updates to allow save in mergeRoiTool

mergeRoiTool.m

@@ -87,6 +87,33 @@ function pushbutton_save_Callback(hObject, eventdata, handles)
 % hObject    handle to pushbutton_save (see GCBO)
 % eventdata  reserved - to be defined in a future version of MATLAB
 % handles    structure with handles and user data (see GUIDATA)
+lungMatrix = handles.lungMatrix;
+
+savePath = [handles.path '/mergeLungROI'];
+fname = handles.curName;
+if exist(savePath,'dir') ~= 7
+    mkdir(savePath);
+end
+try
+    save([savePath '/mergeLung-' fname '.mat'],'lungMatrix')
+    set(handles.checkbox_saved,'Value',1,'BackgroundColor','g');
+    axes(handles.axes1);
+    %warn('here')
+    h = imagesc([0 0; 0 0])
+    
+    %set(h,'HitTest','off')
+    get(h)
+    %set(h,'ButtonDownFcn',@axes1_ButtonDownFcn)
+    handles.needsReload = 1;
+    
+    msgbox('ROI Saved Successfully')
+catch
+    h = warndlg('Save failed.  Nothing saved');
+end
+
+guidata(hObject, handles);
+%% old save function
+%{
 roi = handles.roi;
 
 roiCoords = handles.roiCoords;
@@ -122,6 +149,8 @@ else
     end
 end
 guidata(hObject, handles);
+%}
+% end old save function
 %popup_sel_index = get(handles.popupmenu1, 'Value');
 %{
 switch popup_sel_index
@@ -406,7 +435,7 @@ if lms > -1
         for m=1:size(handles.lungMatrix,2)-1
             xx = n*lms;
             yy = m*lms;
-            switch handles.lungMatrix(n,m,1,handles.currentSlice)
+            switch handles.lungMatrix(m,n,1,handles.currentSlice)
                 case 1
                     cd = [0.2, 0.2, 0.0];
                 case 2
@@ -433,7 +462,7 @@ newim = newim + overlay;
 h = imagesc(newim);
 set(h,'HitTest','off')
 set(h,'PickableParts','none')
-
+set(handles.sliceNum, 'String', num2str(handles.currentSlice));
 set(handles.sliceCount,'String',sprintf('/ %i',size(images,4)));
 if lms > -1
     hold on; for n=0:gridsize:imsize(1); 
@@ -472,7 +501,7 @@ if get(handles.slider2,'Max') ~= 1.1
     h = imagesc(images(:,:,1,get(handles.slider2,'Value')));
     colormap('gray')
     set(h,'ButtonDownFcn',@axes1_ButtonDownFcn);
-
+    redrawImage(hObject,eventdata,handles);
 end
 
 guidata(hObject,handles);
@@ -542,7 +571,7 @@ axes(handles.axes1);
 gridsize = sqrt((x_coord(2)-x_coord(1)).^2 + (y_coord(2)-y_coord(1)).^2);
 gridsize = ceil(gridsize);
 imsize = size(handles.imageMat);
-lungMatrix = zeros(ceil(imsize(1)./gridsize),ceil(imsize(2)./gridsize),imsize(3),imsize(4));
+lungMatrix = zeros(floor(imsize(1)./gridsize),floor(imsize(2)./gridsize),imsize(3),imsize(4));
 handles.lungMatrix = lungMatrix;
 handles.lungGridSize = gridsize;
 hold on; for n=0:gridsize:imsize(1); 
@@ -556,8 +585,9 @@ for n=0:gridsize:imsize(2);
     set(h,'ButtonDownFcn',@axes1_ButtonDownFcn)
 end
 %handles
-guidata(hObject,handles);
 
+guidata(hObject,handles);
+redrawImage(hObject,eventdata,handles);
 %set(gca, 'ButtonDownFcn', @axes1_ButtonDownFcn);
 %ax = gca;
 %im.PickableParts = 'none';
@@ -587,7 +617,8 @@ lungMatLoc = floor(currentBox)
 lmy = floor(lungMatLoc(1)./size(handles.imageMat,2)*lungGridMatSize(2))
 lmx = floor(lungMatLoc(2)./size(handles.imageMat,1)*lungGridMatSize(1))
 currentSlice = get(handles.slider2,'Value');
-handles.lungMatrix(lmy,lmx,1,currentSlice) = mod(handles.lungMatrix(lmy,lmx,1,currentSlice)+1,5);
+currentSlice
+handles.lungMatrix(lmx,lmy,1,currentSlice) = mod(handles.lungMatrix(lmx,lmy,1,currentSlice)+1,5);
 
 handles.lungMatrix(:,:,1,currentSlice);
 guidata(hObject, handles)