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https://github.com/c-sooyoung/fold_slice.git
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117 lines
2.7 KiB
Matlab
117 lines
2.7 KiB
Matlab
import io.image_read
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import io.load_prepared_data
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import io.spec_read
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clear
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addpath ptycho/utils/
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scans=[11745:11763];
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range=[];
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marksaxis_start = 1; % First markMarks used for scan
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marksaxis_step = 0.1; % Step of marks, change of marks from one scan to the next
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usemarksaxis = false;
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use_fluorescence = false;
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use_pilatus = true;
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int=zeros(1,length(scans));
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norm=zeros(1,length(scans));
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xaxis=zeros(1,length(scans));
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marksaxis = [0:numel(xaxis)-1]*marksaxis_step + marksaxis_start;
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S=spec_read('~/Data10/specES1/dat-files/','ScanNr',scans);
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spectra_sum = [];
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for hh=1:length(scans)
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if use_fluorescence
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filename = sprintf('~/Data10/fx123/gccDppConsoleLinux/data/x123_%05d.dat',scans(hh));
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data = image_read(filename);
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if ~isempty(spectra_sum)
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spectra_sum = spectra_sum + sum(data.data,2);
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else
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spectra_sum = sum(data.data,2);
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end
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if ~isempty(range)
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int(hh)=sum(sum(data.data(range,:),1),2);
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else
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int(hh)=sum(sum(data.data(:,:),1),2);
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end
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end
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if use_pilatus
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prepdata_filename = sprintf('~/Data10/analysis/S%05d/S%05d_data_400x400.h5',scans(hh),scans(hh));
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display(sprintf('loading %s',prepdata_filename))
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[I, fmask, ~] = load_prepared_data(prepdata_filename, true);
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this = sum(I, 3).*any(fmask,3);
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trans(hh) = sum(this(:));
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end
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eaxis(hh)=S{hh}.mokev;
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norm(hh)=S{hh}.bpm4i;
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%data_spectrum = sum(data.data,2);
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end
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%
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if usemarksaxis
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axisplot = marksaxis;
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xlabeltext = 'Marks';
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else
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axisplot = eaxis;
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xlabeltext = 'E [keV]';
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end
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if use_fluorescence
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figure(1)
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subplot(2,1,1)
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semilogy(spectra_sum)
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title('Sum of all spectra')
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subplot(2,1,2)
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plot(axisplot,int./norm)
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title('Integrated fluorescence')
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xlabel(xlabeltext)
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% figure(3)
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% subplot(2,1,2)
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% line(eaxis,int./norm)
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% %title('Integrated fluorescence')
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% %xlabel(xlabeltext)
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% xlim([eaxis(1) eaxis(end)])
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% ax1 = gca;
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% ax1_pos = ax1.Position; % position of first axes
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% ax2 = axes('Position',ax1_pos,...
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% 'XAxisLocation','top',...
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% 'YAxisLocation','right',...
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% 'Color','none');
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% line(marksaxis,int./norm,'Parent',ax2,'Color','k')
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% xlim([marksaxis(1) marksaxis(end)])
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end
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if use_pilatus
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xanes=log(norm./trans);
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figure(2)
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title(sprintf('S%05d to S%05d',scans(1),scans(end)))
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subplot(3,1,1)
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plot(axisplot,xanes,'-bo')
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grid on
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subplot(3,1,2)
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% plot(axisplot(1:end-1),diff(xanes),'-bo')
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plot(axisplot,1./xanes,'-bo')
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grid on
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subplot(3,1,3)
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plot(axisplot, xanes,'-bo')
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xlabel(xlabeltext)
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ylabel('log(bpm4i/pilatus\_transmission)')
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grid on
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end
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