% Dave's Sub-program DEPINTL (called by DEPINT - which processes multiple images 
% DEP of beads/dna on INTerdigitated electrodes that via Looping arrangement
% Scottish Parliament election day Th/6/5/1999 D.Bakewell
% NOTES: Direction along electrode strips is referred to as LONGITUDINAL;
% Direction perpendicular to Longitudinal is referred to as TRANSVERSE
%
pmxlng = 720
pmxtrv = 540
switch fmpg
case 1
   i=1:1:pmxtrv;
   k=1:1:pmxlng;
	input2=[];   
   %j=1+(cnt-1)*pmxlng:1:cnt*pmxlng; % use when series of MPEG frames loaded at once 
   j=k; % use when series of MPEG frames loaded one at a time
	input2(i,k)=mpgim(i,j);    
case 2   
	% input file: user input
	switch ffile;
	case 1
   	ifcode = input('enter RGB tif filename WITHOUT  "**.dib":  ','s');
   	ifname = [ifcode ifnum]
      mapA = imread(ifname);
      message=['Reading in DIB file & -> Grayscale']
   	rgb = double(mapA)/255;
		input2 = rgb2gray(rgb); % RGB -> intensity gray
	case 2
   	switch fauto
   	case 1
      	ifcode = input('enter RGB tif filename WITHOUT "**.tif":  ','s');
   	end % end switch fauto INput file CODEname already entered in DEPINT
   	ifname = [ifcode ifnum]
      ifdnam = [ifname '.tif']
      message=['Reading in TIF file & -> Grayscale']
		[r,g,b] = tiffread(ifname);
   	input2 = rgb2gray(r,g,b); % RGB -> intensity gray
	case 3
   	ifcode = input('enter Gray tif filename WITHOUT "**.tif":  ','s');
   	ifname = [ifcode ifnum]
      ifdnam = [ifname '.tif']
      message=['Reading in GRAYSCALE TIF file']
   	input2 = imread(ifdnam,'tif');
		% filename.fmt -> i=pmxtrv x j=pmxlng Uint8 array MATRIX coord sys.
	end % end Flag for FILE
end % end Flag for MPeG
% -------------------------------------------------------------------------
rotatim; % rotate image
switch fauto
   case 1
      ftralo = menu('Vert Per i Av option:','flexible/interpolation','non/integer periods');
   case 2
      ftralo=invar(5)   
   end % end switch fauto      
switch ftralo % average over longitudinal/transverse directions
   case 1
      tralong1; % average using interpolation in transverse, pixel sum longitudinal  
	case 2
      tralong2; % average by constructing non/integer transverse, pixel sum longitudinal 
end % end span vector construction