initial commit

2026-09-17 23:59:11 +09:00 · 2026-08-07 15:56:42 +09:00
commit 91ad25aca9
1012 changed files with 159314 additions and 0 deletions
@@ -0,0 +1,116 @@
+import io.image_read
+import io.load_prepared_data
+import io.spec_read
+
+clear
+
+addpath ptycho/utils/
+
+
+scans=[11745:11763];
+
+range=[];
+
+marksaxis_start = 1;    % First markMarks used for scan
+marksaxis_step = 0.1;  % Step of marks, change of marks from one scan to the next
+usemarksaxis = false;
+
+use_fluorescence = false;
+use_pilatus = true;
+
+int=zeros(1,length(scans));
+norm=zeros(1,length(scans));
+xaxis=zeros(1,length(scans));
+marksaxis = [0:numel(xaxis)-1]*marksaxis_step + marksaxis_start;
+
+S=spec_read('~/Data10/specES1/dat-files/','ScanNr',scans);
+spectra_sum = [];
+for hh=1:length(scans)
+    if use_fluorescence
+        filename = sprintf('~/Data10/fx123/gccDppConsoleLinux/data/x123_%05d.dat',scans(hh));
+        data = image_read(filename);
+        if ~isempty(spectra_sum)
+            spectra_sum = spectra_sum + sum(data.data,2);
+        else 
+            spectra_sum = sum(data.data,2);
+        end
+        if ~isempty(range)
+            int(hh)=sum(sum(data.data(range,:),1),2);
+        else
+            int(hh)=sum(sum(data.data(:,:),1),2);
+        end
+    end
+    if use_pilatus
+
+        prepdata_filename = sprintf('~/Data10/analysis/S%05d/S%05d_data_400x400.h5',scans(hh),scans(hh));
+        display(sprintf('loading %s',prepdata_filename))
+        [I, fmask, ~] = load_prepared_data(prepdata_filename, true);
+        this = sum(I, 3).*any(fmask,3);
+        trans(hh) = sum(this(:));
+    end
+    eaxis(hh)=S{hh}.mokev;
+    norm(hh)=S{hh}.bpm4i;
+    %data_spectrum = sum(data.data,2);
+end
+
+
+
+
+%
+
+if usemarksaxis
+    axisplot = marksaxis;
+    xlabeltext = 'Marks';
+else
+    axisplot = eaxis;
+    xlabeltext = 'E [keV]';
+end
+
+if use_fluorescence
+    figure(1)
+    subplot(2,1,1)
+    semilogy(spectra_sum)
+    title('Sum of all spectra')
+    
+    subplot(2,1,2)
+    plot(axisplot,int./norm)
+    title('Integrated fluorescence')
+    xlabel(xlabeltext)
+    
+%     figure(3)
+%     subplot(2,1,2)
+%     line(eaxis,int./norm)
+%     %title('Integrated fluorescence')
+%     %xlabel(xlabeltext)
+%     xlim([eaxis(1) eaxis(end)])
+%     ax1 = gca;
+%     ax1_pos = ax1.Position; % position of first axes
+%     ax2 = axes('Position',ax1_pos,...
+%     'XAxisLocation','top',...
+%     'YAxisLocation','right',...
+%     'Color','none');
+%     line(marksaxis,int./norm,'Parent',ax2,'Color','k')
+%     xlim([marksaxis(1) marksaxis(end)])
+end
+
+if use_pilatus
+    xanes=log(norm./trans);
+    
+    figure(2)
+    title(sprintf('S%05d to S%05d',scans(1),scans(end)))
+    subplot(3,1,1)
+    plot(axisplot,xanes,'-bo')
+    grid on
+    
+    subplot(3,1,2)
+%     plot(axisplot(1:end-1),diff(xanes),'-bo')
+    plot(axisplot,1./xanes,'-bo')
+    grid on
+    
+    subplot(3,1,3)
+    plot(axisplot, xanes,'-bo')
+    xlabel(xlabeltext)
+    ylabel('log(bpm4i/pilatus\_transmission)')
+    grid on
+    
+end