WiscPlan_olderMV/photonDoseCalc/scripts_m/header2hx.m

function header2hx(headerFileName,imgFileName,amiraScriptFileName)
% Creates an Amira .hx script from a Pinnacle .header file.  The .hx script
% can then be run from inside Amira to open the image.  The central idea is
% that a separate .am file will not have to be created just to view an
% image in Amira, thus saving hard drive space.
%
% Inputs:  headerFileName:  [char]  % location of Pinnacle header file
%          imgFileName: [char] % location of Pinnacle data file
%          amiraScriptFileName: [char] % location of Amira .hx file
%
% Ryan T Flynn 10/26/06

% ensure that the header file has the correct extension
if strcmp(headerFileName,'.header');
    error([headerFileName ' does not have the .header extension.']);
end

% ensure that the data file has the correct extension
if strcmp(imgFileName,'.img');
    error([imgFileName ' does not have the .img extension.']);
end

% ensure that the amira filename has the correct extension
if strcmp(amiraScriptFileName,'.hx');
    error([imgFileName ' does not have the .hx extension.']);
end

fid = fopen(headerFileName,'r');

if fid == -1
    error(['Unable to open ' headerFileName '.']);
end

tline = fgets(fid);
while tline ~= -1
    % check the line for key words
    if length(findstr(tline,'x_dim')) & ~length(findstr(tline,'fname_index_start'))
        eval(tline);  % run the line to get x_dim
    elseif length(findstr(tline,'y_dim'))
        eval(tline);  % run the line to get y_dim
    elseif length(findstr(tline,'z_dim'))
        eval(tline);  % run the line to get z_dim
    elseif length(findstr(tline,'x_pixdim'))
        eval(tline);  % run the line to get x_pixdim
    elseif length(findstr(tline,'y_pixdim'))
        eval(tline);  % run the line to get y_pixdim
    elseif length(findstr(tline,'z_pixdim'))
        eval(tline);  % run the line to get z_pixdim
    elseif length(findstr(tline,'x_start'))
        eval(tline);  % run the line to get x_start
    elseif length(findstr(tline,'y_start'))
        eval(tline);  % run the line to get x_start
    elseif length(findstr(tline,'z_start'))
        eval(tline);  % run the line to get x_start
    elseif length(findstr(tline,'bytes_pix'))
        eval(tline);  % number of bytes per pixel
    elseif length(findstr(tline,'byte_order'))
        eval(tline);  % number of bytes per pixel
    end
    tline = fgets(fid);
end

fclose(fid);

% calculate axes for the image
x = x_start + [0:x_dim-1]*x_pixdim;
y = y_start + [0:y_dim-1]*y_pixdim;
z = z_start + [0:z_dim-1]*z_pixdim;

% deduce the data type of the img file
if bytes_pix == 2
    dataType = 'short 1';
elseif bytes_pix == 4
    dataType = 'float 1';
end

% assign little of big endian byte orders
if byte_order == 0
    byteOrder = 'little';
elseif byte_order == 1
    byteOrder = 'big';
else
    error(['Unknown byte order in ' headerFileName '.']);
end
    
% create the .hx file
fid = fopen(amiraScriptFileName,'w');

% name of the structure that will be opened in Amira
amiraStructName = regexprep(amiraScriptFilleName,'.hx','');

% create Amira script
fprintf(fid,'# Amira Script\n');
fprintf(fid,['remove ' imgFileName '\n']);
fprintf(fid,'\n');
fprintf(fid,'set hideNewModules 0\n');
fprintf(fid,['[ load -raw ' imgFileName ' ' byteOrder ' xfastest ' dataType ' ' num2str(x_dim) ' ' num2str(y_dim) ' ' num2str(z_dim) ...
     ' ' num2str(x(1)) ' ' num2str(x(end)) ' ' num2str(y(1)) ' ' num2str(y(end)) ' ' num2str(z(1)) ' ' num2str(z(end)) ...
     '] setLabel ' imgFileName '\n']);
fprintf(fid,[imgFileName ' setIconPosition 20 10\n']);
fprintf(fid,[imgFileName ' flip 1\n']);  % flip the data along the y-axis
fprintf(fid,[imgFileName ' fire\n']);
fprintf(fid,[imgFileName ' setViewerMask 65535\n']);
fprintf(fid,'set hideNewModules 0\n');
fclose(fid);