metaImageInfo.m

function info = metaImageInfo(fileName, varargin)

%METAIMAGEINFO Read information header of meta image data

%

%   INFO = metaImageInfo(FILENAME)

%   Read and decodes the information stored in metaimage header file.

%

%   Metaimage header files are text files containing parameters name/value

%   pairs in each line. 

%   Example of header file:

%     ObjectType = Image

%     NDims = 3

%     DimSize = 256 256 64

%     ElementType = MET_USHORT

%     HeaderSize = -1

%     ElementSize = 1 1 3

%     ElementSpacing = 1 1 1

%     ElementByteOrderMSB = False

%     ElementDataFile = image.raw

%

%   For information about MetaImage Header format, see:

%   http://www.itk.org/Wiki/MetaIO/Documentation#Quick_Start

%

%   Currently supported tags are:

%     NDims: number of dimensions

%     DimSize 

%     ElementType

%     ElementDataFile

%     HeaderSize

%     ElementSpacing

%     ElementByteOrderMSB

%     ElementNumberOfChannels

%     BinaryData

%     BinaryDataByteOrderMSB

%     CompressedData

%     CompressedDataSize 

%     AnatomicalOrientation

%     CenterOfRotation

%     Offset

%     TransformMatrix

%     ElementDataFile (should be the last tag in the file)

%

%

%   The values supported for 'ElementDataFile' are:

%   * the name of a single data file. Example: 'dataFile.raw'

%   * the keyword 'LIST', followed by the list of file names, one name by

%       line. Example:

%       ElementDataFile = LIST

%       slice-00.tif

%       slice-01.tif

%       slice-02.tif

%       ...

%   * a filename pattern, followed by three values corresponding to index

%       of the first slice, index of the last slice, and step between two

%       consecutive slices. Example: 'slice-%03d.tif 1 50 2'

%   * the 'LOCAL' keyword is not (yet...) supported.

%

%

%   Example

%      info = metaImageInfo('example.hdr');

%      X = metaImageRead(info);

%

%

%   See also

%   metaImageRead, readstack, analyze75info

%

% ------

% Author: David Legland

% e-mail: david.legland@grignon.inra.fr

% Created: 2010-01-27,    using Matlab 7.9.0.529 (R2009b)

% http://www.pfl-cepia.inra.fr/index.php?page=slicer

% Copyright 2010 INRA - Cepia Software Platform.



%   HISTORY

%   2011-08-17 code cleanup, better initialization of spacing





%% Open info file



% If the function is called without argument, open a dialog to read a file

if nargin == 0

    [filename, pathname] = uigetfile(...
        {'*.mha;*.mhd', 'Meta-Image info file (*.mha, *.mhd)'}, ...
        'Open Meta-Image info file');

    

    info = [pathname filename];

    if filename == 0

        return;

    end

end



% add file extension if not present

ext = [];

if length(fileName) > 3

    ext = fileName(end-3:end);

end

if ~strcmp(ext, '.mhd')

    fileName = [fileName '.mhd'];

end



% get base directory

path = fileparts(fileName);



% open the file for reading

f = fopen(fileName, 'rt');

if f == -1

    error(['Could not find the file: ' fileName]);

end





%% Initialisations



% extract key and value of current line

[tag string] = splitLine(fgetl(f));



% check header file contains an image

if ~strcmp(tag, 'ObjectType') || ~strcmp(string, 'Image')

    error('File should contain image data');

end



% default values

info.ObjectType = 'Image';

info.NDims = 0;

info.DimSize = [];

info.ElementType = 'uint8';

info.ElementDataFile = '';



% setup default values for spatial calibration

info.ElementSpacing = [];

info.ElementSize = [];



% default optional values

info.HeaderSize = 0;





%% Loop over lines in the file



while true

    % read current line, if exists

    line = fgetl(f);

    if line == -1

        break

    end



    % extract key and value of current line

    [tag string] = splitLine(line);

    

    % extract each possible tag

    switch tag

        % First, parse required tags

        case 'NDims'

            % number of dimensions. Used for initializing data structure

            nd = parseInteger(string);

            info.NDims = nd;

            

        case 'DimSize'

            info.DimSize = parseIntegerVector(string);

            

        case 'ElementType'

            info.ElementType = string;

            

        case 'HeaderSize'

            info.HeaderSize = parseInteger(string);

            

        case 'ElementDataFile'

            info.ElementDataFile = computeDataFileName(string, f, path);

            % this tag is supposed to be the last one in the tag list

            break;

            

        % Following tags are optional, but often encountered

        

        case 'ElementSize'

            info.ElementSize = parseFloatVector(string);

            

        case 'ElementSpacing'

            info.ElementSpacing = parseFloatVector(string);

            

        case 'ElementByteOrderMSB'

            info.ElementByteOrderMSB = parseBoolean(string);

            

        case 'ElementNumberOfChannels'

            info.ElementNumberOfChannels = parseInteger(string);

            

        case 'BinaryData'

            info.BinaryData = parseBoolean(string);

            

        case 'BinaryDataByteOrderMSB'

            info.BinaryDataByteOrderMSB = parseBoolean(string);

            

        case 'CompressedData'

            info.CompressedData = parseBoolean(string);

            

        case 'CompressedDataSize'

            info.CompressedData = parseIntegerVector(string);

            

        % Some less common tags, used e.g. by Elastix

        

        case 'AnatomicalOrientation'

            info.AnatomicalOrientation = string;

            

        case 'CenterOfRotation'

            info.CenterOfRotation = parseFloatVector(string);

            

        case 'Offset'

            info.Offset = parseFloatVector(string);

            

        case 'TransformMatrix'

            info.TransformMatrix = parseFloatVector(string);

            

        % And unknown tags

        otherwise

            warning('MetaImageInfo:UnknownTag', ...
                ['Unknown tag in MetaImage header: ' tag]);

            info.(tag) = string;

    end

end



fclose(f);





%% Process optional input arguments



while length(varargin) > 1

    info.(varargin{1}) = varargin{2};

    varargin(1:2) = [];

end





%% Cleanup initialization

if isempty(info.ElementSize) || isempty(info.ElementSpacing)

    if ~isempty(info.ElementSize)

        % init spacing from size

        info.ElementSpacing = info.ElementSize;

        

    elseif ~isempty(info.ElementSpacing)

        % init size from spacing

        info.ElementSize = info.ElementSpacing;

        

    else

        % init both spacing and size from dimension

        siz = ones(1, info.NDims);

        info.ElementSize = siz;

        info.ElementSpacing = siz;

        

    end

end





function name = computeDataFileName(string, f, path)

% compute filename or file name list from pattern and current path



% remove eventual trailing spaces

string = strtrim(string);



if strcmpi(string, 'list')

    % read the list of file names and add the path

    tline = fgetl(f);

    name = {};

    i = 1;

    while ischar(tline)

        name{i} = fullfile(path, tline); %#ok<AGROW>

        i = i + 1;

        tline = fgetl(f);

    end

    

elseif ~isempty(strfind(string, ' '))

    % If filename contains spaces, it is parsed to extract indices

    C = textscan(string, '%s %d %d %d');

    pattern = C{1}{1};

    i0 = C{2};

    iend = C{3};

    istep = C{4};

    

    inds = i0:istep:iend;

    

    name = cell(length(inds), 1);

    

    for i=1:length(inds)

        name{i} = fullfile(path, sprintf(pattern, inds(i)));

    end

    

else

    % Simply use the string as the name of the file

    name = fullfile(path, string);

end





function [tag string] = splitLine(line)

[tag remain] = strtok(line, '=');

tag = strtrim(tag);

string = strtrim(strtok(remain, '='));



function b = parseBoolean(string)

b = strcmpi(string, 'true');



function v = parseInteger(string)

v = sscanf(string, '%d');



function v = parseIntegerVector(string)

v = sscanf(string, '%d', inf)';



function v = parseFloatVector(string)

v = sscanf(string, '%f', inf)';