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% SAVE_MERGED_PROJECTIONS save projections generated from tomography to be loaded as initial guess in
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% ptychography , projections are saved to the same path from where they were loaded
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% just with a differenent suffix
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%
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% save_merged_projections(par,stack_object, volData_c, theta, total_shift, name_sufix)
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%
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% Inputs:
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% **par - tomography parameters structure
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% **stack_object - array of complex valued projections
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% **volData_c - complex valued sample reconstruction
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% **theta - measured angles
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% **total_shift - reconstructed shift of the projections
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% **name_sufix - extra sufix added to the saved projections
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% *returns*
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% ++prepared_objects - prepared lsit of structures for 3D ptychotomo
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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) 2018 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 prepared_objects = save_merged_projections(par,stack_object, theta, total_shift, name_sufix)
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import ptycho.*
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import utils.*
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import io.*
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import plotting.imagesc3D
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scanstomo = par.scanstomo;
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num_proj = length(scanstomo);
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verbose(0,'Checking available files')
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verbose(0); % make it quiet
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missing_projections = [];
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proj_file_names = cell(length(scanstomo),1);
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for num = 1:length(scanstomo)
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progressbar(num, length(scanstomo))
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path = find_projection_files_names(par, scanstomo(num));
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if isempty(path)
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missing_projections(end+1) = num;
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continue
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end
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% take the last file fitting the constraints
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proj_file_names{num} = path;
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end
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verbose(par.verbose_level); % return to original settings
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if ~isempty(missing_projections)
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verbose(1,['Did not find following scans:', num2str(missing_projections)])
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end
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[Nx,Ny,~] = size(stack_object);
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verbose(1,'Preparing projections')
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for num = 1:num_proj
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progressbar(num, num_proj)
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[filepath,name, ext] = fileparts(proj_file_names{num});
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out_name = [name,'_',name_sufix];
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fullpath = [filepath, '/', out_name,'.mat'];
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% load original data
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d = io.load_ptycho_recons(proj_file_names{num}, 'recon');
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positions = h5read(proj_file_names{num}, '/reconstruction/p/positions')';
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obj_size = size(d.object);
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object = zeros(obj_size,'like',stack_object);
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object(1:min(end,Nx),1:min(end,Ny)) = ...
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stack_object(1:min(end,obj_size(1)),1:min(end,obj_size(2)),num);
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% load the complex projections from fp16 precision if used
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object = fp16.get(object);
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%% prepare structure for ptychtomo solver
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prepared_objects{num}.object = object;
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prepared_objects{num}.positions = positions;
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prepared_objects{num}.illum_sum = [];
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prepared_objects{num}.weight = [];
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prepared_objects{num}.angle = theta(num);
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prepared_objects{num}.position_offset = round(total_shift(num,:));
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% testme
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prepared_objects{num}.probe = utils.imshift_fft(d.probe, total_shift(num,:) -round(total_shift(num,:))) ;
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prepared_objects{num}.scan_id = scanstomo(num);
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prepared_objects{num}.proj_id = num;
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% phase removal in probe
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[~,~, gamma_x, gamma_y] = utils.stabilize_phase(d.object,object, 'binning', 8);
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% remove ramp from probe as well
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xramp = pi*(linspace(-1,1,par.asize(1)))';
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yramp = pi*(linspace(-1,1,par.asize(2)));
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c_offset = xramp.*gamma_x*par.asize(1) + yramp.*gamma_y*par.asize(2);
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prepared_objects{num}.probe = prepared_objects{num}.probe .* exp(1i*c_offset);
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% plotting.imagesc3D( angle(d.object .* conj(object(1:4:end,1:4:end)) ))
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%drawnow
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end
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end
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