%LOAD_PTYCHO_RECONS Load data from cxs/h5 or mat file and return it as % structure, single dataset or directly into the workspace. % An additional argument can be passed to select subsections of the data. % Loading single datasets is only supported for at least 2 output % arguments. % % file... path to cxs/h5 or mat file % % *optional* % section... 'full', 'probe', 'object', 'recon' or 'p' to select % subsections of the data; default: 'full' % % EXAMPLES: % %% recommended usage %% % % load into a structure % S = load_ptycho_recons('./recon.h5'); % % % load a subset % S = load_ptycho_recons('./recon.h5', 'probe'); % % % load into single datasets % [object, probe, p] = load_ptycho_recons('./recon.h5'); % % %% not recommended, only works in 'base' workspace %% % % load directly into workspace % load_ptycho_recons('./recon.h5'); % % % full = object, probe (current scan) and p % recon = object and probe (current scan) % probe = probe (current scan) % object = object (current scan) % % Academic License Agreement % % Source Code % % Introduction % • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR") % will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS % ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM"). % % Terms and Conditions of the LICENSE % 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions % hereinafter set out and until termination of this license as set forth below. % 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements % or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the % LICENSEE’s responsibility to ensure its proper use and the correctness of the results.” % 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR % A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT % HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE % OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM. % 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively, % "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same % license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for % profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged % in the commercial use, application or exploitation of works similar to the PROGRAM. % 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into % another computing language: % "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul % Scherrer Institut, Switzerland." % % Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map: % P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008). % (doi: 10.1126/science.1158573), % for maximum likelihood: % P. Thibault and M. Guizar-Sicairos, Maximum-likelihood refinement for coherent diffractive imaging, New J. Phys. 14, 063004 (2012). % (doi: 10.1088/1367-2630/14/6/063004), % for mixed coherent modes: % P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806), % and/or for multislice: % E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016). % (doi: 10.1364/OE.24.029089). % 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the % names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case. % 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE % agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to % make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies: % © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017. % 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein. % 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate % to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents, % in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software % in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program. % 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before % the courts of Zürich, Switzerland. function varargout = load_ptycho_recons( filename_with_path, varargin ) import io.HDF.hdf5_load varargout = {}; if ~ischar(filename_with_path) error('First argument has to be string') end filename_with_path = utils.abspath(filename_with_path); if ~exist(filename_with_path, 'file') error('Could not find reconstruction file %s', filename_with_path) end if nargin > 1 switch varargin{1} case {'pr'; 'probe'; 'probes'} section = 'probe'; case {'ob'; 'obj'; 'objects'} section = 'object'; otherwise section = varargin{1}; end else section = 'full'; end if ~nargout output = 0; elseif nargout >=2 output = 2; else output = 1; end function assign_struct(val, val_name) switch output case 1 varargout{1}.(val_name) = val; case 2 varargout{end+1} = val; otherwise assignin('base', val_name, val); end end function assign_val(struc) switch output case 1 varargout{1} = struc; case 2 if isfield(struc, 'object') varargout{end+1} = struc.object; end if isfield(struc, 'probe') varargout{end+1} = struc.probe; end if isfield(struc, 'p') varargout{end+1} = struc.p; end otherwise fn = fieldnames(struc); for ii=1:length(fn) assignin('base', fn{ii}, struc.(fn{ii})) end end end % check if it is a .mat file or a .cxs file [~, ~, ext] = fileparts(filename_with_path); switch ext case '.mat' switch section case 'recon' S = load(filename_with_path, 'object', 'probe'); assign_val(S); case 'full' S = load(filename_with_path); assign_val(S); case 'object' S = load(filename_with_path, 'object'); assign_val(S); case 'probe' S = load(filename_with_path, 'probe'); size(S) assign_val(S); case 'p' S = load(filename_with_path, 'p'); assign_val(S); otherwise error('Unknown data section %s', section); end case {'.cxs','.h5'} if io.HDF.hdf5_dset_exists(filename_with_path, 'object', '/reconstruction', true) h5_path = '/reconstruction'; else h5_path = ''; end % reconstruction switch section case 'recon' % load object h = hdf5_load(filename_with_path, [h5_path '/object']); assign_struct(load_data_cell(h), 'object'); % load probe h = hdf5_load(filename_with_path, [h5_path '/probes']); assign_struct(load_data_cell(h), 'probe'); case 'full' % load object h = hdf5_load(filename_with_path, [h5_path '/object']); assign_struct(load_data_cell(h), 'object'); % load probe h = hdf5_load(filename_with_path, [h5_path '/probes']); assign_struct(load_data_cell(h), 'probe'); % load p p = convert2p(hdf5_load(filename_with_path, '/reconstruction/p', '-c')); if io.HDF.hdf5_dset_exists(filename_with_path, 'meta_all', '/measurement', true) p.meta = hdf5_load(filename_with_path, '/measurement/meta_all', '-c'); elseif io.HDF.hdf5_dset_exists(filename_with_path, 'spec_all', '/measurement', true) p.meta = hdf5_load(filename_with_path, '/measurement/spec_all', '-c'); end assign_struct(p, 'p'); case 'object' % load object h = hdf5_load(filename_with_path, [h5_path '/object']); assign_struct(load_data_cell(h), 'object'); case 'probe' % load probe h = hdf5_load(filename_with_path, [h5_path '/probes']); assign_struct(load_data_cell(h), 'probe'); case 'p' % load p p = convert2p(hdf5_load(filename_with_path, '/reconstruction/p', '-c')); if io.HDF.hdf5_dset_exists(filename_with_path, 'meta_all', '/measurement', true) p.meta = hdf5_load(filename_with_path, '/measurement/meta_all', '-c'); elseif io.HDF.hdf5_dset_exists(filename_with_path, 'spec_all', '/measurement', true) p.meta = hdf5_load(filename_with_path, '/measurement/spec_all', '-c'); end assign_struct(p, 'p'); otherwise error('Unknown data section %s', section); end otherwise error('Unknown ptycho datatype %s.', ext) end end function tmp = load_data_cell(h) fn = fieldnames(h); num_end = str2double(subsref(strsplit(fn{1}, '_'), struct('type', '{}', 'subs',{{length(strsplit(fn{1},'_'))}}))); if length(fn)==2 && (strcmpi(fn{1}, 'i') || strcmpi(fn{1}, 'r')) tmp = permute(h.r + 1i*h.i, [2,1,3,4]); elseif isnumeric(num_end) && ~isnan(num_end) for ii=1:length(fn) if isstruct(h.(fn{ii})) tmp{ii} = load_data_cell(h.(fn{ii})); else if isnumeric(h.(fn{ii})) tmp{ii} = double(h.(fn{ii})); else tmp{ii} = h.(fn{ii}); end end end % tmp = h; else for ii=1:length(fn) if isstruct(h.(fn{ii})) tmp.(fn{ii}) = load_data_cell(h.(fn{ii})); else if isnumeric(h.(fn{ii})) tmp.(fn{ii}) = double(h.(fn{ii})); else tmp.(fn{ii}) = h.(fn{ii}); end end end end end function tmp = convert2p(h) fn = fieldnames(h); for ii=1:length(fn) if isstruct(h.(fn{ii})) h.(fn{ii}) = load_data_cell(h.(fn{ii})); elseif isnumeric(h.(fn{ii})) h.(fn{ii}) = double(h.(fn{ii})); else continue; end end tmp = h; % object for ii=1:length(h.objects) tmp.object{ii} = permute(h.objects{ii}, [2 1 3 4]); end tmp = rmfield(tmp, 'objects'); % probes pr = tmp.probes; tmp.probes = []; for ii=1:length(pr) tmp.probes(:,:,ii,:) = permute(pr{ii}, [2 1 3 4]); end % positions tmp.positions = transpose(tmp.positions); tmp.positions_real = transpose(tmp.positions_real); tmp.positions_orig = transpose(tmp.positions_orig); % ctr tmp.ctr = transpose(tmp.ctr); end