added a test folder for the medAlign function

medAlign_new/batchMedAlignWithTemporalBinning.m

@@ -0,0 +1,98 @@
+
+nSubIm = 10;
+
+% set a query directory
+dir_query = '/storage/letz/Data/Data/Leona_Enke/20160726_L59/imaging';
+dir_output = '/storage/letz/Data/Data/Leona_Enke/20160726_L59/imaging';
+
+% level one
+[dir_list, dir_count] = getDirsFromDir(dir_query);
+
+d = 1;
+
+for d = 1 : dir_count
+
+    % sub dir name
+    sub_dir = [dir_query, filesep, dir_list{d}];
+    subdir_list = getDirsFromDir(sub_dir);
+    disp(d);
+
+    % remove finished
+    idx_rmv = strncmp('aligned',subdir_list,7);
+    subdir_list(idx_rmv) = [];
+    subdir_count = size(subdir_list,1);
+
+    % loop through sub dirs
+    for k = 10 : subdir_count
+
+
+
+        % current id
+        folder_id = sscanf(subdir_list{k},'Untitled%03d');
+
+
+
+
+        % Compose image stack from filenames
+
+        filePrefixGreen = 'ChanA_0001_0001_0001_'; %Gruen Kanal
+        filePrefixRed = 'ChanB_0001_0001_0001_'; %Rote Kanal
+
+        m = dir([sub_dir,filesep,subdir_list{k},filesep,'ChanB_0001_0001_0001_*.tif']);
+        nImages = size(m,1);
+
+        file_image = [sub_dir,filesep,subdir_list{k},filesep,'ChanB_0001_0001_0001_0001.tif'];
+        im = imread(file_image);
+
+
+        %Assembling Red Image stack
+        allIm = zeros(size(im,1),size(im,2),nImages);
+        for i = 1:nImages
+            filename= sprintf([sub_dir,filesep,subdir_list{k},filesep,filePrefixRed,'%04u.tif'],i);
+            allIm(:,:,i) = imread(filename);
+        end
+
+        %temporal binning on red image stack
+        class_red = class(allIm);
+        allIm = cast(binning(allIm, [1 1 2], 'mean'), class_red);
+
+        %Realignment
+        [rs, cs] = medAlign(allIm, nSubIm, 50, -inf);
+
+        %Rotation and translation on red channel
+        filename= sprintf('%s%s%s%sred%03d.tif',dir_output,filesep,dir_list{d},filesep,folder_id);
+        for i = 1:nImages/2
+            registered(:,:,i) = circshift(allIm(:,:,i),[rs(i),cs(i)]);
+            imwrite(uint16(registered(:,:,i)),filename, 'tif','WriteMode','append');
+        end
+
+
+        %Assembling Green Image stack
+        allIm = zeros(size(im,1),size(im,2),nImages);
+        for i = 1:nImages
+            filename= sprintf([sub_dir,filesep,subdir_list{k},filesep,filePrefixGreen,'%04u.tif'],i);
+            allIm(:,:,i) = imread(filename);
+        end
+
+        %temporal binning on green image stack
+        class_red = class(allIm);
+        allIm = cast(binning(allIm, [1 1 2], 'mean'), class_red);
+
+        %Rotation and translation on green channel
+        filename= sprintf('%s%s%s%sgreen%03d.tif',dir_output,filesep,dir_list{d},filesep,folder_id);
+        %filename= sprintf([dir_output,filesep,filePrefixGreen,'_cc.tif'],i);
+        for i = 1:nImages/2
+            registered(:,:,i) = circshift(allIm(:,:,i),[rs(i),cs(i)]);
+            imwrite(uint16(registered(:,:,i)),filename, 'tif','WriteMode','append');
+        end
+
+
+
+    end
+
+
+
+
+
+end
+

medAlign_new/binning.m

@@ -0,0 +1,149 @@
+function A = binning(A,bin,fun_str)
+%
+% A=binning(A,bin,fun)
+%
+% This function rearranges the array A according to the specifications
+% of the vector bin. In the first dimension of the generated temporary 
+% array the bin elements from all dimension are arranged. By applying 
+% functions like 'sum', 'mean' or 'std' to the first dimension, a real
+% binning ('sum'), a averaging ('mean') and error calculations can be
+% done. 
+%
+% A=binning(A,bin) The input array 'A' is binned by the vector 'bin'.
+% If 'bin' is a scalar, 'bin' elements in each dimenion of 'A' are
+% summarized.
+%
+% Note: The input array 'A' is cut to the maxial integer factor of
+% 'bin'. 
+%
+% A=binning(A,bin,fun) The function 'fun' is applied to the first
+% dimension of the rearranged array. Beside the real binning with the
+% function 'sum' a number of additional functions can be applied. Up
+% to now the following functions are implemented:
+% 'sum', 'mean', 'prod'
+% 
+% Special comment:
+% The functionality can be easily extended by implementing additional
+% functions, or due to the time consuming permutations by the
+% combination of appropriate functions like 'mean' and 'std'.
+%
+% Author: A. Zeug (last modified 19.07.2007)
+% Version: 2.0.0
+
+% comments to: azeug@gwdg.de
+
+tic; t1=toc;
+%% Input validation
+if nargin < 3
+  fun_str='sum';
+  fun_type = 1;
+elseif sum(strcmp(fun_str,{'sum';'mean';'prod'}))>0
+  fun_type = 1;
+elseif sum(strcmp(fun_str,{'std';'var'}))>0
+  fun_type = 2;
+else
+  error('Function not implemented yet')
+end
+fun=str2func(fun_str); % defines function type
+
+if nargin < 1
+  help binning
+  return
+elseif nargin < 2
+  error('Please specify binning vector.')
+end
+
+%% bin vector dimension
+trans = false;
+dims  = ndims(A);
+if isvector(A)
+  dims = 2;
+  if size(A,2)==1; trans = true; end
+end
+if length(bin)==1; 
+  bin = bin * ones(1, dims); 
+elseif length(bin)~=dims;
+  error('Wrong length of binning vector.')
+end
+
+%% resizing of A to fit bin
+sz=size(A);
+if dims==1; sz=length(A); end
+bin=min([sz;bin]);
+for i=1:dims
+  index{i}=1:(bin(i)*floor(sz(i)/bin(i)));
+end
+A = A(index{:});
+
+%% reshaping A
+sz = size(A); if dims==1; sz = length(A); end
+v = []; sz_new = sz./bin;
+for i=1:dims
+  v=[v, bin(i), sz_new(i)];
+end
+A=reshape(A,v);
+
+%% Calculate binning
+if fun_type==1
+  % standard type 'sum', 'mean','prod' 
+  for i=1:dims
+      if isequal(fun, @sum)
+          A=fun(A,(2*i-1),'native');
+      else
+          A=fun(A,(2*i-1));
+      end
+  end
+else
+  % type 'std', 'var'
+  % need to reshape again to calc function at ones
+  v = [];
+  for i=1:dims
+    v=[v, i, dims+i];
+  end
+  A = permute(A, v);
+  A = reshape(A, [prod(bin) sz_new]);
+  try
+    A = fun( double(A) );
+  catch
+    t=toc; fprintf('(%07.3fs) binning: direct calculation failed, start subsequential method (%0.5fs)\n',t,t-t1); t1=t;
+    try
+      A1 = zeros(sz_new,'double');
+      fun1 = @double;
+    catch
+      t=toc; fprintf('(%07.3fs) binning: calculating %s with double precession failed, try single (%0.5fs)\n',t,func2str(fun),t-t1); t1=t;
+      A1 = zeros(sz_new, 'single');
+      fun1 = @single;
+    end
+    h = waitbar(0,'Please wait...','Name','binning: Plese Wait!');
+    % subsequential calculation
+    sub_dim = find(sz_new == max(sz_new));
+    for i = 1:dims; cc{i}=':'; end
+    step = floor(1E6 / (prod(sz_new(sz_new < max(sz_new)))*prod(bin)));
+    for ii = 0:step:sz_new(sub_dim) % subsequentially...
+      waitbar(ii/sz_new(sub_dim),h,['Calculated binning: ' num2str(100*ii/sz_new(sub_dim),'%0.2f') '%']);
+      ii_end = min(sz_new(sub_dim), ii+step) - ii;
+      cc{sub_dim}=(1:ii_end)+ii;
+      A1(cc{:}) = fun(fun1(A(:,cc{:})));
+    end
+    A = A1;
+    delete(h); drawnow;
+    t=toc; fprintf('(%07.3fs) binning: calculation with %s precession susseed (%0.5fs)\n',t,func2str(fun1),t-t1); t1=t;
+  end
+end
+
+%
+%A = reshape(A, sz_new);
+
+if dims==1 
+  A=squeeze(A);
+  if trans==true
+    A=A';
+  end
+else
+  A = reshape(A, sz_new);
+
+end
+
+
+
+