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% 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