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ptycho/utils/load_ptycho_recons.m
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%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