merged the dev_newInfo branch with master

Internal/ag.m

@@ -1,4 +1,4 @@
-function [im,im_min,imax] = ag (im,imin,imax)
+function [im,imin,imax] = ag (im,imin,imax)
 % ag : autogain, it increases the contrast of image im, using imin and imax.
 % It subtracts the the minimum from of the image, divides by the max and
 % then normalizes to 255.
@@ -31,25 +31,33 @@
 
 im = double(im);
 
+
+
 im(isinf(im(:))) = nan;
 
-if exist( 'imin', 'var') && ~isempty(  imin )
-    im_min = imin;
+if ~exist( 'imin', 'var') || isempty( imin ) 
+    imin = min( im(:) );
 else
-    im_min = min(im(:));
+    imin = double( imin );
 end
 
-if ~exist( 'imax', 'var') || isempty(imax)
-    imax = max(im(:));
+
+if ~exist( 'imax', 'var') || isempty( imax )
+    imax = max( im(:) );
+else
+    imax = double( imax );    
 end
+
+if imin == imax 
+    if imin > 0 
+        im = im/imax;
+    end
+else
+    im = (im-imin)/(imax-imin);
+end
+
+% autogain and normalization to uint8
+im = uint8(255*im);
 
-im_max = imax-im_min;
-
-% subtract min
-im = im - double(im_min);
-
-
-   % autogain and normalization to uint8
-im = uint8(255*im/double(im_max));
 
 end

Internal/intFixFields.m

@@ -0,0 +1,22 @@
+function CONST = intFixFields( CONST, CONST0 )
+% This function adds fields that exist in CONST0 but do not exist in CONST
+% to CONST
+if isstruct( CONST0 )
+    C0n = fieldnames( CONST0 );
+
+    for ii = 1:numel( C0n )
+
+        if isfield( CONST, C0n{ii} )
+            CONST = setfield( CONST, C0n{ii}, ...
+                intFixFields( getfield( CONST, C0n{ii} ),...
+                              getfield( CONST0, C0n{ii}) ) );
+        else
+            CONST = setfield( CONST, C0n{ii},  getfield( CONST0, C0n{ii}));
+        end
+
+    end
+%else
+%    CONST = CONST0;
+end
+
+end

Internal/intFixFileName.m

@@ -0,0 +1,22 @@
+function name_mod = intFixFileName( name, str_end) 
+% Fixes a file name by adding the suffix str_end if it doesn't already
+% exist
+if str_end(1) ~= '.'
+   str_end =  ['.',str_end];
+end
+
+ns = numel( str_end );
+nn = numel( name );
+
+% check file name length
+if ns > nn
+    name_mod = [ name, str_end];
+elseif ~strcmp( name( [end-ns+1:end] ), str_end )
+    name_mod = [ name, str_end];
+else
+    name_mod = [ name ];
+end
+
+end
+
+

Internal/intGetChannelNum.m

@@ -0,0 +1,17 @@
+function nnc = intGetChannelNum( data )
+%% comp number of fluor channels
+
+nc = numel(find(~cellfun('isempty',strfind(fieldnames(data),'fluor'))));
+nnc = 0;
+
+for jj = 1:nc
+
+    fluorName =  ['fluor',num2str(jj)];
+
+    if isfield( data, fluorName )
+        nnc = nnc + 1;
+    end
+
+end
+
+end

Internal/intImRead.m

@@ -0,0 +1,24 @@
+function im = intImRead(out_name)
+% More flexible method for loading images... if the file is a mat file, it
+% will load the image in that... else it uses imread
+im = [];
+
+if numel(out_name) > 4
+    if strcmp(out_name([end-3:end]), '.mat' )
+        tmp = load(  out_name );
+        if isfield( tmp, 'im' );
+            im  = tmp.im;
+        end
+    elseif strcmp(out_name([end-3:end]), '.tif' )
+        im = imread( out_name );
+    end
+end
+
+
+if numel(size(im)) > 2
+    disp('Images are in color - attempting to convert to monochromatic.');
+    im = convertToMonochromatic(im);
+end
+end
+
+

Internal/intImWrite.m

@@ -0,0 +1,15 @@
+function intImWrite(im,out_name) 
+% More flexible metho of writing images. Can use save if the image name is
+% .mat.
+if numel( out_name ) > 4
+if strcmp( out_name(end-3:end), '.mat' )
+   out_name = intFixFileName( out_name, '.mat' );
+   save(  out_name, 'im' );            
+else
+   out_name = intFixFileName( out_name, '.tif' ); 
+   imwrite(uint16(im), out_name ,'tif','Compression', 'none');
+end
+
+end
+
+

Internal/intMakeMinMax.m

@@ -0,0 +1,6 @@
+    function minmax = intMakeMinMax( im )
+        minner = medfilt2( im, [2,2], 'symmetric' );
+        maxxer = max( minner(:));
+        minner = min( minner(:));
+        minmax = [minner,maxxer];
+    end

Internal/intRange.m

@@ -0,0 +1,6 @@
+function ranger = intRange( im, CDFr )
+% put max and min in range
+
+ranger = [min( im ),max( im )];
+
+end

Internal/intShiftIm.m

@@ -44,4 +44,6 @@
 
 imOut  = (real(ifft2(fftB).*exp(-1i*phase)));
 
+%imOut2 = imtranslate( imIn, -out([4,3]),'FillValues', mean(imIn(:)));
+
 end

Internal/intShiftImMod.m

@@ -0,0 +1,52 @@
+function imOut = intShiftIm( imIn, out )
+%% intShiftIm: shifts image 'imIn' by the parameters in 'out'
+% out is produced by intAlignIm( imA, imB, precision ).
+%
+% INPUT :
+%   imIn : input image
+%   out : output of intAlignIm,
+%       where the 3rd element is the row_shift and 4th and col_shift
+%
+% OUTPUT :
+%   imOut : shifted image
+%
+% Copyright (C) 2016 Wiggins Lab 
+% Written by Paul Wiggins.
+% University of Washington, 2016
+% This file is part of SuperSegger.
+% 
+% SuperSegger is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+% 
+% SuperSegger is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+% 
+% You should have received a copy of the GNU General Public License
+% along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
+
+% 
+% fftB = fft2(imIn); % fourier transform
+% 
+% deltar = out(3); % net_row_shift in subpixel
+% deltac = out(4); % net_col_shift in subpixel
+% 
+% phase = 0;
+% [nr,nc] = size(imIn); % nr : num of rows, nc : num of columns
+% Nr = ifftshift(-fix(nr/2):ceil(nr/2)-1); % swaps the left and right halves
+% Nc = ifftshift(-fix(nc/2):ceil(nc/2)-1);
+% [Nc,Nr] = meshgrid(Nc,Nr);
+% 
+% fftB = fftB.*exp(1i*2*pi*(deltar*Nr/nr+deltac*Nc/nc));
+% 
+% imOut  = (real(ifft2(fftB).*exp(-1i*phase)));
+%
+% This re-implementation uses the matlab built in imtranslate.
+
+
+imOut = imtranslate( imIn, -out([4,3]),'FillValues', mean(imIn(:)));
+
+end

Internal/isRightNameFormat.m

@@ -26,12 +26,12 @@
 % along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
 
 
-contents = dir([dirname,filesep,'*.tif']);
+contents = dir([dirname,filesep,'*.tif*']);
 filenames = {contents.name}';
 
-nameWithXy=regexpi(filenames,'t\d+xy\d+c\d+.tif','once');
-nameWithoutXy=regexpi(filenames,'t\d+c\d+.tif','once');
-nameWithoutt=regexpi(filenames,'xy\d+c\d+.tif','once');
+nameWithXy=regexpi(filenames,'t\d+xy\d+c\d+.tif+','once');
+nameWithoutXy=regexpi(filenames,'t\d+c\d+.tif+','once');
+nameWithoutt=regexpi(filenames,'xy\d+c\d+.tif+','once');
 
 numWithXy =  sum(~cellfun('isempty',nameWithXy));
 numWithoutXY = sum(~cellfun('isempty',nameWithoutXy));

batch/BatchSuperSeggerOpti.m

@@ -119,7 +119,7 @@ function BatchSuperSeggerOpti(dirname_,skip,clean_flag,res,startEnd,showWarnings
 % align frames
 if exist( dirname_, 'dir' )
     if exist( [dirname_,filesep,'raw_im'] ,'dir') && ...
-            (numel(dir ([dirname_,filesep,'raw_im',filesep,'*.tif'])) || ...
+            (numel(dir ([dirname_,filesep,'raw_im',filesep,'*.tif*'])) || ...
             exist([dirname_,filesep,'raw_im',filesep,'cropbox.mat'],'file'))
         disp('BatchSuperSeggerOpti : images already aligned');
         if exist([dirname_,filesep,'raw_im',filesep,'cropbox.mat'],'file')
@@ -128,7 +128,7 @@ function BatchSuperSeggerOpti(dirname_,skip,clean_flag,res,startEnd,showWarnings
         else
             crop_box_array = cell(1,10000);
         end
-    elseif numel(dir ([dirname_,filesep,'*.tif']))
+    elseif numel(dir ([dirname_,filesep,'*.tif*']))
         % check naming convention
         if ~isRightNameFormat(dirname_)
             disp('Images in incorrect naming format. Using convertImageNames to convert names.')
@@ -139,8 +139,8 @@ function BatchSuperSeggerOpti(dirname_,skip,clean_flag,res,startEnd,showWarnings
         if CONST.align.ALIGN_FLAG
             crop_box_array = trackOptiAlignPad( dirname_,...
                 CONST.parallel.parallel_pool_num, CONST);
-            movefile( [dirname_,filesep,'*.tif'], [dirname_,filesep,'raw_im'] ) % moves images to raw_im
-            movefile( [dirname_,'align',filesep,'*.tif'], [dirname_,filesep]); % moves aligned back to main folder
+            movefile( [dirname_,filesep,'*.tif*'], [dirname_,filesep,'raw_im'] ) % moves images to raw_im
+            movefile( [dirname_,'align',filesep,'*.tif*'], [dirname_,filesep]); % moves aligned back to main folder
             rmdir( [dirname_,'align'] ); % removes _align directory
         else
             copyfile( [dirname_,filesep,'*.tif'], [dirname_,filesep,'raw_im'] ) % moves images to raw_im
@@ -251,7 +251,7 @@ function intProcessXY( dirname_xy, skip, nc, num_c, clean_flag, ...
 % processor all the information it needs to process the images.
 
 % Initialization
-file_filter = '*.tif';
+file_filter = '*.tif*';
 verbose = CONST.parallel.verbose;
 
 % get header to show xy position

batch/convertImageNames.m

@@ -43,11 +43,11 @@ function convertImageNames(dirname, basename, timeFilterBefore, ...
 % along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
 
 
-images = dir([dirname,filesep,'*.tif']);
+images = dir([dirname,filesep,'*.tif*']);
 
 % directory to move original images
 dirOriginal  = [dirname,filesep,'original',filesep] ;
-imagesInOrig = dir([dirOriginal,filesep,'*.tif']);
+imagesInOrig = dir([dirOriginal,filesep,'*.tif*']);
 
 elementsTime='t';
 elementsXY ='xy';
@@ -87,10 +87,13 @@ function convertImageNames(dirname, basename, timeFilterBefore, ...
 end
 
 if isempty(imagesInOrig) % move original images
-    movefile([dirname,filesep,'*.tif'],dirOriginal); % move all images to dir original
+
+
+    movefile([dirname,filesep,'*.tif*'],dirOriginal); % move all images to dir original
+
 end
 
-images = dir([dirOriginal,filesep,'*.tif']);
+images = dir([dirOriginal,filesep,'*.tif*']);
 
 % go through every image
 for j = 1: numel (images)
@@ -186,4 +189,4 @@ function convertImageNames(dirname, basename, timeFilterBefore, ...
     numbers = str2double(pattern);
 end
 
-end
+end

batch/processExp.m

@@ -90,6 +90,7 @@ function processExp( dirname )
 CONST.trackOpti.NEIGHBOR_FLAG = false; % calculate number of neighbors (default = false)
 CONST.imAlign.AlignChannel = 1; % change this if you want the images to be aligned to fluorescence channel
 
+CONST.view.fluorColor = {'y','r','b'};
 
 %% Skip Frames for Segmentation
 % For fast time-lapse or slow growth you can skip phase image frames 

batch/superSeggerGui.m

@@ -315,6 +315,7 @@ function end_step_CreateFcn(hObject, eventdata, handles)
 
 % Hint: edit controls usually have a white background on Windows.
 %       See ISPC and COMPUTER.
+
 if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
     set(hObject,'BackgroundColor','white');
 end