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ptycho/+detector/+virtual/private/fourier_ptycho_data.m
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%FOURIER_PTYCHO_DATA
% Prepare and adjust artificial data for Fourier Ptychography
% 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 [ sim ] = fourier_ptycho_data( sim )
import utils.*
%% first create the illumination of the sample in real-space
sz = size(sim.simulation.obj{1});
objpix = sim.lambda*sim.z_lens./(sim.asize.*sim.dx_spec);
illum_dim = round(sim.simulation.illumination/2./objpix);
maxdim = round(max([sz illum_dim]));
if maxdim == max(illum_dim)
maxdim = round(maxdim *1.1);
end
aperture = prop_free_nf(fftshift(filt2d_pad(maxdim, illum_dim(1), illum_dim(1)-3, 'circ')), sim.lambda, 1e-3, objpix);
illum = crop_pad(aperture, sz);
%% propagate to the objective lens
if sim.simulation.prop_from_focus
sim.simulation.obj{1} = fftshift(prop_free_nf(fft2(ifftshift(sim.simulation.obj{1} .* illum)),sim.lambda, sim.prop_from_focus, sim.dx_spec))./sqrt(sz(1)*sz(2));
else
sim.simulation.obj{1} = fftshift(fft2(ifftshift(sim.simulation.obj{1} .* illum)))./sqrt(sz(1)*sz(2));
end
end
ptycho/+detector/+virtual/private/generate_virtual_object.m
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% [object] = generate_virtual_object(dataset, img_path, Npix, angle)
% create a virtual thickness map that can be used to generate test object
% for ptycho
% Inputs:
% dataset - number or string with name
% img_path - path to folder with source images
% Npix - size of the output ptrojections
% angle - rotation of the 3D object
% Outputs:
% object - normalized thickness map
% Publications most relevant to the Difference-Map implementation
% + P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer,
% "High-Resolution Scanning X-ray Diffraction Microscopy," Science 321, 379-382 (2008)
% + P. Thibault, M. Dierolf, O. Bunk, A. Menzel, F. Pfeiffer,
% "Probe retrieval in ptychographic coherent diffractive imaging,"
% Ultramicroscopy 109, 338–343 (2009)
%
% Publications most relevant to the Maximum Likelihood refinement
% + M. Guizar-Sicairos and J. R. Fienup, "Phase retrieval with transverse
% translation diversity: a nonlinear optimization approach," Opt. Express 16, 7264-7278 (2008)
% + P. Thibault and M. Guizar-Sicairos, "Maximum-likelihood refinement for
% coherent diffractive imaging," New J. Phys. 14, 063004 (2012).
% 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 [object] = generate_virtual_object(p, dataset, img_path, Npix, angle)
%% preload some artificial object
switch dataset
case 1
%% MONA LISA
object = imread(fullfile(img_path, 'ML512.jpg'));
object = double(object(:,:,1));
object = double(object)./double(max(object(:)));
case 2
%% autumn
object = imread('autumn.tif');
object = double(object(:,:,1));
object = double(object)./double(max(object(:)));
case 3
%% camera man
object = imread('autumn.tif');
object = double(object(:,:,1));
object = double(object)./double(max(object(:)));
case 4
%% test pattern
object = imread('testpat1.png');
object = double(object(:,:,1));
object = double(object)./double(max(object(:)));
case 5
%% USAF target
object = 255-imread(fullfile(img_path, 'USAF-1951.png'));
object = single(object(:,:,1) < 128);
case 6
%% MANDRIL
object = imread(fullfile(img_path, 'mandrill.png'));
object = double(object)./double(max(object(:)));
case 7
%% CHIP
object = imread(fullfile(img_path, 'chip_phantom.png'));
object = single(object(:,:,1)) / 255;
case 8
%% Snellen chart
object = imread(fullfile(img_path, 'Snellen_chart.png'));
object = single(object(1:2:end,1:2:end,1) > 50);
object = utils.crop_pad(object, size(object)+10,1);
case '3D_phantom'
%% create a phantom that looks like a porous material and henerate projections from it,
import utils.*
import math.*
% Nx = ceil(Npix(1)/128)*128;
% Nz = ceil(Npix(2)/128)*128;
% Ny = Nx;
Nx = 512;
Ny = 512;
Nz = 512;
if check_option(p, 'use_gpu')
dtype = gpuArray.ones(1,'single');
verbose(0,'Processing phantom on GPU')
else
dtype = ones(1,'single');
end
phantom_filename = fullfile(img_path, sprintf('glass_data_%ipx.mat', Nx));
try
d = load(phantom_filename);
volData = single(d.volData)/255; % convert from uint8 to singles
[Nx, Ny, Nlayers] = size(volData);
catch
verbose(0, 'Cached phantom not availible in %s', phantom_filename)
disp('Creating phantom')
% create a phantom that looks like a porous material
rng default
volData = randn([Nx, Ny, Nz],'like', dtype);
utils.progressbar(1,6);
volData = imgaussfilt3_fft(volData, 2);
utils.progressbar(2, 6);
volData = volData / max(abs(volData(:)));
utils.progressbar(3,6);
volData = single(volData <= 0);
utils.progressbar(5, 6);
% volData = volData*0.2 + 0.8; % add some background
% store as uint8 to save space
volData = uint8(volData/max(volData(:)) * 255);
if isa(volData, 'gpuArray')
volData = gather(volData);
end
try; save('-v6', phantom_filename, 'volData'); end
volData = single(volData)/255;
utils.progressbar(6, 6);
end
if ~isempty(angle)
verbose(0,'Phantom volume is rotated by %6.3g degrees', angle)
if check_option(p, 'use_gpu')
volData = gpuArray(volData);
end
% apply circular mask
xgrid = -Nx/2+1 : Nx/2;
ygrid = -Ny/2+1 : Ny/2;
[X,Y] = meshgrid(ygrid, xgrid);
air_gap = 200; % pixels
volData = volData .* imgaussfilt(single(X.^2+Y.^2 < (Nx/2 - air_gap/2)^2), 3);
% rotate the volume using FFT (volData is real valued at this point)
volData = utils.imrotate_ax_fft(volData, angle, 3);
volData = max(0,min(volData,1));
end
object = 1-permute(volData, [3,1,2]);
otherwise
error('Sorry, sample %d is missing. Feel free to add it!', dataset)
end
if size(object,3) == 1
% in case of a simple 2D object replicate the pattern to avoid void
% space around
object = repmat(object, 5,5);
end
%% adjust the object to the requested size and surround by empty space
object = utils.crop_pad(object, Npix, mean(mean(mean(object(:,[1,end],:)))));
object = reshape(object,size(object,1), size(object,2),1,size(object,3));
end
ptycho/+detector/+virtual/private/randpoisson.m
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function out=randpoisson(inarray,thresh);␍% function out=randpoisson(inarray,thresh);␍% outputs an array of poisson-distributed numbers with mean equal to inarray␍% For inarray values above the threshold thresh (default=32),␍% use a quick-and-dirty version of the gaussian method,␍% but with negatives clipped to zero␍% J.R. Fienup 10/22/99␍␍␍if nargin < 1, ␍ error('Requires at least one input argument.'); ␍end␍␍if exist('thresh')~=1, thresh=32; end␍␍out=inarray;␍% High-count pixels - use Gaussian approach␍gtthresh=find(inarray>thresh);␍if ~isempty(gtthresh),␍ out(gtthresh)=inarray(gtthresh) + sqrt(inarray(gtthresh)).*randn(size(inarray(gtthresh)));␍ out(gtthresh)=round(max(0,out(gtthresh)));␍end␍% Low-count pixels - this goes into the counting-experiment method␍␍ltthresh=find(inarray<=thresh);␍if ~isempty(ltthresh)␍ lamda=inarray(ltthresh); % segregate low-value pixels to speed computation␍ % Now dealing with a 1-D column vector that will merge into n-D array out later on␍ %Initialize r to zero.␍ r = zeros(size(lamda)); % output array for ltthresh pixels␍ p = zeros(size(lamda));␍ ind = true(size(lamda));␍ ␍ while any(ind)␍ p(ind) = p(ind) - log(rand(length(ind),1)); % note, do repeatedly calculate over all of lamda␍ ind = find(p < lamda); % Q: does this k index over ␍ r(ind) = r(ind) + 1;␍ end␍␍ ␍ % Return NaN if lamda is not positive -- to do this, un-comment what follows (gives zero now).␍ ␍% tmp = NaN;␍% if any(any(any(lamda <= 0)));␍% if prod(size(lamda) == 1), % i.e., a single pixel?␍% r = tmp(ones(size(lamda)));␍% else␍% k = find(lamda <= 0);␍% r(k) = tmp(ones(size(k)));␍% end␍% end␍␍ out(ltthresh)=r; % Merge low-value-pixel results with large-value-pixel results␍ ␍end; % of if length(ltthresh)>0␍␍end␍␍