% IMAGESC_HSV for plotting complex valued arrays , similar to imagesc3D but with more options % imagesc_hsv(varargin) % % ** varargin see the code % % 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 mixed coherent modes: % P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806), % for LSQ-ML method % M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018 % for OPRP method % M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369 % 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). % 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 imagesc_hsv(varargin) import utils.* import math.* par = inputParser; par.addOptional('data', []) par.addParameter('scale', nan , @isnumeric ) par.addParameter('clim', [] , @isnumeric ) par.addParameter('inverse', false , @islogical ) % use white background par.addParameter('show_ROI', false , @islogical ) % show only intersting area par.addParameter('points', [] , @isnumeric ) % plot dots par.addParameter('enhance_contrast', false , @islogical ) % plot dots par.addParameter('axis', [] , @isnumeric ) % plot dots par.addParameter('stabilize_phase', true , @islogical ) % plot dots par.addParameter('show', true , @islogical ) % plot dots par.parse(varargin{:}) r = par.Results; data = r.data; clim = r.clim; if all(data(:) == 0) warning('Empty data to plot') return end [W,H] = size(data); if ~isempty(r.axis) X = linspace(r.axis(1),r.axis(2),W)*1e6; Y = linspace(r.axis(3),r.axis(4),H)*1e6; else if ~isnan(r.scale) scale = ones(2,1).*r.scale(:); X = [-W/2:W/2-1]* scale(1)*1e6; Y = [-H/2:H/2-1]* scale(2)*1e6; else X = 1:W; Y = 1:H; end end if r.show_ROI asum = abs(sum(data,3)); try T1 = (graythresh_new((sum(asum,1)))); T2 = (graythresh_new((sum(asum,2)))); asum(:,sum(asum,1) < T1) = 0; asum(sum(asum,2) < T2,:) = 0; [ROI] = get_ROI(asum > 0.01*quantile(asum(:), 0.99), 0); data = data(ROI{:}); X = X(ROI{1}); Y = Y(ROI{2}); catch warning('ROI estimation failed') end end [W,H] = size(data); if ~isempty(clim) ind_min = abs(data) < clim(1); ind_max = abs(data) > clim(2); data(ind_min) = data(ind_min) ./ abs(data(ind_min)) * clim(1); data(ind_max) = data(ind_max) ./ abs(data(ind_max)) * clim(2); end adata = abs(data); alpha = 1e-3; tmp= sort(adata(:)); MAX = tmp(ceil(end*(1-alpha))); ind = adata > MAX; data(ind) = MAX * data(ind) ./ abs(data(ind)); if r.enhance_contrast data = data ./ sqrt(alpha+abs(data)); clim = sqrt(clim); end if r.stabilize_phase data = stabilize_phase(data, abs(data), abs(data), 'remove_ramp', false); end adata = abs(data); if isempty(clim) range = sp_quantile(adata(:), [1e-2, 1-1e-2],10); else range = clim; end %clim adata = (adata - range(1) ) ./ ( range(2) - range(1) ); ang_data = angle(data); if r.enhance_contrast && r.stabilize_phase ang_range = max(abs(sp_quantile(ang_data(:), [1e-2, 1-1e-2],10))); ang_range = max(1e-3, ang_range); ang_data = 2*pi*ang_data ./ (2* ang_range); end if r.inverse hue = mod(ang_data+1.5*pi, 2*pi)/(2*pi); hsv_data = [ hue(:) , adata(:), ones(W*H,1) ]; else hue = mod(ang_data+2.5*pi, 2*pi)/(2*pi); hsv_data = [ hue(:) , ones(W*H,1), adata(:) ]; end hsv_data = min(max(0, hsv_data),1); rgb_data = hsv2rgb(hsv_data); rgb_data = reshape(rgb_data, W,H,3); rgb_data = min(1,rgb_data); if r.show hh = imagesc(Y,X, rgb_data ); axis image end if r.show % Get the parent Axes of the image axis image if ~isempty(r.points) && ~any(isnan(r.scale)) hold on points = r.scale.*1e6.*r.points; plot( points(:,1),points(:,2), '.w') hold off end end end