% TRALONG1 1 called by DEPINTL sets up TRAnsverse vectors rep. electdes & gaps, 
% by requsting edge pnts & spec. pnts, sums LONGitdinl dirn then transvrs drctn thn
% INTERPOLATES -> av. intensities over 1/2 el wdth & gap D. Bakewell Tu/4/5/1999
% most recent update 21:35 Sa/21/7/2001 
imagmous1;
fredo = 1; % Flag begin processing that can be REDOne if unsatisfactory
while fredo == 1;
   [r,c]=size(rotimag);
	suml = sum(rotimag,2)/pmxlng;
	% SUMs rotated intens matix 'rotimag' 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
   % generate interpolation vectors
   % Integer VECtor Transverse direction on elctrd plne (1 row x pmxtrv colmns)
   switch fauto
   case 1
          ipolqrt=50 % for PhD thesis publication
         %ipolqrt=input('no. resolutn points for HALF electrode = HALF gap (eg 30) = ');
      case 2
         ipolqrt=invar(7);   
   end % end switch fauto      
   ipolhlf=round(2*ipolqrt);
   ipolper=round(2*ipolhlf);
   ipoltot = round(mp*ipolper);
   for n=1:1:edgpnts-1;
    	for p=1:1:ipolhlf;
      	pn=round(ipolhlf*n + p - ipolhlf);
      	ypolvec(pn)=y(n) + (y(n+1)-y(n))*p/ipolhlf;
      end % p
   end % n
   pnmax=round(ipolhlf*(edgpnts-1));
   pnvec=1:1:pnmax;
	t = 1:1:pmxtrv; % Integer VECtor Transverse direction on elctrd plne (1 row x pmxtrv colmns)
	ipolsuml = interp1(t,suml,ypolvec,'linear'); % interpolate suml  
	smlmaxr=round(max(suml));
	smlminr=round(min(suml));
	smldifr=smlmaxr-smlminr;
	pvec = smlminr:smldifr/200:smlmaxr;
   fvecgen = 1; % Flag for VECtor GENeration
   switch fauto
      case 1
         dummy = menu('    ','Press to continue');
      case 2
         pause(2)
   end % end switch fauto
	%	display sum longitudinal
	k = []; figure ; plot(suml',t');axis ij; %
   switch fauto
      case 1
         dummy = menu('    ','Press to continue');
      case 2
         pause(2)
   end % end switch fauto
   figure;    plot(ipolsuml',pnvec');axis ij;
   switch fauto
      case 1
         dummy = menu('    ','Press to continue');
      case 2
         pause(1)
   end % end switch fauto
	% plot(smlminr',y(n)','g+')
   hold off
   close; close;
	% sum suml -> sumt for two Transverse regions A & B
	Ai=0;
	Bi=0;
	p=0;
	q=0;
	sumAt=0;
	sumBt=0;
	for p = 1:1:ipolhlf;
   	sumA=0;
   	sumB=0;
		for k=1:1:mp;
   		Ai = p-1 + ipolqrt + round((k-1)*ipolper);
         ipvecA = ipolsuml(Ai);
         sumA=ipvecA + sumA;
   		Bi = Ai + ipolhlf;
   		ipvecB = ipolsuml(Bi);
			sumB=ipvecB + sumB;
		end
	sumAt(p)=sumA/double(mp); 	sumBt(p)=sumB/double(mp);
	end
	p =  1:1:ipolhlf; 	q = ipolhlf:-1:1;
   figure; plot(sumAt,p',sumBt,q');axis ij;
   switch fauto
      case 1
         dummy = menu('Press to','Add 2 profiles & plot');
      case 2
         pause(3)
   end % end switch fauto
	hold off
	sumBTt(p)=sumBt(q);
	sumCy=(sumAt + sumBTt)/double(2);
	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)
   pause(2)
   figure
   plot(p,sumCy)
   pause(2)
   switch fauto
      case 1
         fcont = menu('Press to','Re-process data/plot','Store results','End only');
      case 2
         fcont = 2;
      end
   hold off
   close
   close
   close
   %
   switch fcont
   case 1
      imshow(rotimag)
      hold on
      truesize
	   %[xi,yi] = ginput(1);
      plot(x,y,'c+','EraseMode','none')
      hold on
      fpoint2 = 2;
   		while fpoint2 == 2;
      	pntval = menu('POINT to be repositioned','None','1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20');
      	switch pntval
         case 1
            fpoint = 1
      		otherwise
               pntvlc=round(pntval-1);
      			yi=y(pntvlc)
      			ynew=input('New value of point = ')
               y(pntvlc)=ynew
               xnew=x(pntvlc)
               plot(xnew,ynew,'r+','EraseMode','none')
               hold on
               fpoint2 = menu('last point: satsfid wth selections?','Yes','No');
            end % switch pntval
         end % end fpoint2 while
      vwgset = 2
      hold off
%      
   case 2
      switch fauto
      case 1
       offset=7
       of=1:1:offset
       ed=1:1:edgpnts
       edoff=offset+1:1:edgpnts+offset
       ouvar=zeros(1,edgpnts);
       ouvar(1)=ffile
       ouvar(2)=fcolor
       ouvar(3)=frotate
       ouvar(4)=rotang
       ouvar(5)=ftralo
       ouvar(6)=mp
       ouvar(7)=ipolqrt
       ouvar(edoff)=y(ed)
      ofnam = [ifcode '.dat']
      dlmwrite(ofnam,ouvar, ';') % output data (ASCII) wth ifname of tif image set 
      ofnamc= [ifname 'Cy.dat']   
      dlmwrite(ofnamc,sumCy, ';')
   	case 2
      ofnamc= [ifcode 'Cyt.dat']; % creates matric with no. rows = no. images, 1st column rep. time (secs),
      % other other columns representing profiles (at each point).
      sumCyt(cnt,1)=time;
      sumCyt(cnt,p+1)=sumCy(1,p);
      dlmwrite(ofnamc,sumCyt, ';');
      end % end switch auto
%
    case 3  
    end
    switch fauto
       case 1
          fredo=menu('start again?','Yes','No')
       case 2
          fredo=2;
       end % end switch auto     
end % end main program loop: fredo while
close
close
close