% TRALONG2 option 2 called by DEPINTL; sets up TRAnsverse vectors rep. electrode periods, 
% assuming either integer or non-integer periodic electrode widths and gaps then 
% i.e. NO interpolation then sums LONGitudinal dirn then transverse direction (using constrctd vectors). 
% D. Bakewell Mo/15/2/1999
fflag=menu('Enter electrode prmtrs:','K/brd & mouse','K/brd - only','mouse only');
vwgset=fflag-1
fredo = 1 % Flag begin processing that can be REDOne if unsatisfactory
while fredo == 1
   fpoint1 = 2;
    while fpoint1 == 2;
    switch vwgset
    case 0 % select wr, gr, mp, frmula from keyboard or ASCII, & yr(1) mouse 
      mouskbr; 
    case 1 % select from keyboard or memory
      kbrmem;
    case 2 % selecting from mouse
      imagmous;
    	% for case 3 determining the points & SETting Variables W, G etc
   	yr=round(y) % compute Rounded vector of 6 pnts chosen
		% Calculate w=electrode width, g=inter-electrode spacing
		dummy3 = menu('Calc av elctrd width & gap choose numbr of periods','1','2','3','4','5','6','7','8','9','10');
		mp=double(dummy3);
		mp1=mp+1
		if frmula == 1 % select points 1,3,4,6 elctrd -> gap & 2,5 gap -> elctrd
   		g=(y(3)-y(2)+y(6)-y(5))/2 % electrode Gap average
   		w=(y(2)-y(1)+y(5)-y(4))/2 % electrode Width average
		else
   		%if frmula == 2 select points 1,3,4,6 gap -> elctrd & 2,5 elctrd -> gap & 
   		w=(y(3)-y(2)+y(6)-y(5))/2 % electrode Width average
   		g=(y(2)-y(1)+y(5)-y(4))/2 % electrode Gap average
		end
		wg=w+g
   	wr=round(w)			% Discrete or ROUNDed w & g
   	gr=round(g)
   	wgr=wr+gr
      vwgset = 3
       % 			---------------
case 3 % vwgset = 3  Variables  W, G etc have been set, now more computation 
   dummy = menu('depintl, line 65 ','Press to continue');
   	imagcomplt;
	end % end switch vwgset 0,1,& or 2 
end % end fpoint1 while
jump = 2 % jump ahead to summing & plotting
switch jump
   case 1
% increase size of image so w & g are integer amounts
   xs = num2str(x); % NUM2STR(X) converts matrix X into string repr ~ 4 digits
   ys = num2str(y);
   xr = round(x);   
   yr = round(y);
   p=1:1:4;
   j = yr(p); % convert chosen POINTs from PIXEL coord sys to MATRIX  
   i = xr(p);
   jim=input2(j,i);
   djim=diag(jim);  
   gvald  = double(djim'); % convert Unit8 @ chosen coord to Double precis 
   gvr = num2str(gvald); % read value of 4 pixel
   c=0;
   fpoint3 = 2
   while fpoint3 == 1
      c=c+1
      cs=num2str(c)
      line20 = ['point no. 'cs ' pixel: x=' xs(c) ', y=' ys(c) ' & value=' gvr(c)];
  		display3 = [line20]      
    	figure
      axis off
      text(0.4,0.8,display3);
      dummy = menu('do you wish to select more points?','Yes','No');
      fpoint3 = dummy;
   end % fpoint3 while
   close
% end 
hold off
nmax=n
% text(0,0.5,display1)
var1 = max(input2);
var2 = max(var1);
[m,n] = size(input2);
%	display4 = input2;
imshow(input2);
pause(1);
switch fflag
   case 1
      surf(input2);axis equal;shading interp;view(2)
      pause(2)
      close
   end
end % end switch jump

suml = sum(input2,2); %  SUMs intensity matix 'input2' over j in MATRIX coord. sys.
   % i.e along ea row or Longitud x dirctn in PIXEL cord sys relatng to electrode strips
   % GENerate VECtor (pmxtrv rows x 1 column) from chosen points for plot sumj
smlmaxr=round(max(suml));
smlminr=round(min(suml));
smldifr=smlmaxr-smlminr;
pvec = smlminr:smldifr/200:smlmaxr;
t = 1:1:pmxtrv; % Integer VECtor Transverse direction on elctrd plne (1 row x pmxtrv colmns)
 fvecgen = 1; % Flag for VECtor GENeration
dummy = menu('    ','Press to continue');
%	display4 = sumhoriz
k = [];
figure
plot(suml',t');axis ij; % 
hold on
	for k = 1:1:mp1
  plot(smlminr',ye1vr(k)','g+',pvec',ye1v(k)','g--')
  plot(smlminr',ye2vr(k)','r+',pvec',ye2v(k)','r--')
  plot(smlminr',ym1vr(k)','b+',pvec',ym1v(k)','b--')
  plot(smlminr',ym2vr(k)','m+',pvec',ym2v(k)','m--')
  	end
choice3=menu('Now transverse av.','variable integer periods','same integer periods');
hold off
%close
%print suml-f
%  Take average of intesities over electrode periods
% organise Vertical (matrix i) summing spans, number = 2 x mp = 2xno peroids
% Current aim is to evaluate accumulation over 1 period (w + g) which consists of 
% two sub-periods, each (w + g)/2, A & B which -> accum. over 1 sub-period (w + g)/2. 
% 1. First option is to use w,g e {R+} -> where periods may/not same no. elements
switch choice3;
case 1   
k=[];
int1 = []
int2 = []
k = 1:1:mp
int1(k)=abs(floor(ym1v(k))-ceil(ym1v(k))+1) % avoids counting same point twice (0,1)
int2(k)=abs(floor(ym2v(k))-ceil(ym2v(k))+1) % avoids counting same point twice (0,1)
pAst(k)=ceil(ym1v(k)) + int1(k)	% Point of region A STart
pAnd(k)=floor(ym2v(k))				% Point of region A eND
pBst(k)=ceil(ym2v(k)) + int2(k)	% Point of region B STart	
pBnd(k)=floor(ym1v(k+1))			% Point of region B eND
% 2. Other option is to use w,g e {R+} -> where All periods have same no. elements
% which means 
case 2  
   k=[];
   k=1:1:mp
   switch fwrop % Flag for wr ODD parity (= 1 Odd, 0 even)
   case 0 % w is even => regions A & B are w/2 elements
      pAst(k)=ym1vr(k)
      pBnd(k)=ym1vr(k+1)
   case 1 % w is odd  => regions A & B are w/2 + extra element
      pAst(k)=floor(ym1vr(k))
      pBnd(k)= ceil(ym1vr(k+1))
   end
   switch fgrop
   case 0 % g is even => regions A & B are g/2 elements 
      pAnd(k)=ym2vr(k)
      pBst(k)=ym2vr(k)
   case 1 % g is odd  => regions A & B are g/2 + extra element
      pAnd(k)= ceil(ym2vr(k))
      pBst(k)=floor(ym2vr(k))
   end
end % switch choice3
% 3. Constructing  SPaN vectors and summing the suml elements over ml periodic str.
pAspn(k)=pAnd(k)-pAst(k);			% point A SPaN	
pBspn(k)=pBnd(k)-pBst(k);			% point B SPaN
pAav=mean(pAspn)
pBav=mean(pBspn)
pAstd=std(pAspn)
pBstd=std(pBspn)
% sum suml -> sumt for two regions A & B
p=0;
q=0;
sumAt=0;
sumBt=0;
p = 1:1:pAspn(1)
   for k=1:1:mp;
   pAst1 = pAst(k) + p-1;
   sumAt=suml(pAst1) + sumAt;
	end
q = 1:1:pBspn(1)
   for k=1:1:mp;
   pBst1 = pBst(k) + q-1;
   sumBt=suml(pBst1) + sumBt;
end
pAst1
pBst1
   % plot
   switch choice3
   case 1
   	pr=pAspn(1):-1:1
   	prr=pAspn(1)+1:-1:2
   	figure
   	plot(sumAt,p',sumBt,pr',sumBt,prr');axis ij;
   case 2
      qr=pBspn(1):-1:1 % q vector Reflected about horizontal
      plot(sumAt,p',sumBt,qr');axis ij;
   end
   dummy = menu('Press to','Re-process data/plot','Add two plots');
   fredo=dummy 
   hold off
   switch fredo
   case 1
      imshow(input2)
      hold on
      truesize
      wr
      wr=input('integer input wr = ') % enter new values for reprocessing image
      gr
      gr=input('integer input gr = ')
      wgr=wr+gr
      yr(1)
      yr1=input('integer input yr(1) = ')
      yr(1)=round(yr1)
      vwgset = 2
      hold off
   case 2
      sumBTt(q)=sumBt(qr)
      sumCy=sumAt + sumBTt'
      figure
      plot(sumCy,p');axis ij; % sum of Collected solute (along Longitudinal) as a
      % function of Transverse direction (also called Y to avoid confusion with time)
      choice = menu('Satisfactory:store results','Yes','no');
      switch choice
      case 1
         ouvar=zeros(1,5);
         ouvar(1)=wr;
         ouvar(2)=gr;
         ouvar(3)=yr(1);
         ouvar(4)=mp;
         ouvar(5)=frmula;
         ofnam = [ifname '.dat']
      dlmwrite(ofnam,ouvar, ';') % output data (ASCII) wth ifname of tif image  
      ofnamc= [ifname 'Cy.dat']   
      dlmwrite(ofnamc,sumCy, ';')
      %print sumCy-f
   	end
   end
end % end main program loop: fredo while

close
close
close