diff --git a/zUtil_ID19/mncf.m b/zUtil_ID19/mncf.m
new file mode 100755
index 0000000000000000000000000000000000000000..d5d5fb1f2eebc69e31b9dc1dff84de58b4109177
--- /dev/null
+++ b/zUtil_ID19/mncf.m
@@ -0,0 +1,127 @@
+function mt = mncf(opt, varargin)
+% function mt = mncf(opt, varargin)
+%
+% Input:
+% opt : camera-setup
+% 1: july 97, 10um set-up
+% 2: april 98, 1.93um pixel set-up: optique 10x + 25um YAG
+% 3: august 98, 0.932um pixel set-up: optique 10x + eyepiece + 25um YAG
+% 4: september 97, 0.7 um pixel set-up: 20* YAG 5um
+% 5: november 98, 0.5 um pixel set-up: optique 20x + eyepiece + LAG 3um
+% 6: november 99, 0.394 um pixe set-up: optique 20x + eyepiece + LAG 6mu
+% 7: november 2001, 1 micron setup with 0.69um pixelsize (2048 ccd): 10x optics + eyepiece + 25um YAG
+% 8: for testing
+% 9: for fits
+% Optional Input:
+% m : number of row samples
+% n : number of column samples
+% oversampling : samplerate is fixed by oversamp, sigmas expressed in pixels,
+% changing n changes the width of the window and sampling rate
+% in frequency space
+% dimmensions: 1 | {2} create 1-dim mtf plot or 2-dim mtf map
+
+ conf = struct( ...
+ 'size', 11, ...
+ 'oversampling', 1, ...
+ 'dimensions', 2, ...
+ 'p', []);
+ conf = parse_pv_pairs(conf, varargin);
+
+ switch (opt)
+ case 1
+ % july 97, 10 mu set-up
+ mi = 0.01;
+ ma = 1;
+ p = [0.5884, 0.9093, 0.3570, 2.8537, 0.0352, 49.3503, 748.8534];
+ case 2
+ % april 98, 1.93 um pixel set-up: optique 10x + 25um YAG
+ mi = 0.0117;
+ ma = 0.9862;
+ p = [0.4327, 0.9147, 0.2296, 7.9874, 0.1683, 54.6962, 197.9522];
+ case 3
+ % august 98, 0.932 mu pixel set-up: optique 10x + eyepiece 2x + 25um YAG
+ %mi = 0.0149;
+ %ma = 0.996;
+ %p = [0.4723 1.3329 0.2154 5.8018 0.1569 56.1836 268.3804];
+
+ %best 100 columns:
+ %mi = 0.0151;
+ %ma = 0.994;
+ %p = [0.4530 1.2271 0.2279 5.2286 0.1550 52.5938 255.9305];
+
+ %measurement in february 99 - optimised uptilt of GaAs
+ mi = 0.013;
+ ma = 0.984;
+ p = [0.5985, 0.9903, 0.1622, 8.4452, 0.1423, 41.2661, 375.8298];
+ case 4
+ % september 97 0.7 um pixel set-up: optique 20x + eyepiece 1.6x + YAG 5um
+ mi = 0.0214;
+ ma = 0.9841;
+ p = [0.3396, 1.2313, 0.2130, 10.4607, 0.1801, 51.0301, 240.2380];
+ case 5
+ % november 98 0.5 um pixel set-up: optique 20x + eyepiece 2x + LAG 3um
+ mi = 0.022;
+ ma = 1.001;
+ p = [0.4182, 1.6436, 0.2293, 12.4082, 0.1922, 288.6455, 67.6439];
+ case 6
+ % november 99 0.394 um pixel set-up: optique 20x + eyepiece 2x + LAG 6um
+ mi = 0.005;
+ ma = 0.996;
+ p = [0.6023, 1.6800, 0.2545, 5.0455, 0.1051, 29.9829, 235.2297];
+ case 7
+ % november 2001, 1 micron setup with 0.69um pixelsize (2048 ccd): 10x optic
+ % determined with jofit and a defocus series
+ mi = 0;
+ ma = 1;
+ p = [0.3978, 1.0493, 0.4608, 3.4978, 0.0674, 17.8457, 679.3300];
+ case 8
+ % for testing
+ mi = 0;
+ ma = 1;
+ p = [0.3246, 1.1299, 0.4810, 3.4915, 0.1187, 15.4062, 729.8940];
+ case 9
+ % for fits
+ mi = 0;
+ ma = 1;
+ p = conf.p;
+ case 10
+ mi = 0;
+ ma = 1;
+ p = [0.5305, 1.5617, 0.4765, 7.4535, -0.0676, 15.7088, 683.5288];
+ end
+
+ % a's are the widths in erfc = sqrt(2)*sigma
+ a1 = p(2) * conf.oversampling;
+ a2 = p(4) * conf.oversampling;
+ a3 = p(6) * conf.oversampling;
+ a4 = p(7) * conf.oversampling;
+
+ % b's are weigths
+ b1 = p(1);
+ b2 = p(3);
+ b3 = p(5);
+ b4 = ma - mi - p(1) - p(3) - p(5);
+
+ n = conf.size;
+ m = conf.size;
+
+ switch (conf.dimensions)
+ case 1
+ f = (0:1/n:0.5)';
+ mt = b1 * exp(-(pi * a1 * f) .^ 2) + b2 * exp(-(pi * a2 * f) .^ 2) + b3 * exp(-(pi * a3 * f) .^2 ) + b4 * exp(-(pi * a4 * f) .^ 2);
+ mt = [mt; flipud(mt(2:n/2))];
+ mt(1) = 1;
+ case 2
+ [x, y] = meshgrid(0:1/n:0.5, 0:1/m:0.5);
+ f2 = x .^ 2 + y .^ 2;
+ mt = b1 * exp(-(pi * a1) ^ 2 * f2) + b2 * exp(-(pi * a2) ^ 2 * f2) + b3 * exp(-(pi * a3) ^ 2 * f2) + b4 * exp(-(pi * a4) ^ 2 * f2);
+ mt = [ ...
+ mt, fliplr(mt(:, 2:floor(n/2))); ...
+ flipud(mt(2:floor(m/2), :)), rot90(mt(2:floor(m/2), 2:floor(n/2)),2)];
+ mt(1, 1) = 1;
+ otherwise
+ error([mfilename ':wrong_argument'], 'Dimemsions must be 1 or 2');
+ end
+end
+
+
diff --git a/zUtil_Imaging/GtPSF.m b/zUtil_Imaging/GtPSF.m
index 054889db182c5e7c182c857421547f63339727b7..57d6c200aeadd3d4e78aca444da8d1d990680600 100644
--- a/zUtil_Imaging/GtPSF.m
+++ b/zUtil_Imaging/GtPSF.m
@@ -10,10 +10,16 @@ classdef GtPSF < handle
is_projection_invariant = true;
image_size = [];
+ use_otf = true;
+
data_type = 'single';
end
methods (Access = public)
+ function self = GtPSF(varargin)
+ self = parse_pv_pairs(self, varargin);
+ end
+
function set_psf_direct(self, psf_d, image_size)
self.reset();
@@ -33,7 +39,7 @@ classdef GtPSF < handle
psfs_norm = 1 ./ sum(sum(abs(psf_d), 1), 3);
psf_d = bsxfun(@times, psf_d, psfs_norm);
- self.psf_direct = psf_d;
+ self.psf_direct = cast(psf_d, self.data_type);
if (exist('image_size', 'var') && ~isempty(image_size))
self.image_size = image_size;
end
@@ -48,7 +54,7 @@ classdef GtPSF < handle
self.is_projection_invariant = size(psf_d, 2) == 1;
% if we know the images sizes, we can already compute the OTF
- if (~isempty(image_size))
+ if (~isempty(self.image_size))
self.init_otfs();
end
end
@@ -56,13 +62,21 @@ classdef GtPSF < handle
function imgs = apply_psf_direct(self, imgs)
self.check_incoming_images(imgs);
- imgs = self.apply_otf(imgs, true);
+ if (self.use_otf)
+ imgs = self.apply_otf(imgs, true);
+ else
+ imgs = self.apply_psf(imgs, true);
+ end
end
function imgs = apply_psf_transpose(self, imgs)
self.check_incoming_images(imgs);
- imgs = self.apply_otf(imgs, false);
+ if (self.use_otf)
+ imgs = self.apply_otf(imgs, false);
+ else
+ imgs = self.apply_psf(imgs, false);
+ end
end
end
@@ -132,7 +146,7 @@ classdef GtPSF < handle
self.image_size = imgs_size;
end
- if (isempty(self.otf_direct))
+ if (isempty(self.otf_direct) && self.use_otf)
self.init_otfs();
end
end
@@ -164,5 +178,21 @@ classdef GtPSF < handle
imgs = real(imgs);
end
+
+ function imgs = apply_psf(self, imgs, is_direct)
+ if (is_direct || self.is_symmetric)
+ psf = self.psf_direct;
+ else
+ psf = self.psf_transpose;
+ end
+
+ if (self.is_projection_invariant)
+ imgs = convn(imgs, psf, 'same');
+ else
+ for ii_i = 1:size(imgs, 2)
+ imgs(:, ii_i, :) = convn(imgs(:, ii_i, :), psf(:, ii_i, :), 'same');
+ end
+ end
+ end
end
end
\ No newline at end of file
diff --git a/zUtil_Imaging/gtOTFGetMeasured.m b/zUtil_Imaging/gtOTFGetMeasured.m
new file mode 100755
index 0000000000000000000000000000000000000000..606df765aa1fb814a4cde2c9d458e01676b63f0f
--- /dev/null
+++ b/zUtil_Imaging/gtOTFGetMeasured.m
@@ -0,0 +1,126 @@
+function [otf, psf] = gtOTFGetMeasured(opt, varargin)
+% function mt = gtOTFGetMeasured(opt, varargin)
+%
+% Input:
+% opt : camera-setup
+% 1: july 97, 10um set-up
+% 2: april 98, 1.93um pixel set-up: optique 10x + 25um YAG
+% 3: august 98, 0.932um pixel set-up: optique 10x + eyepiece + 25um YAG
+% 4: september 97, 0.7 um pixel set-up: 20* YAG 5um
+% 5: november 98, 0.5 um pixel set-up: optique 20x + eyepiece + LAG 3um
+% 6: november 99, 0.394 um pixe set-up: optique 20x + eyepiece + LAG 6mu
+% 7: november 2001, 1 micron setup with 0.69um pixelsize (2048 ccd): 10x optics + eyepiece + 25um YAG
+% 8: for testing
+% 9: for fits
+% Optional Input:
+% m : number of row samples
+% n : number of column samples
+% oversampling : samplerate is fixed by oversamp, sigmas expressed in pixels,
+% changing n changes the width of the window and sampling rate
+% in frequency space
+%
+% Derived from a modified version of the function: mncf from
+% Wolfgang/Peter's matlab functions
+
+ conf = struct( ...
+ 'size', 11, ...
+ 'oversampling', 1, ...
+ 'p', []);
+ conf = parse_pv_pairs(conf, varargin);
+
+% if (mod(conf.size, 2) ~= 1)
+% error([mfilename ':wrong_argument'], ...
+% 'The OTF should have an odd size');
+% end
+
+ switch (opt)
+ case 1
+ % july 97, 10 mu set-up
+ mi = 0.01;
+ ma = 1;
+ p = [0.5884, 0.9093, 0.3570, 2.8537, 0.0352, 49.3503, 748.8534];
+ case 2
+ % april 98, 1.93 um pixel set-up: optique 10x + 25um YAG
+ mi = 0.0117;
+ ma = 0.9862;
+ p = [0.4327, 0.9147, 0.2296, 7.9874, 0.1683, 54.6962, 197.9522];
+ case 3
+ % august 98, 0.932 mu pixel set-up: optique 10x + eyepiece 2x + 25um YAG
+ %mi = 0.0149;
+ %ma = 0.996;
+ %p = [0.4723 1.3329 0.2154 5.8018 0.1569 56.1836 268.3804];
+
+ %best 100 columns:
+ %mi = 0.0151;
+ %ma = 0.994;
+ %p = [0.4530 1.2271 0.2279 5.2286 0.1550 52.5938 255.9305];
+
+ %measurement in february 99 - optimised uptilt of GaAs
+ mi = 0.013;
+ ma = 0.984;
+ p = [0.5985, 0.9903, 0.1622, 8.4452, 0.1423, 41.2661, 375.8298];
+ case 4
+ % september 97 0.7 um pixel set-up: optique 20x + eyepiece 1.6x + YAG 5um
+ mi = 0.0214;
+ ma = 0.9841;
+ p = [0.3396, 1.2313, 0.2130, 10.4607, 0.1801, 51.0301, 240.2380];
+ case 5
+ % november 98 0.5 um pixel set-up: optique 20x + eyepiece 2x + LAG 3um
+ mi = 0.022;
+ ma = 1.001;
+ p = [0.4182, 1.6436, 0.2293, 12.4082, 0.1922, 288.6455, 67.6439];
+ case 6
+ % november 99 0.394 um pixel set-up: optique 20x + eyepiece 2x + LAG 6um
+ mi = 0.005;
+ ma = 0.996;
+ p = [0.6023, 1.6800, 0.2545, 5.0455, 0.1051, 29.9829, 235.2297];
+ case 7
+ % november 2001, 1 micron setup with 0.69um pixelsize (2048 ccd): 10x optic
+ % determined with jofit and a defocus series
+ mi = 0;
+ ma = 1;
+ p = [0.3978, 1.0493, 0.4608, 3.4978, 0.0674, 17.8457, 679.3300];
+ case 8
+ % for testing
+ mi = 0;
+ ma = 1;
+ p = [0.3246, 1.1299, 0.4810, 3.4915, 0.1187, 15.4062, 729.8940];
+ case 9
+ % for fits
+ mi = 0;
+ ma = 1;
+ p = conf.p;
+ case 10
+ mi = 0;
+ ma = 1;
+ p = [0.5305, 1.5617, 0.4765, 7.4535, -0.0676, 15.7088, 683.5288];
+ otherwise
+ error([mfilename ':wrong_argument'], ...
+ 'Not recognized option: %d', opt)
+ end
+
+ % a's are the widths in erfc = sqrt(2)*sigma
+ a = (pi .* p([2 4 6 7]) .* conf.oversampling) .^ 2;
+ a = reshape(a, 1, 1, []);
+
+ % b's are weigths
+ b = [p([1 3 5]), (ma - mi - sum(p([1 3 5])))];
+ b = reshape(b, 1, 1, []);
+
+ grid_points = linspace(-0.5, 0.5, conf.size);
+ [x, y] = meshgrid(grid_points, grid_points);
+ otf = x .^ 2 + y .^ 2;
+ otf = bsxfun(@times, otf, a);
+ otf = exp(-otf);
+ otf = sum(bsxfun(@times, otf, b), 3);
+
+ center_pos = floor(conf.size / 2) + 1;
+ otf(center_pos, center_pos) = 1;
+
+ otf = ifftshift(otf);
+
+ psf = real(ifft2(otf));
+ psf = fftshift(psf);
+end
+
+