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https://github.com/c-sooyoung/fold_slice.git
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211 lines
8.8 KiB
Matlab
211 lines
8.8 KiB
Matlab
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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% Function:
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%
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% dose_calc(ptycho_recon, ptycho_data, param)
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%
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% Description:
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%
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% The function (1) takes one reconstruction and its data and estimate the
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% dose (2) saves the dose estimation into a .txt file.
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%
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% Input:
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%
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% ptycho_recon: reconstruction, including object, probe, and p
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% ptycho_data: data for the reconstruction
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% param_dose.mu = 1/(451*1e-6); % 1/attenuation_length in 1/m (for CH2 @6.2keV)
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% % 1/(152.7*1e-6) for zeolite Na2Al2Si3O102H4O with 2 g/cm3 density at 6.2 keV
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% param_dose.rho = 1000; % Density in kg/m^3
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% param_dose.setup_transmission = 0.55; % Intensity transmission of sample
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% % (e.g. air path after the sample, windows, He, detector efficiency)
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% % 0.943 for 700 cm He gas at 760 Torr and 295 K @ 6.2 keV
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% % 0.780 for 10 cm air at 760 Torr and 295 K @ 6.2 keV
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% % 0.976 for 13 micron Kapton (polymide) with 1.43
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% % g/cm3 @ 6.2 keV
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% % 0.841 for 7 micron muskovite mica
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% % (KAl3Si3O11.8H1.8F0.2) with 2.76 g/cm3 @ 6.2 keV
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% % 0.914 for 5 cm of air at 6.2 keV 750 Torr 295 K
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% % 0.55 for 300 micron of mylar C10H8O4 with density 1.38 g/cm3 at 6.2 keV
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% param_dose.overhead = 0.0; % Extra dose during movement overhead, only applicable
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% % if shutter is not closed between exposures
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% param_dose.fmask
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% param_dose.scan_number
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% param_dose.num_proj
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% param_dose.output_folder (default: ./)
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%
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% Output:
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%
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% one jpg for one_data_frame
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% one jpg for photons_per_shot_all
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% one jpg for photons_per_obj_pix
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% one txt for dose_estimate
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%
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% 2017-03-30
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%*-----------------------------------------------------------------------*
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%| |
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%| Except where otherwise noted, this work is licensed under a |
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%| Creative Commons Attribution-NonCommercial-ShareAlike 4.0 |
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%| International (CC BY-NC-SA 4.0) license. |
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%| |
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%| Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch) |
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%| |
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%| Author: CXS group, PSI |
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%*-----------------------------------------------------------------------*
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% You may use this code with the following provisions:
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%
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% If the code is fully or partially redistributed, or rewritten in another
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% computing language this notice should be included in the redistribution.
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%
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% If this code, or subfunctions or parts of it, is used for research in a
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% publication or if it is fully or partially rewritten for another
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% computing language the authors and institution should be acknowledged
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% in written form in the publication: “Data processing was carried out
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% using the “cSAXS matlab package” developed by the CXS group,
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% Paul Scherrer Institut, Switzerland.”
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% Variations on the latter text can be incorporated upon discussion with
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% the CXS group if needed to more specifically reflect the use of the package
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% for the published work.
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%
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% A publication that focuses on describing features, or parameters, that
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% are already existing in the code should be first discussed with the
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% authors.
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%
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% This code and subroutines are part of a continuous development, they
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% are provided “as they are” without guarantees or liability on part
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% of PSI or the authors. It is the user responsibility to ensure its
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% proper use and the correctness of the results.
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function dose_calc(ptycho_recon, ptycho_data, param)
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import utils.*
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%Estimating detected photons
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probe = ptycho_recon.probe;
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object = ptycho_recon.object;
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p = ptycho_recon.p;
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data = ptycho_data.data;
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fmask = ptycho_data.fmask;
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if isfield(param,'mu') && isfield(param,'rho') && isfield(param,'setup_transmission') && isfield(param,'overhead')
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mu = param.mu;
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rho = param.rho;
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setup_transmission = param.setup_transmission;
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overhead = param.overhead;
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else
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error('Please specify param.mu, param.rho, param.setup_transmission, and param.overhead.\n');
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end
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if isfield(param,'num_proj')
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num_proj = param.num_proj;
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else
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verbose(0,'Using num_proj = 1');
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num_proj = 1;
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end
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if isfield(param,'scan_number')
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scan_number = param.scan_number;
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else
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scan_number = [];
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end
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if isfield(param,'output_folder')
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output_folder = param.output_folder;
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else
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verbose(0,'Using output_folder = ./');
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output_folder = '.';
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end
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data = data .* fmask;
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photons_per_shot_all = sum(sum(data));
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photons_per_shot = max(photons_per_shot_all);
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%Normalizing probe to photons per shot
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probe_norm = sum(abs(probe).^2,3);
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probe_norm = probe_norm/sum(probe_norm(:));
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probe_norm = probe_norm*photons_per_shot;
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%
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asize = size(probe);
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%objaux = object*0;
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illum_sum = zeros(size(object,1)+10,size(object,2)+10);
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scanfirstindex = [1 cumsum(p.numpts)+1]; % First index for scan number
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for ii = 1:p.numscans
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p.scanindexrange(ii,:) = [scanfirstindex(ii) scanfirstindex(ii+1)-1];
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p.scanidxs{ii} = p.scanindexrange(ii,1):p.scanindexrange(ii,end);
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end
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for ii = p.scanidxs{1}
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Indy = round(p.positions(ii,1)) + [1:asize(1)];
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Indx = round(p.positions(ii,2)) + [1:asize(2)];
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illum_sum(Indy,Indx) = illum_sum(Indy,Indx)+probe_norm;
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end
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illum_sum = illum_sum(asize(1)/2:end-asize(1)/2,asize(2)/2:end-asize(2)/2);
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% in case of laminography the field of view isnot rectangular ->
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% exclude the empty regions in the illumination function
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illum_mask = illum_sum > mean(illum_sum) * 0.1;
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flux_in_area = sum(sum(illum_sum .* illum_mask)); %photons
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area = sum(illum_mask(:))*p.dx_spec(1)^2; % meters^2
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I = flux_in_area/area; %ph/meters^2
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hv = 9.9334947e-16*(p.energy/6.2); %6.2keV in joules
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D = mu*I*hv*num_proj/rho;
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D_with_gas = D/setup_transmission;
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D_with_overhead = D_with_gas*(1+overhead);
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verbose(0,'**********************************************')
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verbose(0,'Dose report for %d projections, Scan %d',num_proj, scan_number)
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verbose(0,'**********************************************')
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verbose(0,'Measured photons per frame = %.2e photons',photons_per_shot);
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verbose(0,'N_0 used for imaging for one projection = %.2e photons/micron^2',I*1e-12);
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verbose(0,'Dose used for imaging, D = %.2e Gy',D)
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verbose(0,'Accounting for experiment transmission, D = %.2e Gy',D_with_gas)
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verbose(0,'Accounting for experiment transmission and overhead, D = %.2e Gy',D_with_overhead)
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%=======================
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figure(1); clf
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plotting.imagesc3D(log10(1+data));
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caxis([0,log10(max(data(:)))])
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colormap(plotting.franzmap); colorbar
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axis xy equal tight
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title('Data frames, log10')
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filename = fullfile(output_folder,sprintf('/%s_one_data_frame.jpg',p.run_name));
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verbose(1,'saving %s',filename);
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print('-djpeg','-r300',filename);
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figure(2); clf
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plot(squeeze(photons_per_shot_all)); grid on;
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title(['Number of measured photons per frame = ' num2str(photons_per_shot)]);
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filename = fullfile(output_folder,sprintf('/%s_photons_per_shot_all.jpg',p.run_name));
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verbose(1,'saving %s',filename);
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print('-djpeg','-r300',filename);
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figure(3); clf
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imagesc(illum_sum)
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colormap(plotting.franzmap); colorbar
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axis image xy
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title('Photons per pixel of the object')
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filename = fullfile(output_folder,sprintf('/%s_photons_per_obj_pix.jpg',p.run_name));
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verbose(1,'saving %s',filename);
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print('-djpeg','-r300',filename);
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%=======================
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filename = fullfile(output_folder,sprintf('/%s_dose_estimate_S%05d.txt',p.run_name, scan_number));
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fid = fopen(filename,'w');
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fprintf(fid,'Scan = %d\n',scan_number);
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fprintf(fid,'Measured photons per frame = %.3e\n',photons_per_shot);
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fprintf(fid,'N_0 used for imaging for one projection (I*1e-12) = %.3e photons/micron^2\n',I*1e-12);
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fprintf(fid,'num_proj = %d\n',num_proj);
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fprintf(fid,'hv = %.5e\n\n',hv);
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fprintf(fid,'D = mu*I*hv*num_proj/rho \n');
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fprintf(fid,'D_with_gas = D/setup_transmission \n');
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fprintf(fid,'D_with_overhead = D_with_gas*(1+overhead) \n\n');
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fprintf(fid,'If mu = %.3e m^-1, rho = %.3e kg/m^3, setup_transmission = %.3f, then:\n', mu, rho, setup_transmission);
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fprintf(fid,'Accounting for experiment transmission, D_with_gas = %.3e Gy = %.3f MGy\n\n', D_with_gas, D_with_gas/1e6);
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fprintf(fid,'asize = %d, pixel size = %.4f nm\n', asize(1), p.dx_spec(1)*1e9);
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fclose(fid); |