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Currently the code works, but I'm no Matlab expert, and wrote it entirely through google/hack&slashing my way into a successful form. Unfortunately it's slow, and it probably not written with good style.

I was hoping that anyone would be able to tell me how I can improve the code. I don't think that you'll need a video file or calibration file, but if it would help I can include it. I am also curious whether there is a better way to output data to an XLS file than writing in the title/values.

I'm mainly conserned about style and efficiency.

%profile off
%profile clear
clear all;
set(0,'ShowHiddenHandles','on')
delete(get(0,'Children')) % Delete any currently open figures
%profile on
%Input user specified filename
[filename, pathname] = uigetfile('*.avi', 'Select a video file');
if isequal(filename,0)
 disp('User selected Cancel')
else
 disp(['User selected: ', fullfile(pathname, filename)]); 
end
% [~,~,ext]=fileparts(filename);
dataFileName={filename};
nab=fullfile(pathname, filename);
[filename, pathname] = uigetfile({'*.xlsx'},'Select the calibration file'); % choose name and location of Excel calibration file 
if isequal(filename,0)
 disp('User selected Cancel');
else
 disp(['User selected: ', fullfile(pathname, filename)]); 
end
[pathstr,name,ext]=fileparts(filename);
calfile=fullfile(pathname, filename);
% read the calibration file specifically
interval = xlsread(calfile,'Calibration','B1');
repeats = xlsread(calfile,'Calibration','B2');
pixels_per_mm = xlsread(calfile,'Calibration','B8');
stainValue = xlsread(calfile,'Calibration','B10');
maxFrames = xlsread(calfile,'Calibration','B23');
maxstainNum = xlsread(calfile,'Calibration','B24');
densityBlood = xlsread(calfile,'Calibration','B41');
surftBlood = xlsread(calfile,'Calibration','B42');
densityAir = xlsread(calfile,'Calibration','B35') ;
visAir = xlsread(calfile,'Calibration','B36');
dsFrame = xlsread(calfile,'Calibration','B14') ; % frame for first dispensing of fluid
tsFrame = xlsread(calfile,'Calibration','B15') ; % frame for first image analysis tracking
% read the calibration file generally
[ndata, col1] = xlsread(calfile,'Calibration','A:A');
[col2, tt] = xlsread(calfile,'Calibration','B:B');
[ndata2, col3] = xlsread(calfile,'Calibration','C:C');
% Read the video file 
spatterObj = VideoReader(nab); 
 
nframes = spatterObj.NumberOfFrames; % determine the number of frames 
if nframes > maxFrames % restrict the total number of frames to process to maxFrames
 nframes = maxFrames;
end
I = read(spatterObj, 1);
%onlystains = zeros([size(I,1) size(I,2) 3 nframes], class(I)); % zero the array
onlystains = zeros([size(I,1) size(I,2) 3 nframes], 'like', I); % replace "class(I)" with I. 
figure(100) % set up figure to plot
%hold on
x=0;
for k = tsFrame : nframes % process video file, frame by frame from the selected first frame
 singleFrame = read(spatterObj, k);
 % Convert to grayscale
 I = rgb2gray(singleFrame);
 I2 = imadjust(I);
 % convert to binary image
 %level = graythresh(I);
 frame = im2bw(I2,stainValue);
 % Invert image so stains are white objects on black background
 frame=~frame;
 % filter all objects with less than minNumpixels to clean background
 minNumpixels = 500;
 frame = bwareaopen(frame, minNumpixels);
 % fill any holes in object(s)
 frame = imfill(frame,'holes');
 if k == tsFrame
 displaystains = frame; 
 else
 displaystains = displaystains + frame;
 end
 imshow(displaystains, 'InitialMagnification',100);
 % locate stains in the kth frame
 L = logical(frame);%convert array into logicals
 if any(L(:))
 props = regionprops(L, {'Centroid','FilledArea','Eccentricity','Orientation','EquivDiameter','MajorAxisLength','MinorAxisLength','Perimeter'});
 end
 numObj = numel(props); % number of stains in the frame
 %nn(k)=numObj; % number of stains in kth frame
 mj = 0;
 parentStainMax=0;
 % store stain data from each frame and plot in figure
 %should preallocate size of the array with zeroes, to avoid
 %copying etc
 stainData = zeros(numObj,10);
 for stain = 1 : numObj
 if props(stain).Centroid(1) > 0 % can use whole image
 stainData(stain,1) = props(stain).Centroid(1); % x-coord of stain
 stainData(stain,2) = props(stain).Centroid(2); % y coord of stain
 stainData(stain,3) = props(stain).FilledArea; % stain size (filled)
 stainData(stain,4) = props(stain).Eccentricity; % ratio of distance between ellipse foci and major axis length, =0 for circle
 stainData(stain,5) = props(stain).Orientation; % angle bewteen major axis of ellipse and x-axis
 stainData(stain,6) = props(stain).EquivDiameter; % average diameter (non-filled)
 stainData(stain,7) = props(stain).MajorAxisLength; % length of major axis
 stainData(stain,8) = props(stain).MinorAxisLength; % length of minor axis
 stainData(stain,9) = props(stain).Perimeter; % perimeter
 stainData(stain,10) = k; % time - must be the last parameter in the list
 
 end
 if stainData(stain,3)> parentStainMax % find the parent stain (the largest object)
 parentStainNo(k) = stain;
 parentStainMax=stainData(stain,3);
 parentStain(k)=stainData(stain,3)/(pixels_per_mm)^2; % store stain areas in mm^2
 AR(k)=stainData(stain,8)/stainData(stain,7); % aspect ratio
 peri(k)=stainData(stain,9)/(pixels_per_mm); % perimeter of stain in mm
 circ (k)=peri(k)^2/(4*pi()*parentStain(k)); % compactness
 K(k)=k; % frame number
 end
 end
end
X=parentStain;
%Ktrim=K(dsFrame:nframes);
figure(101)
h3 = plot(K,parentStain); % plot the change in area vs frame number
%hold off
% Invert Matrices
stainxCol = X.';
kCol = K.';
for n=1:nframes
 if n < tsFrame
 Time(n) = 0;
 else
 Time(n) = interval*(kCol(n)-dsFrame);
 end
end
timeCol = Time.';
stainDiamCol = 2*sqrt(stainxCol/pi());
ARCol=AR.';
periCol=peri.';
circCol=circ.';
figure(101) 
 h3 = plot(Time,X); % plot the stain area vs time
% Write to excel spreadsheet
[filename, pathname] = uiputfile('*.xlsx','Save as'); % choose name and location of Excel file to save results in
stainresults = fullfile(pathname, filename);
message1 = 'Please wait while I write the data to Excel...';
h = msgbox(message1);
hExcel = actxserver('Excel.Application');
hExcel.SheetsInNewWorkbook = 1; % Limits number of sheets in about-to-be created workbook to 1
EW = hExcel.Workbooks.Add; % Starts a new workbook (not named yet)
EW.SaveAs(stainresults) % Name and close file
EW.Close
hExcel.Quit
Title1 = {'Calibration Data'};
Title2 = {'File Name: '};
xlswrite(stainresults,Title1,'Sheet1','A1')
xlswrite(stainresults,Title2,'Sheet1','B1')
xlswrite(stainresults,dataFileName,'Sheet1','C1')
xlswrite(stainresults,col1,'Sheet1','A3');
xlswrite(stainresults,col2,'Sheet1','B3');
xlswrite(stainresults,col3,'Sheet1','C3');
header3 = {'Frame', 'Time','Stain diameter','Stain Area', 'aspect ratio','perimeter','compactness' };
header4 = {'', '(sec)', '(mm)', '(mm^2)', '', '(mm)'};
 sheetRef = 'stain '; 
 xlswrite(stainresults,header3,sheetRef,'A1'); % write the column headings 
 xlswrite(stainresults,header4,sheetRef,'A2');
 comb = [kCol,timeCol,stainDiamCol,stainxCol,ARCol,periCol,circCol];
 xlswrite(stainresults,comb,sheetRef,'A3'); % write the data
 
message2 = 'Finished writing data';
h = msgbox(message2);
%profile off
%profsave(profile('info'),'Profile_0.1_preallocating')

Ive also included the pastebin link if you want syntax highlighting. http://pastebin.com/CCFcH893#

Currently the code works, but I'm no Matlab expert, and wrote it entirely through google/hack&slashing my way into a successful form. Unfortunately it's slow, and it's probably not written with good style.

I was hoping that anyone would be able to tell me how I can improve the code. I don't think that you'll need a video file or calibration file, but if it would help I can include it. I am also curious whether there is a better way to output the data to an XLS file than writing in the title/values.

I'm mainly concerned about style and efficiency.

%profile off
%profile clear
clear all;
set(0,'ShowHiddenHandles','on')
delete(get(0,'Children')) % Delete any currently open figures
%profile on
%Input user specified filename
[filename, pathname] = uigetfile('*.avi', 'Select a video file');
if isequal(filename,0)
 disp('User selected Cancel')
else
 disp(['User selected: ', fullfile(pathname, filename)]); 
end
% [~,~,ext]=fileparts(filename);
dataFileName={filename};
nab=fullfile(pathname, filename);
[filename, pathname] = uigetfile({'*.xlsx'},'Select the calibration file'); % choose name and location of Excel calibration file 
if isequal(filename,0)
 disp('User selected Cancel');
else
 disp(['User selected: ', fullfile(pathname, filename)]); 
end
[pathstr,name,ext]=fileparts(filename);
calfile=fullfile(pathname, filename);
% read the calibration file specifically
interval = xlsread(calfile,'Calibration','B1');
repeats = xlsread(calfile,'Calibration','B2');
pixels_per_mm = xlsread(calfile,'Calibration','B8');
stainValue = xlsread(calfile,'Calibration','B10');
maxFrames = xlsread(calfile,'Calibration','B23');
maxstainNum = xlsread(calfile,'Calibration','B24');
densityBlood = xlsread(calfile,'Calibration','B41');
surftBlood = xlsread(calfile,'Calibration','B42');
densityAir = xlsread(calfile,'Calibration','B35') ;
visAir = xlsread(calfile,'Calibration','B36');
dsFrame = xlsread(calfile,'Calibration','B14') ; % frame for first dispensing of fluid
tsFrame = xlsread(calfile,'Calibration','B15') ; % frame for first image analysis tracking
% read the calibration file generally
[ndata, col1] = xlsread(calfile,'Calibration','A:A');
[col2, tt] = xlsread(calfile,'Calibration','B:B');
[ndata2, col3] = xlsread(calfile,'Calibration','C:C');
% Read the video file 
spatterObj = VideoReader(nab); 
 
nframes = spatterObj.NumberOfFrames; % determine the number of frames 
if nframes > maxFrames % restrict the total number of frames to process to maxFrames
 nframes = maxFrames;
end
I = read(spatterObj, 1);
%onlystains = zeros([size(I,1) size(I,2) 3 nframes], class(I)); % zero the array
onlystains = zeros([size(I,1) size(I,2) 3 nframes], 'like', I); % replace "class(I)" with I. 
figure(100) % set up figure to plot
%hold on
x=0;
for k = tsFrame : nframes % process video file, frame by frame from the selected first frame
 singleFrame = read(spatterObj, k);
 % Convert to grayscale
 I = rgb2gray(singleFrame);
 I2 = imadjust(I);
 % convert to binary image
 %level = graythresh(I);
 frame = im2bw(I2,stainValue);
 % Invert image so stains are white objects on black background
 frame=~frame;
 % filter all objects with less than minNumpixels to clean background
 minNumpixels = 500;
 frame = bwareaopen(frame, minNumpixels);
 % fill any holes in object(s)
 frame = imfill(frame,'holes');
 if k == tsFrame
 displaystains = frame; 
 else
 displaystains = displaystains + frame;
 end
 imshow(displaystains, 'InitialMagnification',100);
 % locate stains in the kth frame
 L = logical(frame);%convert array into logicals
 if any(L(:))
 props = regionprops(L, {'Centroid','FilledArea','Eccentricity','Orientation','EquivDiameter','MajorAxisLength','MinorAxisLength','Perimeter'});
 end
 numObj = numel(props); % number of stains in the frame
 %nn(k)=numObj; % number of stains in kth frame
 mj = 0;
 parentStainMax=0;
 % store stain data from each frame and plot in figure
 %should preallocate size of the array with zeroes, to avoid
 %copying etc
 stainData = zeros(numObj,10);
 for stain = 1 : numObj
 if props(stain).Centroid(1) > 0 % can use whole image
 stainData(stain,1) = props(stain).Centroid(1); % x-coord of stain
 stainData(stain,2) = props(stain).Centroid(2); % y coord of stain
 stainData(stain,3) = props(stain).FilledArea; % stain size (filled)
 stainData(stain,4) = props(stain).Eccentricity; % ratio of distance between ellipse foci and major axis length, =0 for circle
 stainData(stain,5) = props(stain).Orientation; % angle bewteen major axis of ellipse and x-axis
 stainData(stain,6) = props(stain).EquivDiameter; % average diameter (non-filled)
 stainData(stain,7) = props(stain).MajorAxisLength; % length of major axis
 stainData(stain,8) = props(stain).MinorAxisLength; % length of minor axis
 stainData(stain,9) = props(stain).Perimeter; % perimeter
 stainData(stain,10) = k; % time - must be the last parameter in the list
 
 end
 if stainData(stain,3)> parentStainMax % find the parent stain (the largest object)
 parentStainNo(k) = stain;
 parentStainMax=stainData(stain,3);
 parentStain(k)=stainData(stain,3)/(pixels_per_mm)^2; % store stain areas in mm^2
 AR(k)=stainData(stain,8)/stainData(stain,7); % aspect ratio
 peri(k)=stainData(stain,9)/(pixels_per_mm); % perimeter of stain in mm
 circ (k)=peri(k)^2/(4*pi()*parentStain(k)); % compactness
 K(k)=k; % frame number
 end
 end
end
X=parentStain;
%Ktrim=K(dsFrame:nframes);
figure(101)
h3 = plot(K,parentStain); % plot the change in area vs frame number
%hold off
% Invert Matrices
stainxCol = X.';
kCol = K.';
for n=1:nframes
 if n < tsFrame
 Time(n) = 0;
 else
 Time(n) = interval*(kCol(n)-dsFrame);
 end
end
timeCol = Time.';
stainDiamCol = 2*sqrt(stainxCol/pi());
ARCol=AR.';
periCol=peri.';
circCol=circ.';
figure(101) 
 h3 = plot(Time,X); % plot the stain area vs time
% Write to excel spreadsheet
[filename, pathname] = uiputfile('*.xlsx','Save as'); % choose name and location of Excel file to save results in
stainresults = fullfile(pathname, filename);
message1 = 'Please wait while I write the data to Excel...';
h = msgbox(message1);
hExcel = actxserver('Excel.Application');
hExcel.SheetsInNewWorkbook = 1; % Limits number of sheets in about-to-be created workbook to 1
EW = hExcel.Workbooks.Add; % Starts a new workbook (not named yet)
EW.SaveAs(stainresults) % Name and close file
EW.Close
hExcel.Quit
Title1 = {'Calibration Data'};
Title2 = {'File Name: '};
xlswrite(stainresults,Title1,'Sheet1','A1')
xlswrite(stainresults,Title2,'Sheet1','B1')
xlswrite(stainresults,dataFileName,'Sheet1','C1')
xlswrite(stainresults,col1,'Sheet1','A3');
xlswrite(stainresults,col2,'Sheet1','B3');
xlswrite(stainresults,col3,'Sheet1','C3');
header3 = {'Frame', 'Time','Stain diameter','Stain Area', 'aspect ratio','perimeter','compactness' };
header4 = {'', '(sec)', '(mm)', '(mm^2)', '', '(mm)'};
 sheetRef = 'stain '; 
 xlswrite(stainresults,header3,sheetRef,'A1'); % write the column headings 
 xlswrite(stainresults,header4,sheetRef,'A2');
 comb = [kCol,timeCol,stainDiamCol,stainxCol,ARCol,periCol,circCol];
 xlswrite(stainresults,comb,sheetRef,'A3'); % write the data
 
message2 = 'Finished writing data';
h = msgbox(message2);
%profile off
%profsave(profile('info'),'Profile_0.1_preallocating')

I've also included the pastebin link (http://pastebin.com/CCFcH893# ) if you want syntax highlighting.

Im not really certain whether this is OK, but I'm looking for some code advice- particularly around style and efficiency. the code takes a video (a drop onto a fabric surface) and I want it to return the area of the drop.

Currently the code works, but I'm no matlab expert, and wrote it entirely through google/hack&slashing my way into a successful form. Unfortunately it's slow, and it probably not written with good style.

I was hoping that anyone (who actually knows what they're doing) would be able to tell me how I could improve the code. I don't think that you'll need a video file or calibration file, but if it would help I can include it. I am also curious whether there is a better way to output data to an XLS file than writing in the title/values.

The code below takes a video as input (a drop onto a fabric surface) and I want it to return the area of the drop.

Currently the code works, but I'm no Matlab expert, and wrote it entirely through google/hack&slashing my way into a successful form. Unfortunately it's slow, and it probably not written with good style.

I was hoping that anyone would be able to tell me how I can improve the code. I don't think that you'll need a video file or calibration file, but if it would help I can include it. I am also curious whether there is a better way to output data to an XLS file than writing in the title/values.

I'm mainly conserned about style and efficiency.