create new folder for stage functions.

create 'ludl' and 'prior' subfolder for each system. 
In main directory, create if statement in stage functions to switch between systems

Author: qigongFDA

Administrator_Input_Screen.m

@@ -51,7 +51,7 @@ function Administrator_Input_Screen_OpeningFcn(hObject, eventdata, handles, vara
     handles.myData.wsi_files = [];
     handles.myData.graphics = struct;
 
-    addpath('gui_graphics', 'icc_profiles', 'tasks');
+    addpath('gui_graphics', 'icc_profiles', 'tasks','stages/Prior','stages/Ludl');
 
     handles.myData.sourcedir = [cd, '\'];
 
@@ -215,7 +215,6 @@ function ExtractROIsButtonPressed(hObject, eventdata, handles) %#ok<DEFNU>
         handles.myData.tasks_out{i} = taskinfo;
 
     end
-    
     guidata(handles.Administrator_Input_Screen, handles);
     close(wtb);
 
@@ -442,25 +441,15 @@ function align_eye_cam(handles) %#ok<*INUSD>
 
 function position_eye_callback(hObject, eventdata) %#ok<*INUSD>
 handles = guidata(findobj('Tag','Administrator_Input_Screen'));
-stage_label = handles.myData.stage.label;
-if strcmp(stage_label(end-4:end),'Prior')
-    stage=stage_get_pos_prior(handles.myData.stage);
-else
-    stage=stage_get_pos(handles.myData.stage);
-end
+stage=stage_get_pos(handles.myData.stage);
 Pos=stage.Pos;
 set(hObject, 'UserData', Pos);
 
 end
 
 function position_cam_callback(hObject, eventdata)
 handles = guidata(findobj('Tag','Administrator_Input_Screen'));
-stage_label = handles.myData.stage.label;
-if strcmp(stage_label(end-4:end),'Prior')
-    stage=stage_get_pos_prior(handles.myData.stage);
-else
-    stage=stage_get_pos(handles.myData.stage);
-end
+stage=stage_get_pos(handles.myData.stage);
 Pos=stage.Pos;
 set(hObject, 'UserData', Pos);
 
@@ -538,12 +527,7 @@ function ModeSelectionPopUpMenu_Callback(hObject, eventdata, handles) %#ok<DEFNU
             set(hObject_configure_camera, ...
                 'Enable', 'on', ...
                 'String', 'Configure Camera');
-            stage_label = handles.myData.stage.label;
-            if strcmp(stage_label(end-4:end),'Prior')
-                handles.myData.stage = stage_get_pos_prior(handles.myData.stage);
-            else
-                handles.myData.stage = stage_get_pos(handles.myData.stage); %#ok<NASGU>
-            end
+            handles.myData.stage = stage_get_pos(handles.myData.stage); %#ok<NASGU>
             if handles.myData.stage.Pos == 0
                 return
             end

Camera_stage_review.m

@@ -95,12 +95,7 @@ function Take_image_Callback(hObject, eventdata, handles)
 
    img=camera_take_image(handles.cam);
    if handles.stageflag==1
-       if strcmp(handles.mode_desc(end-4:end),'Prior')
-           handles.stage = stage_get_pos_prior(handles.stage);
-       else
-           handles.stage = stage_get_pos(handles.stage);
-       end
-      
+       handles.stage = stage_get_pos(handles.stage);
        x = handles.stage.Pos(1);
        y = handles.stage.Pos(2);
        set(handles.current_position_x,'String',x);
@@ -142,12 +137,7 @@ function Move_stage_Callback(hObject, eventdata, handles)
 % eventdata  reserved - to be defined in a future version of MATLAB
 % handles    structure with handles and user data (see GUIDATA)
 stage_new = [str2num(handles.target_position_x),str2num(handles.target_position_y)];
-if strcmp(handles.mode_desc(end-4:end),'Prior')
-    handles.stage = stage_move_prior(handles.stage,stage_new);
-else
-    handles.stage = stage_move(handles.stage,stage_new);
-end
-%handles.stage = stage_move(handles.stage,stage_new);
+handles.stage = stage_move(handles.stage,stage_new);
 set(handles.current_position_x,'String',handles.target_position_x);
 set(handles.current_position_y,'String',handles.target_position_y);
 handles.position_flag_y=0;
@@ -214,12 +204,7 @@ function Get_position_Callback(hObject, eventdata, handles)
 % hObject    handle to Get_position (see GCBO)
 % eventdata  reserved - to be defined in a future version of MATLAB
 % handles    structure with handles and user data (see GUIDATA)
-if strcmp(handles.mode_desc(end-4:end),'Prior')
-    handles.stage = stage_get_pos_prior(handles.stage);
-else
-    handles.stage = stage_get_pos(handles.stage);
-end
-%handles.stage = stage_get_pos(handles.stage);
+handles.stage = stage_get_pos(handles.stage);
 x = handles.stage.Pos(1);
 y = handles.stage.Pos(2);
 set(handles.current_position_x,'String',x);
@@ -276,15 +261,9 @@ function Choose_System_Callback(hObject, eventdata, handles)
 mode_desc = deblank(modes{mode_index});
 handles.mode_desc = mode_desc;
 if mode_index ~= 1  
-    if strcmp(handles.mode_desc(end-4:end),'Prior')
-        handles.stage=stage_open_prior(mode_desc);
-        handles.stage = stage_set_origin_prior(handles.stage);
-        handles.stage=stage_move_prior(handles.stage,[5000,5000]);
-    else
-        handles.stage=stage_open(mode_desc);
-        handles.stage = stage_set_origin(handles.stage);
-        handles.stage=stage_move(handles.stage,[50000,50000]);
-    end
+    addpath('stages/Prior','stages/Ludl');
+    handles.stage=stage_open(mode_desc);
+    handles.stage = stage_set_origin(handles.stage);
     set(handles.Get_position,'Enable','on');
     set(handles.current_position_x,'Enable','on');
     set(handles.current_position_y,'Enable','on');
@@ -380,7 +359,7 @@ function Choose_Camera_Callback(hObject, eventdata, handles)
             settings.cam_kind = char('USB');
             settings.cam_format=char('F7_RGB_1224x1024_Mode1');
         else
-             settings.cam_kind = char('firewire');
+             settings.cam_kind = char('Firewire');
              settings.cam_format=char('RGB24_1024x768');
         end
         settings.reticleID=char('KR-871');

GUI.m

@@ -180,7 +180,7 @@ function GUI_OpeningFcn(hObj, eventdata, handles, varargin)
     % The mode_index and the filename for the test are extracted from the
     % cell structure varargin. varargin stores the input arguments for the
     % whole Matlab application
-    addpath('gui_graphics', 'icc_profiles', 'tasks');
+    addpath('gui_graphics', 'icc_profiles', 'tasks','stages/Prior','stages/Ludl');
     handles_old = varargin{1};
     handles.Administrator_Input_Screen = handles_old.Administrator_Input_Screen;
     myData = handles_old.myData;
@@ -198,7 +198,6 @@ function GUI_OpeningFcn(hObj, eventdata, handles, varargin)
     handles.reticle = 1;
     settings = myData.settings;
     guidata(handles.GUI, handles)
-    
     % Open communications to camera and begin preview
     % Open communications to stage
     switch myData.mode_desc
@@ -213,13 +212,7 @@ function GUI_OpeningFcn(hObj, eventdata, handles, varargin)
                 % close(cam_figure)
 
                 % Open communications to stage
-                stage_label = handles.myData.stage.label;
-                if strcmp(stage_label(end-4:end),'Prior')
-                    handles.myData.stage = stage_open_prior(handles.myData.stage.label);
-                else
                     handles.myData.stage = stage_open(handles.myData.stage.label);
-                end
-                %handles.myData.stage = stage_open(handles.myData.stage.label);
                 % To close:
                 % delete(handles.stage)
                 % If communications with the stage cannot be established,
@@ -562,13 +555,7 @@ function NextButtonPressed(hObj, eventdata, handles) %#ok<DEFNU>
                 end
                 taskinfo.stage_x = stage_new(1);
                 taskinfo.stage_y = stage_new(2);
-                stage_label = handles.myData.stage.label;
-                if strcmp(stage_label(end-4:end),'Prior')
-                    myData.stage = stage_move_prior(myData.stage,stage_new, myData.stage.handle);
-                else
-                    myData.stage = stage_move(myData.stage,stage_new, myData.stage.handle);
-                end
-                %myData.stage = stage_move(myData.stage,stage_new, myData.stage.handle);
+                myData.stage = stage_move(myData.stage,stage_new, myData.stage.handle);
                 taskimage_load(hObj);
                 handles = guidata(handles.GUI);
                 set(handles.iH,'visible','off');
@@ -736,13 +723,7 @@ function ResetViewButtonPressed(hObj, eventdata, handles) %#ok<DEFNU>
             set(handles.NextButton,'enable','off');
             set(handles.Fast_Register_Button,'enable','off');
             set(handles.Best_Register_Button,'enable','off');
-            stage_label = handles.myData.stage.label;
-            if strcmp(stage_label(end-4:end),'Prior')
-                handles.myData.stage = stage_move_prior(handles.myData.stage,target_pos,handles.myData.stage.handle);
-            else
-                handles.myData.stage = stage_move(handles.myData.stage,target_pos,handles.myData.stage.handle);
-            end
-            %handles.myData.stage = stage_move(handles.myData.stage,target_pos,handles.myData.stage.handle);
+            handles.myData.stage = stage_move(handles.myData.stage,target_pos,handles.myData.stage.handle);
             set(handles.NextButton,'enable',currentNextStatus);
             set(handles.Fast_Register_Button,'enable','on');
             set(handles.Best_Register_Button,'enable','on');
@@ -798,13 +779,7 @@ function Fast_Register_Button_Callback(hObject, eventdata, handles) %#ok<DEFNU>
     [roi_h, roi_w] = size(roi_image);
 
     % Get the stage position
-    stage_label = handles.myData.stage.label;
-    if strcmp(stage_label(end-4:end),'Prior')
-        handles.myData.stage = stage_get_pos_prior(handles.myData.stage,myData.stage.handle);
-    else
-        handles.myData.stage = stage_get_pos(handles.myData.stage,myData.stage.handle); 
-    end
-   % handles.myData.stage = stage_get_pos(handles.myData.stage,myData.stage.handle);
+    handles.myData.stage = stage_get_pos(handles.myData.stage,myData.stage.handle); 
     stage_current = int64(handles.myData.stage.Pos);
 
     % Cross correlate the stage and wsi images
@@ -833,12 +808,7 @@ function Fast_Register_Button_Callback(hObject, eventdata, handles) %#ok<DEFNU>
     stage_new = stage_current + offset_roi;
     offset_stage = int64(myData.settings.offset_stage);
     stage_new = stage_new - offset_stage;
-    if strcmp(stage_label(end-4:end),'Prior')
-        handles.myData.stage = stage_move_prior(handles.myData.stage,stage_new, handles.myData.stage.handle);
-    else
-        handles.myData.stage = stage_move(handles.myData.stage,stage_new, handles.myData.stage.handle);
-    end
-    %handles.myData.stage = stage_move(handles.myData.stage,stage_new, handles.myData.stage.handle);
+    handles.myData.stage = stage_move(handles.myData.stage,stage_new, handles.myData.stage.handle);
 catch ME
     error_show(ME)
 end
@@ -1102,25 +1072,12 @@ function Best_Register_Button_Callback(hObject, eventdata, handles)
     [roi_h, roi_w] = size(roi_image);
 
     % Get the stage position and snap a picture: cam_image
-    stage_label = handles.myData.stage.label;
-    if strcmp(stage_label(end-4:end),'Prior')
-        handles.myData.stage = stage_get_pos_prior(handles.myData.stage,handles.myData.stage.handle);
-    else
-        handles.myData.stage = stage_get_pos(handles.myData.stage,handles.myData.stage.handle); 
-    end
-      %  handles.myData.stage = stage_get_pos(handles.myData.stage,handles.myData.stage.handle);
+    handles.myData.stage = stage_get_pos(handles.myData.stage,handles.myData.stage.handle); 
     stage_current = int64(handles.myData.stage.Pos);
     offset_stage = int64(myData.settings.offset_stage);
     stage_new = stage_current + offset_stage;
-    if strcmp(stage_label(end-4:end),'Prior')
-        handles.myData.stage = stage_move_prior(handles.myData.stage,stage_new,handles.myData.stage.handle);
-        handles.myData.stage = stage_get_pos_prior(handles.myData.stage,handles.myData.stage.handle);
-    else
-        handles.myData.stage = stage_move(handles.myData.stage,stage_new,handles.myData.stage.handle);
-        handles.myData.stage = stage_get_pos(handles.myData.stage,handles.myData.stage.handle); 
-    end
-    %handles.myData.stage = stage_move(handles.myData.stage,stage_new,handles.myData.stage.handle);
-    %handles.myData.stage = stage_get_pos(handles.myData.stage,handles.myData.stage.handle);
+    handles.myData.stage = stage_move(handles.myData.stage,stage_new,handles.myData.stage.handle);
+    handles.myData.stage = stage_get_pos(handles.myData.stage,handles.myData.stage.handle); 
     stage_current = int64(handles.myData.stage.Pos);
     cam_image = camera_take_image(handles.cam);
 
@@ -1174,12 +1131,7 @@ function Best_Register_Button_Callback(hObject, eventdata, handles)
     stage_new = stage_current + offset_roi;
     offset_stage = int64(myData.settings.offset_stage);
     stage_new = stage_new - offset_stage;
-    if strcmp(stage_label(end-4:end),'Prior')
-        handles.myData.stage = stage_move_prior(handles.myData.stage,stage_new, handles.myData.stage.handle);
-    else
-        handles.myData.stage = stage_move(handles.myData.stage,stage_new, handles.myData.stage.handle);
-    end
-    %handles.myData.stage = stage_move(handles.myData.stage,stage_new, handles.myData.stage.handle);
+    handles.myData.stage = stage_move(handles.myData.stage,stage_new, handles.myData.stage.handle);
 catch ME
     error_show(ME)
 end

Stage_Allighment.m

@@ -39,23 +39,13 @@ function Stage_Allighment_OpeningFcn(hObject, eventdata, handles, varargin) %#ok
     reg_flag = current.reg_flag; %#ok<NASGU>
     slot_i = current.slot_i;
     wsi_info = myData.wsi_files{slot_i};
-    
+    addpath('stages/Prior','stages/Ludl');
     % Initiate the camera preview window
     % handles.cam = camera object
     if myData.yesno_micro==1
         handles.cam = camera_open(settings.cam_kind,settings.cam_format);
         handles.cam_figure = camera_preview(handles.cam, settings);
-        stage_label = myData.stage.label;
-        if strcmp(stage_label(end-4:end),'Prior')
-            myData.stage = stage_set_origin_prior(myData.stage);
-            myData.stage=stage_move_prior(myData.stage,[5000,5000]);
-        else
-            myData.stage = stage_set_origin(myData.stage);
-            myData.stage=stage_move(myData.stage,[50000,50000]);
-        end
-        %myData.stage = stage_set_origin(myData.stage);
-        %myData.stage=stage_move(myData.stage,[50000,50000]);
-        
+        myData.stage = stage_set_origin(myData.stage);       
     end
 
     % Set the default size of the window and the axes
@@ -298,13 +288,7 @@ function take_stage(hObject, eventdata, handles)
 
     % Get stage position_i and camera image
     if handles.myData.yesno_micro==1
-        stage_label = handles.myData.stage.label;
-        if strcmp(stage_label(end-4:end),'Prior')
-            myData.stage = stage_get_pos_prior(myData.stage);
-        else
-            myData.stage = stage_get_pos(myData.stage);
-        end
-        %myData.stage = stage_get_pos(myData.stage);
+        myData.stage = stage_get_pos(myData.stage);
         temp = myData.stage.Pos;
         current.cam_x0 = temp(1);
         current.cam_y0 = temp(2);
@@ -678,13 +662,7 @@ function take_stage1_Callback(hObject, eventdata, handles) %#ok<DEFNU>
 
     if handles.current.load_stage_data(1) == 1
         display('automatically navigate to position 1')
-        stage_label = handles.myData.stage.label;
-        if strcmp(stage_label(end-4:end),'Prior')
-            handles.myData.stage=stage_move_prior(handles.myData.stage,handles.myData.stagedata.stage_positions(1,:));     
-        else
-            handles.myData.stage=stage_move(handles.myData.stage,handles.myData.stagedata.stage_positions(1,:));     
-        end
-        %handles.myData.stage=stage_move(handles.myData.stage,handles.myData.stagedata.stage_positions(1,:));     
+        handles.myData.stage=stage_move(handles.myData.stage,handles.myData.stagedata.stage_positions(1,:));       
         set(handles.take_stage1,'String','Take Stage Position 1');
         handles.current.load_stage_data(1) = 2;
         guidata(handles.Stage_Allighment,handles);
@@ -724,14 +702,7 @@ function take_stage2_Callback(hObject, eventdata, handles) %#ok<DEFNU>
 
     if handles.current.load_stage_data(2) == 1
         display('automatically navigate to position 2')
-        stage_label = handles.myData.stage.label;
-        if strcmp(stage_label(end-4:end),'Prior')
-            handles.myData.stage=stage_move_prior(handles.myData.stage,handles.myData.stagedata.stage_positions(2,:));     
-        else
-            handles.myData.stage=stage_move(handles.myData.stage,handles.myData.stagedata.stage_positions(2,:));     
-        end
-        %handles.myData.stage=stage_move(handles.myData.stage,handles.myData.stagedata.stage_positions(2,:));
-        
+        handles.myData.stage=stage_move(handles.myData.stage,handles.myData.stagedata.stage_positions(2,:));           
         set(handles.take_stage2,'String','Take Stage Position 2');
         handles.current.load_stage_data(2) = 2;
         guidata(handles.Stage_Allighment,handles);
@@ -769,14 +740,7 @@ function take_stage3_Callback(hObject, eventdata, handles) %#ok<DEFNU>
 
     if handles.current.load_stage_data(3) == 1
         display('automatically navigate to position 3')
-        stage_label = handles.myData.stage.label;
-        if strcmp(stage_label(end-4:end),'Prior')
-            handles.myData.stage=stage_move_prior(handles.myData.stage,handles.myData.stagedata.stage_positions(3,:));     
-        else
-            handles.myData.stage=stage_move(handles.myData.stage,handles.myData.stagedata.stage_positions(3,:));     
-        end
-        %handles.myData.stage=stage_move(handles.myData.stage,handles.myData.stagedata.stage_positions(3,:));
-        
+        handles.myData.stage=stage_move(handles.myData.stage,handles.myData.stagedata.stage_positions(3,:));     
         set(handles.take_stage3,'String','Take Stage Position 3');
         handles.current.load_stage_data(3) = 2;
         guidata(handles.Stage_Allighment,handles);

camera_open.m

@@ -27,7 +27,7 @@
     delete(objects);
     if strcmp( cam_kind,'USB')
        cam_adaptor = 'pointgrey';
-    elseif strcmp( cam_kind,'firewire')
+    elseif strcmp( cam_kind,'Firewire')
        cam_adaptor = 'dcam';
     end
     % Create the video object to communicate with the camera 

sample_inputfiles/thorlabs20x-axioplan2i.dapsi

@@ -38,6 +38,7 @@ wsi_slot_1       = C:\000_whole_slides\100113_ThorLabs_20x.ndpi
 rgb_lut_slot_1   = icc_profiles\rgb_lut_identity.txt
 label_pos        = 6
 reticleID        = KR-32536
+cam_kind	 = Firewire
 cam_format       = RGB24_1024x768
 cam_pixel_size   = 6.9
 mag_cam          = 1.0

sample_inputfiles/thorlabs20x-axioplan2i_RK871.dapsi

@@ -38,6 +38,7 @@ wsi_slot_1       = C:\000_whole_slides\100113_ThorLabs_20x.ndpi
 rgb_lut_slot_1   = icc_profiles\rgb_lut_identity.txt
 label_pos        = 6
 reticleID        = KR-871
+cam_kind	 = Firewire
 cam_format       = RGB24_1024x768
 cam_pixel_size   = 6.9
 mag_cam          = 1.0

sample_inputfiles/thorlabs20x-olympus.dapsi

@@ -38,6 +38,7 @@ wsi_slot_1       = C:\000_whole_slides\100113_ThorLabs_20x.ndpi
 rgb_lut_slot_1   = icc_profiles\rgb_lut_identity.txt
 label_pos        = 12
 reticleID        = KR-32536
+cam_kind	 = Firewire
 cam_format       = RGB24_1024x768
 cam_pixel_size   = 6.9
 mag_cam          = 0.5

sample_inputfiles/tissue40x-8B-axioplan2i.dapsi

@@ -44,6 +44,7 @@ wsi_slot_1       = C:\000_whole_slides\tissue40x-8B.ndpi
 rgb_lut_slot_1   = icc_profiles\rgb_lut_gamma_inv1p8.txt
 label_pos        = 6
 reticleID        = KR-871
+cam_kind	 = Firewire
 cam_format       = RGB24_1024x768
 cam_pixel_size   = 6.9
 mag_cam          = 1.0

sample_inputfiles/tissue40x-8B-olympus.dapsi

@@ -38,6 +38,7 @@ wsi_slot_1       = C:\000_whole_slides\tissue40x-8B.ndpi
 rgb_lut_slot_1   = icc_profiles\rgb_lut_gamma_inv1p8.txt
 label_pos        = 12
 reticleID        = KR-32536
+cam_kind	 = Firewire
 cam_format       = RGB24_1024x768
 cam_pixel_size   = 6.9
 mag_cam          = 0.5