HDF Compound Data and “strings”
Hi,
I’m migrating code to Matlab. The data format from the previous language writes out an HDF file, with a compound datatype. This is not the way I would choose to do this in Matlab, I love the higher level functions and almost never touch the lower level ones. However, I’d like to make the new code backwards compatible with previous data which means I also need the compound datatype. It includes strings. I know HDF supports this, but it’s unclear that Matlab supports putting this into an HDF file.
The error message I get is:
Error using hdf5lib2
The class of input data must be integer instead of char when the HDF5 class is H5T_STD_I8LE.
Error in H5D.write (line 100)
H5ML.hdf5lib2(‘H5Dwrite’, varargin{:});
Error in hdfhell2p0 (line 53)
H5D.write(dsetid, cid, ‘H5S_ALL’, ‘H5S_ALL’, ‘H5P_DEFAULT’, params);
I can only assume it’s upset by the char arrays/strings. I’ve tried different versions of creating the strings. I found a piece that said they had to be characters, not strings, so I converted them. I found another that said they had to be uniform in length, so I set a specific length. This one doesn’t make sense to me since I’m only doinn a single value, but hey, grasping at straws.
If i remove the strings/charcters, it works.
So, is there a way to keep the strings and if so, what am I missing?
%%make up a mixed structure
params.floc = ‘C:Folder1’;
params.fname = ‘fname.txt’;
params.value = 10;
%%actual code
outname = ‘test09.h5’;
plist = ‘H5P_DEFAULT’;
fNames = fieldnames(params);
for ii = 1:numel(fNames)
temp = params.(fNames{ii});
if ~isnan(str2double(temp))
params.(fNames{ii}) = str2double(temp);
Vsize(ii) = 8;
Vclass{ii} = ‘H5T_NATIVE_DOUBLE’;
elseif ischar(temp)
temp = char(pad(params.(fNames{ii}),15,’right’));
params.(fNames{ii}) = temp;
Vsize(ii) = strlength(temp);
Vclass{ii}= ‘H5T_NATIVE_CHAR’;
end
end
H5F.create(outname, ‘H5F_ACC_TRUNC’, ‘H5P_DEFAULT’, ‘H5P_DEFAULT’);
fid = H5F.open(outname,’H5F_ACC_RDWR’,plist);
H5G.create(fid,’/SETTINGS’,plist,plist,plist);
gid = H5G.open(fid,’/SETTINGS’);
cid = H5T.create(‘H5T_COMPOUND’, sum(Vsize));
for ii = 1:numel(fNames)
if ii == 1
H5T.insert(cid, fNames{ii}, 0, H5T.copy(Vclass{ii}));
else
if strcmp(Vclass{ii},’H5T_NATIVE_CHAR’)
string_type = H5T.array_create(H5T.copy(‘H5T_NATIVE_CHAR’), 1, 20);
H5T.insert(cid, fNames{ii}, sum(Vsize(1:(ii-1))), string_type)
else
H5T.insert(cid, fNames{ii}, sum(Vsize(1:(ii-1))), H5T.copy(Vclass{ii}));
end
end
end
dsid = H5S.create_simple(1,1,[]);
dsetid = H5D.create(fid, ‘/SETTINGS/PASS’, cid, dsid, ‘H5P_DEFAULT’);
H5D.write(dsetid, cid, ‘H5S_ALL’, ‘H5S_ALL’, ‘H5P_DEFAULT’, params);
H5D.close(dsetid)
H5S.close(did)
H5T.close(cid)
H5G.close(gid)
H5F.close(fid)Hi,
I’m migrating code to Matlab. The data format from the previous language writes out an HDF file, with a compound datatype. This is not the way I would choose to do this in Matlab, I love the higher level functions and almost never touch the lower level ones. However, I’d like to make the new code backwards compatible with previous data which means I also need the compound datatype. It includes strings. I know HDF supports this, but it’s unclear that Matlab supports putting this into an HDF file.
The error message I get is:
Error using hdf5lib2
The class of input data must be integer instead of char when the HDF5 class is H5T_STD_I8LE.
Error in H5D.write (line 100)
H5ML.hdf5lib2(‘H5Dwrite’, varargin{:});
Error in hdfhell2p0 (line 53)
H5D.write(dsetid, cid, ‘H5S_ALL’, ‘H5S_ALL’, ‘H5P_DEFAULT’, params);
I can only assume it’s upset by the char arrays/strings. I’ve tried different versions of creating the strings. I found a piece that said they had to be characters, not strings, so I converted them. I found another that said they had to be uniform in length, so I set a specific length. This one doesn’t make sense to me since I’m only doinn a single value, but hey, grasping at straws.
If i remove the strings/charcters, it works.
So, is there a way to keep the strings and if so, what am I missing?
%%make up a mixed structure
params.floc = ‘C:Folder1’;
params.fname = ‘fname.txt’;
params.value = 10;
%%actual code
outname = ‘test09.h5’;
plist = ‘H5P_DEFAULT’;
fNames = fieldnames(params);
for ii = 1:numel(fNames)
temp = params.(fNames{ii});
if ~isnan(str2double(temp))
params.(fNames{ii}) = str2double(temp);
Vsize(ii) = 8;
Vclass{ii} = ‘H5T_NATIVE_DOUBLE’;
elseif ischar(temp)
temp = char(pad(params.(fNames{ii}),15,’right’));
params.(fNames{ii}) = temp;
Vsize(ii) = strlength(temp);
Vclass{ii}= ‘H5T_NATIVE_CHAR’;
end
end
H5F.create(outname, ‘H5F_ACC_TRUNC’, ‘H5P_DEFAULT’, ‘H5P_DEFAULT’);
fid = H5F.open(outname,’H5F_ACC_RDWR’,plist);
H5G.create(fid,’/SETTINGS’,plist,plist,plist);
gid = H5G.open(fid,’/SETTINGS’);
cid = H5T.create(‘H5T_COMPOUND’, sum(Vsize));
for ii = 1:numel(fNames)
if ii == 1
H5T.insert(cid, fNames{ii}, 0, H5T.copy(Vclass{ii}));
else
if strcmp(Vclass{ii},’H5T_NATIVE_CHAR’)
string_type = H5T.array_create(H5T.copy(‘H5T_NATIVE_CHAR’), 1, 20);
H5T.insert(cid, fNames{ii}, sum(Vsize(1:(ii-1))), string_type)
else
H5T.insert(cid, fNames{ii}, sum(Vsize(1:(ii-1))), H5T.copy(Vclass{ii}));
end
end
end
dsid = H5S.create_simple(1,1,[]);
dsetid = H5D.create(fid, ‘/SETTINGS/PASS’, cid, dsid, ‘H5P_DEFAULT’);
H5D.write(dsetid, cid, ‘H5S_ALL’, ‘H5S_ALL’, ‘H5P_DEFAULT’, params);
H5D.close(dsetid)
H5S.close(did)
H5T.close(cid)
H5G.close(gid)
H5F.close(fid) Hi,
I’m migrating code to Matlab. The data format from the previous language writes out an HDF file, with a compound datatype. This is not the way I would choose to do this in Matlab, I love the higher level functions and almost never touch the lower level ones. However, I’d like to make the new code backwards compatible with previous data which means I also need the compound datatype. It includes strings. I know HDF supports this, but it’s unclear that Matlab supports putting this into an HDF file.
The error message I get is:
Error using hdf5lib2
The class of input data must be integer instead of char when the HDF5 class is H5T_STD_I8LE.
Error in H5D.write (line 100)
H5ML.hdf5lib2(‘H5Dwrite’, varargin{:});
Error in hdfhell2p0 (line 53)
H5D.write(dsetid, cid, ‘H5S_ALL’, ‘H5S_ALL’, ‘H5P_DEFAULT’, params);
I can only assume it’s upset by the char arrays/strings. I’ve tried different versions of creating the strings. I found a piece that said they had to be characters, not strings, so I converted them. I found another that said they had to be uniform in length, so I set a specific length. This one doesn’t make sense to me since I’m only doinn a single value, but hey, grasping at straws.
If i remove the strings/charcters, it works.
So, is there a way to keep the strings and if so, what am I missing?
%%make up a mixed structure
params.floc = ‘C:Folder1’;
params.fname = ‘fname.txt’;
params.value = 10;
%%actual code
outname = ‘test09.h5’;
plist = ‘H5P_DEFAULT’;
fNames = fieldnames(params);
for ii = 1:numel(fNames)
temp = params.(fNames{ii});
if ~isnan(str2double(temp))
params.(fNames{ii}) = str2double(temp);
Vsize(ii) = 8;
Vclass{ii} = ‘H5T_NATIVE_DOUBLE’;
elseif ischar(temp)
temp = char(pad(params.(fNames{ii}),15,’right’));
params.(fNames{ii}) = temp;
Vsize(ii) = strlength(temp);
Vclass{ii}= ‘H5T_NATIVE_CHAR’;
end
end
H5F.create(outname, ‘H5F_ACC_TRUNC’, ‘H5P_DEFAULT’, ‘H5P_DEFAULT’);
fid = H5F.open(outname,’H5F_ACC_RDWR’,plist);
H5G.create(fid,’/SETTINGS’,plist,plist,plist);
gid = H5G.open(fid,’/SETTINGS’);
cid = H5T.create(‘H5T_COMPOUND’, sum(Vsize));
for ii = 1:numel(fNames)
if ii == 1
H5T.insert(cid, fNames{ii}, 0, H5T.copy(Vclass{ii}));
else
if strcmp(Vclass{ii},’H5T_NATIVE_CHAR’)
string_type = H5T.array_create(H5T.copy(‘H5T_NATIVE_CHAR’), 1, 20);
H5T.insert(cid, fNames{ii}, sum(Vsize(1:(ii-1))), string_type)
else
H5T.insert(cid, fNames{ii}, sum(Vsize(1:(ii-1))), H5T.copy(Vclass{ii}));
end
end
end
dsid = H5S.create_simple(1,1,[]);
dsetid = H5D.create(fid, ‘/SETTINGS/PASS’, cid, dsid, ‘H5P_DEFAULT’);
H5D.write(dsetid, cid, ‘H5S_ALL’, ‘H5S_ALL’, ‘H5P_DEFAULT’, params);
H5D.close(dsetid)
H5S.close(did)
H5T.close(cid)
H5G.close(gid)
H5F.close(fid) h5, hdf, compound data type, strings and hdf MATLAB Answers — New Questions
