Snirf writing (#117)

function gid = HDF5_CreateGroup(fid, group)

if strcmp(group, '/') || strcmp(group, '\')

    gid = H5G.open(fid, '/');

    return

end

try

    gid = H5G.open(fid, group);

catch

    rootgroup = fileparts(group);

    gid = HDF5_CreateGroup(fid, rootgroup);

    gid = H5G.create(gid, group, 'H5P_DEFAULT','H5P_DEFAULT','H5P_DEFAULT');

end

function err = HDF5_DatasetWrite(fname, location, data)

if exist(fname,'file')

    fid = H5F.open(fname, 'H5F_ACC_RDWR', 'H5P_DEFAULT');

else

    fid = H5F.create(fname, 'H5F_ACC_TRUNC', 'H5P_DEFAULT', 'H5P_DEFAULT');

end

if fid<0

    err = -1;

    return;

end

% Create group where dataset is located

group = filesepStandard(fileparts(location), 'nameonly');

gid = CreateGroup(fid, group);

if gid < 0

    err = -1;

    return;

end

% Update dataset

err = WriteDataset(fid, location, data);

% ----------------------------------------------------------------

function gid = CreateGroup(fid, group)

if group == '/'

    gid = H5G.open(fid, '/');

    return;

end

try

    gid = H5G.open(fid, group);

catch

    [rootgroup, group] = filesepStandard(fileparts(group));

    gid = CreateGroup(fid, rootgroup);

    gid = H5G.create(gid, group, 'H5P_DEFAULT','H5P_DEFAULT','H5P_DEFAULT');

end

% --------------------------------------------------------------

function err = WriteDataset(fid, location, data)

err = 0;

% data = HDF5_Transpose(data);

dims = size(data);

h5_dims = fliplr(dims);

unlimited = H5ML.get_constant_value('H5S_UNLIMITED');

h5_maxdims = [unlimited, unlimited];

if isnumeric(data)

    type_id = H5T.copy('H5T_NATIVE_DOUBLE');

elseif ischar(data)

    type_id = H5T.copy('H5T_C_S1'); 

else

    err = -1;

    return;

end

space_id = H5S.create_simple(2, h5_dims, h5_maxdims);

proplist_id = H5P.create('H5P_DATASET_CREATE');

% Open or create dataset

try

    dset_id = H5D.open(fid, location);

    H5D.set_extent(dset_id, h5_dims);

catch

    H5P.set_chunk(proplist_id, h5_dims);

    dset_id = H5D.create(fid, location, type_id, space_id, proplist_id);

end

file_space_id = H5D.get_space(dset_id);

% Write dataset

% H5D.write(dset_id, type_id, space_id, file_space_id, proplist_id, data);

H5D.write(dset_id, type_id, space_id, file_space_id, 'H5P_DEFAULT', data);

% Close space, type, dataset and file

H5S.close(space_id);

H5T.close(type_id);

H5D.close(dset_id);

H5F.close(fid);

% ----------------------------------------------------------------

function [dset_id, type_id, space_id, proplist_id] = CreateDataset(fid, location, h5_dims)

h5_maxdims = h5_dims;

type_id = H5T.copy('H5T_NATIVE_DOUBLE');

space_id = H5S.create_simple(2, h5_dims, h5_maxdims);

proplist_id = H5P.create('H5P_DATASET_CREATE');

H5P.set_chunk(proplist_id, [h5_dims(1), h5_dims(2)]);

dset_id = H5D.create(fid, location, type_id, space_id, proplist_id);

function HDF5_DatasetWriteStrings(fname, location, data)

if ~exist(fname, 'file')

    fid = H5F.create(fname, 'H5F_ACC_TRUNC', 'H5P_DEFAULT', 'H5P_DEFAULT');

else

    fid = H5F.open(fname,'H5F_ACC_RDWR','H5P_DEFAULT');

end

if iscell(data)

    data = cell2str_new(data);

end

filetype = H5T.copy('H5T_FORTRAN_S1'); 

H5T.set_size(filetype, size(data,2)); 

memtype = H5T.copy('H5T_C_S1'); 

H5T.set_size(memtype, size(data,2)); 

% Create dataspace. Setting maximum size to [] sets the maximum 

% size to be the current size. 

space = H5S.create_simple(1, size(data,1), []); 

% Create the dataset and write the string data to it. 

try

    dset = H5D.create(fid, location, filetype, space, 'H5P_DEFAULT'); 

catch

    dset = H5D.open(fid, location);

end

% Transpose the data to match the layout in the H5 file to match C 

% generated H5 file. 

H5D.write(dset, memtype, 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT',  data'); 

% Close and release resources. 

H5D.close(dset); 

H5S.close(space); 

H5T.close(filetype); 

H5T.close(memtype); 

H5F.close(fid); 

function h5save(fname, varval, varname)

if nargin==1

    varname = '';

end

if exist(fname, 'file')

    delete(fname);

end

fid = H5F.create(fname, 'H5F_ACC_TRUNC', 'H5P_DEFAULT', 'H5P_DEFAULT');

H5F.close(fid);

h5savevar(fname, varval, varname);

% ---------------------------------------------------------------------------

function h5savevar(fname, varval, varname)

% Simple matrices: uint, int, double, char, etc

if ~isstruct(varval) && ~isobject(varval)

    % Create new leaf variable if it doesn't exist. 

    if ~exist(fname, 'file') || ~h5exist(h5info(fname), varname)

        % Since HDF5 does not support empty or null variable, if varval is null 

        % add a _0 suffix to the var name and then don't write to it.          

        if ~isempty(varval)

            hdf5write(fname, varname, varval, 'WriteMode','append');

        else

            varname_0 = eval( sprintf('''%s_0'';', varname) );

            hdf5write(fname, varname_0, 0, 'WriteMode','append');

        end

    end

% Structs and Classes

else

    for jj=1:length(varval)

        props = propnames(varval(jj));

        for ii=1:length(props)

            if isempty(varname) || varname(1)=='/'

                subvarname = sprintf('%s_%d/%s', varname, jj, props{ii});

            else

                subvarname = sprintf('/%s_%d/%s', varname, jj, props{ii});

            end

            subvar = eval( sprintf('varval(jj).%s', props{ii}) );

            h5savevar(fname, subvar, subvarname);

        end

    end

end

function h5write_safe(fname, name, val)

if ~isempty(val)

    h5create(fname, name, [size(val,1), size(val,2)]);

    h5write(fname, name, val);

end