test statΒΆ

function test_suite = test_stat
% tests for cosmo_stat
%
% #   For CoSMoMVPA's copyright information and license terms,   #
% #   see the COPYING file distributed with CoSMoMVPA.           #
    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
        test_functions=localfunctions();
    catch % no problem; early Matlab versions can use initTestSuite fine
    end
    initTestSuite;


function r=randint(x)
    r=ceil(rand()*x+10);

function test_stat_correspondence
    is_matlab=cosmo_wtf('is_matlab');

    if isempty(which('ttest'))
        cosmo_notify_test_skipped('ttest is not available');
        return
    end

    % test conformity with matlab's stat functions
    ntargets=randint(5);
    nchunks=randint(5);
    ds=cosmo_synthetic_dataset('nchunks',nchunks,'ntargets',ntargets,'sigma',0);
    ds.samples=randn(size(ds.samples)); % full random data
    ds=cosmo_slice(ds,[2 5 6],2);
    [ns,nf]=size(ds.samples);

    f=zeros(1,nf);
    p=zeros(1,nf);


    for k=1:nf
        if is_matlab
            [p(k),tab]=anova1(ds.samples(:,k), ds.sa.targets, 'off');
            f(k)=tab{2,5};
            df=[tab{2:3,3}];
        else
            [p(k),f(k),df_b,df_w]=anova(ds.samples(:,k), ds.sa.targets);
            df=[df_b df_w];
        end
    end
    % f stat

    ds.sa.chunks=(1:ns)';
    ff=cosmo_stat(ds,'F');
    assertVectorsAlmostEqual(f,ff.samples);
    assertEqual(ff.sa.stats,{sprintf('Ftest(%d,%d)',df)});

    pp=cosmo_stat(ds,'F','p');
    assertVectorsAlmostEqual(p,pp.samples);

    ds.sa.chunks(:)=1;
    assertExceptionThrown(@()cosmo_stat(ds,'F'),'');

    % t stat
    tails={'p','left','right','both'};
    for k=1:numel(tails)
        % one-sample ttest
        assertExceptionThrown(@()cosmo_stat(ds,'t'),'');
        ds1=ds;
        ds1.sa.targets(:)=10;
        ds1.sa.chunks=(1:ns)';

        tail=tails{k};


        if strcmp(tail,'p')
            ttest_arg=cell(0);
        else
            ttest_arg={'tail',tail};
        end

        % test t-statistic
        [h,p,ci,stats]=ttest_wrapper(ds.samples,0,ttest_arg{:});

        tt=cosmo_stat(ds1,'t');
        assertVectorsAlmostEqual(stats.tstat,tt.samples);
        assertEqual(tt.sa.stats,{sprintf('Ttest(%d)',stats.df(1))});

        pp=cosmo_stat(ds1,'t',tail);
        assertVectorsAlmostEqual(p,pp.samples);

        ds1.sa.chunks(:)=1;
        assertExceptionThrown(@()cosmo_stat(ds1,'t'),'');

        % two-sample (unpaired) ttest
        ds2=ds;
        i=randperm(ns)';
        ds2.sa.targets=mod(i,2)+1;
        ds2.sa.chunks=i;
        ds_sp=cosmo_split(ds2,'targets');
        x=ds_sp{1}.samples;
        y=ds_sp{2}.samples;

        [h,p,ci,stats]=ttest2_wrapper(x,y,ttest_arg{:});
        tt=cosmo_stat(ds2,'t2');

        assertVectorsAlmostEqual(stats.tstat,tt.samples);
        assertEqual(tt.sa.stats,{sprintf('Ttest(%d)',stats.df(1))});


        pp=cosmo_stat(ds2,'t2',tail);
        assertVectorsAlmostEqual(p,pp.samples);

        ds2.sa.chunks(1)=ds2.sa.chunks(1)+1;
        assertExceptionThrown(@()cosmo_stat(ds1,'t2'),'');

        ds2.sa.chunks(1)=ds2.sa.chunks(1)-1;
        ds2.sa.targets(1)=ds2.sa.targets(1)+1;
        assertExceptionThrown(@()cosmo_stat(ds1,'t2'),'');
        ds2.sa.targets(:)=1;
        assertExceptionThrown(@()cosmo_stat(ds1,'t2'),'');

    end

    assertExceptionThrown(@()cosmo_stat(ds,'t2'),'');
    assertExceptionThrown(@()cosmo_stat(ds,'t'),'');


function test_stat_contrast()
    ds=cosmo_synthetic_dataset('nchunks',6,'ntargets',4,'sigma',0);
    ds.sa.contrast=zeros(size(ds.sa.targets));
    ds.sa.contrast(ds.sa.targets==2)=1;
    ds.sa.contrast(ds.sa.targets==4)=-1;
    chunks=ds.sa.chunks;
    ds.sa.chunks=chunks*6+ds.sa.targets;

    res=cosmo_stat(ds,'F','z');
    assertElementsAlmostEqual(res.samples,...
                    [0.2695 0.9675 -0.8770 -1.0542 0.9173 1.2814],...
                    'absolute',1e-4);

    % test exceptions
    aet=@(varargin)assertExceptionThrown(@()...
                            cosmo_stat(varargin{:}),'');

    ds2=cosmo_slice(ds,ds.sa.contrast~=0);
    aet(ds2,'t');
    aet(ds2,'t2');

    ds.sa.contrast(1)=1;
    aet(ds,'F');

    ds.sa.contrast(ds.sa.targets==1)=1;
    aet(ds,'F');

    % within subject F
    ds.sa.chunks=chunks;
    aet(ds,'F');
    aet(ds,'t');
    aet(ds,'t2');

function [h,p,ci,stats]=ttest_wrapper(varargin)
    [h,p,ci,stats]=general_ttestX_wrapper(@ttest,varargin{:});

function [h,p,ci,stats]=ttest2_wrapper(varargin)
    [h,p,ci,stats]=general_ttestX_wrapper(@ttest2,varargin{:});

function [h,p,ci,stats]=general_ttestX_wrapper(func,varargin)
    args=varargin;
    switch nargin(func)
        case {5,6}
            % old Matlab
            args=remove_keys_from_arguments(2,{'alpha','tail','dim'},args);
        case -3
            % GNU Octave and recent Matlab

        otherwise
            assert(false);
    end

    [h,p,ci,stats]=func(args{:});

function short_args=remove_keys_from_arguments(skip_count,keys,args)
    n=numel(keys);
    short_args=cell(1,skip_count+n);
    short_args(1:skip_count)=args(1:skip_count);
    for k=1:n
        key=keys{k};
        i=strmatch(key,args((skip_count+1):2:end));
        if isempty(i)
            short_arg=[];
        else
            short_arg=args{skip_count+i*2};
        end
        short_args{skip_count+k}=short_arg;
    end

function test_stat_no_division_by_zero_error()
    [lastmsg,lastid]=lastwarn();
    cleaner=onCleanup(@()lastwarn(lastmsg,lastid));
    lastwarn('');

    ds=cosmo_synthetic_dataset('ntargets',1,'nchunks',1);
    ds.samples(:)=0;

    cosmo_stat(ds,'t','z');
    assertEqual(lastwarn(),'');

function test_stat_same_nan_fstat()
    ds=cosmo_synthetic_dataset('nchunks',4,'ntargets',3);
    ds.samples(ds.sa.chunks==3,[1 3 5])=NaN;

    stat=cosmo_stat(ds,'F'); % should be ok
    assertEqual(isnan(stat.samples),any(isnan(ds.samples),1));





function test_stat_exceptions()
    ds=cosmo_synthetic_dataset('ntargets',3);
    aet=@(varargin)assertExceptionThrown(@()...
                            cosmo_stat(varargin{:}),'');
    aet(ds,'foo');
    aet(ds,'F','foo');
    aet(ds,'t');

    ds2=cosmo_slice(ds,ds.sa.targets==1);
    aet(ds2,'F');
    aet(ds2,'t2');

function test_stat_missing_values()
    % assuming that cosmo_stat works well with no NaNs, try it
    % with some missing values

    output_labels={'','p','z','left','right'};
    n_outputs=numel(output_labels);

    for k=1:5
        switch k
            % sa_label_func (below) takes the number of chunks and
            % returns a statistic sa label

            case 1
                stat_name='t';
                ntargets=1;
                is_between=true;
                sa_label_func=@(x)sprintf('Ttest(%d)',x-1);

            case 2
                stat_name='t';
                ntargets=2;
                is_between=false;
                sa_label_func=@(x)sprintf('Ttest(%d)',x-1);

            case 3
                stat_name='t2';
                ntargets=2;
                is_between=true;
                sa_label_func=@(x)sprintf('Ttest(%d)',x-2);

            case 4
                stat_name='F';
                ntargets=randint(5);
                is_between=true;
                sa_label_func=@(x)sprintf('Ftest(%d,%d)',...
                                    ntargets-1,x-ntargets);

            case 5
                stat_name='F';
                ntargets=randint(5);
                is_between=false;
                sa_label_func=@(x)sprintf('Ftest(%d,%d)',...
                                    ntargets-1,x*(ntargets-1)-ntargets+1);

            otherwise
                assert(false)
        end

        nchunks=randint(10);

        % make dataset with some elements set to NaN
        ds=cosmo_synthetic_dataset('ntargets',ntargets,...
                                    'nchunks',nchunks);
        if is_between
            nchunks=numel(ds.sa.chunks);
            ds.sa.chunks(:)=1:nchunks;
        end

        [nsamples,nfeatures]=size(ds.samples);


        % at least one column has no NaN values

        attempt=100;
        while true
            attempt=attempt-1;
            if attempt==0
                error('unable to generate data');
            end

            % add some NaNs
            nan_ratio=.1+rand()*.2;

            non_nan_col=ceil(1+rand()*(nfeatures-1));
            for col=1:nfeatures
                if col==non_nan_col
                    continue;
                elseif col==1
                    % at least one NaN
                    ds.samples(ds.sa.chunks==1)=NaN;
                else
                    % subset of chunks set to NaN
                    [unused,idx]=sort(rand(1,nchunks));
                    nan_chunks=idx(1:ceil(nan_ratio*nchunks));

                    msk=any(bsxfun(@eq,nan_chunks,ds.sa.chunks),2);
                    ds.samples(msk,col)=NaN;
                end
            end

            % verify there are some NaNs
            has_nan=any(isnan(ds.samples(:)));
            not_all_are_nan=any(any(~isnan(ds.samples),1));

            if has_nan && not_all_are_nan
                break;
            end
        end

        for i_output=1:n_outputs
            output_label=output_labels{i_output};
            result_all=cosmo_stat(ds,stat_name,output_label);

            % check values for each feature
            for col=1:nfeatures
                ds_full=cosmo_slice(ds,col,2);
                ds_non_nan=cosmo_slice(ds_full,...
                                ~isnan(ds_full.samples));

                result=cosmo_stat(ds_non_nan,stat_name,output_label);
                assertEqual(size(result.samples),[1 1]);


                if isempty(output_label) && any(isnan(ds_full.samples))
                    expected_value=NaN;
                else
                    expected_value=result.samples;
                end

                assertElementsAlmostEqual(result_all.samples(:,col),...
                                                expected_value)
            end

            % check sa
            return_raw_stat=isempty(output_label);
            if return_raw_stat
                % generate label with 'Ttest' or 'Ftest'
                sa_label=sa_label_func(nchunks);
            else
                if strcmp(output_label,'z')
                    sa_label='Zscore()';
                else
                    sa_label='Pval()';
                end
            end

            expected_sa=struct();
            expected_sa.stats={sa_label};
            assertEqual(result_all.sa,expected_sa);

            % ensure that if targets for one condition are all NaN, then
            % output is NaN
            nan_ds=ds;
            msk=nan_ds.sa.targets==max(nan_ds.sa.targets);
            nan_ds.samples(msk,:)=NaN;

            result_all_nan=cosmo_stat(nan_ds,stat_name,output_label);
            assertEqual(result_all_nan.samples,zeros(1,nfeatures)+NaN);


            % set one target to NaN; if unbalance the resulting
            % sample must be NaN
            tiny_ds=cosmo_slice(ds,1,2);
            tiny_ds.samples=randn(size(tiny_ds.samples));

            result=cosmo_stat(tiny_ds,stat_name,output_label);
            assert(~isnan(result.samples));

            msk=tiny_ds.sa.chunks==1 & tiny_ds.sa.targets==1;
            assert(sum(msk)==1);
            tiny_ds.samples(msk)=NaN;

            result=cosmo_stat(tiny_ds,stat_name,output_label);
            must_be_nan=return_raw_stat || ~is_between;
            assertEqual(must_be_nan,isnan(result.samples))
        end
    end


function test_stat_regression()
% using pre-generated data
    ds=cosmo_synthetic_dataset('nchunks',6,'ntargets',4,'sigma',0);
    ds=cosmo_slice(ds,[2 6],2);

    params=get_stat_regression_params();
    for k=1:numel(params)
        param=params{k};

        args=param{1};
        targets=param{2}{1};
        is_between=param{2}{2};
        should_raise_error=param{2}{3};

        ds_sel=cosmo_slice(ds,cosmo_match(ds.sa.targets,targets));

        if is_between
            ds_sel.sa.chunks=ds_sel.sa.chunks+6*ds_sel.sa.targets;
        end

        stat_func=@()cosmo_stat(ds_sel,args{:});
        if should_raise_error
            assertExceptionThrown(stat_func,'');
            continue;
        end

        result=stat_func();

        samples=param{3}{1};
        assertElementsAlmostEqual(result.samples,samples,'absolute',1e-4);
        stat_sa=struct();
        stat_sa.stats=param{3}(2);
        assertEqual(result.sa,stat_sa);

        % test errors for wrong assignment of chunks and targets
        if is_between
            ds_sel.sa.chunks(1)=ds_sel.sa.chunks(2);
            assertExceptionThrown(@()cosmo_stat(ds_sel,args{:}),'');
        else
            ds_sel.sa.chunks(ds_sel.sa.chunks==2)=1;
            assertExceptionThrown(@()cosmo_stat(ds_sel,args{:}),'');
        end

    end


function params=get_stat_regression_params()
    % parameters to test regressions in stat test; format:
    % {{stat_name, output_stat_name},...
    %   {targets,is_between_test,should_raise_error},...
    %   {samples,.sa.stats{}}}
    %
    % based on input dataset generated by:
    % ds=cosmo_synthetic_dataset('nchunks',6,'ntargets',4,'sigma',0);
    % ds=cosmo_slice(ds,[2 6],2);
    params={{{'F',''},...
                {[1 2 3 4 ],0,0}...
                {[1.63475 2.00315],'Ftest(3,15)'}}
            {{'F','z'},...
                {[1 2 3 4 ],0,0}...
                {[0.76051 1.00751],'Zscore()'}}
            {{'F','p'},...
                {[1 2 3 4 ],0,0}...
                {[0.22348 0.15684],'Pval()'}}
            {{'F','left'},...
                {[1 2 3 4 ],0,0}...
                {[0.77652 0.84316],'Pval()'}}
            {{'F','right'},...
                {[1 2 3 4 ],0,0}...
                {[0.22348 0.15684],'Pval()'}}
            {{'F','both'},...
                {[1 2 3 4 ],0,0}...
                {[0.44695 0.31369],'Pval()'}}
            {{'t2',''},...
                {[3 4 ],0,1}...
                '<should raise error>'}
            {{'t2','z'},...
                {[3 4 ],0,1}...
                '<should raise error>'}
            {{'t2','p'},...
                {[3 4 ],0,1}...
                '<should raise error>'}
            {{'t2','left'},...
                {[3 4 ],0,1}...
                '<should raise error>'}
            {{'t2','right'},...
                {[3 4 ],0,1}...
                '<should raise error>'}
            {{'t2','both'},...
                {[3 4 ],0,1}...
                '<should raise error>'}
            {{'t',''},...
                {[3 4 ],0,0}...
                {[-0.47494 -0.73292],'Ttest(5)'}}
            {{'t','z'},...
                {[3 4 ],0,0}...
                {[-0.44704 -0.68000],'Zscore()'}}
            {{'t','p'},...
                {[3 4 ],0,0}...
                {[0.65485 0.49650],'Pval()'}}
            {{'t','left'},...
                {[3 4 ],0,0}...
                {[0.32742 0.24825],'Pval()'}}
            {{'t','right'},...
                {[3 4 ],0,0}...
                {[0.67258 0.75175],'Pval()'}}
            {{'t','both'},...
                {[3 4 ],0,0}...
                {[0.65485 0.49650],'Pval()'}}
            {{'F',''},...
                {[1 2 3 4 ],1,0}...
                {[1.84801 1.07461],'Ftest(3,20)'}}
            {{'F','z'},...
                {[1 2 3 4 ],1,0}...
                {[0.95018 0.29948],'Zscore()'}}
            {{'F','p'},...
                {[1 2 3 4 ],1,0}...
                {[0.17101 0.38229],'Pval()'}}
            {{'F','left'},...
                {[1 2 3 4 ],1,0}...
                {[0.82899 0.61771],'Pval()'}}
            {{'F','right'},...
                {[1 2 3 4 ],1,0}...
                {[0.17101 0.38229],'Pval()'}}
            {{'F','both'},...
                {[1 2 3 4 ],1,0}...
                {[0.34202 0.76457],'Pval()'}}
            {{'t2',''},...
                {[3 4 ],1,0}...
                {[-0.51279 -0.50269],'Ttest(10)'}}
            {{'t2','z'},...
                {[3 4 ],1,0}...
                {[-0.49693 -0.48727],'Zscore()'}}
            {{'t2','p'},...
                {[3 4 ],1,0}...
                {[0.61924 0.62607],'Pval()'}}
            {{'t2','left'},...
                {[3 4 ],1,0}...
                {[0.30962 0.31303],'Pval()'}}
            {{'t2','right'},...
                {[3 4 ],1,0}...
                {[0.69038 0.68697],'Pval()'}}
            {{'t2','both'},...
                {[3 4 ],1,0}...
                {[0.61924 0.62607],'Pval()'}}
            {{'t',''},...
                {[4 ],1,0}...
                {[-0.65552 0.32687],'Ttest(5)'}}
            {{'t','z'},...
                {[4 ],1,0}...
                {[-0.61117 0.30942],'Zscore()'}}
            {{'t','p'},...
                {[4 ],1,0}...
                {[0.54109 0.75700],'Pval()'}}
            {{'t','left'},...
                {[4 ],1,0}...
                {[0.27055 0.62150],'Pval()'}}
            {{'t','right'},...
                {[4 ],1,0}...
                {[0.72945 0.37850],'Pval()'}}
            {{'t','both'},...
                {[4 ],1,0}...
                {[0.54109 0.75700],'Pval()'}}};