This is work for the open source release (see #140)

Remove obsolete classes and clean up others keeping only core
funcionality. Still retain Sandpit class

More clean up and resharper work
atruskie added a commit that referenced this issue Jan 27, 2018
This commit deletes all Matlab, RCode, and most importantly
all the binaries from the ExtraAssemblies directory.

This commit will be used as the basis for cleaning out binary files
in the open source release. See #140 (https://github.com/QutBioacoustics/audio-analysis/issues/140)

There is more code to delete but nearly all the files that need
to be **cleaned** are removed in this commit.

Please note: we have internal backups of this repository as well
as an online backup here at https://github.com/QutBioacoustics/audio-analysis-archive

 Please enter the commit message for your changes. Lines starting
 with '#' will be ignored, and an empty message aborts the commit.

 On branch master
 Your branch is up to date with 'origin/master'.

 Changes to be committed:
	deleted:    AudioAnalysis/AED/Test/matlab/BAC2_20071015-045040.wav
	deleted:    AudioAnalysis/AED/Test/matlab/BAC2_20071015-045040/AE1.csv
	deleted:    AudioAnalysis/AED/Test/matlab/BAC2_20071015-045040/AE2.csv
	deleted:    AudioAnalysis/AED/Test/matlab/BAC2_20071015-045040/AE3.csv
	deleted:    AudioAnalysis/AED/Test/matlab/BAC2_20071015-045040/I1.csv
	deleted:    AudioAnalysis/AED/Test/matlab/BAC2_20071015-045040/I2.csv
	deleted:    AudioAnalysis/AED/Test/matlab/BAC2_20071015-045040/I3.csv
	deleted:    AudioAnalysis/AED/Test/matlab/BAC2_20071015-045040/I4.csv
	deleted:    AudioAnalysis/AED/Test/matlab/BAC2_20071015-045040/I5.csv
	deleted:    AudioAnalysis/AED/Test/matlab/BAC2_20071015-045040/I6.csv
	deleted:    AudioAnalysis/AED/Test/matlab/GParrots_JB2_20090607-173000.wav_minute_10.wav
	deleted:    AudioAnalysis/AED/Test/matlab/GParrots_JB2_20090607-173000.wav_minute_3/AE1.csv
	deleted:    AudioAnalysis/AED/Test/matlab/GParrots_JB2_20090607-173000.wav_minute_3/AE2.csv
	deleted:    AudioAnalysis/AED/Test/matlab/GParrots_JB2_20090607-173000.wav_minute_3/AE3.csv
	deleted:    AudioAnalysis/AED/Test/matlab/GParrots_JB2_20090607-173000.wav_minute_3/EPRAE.csv
	deleted:    AudioAnalysis/AED/Test/matlab/GParrots_JB2_20090607-173000.wav_minute_3/EPRCandidates.csv
	deleted:    AudioAnalysis/AED/Test/matlab/GParrots_JB2_20090607-173000.wav_minute_3/EPRresults.csv
	deleted:    AudioAnalysis/AED/Test/matlab/GParrots_JB2_20090607-173000.wav_minute_3/EPRtemplatebottomlefts.csv
	deleted:    AudioAnalysis/AED/Test/matlab/GParrots_JB2_20090607-173000.wav_minute_3/EPRtemplatecentroids.csv
	deleted:    AudioAnalysis/AED/Test/matlab/GParrots_JB2_20090607-173000.wav_minute_3/I1.csv
	deleted:    AudioAnalysis/AED/Test/matlab/GParrots_JB2_20090607-173000.wav_minute_3/I2.csv
	deleted:    AudioAnalysis/AED/Test/matlab/GParrots_JB2_20090607-173000.wav_minute_3/I3.csv
	deleted:    AudioAnalysis/AED/Test/matlab/GParrots_JB2_20090607-173000.wav_minute_3/I4.csv
	deleted:    AudioAnalysis/AED/Test/matlab/GParrots_JB2_20090607-173000.wav_minute_3/I5.csv
	deleted:    AudioAnalysis/AED/Test/matlab/GParrots_JB2_20090607-173000.wav_minute_3/I6.csv
	deleted:    AudioAnalysis/AED/Test/matlab/SPT/Female1_HoneymoonBay_StBees_20081027-023000.wav
	deleted:    AudioAnalysis/AED/Test/matlab/SPT/I3.csv
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	deleted:    AudioAnalysis/AED/Test/matlab/SPT/peaksI3_h.csv
	deleted:    AudioAnalysis/Matlab/AED/do_acoustic_event_detection.m
	deleted:    AudioAnalysis/Matlab/AED/do_acoustic_event_detection_GP.m
	deleted:    AudioAnalysis/Matlab/AED/get_acoustic_events.m
	deleted:    AudioAnalysis/Matlab/AED/image_thresh_bw.m
	deleted:    AudioAnalysis/Matlab/AED/join_horizontal_lines.m
	deleted:    AudioAnalysis/Matlab/AED/join_vertical_lines.m
	deleted:    AudioAnalysis/Matlab/AED/mode_intensity_thresh.m
	deleted:    AudioAnalysis/Matlab/AED/mode_large_area_threshold.m
	deleted:    AudioAnalysis/Matlab/AED/mode_small_area_threshold.m
	deleted:    AudioAnalysis/Matlab/AED/separate_large_AEs_areas.m
	deleted:    AudioAnalysis/Matlab/Common/computeSPT.m
	deleted:    AudioAnalysis/Matlab/Common/getAcousticEventPixels.m
	deleted:    AudioAnalysis/Matlab/Common/showImage.m
	deleted:    AudioAnalysis/Matlab/Common/showImageChooseColour.m
	deleted:    AudioAnalysis/Matlab/Common/wavToSpectrogram.m
	deleted:    AudioAnalysis/Matlab/Common/withoutSubbandModeIntensities.m
	deleted:    AudioAnalysis/Matlab/EPR/Ground Parrot/GParrots_JB2_20090607-173000.wav_minute_3.wav
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	deleted:    AudioAnalysis/Matlab/EPR/Ground Parrot/GParrots_JB2_20090607-173000.wav_minute_3.wav_Intensity_Thresh_3dB_Small_area_thresh_max_100_template72.mat
	deleted:    AudioAnalysis/Matlab/EPR/Ground Parrot/GParrots_JB2_20090607-173000.wav_minute_8.wav
	deleted:    AudioAnalysis/Matlab/EPR/Ground Parrot/GParrots_JB2_20090607-173000.wav_minute_8.wav.png
	deleted:    AudioAnalysis/Matlab/EPR/Ground Parrot/GParrots_JB2_20090607-173000.wav_minute_8.wav_Intensity_Thresh_3dB_Small_area_thresh_max_100.xls
	deleted:    AudioAnalysis/Matlab/EPR/Ground Parrot/GParrots_JB2_20090607-173000.wav_minute_8.wav_Intensity_Thresh_6dB_Small_area_thresh_max_100_template52.mat
	deleted:    AudioAnalysis/Matlab/EPR/Ground Parrot/Matching_GParrots_JB2_20090607-173000.wav_minute_3.wav_Intensity_Thresh_3dB_Small_area_thresh_max_100_template72.xls
	deleted:    AudioAnalysis/Matlab/EPR/Ground Parrot/Matching_GParrots_JB2_20090607-173000.wav_minute_8.wav_Intensity_Thresh_6dB_Small_area_thresh_max_100_template52.xls
	deleted:    AudioAnalysis/Matlab/EPR/Ground Parrot/examine_all_AE_results.m
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	deleted:    AudioAnalysis/Matlab/EPR/Ground Parrot/old/ground_parrot_image_template_47.mat
	deleted:    AudioAnalysis/Matlab/EPR/Ground Parrot/scan_image_for_AEs.m
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	deleted:    AudioAnalysis/Matlab/EPR/Koala/Honeymoon Bay - St Bees_20080905-001000.wav
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	deleted:    AudioAnalysis/Matlab/EPR/Koala/Top Knoll - St Bees_20080912-213000.wav
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	deleted:    AudioAnalysis/Matlab/EPR/Koala/examine_all_AE_results.m
	deleted:    AudioAnalysis/Matlab/EPR/Koala/koala_template_example.m
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	deleted:    AudioAnalysis/Matlab/EPR/Koala/scan_image_for_AEs_koala.m
	deleted:    AudioAnalysis/Matlab/EPR/Koala/subband_mode_intensities.m
	deleted:    AudioAnalysis/Matlab/EPR/Koala/template_matching_using_distance_koala.m
	deleted:    AudioAnalysis/Matlab/Jie/MIML anaysis for frog call classification/AED.m
	deleted:    AudioAnalysis/Matlab/Jie/MIML anaysis for frog call classification/AEDFodor.m
	deleted:    AudioAnalysis/Matlab/Jie/MIML anaysis for frog call classification/AEDJie.m
	deleted:    AudioAnalysis/Matlab/Jie/MIML anaysis for frog call classification/AEDLasseck.m
	deleted:    AudioAnalysis/Matlab/Jie/MIML anaysis for frog call classification/AEDPotamitis.m
	deleted:    AudioAnalysis/Matlab/Jie/MIML anaysis for frog call classification/MIL.m
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atruskie pushed a commit that referenced this issue Jan 30, 2018
This is work for the open source release (see #140)
Remove obsolete classes and clean up others keeping only core
funcionality. Still retain Sandpit class
More clean up and resharper work
Original hash: 88715b7
atruskie added a commit that referenced this issue Feb 2, 2018
The directories and files are mostly organized now according to de facto standard for organizing code. This work is completed partially for #140

Please note: this is not a functional commit. It in no way is buildable.
atruskie added a commit that referenced this issue Feb 2, 2018
This commit removes obsolete projects. The projects removed:

- AudioBrowser was a GUI developed for viewing LDFC spectrograms but is now unmaintained
- Dong.Felt is code that belonged to Xueyan Dong. Relvant code, mainly calculation of ridges, has been previously ported.
- QutBioacosutics.Xie is code that belonged to Jie Xie. It is not clear whether this code has been reused, but it is unmaintained.
- FELT/* projects were code created by Anthony Truskinger. The code is no longer functional and since being written has been superseeded by better techniques

All the code deleted here has been backed up in the archive copy of audio-analysis.

This is work done for #140 - open sourcing our code. This commit is non-buildable.
@atruskie atruskie added this to the Open Source milestone Feb 2, 2018
atruskie added a commit that referenced this issue Feb 15, 2018
The work done in 864f7a4 to reorganize the solution for our open source release (see #140) was left incomplete because various dependencies needed to be replaced.

This commit fixes nearly all tests (with the exception of one test which is now detailed in #146).

This commit also:
- Replaces our chosen cloning library (GerorgeCloney) with a newer one that can clone `FileInfo`s via reflection
- Fixes a bug from 72aab48 where `FrequencyScaleType` property did not match the name used in the config files
- The changed FFT calculation produced very very small changes in anything that depends on the FFT. I either recalculated our expected binary matrices, or for most failing cases added a delta threshold to the comparison. I found 1E-9 was plenty of delta and three orders of magnitude smaller than any change we could notice
- I adjusted the build to ensure audio tools are copied to test output
atruskie added a commit that referenced this issue Feb 15, 2018
The F# unit tests were broken in 864f7a4. This commit ensures they work again.

Work for #140
atruskie added a commit that referenced this issue Feb 17, 2018
I went through and applied as many automatic rules as I could. Work for #140
atruskie added a commit that referenced this issue Feb 17, 2018
Also cleans up the main README a bit.

Work done for #140
atruskie added a commit that referenced this issue Mar 1, 2018
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atruskie commented Mar 5, 2018

This was finally completed in 6ea3cbb

@atruskie atruskie closed this as completed Mar 5, 2018
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