Added implementation for image resizing in CONST file.

batch/trackOptiResize.m

@@ -50,7 +50,7 @@
         image_name  = contents(i).name;
         image_folder = contents(i).folder;
         disp(image_name);
-        im = imread([image_folder,'/',image_name]);
+        im = intImRead([image_folder,'/',image_name]);
         out_name = [targetd, image_name];
         imwrite(imresize(im,scale), out_name, 'TIFF');        
     end

batch/trackOptiSkipMerge.m

@@ -142,7 +142,7 @@ function intSkipPar(i,dirname_xy,nameInfo,nt,nc,nz,skip,num_c,num_z)
 for k = 2:num_z
     nameInfo_tmp.npos(4,1) = nz(k);
     name  = MakeFileName(nameInfo_tmp);
-    phase =  min(phase, double(imread( [dirname_xy,'phase',filesep,name] )));
+    phase =  min(phase, double(intImRead( [dirname_xy,'phase',filesep,name] )));
 end
 
 % Loads the reference _err file for the image already segmented
@@ -174,7 +174,7 @@ function intSkipPar(i,dirname_xy,nameInfo,nt,nc,nz,skip,num_c,num_z)
         nameInfo_tmp.npos(2,1) = nc(k);
         nameInfo_tmp.npos(4,1) = 1;
         name = MakeFileName( nameInfo_tmp );
-        fluorImage = imread( [dirname_xy,'fluor',num2str(nc(k)-1),filesep,name]);
+        fluorImage = intImRead( [dirname_xy,'fluor',num2str(nc(k)-1),filesep,name]);
         data.(['fluor',num2str(nc(k)-1)]) = fluorImage;
 
         imRange(:,k) = intRange( fluorImage(:) );

batch/tryDifferentConstants.m

@@ -42,7 +42,7 @@
 % imfinfo()
 
 if strcmp(filename(end-3:end), '.tif')
-    tempImage = imread(filename);
+    tempImage = intImRead(filename);
 else % it is a folder
     filename = fixDir(filename);
     images = dir([filename,'*c1*.tif']);
@@ -55,7 +55,7 @@
     else
         lastPhaseImage = images(end).name;
     end
-    tempImage = imread([filename,lastPhaseImage]);  
+    tempImage = intImRead([filename,lastPhaseImage]);  
 end
 
 phase = intCropImage (tempImage);  

dev-lab/trackOptiZMerge.m

@@ -77,7 +77,7 @@ function trackOptiZMerge( dirname, targetname, CONST, dz )
 
 %% Load up first images and get the size
 
-im = imread( [dirname,contents(1).name] );
+im = intImRead( [dirname,contents(1).name] );
 
 if numel(size(im)) > 2
     im = im(:,:,2);
@@ -162,7 +162,7 @@ function intDoTimeStep( it, data, nnxy )
         nameInfo_in.npos(:,1) = [it; ic; nnxy; iz];
         in_name =  [data.dirname, MakeFileName(nameInfo_in)];
 
-        tmp = imread( in_name );
+        tmp = intImRead( in_name );
 
         if numel(size(tmp)) > 2
             tmp = tmp(:,:,2);

segmentation/doSeg.m

@@ -69,16 +69,17 @@
     nameInfo_tmp.npos(4,1) = 1; % z value
     name = MakeFileName(nameInfo_tmp);
     namePhase = [dirname_xy,'phase',filesep,name];    
-    phase = intImRead( namePhase );
-
+    phase = intImLoader( namePhase, CONST );
+        
     if num_z > 1 % if there are z frames
         phaseCat = zeros( [size(phase), num_z], 'uint16' );
         phaseCat(:,:,1) = phase;
 
         for iz = 2:num_z
             nameInfo_tmp.npos(4,1) = iz;
             name = MakeFileName(nameInfo_tmp);
-            phaseCat(:,:,iz) = intImRead( [dirname_xy,'phase',filesep,name] );
+            phaseCat(:,:,iz) = intImLoader( ...
+                [dirname_xy,'phase',filesep,name], CONST );
         end        
         phase = mean( phaseCat, 3);      
     end
@@ -110,7 +111,8 @@
             nameInfo_tmp.npos(2,1) = nc(k);
             nameInfo_tmp.npos(4,1) = 1;
             name = MakeFileName( nameInfo_tmp );
-            fluor_tmp = intImRead( [dirname_xy,'fluor',num2str(nc(k)-1),filesep,name] );         
+            fluor_tmp = intImLoader( [dirname_xy,...
+                'fluor',num2str(nc(k)-1),filesep,name], CONST );         
             data.(['fluor',num2str(nc(k)-1)])=fluor_tmp;        
 
             imRange(:,k) = intRange( fluor_tmp(:) );
@@ -124,4 +126,5 @@
     disp([dataname, ' already exists.']);
 end
 
-end
+end
+

segmentation/intImLoader.m

@@ -0,0 +1,16 @@
+function im = intImLoader( imname, CONST )
+%UNTITLED Summary of this function goes here
+%   Detailed explanation goes here
+
+ tmp_im = intImRead( imname );
+
+ if isfield( CONST.superSeggerOpti, 'rescale' ) && ...
+            CONST.superSeggerOpti.rescale ~= 1
+        im = imresize( tmp_im, CONST.superSeggerOpti.rescale );
+    else
+        im = tmp_im;
+ end
+
+
+end
+

trainingConstants/modifyConstValuesGUI.m

@@ -209,7 +209,7 @@ function image_folder_ClickedCallback(hObject, eventdata, handles)
 [imageName,directoryName , ~] = uigetfile('*.tif', 'Pick an image file');
 if imageName~=0
     handles.directory.String = [directoryName,filesep,imageName];
-    settings_mod.phaseImage = imread(handles.directory.String);
+    settings_mod.phaseImage = intImRead(handles.directory.String);
     axes(handles.viewport_modify);
     imshow(settings_mod.phaseImage,[]);
 end
@@ -517,7 +517,7 @@ function run_Callback(hObject, eventdata, handles)
 if numel(imageName)<3 || ~strcmp(imageName(end-3:end), '.tif')
     image_folder_ClickedCallback([],[],handles);
 end
-phaseIm = imread(handles.directory.String);
+phaseIm = intImRead(handles.directory.String);
 
 set(gcf,'Pointer','watch');
 settings_mod.data = superSeggerOpti(phaseIm,[],0,CONST);

trainingConstants/trainingGui.m

@@ -753,7 +753,7 @@ function loadData(frameNumber)
         settings_train.currentData = load([settings_train.loadDirectory,settings_train.loadFiles(frameNumber).name]);
     end
 else
-    settings_train.currentData = imread([settings_train.imageDirectory,settings_train.loadFiles(frameNumber).name]);
+    settings_train.currentData = intImRead([settings_train.imageDirectory,settings_train.loadFiles(frameNumber).name]);
 end
 settings_train.currentIsBad = strfind(settings_train.loadFiles(frameNumber).name, '_mod.mat');
 
@@ -865,7 +865,7 @@ function makeData_Callback(hObject, eventdata, handles)
     cropY = ceil(handles.viewport_train.YLim(1):handles.viewport_train.YLim(2) - 1);
 
     for i = 1:settings_train.frameSkip:maxFrames
-        tempImage = imread([settings_train.imageDirectory,settings_train.loadFiles(i).name]);
+        tempImage = intImRead([settings_train.imageDirectory,settings_train.loadFiles(i).name]);
         saveName = [newDir, filesep, settings_train.loadFiles(i).name];
         imwrite( tempImage(cropY, cropX), saveName, 'TIFF' );
     end
@@ -977,7 +977,7 @@ function save_cut_Callback(hObject, eventdata, handles)
 i = settings_train.frameNumber;
 filename =[ settings_train.imageDirectory,filesep,settings_train.loadFiles(i).name];
 
-tempImage = imread([filename]);
+tempImage = intImRead([filename]);
 saveName = [filename];
 imwrite( tempImage(cropY, cropX), saveName, 'TIFF' );
 

viz/fixFlags.m

@@ -133,7 +133,7 @@
 
 % modifies the transparency of the phase/mask - use as double from 0 - 1
 if ~isfield(FLAGS, 'level');
-    FLAGS.level = 0.8*ones([1,10]);
+    FLAGS.level = 0.5*ones([1,10]);
 end
 
 % modifies the transparency of the phase/mask - use as double from 0 - 1

viz/superSeggerViewerGui.m

@@ -37,7 +37,7 @@
     gui_mainfcn(gui_State, varargin{:});
 end
 
-function disable_all_panels (hObject,handles)
+function disable_all_panels (~,handles)
 set(findall(handles.gate_options_text, '-property', 'enable'), 'enable', 'off')
 set(findall(handles.output_options_text, '-property', 'enable'), 'enable', 'off')
 set(findall(handles.display_options_text, '-property', 'enable'), 'enable', 'off')
@@ -131,6 +131,9 @@ function initImage(hObject, handles) % Not updated
 handles.num_errs = 0;
 handles.canUseErr = 0;
 
+axes(handles.axes1);
+axis tight
+cla;
 
 if (nargin<1 || isempty(handles.image_directory.String))
     handles.image_directory.String = pwd;
@@ -147,8 +150,7 @@ function initImage(hObject, handles) % Not updated
 
 file_filter = '';
 CONST = [];
-axis tight
-cla;
+
 
 dirname = fixDir(dirname);
 dirname0 = dirname;
@@ -238,21 +240,21 @@ function initImage(hObject, handles) % Not updated
 handles.cell_poles.Value = FLAGS.p_flag;
 handles.legend_box.Value = FLAGS.legend;
 handles.outline_cells.Value = FLAGS.Outline_flag;
-handles.foci_box.Value = FLAGS.s_flag;
-handles.scores_foci.Value = FLAGS.scores_flag;
-
 if FLAGS.f_flag
+    handles.foci_box.Value = FLAGS.s_flag(FLAGS.f_flag);
+    handles.scores_foci.Value = FLAGS.scores_flag;
     handles.filt.Value = FLAGS.filt(FLAGS.f_flag);
+    handles.phase_flag.Value = FLAGS.phase_flag(FLAGS.f_flag);
 else
     handles.filt.Value = 0;
 end
+
 handles.region_outlines.Value = FLAGS.P_flag;
 handles.region_scores.Value = FLAGS.regionScores;
 handles.use_seg_files.Value = FLAGS.useSegs;
 handles.show_daughters.Value = FLAGS.showDaughters;
 handles.show_mothers.Value = FLAGS.showMothers;
 handles.show_linking.Value = FLAGS.showLinks;
-handles.phase_flag.Value = FLAGS.phase_flag;
 handles.phase_level_txt.String = num2str(FLAGS.phase_level);
 handles.composite.Value = FLAGS.composite;
 if exist('nn','var');