modify constants gui and loadConstants now loads anything in the sett…

…ings folder

batch/superSeggerGui.m

@@ -40,10 +40,19 @@
 
 function superSeggerGui_OpeningFcn(hObject, eventdata, handles, varargin)
 handles.output = hObject;
+load_listbox(handles)
 set(handles.figure1, 'units', 'normalized', 'position', [0.25 0.2 0.35 0.7])
 guidata(hObject, handles);
 
 
+function load_listbox(handles)
+[possibleConstants] = getConstantsList();
+[sorted_names,sorted_index] = sortrows({possibleConstants.resFlag}');
+handles.file_names = sorted_names;
+handles.sorted_index = sorted_index;
+set(handles.constants_list,'String',handles.file_names,...
+	'Value',1)
+
 function varargout = superSeggerGui_OutputFcn(hObject, eventdata, handles)
 varargout{1} = handles.output;
 
@@ -105,40 +114,12 @@ function segment_images_Callback(hObject, eventdata, handles)
     return
 end
 
-if (handles.ec60.Value + handles.ec100.Value + handles.pa100.Value + ...
-        handles.pa60.Value + ...
-        handles.bay60.Value+handles.eclb60.Value) > 1
-    errordlg ('Please select only one constant.')
-    return
-end
-
-text = '';
-
-if handles.ec60.Value;
-    text = '60XEc';
-elseif handles.ec100.Value;
-    text = '100XEc';
-elseif handles.pa100.Value;
-    text = '100XPa';
-elseif handles.pa60.Value;
-    text = '60XPa';
-elseif handles.eclb60.Value;
-    text = '60XEcLB';
-elseif handles.bay60.Value;
-    text = '60XBay';
-end
-
-
-% get values for constants
+% load constants
 parallel = handles.parallel_flag.Value;
-if ~strcmp(text,'');
-    CONST = loadConstantsNN(text, parallel);
-elseif isfield(handles,'CONST') && ~isempty(handles.CONST)
-    CONST = handles.CONST;
-else
-    errordlg ('No constants selected');
-    return
-end
+resValue = get(handles.constants_list,'Value');
+res = handles.constants_list.String{resValue};
+CONST = loadConstantsNN (res,parallel);
+
 
 % set constants
 CONST.trackOpti.NEIGHBOR_FLAG = handles.neighbor_flag.Value;
@@ -151,7 +132,6 @@ function segment_images_Callback(hObject, eventdata, handles)
 CONST.trackOpti.MIN_CELL_AGE = str2num(handles.cell_age.String);
 CONST.trackOpti.REMOVE_STRAY = handles.remove_stray.Value;
 
-
 linkVal = get(handles.link_list,'Value'); 
 if linkVal == 1
     CONST.trackOpti.linkFun =  @multiAssignmentFastOnlyOverlap;
@@ -176,37 +156,8 @@ function bthai60_Callback(hObject, eventdata, handles)
 
 % tries different constants
 function try_constants_Callback(hObject, eventdata, handles)
-resFlags = {};
-if handles.ec60.Value;
-    resFlags{end+1} = '60XEc';
-end
-if handles.ec100.Value;
-    resFlags{end+1} = '100XEc';
-end
-if handles.pa100.Value;
-    resFlags{end+1} = '100XPa';
-end
-if handles.pa60.Value;
-    resFlags{end+1} = '60XPa';
-end
-if handles.bay60.Value;
-    resFlags{end+1} = '60XBay';
-end
-if handles.eclb60.Value;
-    resFlags{end+1} = '60XEcLB';
-end
+tryDifferentConstants(handles.directory.String);
 
-tryDifferentConstants(handles.directory.String, resFlags);
-
-% loads constants that user selects 
-function loadConstMine_Callback(hObject, eventdata, handles)
-if get(hObject,'Value')
-[filename,path] = uigetfile('*.mat', 'Pick a superSegger constants file');
-handles.CONST = load([path,'/',filename]);
-else
-    handles.CONST  = [];
-end
-guidata(hObject, handles)
 
 
 % opens superSeggerViewer
@@ -250,8 +201,6 @@ function cell_age_CreateFcn(hObject, eventdata, handles)
 end
 
 
-
-
 % --- Executes on selection change in constants_list.
 function link_list_Callback(hObject, eventdata, handles)
 % hObject    handle to constants_list (see GCBO)
@@ -269,6 +218,30 @@ function link_list_CreateFcn(hObject, eventdata, handles)
 % eventdata  reserved - to be defined in a future version of MATLAB
 % handles    empty - handles not created until after all CreateFcns called
 
+% Hint: listbox 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
+
+
+
+% --- Executes on selection change in constants_list.
+function constants_list_Callback(hObject, eventdata, handles)
+% hObject    handle to constants_list (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: contents = cellstr(get(hObject,'String')) returns constants_list contents as cell array
+%        contents{get(hObject,'Value')} returns selected item from constants_list
+
+
+% --- Executes during object creation, after setting all properties.
+function constants_list_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to constants_list (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
 % Hint: listbox controls usually have a white background on Windows.
 %       See ISPC and COMPUTER.
 if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

batch/tryDifferentConstants.m

@@ -1,63 +1,66 @@
-function tryDifferentConstants(dirname,resFlags)
+function data = tryDifferentConstants(filename,resFlags)
 % tryDifferentConstants : displays images of cells segmented with
 % different constants set in resFlags. It only does the initial
 % segmentation (only the doSeg part) and not the regions decisions,
 % linking and error resolution that come after.
-% Images need to have the right naming convention - if they don't use 
+% Images need to have the right naming convention - if they don't use
 % renameImages before this script.
 %
 % INPUT :
-%       dirname : directory with images
+%       dirname : directory with images or filename of image (must be .tif)
 % OUTPUT :
 %       data.SegFile: _seg file from segmentation
 %            .res: constants resolution for each seg file
 %
-% Copyright (C) 2016 Wiggins Lab 
+% Copyright (C) 2016 Wiggins Lab
 % Written by Stella Stylianidou
 % 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/>.
 
 % modify this accoding to the constants you want to try
-if nargin < 1 || isempty( dirname ) || strcmp(dirname,'.')
-    dirname = pwd;
+if nargin < 1 || isempty( filename ) || strcmp(filename,'.')
+    filename = pwd;
 end
 
 if ~exist('resFlags','var') || isempty(resFlags)
-%resFlags = {'60XEc','60XA','60XEcLB',...
- %   '60XPa','60XPaM','60XPaM2','60XBthai','100XEc','100XPa'};
-resFlags = {'60XEc','100XEc','60XEcLB','60XBay','60XPa','100XPa'};
+    [possibleConstants] = getConstantsList();
+    resFlags = {possibleConstants.resFlag};
 end
 
 
-
-dirname = fixDir(dirname);
-images = dir([dirname,'*c1*.tif']);
-
-
-if isempty (images)
-    disp('no images found in the directory with c1.tif.Select an image');
-    [lastPhaseImage,dirname , ~] = uigetfile('*.tif', 'Pick an image file');
-    if lastPhaseImage == 0
-        return;
+if strcmp(filename(end-3:end), '.tif')
+    tempImage = imread(filename);
+else % it is a folder
+    filename = fixDir(filename);
+    images = dir([filename,'*c1*.tif']);
+    if isempty (images)
+        disp('no images found in the directory with c1.tif.Select an image');
+        [lastPhaseImage,filename , ~] = uigetfile('*.tif', 'Pick an image file');
+        if lastPhaseImage == 0
+            return;
+        end
+    else
+        lastPhaseImage = images(end).name;
     end
-else
-    lastPhaseImage = images(end).name;
+    tempImage = imread([filename,lastPhaseImage]);  
 end
 
-phase = intCropImage (imread([dirname,lastPhaseImage]));
+phase = intCropImage (tempImage);  
+
+
 numFlags = numel(resFlags);
 numCols = 3;
 numRows = ceil(numFlags / numCols);