avw_hdr_read.m

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function [ avw, machine ] = avw_hdr_read(fileprefix, machine)

% avw_hdr_read - read Analyze format data header (*.hdr)
%
% [ avw, machine ] = avw_hdr_read(fileprefix, [machine])
%
% fileprefix - string filename (without .hdr); the file name
%              can be given as a full path or relative to the
%              current directory.
% 
% machine - a string, see machineformat in fread for details.
%           The default here is 'ieee-le' but the routine
%           will automatically switch between little and big
%           endian to read any such Analyze header.  It
%           reports the appropriate machine format and can
%           return the machine value.
%
% avw.hdr - a struct, all fields returned from the header.
%           For details, find a good description on the web
%           or see the Analyze File Format pdf in the 
%           mri_toolbox doc folder or read this .m file.
%
% This function is called by avw_img_read
% 
% See also avw_hdr_write, avw_hdr_make, avw_view_hdr, avw_view
% 

% $Revision: 1.10 $ $Date: 2004/02/07 01:41:51 $

% Licence:  GNU GPL, no express or implied warranties
% History:  05/2002, [e-mail]
%                    The Analyze format and c code below is copyright 
%                    (c) Copyright, 1986-1995
%                    Biomedical Imaging Resource, Mayo Foundation
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

version = '[$Revision: 1.10 $]';
fprintf('\nAVW_HDR_READ [v%s]\n',version(12:16));  tic;

if ~exist('fileprefix','var'),
    msg = sprintf('...no input fileprefix - see help avw_hdr_read\n\n');
    error(msg);
end
if ~exist('machine','var'), machine = 'ieee-le'; end


if findstr('.hdr',fileprefix),
    % fprintf('...removing .hdr extension from ''%s''\n',fileprefix);
    fileprefix = strrep(fileprefix,'.hdr','');
end
if findstr('.img',fileprefix),
    % fprintf('...removing .img extension from ''%s''\n',fileprefix);
    fileprefix = strrep(fileprefix,'.img','');
end
file = sprintf('%s.hdr',fileprefix);

if exist(file),
    fprintf('...reading %s Analyze format',machine);
    fid = fopen(file,'r',machine);
    avw.hdr = read_header(fid);
    avw.fileprefix = fileprefix;
    fclose(fid);
    
    if ~isequal(avw.hdr.hk.sizeof_hdr,348),
        fprintf('...failed.\n');
        % first try reading the opposite endian to 'machine'
        switch machine,
        case 'ieee-le', machine = 'ieee-be';
        case 'ieee-be', machine = 'ieee-le';
        end
        fprintf('...reading %s Analyze format',machine);
        fid = fopen(file,'r',machine);
        avw.hdr = read_header(fid);
        avw.fileprefix = fileprefix;
        fclose(fid);
    end
    if ~isequal(avw.hdr.hk.sizeof_hdr,348),
        % Now throw an error
        fprintf('...failed.\n');
        msg = sprintf('...size of header not equal to 348 bytes!\n\n');
        error(msg);
    end
else
    msg = sprintf('...cannot find file %s.hdr\n\n',file);
    error(msg);
end

t=toc; fprintf('...done (%5.2f sec).\n',t);

return


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [ dsr ] = read_header(fid)
    
    % Original header structures - ANALYZE 7.5
	%struct dsr
	%       { 
	%       struct header_key hk;            /*   0 +  40       */
	%       struct image_dimension dime;     /*  40 + 108       */
	%       struct data_history hist;        /* 148 + 200       */
	%       };                               /* total= 348 bytes*/
    dsr.hk   = header_key(fid);
    dsr.dime = image_dimension(fid);
    dsr.hist = data_history(fid);
    
return



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [hk] = header_key(fid)
    
    % The required elements in the header_key substructure are: 
    %
	% int sizeof_header   Must indicate the byte size of the header file. 
	% int extents         Should be 16384, the image file is created as 
	%                     contiguous with a minimum extent size. 
	% char regular        Must be 'r' to indicate that all images and 
	%                     volumes are the same size. 
	
	% Original header structures - ANALYZE 7.5
	% struct header_key                      /* header key      */ 
	%       {                                /* off + size      */
	%       int sizeof_hdr                   /*  0 +  4         */
	%       char data_type[10];              /*  4 + 10         */
	%       char db_name[18];                /* 14 + 18         */
	%       int extents;                     /* 32 +  4         */
	%       short int session_error;         /* 36 +  2         */
	%       char regular;                    /* 38 +  1         */
	%       char hkey_un0;                   /* 39 +  1         */
	%       };                               /* total=40 bytes  */
    
    fseek(fid,0,'bof');
    
    hk.sizeof_hdr    = fread(fid, 1,'*int32');  % should be 348!
    hk.data_type     = fread(fid,10,'*char')';
    hk.db_name       = fread(fid,18,'*char')';
    hk.extents       = fread(fid, 1,'*int32');
    hk.session_error = fread(fid, 1,'*int16');
    hk.regular       = fread(fid, 1,'*char')'; % might be uint8
    hk.hkey_un0      = fread(fid, 1,'*uint8')';
    
    % check if this value was a char zero
    if hk.hkey_un0 == 48,
        hk.hkey_un0 = 0;
    end
    
return

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [ dime ] = image_dimension(fid)
    
	%struct image_dimension
	%       {                                /* off + size      */
	%       short int dim[8];                /* 0 + 16          */
    %           /*
    %           dim[0]      Number of dimensions in database; usually 4. 
    %           dim[1]      Image X dimension;  number of *pixels* in an image row. 
    %           dim[2]      Image Y dimension;  number of *pixel rows* in slice. 
    %           dim[3]      Volume Z dimension; number of *slices* in a volume. 
    %           dim[4]      Time points; number of volumes in database
    %           */
	%       char vox_units[4];               /* 16 + 4          */
	%       char cal_units[8];               /* 20 + 8          */
	%       short int unused1;               /* 28 + 2          */
	%       short int datatype;              /* 30 + 2          */
	%       short int bitpix;                /* 32 + 2          */
	%       short int dim_un0;               /* 34 + 2          */
	%       float pixdim[8];                 /* 36 + 32         */
	%			/*
	%				pixdim[] specifies the voxel dimensions:
	%				pixdim[1] - voxel width, mm
	%				pixdim[2] - voxel height, mm
	%				pixdim[3] - slice thickness, mm
    %               pixdim[4] - volume timing, in msec
	%					..etc
	%			*/
	%       float vox_offset;                /* 68 + 4          */
	%       float roi_scale;                 /* 72 + 4          */
	%       float funused1;                  /* 76 + 4          */
	%       float funused2;                  /* 80 + 4          */
	%       float cal_max;                   /* 84 + 4          */
	%       float cal_min;                   /* 88 + 4          */
	%       int compressed;                  /* 92 + 4          */
	%       int verified;                    /* 96 + 4          */
	%       int glmax;                       /* 100 + 4         */