Merge pull request #19 from DIDSR/newsystem

Excellent work adapting the code for new hardware types (prior stage, USB 3 camera) and communications.

Author: brandon-gallas

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);
 
@@ -334,7 +333,7 @@ function align_eye_cam(handles) %#ok<*INUSD>
 try
 
     settings = handles.myData.settings;
-    handles.cam = camera_open(settings.cam_format);
+    handles.cam = camera_open(settings.cam_kind,settings.cam_format);
     handles.cam_figure = camera_preview(handles.cam, settings);
     pos_eye = [0,0];
     pos_cam = [0,0];
@@ -528,7 +527,6 @@ function ModeSelectionPopUpMenu_Callback(hObject, eventdata, handles) %#ok<DEFNU
             set(hObject_configure_camera, ...
                 'Enable', 'on', ...
                 'String', 'Configure Camera');
-            
             handles.myData.stage = stage_get_pos(handles.myData.stage); %#ok<NASGU>
             if handles.myData.stage.Pos == 0
                 return
@@ -545,7 +543,7 @@ function ModeSelectionPopUpMenu_Callback(hObject, eventdata, handles) %#ok<DEFNU
 
             % Determine and derive additional camera settings
             if handles.myData.yesno_micro==1
-                cam=camera_open();
+                cam=camera_open(settings.cam_kind,settings.cam_format);
                 if cam == 0
                     return
                 end

Camera_stage_review.fig

@@ -22,7 +22,7 @@
 
 % Edit the above text to modify the response to help Camera_stage_review
 
-% Last Modified by GUIDE v2.5 29-Jun-2015 15:59:11
+% Last Modified by GUIDE v2.5 25-Apr-2016 16:52:17
 
 % Begin initialization code - DO NOT EDIT
 gui_Singleton = 1;
@@ -54,24 +54,18 @@ function Camera_stage_review_OpeningFcn(hObject, eventdata, handles, varargin)
 % varargin   command line arguments to Camera_stage_review (see VARARGIN)
 
 % Choose default command line output for Camera_stage_review
-settings.mag_cam=1;
-settings.cam_pixel_size=6.9;
-settings.cam_format=char('RGB24_1024x768');
-settings.reticleID=char('KR-871');
-settings.cam_mask = reticle_make_mask(...
-        settings.reticleID,...
-        settings.cam_pixel_size/settings.mag_cam,...
-        [0,0]);
-handles.cam=camera_open(settings.cam_format);
-camera_image_display(handles,handles.cam,settings);
-handles.imagenumber = 1;
-handles.position_flag_y=0;
-handles.position_flag_x=0;
-handles.stageflag=0;
-handles.firsttime = 1;
-handles.output=hObject;
-% Update handles structure
-guidata(hObject, handles);
+    desc = {'\bfWelcome'...
+    ,'Please choose the camera format'};
+    welcome_page(handles,desc );
+    set(handles.Take_image,'Enable','off');
+    handles.imagenumber = 1;
+    handles.position_flag_y=0;
+    handles.position_flag_x=0;
+    handles.stageflag=0;
+    handles.firsttime = 1;
+    handles.output=hObject;
+    % Update handles structure
+    guidata(hObject, handles);
 end
 
 % UIWAIT makes Camera_stage_review wait for user response (see UIRESUME)
@@ -266,15 +260,17 @@ function Choose_System_Callback(hObject, eventdata, handles)
 mode_index = get(handles.Choose_System, 'Value');
 mode_desc = deblank(modes{mode_index});
 handles.mode_desc = mode_desc;
-handles.stage=stage_open(mode_desc);
-handles.stage = stage_set_origin(handles.stage);
-handles.stage=stage_move(handles.stage,[50000,50000]);
-set(handles.Get_position,'Enable','on');
-set(handles.current_position_x,'Enable','on');
-set(handles.current_position_y,'Enable','on');
-set(handles.target_position_x,'Enable','on');
-set(handles.target_position_y,'Enable','on');
-handles.stageflag=1;
+if mode_index ~= 1  
+    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');
+    set(handles.target_position_x,'Enable','on');
+    set(handles.target_position_y,'Enable','on');
+    handles.stageflag=1;
+end
 guidata(hObject, handles);   
 end
 
@@ -299,7 +295,9 @@ function camera_image_display(handles,vid, settings)
     imWidth = vidRes(1);
     imHeight = vidRes(2);
     set(handles.ImageAxes,'Units', 'pixels')
-    set(handles.ImageAxes,'Position', [5, 5, imWidth, imHeight]);
+    startWidth = floor((1252-imWidth)/2);
+    startHeight = floor((1051-imHeight)/2);
+    set(handles.ImageAxes,'Position', [startWidth, startHeight, imWidth, imHeight]);
     hImage = image( uint8(zeros(imHeight, imWidth, nBands) ),'parent', handles.ImageAxes);
     set(hImage, 'UserData', settings)
     setappdata(hImage,'UpdatePreviewWindowFcn',@preview_image_with_cross); 
@@ -347,5 +345,83 @@ function preview_image_with_cross(obj, event, himage)
 end
 
 
+% --- Choose camera format
+function Choose_Camera_Callback(hObject, eventdata, handles)
+try
+    settings.mag_cam=1;
+    settings.cam_pixel_size=6.9;
+    modes=get(handles.Choose_Camera,'String');
+    mode_index = get(handles.Choose_Camera, 'Value');
+    cam_mode = deblank(modes{mode_index});
+    if mode_index ~= 1  
+        handles.cam_mode = cam_mode;
+        if strcmp(handles.cam_mode(1:3),'USB')
+            settings.cam_kind = char('USB');
+            settings.cam_format=char('F7_RGB_1224x1024_Mode1');
+        else
+             settings.cam_kind = char('Firewire');
+             settings.cam_format=char('RGB24_1024x768');
+        end
+        settings.reticleID=char('KR-871');
+        settings.cam_mask = reticle_make_mask(...
+                settings.reticleID,...
+                settings.cam_pixel_size/settings.mag_cam,...
+                [0,0]);
+        handles.cam=camera_open(settings.cam_kind,settings.cam_format);
+        camera_image_display(handles,handles.cam,settings);
+        set(handles.Take_image,'Enable','on');
+    else
+        desc = {'\bfWelcome'...
+            ,'Please choose the camera format'};
+        welcome_page(handles, desc);
+        set(handles.Take_image,'Enable','off');
+    end
+    guidata(hObject, handles);
+catch ME
+    error_show(ME)
+end
 
+end
+
+% --- Executes during object creation, after setting all properties.
+function Choose_Camera_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to Choose_Camera (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
 
+% Hint: popupmenu 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
+end
+function  welcome_page(handles, desc)
+try
+   % This function creates an image with text to be displayed to the user
+     set(handles.ImageAxes,...
+         'Units', 'pixels',...
+         'Position', [1, 1, 1252, 1051],...
+         'Visible', 'off');
+    position = int64(get(handles.ImageAxes, 'Position'));
+    temp_image = ones([position(4), position(3), 3])-.5;
+    i=(1:double(position(3)))/double(position(3));
+    for j=1:position(4)
+        temp_image(j,:,1) = i;
+    end
+    img_object = image(temp_image, 'Parent', handles.ImageAxes); %#ok<NASGU>
+    axis image
+    set(handles.ImageAxes, 'Visible', 'off');
+    fontsize=0.05;
+    text('Parent', handles.ImageAxes,...
+        'FontName', 'Times',...
+        'FontUnits', 'normalized',...
+        'FontSize', fontsize,...
+        'HorizontalAlignment', 'center',...
+        'VerticalAlignment', 'middle',...
+        'Position', [position(3)/2, position(4)/2],...
+        'String', desc);
+   
+catch ME
+    error_show(ME)
+end
+end

Camera_stage_review.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;
@@ -198,22 +198,21 @@ 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
         case 'MicroRT'
             if myData.yesno_micro==1
                 % Open communications to camera and begin preview
-                handles.cam=camera_open();
+                handles.cam=camera_open(settings.cam_kind,settings.cam_format);
                 handles.cam_figure = ...
                     camera_preview(handles.cam, settings);
                 % To close:
                 % delete handles.cam
                 % close(cam_figure)
 
                 % Open communications to stage
-                handles.myData.stage = stage_open(handles.myData.stage.label);
+                    handles.myData.stage = stage_open(handles.myData.stage.label);
                 % To close:
                 % delete(handles.stage)
                 % If communications with the stage cannot be established,
@@ -780,7 +779,7 @@ function Fast_Register_Button_Callback(hObject, eventdata, handles) %#ok<DEFNU>
     [roi_h, roi_w] = size(roi_image);
 
     % Get the stage position
-    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
@@ -809,7 +808,6 @@ 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;
-    
     handles.myData.stage = stage_move(handles.myData.stage,stage_new, handles.myData.stage.handle);
 catch ME
     error_show(ME)
@@ -1074,12 +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
-    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;
     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_get_pos(handles.myData.stage,handles.myData.stage.handle); 
     stage_current = int64(handles.myData.stage.Pos);
     cam_image = camera_take_image(handles.cam);
 
@@ -1133,7 +1131,6 @@ 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;
-    
     handles.myData.stage = stage_move(handles.myData.stage,stage_new, handles.myData.stage.handle);
 catch ME
     error_show(ME)

GUI.m

@@ -182,6 +182,14 @@ function Load_Input_File(handles)
     end
     tline = fgets(fid);
     [setting_name, setting_value]=strread(tline, '%s %s', 'delimiter', '=');
+    name = 'cam_kind';
+    if strcmp(strtrim(setting_name),name)==1
+        settings.cam_kind=char(setting_value);
+    else
+        io_error(name);
+    end
+    tline = fgets(fid);
+    [setting_name, setting_value]=strread(tline, '%s %s', 'delimiter', '=');
     name = 'cam_format';
     if strcmp(strtrim(setting_name),name)==1
         settings.cam_format=char(setting_value);

Load_Input_File.m

@@ -3,7 +3,7 @@
 
     success = 0;
 
-    for i=1:1:12
+    for i=1:1:20
         Ports{i}=strcat('COM',num2str(i));
     end
 

SerialPortSetUp.m

@@ -39,15 +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_format);
+        handles.cam = camera_open(settings.cam_kind,settings.cam_format);
         handles.cam_figure = camera_preview(handles.cam, settings);
-        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
@@ -664,7 +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')
-        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);
@@ -704,8 +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')
-        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);
@@ -743,8 +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')
-        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);

Stage_Allighment.m

@@ -1,5 +1,5 @@
 
-function cam=camera_open(cam_format)
+function cam=camera_open(cam_kind,cam_format)
 try
 
     % imaqtool: launches an interactive GUI to allow you to explore,
@@ -25,12 +25,16 @@
     % delete any currently running (stale) video inputs
     objects = imaqfind;
     delete(objects);
-    
+    if strcmp( cam_kind,'USB')
+       cam_adaptor = 'pointgrey';
+    elseif strcmp( cam_kind,'Firewire')
+       cam_adaptor = 'dcam';
+    end
     % Create the video object to communicate with the camera 
     if exist('cam_format','var')
-        cam = videoinput('dcam',1,cam_format) %#ok<NOPRT>
+        cam = videoinput(cam_adaptor,1,cam_format) %#ok<NOPRT>
     else
-        cam = videoinput('dcam',1) %#ok<NOPRT>
+        cam = videoinput(cam_adaptor,1) %#ok<NOPRT>
     end
     imaqhwinfo(cam)
     cam.Tag = 'Microscope Camera Object';
@@ -57,7 +61,9 @@
     % Set value of a video source object property.
     cam_src = getselectedsource(cam);
     cam_src.Tag = 'Microscope Camera Source';
-
+    if strcmp( cam_kind,'USB')
+       cam_src.WhiteBalanceRBMode = 'Off';
+    end
 catch ME
     error_show(ME)
 end