%usage:  data = open_di(file_name)

%This program extracts the data from a NanoScope data file.  The scaled
%results are placed in the matrix data, an N x M x L matrix, where N is
%the number of lines, M is the number of points per line (N = M in most
%cases), and L is the number of simultaneous data channels recorded.
%This program assumes that the first data channel is topgraphy and all
%the other channels are not topography.  The data output is nm for the
%first channel and V for all subsequent channels.

%This program is based on the get_image_data m file which is a part of the
%Carpick Lab Toolbox, with changes made to the data scaling.

%Jennifer R. Hampton  2/16/09

function data = open_di(file_name)

%The scaling of binary data to physical units is based on Appendix B "Data
%File Format" from the NanoScope Command Reference Manual (Section B.6.3)

%The Z scale conversion factors for topography are in the following two
%header lines:
%\@Sens. Zscan: V XXX nm/V
%\@2:Z scale: V [Sens. Zscan] (XXX V/LSB) YYY V

%There will be one version of the second line for each simultaneous data
%channel that is recorded.  For example, a for a friction channel, the
%second header line is:
%\@2:Z scale:  V [Sens. Friction] (XXX V/LSB) YYY V
%The first header line in this case isn't needed:
%\@Sens. Friction: V 1.000000

%To convert from binary (LSB) to hardware units (V), the second line is
%used.  The XXX value in parentheses is the conversion factor that was used
%when the data were taken.  However, a rescaling is performed when the
%data are saved to use the full range of the 2-byte binary data.  So the
%scaling factor to convert saved LSB data to V is
%YYY V/2^16 LSB = YYY V/65536 LSB.

%In the topography case, to convert from hardware units (V) to physical
%units (nm), the first line is used.  The scaling factor is
%XXX nm/V.

%maximum integer stored in 2-byte number
maxlsb = 2^16;

%open file for reading
fid = fopen(file_name,'r');
if (fid == -1)
    disp('Error reading file, exiting');
    return;
end

%locations of scaling factors 
%in nm/V (for topographic data)
scal_data1 = di_header_find(file_name,'\@Sens. Zsens: V');
%in V/LSB for all data
scal_data2 = di_header_find(file_name,'\@2:Z scale: V [Sens.');

%locations of number of points per line
%(number of lines on next header line)
pos_spl = di_header_find(file_name,'\Samps');
%different positions of data sets
pos_data = di_header_find(file_name,'\Data offset');

%number of different data sets
L = length(pos_data);

fseek(fid, pos_spl(1),-1);
line = fgets(fid);
spl = get_num(line);
line = fgets(fid);
linno = get_num(line);

%scaling factor for topographic data in nm/V
fseek(fid,scal_data1,-1);
line = fgets(fid);
scaling1 = get_num(line);

for i = 1:L

    fseek(fid,pos_data(i),-1);
    line = fgets(fid);
    imag_pos = get_num(line);
   
    %scaling factor in V/LSB
    fseek(fid,scal_data2(i),-1);
    line = fgets(fid);
    scaling2 = get_num(line)/maxlsb;
    if i==1
        %combined scaling factor in nm/LSB for topographic data
        scaling = scaling1*scaling2;
    else
        %single scaling factor in V/LSB for nontopographic data
        scaling = scaling2;
    end

    fseek(fid,imag_pos,-1);
    A = fread(fid, [spl linno],'int16');
    data(:,:,i) = rot90(scaling*A);
   
end

fclose('all');