swim/fold_slice
1
0
Fork 0
mirror of https://github.com/c-sooyoung/fold_slice.git synced 2026-09-17 20:39:08 +09:00
Code Issues Packages Projects Releases Wiki Activity

initial commit

Browse Source
This commit is contained in:
swim
2026-08-07 15:56:42 +09:00
commit 91ad25aca9
1012 changed files with 159314 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files
ptycho/+core/prep_h5data.m
+234
View File
@@ -0,0 +1,234 @@
%PREP_H5DATA prepare data and save it to disk
% prep_h5data expects that fmask and fmag already exist, prepares them
% for the C++ code and saves everything to disk.
%
% ** p p structure
%
% see also: core.ptycho_prepare_scans
% 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 prep_h5data(p)
import utils.verbose
import io.HDF.save2hdf5
fmask = p.fmask;
fmag = p.fmag;
single_mask = true;
for ii=1:size(fmask,3)-1
if ~isequaln(fmask(:,:,ii),fmask(:,:,ii+1))
single_mask = false;
break;
end
end
%%%%% Prepare object and probe for hdf5 file %%%%%
for obnum = p.share_object_ID
object_c(obnum) = struct('data',p.object{obnum}(:,:,1));
end
for prnum = p.share_probe_ID
probe_c(prnum) = struct('data',p.probes(:,:,prnum));
end
%%%%% Prepare data for hdf5 file %%%%%
bad_pixels = cell(p.numscans,1);
bad_pixels_index = cell(p.numscans,1);
% Assumes that detector position is the same within a scan
for ii = 1:p.numscans % loop over scans
% Prepare structure for detector %
% Here I detect the module gaps, can be later given by the
% prepare_data function
fmaski = fmask(:,:,p.scanindexrange(ii,1)); % First mask to detect modules (gaps)
auxmodxo = any(fmaski,1);
if auxmodxo(1)
indbeginmodx = 1;
else
indbeginmodx = [];
end
auxmodx = diff(auxmodxo);
indbeginmodx = [indbeginmodx find(auxmodx==1)+1];
nummodx = length(indbeginmodx);
indendmodx = find(auxmodx==-1);
if auxmodxo(end)
indendmodx = [indendmodx p.asize(2)];
end
auxmodyo = any(fmaski,2);
if auxmodyo(1)
indbeginmody = 1;
else
indbeginmody = [];
end
auxmody = diff(auxmodyo);
indbeginmody = [indbeginmody find(auxmody==1).'+1];
nummody = length(indbeginmody);
indendmody = find(auxmody==-1).';
if auxmodyo(end)
indendmody = [indendmody p.asize(1)];
end
modulearray = zeros(nummody*nummodx,4);
fmaskdet = zeros(p.asize); % Module mask for current detector position
counter = 0;
for kk = 1:nummody
for jj = 1:nummodx
counter = counter+1;
numrows = indendmody(kk) - indbeginmody(kk) + 1;
numcols = indendmodx(jj) - indbeginmodx(jj) + 1;
fmaskdet(indbeginmody(kk):indendmody(kk),indbeginmodx(jj):indendmodx(jj))=1;
modulearray(counter,:) = [numrows,numcols,indbeginmody(kk)-1,indbeginmodx(jj)-1]; %% Minus one to go to indexing convention in C
end
end
verbose(3,['Detected ' num2str(nummodx*nummody) ' modules'])
if verbose >= 3
disp([num2str(modulearray)])
end
%%% Here there is the posibility to add bad pixels that are common
%%% to all diffraction patterns. Could be identified in prepare
%%% data
%detector(ii) = struct('rows', uint32(192), 'columns', uint32(192), 'modules', transpose(uint32([192,192,0,0])), 'bad_pixels', transpose(uint32([9,10; 11,12; 13,14])));
detector(ii) = struct('rows', uint32(p.asize(1)), 'columns', uint32(p.asize(2)),...
'modules', transpose(uint32(modulearray)),'bad_pixels',uint32([]));
if ~single_mask
idx = 0;
for jj = p.scanindexrange(ii,1):p.scanindexrange(ii,2) % loop over corresponding diffraction patterns
[y, x] = find(1+fmask(:,:,jj)-fmaskdet==0);
bps = transpose(reshape([y, x], length(x), 2))-1;
idx = length(bps)+idx;
bad_pixels_index{ii} = [bad_pixels_index{ii} idx];
bad_pixels{ii} = [bad_pixels{ii} bps];
end
else
[y, x] = find(1+fmaski-fmaskdet==0);
bad_pixels{ii} = transpose(reshape([y, x], length(x), 2))-1;
end
% Prepare structure for measurement %
% for jj = p.scanindexrange(ii,1):p.scanindexrange(ii,2) % loop over corresponding diffraction patterns
% %%%%% Prepare bad pixels %%%%%
% [y, x] = find(1+fmaski-fmaskdet==0);
% bad_pixels(jj) = transpose(reshape([y, x], length(x), 2))-1;
% measurement(jj) = struct('data', fmag(:,:,jj), 'position', uint32((p.positions(jj,:))),...
% 'object', uint32(p.share_object_ID(ii)-1), 'probe', uint32(p.share_probe_ID(ii)-1),...
% 'detector', uint32(ii-1));
% end
end
%% prepare output
h5_struc = [];
h5_struc.Attributes.format = 2;
for ii=1:size(probe_c,2)
h5_struc.probes(:,ii) = uint64(size(probe_c(ii).data));
end
for ii=1:size(object_c,2)
h5_struc.objects(:,ii) = uint64(size(object_c(ii).data));
end
%% detectors
h5_struc.detector = [];
for ii=1:p.numscans
temp = detector(ii);
h5_struc.detector.(['n' num2str(ii-1)]).Attributes.rows = temp.rows;
h5_struc.detector.(['n' num2str(ii-1)]).Attributes.columns = temp.columns;
if single_mask && ~isempty(bad_pixels{ii})
h5_struc.detector.(['n' num2str(ii-1)]).bad_pixels = bad_pixels{ii};
end
h5_struc.detector.(['n' num2str(ii-1)]).modules = temp.modules;
end
%% measurements
h5_struc.measurement = [];
h5_struc.measurement.Attributes.max_power = 1/p.renorm^2;
for ii=1:p.numscans
% attributes
h5_struc.measurement.(['n' num2str(ii-1)]).Attributes.detector = uint32(ii-1);
h5_struc.measurement.(['n' num2str(ii-1)]).Attributes.probe = uint32(p.share_probe_ID(ii)-1);
h5_struc.measurement.(['n' num2str(ii-1)]).Attributes.object = uint32(p.share_object_ID(ii)-1);
h5_struc.measurement.(['n' num2str(ii-1)]).Attributes.max_sum = uint32(p.max_sum(ii));
% datasets
h5_struc.measurement.(['n' num2str(ii-1)]).positions = uint32(transpose(round(p.positions(p.scanidxs{ii},:))));
h5_struc.measurement.(['n' num2str(ii-1)]).data = permute((fmag(:,:,p.scanidxs{ii})/p.renorm).^2, [2 1 3]);
if ~single_mask
h5_struc.measurement.(['n' num2str(ii-1)]).bad_pixels = bad_pixels{ii};
h5_struc.measurement.(['n' num2str(ii-1)]).bad_pixels_index.Value = uint64(transpose(bad_pixels_index{ii}));
h5_struc.measurement.(['n' num2str(ii-1)]).bad_pixels_index.Attributes.save2hdf5DataShape = size(uint64(transpose(bad_pixels_index{ii})),1);
end
end
%% save to disk
if ~exist(p.prepare_data_path, 'dir')
mkdir(p.prepare_data_path)
end
verbose(2,'Writing H5 data file: %s',[p.prepare_data_path p.prepare_data_filename]);
save2hdf5([p.prepare_data_path p.prepare_data_filename], h5_struc, 'overwrite', true, 'comp', p.io.data_compression);
end