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%WRITE_DATASET write dataset data_name, containing data to ID gid
%*-----------------------------------------------------------------------*
%|                                                                       |
%|  Except where otherwise noted, this work is licensed under a          |
%|  Creative Commons Attribution-NonCommercial-ShareAlike 4.0            |
%|  International (CC BY-NC-SA 4.0) license.                             |
%|                                                                       |
%|  Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch)    |
%|                                                                       |
%|      Author: CXS group, PSI  |
%*-----------------------------------------------------------------------*
% You may use this code with the following provisions:
%
% If the code is fully or partially redistributed, or rewritten in another
% computing language this notice should be included in the redistribution.
%
% If this code, or subfunctions or parts of it, is used for research in a
% publication or if it is fully or partially rewritten for another
% computing language the authors and institution should be acknowledged
% in written form in the publication: “Data processing was carried out
% using the “cSAXS matlab package” developed by the CXS group,
% Paul Scherrer Institut, Switzerland.”
% Variations on the latter text can be incorporated upon discussion with
% the CXS group if needed to more specifically reflect the use of the package
% for the published work.
%
% A publication that focuses on describing features, or parameters, that
% are already existing in the code should be first discussed with the
% authors.
%
% This code and subroutines are part of a continuous development, they
% are provided “as they are” without guarantees or liability on part
% of PSI or the authors. It is the user responsibility to ensure its
% proper use and the correctness of the results.
function write_dataset(data, gid, data_name, plist, varargin)
import io.HDF.*
extend_data = false;
link = false;
link_type = '';
cellstrdata = false;
write_data = true;
if ~isempty(varargin)
comp = varargin{1};
else
comp = true;
end
if nargin > 5
overwrite = varargin{2};
else
overwrite = true;
end
if nargin > 6
data_attr = varargin{3};
else
data_attr = [];
end
if nargin > 7
extend_dim = varargin{4};
else
extend_dim = 0;
end
if nargin > 8
extendable = varargin{5};
else
extendable = false;
end
if nargin > 9
extend_offset = varargin{6};
else
extend_offset = 0;
end
if nargin > 10
extend_maxdims = varargin{7};
else
extend_maxdims = 0;
end
[datatype, data] = get_datatype(data);
filespaceID = [];
function create_dataspace()
if extendable
unlimited = H5ML.get_constant_value('H5S_UNLIMITED');
dims_max = repmat(unlimited, 1, numel(dims));
else
dims_max = dims;
end
if ~extend_dim
if ~extendable
dataspaceID = H5S.create_simple(length(dims), fliplr(dims), fliplr(dims_max));
else
try
datasetID = H5D.open(gid, data_name);
filespaceID = H5D.get_space(datasetID);
[~, spaceDims] = H5S.get_simple_extent_dims(filespaceID);
% spaceDims = fliplr(spaceDims);
start = ones(1,numel(dims))-1;
count = dims;
stride = ones(1, numel(start));
boundsEnd = start + (count).*stride;
new_dims = fliplr(boundsEnd);
H5S.close(filespaceID);
H5D.set_extent(datasetID,new_dims);
filespaceID = H5D.get_space(datasetID);
H5S.select_hyperslab(filespaceID, 'H5S_SELECT_SET', fliplr(start), fliplr(stride), ...
fliplr(count), ones(1,length(start)));
dataspaceID = H5S.create_simple(numel(count),fliplr(count),[]);
extend_data = true;
catch
dataspaceID = H5S.create_simple(length(dims), fliplr(dims), fliplr(dims_max));
end
end
else
try
datasetID = H5D.open(gid, data_name);
filespaceID = H5D.get_space(datasetID);
[~, spaceDims] = H5S.get_simple_extent_dims(filespaceID);
spaceDims = fliplr(spaceDims);
if extend_offset
start = [ones(1,extend_dim-1) extend_offset+1]-1;
else
start = [ones(1,extend_dim-1) spaceDims(end)+1]-1;
end
if numel(spaceDims) > numel(dims)
count = [dims 1];
else
count = dims;
end
stride = ones(1, numel(start));
boundsEnd = start + (count-1).*stride;
if extend_maxdims
boundsStart = spaceDims;
boundsStart(end) = extend_maxdims;
else
boundsStart = spaceDims;
end
new_dims = fliplr(max(boundsStart,boundsEnd+1));
H5S.close(filespaceID);
H5D.set_extent(datasetID,new_dims);
filespaceID = H5D.get_space(datasetID);
H5S.select_hyperslab(filespaceID, 'H5S_SELECT_SET', fliplr(start), fliplr(stride), ...
fliplr(count), ones(1,length(start)));
dataspaceID = H5S.create_simple(numel(count),fliplr(count),[]);
extend_data = true;
catch
unlimited = H5ML.get_constant_value('H5S_UNLIMITED');
maxdims = [dims(1:extend_dim-1) unlimited];
% maxdims = repmat(-1, 1, extend_dim);
if numel(maxdims) > numel(dims)
dims = [dims 1];
end
dataspaceID = H5S.create_simple(length(dims), [fliplr(dims)], fliplr(maxdims));
end
end
end
if strcmp(datatype, 'complex')
%%% prepare compound dataset for complex input data
dims = size(data);
data_temp = data;
data = [];
data.r = real(data_temp);
data.i = imag(data_temp);
create_dataspace();
% Create the required data types
complexType = H5T.copy(get_datatype(data.r));
sz = H5T.get_size(complexType);
% Create the compound datatype for memory.
datatypeID = H5T.create ('H5T_COMPOUND', 2*sz);
H5T.insert (datatypeID, 'r',0, complexType);
H5T.insert (datatypeID, 'i',sz, complexType);
memtype = datatypeID;
data_attr.MATLAB_class = 'complex';
elseif ischar(data)
% check if char is a link
ch_entrs = strsplit(data, ':');
if length(ch_entrs) >= 2
link = true;
if strcmp(ch_entrs{1}, 'ext')
% prepare external link
link_type = 'ext';
elseif strcmp(ch_entrs{1}, 'int_soft')
% prepare internal soft link
link_type = 'int_soft';
elseif strcmp(ch_entrs{1}, 'int_hard')
% prepare internal hard link
link_type = 'int_hard';
end
else
data = {data};
datatypeID = H5T.copy ('H5T_FORTRAN_S1');
H5T.set_size (datatypeID,'H5T_VARIABLE');
memtype = H5T.copy ('H5T_C_S1');
H5T.set_size (memtype, 'H5T_VARIABLE');
dataspaceID = H5S.create ('H5S_SCALAR');
end
elseif iscell(data) || strcmp(datatype, 'char_array')
if iscellstr(data)
cellstrdata = true;
datatypeID = H5T.copy ('H5T_C_S1');
H5T.set_size (datatypeID, 'H5T_VARIABLE');
dgcv = H5ML.get_constant_value('H5S_UNLIMITED');
dataspaceID = H5S.create_simple(1,numel(data),dgcv);
memtype = datatypeID;
plist_cr = H5P.create('H5P_DATASET_CREATE');
H5P.set_chunk(plist_cr,1);
if strcmp(datatype, 'char_array')
data_attr.MATLAB_class = 'char_array';
end
else
write_data = false;
fn_names = cell(1,length(data));
cell_gid = add_groups(gid, data_name, plist, true);
for ii=1:length(data)
fn_names{ii} = sprintf([data_name '_%d'],ii-1);
write_dataset(data{ii}, cell_gid, fn_names{ii}, plist, comp, overwrite);
end
write_attribute(cell_gid, 'cell', 'MATLAB_class');
end
elseif isstruct(data)
write_data = false;
struct_gid = add_groups(gid, data_name, plist, true);
add_content(data, struct_gid, plist, comp, overwrite);
else
datatypeID = H5T.copy(datatype);
dims = size(data);
if isfield(data_attr, 'save2hdf5DataShape')
dims = data_attr.save2hdf5DataShape;
end
% prepare dataspace
create_dataspace();
memtype = 'H5ML_DEFAULT';
end
%%% create groups and write data
if comp && ~iscell(data) && ~ischar(data) && write_data || extend_dim || extendable
% define compression and chunk size
plist_ch = H5P.create('H5P_DATASET_CREATE');
if length(dims)>=3
chunk_dims = [dims(1) dims(2) ones(1, numel(dims)-2)];
else
chunk_dims = dims;
end
h5_chunk_dims = fliplr(chunk_dims);
H5P.set_chunk(plist_ch,h5_chunk_dims);
H5P.set_shuffle(plist_ch);
if comp
H5P.set_deflate(plist_ch,comp);
end
% Try to create a new dataset. If it exists, try to open it.
try
if ~extend_data
if cellstrdata
datasetID = H5D.create(gid,data_name,datatypeID,dataspaceID,plist_cr);
else
datasetID = H5D.create(gid,data_name,datatypeID,dataspaceID,plist_ch);
% create_dataspace();
end
end
catch
if ~overwrite
try
datasetID = H5D.open(gid, data_name);
catch
error('Could not create dataset %s! Try a different name or overwrite the already existing file.', data_name);
end
else
keyboard
error('Dataset %s already exists! Try a different name or overwrite the already existing file.', data_name);
end
end
elseif ~link && write_data
% Same as above but without compression:
% Try to create a new dataset. If it exists, try to open it.
try
if cellstrdata
datasetID = H5D.create(gid,data_name,datatypeID,dataspaceID,plist_cr);
else
datasetID = H5D.create(gid,data_name,datatypeID,dataspaceID,plist);
end
catch
if ~overwrite
try
datasetID = H5D.open(gid, data_name);
catch
error('Could not open dataset %s! Try a different name or overwrite the already existing file.', data_name);
end
else
error('Dataset %s already exists! Try a different name or overwrite the already existing file.', data_name);
end
end
end
if write_data
% write data to disk or link data
if ~link && ~extend_data
H5D.write(datasetID,memtype,'H5S_ALL','H5S_ALL',plist ,data);
% append attributes if needed
if ~isempty(data_attr)
fn = fieldnames(data_attr);
for ii=1:length(fn)
write_attribute(datasetID, data_attr.(fn{ii}), fn{ii}, true);
end
end
H5D.close(datasetID);
elseif extend_data
H5D.write(datasetID,memtype,dataspaceID, filespaceID, plist, data)
elseif strcmp(link_type, 'ext')
H5L.create_external(ch_entrs{2},ch_entrs{3},gid,data_name,plist,plist);
elseif strcmp(link_type, 'int_hard')
error('Currently not supported, sorry!')
% H5L.create_hard(ch_entrs{2},'g3',gid1,'g4',plist,plist);
elseif strcmp(link_type, 'int_soft')
H5L.create_soft(ch_entrs{2},gid,data_name,plist,plist);
end
end
end