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src/Flowcytometer_matlab _code/flowcytometergui.m

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+function varargout = flowcytometergui(varargin)
+% FLOWCYTOMETERGUI MATLAB code for flowcytometergui.fig
+%      FLOWCYTOMETERGUI, by itself, creates a new FLOWCYTOMETERGUI or raises the existing
+%      singleton*.
+%
+%      H = FLOWCYTOMETERGUI returns the handle to a new FLOWCYTOMETERGUI or the handle to
+%      the existing singleton*.
+%
+%      FLOWCYTOMETERGUI('CALLBACK',hObject,eventData,handles,...) calls the local
+%      function named CALLBACK in FLOWCYTOMETERGUI.M with the given input arguments.
+%
+%      FLOWCYTOMETERGUI('Property','Value',...) creates a new FLOWCYTOMETERGUI or raises the
+%      existing singleton*.  Starting from the left, property value pairs are
+%      applied to the GUI before flowcytometergui_OpeningFcn gets called.  An
+%      unrecognized property name or invalid value makes property application
+%      stop.  All inputs are passed to flowcytometergui_OpeningFcn via varargin.
+%
+%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
+%      instance to run (singleton)".
+%
+% See also: GUIDE, GUIDATA, GUIHANDLES
+
+% Edit the above text to modify the response to help flowcytometergui
+
+% Last Modified by GUIDE v2.5 09-Jul-2018 11:27:06
+
+% Begin initialization code - DO NOT EDIT
+gui_Singleton = 1;
+gui_State = struct('gui_Name',       mfilename, ...
+                   'gui_Singleton',  gui_Singleton, ...
+                   'gui_OpeningFcn', @flowcytometergui_OpeningFcn, ...
+                   'gui_OutputFcn',  @flowcytometergui_OutputFcn, ...
+                   'gui_LayoutFcn',  [] , ...
+                   'gui_Callback',   []);
+if nargin && ischar(varargin{1})
+    gui_State.gui_Callback = str2func(varargin{1});
+end
+
+if nargout
+    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
+else
+    gui_mainfcn(gui_State, varargin{:});
+end
+% End initialization code - DO NOT EDIT
+
+
+% --- Executes just before flowcytometergui is made visible.
+function flowcytometergui_OpeningFcn(hObject, eventdata, handles, varargin)
+% This function has no output args, see OutputFcn.
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+% varargin   command line arguments to flowcytometergui (see VARARGIN)
+
+% Choose default command line output for flowcytometergui
+handles.output = hObject;
+s = serial('COM12');
+set(s,'BaudRate',57600);   set(s,'Terminator','#');    
+set(s,'Timeout',30);  %  s.RecordName = 'CytoSerialTxnLog.txt';    
+fopen(s);  % record(s);
+handles.s = s;
+
+msg=strcat(datestr(clock,'yyyy-mm-dd-HHMM'),'m',datestr(clock,'ss'),'s'); 
+fid = fopen(strcat(msg,'.txt'),'w');
+handles.fid = fid;
+if (fid == -1)
+    disp('could not open logging file. You probably need to change working directory to the one where the MATLAB file is located.');
+    return;
+end
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%       Start cam
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+tic
+fprintf(fid, '\r\nStarting camera...');
+% choose which webcam (winvideo-1) and which  mode (YUY2_176x144)
+%vid = videoinput('winvideo', 1, 'RGB32_744x480');
+vid = videoinput('winvideo', 2, 'RGB24_640x480');
+% Configure the object for manual trigger mode.
+triggerconfig(vid, 'manual');
+% only capture one frame per trigger, we are not recording a video
+vid.FramesPerTrigger = 1;
+% output would image in RGB color space
+vid.ReturnedColorspace = 'rgb';
+% tell matlab to start the webcam on user request, not automatically
+triggerconfig(vid, 'manual');
+% we need this to know the image height and width
+vidRes = get(vid, 'VideoResolution');
+% image width
+imWidth = vidRes(1);
+% image height
+imHeight = vidRes(2);
+% number of bands of our image (should be 3 because it's RGB)
+nBands = get(vid, 'NumberOfBands');
+% create an empty image container and show it on axPreview
+hImage = image(zeros(imHeight, imWidth, nBands), 'parent', handles.axPreview);
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% do auto white balance
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+src = getselectedsource(vid);
+% src.BalanceWhiteAuto = 'Continuous';
+% begin the webcam preview
+currzpos = 0;
+preview(vid, hImage);
+% expose the objects so we can handle them in other functions
+handles.vid = vid;
+handles.src = src;
+handles.currz = currzpos;
+guidata(hObject,handles);
+%start(vid);
+drawnow;     
+
+% % set and display the exposure
+% src.ExposureTime  = 360;
+%set(handles.expDisp,'string', src.ExposureTime );
+Time_to_init_cam = toc
+
+% Update handles structure
+guidata(hObject, handles);
+
+% UIWAIT makes flowcytometergui wait for user response (see UIRESUME)
+% uiwait(handles.figure1)
+
+% --- Outputs from this function are returned to the command line.
+function varargout = flowcytometergui_OutputFcn(hObject, eventdata, handles) 
+% varargout  cell array for returning output args (see VARARGOUT);
+% hObject    handle to figure
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Get default command line output from handles structure
+varargout{1} = handles.output;
+
+
+% --- Executes on button press in autofocus.
+function autofocus_Callback(hObject, eventdata, handles)
+% hObject    handle to autofocus (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+s = handles.s; vid = handles.vid; currzpos = handles.currz;
+[~, ~, ~] = focusstack_1(s,vid,currzpos);pause(2)
+
+
+
+
+% --- Executes on button press in moveleft.
+function moveleft_Callback(hObject, eventdata, handles)
+% hObject    handle to moveleft (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+s = handles.s; fprintf(s,'A')
+
+
+% --- Executes on button press in moveright.
+function moveright_Callback(hObject, eventdata, handles)
+% hObject    handle to moveright (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+s = handles.s; fprintf(s,'D')
+
+
+% --- Executes on button press in snapshot.
+function snapshot_Callback(hObject, eventdata, handles)
+% hObject    handle to snapshot (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+vid = handles.vid; 
+snapshot = getsnapshot(vid);
+imwrite(snapshot,'snap.jpg')
+
+function figure1_DeleteFcn(hObject, eventdata, handles)
+% hObject    handle to figure1 (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+if ~isempty(instrfind)
+    fclose(instrfind);
+    delete(instrfind);
+end
+
+try
+    fid=handles.fid;    fclose(fid); 
+    vid = handles.vid;  stoppreview(vid);   delete(vid);
+catch
+    clear all;
+    clc;
+end
+
+%s=handles.s;   fclose(s);  delete(s);
+disp('Killed all before exiting');
+
+
+% --- Executes on button press in startvid.
+function startvid_Callback(hObject, eventdata, handles)
+% hObject    handle to startvid (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+vid = handles.vid;
+vid_trigger = 1; handles.vid_trigger = vid_trigger;
+for x=1:1000
+    snap = getsnapshot(vid)
+    imwrite(strcat('Image_',num2str(x),'.jpg'),snap)
+end
+% aviObject = VideoWriter('newfile.avi','Motion JPEG AVI'); handles.aviObject = aviObject;
+% open(aviObject);
+% while(vid_trigger == 1)
+%     snap = getsnapshot(vid);
+%     writeVideo(aviObject,snap);
+% end
+
+% --- Executes on button press in stopvid.
+function stopvid_Callback(hObject, eventdata, handles)
+% hObject    handle to stopvid (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+aviObject = handles.aviObject;
+handles.vid_trigger = 0;
+close(aviObject);

src/Flowcytometer_matlab _code/focusplane_4.m

@@ -0,0 +1,263 @@
+clear;clc;
+disp('Scan Inializing........')
+tic;
+t1 = toc;
+s = serial('COM3');
+set(s,'BaudRate',57600);   set(s,'Terminator','#');    
+set(s,'Timeout',30);    %s.RecordName = 'CytoSerialTxnLog.txt';    
+fopen(s);  %recweblistord(s);
+msg=strcat(datestr(clock,'yyyy-mm-dd-HHMM'),'m',datestr(clock,'ss'),'s'); 
+fid = fopen(strcat(msg,'.txt'),'w');
+if (fid == -1)
+    disp('could not open logging file. You probably need to change working directory to the one where the MATLAB file is located.');
+    return;
+end
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%       Start cam
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+tic
+disp('\r\nStarting camera...')
+fprintf(fid, '\r\nStarting camera...');
+% choose which webcam (winvideo-1) and which  mode (YUY2_176x144)
+%vid = videoinput('winvideo', 1, 'RGB32_744x480');
+vid = videoinput('gentl', 1, 'BGRA8Packed');
+% Configure the object for manual trigger mode.
+triggerconfig(vid, 'manual');
+% only capture one frame per trigger, we are not recording a video
+vid.FramesPerTrigger = 1;
+% output would image in RGB color space
+vid.ReturnedColorspace = 'rgb';
+% tell matlab to start the webcam on user request, not automatically
+triggerconfig(vid, 'manual');
+% we need this to know the image height and width
+vidRes = get(vid, 'VideoResolution');
+% image width
+imWidth = vidRes(1);
+% image height
+imHeight = vidRes(2);
+% number of bands of our image (should be 3 because it's RGB)
+nBands = get(vid, 'NumberOfBands');
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% do auto white balance
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+src = getselectedsource(vid);
+src.BalanceWhiteAuto = 'Continuous'; 
+
+src.ExposureTime  = 800;
+start(vid);
+Time_to_init_cam = toc
+
+% this is the slide name 
+setslidename = 'Slide';
+
+
+fprintf(s,'J');currxpos = 0;
+fprintf(s,'K');currypos = 0;
+fprintf(s,'L');currzpos = 0;
+pause(0.1);
+disp('Origin is set');
+
+xFoV = round(1280*5.3/(34*0.159));yFoV = round(1024*5.3/(34*0.159));
+xFoV_mm = 0.1995;yFoV_mm = 0.1596;
+
+XPulseRate = 38400;     YPulseRate = 38400 ; 
+Xzadjustdelay = 0.002;
+autoContrTime = 0.1;
+XImDelay = (xFoV / XPulseRate) ;
+YImDelay = (yFoV / YPulseRate) ;
+%at y = 12.5mm line
+Ypos = strcat('+',sprintf('%06d',abs(41359)));
+fprintf(s,'N'); fprintf(s,Ypos);pause(41359/YPulseRate);currypos=41359;
+param_y0 =[];Zval=[];
+xpos1 = 0; xpos2 = 200000;
+[currzpos, temp_var] = focusstack_1(s,vid,currzpos);pause(2)
+tf1 = toc;
+for xpos = xpos1:17986:xpos2
+    Xpos = strcat('+',sprintf('%06d',abs(xpos )));
+    fprintf(s,'B'); fprintf(s,Xpos);pause(17986/XPulseRate)
+    [currzpos, temp_var] = focusstack_2(s,vid,currzpos);
+    Zval = [Zval currzpos]; 
+    snapshot=getsnapshot(vid);
+    disp('saving best focussed snapshot..')
+    imwrite(snapshot,strcat('images/finding_best_region/t7/t7_x_',Xpos,'_',sprintf('%06d',abs(currzpos)),'.bmp'));
+    param_y0 = [param_y0 parameter(snapshot)];    currxpos = xpos;
+end
+disp(toc-tf1)
+xpos = xpos1:17986:xpos2;
+[max_param_y0, Index] = max(param_y0);
+xbest1 = abs(xpos(Index));
+Xbest1 = strcat('+',sprintf('%06d',xbest1));
+fprintf(s,'B'); fprintf(s,Xpos);pause(abs(currxpos-xbest1)/XPulseRate)
+Zfoc1 = Zval(Index);gotoZ(s,Zfoc1,currzpos);currzpos=Zfoc1;param_y1 = []; Zval=[];
+tf2 =toc;
+if(xbest1 <= 17986)
+    for xpos = (xbest1):7194:(xbest1+17986*2)
+        Xpos = strcat('+',sprintf('%06d',abs(xpos )));
+        fprintf(s,'B'); fprintf(s,Xpos);pause(17986/XPulseRate)
+        [currzpos, temp_var] = focusstack_2(s,vid,currzpos);
+        Zval = [Zval currzpos]; 
+        snapshot=getsnapshot(vid);
+        disp('saving best focussed snapshot..')
+        imwrite(snapshot,strcat('images/finding_best_region/t7/t7_x_',Xpos,'_',sprintf('%06d',abs(currzpos)),'.bmp'));
+        param_y1 = [param_y1 parameter(snapshot)];    currxpos = xpos;
+    end
+elseif(xbest1>=200000)
+    for xpos = (xbest1-17986*2):7194:(xbest1)
+        Xpos = strcat('+',sprintf('%06d',abs(xpos )));
+        fprintf(s,'B'); fprintf(s,Xpos);pause(17986/XPulseRate)
+        [currzpos, temp_var] = focusstack_2(s,vid,currzpos);
+        Zval = [Zval currzpos]; 
+        snapshot=getsnapshot(vid);
+        disp('saving best focussed snapshot..')
+        imwrite(snapshot,strcat('images/finding_best_region/t7/t7_x_',Xpos,'_',sprintf('%06d',abs(currzpos)),'.bmp'));
+        param_y1 = [param_y1 parameter(snapshot)];    currxpos = xpos;
+    end
+else
+    for xpos = (xbest1-17986):7194:(xbest1+17986)
+        Xpos = strcat('+',sprintf('%06d',abs(xpos )));
+        fprintf(s,'B'); fprintf(s,Xpos);pause(17986/XPulseRate)
+        [currzpos, temp_var] = focusstack_2(s,vid,currzpos);
+        Zval = [Zval currzpos]; 
+        snapshot=getsnapshot(vid);
+        disp('saving best focussed snapshot..')
+        imwrite(snapshot,strcat('images/finding_best_region/t7/t7_x_',Xpos,'_',sprintf('%06d',abs(currzpos)),'.bmp'));
+        param_y1 = [param_y1 parameter(snapshot)];    currxpos = xpos;
+    end
+end
+disp(toc-tf2)
+xpos = (xbest1-17896):7194:(xbest1+17896);
+param_y1 = (param_y1>0.0999);disp(param_y1)
+target1 = sum(param_y1(1:3)); target2 = sum(param_y1(3:5));
+fprintf(s,'N'); fprintf(s,'0000000');pause(abs(41359)/YPulseRate);
+tf3=toc;
+if((sum(param_y1(2:4))==3))
+    xbest2 = xpos(2);xbest1 = xpos(4);
+    Xbest2 = strcat('+',sprintf('%06d',xbest2));
+    Xbest1 = strcat('+',sprintf('%06d',xbest1));
+    fprintf(s,'B'); fprintf(s,Xbest1);pause((abs(currxpos-xbest1))/XPulseRate);gotoZ(s,Zval(4),currzpos);currzpos=Zval(4);fprintf(s,'R');
+    fprintf(s,'B'); fprintf(s,Xbest2);pause((abs(17986))/XPulseRate);gotoZ(s,Zval(2),currzpos);currzpos=Zval(2);fprintf(s,'E');currxpos = xbest2;
+    fprintf(s,'N'); fprintf(s,'0078719');pause(abs(78719)/YPulseRate);currypos = 78719;
+    [currzpos, temp_var] = focusstack_2(s,vid,currzpos);fprintf(s,'Y');
+    fprintf(s,'Z');
+    xA = xbest2; xB = xbest1;
+    yC = 78719; yB =0;
+    numofX = (xB - xA) / xFoV;       
+    numofY = (yC - yB) / yFoV;
+    while fscanf(s) ~= 'S'
+    end;
+    % NOW TAKING PICTURES
+    rowcount = 0;
+    filecount = 0;
+    
+    msg = '\r\n Starting image capture ...';
+    fprintf(fid, msg);
+    
+    % Dircn = false; %We believe we start from top
+    while(rowcount <= numofY)
+        while(filecount <= numofX)
+            %pause(XImDelay*2);
+            snapshot=getsnapshot(vid);
+            %enh_snapshot=autocontrast(snapshot);
+            filename = strcat(setslidename,'_',num2str(rowcount),'-',num2str(filecount), '.bmp');
+            %imwrite(enh_snapshot,filename);
+            imwrite(snapshot,strcat('images/',filename));
+            filecount = filecount + 1;
+        end
+        % wait for shift by one FoV in Y direction
+        filecount = 0;
+        %pause(YImDelay*2);
+        rowcount = rowcount + 1;
+    end
+elseif(target1>target2)
+    xbest2 = xpos(1);xbest1 = xpos(3);
+    Xbest2 = strcat('+',sprintf('%06d',xbest2));
+    Xbest1 = strcat('+',sprintf('%06d',xbest1));
+    fprintf(s,'B'); fprintf(s,Xbest1);pause((abs(currxpos-xbest1))/XPulseRate);gotoZ(s,Zval(3),currzpos);currzpos=Zval(3);fprintf(s,'R');
+    fprintf(s,'B'); fprintf(s,Xbest2);pause((abs(17986))/XPulseRate);gotoZ(s,Zval(1),currzpos);currzpos=Zval(1);fprintf(s,'E');currxpos = xbest2;
+    fprintf(s,'N'); fprintf(s,'0078719');pause(abs(78719)/YPulseRate);currypos = 78719;
+    [currzpos, temp_var] = focusstack_2(s,vid,currzpos);fprintf(s,'Y');
+    fprintf(s,'Z');
+    xA = xbest2; xB = xbest1;
+    yC = 78719; yB =0;
+    numofX = (xB - xA) / xFoV;       
+    numofY = (yC - yB) / yFoV;
+    while fscanf(s) ~= 'S'
+    end;
+    % NOW TAKING PICTURES
+    rowcount = 0;
+    filecount = 0;
+    
+    msg = '\r\n Starting image capture ...';
+    fprintf(fid, msg);
+    
+    % Dircn = false; %We believe we start from top
+    while(rowcount <= numofY)
+        while(filecount <= numofX)
+            %pause(XImDelay*2);
+            snapshot=getsnapshot(vid);
+            %enh_snapshot=autocontrast(snapshot);
+            filename = strcat(setslidename,'_',num2str(rowcount),'-',num2str(filecount), '.bmp');
+            %imwrite(enh_snapshot,filename);
+            imwrite(snapshot,strcat('images/',filename));
+            filecount = filecount + 1;
+        end
+        % wait for shift by one FoV in Y direction
+        filecount = 0;
+        %pause(YImDelay*2);
+        rowcount = rowcount + 1;
+    end
+elseif(target1<target2)
+    xbest2 = xpos(5);xbest1 = xpos(3);
+    Xbest2 = strcat('+',sprintf('%06d',xbest2));
+    Xbest1 = strcat('+',sprintf('%06d',xbest1));
+    fprintf(s,'B'); fprintf(s,Xbest1);pause((abs(currxpos-xbest1))/XPulseRate);gotoZ(s,Zval(3),currzpos);currzpos=Zval(3);fprintf(s,'E');
+    fprintf(s,'B'); fprintf(s,Xbest2);pause((abs(17986))/XPulseRate);gotoZ(s,Zval(5),currzpos);currzpos=Zval(5);fprintf(s,'R');currxpos = xbest2;
+    fprintf(s,'N'); fprintf(s,'0078719');pause(abs(78719)/YPulseRate);currypos = 78719;
+    [currzpos, temp_var] = focusstack_2(s,vid,currzpos);fprintf(s,'Y');
+    fprintf(s,'Z');
+    xA = xbest1; xB = xbest2;
+    yC = 78719; yB =0;
+    numofX = (xB - xA) / xFoV;       
+    numofY = (yC - yB) / yFoV;
+    while fscanf(s) ~= 'S'
+    end;
+    % NOW TAKING PICTURES
+    rowcount = 0;
+    filecount = 0;
+    
+    msg = '\r\n Starting image capture ...';
+    fprintf(fid, msg);
+    
+    % Dircn = false; %We believe we start from top
+    while(rowcount <= numofY)
+        while(filecount <= numofX)
+            %pause(XImDelay*2);
+            snapshot=getsnapshot(vid);
+            %enh_snapshot=autocontrast(snapshot);
+            filename = strcat(setslidename,'_',num2str(rowcount),'-',num2str(filecount), '.bmp');
+            %imwrite(enh_snapshot,filename);
+            imwrite(snapshot,strcat('images/t7/',filename));
+            filecount = filecount + 1;
+        end
+        % wait for shift by one FoV in Y direction
+        filecount = 0;
+        %pause(YImDelay*2);
+        rowcount = rowcount + 1;
+    end
+else    
+    disp('Slide is not prepared well!!! Please make a good slide..!')
+end
+disp(toc-tf3)
+    
+stop(vid);
+fprintf(s,'N'); fprintf(s,'0000000');
+fprintf(s,'B'); fprintf(s,'0000000');
+fprintf(s,'M'); fprintf(s,'0000000');
+pause(0.1)
+
+if ~isempty(instrfind)
+    fclose(instrfind);
+    delete(instrfind);
+end
+t2 = toc;
+disp((t2-t1)/60)

src/Flowcytometer_matlab _code/focusstack_1.m

@@ -0,0 +1,58 @@
+function [Zval, Variance, currzpos] = focusstack_1(s,vid,z)
+    t1 = toc;currzpos=z;
+    snap = getsnapshot(vid);
+    imwrite(snap,strcat('images/withouthc/snap_at_start','.bmp'))
+    %fprintf(s,'L');
+    %       CRUDE AF. 
+    Z_travel_for_crude = 16000;  crude_step_count = 200;
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    crude_pulse_count = Z_travel_for_crude / crude_step_count;
+    crude_max_var=0;    crude_loc_max_var=0;
+    crude_start_loc = z-(Z_travel_for_crude/2);
+%    gotoZ(s,crude_start_loc,currzpos);pause(1) ;
+    fprintf(s,'M');pause(3)
+%     for i=1: crude_pulse_count/2
+%         fprintf(s,'T');pause(0.35)
+%     end
+    currzpos=crude_start_loc;
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    % now keep going up and taking var
+    crude_curr_loc = crude_start_loc;
+    Variance = []; Zval = [];
+    for i=1: crude_pulse_count     
+        % variance
+        snap = getsnapshot(vid);
+        imwrite(snap,strcat('images/snap_at_',num2str(crude_curr_loc),'.bmp'))
+        crude_img = double(snap);     crude_curr_var=var(crude_img(:));
+        %display(strcat('Variance',num2str(crude_curr_var),'Iter:',num2str(i)))
+        %pause(0.5)
+        Variance = [Variance crude_curr_var];
+        Zval = [Zval crude_curr_loc];
+        if (crude_curr_var > crude_max_var) 
+            crude_max_var = crude_curr_var;
+            crude_loc_max_var = crude_curr_loc;
+        end 
+        % update loc 
+        crude_curr_loc = crude_curr_loc + crude_step_count      ;
+        fprintf(s,'G');pause(0.1) 
+        %gotoZ(s,crude_curr_loc,currzpos); 
+        currzpos=crude_curr_loc;
+    end
+    disp(currzpos)
+    disp(crude_loc_max_var)
+    crude_pulse_count = round(abs(crude_loc_max_var - currzpos)/200);
+    for i=1: crude_pulse_count
+        if(currzpos>crude_loc_max_var)
+            fprintf(s,'T');pause(0.1)  
+            currzpos = currzpos - 200;
+        elseif(currzpos<crude_loc_max_var)
+            fprintf(s,'G');pause(0.1)  
+            currzpos = currzpos + 200;
+        end
+    end
+    pause(1)
+    snap = getsnapshot(vid);
+    imwrite(snap,strcat('images/withouthc/snap_at_end_crude','.bmp'))
+    t2 = toc;
+    disp(t2-t1)
+end

src/Flowcytometer_matlab _code/focusstack_2.m

@@ -0,0 +1,88 @@
+function [Zval, Variance] = focusstack_2(s,vid,z)
+    t1 = toc;currzpos=z;
+    %       fINECRUDE AF. 
+    Z_travel_for_crude = 6000;  crude_step_count = 200;
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    crude_pulse_count = Z_travel_for_crude / crude_step_count;
+    crude_max_var=0;   
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    %        go to starting Z loc (we've hit limit switch via arduino already so its z=0)
+    crude_start_loc = z- (Z_travel_for_crude/2);
+    gotoZ(s,crude_start_loc,currzpos); currzpos=crude_start_loc;
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    % now keep going up and taking var
+    crude_curr_loc = crude_start_loc;
+
+    for i=1: crude_pulse_count     
+        % variance
+        crude_img = double(getsnapshot(vid));     crude_curr_var=var(crude_img(:));
+
+        if (crude_curr_var > crude_max_var) 
+            crude_max_var = crude_curr_var;
+            crude_loc_max_var = crude_curr_loc;
+        end 
+        % update loc 
+        crude_curr_loc = crude_curr_loc + crude_step_count      ;
+        gotoZ(s,crude_curr_loc,currzpos); currzpos=crude_curr_loc;
+    end
+    gotoZ(s,crude_loc_max_var,currzpos);currzpos=crude_loc_max_var;
+    
+    %       fINECRUDE AF. 
+    Z_travel_for_crude = 500;  crude_step_count = 50;
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    crude_pulse_count = Z_travel_for_crude / crude_step_count;
+    crude_max_var=0;   
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    %        go to starting Z loc (we've hit limit switch via arduino already so its z=0)
+    crude_start_loc = currzpos- (Z_travel_for_crude/2);
+    gotoZ(s,crude_start_loc,currzpos);currzpos=crude_start_loc;
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    % now keep going up and taking var
+    crude_curr_loc = crude_start_loc;
+
+    for i=1: crude_pulse_count     
+        % variance
+        crude_img = double(getsnapshot(vid));     crude_curr_var=var(crude_img(:));
+
+        if (crude_curr_var > crude_max_var) 
+            crude_max_var = crude_curr_var;
+            crude_loc_max_var = crude_curr_loc;
+        end 
+        % update loc 
+        crude_curr_loc = crude_curr_loc + crude_step_count      ;
+        gotoZ(s,crude_curr_loc,currzpos);currzpos=crude_curr_loc;
+    end
+    gotoZ(s,crude_loc_max_var,currzpos);currzpos=crude_loc_max_var;
+    
+    % The fine AF begins here
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    Ztotaltravel = 100;     final_go_backpulses = 0 ;
+    currZ = crude_loc_max_var;
+
+    % first go above
+    start_above_loc = currZ- (Ztotaltravel/2);
+    gotoZ(s,start_above_loc,currzpos);currzpos=start_above_loc;
+    
+    % now build the var array
+    localAF_loc_array = zeros(1,Ztotaltravel);   localAF_var_array = zeros(1,Ztotaltravel);
+    localAF_curr_loc = start_above_loc;
+    for q=1:(Ztotaltravel/5)
+        % location
+        localAF_loc_array(q) = localAF_curr_loc;
+        % variance
+        localAF_img = double(getsnapshot(vid)); localAF_var_array(q)=var(localAF_img(:));
+
+        % move and update loc    
+        localAF_curr_loc = localAF_curr_loc + 5;    gotoZ(s,localAF_curr_loc,currzpos);  
+        currzpos=localAF_curr_loc;
+    end  
+
+    % Finally go to the max var location
+    index_of_max_var =  localAF_var_array == max(localAF_var_array);
+    loc_of_max_var = localAF_loc_array(index_of_max_var) - final_go_backpulses  ;    
+    gotoZ(s,loc_of_max_var,currzpos); currzpos=loc_of_max_var;
+    Zval = loc_of_max_var;
+    Variance = max(localAF_var_array);
+    t2 = toc;
+    disp(t2-t1)
+end

src/Flowcytometer_matlab _code/focusstack_3.m

@@ -0,0 +1,60 @@
+function [Zval, Variance] = focusstack_3(s,vid,z)
+    t1 = toc;currzpos=z;
+    %       fINECRUDE AF. 
+    Z_travel_for_crude = 1000;  crude_step_count = 50;
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    crude_pulse_count = Z_travel_for_crude / crude_step_count;
+    crude_max_var=0;   
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    %        go to starting Z loc (we've hit limit switch via arduino already so its z=0)
+    crude_start_loc = z - (Z_travel_for_crude/2);
+    gotoZ(s,crude_start_loc,currzpos); currzpos=crude_start_loc;
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    % now keep going up and taking var
+    crude_curr_loc = crude_start_loc;
+
+    for i=1: crude_pulse_count     
+        % variance
+        crude_img = double(getsnapshot(vid));     crude_curr_var=var(crude_img(:));
+
+        if (crude_curr_var > crude_max_var) 
+            crude_max_var = crude_curr_var;
+            crude_loc_max_var = crude_curr_loc;
+        end 
+        % update loc 
+        crude_curr_loc = crude_curr_loc + crude_step_count      ;
+        gotoZ(s,crude_curr_loc,currzpos); currzpos=crude_curr_loc;
+    end
+    gotoZ(s,crude_loc_max_var,currzpos);currzpos=crude_loc_max_var;
+    
+    % The fine AF begins here
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    Ztotaltravel = 100;     final_go_backpulses = 0 ;
+    currZ = crude_loc_max_var;
+
+    % first go above
+    start_above_loc = currZ - (Ztotaltravel/2);
+    gotoZ(s,start_above_loc,currzpos);currzpos=start_above_loc;
+    % now build the var array
+    localAF_loc_array = zeros(1,Ztotaltravel);   localAF_var_array = zeros(1,Ztotaltravel);
+    localAF_curr_loc = start_above_loc;
+    for q=1:(Ztotaltravel/5)
+        % location
+        localAF_loc_array(q) = localAF_curr_loc;
+        % variance
+        localAF_img = double(getsnapshot(vid)); localAF_var_array(q)=var(localAF_img(:));
+
+        % move and update loc    
+        localAF_curr_loc = localAF_curr_loc + 5;    gotoZ(s,localAF_curr_loc,currzpos); 
+        currzpos=localAF_curr_loc;
+    end  
+
+    % Finally go to the max var location
+    index_of_max_var =  localAF_var_array == max(localAF_var_array);
+    loc_of_max_var = localAF_loc_array(index_of_max_var) - final_go_backpulses  ;    
+    gotoZ(s,loc_of_max_var,currzpos);currzpos=loc_of_max_var;
+    Zval = loc_of_max_var;
+    Variance = max(localAF_var_array);
+    t2 = toc;
+    disp(t2-t1)
+end

src/Flowcytometer_matlab _code/gotoZ.m

@@ -0,0 +1,14 @@
+function gotoZ(s,check,currzpos)
+    ZPulseRate = 38400;
+    if(check<200000 && check>-200000)
+        str = sprintf('%06d',abs(round(check)));     % abs needed so that no +&- in neg numbers
+        if((check) < 0)                 
+            newstr = strcat('-',str);    
+        else
+            newstr = strcat('+',str);
+        end
+        disp(strcat('moving to position:',newstr))
+        % end formatting ---------- -------------------------------------------- 
+        fprintf(s,'M');        fprintf(s, newstr );  pause(0.035);
+    end  
+end

src/Flowcytometer_matlab _code/parameter.m

@@ -0,0 +1,21 @@
+function param = parameter(image)
+    t1 = toc;
+    bw = rgb2gray(image);
+    [Gx, Gy] = imgradientxy(bw);
+    %[Gmag, Gdir] = imgradient(Gx, Gy);
+    gradImage = rgb2gray(imfuse(Gx,Gy));
+    %temp = histeq(gradImage);
+    threshImage = im2bw(gradImage,graythresh(gradImage));
+    [~, radii] = imfindcircles(threshImage,[10 60]);
+    cell_area = round(sum(3.14*(radii.^2)));
+    bg = rgb2gray(imread('bg.jpg'));
+    a = histeq(bw)-bg;
+    level2 = graythresh(a);
+    bgImg = bwareaopen(im2bw(a,level2),800);
+    bg_pixels = sum(sum(bgImg == 1));
+    fg_pixels = (1280 * 1024) - bg_pixels;
+    fg_pixels = fg_pixels - round(0.1*fg_pixels);
+    param = cell_area/fg_pixels;
+    t2 = toc;
+    disp(t2-t1)
+end

src/current_GUIcode.py

@@ -0,0 +1,744 @@
+ # 1. Name of the test is always Malaria
+ # 2. Close button to be checked as abort button
+ # 3. Exceptions for network connection, camera.
+
+ 
+ 
+ 
+ #Things to be worked on:
+ # 1. On window closed by clicking x at top right corner, the application should terminate
+ 
+ # 2. On abort button Clicked, the C++ API should be killed
+ 
+ # 1. Progressbar speed increased with iterations
+ 
+ # (SOLVED) 5. Setting user defined resolutions for image capture in pylon programs
+  
+ # (SOLVED) 9. Auto focus code for variance calculation
+ 
+ # (SOLVED)2. Stopping/killing threads on abort 
+
+ # (SOLVED)8. Adjust time for sending data through FTP that should be by stopping or killing threads while they are sleeping ....  (Same as 2)
+
+ # (SOLVED)3. Focusing window pulse 	
+ 				 
+ # (SOLVED)4. sending data for analysis in progress bar  
+ 
+ # (SOLVED)6. On abort, stop progress bar. 				
+ 
+ # (SOLVED)7. Run focussing only on start up.. Ask jayesh about it..
+ 
+ # (SOLVED)1.Command line executions in os.system for basler camera acquisition
+global ip1
+global ip2
+global ip3
+global batches
+global numframes
+batches=2
+numframes=5000
+ip1="54.191.132.121"
+ip2="54.191.13.206"
+ip3="52.38.126.238"
+#!/usr/bin/python
+import numpy
+#import cv2
+#from pyfirmata import Arduino, util
+from gi.repository import Gtk, GObject
+import time
+from time import sleep
+import os
+import threading
+import sys
+import thread
+from time import sleep
+global count
+global x
+from threading import Thread
+from locale import gettext as _
+import subprocess
+import ftplib
+from ftplib import FTP
+#import gpio
+import datetime
+#global Thread1
+#global Thread2
+global Acquire
+Acquire = False
+global ExitVLCThread
+ExitVLCThread = False
+global Kill
+Kill=False
+global SendCellDataThread
+SendCellDataThread = False
+import Queue
+global error1
+global error2
+global error3
+global test
+global f
+global filename
+global compress
+global st
+error1=0
+error2=0
+error3=0
+q=Queue.Queue(1)
+
+#Create a directory to acquire images. 
+#os.mkdir('/home/odroid/BloodAnalyser/AcquiredData/PatientInformation')
+if os.path.isdir("/home/odroid/BloodAnalyser/AcquiredData/"):
+	os.system("rm -r /home/odroid/BloodAnalyser/AcquiredData/")
+os.mkdir('/home/odroid/BloodAnalyser/AcquiredData/')
+os.mkdir('/home/odroid/BloodAnalyser/AcquiredData/PatientInformation')
+	
+
+class patientID(Gtk.Window):
+	def __init__(self):
+		self.builder = Gtk.Builder()
+		global name
+		global age
+		#Get objects from patient ID Glade file
+		self.builder.add_from_file('./patientID.glade')
+		self.window = self.builder.get_object('entrywindow')
+		self.nextbutton = self.builder.get_object('button1')                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
+		self.okbutton=self.builder.get_object('okbutton')
+		self.name = self.builder.get_object('name')
+		self.age = self.builder.get_object('age')
+		self.entryname=self.builder.get_object('entryname')
+		self.entryage=self.builder.get_object('entryage')
+		self.entrypatientID=self.builder.get_object('entrypatientID')
+		#self.check_editable = Gtk.CheckButton("entryname")
+
+		#self.entryname = Gtk.Entry()
+
+		self.patientID = self.builder.get_object('patientID')
+		self.builder.connect_signals(self)
+		#self.entryname = Gtk.Entry()
+		#self.entryage = Gtk.Entry()
+		#self.entrypatientID = Gtk.Entry()
+		
+		#print(self.entryname.get_text())
+		print('rashmi')
+		
+		self.window.show()
+	def on_okbutton_clicked(self,button):
+		global name
+		global age
+		global patientID
+		global st
+		ts=time.time()
+		#blood=BloodAnalyser()
+		st = datetime.datetime.fromtimestamp(ts).strftime('%Y-%m-%d %H_%M_%S')
+		name=self.entryname.get_text()
+		age=self.entryage.get_text()
+		patientID=self.entrypatientID.get_text()		
+		self.window.hide()
+		#filename=folder.append(st)
+		#filename=filename.append(".txt")
+		global test
+		test="malaria"
+		global filename
+		filename=folder+st+".txt"
+
+			#return
+
+
+class splashScreen(Gtk.Window):     
+    def __init__(self):
+		
+		self.builder = Gtk.Builder()
+		self.builder.add_from_file('./splash.glade')  
+		self.builder.connect_signals(self)
+		self.window = self.builder.get_object('applicationwindow1')
+		self.image1=self.builder.get_object("image1")
+		self.window.show()
+		#self.done=True
+		#GObject.timeout_add(5000,)
+
+		self.window.show
+class AutoFocus(Gtk.Window):
+	def __init__(self):
+		self.builder = Gtk.Builder()
+		self.builder.add_from_file('./AutoFocus.glade')
+		self.builder.connect_signals(self)
+		self.window = self.builder.get_object('AutoFocus_window')
+		self.image1=self.builder.get_object("image1")
+		self.autofocus_pulse=self.builder.get_object("autofocus_pulse")
+
+		self.autofocus_start=False
+		#threading.Thread(target=self.UpdateImages).start()
+		
+	def pulse_invoke(self):
+		#self.window.show()
+
+		try:
+			os.system('v4l2-ctl -c exposure_absolute=1')
+			os.system('mplayer tv:// driver=v4l2:device=/dev/video0')
+
+
+			blood_analyser.vlc_invoke()
+			#return
+		except: 
+			error2=True
+			return error2
+
+	def variance(self):
+		try:
+			os.chdir('/home/odroid/BloodAnalyser/AutoFocus')
+			#os.system("make clean")
+			#os.system("source /opt/pylon4/bin/pylon-setup-env.sh /opt/pylon4")
+			#os.system("make")
+			#os.system("chmod 777 autofocus")
+			#os.system("ls")
+						
+			#itime=time.time()
+			board=Arduino('/dev/ttyACM0')		
+				   
+			#cap = cv2.VideoCapture(0)
+			n=1
+			mylistForward=[]
+			while(n < 50):
+				board.digital[5].write(1)
+				board.digital[6].write(1)
+				# Capture frame-by-frame
+				os.system("mplayer tv:// -tv driver=v4l2:device=/dev/video0:fps=20 --frames=2 -vo png")
+			
+				# Our operations on the frame come here
+
+				frame=cv2.imread('/home/odroid/BloodAnalyser/AutoFocus/00000002.png')
+				#image_file = '/home/rbccps/BloodAnalyser/AutoFocus/focus%d.png'%n
+				self.window.show()
+			
+				self.image1.set_from_file('/home/odroid/BloodAnalyser/AutoFocus/00000002.png')
+				a=numpy.var(frame)
+				print(a)
+				mylistForward.append(a)
+				sleep(0.1)
+				n=n+1
+			maxMeasure=max(mylistForward)
+			maxMeasure = maxMeasure - 40
+			cMeas=0
+			n=0
+			print '**************Motor Moving Backwards*******************'
+			while(n<50):
+				print("While loop entered")
+				if cMeas > maxMeasure:
+					board.digital[5].write(0)
+					break
+				board.digital[5].write(1)
+				board.digital[6].write(0)
+				
+				os.system("mplayer tv:// -tv driver=v4l2:device=/dev/video0:fps=20 --frames=2 -vo png")
+				self.image1.set_from_file('/home/odroid/BloodAnalyser/AutoFocus/00000002.png')
+				frame1=cv2.imread('/home/odroid/BloodAnalyser/AutoFocus/00000002.png')
+				cMeas=numpy.var(frame1)
+				print(cMeas)
+				n=n+1
+				sleep(0.1)
+			board.digital[5].write(0)
+
+				
+			#cv2.destroyAllWindows()
+				
+			#n=cap.release()
+			self.window.hide()
+			print(n)
+			# When everything done, release the capture
+			print("Capture released")
+			maxMeasure= max(mylistForward)
+			blood_analyser.vlc_invoke()
+
+			#cv2.destroyAllWindows()
+
+		except: 
+			global error1
+			print("HARDWARE MISSING")
+			error1=1
+			return error1
+
+
+	
+	def on_timeout(self, user_data):
+
+		if self.activity_mode:
+			self.autofocus_pulse.pulse()
+		else:
+			new_value = self.autofocus_pulse.get_fraction() + 0.01
+
+			if new_value > 1:
+				new_value = 0
+
+			self.progressbar.set_fraction(new_value)
+
+        # As this is a timeout function, return True so that it
+        # continues to get called
+		return True
+
+		
+class quit_window(Gtk.Window):
+	def __init__(self):
+		self.builder = Gtk.Builder()
+		os.chdir('/home/odroid/BloodAnalyser')
+		self.builder.add_from_file('./quit_window.glade')
+		self.builder.connect_signals(self)
+		self.window = self.builder.get_object('quit_window')
+		self.finishbutton = self.builder.get_object('finishbutton')
+		self.another_testbutton = self.builder.get_object('another_testbutton')
+		
+
+	
+	def show_screen(self):
+		self.window.show()
+
+	
+	def on_finishbutton_activate(self, widget):
+		os.system('rm ./celldata.zip')
+		os.system('rm -r ./AcquiredData')
+		os.system('mkdir ./AcquiredData')
+		Gtk.main_quit()
+
+		
+	def on_another_testbutton_activate(self,widget):
+		#os.system('rm ./celldata.zip')
+		#os.system('rm -r ./AcquiredData')
+		#os.system('mkdir ./AcquiredData')
+		print "ANother test selected"
+		self.progressbar.set_fraction(0.0)
+		self.timeout_id = GObject.timeout_add(False, self.on_timeout,None)
+		
+		blood_analyser.start.set_label("START TEST")
+		blood_analyser = BloodAnalyser()
+		#splScr = splashScreen()
+		patient_ID=patientID()
+		Gtk.main()
+
+
+		
+
+
+class BloodAnalyser(Gtk.Window): 
+	
+	def __init__(self):
+		global count 
+		count=0
+		global x
+		x=0
+		self.builder = Gtk.Builder()
+		self.builder.add_from_file('./bloodAnalyser.glade')
+		self.builder.connect_signals(self)
+		self.window = self.builder.get_object('window1')
+		self.window.show()
+		
+
+		self.infectious_disease = self.builder.get_object("infectious_disease")
+		self.hamatological_disorder =self.builder.get_object("hematological")	
+		self.completebloodcount = self.builder.get_object("completebloodcount")
+		self.malaria = self.builder.get_object("malaria")
+		self.dengue = self.builder.get_object("dengue")
+		self.tuberculosis = self.builder.get_object("tuberculosis")
+		self.spherocytosis = self.builder.get_object("spherocytosis")
+		self.sicklecellanemia=self.builder.get_object("sicklecellanemia")
+		self.hereditaryelliptocytosis=self.builder.get_object("hereditaryelliptocytosis")
+		self.start = self.builder.get_object("start")
+		self.progressbar = self.builder.get_object("progressbar")
+		self.image1=self.builder.get_object("image1")
+		self.image2=self.builder.get_object("image2")
+		
+		self.malaria.set_sensitive(True)
+		self.dengue.set_sensitive(True)
+		self.tuberculosis.set_sensitive(True)
+		self.spherocytosis.set_sensitive(False)
+		self.sicklecellanemia.set_sensitive(False)
+		self.hereditaryelliptocytosis.set_sensitive(False)
+		
+
+	def on_infectiousdisease_toggled(self, button):
+		if button.get_active():
+			print "infectious"
+			self.malaria.set_sensitive(True)
+			self.dengue.set_sensitive(True)
+			self.tuberculosis.set_sensitive(True)
+			self.spherocytosis.set_sensitive(False)
+			self.sicklecellanemia.set_sensitive(False)
+			self.hereditaryelliptocytosis.set_sensitive(False)
+			
+		
+		#print "infectious"
+		
+	def on_hematological_toggled(self, button):
+		if button.get_active():
+			print "hematology"
+			self.spherocytosis.set_sensitive(True)
+			self.sicklecellanemia.set_sensitive(True)
+			self.hereditaryelliptocytosis.set_sensitive(True)
+			self.malaria.set_sensitive(False)
+			self.dengue.set_sensitive(False)
+			self.tuberculosis.set_sensitive(False)
+
+	
+	def on_completebloodcount_toggled(self, button):
+		global test
+		test="Complete Blood Count"
+		print "blood count"
+		self.spherocytosis.set_sensitive(False)
+		self.sicklecellanemia.set_sensitive(False)
+		self.hereditaryelliptocytosis.set_sensitive(False)
+		self.malaria.set_sensitive(False) 
+		self.dengue.set_sensitive(False)
+		self.tuberculosis.set_sensitive(False)
+		self.hereditaryelliptocytosis.set_sensitive(False)
+            
+	def on_malaria_toggled(self, widget):
+		
+		if malaria.get_active():
+			global test
+			test="Malaria"
+			print "on"
+        #else:
+        #    print "off"
+	def on_hereditaryelliptocytosis_toggled(self, widget):
+		if hereditaryelliptocytosis.get_active():
+			print "hereditaryelliptocytosis"
+			global test
+			test="hereditaryelliptocytosis"
+			
+	def on_timeout_thread_end(self, user_data):
+		global error1
+		global error2
+		global error3
+		global filename
+		# Error handling if the Motor pulse giving Arduino board is missing
+		if error1==1:
+			dialog = Gtk.MessageDialog(None, 0, Gtk.MessageType.WARNING, Gtk.ButtonsType.OK, "Error!")
+			dialog.format_secondary_text("Required hardware missing!.. Cannot run application")
+			response = dialog.run()
+			
+			self.progressbar.set_fraction(0.0)
+			self.timeout_id = GObject.timeout_add(False, self.on_timeout,None)
+			if response == Gtk.ResponseType.OK:
+				self.window.close()
+				dialog.destroy()
+				self.window.hide()
+				Gtk.main_quit()
+		# Error handling if the camera is not operating properly
+		elif error2==1:
+			dialog = Gtk.MessageDialog(None, 0, Gtk.MessageType.WARNING, Gtk.ButtonsType.OK, "Error!")
+			dialog.format_secondary_text("Camera interface not found!.. Cannot run application")
+			response = dialog.run()
+			
+			self.progressbar.set_fraction(0.0)
+			self.timeout_id = GObject.timeout_add(False, self.on_timeout,None)
+			if response == Gtk.ResponseType.OK:
+				self.window.close()
+				dialog.destroy()
+				self.window.hide()
+				Gtk.main_quit()
+		
+		elif error3==1:
+			dialog = Gtk.MessageDialog(None, 0, Gtk.MessageType.WARNING, Gtk.ButtonsType.OK, "Sending Data Error!")
+			dialog.format_secondary_text("Cannot send data.")
+			response = dialog.run()
+			
+			self.progressbar.set_fraction(0.0)
+			self.timeout_id = GObject.timeout_add(False, self.on_timeout,None)
+			if response == Gtk.ResponseType.OK:
+				self.window.close()
+				dialog.destroy()
+				self.window.hide()
+				Gtk.main_quit()
+				sys.exit()
+			
+		else:	
+			if self.Thread1.is_alive():
+				test_ended = False
+				
+			else:
+				test_ended = True
+				text="Finished Sending Data !"
+				
+			#	text="Data Sent for Analysis"
+				self.progressbar.set_text(text)
+				self.activity=False
+				#print("send_data status=%s",SendCellDataThread)	
+				self.progressbar.set_fraction(0.0)
+				self.timeout_id = GObject.timeout_add(1, self.on_timeout,None)
+		
+		
+				
+				#self.progressbar.set_fraction(0.0)
+				GObject.source_remove(self.timeout_id)				
+				dialog = Gtk.MessageDialog(None, 0, Gtk.MessageType.WARNING, Gtk.ButtonsType.YES_NO, "Test Complete !")
+				dialog.format_secondary_text("Do you want to run another test?")
+				response = dialog.run()
+				if response == Gtk.ResponseType.YES:
+					dialog.destroy()
+					self.window.hide() 
+					Gtk.main_quit()
+
+
+					
+					dialog.destroy()
+				if response == Gtk.ResponseType.NO:
+					dialog.destroy()
+					#os.system('rm ./celldata.zip')
+
+					dialog.destroy()
+					self.window.hide()
+					Gtk.main_quit()
+					sys.exit()
+
+				
+				return False
+			return True   
+
+
+        #print("Button", "was turned", state)
+	def on_start_clicked(self, widget):
+		global count
+		global ExitVLCThread
+		global Acquire
+		global Kill
+		global SendCellDataThread
+		global test
+		global st
+		global name
+		global age
+		global patientID
+		global filename
+		folder=("/home/odroid/BloodAnalyser/AcquiredData/")
+		#filename=folder.append(st)
+		#filename=filename.append(".txt")
+		filename=folder+'PatientInformation'+".txt"
+		f = open(filename,"w") #opens file with name of "test.txt"
+		
+				
+		#f.write("Name:\t")
+		f.write(name)
+		f.write("\n")
+		print(f)
+
+		#f.write("Age:\t")
+		f.write(age)
+		f.write("\n")
+		
+		#f.write("PatientID:\t")
+		f.write(patientID)
+		f.write("\n")
+		
+		#f.write("Test Selected:\t")
+		f.write(test)
+		f.write("\n")
+		f.close()
+		#os.system('7z a /home/odroid/BloodAnalyser/AcquiredData/celldata.7z /home/odroid/BloodAnalyser/AcquiredData/PatientInformation')
+		#self.activity= False
+		#self.ftp_invoke()
+
+		count=count+1
+		print(count)
+		if (count ==1):
+		
+			print("Hello World!")
+			dialog = Gtk.MessageDialog(None, 0, Gtk.MessageType.WARNING, Gtk.ButtonsType.YES_NO, "Reminder! Suitable Cartridge had to be loaded before starting the test.")
+			dialog.format_secondary_text("Do you want to continue?")
+			response = dialog.run()
+			if response == Gtk.ResponseType.YES:
+				dialog.destroy()
+				self.start.set_label("ABORT TEST")
+				print("WARN dialog closed by clicking OK button")
+				
+				Acquire = True
+				print (Acquire)
+				#Kill = True
+				#print(Kill)
+				#global Thread1
+				#global Thread2
+
+				
+				auto_focus=AutoFocus()
+				
+				#auto_focus.window.show()
+				#blood_analyser = BloodAnalyser()
+
+				self.timeout_id_thread_end = GObject.timeout_add(500, self.on_timeout_thread_end, None)
+
+				self.Thread1=threading.Thread(target=auto_focus.pulse_invoke)
+				#self.Thread1.start()
+
+				#self.Thread1=threading.Thread(target=self.vlc_invoke)
+				self.Thread1.daemon=True
+				self.Thread1.start()
+
+            
+            
+			elif response == Gtk.ResponseType.NO:
+				dialog.destroy()
+				print("WARN dialog closed by clicking CANCEL button")
+				count=0
+				
+		else:
+			print(count)
+			dialog = Gtk.MessageDialog(None, 0, Gtk.MessageType.WARNING,Gtk.ButtonsType.YES_NO, "Test in progress!.. Do you still want to abort test?")
+			dialog.format_secondary_text("Click Yes to continue")
+			response = dialog.run()
+			if response == Gtk.ResponseType.YES:
+
+				dialog.destroy()
+				self.window.hide()
+				Gtk.main_quit()
+				os.system('exit()')
+				print("Thread2=")
+				print(SendCellDataThread)
+				os.system("killall vlc")
+				
+				self.start.set_label("START TEST")
+				text2 = " "
+				count = 0
+				self.progressbar.set_text(text2)
+        
+				self.progressbar.set_show_text(text2)
+	
+				self.progressbar.set_fraction(0.0)
+				self.activity= False
+#				self.timeout_id = GObject.timeout_add(0, self.on_timeout,None)
+
+
+				self.start.set_label("START TEST")
+				#os.system('rm ./celldata.zip')
+				os.system('rm -r ./AcquiredData')
+				os.system('mkdir ./AcquiredData')
+				print("WARN dialog closed by clicking OK button")	
+			elif response == Gtk.ResponseType.NO:	
+				count = 0
+				dialog.destroy()		
+			
+	def on_timeout(self, user_data):
+		if self.activity:
+
+			new_value = self.progressbar.get_fraction() + 0.01
+
+			if new_value > 1:                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
+				new_value = 0
+
+			self.progressbar.set_fraction(new_value)
+
+		return True
+		
+
+
+
+    
+	def vlc_invoke(self):
+        #gobject.threads_init()
+		#os.system("v4l2-ctl -c exposure_absolute=1")
+		print ("Vlc invoked")		
+        #similar to time.sleep()
+		#sleep(10)
+		n = 0
+		global error2
+		start_time=time.time()
+		
+		while (True):
+
+			sleep(0.5)
+			print Acquire
+			if Acquire:
+			#print ('while acquire')
+				self.activity= 1
+
+				self.timeout_id = GObject.timeout_add(400, self.on_timeout,None)
+
+				os.chdir('/home/odroid/BloodAnalyser/AcquiredData')
+
+				
+				itime=time.time()
+				i=1
+				
+				print("Time taken to capture =")
+				print(time.time()-itime)				
+				
+
+				
+				os.chdir('/home/odroid/BloodAnalyser/AcquiredData')
+				while(i<batches+1):
+					text2 = "Acquiring Dataset %d"%i
+
+					self.progressbar.set_text(text2)		
+					self.progressbar.set_show_text(text2)
+
+
+					os.mkdir('/home/odroid/BloodAnalyser/AcquiredData/%d'%i)
+					os.chdir('/home/odroid/BloodAnalyser/AcquiredData/%d'%i)
+					
+					os.system("mplayer tv:// -tv driver=v4l2:device=/dev/video0:fps=60 --frames=%d -vo jpeg"%numframes)
+					if i==1:
+						ip=ip1
+
+					elif i==batches:
+						ip=ip2
+						os.system('7z a /home/odroid/BloodAnalyser/AcquiredData/celldata%d.7z /home/odroid/BloodAnalyser/AcquiredData/%d'%(i,i))
+						self.sizewrite(i,ip)
+						os.system("echo odroid | sudo -S scp -i /home/odroid/jayesh1.pem /home/odroid/BloodAnalyser/AcquiredData/celldata%d.7z ubuntu@%s:"%(i,ip2))
+						print('File Uploaded to %s'%ip)
+						return
+
+					a=thread.start_new_thread(self.compress,(i,ip))
+					i=i+1
+					print 'Updating queue'
+
+				self.start.set_sensitive(False)
+
+
+				
+	def compress(self,i,ip):
+		text='Compessing and Sending Dataset %d'%i
+		
+		self.progressbar.set_text(text) 
+		print ('Entered Compression=%d'%i)
+		
+		self.progressbar.set_show_text(text)
+		os.chdir('/home/odroid/BloodAnalyser/AcquiredData/')
+		print(name)
+		
+		
+		start_time=time.time()
+			
+		#if i==1: 
+			
+		os.system('7z a /home/odroid/BloodAnalyser/AcquiredData/celldata%d.7z /home/odroid/BloodAnalyser/AcquiredData/%d'%(i,i))
+		self.sizewrite(i,ip)
+		os.system("echo odroid | sudo -S scp -i /home/odroid/jayesh1.pem /home/odroid/BloodAnalyser/AcquiredData/PatientInformation.txt /home/odroid/BloodAnalyser/AcquiredData/celldata%d.7z ubuntu@%s:"%(i,ip))
+		print('File Uploaded to %s'%ip)
+
+
+
+		print("--- %s seconds ---" % (time.time() - start_time))
+
+
+		
+		
+	def sizewrite(self,i,ip):
+		print "entered write size"
+		size=str(os.path.getsize('/home/odroid/BloodAnalyser/AcquiredData/celldata%d.7z'%i))
+		print ("size of %d file is:%s"%(i,size))
+		f=open('/home/odroid/BloodAnalyser/AcquiredData/sizefile.txt','w')
+		f.write(size)
+		f.close()
+		os.system("echo odroid | sudo -S scp -i /home/odroid/jayesh1.pem /home/odroid/BloodAnalyser/AcquiredData/sizefile.txt ubuntu@%s:"%ip)
+		return
+	
+         
+
+if __name__ == "__main__":
+	#patient_ID=patientID()
+	blood_analyser = BloodAnalyser()
+	splScr = splashScreen()
+	patient_ID=patientID()
+	#quitwindow=quit_window()
+	
+    #If you don't do this, the splash screen will show, but wont render it's contents
+	while Gtk.events_pending():
+		Gtk.main_iteration()
+	GObject.timeout_add(5000, splScr.window.hide)
+	
+
+Gtk.main()

src/server_script_master.py

@@ -0,0 +1,175 @@
+import sys
+import os, time
+import os.path
+global folder
+import threading
+global it
+#from gi.repository import Gtk, GObject
+global Thread1
+global process
+import numpy
+global num_batches
+if len(sys.argv) < 3:
+    print "Invalid arguments"
+    print "Usage  : python server_script_threads.py <instance_id>"
+    print "Example: python server_script_threads.py 3"
+    sys.exit()
+
+instance_id = int(sys.argv[1])
+num_instances = int(sys.argv[2])
+print 'Starting instance id: %d, num_batches:%d'%(instance_id, num_instances)
+
+
+class servercheck():
+
+  i=0
+  path=("/home/ubuntu/")
+  print(path)
+  path_to_watch =os.path.join("/home/ubuntu/")
+  before = dict ([(f, None) for f in os.listdir (path_to_watch)])
+  dir=os.chdir(os.path.join("/home/ubuntu/"))
+  it=time.time()
+
+  while 1:
+    print "Checking for zip file..."
+    time.sleep (1)
+    after = dict ([(f, None) for f in os.listdir (path_to_watch)])
+    added = [f for f in after if not f in before]
+    removed = [f for f in before if not f in after]
+    #print(removed)
+    if removed:
+        print "removed: ", ", ".join (removed)
+
+    if added:
+
+        added_file=", ".join (added)
+        print "added: ", ", ".join (added)
+        i=i+1
+        if i<4:
+            file_name=("celldata.7z")
+            added_file=", ".join (added)
+            if added_file == file_name:
+
+                time.sleep(130)
+                print "Removing celldata folder"
+                os.system("rm -rf celldata")
+
+                print "Unzipping celldata.7z"
+                os.system("7z x celldata.7z")
+
+                print "Removing zip file - celldata.7z"
+                os.system("rm celldata.7z")
+
+                if os.path.isdir("./images"):
+                    os.system("cp -r celldata/* images/")
+                else:
+                    os.mkdir("./images/")
+                    os.system("cp -r celldata/* images/")
+
+                global ProcessThreads
+                ProcessThreads = []
+                print os.getcwd() + '/celldata'
+                numImages = len(os.listdir(os.getcwd() + '/celldata'))
+                print "Number of images in the folder: %d"%numImages
+                numThreads = 5
+                numImagesPerThread = numImages/numThreads
+                print "Starting %d threads- Total images: %d, Images per thread:%d"%(numThreads, numImages, numImagesPerThread)
+
+                image_num_min = 2               # Starting from image 2 as image 1 is always black!
+                                                                                                                              39,5          28%
+                image_num_max = 0
+
+                for i in range (1, numThreads+1):
+
+                    image_num_max = image_num_min + numImagesPerThread
+                    if image_num_max > 10000:
+                        image_num_max=10000
+                    t = threading.Thread(target=process,args=(i, image_num_min, image_num_max))
+                    t.start()
+                    ProcessThreads.append(t)
+                    print 'Started thread %d for images %d to %d'%(i, image_num_min, image_num_max)
+                    image_num_min = image_num_max + 1
+
+                for t in ProcessThreads:
+                                        t.join()
+
+                totalCount = 0
+
+                for i in range (1, numThreads+1):
+                    result_file = 'count' + str(i) + '.txt'
+                    f = open(result_file, 'r')
+                    count_str = f.readline()
+                    count = int(count_str.split("=")[1])
+                    totalCount = totalCount + count
+                    print "Thread:%d, Count:%d, Total Count:%d"%(i, count, totalCount)
+                    os.system("rm -f " + result_file)
+
+                print totalCount
+
+                print totalCount
+
+                writefile(totalCount)
+                #checkcountfiles()
+
+    before=after
+
+    def process(threadId, frame_no_min, frame_no_max):
+        result_file = 'count' + str(threadId) + '.txt'
+         cmd = 'sudo ./run_malariaExecutableArgs.sh /usr/local/MATLAB/MATLAB_Compiler_Runtime/v83/ %d %d %s'%(frame_no_min, frame_no_max, result_file)
+        print "ThreadId: %d, cmd =%s"%(threadId, cmd)
+        os.system(cmd)
+        return
+
+
+    def writefile(count):
+        #testsite_array = []
+        #with open('PatientInformation.txt','r') as my_file:
+        #    testsite_array = my_file.readlines()
+        #count=numpy.sum(testsite_array)
+        file_name = 'Instance' + str(instance_id) + '.txt'
+        f = open(file_name,'w')
+        f.write('%d'%count)
+        f.flush()
+        f.close()
+        cmd = 'sudo scp -i "jayesh1.pem" ' + file_name + ' ubuntu@ec2-54-200-214-228.us-west-2.compute.amazonaws.com:'
+        print cmd
+        os.system(cmd)
+    def checkcountfiles():
+        path = '/home/ubuntu/'
+        files = []
+        countFiles=1
+        iteration=0
+        totalCount=0
+        cellcount=0
+        textf1='Instance'+str(countFiles)+'.txt'
+        textf2='Instance'+str(countFiles+1)+'.txt'
+        textf3='Instance'+str(countFiles+2)+'.txt'
+        while True:
+            print "Checking for count files from Instances"
+            time.sleep(1)
+            if os.path.isfile(textf1) and os.path.isfile(textf2) and os.path.isfile(textf3):
+
+                    #print i
+                    iteration=iteration+1
+                    print countFiles
+                    textf='Instance'+str(iteration)+'.txt'
+
+                    f = open(textf,'r')
+                    count_str = f.readline()
+                    cellcount = int(count_str)
+                    print 'The count of instance %d =%d'%(iteration,cellcount)
+                    totalCount = totalCount + cellcount
+
+                    if iteration == num_instances:
+                        print 'condition met'
+                        print 'total count =%d'%totalCount
+                        file_name="totalCount.txt"
+                        f = open(file_name,'w')
+                        f.write('%d'%totalCount)
+                        f.flush()
+                        f.close()
+                        return
+            else:
+                        print "Count files have not arrived"
+                                                                                                                                       85%
+