added non-relative path references to GetDate while implementing zip...

added non-relative path references to GetDate while implementing zip extraction, adding SetProxyPythonPath.py in phase and links in experiments in phase

poetry.lock

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proxtoolbox/experiments/InputData/Phase/Elser/phase-retrieval-benchmarks-master/CDP-matlab/README

+The matlab code to implement the 2D phase retrieval of the coded diffraction pattern (CDP) problem using the RRR algorithm.
+To run the code, execute the following command in terminal:
+    
+    octave cdp.m
+
+or run the script octave cdp.m in matlab.

proxtoolbox/experiments/InputData/Phase/Elser/phase-retrieval-benchmarks-master/CDP-matlab/RRR_cdp_image.m

+function RRR_cdp_image(b, y, sol, D)
+
+    %% input parameters
+    beta = 0.5 ;
+    epsilon = 1.e-5 ;
+    iter_max = 100000 ;
+    L = size(D, 1) ;
+    height = size(D, 2) ;
+    width = size(D, 3) ;
+
+    %% The inverse of the diagonal terms of 1/n * Hermitian(A) * A
+    inv_diag = zeros(height, width) ;
+    for i = 1:L
+        for j = 1:height
+            for k = 1:width
+                inv_diag(j, k) = inv_diag(j, k) + abs(D(i, j, k))^2 ;
+            end
+        end
+    end
+    inv_diag = 1 ./ inv_diag ;
+
+    iter_arr = [] ;
+    err_arr = [] ;
+    cur_sol = zeros(height, width, 3) ;
+    for iter = 1:iter_max
+        rms_diff = 0. ;
+        norm_y = 0. ;
+        for c = 1:3
+            b_c = squeeze(b(:, :, :, c)) ;
+            y_c = squeeze(y(:, :, :, c)) ;
+            p1 = proj1(D, inv_diag, y_c, L, height, width) ;
+            p2 = proj2(b_c, 2*p1 - y_c) ;
+            delta_y = p2 - p1 ;
+            for k = 1:L
+                rms_diff = rms_diff + norm(squeeze(delta_y(k, :, :)))^2 ;
+                norm_y = norm_y + norm(squeeze(y_c(k, :, :)))^2 ;
+            end
+            y_c = y_c + beta*delta_y ;
+            y(:, :, :, c) = y_c ;
+        end
+
+        rms_diff = beta*sqrt(rms_diff / norm_y) ;
+        if (iter < 10 || mod(iter, 10) == 0)
+            norm1 = 0. ;
+            norm2 = 0. ;
+            for c = 1:3
+                x_c = reshape(squeeze(sol(:, :, c)), height*width, 1) ;
+                y_c = squeeze(y(:, :, :, c)) ;
+                p1 = proj1(D, inv_diag, y_c, L, height, width) ;
+                cur_sol(:, :, c) = Ainv(D, inv_diag, p1, L, height, width) ;
+                x_cur = reshape(squeeze(cur_sol(:, :, c)), height*width, 1) ;
+                norm1 = norm1 + norm(x_c - x_cur*sign(x_cur'*x_c))^2 ;
+                norm2 = norm2 + norm(x_c)^2 ;
+            end
+            filename = ['reconst-cornell-iter', int2str(iter), '.jpg'] ;
+            cur_img = uint8(round(abs(cur_sol))) ;
+            imwrite(cur_img, filename) ;
+            err_val = sqrt(norm1/norm2) ;
+            iter_arr = [iter_arr, iter] ;
+            err_arr = [err_arr, err_val] ;
+            [err_val, rms_diff]
+            if (rms_diff < epsilon)
+                break ;
+            end
+        end
+    end
+
+    fp = fopen('phasing-error.dat', 'w') ;
+    for i = 1:length(err_arr)
+        fprintf(fp, '%d %1.5e\n', iter_arr(i), err_arr(i)) ;
+    end
+    fclose(fp) ;
+end
+
+%% pseudo-inverse of A
+function x1 = Ainv(D, inv_diag, y, L, height, width)
+    x1 = zeros(height, width) ;
+    for l = 1:L
+        x1 = x1 + squeeze(conj(D(l, :, :))) .* ifft2(squeeze(y(l, :, :))) ;
+    end
+    x1 = x1 .* inv_diag ;
+end
+
+%% projections
+function y1 = proj1(D, inv_diag, y, L, height, width)
+    x1 = Ainv(D, inv_diag, y, L, height, width) ;
+    y1 = zeros(L, height, width) ;
+    for i = 1:L
+        y1(i, :, :) = fft2(squeeze(D(i, :, :)) .* x1) ;
+    end
+end
+
+function y2 = proj2(b, y)
+    y2 = b .* sign(y) ;
+end

proxtoolbox/experiments/InputData/Phase/Elser/phase-retrieval-benchmarks-master/CDP-matlab/cdp.m

+L = 3 ;
+stanford = double(imread('stanford.jpg')) ;
+cornell = double(imread('cornell.jpg')) ;
+height = size(cornell, 1) ;
+width = size(cornell, 2) ;
+
+%% generate random coded diffraction pattern
+D = zeros(L, height, width) ;
+for i = 1:L
+    D(i, :, :) = exp(1i*floor(rand(height, width)*4)*pi/2) ;
+end
+
+b = zeros(L, height, width, 3) ;    % data
+y = zeros(L, height, width, 3) ;    % initial guess
+for c = 1:3
+    for i = 1:L
+        phase_mask = squeeze(D(i, :, :)) ;
+        b(i, :, :, c) = abs(fft2(phase_mask .* cornell(:, :, c))) ;
+        y(i, :, :, c) = fft2(phase_mask .* stanford(:, :, c)) ;
+    end
+end
+
+RRR_cdp_image(b, y, cornell, D) ;

proxtoolbox/experiments/InputData/Phase/Elser/phase-retrieval-benchmarks-master/README.md

+## phase retrieval benchmarks
+### RRR: Simple Phase Retrieval
+This program is deliberately minimalist so as not to obscure the structure of the algorithm.
+It needs the [FFTW3 library](http://www.fftw.org).
+
+The program is set up for solving the benchmarks described in:
+> "Benchmark problems for phase retrieval", V. Elser, T.-Y. Lan & T. Bendory
+
+To compile:
+```
+gcc -O2 RRR.c -lm -lfftw3 -o RRR
+```
+
+To run:
+```
+./RRR [datafile] [supp] [powgoal] [beta] [iterlimit] [trials] [resultfile] &
+```
+
+- datafile:	one of the benchmark datafiles (data/data100E, data/data140E, ...)
+- supp:		support size = 8*N, N = 100, 140, ... is the number of atoms
+- powgoal:	fractional power in support
+- beta:		RRR parameter
+- iterlimit:	RRR iteration limit (long int)
+- trials:		number of random starts
+- resultfile:	ASCII file of the iteration counts for each trial
+
+Example:
+```
+./RRR data/data100E 800 .95 .5 1000 5 results100E &
+```
+
+Solutions are written to a file named sol (M x M table of floats).
+
+Send comments, bug reports, to: ve10@cornell.edu

proxtoolbox/experiments/InputData/Phase/Elser/phase-retrieval-benchmarks-master/RRR.c

+/*
+-----------------------------------
+RRR: Simple Phase Retrieval
+-----------------------------------
+
+This program is deliberately minimalist so as not to obscure
+the structure of the algorithm. It needs the FFTW3 library:
+
+	http://www.fftw.org
+
+The program is set up for solving the benchmarks described in:
+
+	"Benchmark problems for phase retrieval", V. Elser, T.-Y. Lan & T. Bendory
+
+To compile:
+
+	gcc -O2 RRR.c -lm -lfftw3 -o RRR
+
+To run:
+
+	./RRR [datafile] [supp] [powgoal] [beta] [iterlimit] [trials] [resultfile] &
+
+datafile:	one of the benchmark datafiles (data100E, data140E, ...)
+supp:		support size = 8*N, N = 100, 140, ... is the number of atoms
+powgoal:	fractional power in support
+beta:		RRR parameter
+iterlimit:	RRR iteration limit (long int)
+trials:		number of random starts
+resultfile:	ASCII file of the iteration counts for each trial
+
+Example:
+
+	./RRR data/data100E 800 .95 .5 1000 5 results100E &
+
+Solutions are written to a file named sol (M x M table of floats).
+
+*/
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <time.h>
+#include <math.h>