smiuser/ofm
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

first commit

Browse Source
This commit is contained in:
moonanjum26
2018-08-10 12:20:31 +05:30
parent 1e59ab21b2
commit efbe825bd9
13 changed files with 1640 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files

BIN
src/Flowcytometer_matlab _code/flowcytometergui.fig Normal file
View File

Binary file not shown.

217
src/Flowcytometer_matlab _code/flowcytometergui.m Normal file
View File

@@ -0,0 +1,217 @@
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);

263
src/Flowcytometer_matlab _code/focusplane_4.m Normal file
View File

@@ -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)

58
src/Flowcytometer_matlab _code/focusstack_1.m Normal file
View File

@@ -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

88
src/Flowcytometer_matlab _code/focusstack_2.m Normal file
View File

@@ -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

60
src/Flowcytometer_matlab _code/focusstack_3.m Normal file
View File

@@ -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

14
src/Flowcytometer_matlab _code/gotoZ.m Normal file
View File

@@ -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

21
src/Flowcytometer_matlab _code/parameter.m Normal file
View File

@@ -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

BIN
src/Time chart .xlsx Normal file
View File

Binary file not shown.

BIN
src/cloud_codeorganization.pptx Normal file
View File

Binary file not shown.

744
src/current_GUIcode.py Normal file
View File

@@ -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()

BIN
src/server_computation.pptx Normal file
View File

Binary file not shown.

175
src/server_script_master.py Normal file
View File

@@ -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%