Fixed Initialize Constants to be dependent on Cell Type

src/MATLAB/+Load/InitializeConstants.m

@@ -25,8 +25,19 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function InitializeConstants()
-%Set all constants here
+%% Set all constants here
 
+global CONSTANTS
+
+im = imread(Helper.GetFullImagePath(1));
+Load.AddConstant('imageSize',size(im),1);
+
+if (~isfield(CONSTANTS,'cellType') || isempty(CONSTANTS.cellType))
+    type = questdlg('Cell Type:','Cell Type','Adult','Hemato','Adult');
+    Load.AddConstant('cellType',type,1);
+end
+
+%% Common Constants
 Load.AddConstant('imageAlpha',                  1.5);
 Load.AddConstant('maxPixelDistance',            40,1);
 Load.AddConstant('maxCenterOfMassDistance',     40,1);
@@ -37,10 +48,25 @@ Load.AddConstant('minFamilyTimeFrame',25, 1);
 Load.AddConstant('maxFrameDifference',          1, 1);
 Load.AddConstant('historySize',                 10, 1);
 Load.AddConstant('clickMargin',                 500, 1);
-Load.AddConstant('timeResolution',10); %in frames per min
+Load.AddConstant('minTrackScore',               0.5,1);
+Load.AddConstant('maxPropagateFrames',          50,1);
+
+%% Particular Constants
+switch CONSTANTS.cellType
+    case 'Adult'
+        Load.AddConstant('timeResolution',              10); %in min per frame
         Load.AddConstant('dMaxCenterOfMass',            40,1);
         Load.AddConstant('dMaxConnectComponent',        40,1);
         Load.AddConstant('dMaxConnectComponentTracker', 20,1);
-Load.AddConstant('minTrackScore',0.5,1);
-Load.AddConstant('maxPropagateFrames',50,1);
+    case 'Hemato'
+        Load.AddConstant('timeResolution',              5); %in min per frame
+        Load.AddConstant('dMaxCenterOfMass',            80,1);
+        Load.AddConstant('dMaxConnectComponent',        80,1);
+        Load.AddConstant('dMaxConnectComponentTracker', 40,1);
+    otherwise
+        Load.AddConstant('timeResolution',              10); %in min per frame
+        Load.AddConstant('dMaxCenterOfMass',            40,1);
+        Load.AddConstant('dMaxConnectComponent',        40,1);
+        Load.AddConstant('dMaxConnectComponentTracker', 20,1);
+end
 end

src/MATLAB/+Load/OpenData.m

@@ -103,11 +103,10 @@ switch answer
         end
         load('LEVerSettings.mat');
         
-        Load.InitializeConstants();
         Load.AddConstant('version',softwareVersion,1);
+        CONSTANTS.cellType = [];
+        Load.InitializeConstants();
         
-        type = questdlg('Cell Type:','Cell Type','Adult','Hemato','Adult');
-        Load.AddConstant('cellType',type,1);
         errOpen = Segmentation.SegAndTrack();
         if(~errOpen)
             opened = 1;
@@ -150,11 +149,6 @@ switch answer
                 return
             end
             
-            if (~isfield(CONSTANTS,'cellType'))
-                type = questdlg('Cell Type:','Cell Type','Adult','Hemeta','Adult');
-                Load.AddConstant('cellType',type,1);
-            end
-            
             errors = mexIntegrityCheck();
             if ( ~isempty(errors) )
                 warndlg('There were database inconsistencies.  LEVer might not behave properly!');
@@ -167,6 +161,8 @@ switch answer
         
         Error.LogAction(['Opened file ' CONSTANTS.matFullFile]);
         
+        Load.InitializeConstants();
+                
         UI.InitializeFigures();
                 
         bUpdated = Load.FixOldFileVersions();

src/MATLAB/+Segmentation/HematoSegmentation.m

-function  HematoSegmentation(imageAlpha)
+function  HematoSegmentation()
 global CONSTANTS CellHulls
 eccentricity = 1.0;
 minVol = 200;
@@ -10,7 +10,7 @@ end
 
 fprintf(1,'Segmentation...');
 
-system(['start HematoSeg.exe ' CONSTANTS.rootImageFolder '* ' num2str(imageAlpha) ' ' num2str(minVol) ' ' num2str(eccentricity) ' .9 && exit']);
+system(['start HematoSeg.exe ' CONSTANTS.rootImageFolder '* ' num2str(CONSTANTS.imageAlpha) ' ' num2str(minVol) ' ' num2str(eccentricity) ' .9 && exit']);
 
 pause(20);
 CellHulls = struct(...
@@ -49,9 +49,6 @@ for i=1:length(dir([CONSTANTS.rootImageFolder '\*.tif']))
     
 end
 
-im = imread(Helper.GetFullImagePath(1));
-Load.AddConstant('imageSize',size(im),1);
-
 for i=1:length(CellHulls)
     [r c] = ind2sub(CONSTANTS.imageSize,CellHulls(i).indexPixels);
     ch = convhull(r,c);

src/MATLAB/+Segmentation/SegAndTrack.m

@@ -57,11 +57,8 @@ function errStatus = SegAndTrack()
     switch CONSTANTS.cellType
         case 'Hemato'
             tic;
-            Segmentation.HematoSegmentation(1.2);
+            Segmentation.HematoSegmentation();
             tSeg = toc;
-            Load.AddConstant('dMaxCenterOfMass',80,1);
-            Load.AddConstant('dMaxConnectComponent',80,1);
-            Load.AddConstant('dMaxConnectComponentTracker',40,1);
             tic;
             Tracker.HematoTracker();
             tTrack = toc;

src/MATLAB/+UI/DrawTree.m

@@ -25,7 +25,7 @@
 
 function DrawTree(familyID)
 
-global CellFamilies HashedCells Figures CONSTANTS CellTracks CellPhenotypes  
+global CellFamilies HashedCells Figures CellPhenotypes  
 
 if ( ~exist('familyID','var') || isempty(familyID) )
     Families.FindLargestTree();
@@ -40,10 +40,6 @@ end
 phenoScratch.phenoColors = hsv(length(CellPhenotypes.descriptions));
 phenoScratch.phenoLegendSet = zeros(length(CellPhenotypes.descriptions),1);
 
-if(~isfield(CONSTANTS,'timeResolution'))
-    CONSTANTS.timeResolution = 10;
-end
-
 if(isempty(CellFamilies(familyID).tracks)),return,end
 
 %let the user know that this might take a while