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eddplot3.m
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% eddplot to visdualize 6BM data.
%
% +1.6 2020/07/26 support plotting of all 10 elements
% +1.5 2020/01/16 support different size (for 10-element detector)
% +1.4 2018/11/27 new detpart format
% +1.3 2018/04/17 add x scaling factor
% +1.2 2018/02/03 switch yscale for 1-D plot
% +1.1 2017/09/20 bug fix
%
% Copyright 2017-2020 Andrew Chuang ([email protected])
% $Revision: 1.6 $ $Date: 2020/07/26 $
function eddplot3(da,opt)
fsa = 13;
fst = 18;
cc = lines(20);
if nargin == 1
opt = '';
end
%%%%%% define default option %%%%%
if isfield(opt,'datalim')
datalim = opt.datalim;
else
% range for (Ch/E/d),(posno),(Intensity)
datalim = {'auto','auto','auto'};
end
if isfield(opt,'normalize')
normalize = opt.normalize;
else
normalize = 0;
end
if isfield(opt,'detno')
detno = opt.detno;
else
detno = 1;
end
if isfield(opt,'phase')
phase = opt.phase;
else
phase = 1;
end
if isfield(opt,'pk')
pk = opt.pk;
else
pk = 5;
end
if isfield(opt,'do_export')
do_export = opt.do_export;
else
do_export = 0;
end
if isfield(opt,'x_unit')
x_unit = lower(opt.x_unit);
else
x_unit = 'ch';
end
if isfield(opt,'yscale')
switch opt.yscale
case 1
y_scale = 'linear';
otherwise
y_scale = 'log';
end
else
y_scale = 'log';
end
if isfield(opt,'xscaling')
x_scaling = opt.xscaling;
else
x_scaling = 1;
end
if isfield(opt,'x_range')
x_range = opt.x_range;
else
x_range = ':';
end
% if isfield(opt,'fig_handle')&&ishandle(opt.fig_handle)
% fig_handle = opt.fig_handle;
% else
% fig_handle = 0;
% end
if isfield(opt,'avg_1D')
avg_1D = opt.avg_1D;
else
avg_1D = 0;
end
if isfield(opt,'title')
title_text = opt.title;
else
title_text = '';
end
if isfield(opt,'dzero')
dzero = opt.dzero;
else
dzero = zeros(1,length(pk))+1;
end
if isfield(opt,'posno')
posno = opt.posno;
else
posno = 1;
end
if isfield(opt,'xoffset')
xoffset = opt.xoffset;
else
xoffset = 0;
end
if isfield(opt,'Eoffset')
Eoffset = opt.Eoffset;
else
Eoffset = [0 0];
end
if isfield(opt,'type')
type = opt.type;
else
type = '2draw';
end
if isfield(opt,'scno')
%scno = opt.scno(1); % only plot one scan at a time. (May.17)
scno = opt.scno;
else
scno = 1;
end
if isfield(da,'Material')
label_peak = 1;
else
label_peak = 0;
end
if ~strcmp(type,'raw')&isfield(da(1),'Material')
pkname = da(1).Material(phase).hkls;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% pre-processing
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if strcmp(type,'2draw')&&size(da(scno).data{detno},1)==1
type = 'raw';
end
if isfield(opt,'Inst')
da(1).Inst = opt.Inst;
elseif ~isfield(da(scno),'Inst')
fprintf('No Instrument parameters provided!!\n');
fprintf('Use default TOA = 3 (deg)\n');
fprintf('Use default Ch2E = [0 0.03 0];\n');
da(scno).Inst.detpar = repmat([3 0 0.03 0],10,1);
end
% calculate E_grid, d_grid
hc = 12.398419057638671;
for i = 1:size(da(1).Inst.detpar,1)
for j = 1:length(scno)
da(scno(j)).Inst.E_grid(i,:) = polyval(flip(da(1).Inst.detpar(i,2:end)), 1:size(da(scno(j)).data{detno},2));
da(scno(j)).Inst.d_grid(i,:) = hc./da(scno(j)).Inst.E_grid(i,:)*0.5/sind(da(1).Inst.detpar(i,1)/2);
end
end
%%%% initiate figure for various types of plot
switch lower(type)
case 'step_plot'
hfig = findall(0,'Tag','edd_fig_step_plot');
if ishandle(hfig)
fig = hfig(1);
clf(fig,'reset');
set(fig,'Tag','edd_fig_step_plot');
else
fig = figure(163);
set(fig,'Position',[900 100 800 600],'Tag','edd_fig_step_plot');
end
figure(163);
case '2draw'
figtag = sprintf('edd_fit_det%d_map',detno(1));
fignum= detno(1)*100+61;
hfig = findall(0,'Tag',figtag);
if ishandle(hfig)
fig=hfig(1);
clf(fig,'reset');
set(fig,'Tag',figtag);
else
fig = figure(fignum);
set(fig,'Position',[50+(detno-1)*50 100 800 600],'Tag',figtag);
end
figure(fignum);
otherwise
figtag = sprintf('edd_fit_det%d_line',detno(1));
fig2num= detno*100+62;
hfig = findall(0,'Tag',figtag);
if ishandle(hfig)
fig = hfig(1);
clf(fig,'reset');
set(fig,'Tag',figtag);
else
fig = figure(fig2num);
set(fig,'Position',[50+(detno-1)*50 700 800 600],'Tag',figtag);
end
figure(fig2num)
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% start ploting
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
cc = lines(100);
ax = axes('parent',hfig,'fontsize',fsa,'box','on');
grid on;
switch lower(type)
case 'cen'
xdata = da(scno).motorpos(x_range)+xoffset;
fprintf('\nAveraged Peak Position (Mean%sStd) for %s\n',char(177),title_text);
for i = 1:length(pk)
ydata = da(scno).fit(phase,pk(i),detno).cen(x_range);
flag = find(ydata~=0);
ydata = ydata(flag);
if normalize == 1 % normalize to mean
line(xdata(flag),((mean(ydata)./ydata)-1)*1E6,'marker','o','color',cc(i,:),'displayname',sprintf('%s',num2str(pkname(pk(i),:))));
%datalim{2} = [-5E3 5E3];
ylabel('Strain (x 10^{-6})');
%display(sprintf('[%s] = %04.8f, ',num2str(pkname(pk(i),:)),mean(ydata)));
fprintf('[%s] = %8.2f %s %8.2f, ',num2str(pkname(pk(i),:)),mean(((ydata./mean(ydata))-1)*1E6),char(177),std(((ydata./mean(ydata))-1)*1E6));
elseif normalize == 0
line(xdata(flag),ydata,'marker','o','color',cc(i,:),'displayname',sprintf('%s',num2str(pkname(pk(i),:))));
ylabel('Peak Center (keV)');
fprintf('[%s] = %8.8f %s %6.4f, ',num2str(pkname(pk(i),:)),mean(ydata),char(177),std(ydata));
elseif normalize == 3 % show absolute diff
line(xdata(flag),ydata-mean(ydata),'marker','o','color',cc(i,:),'displayname',sprintf('%s',num2str(pkname(pk(i),:))));
ylabel('Peak Center (keV)');
fprintf('[%s] = %8.8f %s %6.4f, ',num2str(pkname(pk(i),:)),mean(ydata),char(177),std(ydata));
else % normalize to user defined d_zero
line(xdata(flag),((dzero(pk(i))./ydata)-1)*1E6,'marker','o','color',cc(i,:),'displayname',sprintf('%s',num2str(pkname(pk(i),:))));
%datalim{2} = [-5E3 5E3];
ylabel('Strain (x 10^{-6})');
fprintf('[%s] = %8.2f %s %8.2f, ',num2str(pkname(pk(i),:)),mean((ydata./dzero(pk(i))-1).*1E6),char(177),std((ydata./dzero(pk(i))-1).*1E6));
%std((ydata./dzero(pk(i))-1).*1E6)
end
%display(sprintf('[%s] = %04.8f, ',num2str(pkname(pk(i),:)),mean(ydata)));
end
set(gca,'fontsize',fsa);
xlabel('Position (mm)');
xlim(datalim{1});
ylim(datalim{3});
title(title_text,'fontsize',fst);
leg = legend('toggle');
case 'dspac' % d-spacing was calculated during fitting
if length(scno) > 1
xdata = [];
for i_scno=1:length(scno)
xdata = vertcat(xdata,(da(scno(i_scno)).motorpos(x_range)+xoffset)*x_scaling);
end
else
xdata = (da(scno).motorpos(x_range)+xoffset)*x_scaling;
end
%whos xdata
fprintf('\nAveraged Peak Position (Mean%sStd) for %s\n',char(177),title_text);
for i = 1:length(pk)
%da(scno).fit(phase,pk(i),detno);
if length(scno)>1
ydata = [];
for i_scno = 1:length(scno)
ydata = vertcat(ydata,da(scno(i_scno)).fit(phase,pk(i),detno).dspac(x_range));
end
else
ydata = da(scno).fit(phase,pk(i),detno).dspac(x_range);
end
%whos ydata
flag = find(ydata~=0);
ydata = ydata(flag);
if normalize == 1
line(xdata(flag),((ydata./mean(ydata))-1)*1E6,'marker','o','color',cc(i,:),'displayname',sprintf('%s',num2str(pkname(pk(i),:))));
%datalim{2} = [-5E3 5E3];
ylabel('Strain (x 10^{-6})');
%display(sprintf('[%s] = %04.8f, ',num2str(pkname(pk(i),:)),mean(ydata)));
fprintf('[%s] = %8.2f %s %8.2f,\n',num2str(pkname(pk(i),:)),mean(((ydata./mean(ydata))-1)*1E6),char(177),std(((ydata./mean(ydata))-1)*1E6));
elseif normalize == 0
line(xdata(flag),ydata,'marker','o','color',cc(i,:),'displayname',sprintf('%s',num2str(pkname(pk(i),:))));
ylabel('d-spacing (Angstron)');
fprintf('[%s] = %8.8f %s %6.4f,\n',num2str(pkname(pk(i),:)),mean(ydata),char(177),std(ydata));
else
line(xdata(flag),((ydata./dzero(pk(i)))-1)*1E6,'marker','o','color',cc(i,:),'displayname',sprintf('%s',num2str(pkname(pk(i),:))));
%datalim{2} = [-5E3 5E3];
ylabel('Strain (x 10^{6})');
fprintf('[%s] = %8.2f %s %8.2f,\n',num2str(pkname(pk(i),:)),mean((ydata./dzero(pk(i))-1).*1E6),char(177),std((ydata./dzero(pk(i))-1).*1E6));
%std((ydata./dzero(pk(i))-1).*1E6)
end
%display(sprintf('[%s] = %04.8f, ',num2str(pkname(pk(i),:)),mean(ydata)));
end
set(gca,'fontsize',fsa);
xlabel('Position (mm)');
xlim(datalim{1});
ylim(datalim{3});
title(strjoin(strsplit(title_text,'_'),'\\_'),'fontsize',fst);
leg = legend('toggle');
case 'dspac2' % calculate d-spacing based on tth value
xdata = (da(scno).motorpos(x_range)+xoffset)*x_scaling;
fprintf('\nAveraged Peak Position (Mean%sStd) for %s\n',char(177),title_text);
for i = 1:length(pk)
dspac_cal = hc./(da(scno).fit(phase,pk(i),detno).cen+Eoffset(detno))/2/sind(da(1).Inst.detpar(detno,1)/2);
ydata = dspac_cal(x_range);
flag = find(ydata>0 & ydata<20);
ydata = ydata(flag);
if normalize == 1
line(xdata(flag),((ydata./mean(ydata))-1)*1E6,'marker','o','color',cc(i,:),'displayname',sprintf('%s',num2str(pkname(pk(i),:))));
%datalim{2} = [-5E3 5E3];
ylabel('Strain (x 10^{-6})');
%display(sprintf('[%s] = %04.8f, ',num2str(pkname(pk(i),:)),mean(ydata)));
fprintf('[%s] = %8.2f %s %8.2f, \n',num2str(pkname(pk(i),:)),mean(((ydata./mean(ydata))-1)*1E6),char(177),std(((ydata./mean(ydata))-1)*1E6));
elseif normalize == 0
line(xdata(flag),ydata,'marker','o','color',cc(i,:),'displayname',sprintf('%s',num2str(pkname(pk(i),:))));
ylabel('d-spacing (Angstron)');
ppfit = polyfit(xdata(flag),ydata,1);
fprintf('[%s] = %8.8f %s %6.4f, d_0 = %1.6f\n',num2str(pkname(pk(i),:)),mean(ydata),char(177),std(ydata),ppfit(2));
else
line(xdata(flag),((ydata./dzero(pk(i)))-1)*1E6,'marker','o','color',cc(i,:),'displayname',sprintf('%s',num2str(pkname(pk(i),:))));
%datalim{2} = [-5E3 5E3];
ylabel('Strain (x 10^{6})');
fprintf('[%s] = %8.2f %s %8.2f,\n',num2str(pkname(pk(i),:)),mean((ydata./dzero(pk(i))-1).*1E6),char(177),std((ydata./dzero(pk(i))-1).*1E6));
%std((ydata./dzero(pk(i))-1).*1E6)
end
%display(sprintf('[%s] = %04.8f, ',num2str(pkname(pk(i),:)),mean(ydata)));
end
set(gca,'fontsize',fsa);
xlabel('Position (mm)');
xlim(datalim{1});
ylim(datalim{3});
title(strjoin(strsplit(title_text,'_'),'\\_'),'fontsize',fst);
leg = legend('toggle');
case 'int'
xdata = (da(scno).motorpos+xoffset)*x_scaling;
for i = 1:length(pk)
ydata = da(scno).fit(phase,pk(i)).int;
yref = da(scno).fit(phase,1).int; % use fitst peak as refernce
flag = find(ydata~=0);
ydata = ydata(flag);
if normalize == 0
line(xdata(flag),ydata.*da(1).exp_time,'marker','o','color',cc(i,:),'displayname',sprintf('%s',num2str(pkname(pk(i),:))));
ylabel('Intensity (counts)');
elseif normalize == 1
line(xdata(flag),ydata/max(ydata),'marker','o','color',cc(i,:),'displayname',sprintf('%s',num2str(pkname(pk(i),:))));
ylabel('Normalized Intensity (cps)');
else
line(xdata(flag),ydata./yref(flag),'marker','o','color',cc(i,:),'displayname',sprintf('%s',num2str(pkname(pk(i),:))));
ylabel('Normalized Intensity (cps)');
end
text(0.4,0.95,sprintf('Total count time: %d sec',da(1).exp_time),'sc','fontsize',fsa);
end
set(gca,'fontsize',fsa);
xlabel('Position (mm)');
xlim(datalim{1})
ylim(datalim{3})
title(title_text,'fontsize',fst)
leg = legend('toggle');
case 'fwhm'
xdata = da(scno).motorpos+xoffset;
for i = 1:length(pk)
ydata = da(scno).fit(phase,pk(i)).fwhm;
flag = find(ydata~=0);
line(xdata(flag),ydata(flag),'marker','o','color',cc(i,:),'displayname',sprintf('%s',num2str(pkname(pk(i),:))));
ylabel('FWHM (keV)');
end
set(gca,'fontsize',fsa);
xlabel('Position (mm)');
xlim(datalim{1})
ylim(datalim{3})
title(title_text,'fontsize',fst)
leg = legend('toggle');
case 'raw'
yrange = datalim{3};
switch x_unit
case 'd'
%xxdata = da(point).Inst.d_grid;
%xxdata = da(scno).Inst(detno).d_grid;
xxdata = da(scno).Inst.d_grid(detno,:);
xrange = [0 10];
xlab = sprintf('d (%s)',char(197));
case 'e'
%xxdata = da(point).Inst.E_grid;
%xxdata = da(scno).Inst(detno).E_grid;
xxdata = da(scno).Inst.E_grid(detno,:);
xrange = [0 200];
xlab = sprintf('E (keV)');
case 'ch'
xxdata = 1:size(da(scno).data{detno},2);
xrange = [1 size(da(scno).data{detno},2)];
xlab = sprintf('Channel');
end
if avg_1D
if normalize == 0
yydata = sum(da(scno).data{detno}(posno,:),1)./length(posno);
tx_yax = 'Intensity (counts)';
else
yydata = sum(da(scno).data{detno}(posno,:),1)./length(posno)./da(scno).exp_time;
tx_yax = 'Normalized Intensity (cps)';
end
line(xxdata, yydata,'color',cc(1,:),'marker','.','displayname','raw curve')
else
if normalize == 0
yydata = double(da(scno).data{detno}(posno,:));
tx_yax = 'Intensity (counts)';
else
yydata = double(da(scno).data{detno}(posno,:))./da(scno).exp_time;
%yydata = sum(da(scno).data(posno,:),1)./length(posno);
tx_yax = 'Normalized Intensity (cps)';
end
for k = 1:length(posno)
line(xxdata, yydata(k,:),'color',cc(k,:),'marker','.','displayname',sprintf('pos-%d',posno(k)))
end
end
% if strcmp(x_unit,'d')
% xxx = 0.5:0.001:10;
% yyy = interp1(xxdata,yydata,xxx,'spline');
% line(xxx,yyy,'color','r','marker','o','markersize',3);
% end
% if label_peak
% ccode = {'b' '[0 0.8 0]' '[0.73 0.7 0.7]'};
% %pk_list = [da(point).pkid_fit{:}];
% pk_list = [da(1).pkid_fit{:}];
% for m = 1:length(da(1).Material)
% phase_name_list{m} = da(1).Material(m).name;
% switch x_unit
% case 'd'
% xxsample = da(1).Material(m).d_hkl;
% case 'E'
% xxsample = da(1).Material(m).E_hkl;
% case 'Ch'
% xxsample = da(1).Material(m).Ch_hkl;
% end
% line(xxsample, ones(length(xxsample), 1),'marker','^','color',ccode{m},'markersize',9,'linestyle','none','Displayname',sprintf('%s',da(1).Material(m).name))
% lnfit = line(xxsample(pk_list([da(1).phase_fit{:}]==m)), ones(length(pk_list([da(1).phase_fit{:}]==m)), 1),'marker','o','color','r','markersize',5,'linestyle','none','displayname','peak fitted');
% if m ~= 1; set(get(get(lnfit,'Annotation'),'LegendInformation'),'IconDisplayStyle','off');end
% end
% end
if ~strcmp(datalim{1},'auto'); xrange = datalim{1};end
grid on
set(gca,'yscale',y_scale,'fontsize',fsa,'box','on');
xlabel(xlab)
ylabel(tx_yax)
xlim(xrange);
ylim(yrange);
legend('toggle');
if length(posno)>1
title_text = sprintf('Det-%d, Positon = %d - %d',detno,posno(1),posno(end));
else
title_text = sprintf('Det-%d, Positon = %d',detno,posno(1));
end
title(title_text,'fontsize',fst)
text(0.1,0.05,sprintf('Total count time: %d sec',da(1).exp_time*length(posno)),'sc','fontsize',fsa);
case '2draw'
switch x_unit
case 'ch'
xrange = datalim{1};
yrange = datalim{2}; %yrange = 'auto';
int_range = datalim{3};
if ~strcmp(yrange,'auto'); yrange=yrange+[-0.5 0.5];end
xlab = sprintf('Channel');
xgrid =1:size(da(scno).data{detno},2);
ygrid =1:size(da(scno).data{detno}(:,:),1);
case 'e'
xrange = datalim{1};
yrange = datalim{2}; %yrange = 'auto';
int_range = datalim{3};
if ~strcmp(yrange,'auto'); yrange=yrange+[-0.5 0.5];end
xlab = sprintf('Energy (keV)');
xgrid= da(scno).Inst.E_grid(detno,:);
ygrid = 1:size(da(scno).data{detno}(:,:),1);
case 'd'
xrange = datalim{1};
yrange = datalim{2};
int_range = datalim{3};
if ~strcmp(yrange,'auto'); yrange=yrange+[-0.5 0.5];end
xlab = sprintf('d (Angstron)');
if ~isfield(da(scno),'d_data')
for k = 1:size(da(scno).data{detno}(:,:),1)
da(scno).Inst.d_grid2(detno,:) = 0.4:0.001:10;
xx = da(scno).Inst.d_grid(detno,:);
yy = double(da(scno).data{detno}(k,:));
qy = interp1(xx,yy,da(scno).Inst.d_grid2(detno,:),'spline');
qy(qy<0.1|qy>max(yy)*2)=0;
da(scno).d_data(k,:,detno) = qy;
end
end
xgrid= da(scno).Inst.d_grid2(detno,:);
ygrid = 1:size(da(scno).d_data(:,:,detno),1);
%assignin('base','da',da);
otherwise
fprintf('The desire x_unit: %s is not supported yet!!\n',x_unit);
return;
end
ylab = sprintf('%s (#) steps',da(scno).motorname);
linesap = find(da(scno).log==char(10));
wordsap = find(da(scno).log(1:linesap(1)-1)==' ');
title_text=sprintf('%s',da(scno).log(wordsap(3)+1:linesap(1)-1));
if strcmp(x_unit,'d')
imagesc(xgrid,ygrid,log10(da(scno).d_data(:,:,detno)));
%set(gca,'clim',[]);
else
imagesc(xgrid,ygrid,log10(double(da(scno).data{detno}(:,:))));
end
if ~strcmp(xrange,'auto'); xlim(xrange);end
if ~strcmp(yrange,'auto'); ylim(yrange);end
if ~strcmp(int_range,'auto'); set(gca,'clim',[log10(int_range(1)) log10(int_range(2))]);end
xlabel(xlab,'fontsize',13);
ylabel(ylab,'fontsize',13);
title(strjoin(strsplit(title_text,'_'),'\\_'),'fontsize',17);
case 'step_plot'
title_text=sprintf('%s, %2.3f to %2.3f, %2.3f/step',da(scno).motorname, da(scno).motorpos(1), da(scno).motorpos(end), da(scno).motorstep);
xrange = datalim{1};
yrange = datalim{2};
switch x_unit
case 'ch'
flag = [1:8192]>=xrange(1) & [1:8192] <= xrange(2);
case 'e'
% use only det-1 to calculate sum range
flag = da(scno).Inst.E_grid(1,:) >=xrange(1) & da(scno).Inst.E_grid(1,:) <= xrange(2);
case 'd'
% use only det-1 to calculate sum range
flag = da(scno).Inst.d_grid(1,:) >=xrange(1) & da(scno).Inst.d_grid(1,:) <= xrange(2);
otherwise
fprintf('unknown x_unit, not ready yet!!\n');
return
end
if sum(flag)==0
flag = 1;
end
%length(da(scno).data)
if normalize
yy1data = sum(da(scno).data{1}(:,flag),2)/max(sum(da(scno).data{1}(:,flag),2));
yy2data = sum(da(scno).data{2}(:,flag),2)/max(sum(da(scno).data{2}(:,flag),2));
else
yy1data = sum(da(scno).data{1}(:,flag),2);
yy2data = sum(da(scno).data{2}(:,flag),2);
end
xxdata = da(scno).motorpos;
line(xxdata,yy1data,'marker','o','color',cc(1,:),'Displayname','Det-1');
line(xxdata,yy2data,'marker','o','color',cc(2,:),'Displayname','Det-2');
xlabel(sprintf('%s position (mm)',da(scno).motorname),'fontsize',15);
ylabel(sprintf('Sum Intensity'),'fontsize',15);
title(strjoin(strsplit(title_text,'_'),'\\_'),'fontsize',17);
otherwise
fprintf('Selected plot type is not supported');
end