Clean up: consistently use spaces instead of tabs (Matlab standard), remove...

Clean up: consistently use spaces instead of tabs (Matlab standard), remove author and last-modified-notes, formatting fixes

functions/auxiliary/centeredGrid.m

@@ -59,29 +59,26 @@ function varargout = centeredGrid(N, dx, computeMeshgrid)
 %
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
-%
-%
-% Last modified on March 19 2019 by Simon Maretzke
 
 % Default: unit spacing
 if nargin < 2
-	dx = 1;
+    dx = 1;
 end
 dx = dx(:).' .* ones([1,numel(N)]);
 ndim = numel(N);
 
 % Grid in Fourier space
 for jj = 1:ndim
-	x{jj} = ( -(0.5*(N(jj)-1)) : (0.5*(N(jj)-1)) ) * dx(jj);
+    x{jj} = ( -(0.5*(N(jj)-1)) : (0.5*(N(jj)-1)) ) * dx(jj);
 end
 
 % Optionally assemble ndgrid (occupies more memory!)
 if nargin == 3 && computeMeshgrid
-	[x{:}] = ndgrid(x{:});
+    [x{:}] = ndgrid(x{:});
 elseif ndim > 1
-	for jj = 1:ndim
-		x{jj} = reshape( x{jj}, [ones([1,jj-1]), N(jj), ones([1,ndim-jj])] );
-	end
+    for jj = 1:ndim
+        x{jj} = reshape( x{jj}, [ones([1,jj-1]), N(jj), ones([1,ndim-jj])] );
+    end
 end
 
 % Unpack cell-array

functions/auxiliary/combineInFourierspace.m

@@ -68,23 +68,17 @@ function combinedImage = combineInFourierspace(highFrequencyImage,lowFrequencyIm
 %
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
-%
-% Original author: Martin Krenkel
-% Last modified on March 22 2019 by Mareike Toepperwien
 
+% default settings
 defaults.combineCutoff = 0.1;
 defaults.combineSigma = 0.01;
-
-
 if (nargin == 0)
     combinedImage = defaults;
     return
 end
-
 if (nargin < 3)
     settings = struct;
 end
-
 settings = completeStruct(settings, defaults);
 
 
@@ -106,6 +100,5 @@ fftLowFrec = fft2(lowFrequencyImage);
 % result
 combinedImage = ifft2((1-weight).*fftHighFrec+weight.*fftLowFrec);
 
-
 end
 

functions/auxiliary/completeStruct.m

@@ -48,20 +48,17 @@ function sNew = completeStruct(s, sRef)
 %
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
-%
-%
-% Last modified on March 16 2019 by Simon Maretzke
 
 sNew = s;
 fnames =  fieldnames(sRef);
 for jj = 1:length(fnames);
-	fname = fnames{jj};
-	x = getfield(sRef, fname);
-	if ~isfield(sNew, fname)
-		sNew = setfield(sNew, fname, x);
-	else if isstruct(x)	% recursively apply the completion to sub-structs
-		sNew = setfield(sNew, fname, completeStruct(getfield(sNew, fname), x));
-	end
+    fname = fnames{jj};
+    x = getfield(sRef, fname);
+    if ~isfield(sNew, fname)
+        sNew = setfield(sNew, fname, x);
+    else if isstruct(x)    % recursively apply the completion to sub-structs
+        sNew = setfield(sNew, fname, completeStruct(getfield(sNew, fname), x));
+    end
 end
 
 end

functions/auxiliary/croparray.m

@@ -50,13 +50,10 @@ function arrayCropped = croparray(array, cropPre, cropPost)
 %
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
-%
-%
-% Last modified on March 12 2019 by Simon Maretzke
 
 % Default: symmetric cropping
 if nargin < 3
-	cropPost = cropPre;
+    cropPost = cropPre;
 end
 
 N = size(array);
@@ -70,11 +67,11 @@ cropPost = [cropPost(:).', zeros([1,ndim-numel(cropPost)])];
 % Crop array dimension by dimension
 arrayCropped = array;
 for dim = 1:ndim
-	if cropPre(dim) > 0 || cropPost(dim) > 0
-		c1 = repmat({':'}, [dim-1,1]);
-		c2 = repmat({':'}, [ndim-dim,1]);
-		arrayCropped = arrayCropped(c1{:}, cropPre(dim)+1:N(dim)-cropPost(dim), c2{:});
-	end
+    if cropPre(dim) > 0 || cropPost(dim) > 0
+        c1 = repmat({':'}, [dim-1,1]);
+        c2 = repmat({':'}, [ndim-dim,1]);
+        arrayCropped = arrayCropped(c1{:}, cropPre(dim)+1:N(dim)-cropPost(dim), c2{:});
+    end
 end
 
 end

functions/auxiliary/fftfreq.m

@@ -55,29 +55,26 @@ function varargout = fftfreq(N, dx, computeMeshgrid)
 %
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
-%
-%
-% Last modified on March 19 2019 by Simon Maretzke
 
 % Default: unit spacing
 if nargin < 2
-	dx = 1;
+    dx = 1;
 end
 dx = dx(:).' .* ones([1,numel(N)]);
 ndim = numel(N);
 
 % Grid in Fourier space
 for jj = 1:ndim
-	xi{jj} = ifftshift( ( -floor(0.5*N(jj)) : floor(0.5*(N(jj)-1)) ).' * ( 2*pi / (N(jj)*dx(jj)) ) );
+    xi{jj} = ifftshift( ( -floor(0.5*N(jj)) : floor(0.5*(N(jj)-1)) ).' * ( 2*pi / (N(jj)*dx(jj)) ) );
 end
 
 % Optionally assemble ndgrid (occupies more memory!)
 if nargin == 3 && computeMeshgrid
-	[xi{:}] = ndgrid(xi{:});
+    [xi{:}] = ndgrid(xi{:});
 elseif ndim > 1
-	for jj = 1:ndim
-		xi{jj} = reshape( xi{jj}, [ones([1,jj-1]), N(jj), ones([1,ndim-jj])] );
-	end
+    for jj = 1:ndim
+        xi{jj} = reshape( xi{jj}, [ones([1,jj-1]), N(jj), ones([1,ndim-jj])] );
+    end
 end
 
 % Unpack cell-array

functions/auxiliary/fftfreqNormSq.m

@@ -40,8 +40,6 @@ function XiSq = fftfreqNormSq(N, dx)
 %
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
-%
-% Last modified on May 15 2019 by Simon Maretzke
 
 
 % Default: Standard grid spacing assigned by function fftfreq.

functions/auxiliary/getSlice.m

@@ -48,8 +48,6 @@ function arraySlice = getSlice(array, sliceIdx, dim)
 %
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
-%
-% Last modified on March 13 2019 by Simon Maretzke
 
 ndim = ndims(array);
 c1 = repmat({':'}, [dim-1,1]);

functions/auxiliary/gpusupport/checkGPUSupport.m

@@ -24,10 +24,6 @@ function gpuIsAvailable = checkGPUSupport()
 %
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
-%
-%
-% Author: Simon Maretzke
-% Last checked and modified: April 24 2019
 
 try
     gpuDevice();
@@ -35,4 +31,5 @@ try
 catch ME
     gpuIsAvailable = false;
 end
+
 end

functions/auxiliary/gpusupport/gatherIf.m

@@ -31,12 +31,9 @@ function array = gatherIf(array, condition)
 %
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
-%
-%
-% Author: Simon Maretzke
-% Last checked and modified: April 24 2019
 
 if condition
     array = gather(array);
 end
+
 end

functions/auxiliary/gpusupport/gatherIfOnGPU.m

@@ -29,10 +29,7 @@ function arrayOnHost = gatherIfOnGPU(array)
 %
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
-%
-%
-% Author: Simon Maretzke
-% Last checked and modified: April 24 2019
 
 arrayOnHost = gatherIf(array, isOnGPU(array));
+
 end

functions/auxiliary/gpusupport/gpuArrayIf.m

@@ -32,13 +32,10 @@ function arrayOnGPUIf = gpuArrayIf(array, condition)
 %
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
-%
-%
-% Author: Simon Maretzke
-% Last checked and modified: April 24 2019
 
 arrayOnGPUIf = array;
 if condition
     arrayOnGPUIf = gpuArray(arrayOnGPUIf);
 end
+
 end

functions/auxiliary/gpusupport/isOnGPU.m

@@ -29,10 +29,7 @@ function arrayIsOnGPU = isOnGPU(array)
 %
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
-%
-%
-% Author: Simon Maretzke
-% Last checked and modified: April 24 2019
 
 arrayIsOnGPU = strcmp(class(array), 'gpuArray');
+
 end

functions/auxiliary/imageToPolarCoords.m

@@ -21,7 +21,7 @@ function [imPolar, R, Phi] = imageToPolarCoords(im, settings)
 %     If numAngles == [], a suitable number is determined based on the size of the input image.
 % interpMethod : interpMethod = 'linear'
 %     The interpolation method used in the image-transformation. The admissible choices are
-%	  the same as for the MATLAB-functions interp1, interp2, etc.
+%     the same as for the MATLAB-functions interp1, interp2, etc.
 %
 % Returns 
 % ------- 
@@ -64,9 +64,6 @@ function [imPolar, R, Phi] = imageToPolarCoords(im, settings)
 %
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
-%
-%
-% Last modified on March 13 2019 by Simon Maretzke
 
 % Default settings
 defaults.numAngles = [];
@@ -74,12 +71,12 @@ defaults.numRadii = [];
 defaults.interpMethod = 'linear';
 
 if (nargin == 0)
-	imPolar = defaults;
-	return
+    imPolar = defaults;
+    return
 end
 
 if (nargin < 2)
-	settings = struct;
+    settings = struct;
 end
 settings = completeStruct(settings, defaults);
 
@@ -88,10 +85,10 @@ N = size(im);
 
 % If radial and/or angular resolutions are not assigned, choose automatically
 if isempty(settings.numRadii)
-	numRadii = 0.5*min(N);
+    numRadii = 0.5*min(N);
 end
 if isempty(settings.numAngles)
-	numAngles = 2*numRadii;
+    numAngles = 2*numRadii;
 end
 
 % Construct polar-equispaced coordinate grid

functions/auxiliary/initOctave.m

@@ -30,14 +30,14 @@ function [] = initOctave()
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 if isOctave
-	% Load additional (dummy-)functions that are needed but not natively implemented in OCTAVE
-	addpath(fullfile(fileparts(mfilename('fullpath')), '..', '..', 'octave'));
+    % Load additional (dummy-)functions that are needed but not natively implemented in OCTAVE
+    addpath(fullfile(fileparts(mfilename('fullpath')), '..', '..', 'octave'));
 
-	% Load image-processing toolbox
-	pkg load image;
+    % Load image-processing toolbox
+    pkg load image;
 else
-	error(['This function performs the required initialization to run the toolbox in OCTAVE ', ...
-	       'and is not meant to be called from within MATLAB.']);
+    error(['This function performs the required initialization to run the toolbox in OCTAVE ', ...
+           'and is not meant to be called from within MATLAB.']);
 end
 
 end

functions/auxiliary/isOctave.m

@@ -28,6 +28,6 @@ function calledFromOctave = isOctave()
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-	calledFromOctave = exist('OCTAVE_VERSION');
+calledFromOctave = exist('OCTAVE_VERSION');
 
 end

functions/auxiliary/kaiserBesselWindow.m

@@ -49,9 +49,6 @@ function window = kaiserBesselWindow(N, beta)
 %
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
-%
-% Original author: Klaus Giewekemeyer
-% Last modified on March 11 2019 by Simon Maretzke
 
 if nargin < 2
     beta = 8;

functions/auxiliary/makeSizeFFTfriendly.m

@@ -23,7 +23,7 @@ function N_FFTfriendly = makeSizeFFTfriendly(N)
 %
 % .. code-block:: matlab
 %
-%     N = [2053, 1031];	% these sizes are primes
+%     N = [2053, 1031]; % these sizes are primes
 %     N_FFTfriendly = makeSizeFFTfriendly(N);
 %     disp(N_FFTfriendly);
 %
@@ -54,11 +54,11 @@ function N_FFTfriendly = makeSizeFFTfriendly(N)
 
 N_FFTfriendly = N;
 for jj = 1:numel(N)
-	n = N(jj);
-	while(max(factor(n)) > 7)
-		n = n + 1;
-	end
-	N_FFTfriendly(jj) = n;
+    n = N(jj);
+    while(max(factor(n)) > 7)
+        n = n + 1;
+    end
+    N_FFTfriendly(jj) = n;
 end
 
 end

functions/auxiliary/scale01.m

@@ -45,11 +45,9 @@ function scaledImage = scale01(image)
 %
 % You should have received a copy of the GNU General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
-%
-% Original authors: Martin Krenkel and Mareike Toepperwien
-% Last modified on March 26 2019 by Mareike Toepperwien
 
-    scaledImage = image-min(image(:));
-    scaledImage = scaledImage/max(scaledImage(:));
+scaledImage = image-min(image(:));
+scaledImage = scaledImage/max(scaledImage(:));
+
 end
 

functions/fresnelPropagation/FresnelPropagator.m

@@ -92,205 +92,207 @@ classdef FresnelPropagator
 % along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
     
-    properties (SetAccess = 'private')
-        
-		settings;
-		sizeIn;
-		fresnelNumbers
-        numDistances;
-        numDims;
-        padPre;
-        padPost;
-        cropPre;
-        cropPost;
-        propKernel;
-        
-    end	 % end properties
+properties (SetAccess = 'private')
     
+    settings;
+    sizeIn;
+    fresnelNumbers
+    numDistances;
+    numDims;
+    padPre;
+    padPost;
+    cropPre;
+    cropPost;
+    propKernel;
     
-    methods
-        %% Constructor
-        function obj = FresnelPropagator(sizeIn, fresnelNumbers, settings)
+end % end properties
 
-            if nargin < 3
-                settings = struct;
-            end
-            obj.settings = completeStruct(settings, FresnelPropagator.defaultSettings());
-            
-			obj.sizeIn = sizeIn;
-            obj.fresnelNumbers = fresnelNumbers;
-            obj.numDims = numel(obj.sizeIn);
-            obj.numDistances = size(fresnelNumbers,2);
-            
 
-            % Check consistency of input-parameters
-            %
-            % Input-, output- and padded array sizes
-            if isempty(obj.settings.sizePad)
-                obj.settings.sizePad = sizeIn;
-            elseif numel(obj.settings.sizePad) ~= numel(sizeIn) || any(obj.settings.sizePad < sizeIn)
-                error('settings.sizePad must be of the same length as sizeIn and settings.sizePad >= sizeIn.');
-            end
-            if isempty(obj.settings.sizeOut)
-                obj.settings.sizeOut = obj.settings.sizePad;
-            elseif numel(obj.settings.sizeOut) ~= numel(sizeIn) || any(obj.settings.sizeOut > obj.settings.sizePad)
-                error('settings.sizeOut must be of the same length as sizeIn and settings.sizeOut <= settings.sizePad.');
-            end
-            %
-            % Check sanity of Fresnel numbers
-            if size(obj.fresnelNumbers,1) > 1 && size(obj.fresnelNumbers,1) ~= numel(sizeIn)
-                error(['size(fresnelNumbers,1) must be either 1 (no astigmatism) or equal', ...
-	       		       ' to the number of dimensions numel(sizeIn) (possibly astigmatic setting).']);
-            end
-            %
-            % Check whether GPU-computations are possible
-            if obj.settings.gpuFlag && ~checkGPUSupport();
-                warning(['Unable to initialize GPU. Fresnel-propagation will be performed on CPU instead. ', ...
-                    'Set settings.gpuFlag = false to suppress this warning.']);
-				obj.settings.gpuFlag = false;
-            end
-
-
-			% Ensure that Fresnel-propagation will be performed in the correct precision (single/double)
-			% by casting Fresnel numbers to single/double
-			if obj.settings.singlePrecision
-				obj.fresnelNumbers = single(obj.fresnelNumbers);
-			else
-				obj.fresnelNumbers = double(obj.fresnelNumbers);
-			end
-            
-            
-            % Determine padding- and cropping-amounts (and whether to pad/crop at all)
-            obj.padPre = ceil((obj.settings.sizePad-obj.sizeIn)/2);
-            obj.padPost = floor((obj.settings.sizePad-obj.sizeIn)/2);
-            obj.cropPre = ceil((obj.settings.sizePad-obj.settings.sizeOut)/2);
-            obj.cropPost = floor((obj.settings.sizePad-obj.settings.sizeOut)/2);
+methods
 
+    %% Constructor
+    function obj = FresnelPropagator(sizeIn, fresnelNumbers, settings)
 
-            % Construct propagation kernel to be applied in Fourier-space
-            for idxFresnel = 1:obj.numDistances
-                obj.propKernel{idxFresnel} = fresnelPropagationKernel(obj.settings.sizePad, obj.fresnelNumbers(:,idxFresnel), obj.settings);
-            end
-            obj.propKernel = cat(obj.numDims+1, obj.propKernel{:});
-            
-        end %end constructor
+        if nargin < 3
+            settings = struct;
+        end
+        obj.settings = completeStruct(settings, FresnelPropagator.defaultSettings());
         
+        obj.sizeIn = sizeIn;
+        obj.fresnelNumbers = fresnelNumbers;
+        obj.numDims = numel(obj.sizeIn);
+        obj.numDistances = size(fresnelNumbers,2);
         
 
+        % Check consistency of input-parameters
+        %
+        % Input-, output- and padded array sizes
+        if isempty(obj.settings.sizePad)
+            obj.settings.sizePad = sizeIn;
+        elseif numel(obj.settings.sizePad) ~= numel(sizeIn) || any(obj.settings.sizePad < sizeIn)
+            error('settings.sizePad must be of the same length as sizeIn and settings.sizePad >= sizeIn.');
+        end
+        if isempty(obj.settings.sizeOut)
+            obj.settings.sizeOut = obj.settings.sizePad;
+        elseif numel(obj.settings.sizeOut) ~= numel(sizeIn) || any(obj.settings.sizeOut > obj.settings.sizePad)
+            error('settings.sizeOut must be of the same length as sizeIn and settings.sizeOut <= settings.sizePad.');
+        end
+        %
+        % Check sanity of Fresnel numbers
+        if size(obj.fresnelNumbers,1) > 1 && size(obj.fresnelNumbers,1) ~= numel(sizeIn)
+            error(['size(fresnelNumbers,1) must be either 1 (no astigmatism) or equal', ...
+                      ' to the number of dimensions numel(sizeIn) (possibly astigmatic setting).']);
+        end
+        %
+        % Check whether GPU-computations are possible
+        if obj.settings.gpuFlag && ~checkGPUSupport();
+            warning(['Unable to initialize GPU. Fresnel-propagation will be performed on CPU instead. ', ...
+                'Set settings.gpuFlag = false to suppress this warning.']);
+            obj.settings.gpuFlag = false;
+        end
 
-        function imProp = propagate(obj, im)
-		% PROPAGATE Fresnel-propagates a given image according to the internal parameters 
-		% (Fresnel-numbers, padding, etc) of the Fresnel-propagator object.
-		% 
-		%    ``imProp = propagate(im)``
-
-            % Transfer to GPU if required
-            imProp = gpuArrayIf(im, obj.settings.gpuFlag && ~isOnGPU(im));
-            
-            % Optional padding
-			if any(obj.settings.sizePad ~= obj.sizeIn)
-				imProp = padarray(padarray(imProp, obj.padPre, obj.settings.padVal, 'pre'), ...
-				                  obj.padPost, obj.settings.padVal, 'post');
-			end
-            
-            % Propagation step
-			imProp = obj.iFT(obj.propKernel .* fftn(imProp));
 
-            
-            % Optional cropping
-			if any(obj.settings.sizePad ~= obj.settings.sizeOut)
-            	imProp = croparray(imProp, obj.cropPre, obj.cropPost);
-			end
-            
-            % Transfer back from GPU to host if required
-            imProp = gatherIf(imProp, obj.settings.gpuFlag && ~isOnGPU(im));
+        % Ensure that Fresnel-propagation will be performed in the correct precision (single/double)
+        % by casting Fresnel numbers to single/double
+        if obj.settings.singlePrecision
+            obj.fresnelNumbers = single(obj.fresnelNumbers);
+        else
+            obj.fresnelNumbers = double(obj.fresnelNumbers);
         end
         
         
-        function imBack = backPropagate(obj, im)
-		% BACKPROPAGATE Fresnel-back-propagates a given image, i.e. applies the inverse
-		% operation to propagate. In the case of Fresnel-propagation to more than one
-		% plane, the result is the sum of the back-propagated images from each of the planes. 
-		% 
-		%    ``imBack = backPropagate(im)``
+        % Determine padding- and cropping-amounts (and whether to pad/crop at all)
+        obj.padPre = ceil((obj.settings.sizePad-obj.sizeIn)/2);
+        obj.padPost = floor((obj.settings.sizePad-obj.sizeIn)/2);
+        obj.cropPre = ceil((obj.settings.sizePad-obj.settings.sizeOut)/2);
+        obj.cropPost = floor((obj.settings.sizePad-obj.settings.sizeOut)/2);
 
-            % Transfer to GPU if required
-            imBack = gpuArrayIf(im, obj.settings.gpuFlag && ~isOnGPU(im));
-            
-            
-            % Padding from size obj.settings.sizeOut to obj.settings.sizePad
-            if any(obj.settings.sizePad ~= obj.settings.sizeOut)
-				imBack = padarray(padarray(imBack, obj.cropPre, obj.settings.padVal, 'pre'), ...
-            	                  obj.cropPost, obj.settings.padVal, 'post');
-            end 
 
-            % Back-propagation step (plus summation in the case of multiple Fresnel-numbers)
-            imBack = conj(obj.propKernel) .* obj.FT(imBack);
-            if obj.numDistances > 1
-                imBack = sum(imBack, obj.numDims+1);
-            end
-            imBack = ifftn(imBack);
-            
-            % Cropping from size obj.sizePad to obj.sizeIn
-            if any(obj.settings.sizePad ~= obj.sizeIn)