Filesepfix

example/KHU_example.m

@@ -7,11 +7,11 @@
 
 %load boundary voltages of baseline recording, cleaning the data and
 %plotting
-[BV_baseline, KHUs_baseline]=KHU_Load('..\resources\data\KHU\B1',1,1);
+[BV_baseline, KHUs_baseline]=KHU_Load('../resources/data/KHU/B1',1,1);
 
 %% load Perturbation
 
 %load boundary voltages of baseline recording, cleaning the data but not
 %plotting
-[BV_perturbation, KHUs_perturbation]=KHU_Load('..\resources\data\KHU\P1',1,0);
+[BV_perturbation, KHUs_perturbation]=KHU_Load('../resources/data/KHU/P1',1,0);
 

example/ScouseTom_example.m

@@ -7,19 +7,19 @@
 
 %load boundary voltages of resistor phantom recording. The log files
 %generated by the ScouseTom ssytem are located in same directory
-[BVstruc_TD]=ScouseTom_Load('..\resources\data\ScouseTom\forreal_2_clean.bdf');
+[BVstruc_TD]=ScouseTom_Load('../resources/data/ScouseTom/forreal_2_clean.bdf');
 
 %% load Multifrequency data
 
 %load boundary voltages of resistor phantom recording using multiple
 %frequecies. The log files generated by the ScouseTom system is located in
 %the same directory
-[BVstruc_MF]=ScouseTom_Load('..\resources\data\ScouseTom\MultiFreq.bdf');
+[BVstruc_MF]=ScouseTom_Load('../resources/data/ScouseTom/MultiFreq.bdf');
 
 %% load contact impedance check
 
 % perform contact impedance check on data collected on scalp with EEG
 % electrodes. This code is a bit different as we want to estimate the
 % contact impedance and plot it quickly. The protocol is also independent
 % of that set by the ExpSetup
-[Zout]=ScouseTom_Load('..\resources\data\ScouseTom\S1a_Z4.bdf');
+[Zout]=ScouseTom_Load('../resources/data/ScouseTom/S1a_Z4.bdf');

example/SwissTom_example.m

@@ -7,4 +7,4 @@
 
 %load boundary voltages of resistor phantom recording. Removing injected
 %channels, saturated channels, and plotting data
-[STout]=SwissTom_Load('..\resources\data\Swisstom\r-phantom.eit',1,1,1);
+[STout]=SwissTom_Load('../resources/data/Swisstom/r-phantom.eit',1,1,1);

src/matlab/KHU_Load.m

@@ -359,7 +359,7 @@
 KHU.info=info;
 
 %get the name for the new files
-k=strfind(dirname,filesep);
+k=strfind(dirname,'/');
 newnamestr=dirname(k(end)+1:end);
 
 

tests/Test_ScouseTom.m

@@ -0,0 +1,163 @@
+% test code is functioning on real examples. Requires files from https://doi.org/10.5281/zenodo.4783547
+
+datadir='I:/Load_data_testing/';
+%datadir='data/';
+%% load bdfs
+
+somethingwentwrong=0;
+
+
+try
+    BVs=ScouseTom_Load([datadir 'Baseline1.bdf']);
+catch err
+    fprintf(2,'error on initial test\n');
+    somethingwentwrong=1;
+    fprintf(2, '%s\n', getReport(err, 'extended'));
+end
+
+disp('=================================================');
+disp('=================================================');
+disp('=================================================');
+
+try
+    BVs=ScouseTom_Load([datadir 'Baseline1_missingstart.bdf']);
+catch err
+    fprintf(2,'error on missing start test\n');
+    somethingwentwrong=1;
+    fprintf(2, '%s\n', getReport(err, 'extended'));
+end
+
+disp('=================================================');
+disp('=================================================');
+disp('=================================================');
+
+try
+    BVs=ScouseTom_Load([datadir 'Baseline1_missingend.bdf']);
+catch err
+    fprintf(2,'error on missing end test\n');
+    somethingwentwrong=1;
+    fprintf(2, '%s\n', getReport(err, 'extended'));
+end
+
+disp('=================================================');
+disp('=================================================');
+disp('=================================================');
+
+try
+    BVs=ScouseTom_Load([datadir 'Baseline1_missingboth.bdf']);
+catch err
+    fprintf(2,'error on missing both test\n');
+    somethingwentwrong=1;
+    fprintf(2, '%s\n', getReport(err, 'extended'));
+end
+
+disp('=================================================');
+disp('=================================================');
+disp('=================================================');
+%% multifreq
+
+try
+    BVs=ScouseTom_Load([datadir 'MultiFreq.bdf']);
+catch err
+    fprintf(2,'error on Multifreq test\n');
+    somethingwentwrong=1;
+    fprintf(2, '%s\n', getReport(err, 'extended'));
+end
+
+disp('=================================================');
+disp('=================================================');
+disp('=================================================');
+
+try
+    BVs=ScouseTom_Load([datadir 'MultiFreq_missingstart.bdf']);
+catch err
+    fprintf(2,'error on Multifreq missing start test\n');
+    somethingwentwrong=1;
+    fprintf(2, '%s\n', getReport(err, 'extended'));
+end
+
+disp('=================================================');
+disp('=================================================');
+disp('=================================================');
+
+try
+    BVs=ScouseTom_Load([datadir 'MultiFreq_missingend.bdf']);
+catch err
+    fprintf(2,'error on Multifreq missing end test\n');
+    somethingwentwrong=1;
+    fprintf(2, '%s\n', getReport(err, 'extended'));
+end
+
+disp('=================================================');
+disp('=================================================');
+disp('=================================================');
+
+try
+    BVs=ScouseTom_Load([datadir 'MultiFreq_missingboth.bdf']);
+catch err
+    fprintf(2,'error on Multifreq missing both test\n');
+    somethingwentwrong=1;
+end
+
+disp('=================================================');
+disp('=================================================');
+disp('=================================================');
+
+%% Z check
+try
+    Z=ScouseTom_Load([datadir 'firstinnir_zcheck_1.bdf']);
+catch err
+    fprintf(2,'error on Z load \n');
+    somethingwentwrong=1;
+    fprintf(2, '%s\n', getReport(err, 'extended'));
+end
+
+
+%% AC check
+
+try
+    BVs=ScouseTom_Load([datadir 'rptest2.eeg']);
+catch err
+    fprintf(2,'error on Actichamp test 1\n');
+    somethingwentwrong=1;
+end
+
+disp('=================================================');
+disp('=================================================');
+disp('=================================================');
+
+try
+    BVs=ScouseTom_Load([datadir 'rptest3.eeg']);
+catch err
+    fprintf(2,'error on Actichamp test 2\n');
+    somethingwentwrong=1;
+end
+
+disp('=================================================');
+disp('=================================================');
+disp('=================================================');
+
+
+%% Big file
+
+try
+    BVs=ScouseTom_Load([datadir 'RealThing_NIRFACE_2.bdf']);
+catch err
+    fprintf(2,'error on Multifreq big file test\n');
+    somethingwentwrong=1;
+end
+
+disp('=================================================');
+disp('=================================================');
+disp('=================================================');
+
+
+
+%% did it work?
+
+if somethingwentwrong
+    fprintf(2,'Oh No! SOMETHING WENT WRONG!\n');
+else
+    fprintf('YAY! IT WORKED :)\n');
+end
+

tests/data/readme.md

@@ -0,0 +1,2 @@
+# Test dataset
+Put files from [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4783527.svg)](https://doi.org/10.5281/zenodo.4783527) in this directory to run tests

tests/filters/check_acc.m

@@ -0,0 +1,121 @@
+function [ Amp_error, Phase_error,Vsig,Vsigdemod,Filt,trim_demod] = check_acc( Fc,InjTime,Amp_Inj,Amp_Meas,InjPhase,MeasPhaseDiff,DCoffset,DCoffsetInj, Padsec, Fs,decimate_factor)
+    %UNTITLED Summary of this function goes here
+    %   Detailed explanation goes here
+
+    %%
+    inj = [ 2 4];
+
+    if exist('DCoffset','var') == 0 || isempty(DCoffset)
+        DCoffset=0;
+    end
+
+    if exist('DCoffsetInj','var') == 0 || isempty(DCoffsetInj)
+        DCoffsetInj=0;
+    end
+
+
+    BW=100;
+    chn=5;
+
+    if exist('Padsec','var') == 0 || isempty(Padsec)
+        Padsec=4;
+    end
+
+    if exist('Fs','var') == 0 || isempty(Fs)
+        Fs=16384;
+    end
+
+    if exist('decimate_factor','var') == 0 || isempty(decimate_factor)
+        decimate_factor=0;
+    end
+
+
+    %% Create ideal values, and voltages
+
+    AmpActual= repmat(Amp_Meas,chn,1);
+    AmpActual(inj)=Amp_Inj;
+
+    a=MeasPhaseDiff;
+
+    %force normal valus of deg
+    a = mod(a,360); % [0 2pi)
+
+    % shift
+    jj = a > 180;
+    a(jj) = a(jj) - 360;
+    jj = a < 0 - 180;
+    a(jj) = a(jj) + 360;
+
+    MeasPhaseDiff_corr = a;
+
+    MeasPhase = InjPhase + MeasPhaseDiff_corr; %deg
+    PhaseActual= repmat(MeasPhaseDiff_corr,chn,1);
+    PhaseActual(inj)=0;
+
+    Totaltime=ceil(InjTime + 2*Padsec);
+    t = 0:1/Fs:Totaltime-1/Fs;
+    %make sin wave
+
+    v_m= Amp_Meas*sin(2*pi*Fc*t+(pi*MeasPhase/180))+DCoffset;
+
+    % change amplitude
+    v_i=Amp_Inj*sin(2*pi*Fc*t+(pi*InjPhase/180))+DCoffsetInj;
+
+
+    %%
+    V=repmat(v_m,chn,1);
+
+    V(inj(1),:) = v_i;
+    V(inj(2),:) = v_i;
+
+    V=V';
+
+    %% decimate now if we want to
+
+    if decimate_factor
+        for iChn = 1 :size(V,2)
+            Vtmp(:,iChn) = decimate(V(:,iChn),decimate_factor);
+        end
+        Fs=Fs/decimate_factor;
+        V=Vtmp;
+    end
+
+    %%
+
+
+    %pad with a second of data either side, so the hilbert is more realistic
+    datastart = round(Padsec*Fs);
+    dataend = round((Padsec+InjTime)*Fs);
+
+    V(1:datastart,:)=V(1:datastart,:)*0.1;
+    V(dataend:end,:)=V(dataend:end,:)*0.1;
+
+    InjectionWindows =[datastart dataend];
+
+
+    %%
+    %find the corresponding filter settings
+    [trim_demod,Filt,Fc_found]=ScouseTom_data_GetFilterTrim(V(datastart:dataend,inj(1)),Fs,[],[],[]);
+
+    Vsig = V(datastart:dataend,inj(1));
+
+    [ Vdata_demod,Pdata_demod ] = ScouseTom_data_DemodHilbert( V,Filt);
+    Vsigdemod = Vdata_demod(datastart:dataend,inj(1));
+
+    %%
+    [Vmag,PhaseRaw,VmagSTD,PhaseRawSTD]=ScouseTom_data_getBV(Vdata_demod,Pdata_demod,trim_demod,InjectionWindows);
+    % [Vmag,PhaseRaw,VmagSTD,PhaseRawSTD]=ScouseTom_data_getBVChunk(Datafilt,trim_demod,InjectionWindows);
+
+
+    [Phase]=ScouseTom_data_PhaseEst(PhaseRaw,inj,1);
+
+    Phase_deg=(180/pi) * (Phase);
+
+    Phase_error = PhaseActual - Phase_deg';
+
+    Amp_error = AmpActual - Vmag';
+
+    fprintf('Amp error : %.6f, Phase error : %.6f\n',mean(Amp_error),mean(Phase_error));
+    end
+
+