loadh5.m

function varargout = loadh5(filename, varargin)
%
%    [data, meta] = loadh5(filename)
%    [data, meta] = loadh5(root_id)
%    [data, meta] = loadh5(filename, rootpath)
%    [data, meta] = loadh5(filename, rootpath, options)
%    [data, meta] = loadh5(filename, options)
%    [data, meta] = loadh5(filename, 'Param1',value1, 'Param2',value2,...)
%
%    Load data in an HDF5 file to a MATLAB structure.
%
%    author: Qianqian Fang (q.fang <at> neu.edu)
%
%    input
%        filename
%            Name of the file to load data from
%        root_id: an HDF5 handle (of type 'H5ML.id' in MATLAB)
%        rootpath : (optional)
%            Root path to read part of the HDF5 file to load
%        options: (optional) a struct or Param/value pairs for user specified options
%            Order: 'creation' - creation order (default), or 'alphabet' - alphabetic
%            Regroup: [0|1]: if 1, call regrouph5() to combine indexed
%                  groups into a cell array
%            PackHex: [1|0]: convert invalid characters in the group/dataset
%                  names to 0x[hex code] by calling encodevarname.m;
%                  if set to 0, call getvarname
%            ComplexFormat: {'realKey','imagKey'}: use 'realKey' and 'imagKey'
%                  as possible keywords for the real and the imaginary part
%                  of a complex array, respectively (sparse arrays not supported);
%                  a common list of keypairs is used even without this option
%            Transpose: [1|0] - if set to 1 (default), the row-majored HDF5
%                  datasets are transposed (to column-major) so that the
%                  output MATLAB array has the same dimensions as in the
%                  HDF5 dataset header.
%
%    output
%        data: a structure (array) or cell (array)
%        meta: optional output to store the attributes stored in the file
%
%    example:
%        a={rand(2), struct('va',1,'vb','string'), 1+2i};
%        saveh5(a,'test.h5');
%        a2=loadh5('test.h5')
%        a3=loadh5('test.h5','regroup',1)
%        isequaln(a,a3.a)
%        a4=loadh5('test.h5','/a1')
%
%    This function was adapted from h5load.m by Pauli Virtanen <pav at iki.fi>
%    This file is part of EasyH5 Toolbox: https://github.com/NeuroJSON/easyh5
%
%    License: GPLv3 or 3-clause BSD license, see https://github.com/NeuroJSON/easyh5 for details
%

path = '';
if (bitand(length(varargin), 1) == 0)
    opt = varargin2struct(varargin{:});
elseif (length(varargin) >= 3)
    path = varargin{1};
    opt = varargin2struct(varargin{2:end});
elseif (length(varargin) == 1)
    path = varargin{1};
end

opt.dotranspose = jsonopt('Transpose', 1, opt);
opt.stringarray = jsonopt('StringArray', 0, opt);
opt.rootpath = path;

if (exist('OCTAVE_VERSION', 'builtin') ~= 0)
    [varargout{1:nargout}] = load(filename, '-hdf5');
    if (opt.dotranspose)
        varargout{1} = transposemat(varargout{1});
    end
    return
end

if (isa(filename, 'H5ML.id'))
    loc = filename;
else
    try
        loc = H5F.open(filename, 'H5F_ACC_RDONLY', 'H5P_DEFAULT');
    catch ME
        error('fail to open file');
    end
end

if (~(isfield(opt, 'complexformat') && iscellstr(opt.complexformat) && numel(opt.complexformat) == 2))
    opt.complexformat = {'Real', 'Imag'};
end

opt.releaseid = 0;
vers = ver('MATLAB');
if (~isempty(vers))
    opt.releaseid = datenum(vers(1).Date);
end

if ((isfield(opt, 'order') && strcmpi(opt.order, 'alphabet'))  || opt.releaseid < datenum('1-Jan-2015'))
    opt.order = 'H5_INDEX_NAME';
else
    opt.order = 'H5_INDEX_CRT_ORDER';
end

try
    if (nargin > 1 && ~isempty(path))
        try
            rootgid = H5G.open(loc, path);
            [varargout{1:nargout}] = load_one(rootgid, opt);
            H5G.close(rootgid);
        catch
            [gname, dname] = fileparts(path);
            rootgid = H5G.open(loc, gname);
            [status, res] = group_iterate(rootgid, dname, struct('data', struct, 'meta', struct, 'opt', opt));
            if (nargout > 0)
                varargout{1} = res.data;
            elseif (nargout > 1)
                varargout{2} = res.meta;
            end
            H5G.close(rootgid);
        end
    else
        [varargout{1:nargout}] = load_one(loc, opt);
    end
    H5F.close(loc);
catch ME
    H5F.close(loc);
    rethrow(ME);
end

if (jsonopt('Regroup', 0, opt))
    if (nargout >= 1)
        varargout{1} = regrouph5(varargout{1});
    elseif (nargout >= 2)
        varargout{2} = regrouph5(varargout{2});
    end
end

if (isfield(opt, 'jdata') && opt.jdata && nargout >= 1)
    varargout{1} = jdatadecode(varargout{1}, 'Base64', 0, opt);
end

% --------------------------------------------------------------------------
function [data, meta] = load_one(loc, opt)

data = struct();
meta = struct();
inputdata = struct('data', data, 'meta', meta, 'opt', opt);

% Load groups and datasets
try
    [status, count, inputdata] = H5L.iterate(loc, opt.order, 'H5_ITER_INC', 0, @group_iterate, inputdata);
catch ME
    if (strcmp(opt.order, 'H5_INDEX_CRT_ORDER'))
        [status, count, inputdata] = H5L.iterate(loc, 'H5_INDEX_NAME', 'H5_ITER_INC', 0, @group_iterate, inputdata);
    else
        rethrow(ME);
    end
end

data = inputdata.data;
meta = inputdata.meta;

% --------------------------------------------------------------------------
function [status, res] = group_iterate(group_id, objname, inputdata)
status = 0;
attr = struct();

encodename = jsonopt('PackHex', 1, inputdata.opt);

try
    data = inputdata.data;
    meta = inputdata.meta;

    % objtype index
    info = H5G.get_objinfo(group_id, objname, 0);
    objtype = info.type;
    objtype = objtype + 1;

    if objtype == 1
        % Group
        name = regexprep(objname, '.*/', '');

        group_loc = H5G.open(group_id, name);
        try
            [sub_data, sub_meta] = load_one(group_loc, inputdata.opt);
            H5G.close(group_loc);
        catch ME
            H5G.close(group_loc);
            rethrow(ME);
        end
        if (encodename)
            name = encodevarname(name);
        else
            name = genvarname(name);
        end
        data.(name) = sub_data;
        meta.(name) = sub_meta;

    elseif objtype == 2
        % Dataset
        name = regexprep(objname, '.*/', '');

        dataset_loc = H5D.open(group_id, name);
        try
            sub_data = H5D.read(dataset_loc, ...
                                'H5ML_DEFAULT', 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT');
            try
                [status, count, attr] = H5A.iterate(dataset_loc, 'H5_INDEX_NAME', 'H5_ITER_INC', 0, @getattribute, attr);
            catch
                attr = [];
            end
            H5D.close(dataset_loc);
        catch exc
            H5D.close(dataset_loc);
            rethrow(exc);
        end
        if (ischar(sub_data) && numel(sub_data) > 1 && sub_data(end) == 0)
            sub_data = sub_data(1:end - 1);
        end

        if ((isnumeric(sub_data) && inputdata.opt.dotranspose) || (iscell(sub_data) && length(sub_data) > 1))
            sub_data = permute(sub_data, ndims(sub_data):-1:1);
        end
        sub_data = fix_data(sub_data, attr, inputdata.opt);
        if (encodename)
            name = encodevarname(name);
        else
            name = genvarname(name);
        end
        data.(name) = sub_data;
        meta.(name) = attr;
    end
catch ME
    rethrow(ME);
end
res = struct('data', data, 'meta', meta, 'opt', inputdata.opt);

% --------------------------------------------------------------------------
function data = fix_data(data, attr, opt)
% Fix some common types of data to more friendly form.

if isstruct(data)
    fields = fieldnames(data);

    if (length(intersect(fields, {'SparseIndex', opt.complexformat{1}})) == 2)
        if isnumeric(data.SparseIndex) && isnumeric(data.(opt.complexformat{1}))
            if (nargin > 1 && isstruct(attr))
                if (isfield(attr, 'SparseArraySize'))
                    spd = sparse(1, prod(attr.SparseArraySize));
                    if (isfield(data, opt.complexformat{2}))
                        spd(data.SparseIndex) = complex(data.(opt.complexformat{1}), data.(opt.complexformat{2}));
                    else
                        spd(data.SparseIndex) = data.(opt.complexformat{1});
                    end
                    data = reshape(spd, attr.SparseArraySize(:)');
                    return
                end
            end
        end
    else
        if (numel(opt.complexformat) == 2 && length(intersect(fields, opt.complexformat)) == 2)
            if isnumeric(data.(opt.complexformat{1})) && isnumeric(data.(opt.complexformat{2}))
                data = data.(opt.complexformat{1}) + 1j * data.(opt.complexformat{2});
            end
        else
            % if complexformat is not specified or not found, try some common complex number storage formats
            if (length(intersect(fields, {'Real', 'Imag'})) == 2)
                if isnumeric(data.Real) && isnumeric(data.Imag)
                    data = data.Real + 1j * data.Imag;
                end
            elseif (length(intersect(fields, {'real', 'imag'})) == 2)
                if isnumeric(data.real) && isnumeric(data.imag)
                    data = data.real + 1j * data.imag;
                end
            elseif (length(intersect(fields, {'Re', 'Im'})) == 2)
                if isnumeric(data.Re) && isnumeric(data.Im)
                    data = data.Re + 1j * data.Im;
                end
            elseif (length(intersect(fields, {'re', 'im'})) == 2)
                if isnumeric(data.re) && isnumeric(data.im)
                    data = data.re + 1j * data.im;
                end
            elseif (length(intersect(fields, {'r', 'i'})) == 2)
                if isnumeric(data.r) && isnumeric(data.i)
                    data = data.r + 1j * data.i;
                end
            end
        end
    end
end

if (isa(data, 'uint8') || isa(data, 'int8'))
    if (nargin > 1 && isstruct(attr))
        if (isfield(attr, 'MATLABObjectClass'))
            data = getArrayFromByteStream(data); % use undocumented function
        end
    end
end

% handeling string arrays (or cell of char strings)
if (iscell(data) && length(data) > 1)
    if (all(cellfun(@ischar, data)) && exist('string') && opt.stringarray)
        data = string(data);
    end
end

% --------------------------------------------------------------------------
function [status, dataout] = getattribute(loc_id, attr_name, info, datain)
status = 0;
attr_id = H5A.open(loc_id, attr_name, 'H5P_DEFAULT');
datain.(attr_name) = H5A.read(attr_id, 'H5ML_DEFAULT');
H5A.close(attr_id);
dataout = datain;