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Fix several bugs
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@hagenw
hagenw committed Oct 11, 2018
1 parent 4057fbf commit 37143cc
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Showing 126 changed files with 4,284 additions and 875 deletions.
6 changes: 4 additions & 2 deletions AuditoryMachineLearningTrainingTestingPipeline/src/+BlockCreators/Base.m
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Original file line number Diff line number Diff line change
Expand Up @@ -53,8 +53,9 @@ function process( obj, wavFilepath )
%% -------------------------------------------------------------------------------

% override of Core.IdProcInterface's method
function fileProcessed = hasFileAlreadyBeenProcessed( ~, ~ )
function [fileProcessed,cacheDir] = hasFileAlreadyBeenProcessed( ~, ~ )
fileProcessed = false;
cacheDir = [];
end
%% -------------------------------------------------------------------------------

Expand Down Expand Up @@ -130,11 +131,12 @@ function delete( obj )
%% -------------------------------------------------------------------------------
function processInternal( obj, varargin )
obj.inputProc.sceneId = obj.sceneId;
in = obj.loadInputData( obj.curWavFilepath, 'afeData', 'annotations' );
if nargin < 2 || any( strcmpi( 'afeBlocks', varargin ) )
in = obj.loadInputData( obj.curWavFilepath, 'afeData', 'annotations' );
[obj.blockAnnotations,obj.afeBlocks] = ...
obj.blockify( in.afeData, in.annotations );
else
in = obj.loadInputData( obj.curWavFilepath, 'annotations' );
obj.blockAnnotations = obj.blockify( in.afeData, in.annotations );
end
end
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55 changes: 55 additions & 0 deletions AuditoryMachineLearningTrainingTestingPipeline/src/+BlockCreators/FullFileBlockCreator.m
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Original file line number Diff line number Diff line change
@@ -0,0 +1,55 @@
classdef FullFileBlockCreator < BlockCreators.Base
%
%% -----------------------------------------------------------------------------------
properties (SetAccess = private)
end

%% -----------------------------------------------------------------------------------
methods

function obj = FullFileBlockCreator()
obj = obj@BlockCreators.Base( inf, 0 );
end
%% -------------------------------------------------------------------------------

end

%% -----------------------------------------------------------------------------------
methods (Access = protected)

function outputDeps = getBlockCreatorInternOutputDependencies( obj )
outputDeps.v = 1;
end
%% -------------------------------------------------------------------------------

function [blockAnnots,afeBlocks] = blockify( obj, afeData, annotations )
currentDependencies = obj.getOutputDependencies();
sceneConfig = currentDependencies.preceding.preceding.sceneCfg;
annotations = BlockCreators.StandardBlockCreator.extendAnnotations( ...
sceneConfig, annotations );
anyAFEsignal = afeData(1);
if isa( anyAFEsignal, 'cell' ), anyAFEsignal = anyAFEsignal{1}; end;
streamLen_s = double( size( anyAFEsignal.Data, 1 ) ) / anyAFEsignal.FsHz;
if nargout > 1
afeBlocks = {afeData};
end
blockAnnots = annotations;
blockAnnots.blockOnset = 0;
blockAnnots.blockOffset = streamLen_s;
end
%% -------------------------------------------------------------------------------

end
%% -----------------------------------------------------------------------------------

methods (Static)

%% -------------------------------------------------------------------------------
%% -------------------------------------------------------------------------------

end

end



60 changes: 54 additions & 6 deletions AuditoryMachineLearningTrainingTestingPipeline/src/+BlockCreators/MeanStandardBlockCreator.m
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@
function outputDeps = getBlockCreatorInternOutputDependencies( obj )
outputDeps.sbc = getBlockCreatorInternOutputDependencies@...
BlockCreators.StandardBlockCreator( obj );
outputDeps.v = 1;
outputDeps.v = 3;
end
%% -------------------------------------------------------------------------------

Expand All @@ -32,6 +32,10 @@
blockAnnots = blockify@BlockCreators.StandardBlockCreator( ...
obj, afeData, annotations );
end
[blockAnnots(:).nrj] = deal(struct('t',[],'nrj',[]));
[blockAnnots(:).nrjOthers] = deal(struct('t',[],'nrjOthers',[]));
[blockAnnots(:).srcSNRactive] = deal(struct('t',[],'srcSNRactive',[]));
[blockAnnots(:).srcSNR2] = deal(struct('t',[],'srcSNR2',[]));
aFields = fieldnames( blockAnnots );
isSequenceAnnotation = cellfun( @(af)(...
isstruct( blockAnnots(1).(af) ) && ...
Expand All @@ -40,30 +44,74 @@
), aFields );
sequenceAfields = aFields(isSequenceAnnotation);
for ii = 1 : numel( blockAnnots )
blockAnnots(ii) = ...
BlockCreators.MeanStandardBlockCreator.adjustPreMeanAnnotations( ...
blockAnnots(ii) );
for jj = 1 : numel( sequenceAfields )
seqAname = sequenceAfields{jj};
annot = blockAnnots(ii).(seqAname);
if length( annot.t ) == size( annot.(seqAname), 1 )
if iscell( annot.(seqAname) )
annotSeq = annot.(seqAname);
if length( annot.t ) == size( annotSeq, 1 )
if iscell( annotSeq )
as_szs = cellfun( @(c)( size( c, 2 ) ), annotSeq(1,:) );
blockAnnots(ii).(seqAname) = ...
cellSqueezeFun( @mean, annot.(seqAname), 1, true );
mat2cell( nanmean( cell2mat( annotSeq ), 1 ), 1, as_szs );
else
blockAnnots(ii).(seqAname) = mean( annot.(seqAname), 1 );
blockAnnots(ii).(seqAname) = nanmean( annotSeq, 1 );
end
else
error( 'unexpected annotations sequence structure' );
end
end
blockAnnots(ii) = ...
BlockCreators.MeanStandardBlockCreator.extendMeanAnnotations( ...
blockAnnots(ii) );
end
end
%% -------------------------------------------------------------------------------
%% -------------------------------------------------------------------------------

end
%% -----------------------------------------------------------------------------------

methods (Static)

%% -------------------------------------------------------------------------------

% TODO: this is the wrong place for the annotation computation; it
% should be done in SceneEarSignalProc -- and is now here, for the
% moment, to avoid recomputation with SceneEarSignalProc.

function avgdBlockAnnots = extendMeanAnnotations( avgdBlockAnnots )
srcsGlobalRefEnergyMeanChannel = cellfun( ...
@(c)(sum(c) ./ 2 ), avgdBlockAnnots.globalSrcEnergy );
srcsGlobalRefEnergyMeanChannel_db = 10 * log10( srcsGlobalRefEnergyMeanChannel );
haveSrcsEnergy = srcsGlobalRefEnergyMeanChannel_db > -40;
isAmbientSource = isnan( avgdBlockAnnots.srcAzms );
haveSrcsEnergy(isAmbientSource) = [];
avgdBlockAnnots.nActivePointSrcs = single( sum( haveSrcsEnergy ) );
avgdBlockAnnots.srcSNR2 = 10 * log10( avgdBlockAnnots.nrj ./ avgdBlockAnnots.nrjOthers );
avgdBlockAnnots.nrj = 10 * log10( avgdBlockAnnots.nrj );
avgdBlockAnnots.nrjOthers = 10 * log10( avgdBlockAnnots.nrjOthers );
avgdBlockAnnots.globalSrcEnergy = cellfun( @(c)(10 * log10( c )), ...
avgdBlockAnnots.globalSrcEnergy, 'UniformOutput', false );
end
%% -------------------------------------------------------------------------------

% TODO: this is the wrong place for the annotation computation; it
% should be done in SceneEarSignalProc -- and is now here, for the
% moment, to avoid recomputation with SceneEarSignalProc.

function annotations = adjustPreMeanAnnotations( annotations )
annotations.srcSNRactive.t = annotations.globalSrcEnergy.t;
annotations.srcSNRactive.srcSNRactive = annotations.srcSNR_db.srcSNR_db;
allSrcsInactive = annotations.nActivePointSrcs.nActivePointSrcs == 0;
annotations.srcSNRactive.srcSNRactive(allSrcsInactive,:) = nan;
annotations.srcSNRactive.srcSNRactive = annotations.srcSNRactive.srcSNRactive;
annotations.nrj.t = annotations.globalSrcEnergy.t;
annotations.nrj.nrj = 10.^(annotations.nrj_db.nrj_db./10);
annotations.nrjOthers.t = annotations.globalSrcEnergy.t;
annotations.nrjOthers.nrjOthers = 10.^(annotations.nrjOthers_db.nrjOthers_db./10);
end
%% -------------------------------------------------------------------------------

end
Expand Down
55 changes: 53 additions & 2 deletions AuditoryMachineLearningTrainingTestingPipeline/src/+BlockCreators/StandardBlockCreator.m
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Original file line number Diff line number Diff line change
Expand Up @@ -18,11 +18,15 @@
methods (Access = protected)

function outputDeps = getBlockCreatorInternOutputDependencies( obj )
outputDeps.v = 2;
outputDeps.v = 4;
end
%% -------------------------------------------------------------------------------

function [blockAnnots,afeBlocks] = blockify( obj, afeData, annotations )
currentDependencies = obj.getOutputDependencies();
sceneConfig = currentDependencies.preceding.preceding.sceneCfg;
annotations = BlockCreators.StandardBlockCreator.extendAnnotations( ...
sceneConfig, annotations );
anyAFEsignal = afeData(1);
if isa( anyAFEsignal, 'cell' ), anyAFEsignal = anyAFEsignal{1}; end;
streamLen_s = double( size( anyAFEsignal.Data, 1 ) ) / anyAFEsignal.FsHz;
Expand Down Expand Up @@ -80,13 +84,60 @@
blockAnnots = flipud( blockAnnots );
end
%% -------------------------------------------------------------------------------

end
%% -----------------------------------------------------------------------------------

methods (Static)

%% -------------------------------------------------------------------------------

% TODO: this is the wrong place for the annotation computation; it
% should be done in SceneEarSignalProc -- and is now here, for the
% moment, to avoid recomputation with SceneEarSignalProc.

function annotations = extendAnnotations( sceneConfig, annotations )
annotations.srcSNR_db.t = annotations.globalSrcEnergy.t;
annotations.srcSNR_db.srcSNR_db = zeros( size( annotations.globalSrcEnergy.globalSrcEnergy ) );
annotations.nrj_db.t = annotations.globalSrcEnergy.t;
annotations.nrj_db.nrj_db = zeros( size( annotations.globalSrcEnergy.globalSrcEnergy ) );
annotations.nrjOthers_db.t = annotations.globalSrcEnergy.t;
annotations.nrjOthers_db.nrjOthers_db = zeros( size( annotations.globalSrcEnergy.globalSrcEnergy ) );
annotations.nActivePointSrcs.t = annotations.globalSrcEnergy.t;
annotations.nActivePointSrcs.nActivePointSrcs = zeros( size( annotations.globalSrcEnergy.globalSrcEnergy ) );
if std( sceneConfig.snrRefs ) ~= 0
error( 'AMLTTP:usage:snrRefMustBeSame', 'different snrRefs not supported' );
end
snrRef = sceneConfig.snrRefs(1);
nSrcs = size( annotations.globalSrcEnergy.globalSrcEnergy, 2 );
srcsGlobalRefEnergyMeanChannel = zeros( ...
size( annotations.globalSrcEnergy.globalSrcEnergy ) );
for ss = 1 : nSrcs
srcsGlobalRefEnergyMeanChannel(:,ss) = mean( ...
cell2mat( annotations.globalSrcEnergy.globalSrcEnergy(:,ss) ), 2 );
end
srcsGlobalRefEnergyMeanChannel_db = 10 * log10( srcsGlobalRefEnergyMeanChannel );
snrRefNrjOffsets = cell2mat( annotations.globalNrjOffsets.globalNrjOffsets ) ...
- annotations.globalNrjOffsets.globalNrjOffsets{snrRef};
annotations.globalNrjOffsets = snrRefNrjOffsets;
for ss = 1 : nSrcs
otherIdxs = 1 : size( srcsGlobalRefEnergyMeanChannel, 2 );
otherIdxs(ss) = [];
srcsCurrentSrcRefEnergy_db = srcsGlobalRefEnergyMeanChannel_db ...
- snrRefNrjOffsets(ss);
srcsCurrentSrcRefEnergy = 10.^(srcsCurrentSrcRefEnergy_db./10);
sumOtherSrcsEnergy = sum( srcsCurrentSrcRefEnergy(:,otherIdxs), 2 );
sumOthersSrcsEnergy_db = 10 * log10( sumOtherSrcsEnergy );
annotations.nrjOthers_db.nrjOthers_db(:,ss) = single( sumOthersSrcsEnergy_db );
annotations.nrj_db.nrj_db(:,ss) = single( srcsCurrentSrcRefEnergy_db(:,ss) );
annotations.srcSNR_db.srcSNR_db(:,ss) = single( ...
srcsCurrentSrcRefEnergy_db(:,ss) - sumOthersSrcsEnergy_db );
end
haveSrcsEnergy = srcsGlobalRefEnergyMeanChannel_db > -40;
isAmbientSource = all( isnan( annotations.srcAzms.srcAzms ), 1 );
haveSrcsEnergy(:,isAmbientSource) = [];
annotations.nActivePointSrcs.nActivePointSrcs = single( sum( haveSrcsEnergy, 2 ) );
end
%% -------------------------------------------------------------------------------

end
Expand Down
11 changes: 8 additions & 3 deletions AuditoryMachineLearningTrainingTestingPipeline/src/+Core/DataPipeProc.m
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ function connectToOutputFrom( obj, outputtingProc )
end
%% ----------------------------------------------------------------

function checkDataFiles( obj, otherOverlay )
function cacheDirs = checkDataFiles( obj, otherOverlay )
fprintf( '\nChecking file list: %s\n%s\n', ...
obj.dataFileProcessor.procName, ...
repmat( '=', 1, 20 + numel( obj.dataFileProcessor.procName ) ) );
Expand All @@ -64,8 +64,13 @@ function checkDataFiles( obj, otherOverlay )
obj.dataFileProcessor.getSingleProcessCacheAccess();
DataProcs.MultiSceneCfgsIdProcWrapper.doEarlyHasProcessedStop( true, false );
end
fileHasBeenProcessed = ...
obj.dataFileProcessor.hasFileAlreadyBeenProcessed( dataFile.fileName );
if nargout > 0 && ~exist( 'cacheDirs', 'var' )
[fileHasBeenProcessed,cacheDirs] = ...
obj.dataFileProcessor.hasFileAlreadyBeenProcessed( dataFile.fileName );
else
fileHasBeenProcessed = ...
obj.dataFileProcessor.hasFileAlreadyBeenProcessed( dataFile.fileName );
end
if ii == 1
DataProcs.MultiSceneCfgsIdProcWrapper.doEarlyHasProcessedStop( true, true );
obj.dataFileProcessor.saveCacheDirectory();
Expand Down
9 changes: 5 additions & 4 deletions AuditoryMachineLearningTrainingTestingPipeline/src/+Core/IdCacheDirectory.m
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Original file line number Diff line number Diff line change
Expand Up @@ -148,7 +148,7 @@ function loadCacheDirectory( obj, filename )
end
%% -------------------------------------------------------------------------------

function maintenance( obj )
function maintenance( obj, deleteEmpties )
cDirs = dir( [obj.topCacheDirectory filesep 'cache.*'] );
cacheDirs = cell( 0, 3 );
fprintf( '-> read cache folders\n' );
Expand All @@ -159,7 +159,7 @@ function maintenance( obj )
pause;
else
cdContents = dir( [obj.topCacheDirectory filesep cDirs(ii).name filesep '*.mat'] );
if all( strcmpi( 'cfg.mat', {cdContents.name} ) | strcmpi( 'fdesc.mat', {cdContents.name} ) )
if deleteEmpties && all( strcmpi( 'cfg.mat', {cdContents.name} ) | strcmpi( 'fdesc.mat', {cdContents.name} ) )
rmdir( [obj.topCacheDirectory filesep cDirs(ii).name], 's' );
fprintf( 'deleting empty cache folder ' );
else
Expand Down Expand Up @@ -310,11 +310,12 @@ function maintenance( obj )
end
%% -------------------------------------------------------------------------------

function standaloneMaintain( cacheTopDir )
function standaloneMaintain( cacheTopDir, deleteEmpties )
if nargin < 2, deleteEmpties = true; end
cache = Core.IdCacheDirectory();
cache.setCacheTopDir( cacheTopDir );
cache.loadCacheDirectory();
cache.maintenance();
cache.maintenance( deleteEmpties );
end
%% -------------------------------------------------------------------------------

Expand Down
28 changes: 26 additions & 2 deletions AuditoryMachineLearningTrainingTestingPipeline/src/+Core/IdProcInterface.m
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Original file line number Diff line number Diff line change
Expand Up @@ -118,9 +118,17 @@ function init( obj )
end
%% -------------------------------------------------------------------------------

function fileProcessed = hasFileAlreadyBeenProcessed( obj, wavFilepath )
function [fileProcessed,cacheDir] = hasFileAlreadyBeenProcessed( obj, wavFilepath )
if isempty( wavFilepath ), fileProcessed = false; return; end
fileProcessed = exist( obj.getOutputFilepath( wavFilepath ), 'file' );
cacheFile = obj.getOutputFilepath( wavFilepath );
if obj.forceCacheRewrite
fileProcessed = false;
else
fileProcessed = exist( cacheFile, 'file' );
end
if nargout > 1
cacheDir = fileparts( cacheFile );
end
end
%% -------------------------------------------------------------------------------

Expand Down Expand Up @@ -222,6 +230,22 @@ function save( obj, wavFilepath, out )

end

%% --------------------------------------------------------------------
methods (Static)

function b = forceCacheRewrite( newValue )
persistent fcrw;
if isempty( fcrw )
fcrw = false;
end
if nargin > 0
fcrw = newValue;
else
b = fcrw;
end
end

end
%% -----------------------------------------------------------------------------------
methods (Abstract)
process( obj, wavFilepath )
Expand Down

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