Tissue imager

src/+mic/+camera/@IMGSourceCamera/IMGSourceCamera.m

@@ -273,6 +273,7 @@
         TriggerMode;        %   trigger mode for Hamamatsu sCMOS camera
         DefectCorrection;   %   defect correction  for Hamamatsu sCMOS camera
         GuiDialog;
+        AquisitionType = 'capture';
     end
 
     methods
@@ -585,6 +586,10 @@ function setCamProperties(obj,Infield)
                 obj.ReadyForAcq=0;
                 obj.SequenceLength=in;
         end
+
+        function fireTrigger(obj)
+            trigger(obj.CameraHandle);
+        end
 
     end
 

src/+mic/+camera/@IMGSourceCamera/getcamera.m

@@ -1,5 +1,8 @@
 function getcamera(obj)
 H=imaqhwinfo;
+if isempty(H.InstalledAdaptors)
+    error('No image acquisition adaptors found. Please install hardware support packages.');
+end
 ADname=H.InstalledAdaptors{1};
 info=imaqhwinfo(ADname);
 

src/+mic/+camera/@abstract/abstract.m

@@ -319,7 +319,7 @@ function delete(obj)
             end
 
             %scaling
-            mx=double(max(max(im)));
+            mx=double(max(max(im)))+1;
             mn=double(min(min(im)));
             if obj.AutoScale
                 %im = single(im-mn)/(mx-mn);

src/+mic/@KuriosFilter/KuriosFilter.m

@@ -0,0 +1,183 @@
+classdef KuriosFilter < mic.abstract
+
+    properties (SetAccess=protected)
+        InstrumentName = 'KuriosFilter';
+        Serial;
+        FilterType;
+        BWModes;
+    end
+
+    properties
+        Wavelength;
+        BandwidthMode;
+        OutputMode;
+        MaxWavelength;
+        MinWavelength;
+        StartGUI;
+    end
+
+    methods
+
+        function obj = KuriosFilter(SerialPort)
+            s = serialportfind(Tag=SerialPort);
+            if isempty(s)
+                s = serialport(SerialPort,115200,Tag=SerialPort);
+            else
+                delete(s);
+                s = serialport(SerialPort,115200,Tag=SerialPort);
+            end
+
+            configureTerminator(s,"CR")
+            obj.Serial=s;
+
+            obj.send("*IDN?")
+            response = readline(s);
+            disp("Opening: " + response);
+
+            obj.send("ST?")
+            eval(readline(s)+';')
+            disp("Initializing...")
+            while ST == 0
+                obj.send("ST?")
+                pause(1)
+                eval(readline(s)+';');
+            end
+            disp("Warm up to 40 degree.")
+            while ST == 1
+                obj.send("ST?")
+                pause(1)
+                eval(readline(s)+';')
+            end
+            if ST == 2
+                disp("Ready")
+            end
+
+
+            obj.send("OH?")
+
+            response = readline(s);
+            eval(response+';');
+            OH_bit = bitget(OH,16:-1:1,'int16');
+            if OH_bit(8)==1
+                obj.FilterType = 'Visible';
+            elseif OH_bit(7)==1
+                obj.FilterType = 'NIR';
+            end
+
+            BWModes = {};
+            if OH_bit(16) == 1
+                BWModes = [BWModes,'BLACK'];
+            end
+            if OH_bit(15) == 1
+                BWModes = cat(BWModes,'WIDE');
+            end
+            if OH_bit(14) == 1
+                BWModes = cat(BWModes,'MEDIUM');
+            end
+            if OH_bit(13) == 1
+                BWModes = [BWModes,'NARROW'];
+            end
+            obj.BWModes = BWModes;
+
+            %set output mode to manual
+            obj.send("OM=1")
+            obj.OutputMode = "Manual";
+
+            %set Bandwidth mode to narrow
+            obj.send("BW=8")
+            obj.BandwidthMode = "NARROW";
+
+            %get wavelength range
+            obj.send("SP?")
+            %pause(1)
+            eval(readline(s)+';');
+            %pause(2)
+            eval(readline(s)+';');
+            obj.MaxWavelength=WLmax;
+            obj.MinWavelength=WLmin;
+
+            %get current wavelength
+            obj.send("WL?")
+            %pause(0.1)
+            eval(readline(s)+';')
+            obj.Wavelength = WL;
+
+        end
+
+
+        function send(obj,Message)
+            flush(obj.Serial)
+            writeline(obj.Serial,Message)
+            pause(0.1)
+        end
+
+        function setWavelength(obj,Wavelength)
+            Wavelength = round(Wavelength);
+            if Wavelength<obj.MinWavelength
+                warning("Wavelength is too small, set to %d nm", obj.MinWavelength)
+                Wavelength = obj.MinWavelength;
+            end
+
+            if Wavelength>obj.MaxWavelength
+                warning("Wavelength is too large, set to %d nm", obj.MaxWavelength)
+                Wavelength = obj.MaxWavelength;
+            end
+
+            obj.send("WL="+num2str(Wavelength))
+            obj.Wavelength = Wavelength;
+        end
+
+        function setBWmode(obj,BWmode)
+            if ~ismember(BWmode,obj.BWModes)
+                error('mic.KuriosFilter: setBWmode: available bandwidth modes are %s',strjoin(obj.BWModes,','))
+            end
+             switch BWmode
+                 case "BLACK"
+                     obj.send("BW=1")
+                 case "WIDE"
+                     obj.send("BW=2")
+                 case "MEDIUM"
+                     obj.send("BW=4")
+                 case "NARROW"
+                     obj.send("BW=8")
+             end
+             obj.BandwidthMode = BWmode;
+        end
+
+        function delete(obj)
+            flush(obj.Serial)
+            delete(obj.Serial)
+        end
+
+        function  [Attributes,Data,Children]=exportState(obj)
+            % Export the object current state
+            Attributes.Wavelength=obj.Wavelength;
+            Attributes.BandwidthMode=obj.BandwidthMode;
+            % no Data is saved in this class
+            Data=[];
+            Children=[];
+        end
+    end
+
+        methods (Static=true)
+        function funcTest(SerialPort)
+            % Unit test of object functionality
+
+            if nargin<1
+                error('mic.KuriosFilter::SerialPort must be defined')
+            end
+
+            %Creating an Object and Testing setPower, on, off
+            fprintf('Creating Object\n')
+            TF=mic.KuriosFilter(SerialPort);
+            fprintf('Set to minimum wavelength\n')
+            TF.setWavelength(TF.MinWavelength);
+            fprintf('Delete Object\n')
+            %Test Destructor
+            delete(TF);
+            clear TF;
+
+        end
+    end
+
+end

src/+mic/@KuriosFilter/gui.m

@@ -0,0 +1,100 @@
+function guiFig = gui(obj)
+%gui Graphical User Interface foe attenuator
+
+%Prevent opening more than one figure for same instrument
+if ishandle(obj.GuiFigure)
+    guiFig = obj.GuiFigure;
+    figure(obj.GuiFigure);
+    return
+end
+
+
+%Open figure
+guiFig = figure('NumberTitle','off','Resize','off','Units','pixels','MenuBar','none',...
+    'ToolBar','none','Visible','on', 'Position',[100 200 450 190]);
+
+%Construct the components
+handles.output = guiFig;
+guidata(guiFig,handles);
+
+minWavelength=obj.MinWavelength;
+maxWavelength=obj.MaxWavelength;
+Nstep = maxWavelength-minWavelength-1;
+
+handles.sliderWavelength=uicontrol('Parent',guiFig,'Style','slider','units','pixels','Min',minWavelength,...
+    'Max',maxWavelength,'Value',minWavelength,'SliderStep',[1/Nstep 1/Nstep],...
+    'Position', [118 44 200 35],'Callback',@sliderfn);
+handles.textminWavelength = uicontrol('Style','text','String','Min',...
+    'Position',[35 60,80,20],'FontSize',10);
+handles.valueminWavelength = uicontrol('Style','text','String',[num2str(minWavelength),' ','nm'],...
+    'Position',[48 40,70,20]);
+handles.textmaxWavelength = uicontrol('Style','text','String','Max',...
+    'Position',[325 60,80,20],'FontSize',10);
+handles.valuemaxWavelength = uicontrol('Style','text','String',[num2str(maxWavelength),' ','nm'],...
+   'Position',[337 40,70,20]);
+handles.textSetWavelength = uicontrol('Style','text','String','Set Wavelength',...
+    'Position',[50 100,150,20],'FontSize',10);
+handles.SetWavelength = uicontrol('Style','edit','String',num2str(minWavelength),...
+    'Position',[190 97,80,25],'FontSize',10,'Callback',@setWavelength);
+handles.textWavelengthUnit=uicontrol('Style','text','String','nm',...
+    'Position',[270 100,50,20],'FontSize',10);
+
+handles.textSetBWmode = uicontrol('Style','text','String','Set Bandwidth Mode',...
+    'Position',[50 130,150,20],'FontSize',10);
+handles.SetBWMode = uicontrol('Style','popupmenu','String',obj.BWModes,...
+    'Position',[190 127,120,25],'FontSize',10,'Callback',@setBWmode);
+
+
+% Create a property based on GuiFigure
+obj.GuiFigure = guiFig;
+obj.GuiFigure.Name = obj.InstrumentName;
+
+%Prevent closing after a 'close' or 'close all'
+obj.GuiFigure.HandleVisibility='off';
+
+%Save Propeties upon close
+obj.GuiFigure.CloseRequestFcn = @closeFigure;
+
+%Initialize GUI properties
+properties2gui();
+
+    function closeFigure(~,~)
+        gui2properties();
+        delete(obj.GuiFigure);
+    end
+
+    function sliderfn(h,~)
+        sliderValue=round(get(h,'Value'));
+        set(handles.SetWavelength,'String',num2str(sliderValue))
+        obj.setWavelength(sliderValue)
+        %gui2properties();
+    end
+
+    function setWavelength(h,~)
+        textValue=str2double(get(h,'String'));
+        set(handles.sliderWavelength,'Value',textValue)
+        obj.setWavelength(textValue)
+        %gui2properties()
+    end
+
+    function setBWmode(h,~)
+        idx = get(h,'value');
+        obj.setBWmode(obj.BWModes{idx})
+    end
+
+%%  All figure have these functions but will be different contents
+
+    function gui2properties()
+        %obj.Wavelength=str2double(get(handles.SetWavelength,'String'));
+    end
+
+    function properties2gui()
+        if isempty(obj.Wavelength) || isnan(obj.Wavelength)
+            obj.Wavelength=obj.MinWavelength;
+        end
+        idx = find(strcmp(obj.BWModes, obj.BandwidthMode));
+        set(handles.SetBWMode,'value',idx)
+        set(handles.sliderWavelength,'Value',obj.Wavelength)
+        set(handles.SetWavelength,'String',num2str(obj.Wavelength));
+    end
+end