addpath /research/src/DNAdesign
addpath /research/src/AFMutils

% filepath = '/research/windows/backups/afm/d/Rizal/03-06-23/mov0623a.043'
% rawim = showafm(filepath,0);

% filepath = '/research/windows/backups/afm/d/Rizal/02-08-03/real0803.';
% rawim = showafm(sprintf('%s%03d',filepath, 032),0);

% filepath = '~winfree/Research/DNA/AFM_old/data.rizal/02-07-20/QBOX.097';
% rawim = showafm(filepath, 0);
filepath = '~winfree/Research/DNA/AFM_old/data.rizal/02-07-20/QBOX.091';
% filepath = '~winfree/Research/DNA/AFM_old/data.rizal/02-07-21/HIGHRES.007';
rawim = showafm(filepath, 0);

figure (1)
    imagesc (rawim)
    colormap gray
    truesize
    title 'raw image'
    
    showafm(filepath,1);
    
% adjust image so that all values are positive
low = min(min(rawim))
high = max(max(rawim))
rawim = rawim - low;
% rotate matrix by 90 degrees so that each former row is now a column
temp = rot90(rawim, 1);
% perform fft on each column
ftemp = fft(temp);

% apply some filter to the frequency domain

% % attempt at a butterworth filter: failed.
% d = fdesign.lowpass;
% hd = butter(d);
% ftemp = filter(hd, ftemp);

ftemp(1,:) = 0;
%ftemp(2,:) = ftemp(2,:) / 2;

% perform inverse transform
temp = ifft(ftemp);

% rotate matrix by -90 degrees so that the matrix is restored
temp = rot90(temp, -1);

temp_real = real (temp);
figure (2)
    imagesc (temp_real)
    colormap gray
    truesize
    title 'real portion'

temp_mag = abs (temp);
% high = max(max(temp_mag))
% temp_mag = high - temp_mag;
figure (3)
    imagesc (temp_mag)
    colormap gray
    truesize
    title 'magnitude'


high = max(max(temp_real));
temp_real = temp_real ./ high;
high = max(max(temp_mag));
temp_mag = temp_mag ./ high;
temp = temp_real + temp_mag;
figure (4)
    imagesc (temp)
    colormap gray
    truesize
    title 'final result = real + mag'

% try something else to remove differences between line intesities.
%[r,c] = size(rawim);
%temp = zeros([r,c]);
%for i = 1:r
%	temp(r,:) = histeq(rawim(r,:));
%end
%temp = histeq(temp);
% fails miserably.

t = graythresh(temp);
temp = im2bw(temp, t);

figure(5)
	imagesc(temp)
	colormap gray
	truesize
	title 'thresholded image'

    
pause;
close all;