Changing to .png and commenting bin

+ Changed output format to png, tiff was occupying too much space
+ Cleaning descriptions in functions

bin/Murat_body.m

@@ -20,18 +20,22 @@
 %    energyRatioBodyCoda_i:     energy ratio between body and coda waves
 %    energyRatioCodaNoise_i:    energy ratio between coda waves and noise
 
+% Redefine windows with sampling for noise and direct waves
 int                     =   bodyWindow*srate_i;
 lc                      =   length(cursorCodaStart_i:cursorCodaEnd_i);
 cursor0                 =	floor(startNoise*srate_i);
 cursor0_1               =   floor(cursor0 + int);
 cursor2                 =   floor(cursorPick_i + int-1);
 
+% Direct wave normalised by window length
 spamp                   =...
     trapz(sp_i(cursorPick_i:cursor2,:))/int;
 
+% Noise pre-pick normalised by window length
 spampn                  =...
     trapz(sp_i(cursor0:cursor0_1,:))/int;
 
+% Coda normalised by window length
 spampc                  =...
     trapz(sp_i(cursorCodaStart_i:cursorCodaEnd_i,:))/lc;
 

bin/Murat_codaCheck.m

@@ -25,31 +25,37 @@
 %    cursorCodaStart_i:     coda starting time after check on trace
 %    cursorCodaEnd_i:       coda end time after check on trace
 
+%Define envelope duration
 t00                                             =   tempis(1);
 lengthTempis                                    =   length(tempis);
 
+% Method peak is generally valid for active seismics
 if isequal(peakDelayMethod,'Peak')
 
     tCoda_i                                     =...
         (pktime_i-originTime_i)+peakDelay_i;
-
+
+% Method constant is the most used in small local tomography 
 elseif isequal(peakDelayMethod,'Constant')
 
     tCoda_i                                     =   tCm;
-
+
+% Method travel is the standard at the regional scale
 elseif isequal(peakDelayMethod,'Travel')
 
     tCoda_i                                     =...
         originTime_i+ tCm*(pktime_i-originTime_i);
 
 end
 
+% Define the indexes along the seismogram
 cursorCodaStart_i                               =...
     floor((originTime_i - t00 + tCoda_i) * srate_i - 1);
 
 cursorCodaEnd_i                                 =...
     floor(cursorCodaStart_i + tWm * srate_i - 1);
 
+% Some seismograms are not long enough so you consider a shorter window
 if cursorCodaEnd_i > lengthTempis
     cursorCodaEnd_i                             =   lengthTempis;
 end

bin/Murat_inversion.m

@@ -130,7 +130,7 @@
     modv_Qc(rcQc_k,4,k)             =   mQc;
 
     saveas(LcQc,fullfile(FPath, FLabel,'Tests/LCurve',FName));
-    saveas(LcQc,fullfile(FPath, FLabel,'Tests/LCurve',FName),'tif');
+    saveas(LcQc,fullfile(FPath, FLabel,'Tests/LCurve',FName),'png');
     close(LcQc)
 
     %%
@@ -181,7 +181,7 @@
     modv_Q(rcQ_k,4,k)             =   mQ;
 
     saveas(LcCN,fullfile(FPath, FLabel,'Tests/LCurve',FName));
-    saveas(LcCN,fullfile(FPath, FLabel,'Tests/LCurve',FName),'tif');
+    saveas(LcCN,fullfile(FPath, FLabel,'Tests/LCurve',FName),'png');
     close(LcCN)
 
     %% Checkerboards and spike inputs and checkerboard inversion

bin/Murat_lsqlinQmean.m

@@ -3,30 +3,32 @@
 % function [d1, const_Qc_k, constQmean_k, equationQ]   =...
 %     Murat_lsqlinQmean(tCm,tWm,Q_k,cf_k,sped,luntot_k,time0_k,rapsp_k)
 %
-% INVERTS with weighted tikhonov and creates L-curve and data for Q.
+% INVERTS with minimum least squares to obtain average Q
 %
 % Input parameters:
-%    tCm:           lapse time
-%    tWm:           coda window
-%    Q_k:           inverse Qc
+%    tCm:           starting coda time
+%    tWm:           coda window length
+%    Q_k:           average coda attenuation
 %    cf_k:          central frequency
 %    sped:          spectral decay
-%    luntot_k:      total ray length
-%    time0_k:       total travel time
-%    rapsp_k:       energy ratio
-%    
-% Output parameters:
-%    d1:            data for average Q inversion
-%    const_Qc_k:    constant for average Q inversion depending on Qc
-%    constQmean_k:  average geometrical spreading and Q
-%    equationQ:     sum of all three terms of the CN equation
+%    luntot_k:      total length per frequency
+%    time0_k:       travel time per frequency
+%    rapsp_k:       energy ratio per frequency
 %
+% Output parameters:
+%    d1:            data for the inversion - variations from average
+%    const_Qc_k:    constant obtained using the average source-station Qc
+%    constQmean_k:  contains geometrical spreading, Q, uncertainties
+%    equationQ:     equation to be compared with data in test
+
 %%
 % Data creation for the true inversion, removing the pre-calculated
 % parameters.
+
+% Include info on Qc
 const_Qc_k                      =   (tCm+tWm/2).^-sped...
                                     .*exp(-2*pi*Q_k*cf_k.*(tCm+tWm/2));
-
+% Data vector for inversion of average Q
 d0                              =...
                     log(rapsp_k)/2/pi/cf_k + log(const_Qc_k)/2/pi/cf_k;
 
@@ -35,13 +37,16 @@
 
 cova                            =   (G'*G)^(-1)*G'*cov(d0)*G*(G'*G)^(-1);
 
+% Storing inverted parameters
 constQmean_k(:,1)               =   lsqlin(G,d0(:,1));
 constQmean_k(:,2)               =   sqrt(diag(cova));
 
+% Calculate data vector for average Q and geometrical spreading
 d1                              =	d0  + ...
                             constQmean_k(1,1)*log(luntot_k)/2/pi/cf_k...
                             + time0_k*constQmean_k(2,1);
 
+% Equation for average Q to fit data
 equationQ                       =   -log(const_Qc_k)...
                                     -constQmean_k(1,1)*log(luntot_k)...
                                     -2*pi*cf_k*time0_k*constQmean_k(2,1);

bin/Murat_plot.m

@@ -71,7 +71,7 @@
     storeFolder                     =   'Tests';
     pathFolder                      =...
         fullfile(FPath,FLabel,storeFolder,FName_Cluster);
-    saveas(clustering,pathFolder,'tif');
+    saveas(clustering,pathFolder,'png');
     close(clustering)
 end
 
@@ -105,7 +105,7 @@
         ending,evestaz_pd,x,y,z,FName_peakDelay);
     pathFolder                      =...
         fullfile(FPath,FLabel,storeFolder,FName_peakDelay);
-    saveas(rays_peakDelay,pathFolder,'tif');
+    saveas(rays_peakDelay,pathFolder,'png');
     close(rays_peakDelay)
 
     %%
@@ -117,7 +117,7 @@
         Murat_imageRays(rma_Q,origin,ending,evestaz_Q,x,y,z,FName_Q);
     pathFolder                      =...
         fullfile(FPath, FLabel, storeFolder, FName_Q);
-    saveas(rays_Q,pathFolder,'tif');
+    saveas(rays_Q,pathFolder,'png');
     close(rays_Q)
 
     %%
@@ -163,7 +163,7 @@
     Qc_analysis                     =   Murat_imageCheckQc(Qm_k,RZZ_k,...
         residualQc_k,luntot_Qc,Ac,sizeTitle,Qc_title,QcM);
     saveas(Qc_analysis, fullfile(FPath,FLabel,storeFolder,...
-        ['Qc_analysis_' fcName '_Hz']),'tif');
+        ['Qc_analysis_' fcName '_Hz']),'png');
     saveas(Qc_analysis, fullfile(FPath,FLabel,storeFolder,...
         ['Qc_analysis_' fcName '_Hz']));
     close(Qc_analysis)
@@ -179,7 +179,7 @@
     pd_analysis                     =   Murat_imageCheckPeakDelay(...
     time0PD,fitrobust_k,peakData_k,sizeTitle,pd_title);
     saveas(pd_analysis, fullfile(FPath,FLabel,storeFolder,...
-        ['PD_analysis_' fcName '_Hz']),'tif');
+        ['PD_analysis_' fcName '_Hz']),'png');
     saveas(pd_analysis, fullfile(FPath,FLabel,storeFolder,...
         ['PD_analysis_' fcName '_Hz']));
     close(pd_analysis)
@@ -208,7 +208,7 @@
         Murat_imageCheckCN(equationQ,residualQ_k,d1,spreadAverageQ,...
         luntot_k,time0_k,energyRatio_k,A_k,Edirect_k,CN_title);
     saveas(CN_analysis, fullfile(FPath,FLabel,storeFolder,...
-        ['CN_analysis_' fcName '_Hz']),'tif');
+        ['CN_analysis_' fcName '_Hz']),'png');
     saveas(CN_analysis, fullfile(FPath,FLabel,storeFolder,...
         ['CN_analysis_' fcName '_Hz']));
     close(CN_analysis)
@@ -447,5 +447,5 @@
 QcFrequency                         =   Murat_imageQcFrequency(cf,...
     averageQcFrequency,sizeTitle,Qcf_title);
 FName                               =   'Qc_vs_frequency';
-saveas(QcFrequency, fullfile(FPath,FLabel,storeFolder,FName),'tif');
+saveas(QcFrequency, fullfile(FPath,FLabel,storeFolder,FName),'png');
 close all

bin/Murat_saveFigures.m

@@ -4,7 +4,7 @@ function  Murat_saveFigures(figureName,Path)
 %
 %	Input Parameters:
 %       figureName:             Matlab 3D plot
-%       Path:                   name of sections (tif) and figure (fig)
+%       Path:                   name of sections (png) and figure (fig)
 %
 %   Output:
 %       Three sections and 1 3D figure
@@ -13,11 +13,11 @@ function  Murat_saveFigures(figureName,Path)
 saveas(figureName,Path);    
 view(90,0)
 ytickangle(45)
-saveas(figureName,[Path '_SN'], 'tif');
+saveas(figureName,[Path '_SN'], 'png');
 view(0,0)
 xtickangle(45)
-saveas(figureName,[Path '_WE'], 'tif');
+saveas(figureName,[Path '_WE'], 'png');
 view(0,90)
-saveas(figureName,[Path '_H'], 'tif');
+saveas(figureName,[Path '_H'], 'png');
 close(figureName)
 end

bin/Murat_saveFigures_2panels.m

@@ -4,7 +4,7 @@ function  Murat_saveFigures_2panels(figureName,Path)
 %
 %	Input Parameters:
 %       figureName:             Matlab 3D plot
-%       Path:                   name of sections (tif) and figure (fig)
+%       Path:                   name of sections (png) and figure (fig)
 %
 %   Output:
 %       Three sections and 1 3D figure with 2 panels
@@ -18,21 +18,21 @@ function  Murat_saveFigures_2panels(figureName,Path)
 ax2             =   subplot(1,2,2);
 view(ax2,90,0)
 ytickangle(45)
-saveas(figureName,[Path '_SN'], 'tif');
+saveas(figureName,[Path '_SN'], 'png');
 
 ax1             =   subplot(1,2,1);
 view(ax1,0,0)
 xtickangle(45)
 ax2             =   subplot(1,2,2);
 view(ax2,0,0)
 xtickangle(45)
-saveas(figureName,[Path '_WE'], 'tif');
+saveas(figureName,[Path '_WE'], 'png');
 
 ax1             =   subplot(1,2,1);
 view(ax1,0,90)
 ax2             =   subplot(1,2,2);
 view(ax2,0,90)
-saveas(figureName,[Path '_H'], 'tif');
+saveas(figureName,[Path '_H'], 'png');
 
 close(figureName)