this is for holding javascript data
System Administrator Added MATIN utilities for Matlab
about 10 years ago
Commit id: 8d78482ec70e7f9f4689f19ab11502cd11a887cb
deletions | additions
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..73770aa
--- /dev/null
+++ b/.gitignore
...
_site
*.h5
*.fig
*.mat
/Data
temp.yml
*~
diff --git a/MATLAB/HDF5/MakeFakeFile.m b/MATLAB/HDF5/MakeFakeFile.m
new file mode 100644
index 0000000..3dd1fd6
--- /dev/null
+++ b/MATLAB/HDF5/MakeFakeFile.m
...
hh = 'something.h5';
delete(hh);
nms = {'/Dataset1/aggregate','/Dataset1/spatial','/Dataset1/Workflow1/aggregate', ...
'/Dataset2/aggregate','/Dataset2/spatial','/Dataset2/Workflow1/aggregate','/Dataset2/Workflow2/spatial'};
for dd = 1 : numel(nms);
dset = nms{dd};
if ~exist( hh,'file');
fo = H5F.create(hh);
else
fo = H5F.open(hh,'H5F_ACC_RDWR','H5P_DEFAULT');
end
try
gid=H5G.create(fo,fileparts(dset),'H5P_DEFAULT','H5P_DEFAULT','H5P_DEFAULT');H5G.close(gid);
s.link = 'http://www.theinternet.com';
h5writeatt( hh, fileparts(dset), 'location',s.link );
catch
disp('group exists')
end
H5F.close(fo);
% h5create(hh,dset,[1 1]);
S = struct('Var1',rand(1),'Huh',rand(1),'Pressure',rand(1));
h5writecompound( hh, nms{dd}, S);
end
diff --git a/MATLAB/HDF5/h5writeattcompound.m b/MATLAB/HDF5/h5writeattcompound.m
new file mode 100644
index 0000000..94507f0
--- /dev/null
+++ b/MATLAB/HDF5/h5writeattcompound.m
...
function h5writeattcompound( fn, dset, attname, DATA )
% An improved version of the matlab function h5write. Natively, h5write lacks the
% ability to write structures to HDF5 files.
%
% INPUTS:
% fn - file name where the data is written to.
% dset - name of the dataset in the HDF5 that the data is being stored as
% DATA - allows structures are all h5write native datatypes to be written.
% if DATA is a structure then the information is written as a
% compound datatype. The size of each field should be the same.
if isstruct( DATA )
if exist( fn, 'file')
fo = H5F.open(fn,'H5F_ACC_RDWR','H5P_DEFAULT');
else
fo = H5F.create(fn);
end
fields = fieldnames(DATA);
sz = size( getfield( DATA, fields{1}));
tid = H5T.create('H5T_COMPOUND',numel(fields)*8);
ii = 1;
H5T.insert(tid,fields{ii},(ii-1)*8,'H5T_NATIVE_DOUBLE');
ii = 2;
strType = H5T.copy( 'H5T_C_S1' );
H5T.set_size(strType, numel(getfield( DATA, fields{ii})) );
% DATA = setfield( DATA, fields{ii}, getfield( DATA, fields{ii} ) );
H5T.insert(tid,fields{ii},(ii-1)*8,strType);
sid = H5S.create_simple( numel(sz), fliplr(sz), fliplr(sz) );
% dset = horzcat(dset, num2str(round(rand(1)*1e5)));
did = H5D.open( fo, dset);
aid = H5A.create( did, attname, tid, sid, H5P.create('H5P_ATTRIBUTE_CREATE'));
H5A.write( aid, tid, DATA );
H5A.close(aid)
H5S.close(sid)
H5D.close(did)
H5T.close(tid)
H5F.close(fo);
elseif ischar(DATA)
if exist( fn, 'file')
fo = H5F.open(fn,'H5F_ACC_RDWR','H5P_DEFAULT');
else
fo = H5F.create(fn);
end
SDIM = size(DATA,2);
filetype = H5T.copy ('H5T_FORTRAN_S1');
H5T.set_size (filetype, SDIM );
memtype = H5T.copy ('H5T_C_S1');
H5T.set_size (memtype, SDIM );
% Create dataspace. Setting maximum size to [] sets the maximum
% size to be the current size.
%
dims = size(DATA,1);
space = H5S.create_simple (1,fliplr( dims), []);
%
% Create the attribute and write the string data to it.
%
if strcmp( dset, '/');
attr = H5A.create (fo, attname, filetype, space, 'H5P_DEFAULT');
H5A.write (attr, memtype, DATA');
else
did = H5D.open( fo, dset );
attr = H5A.create (fo, attname, filetype, space, 'H5P_DEFAULT');
H5A.write (attr, memtype, DATA');
H5D.close (did);
end
%
% Close and release resources.
%
H5A.close (attr);
H5S.close (space);
H5T.close (filetype);
H5T.close (memtype);
H5F.close ( fo );
else
h5writeatt( fn,dset, attname, DATA);
end
end
diff --git a/MATLAB/HDF5/h5writecompound.m b/MATLAB/HDF5/h5writecompound.m
new file mode 100644
index 0000000..7dd1c4a
--- /dev/null
+++ b/MATLAB/HDF5/h5writecompound.m
...
function h5writecompound( fn, dset, DATA )
% An improved version of the matlab function h5write. Natively, h5write lacks the
% ability to write structures to HDF5 files.
%
% INPUTS:
% fn - file name where the data is written to.
% dset - name of the dataset in the HDF5 that the data is being stored as
% DATA - allows structures are all h5write native datatypes to be written.
% if DATA is a structure then the information is written as a
% compound datatype. The size of each field should be the same.
flds = fieldnames( DATA );
for ii = 1 : numel( flds )
switch class( getfield( DATA, flds{ii} ) )
case 'int8'
hdftype{ii} = 'H5T_STD_I8LE';
hdfbyte(ii) = 1;
case 'int16'
hdftype{ii} = 'H5T_STD_I16LE';
hdfbyte(ii) = 2;
case 'int32'
hdftype{ii} = 'H5T_STD_I32LE';
hdfbyte(ii) = 4;
case 'uint8'
hdftype{ii} = 'H5T_STD_I8LE';
hdfbyte(ii) = 1;
case 'int16'
hdftype{ii} = 'H5T_STD_I16LE';
hdfbyte(ii) = 2;
case 'uint32'
hdftype{ii} = 'H5T_STD_U32LE';
hdfbyte(ii) = 4;
otherwise
hdftype{ii} = 'H5T_NATIVE_DOUBLE';
hdfbyte(ii) = 8;
end
end
cumhdfbyte = [0 , cumsum(hdfbyte)];
if isstruct( DATA )
if exist( fn, 'file')
fo = H5F.open(fn,'H5F_ACC_RDWR','H5P_DEFAULT');
else
fo = H5F.create(fn);
end
fields = fieldnames(DATA);
sz = size( getfield( DATA, fields{1}));
tid = H5T.create('H5T_COMPOUND', sum(hdfbyte));
for ii = 1 : numel( fields )
H5T.insert(tid,fields{ii},cumhdfbyte(ii),hdftype{ii});
if ~all( sz == size( getfield( DATA, fields{ii})))
error('The size of the elements in the data structure must be the same. The data was not written.')
H5T.close(tid)
H5F.close(fo);
end
end
sid = H5S.create_simple( numel(sz), fliplr(sz), fliplr(sz) );
% dset = horzcat(dset, num2str(round(rand(1)*1e5)));
dset
did = H5D.create( fo, dset, tid, sid, 'H5P_DEFAULT');
H5D.write( did, tid, 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT', DATA );
H5D.close(did)
H5S.close(sid)
else
h5create( fn,dset, DATA, size(DATA) );
end
end
diff --git a/MATLAB/api/AddTags.m b/MATLAB/api/AddTags.m
new file mode 100644
index 0000000..45c827e
--- /dev/null
+++ b/MATLAB/api/AddTags.m
...
function S = AddTags( S,varargin );
if isfield(S,'tags')
S.tags = cat(1,S.tags, varargin{:});
else
S.tags = varargin{:};
end
diff --git a/MATLAB/api/AttachDictionary.m b/MATLAB/api/AttachDictionary.m
new file mode 100644
index 0000000..3451619
--- /dev/null
+++ b/MATLAB/api/AttachDictionary.m
...
function YAML = attachDictionary( YAML, workflow, dictionary )
% if workflow is empty then work on the raw
% dict goes in the top level of YAML
%
% if workflow has a value then look for the workflow name
persistent crap
numel(crap)
if numel( workflow ) == 0;
cc = {'output'};
israw = true;
else
cc = {'workflow', 'output'};
israw = false;
end
% run over the aggregate values
if israw
YAML.dict = dictionary;
else
for ii = 1 : numel( YAML.aggregate )
if isfield( YAML.aggregate{ii}, 'workflow' )
for jj = 1 : numel( YAML.aggregate{ii}.workflow )
wf = fliplr( strtok( fliplr( YAML.aggregate{ii}.workflow{jj}.native ), '/' ) );
if strcmp( wf, workflow )
YAML.aggregate{ii}.workflow{jj}.dict = dictionary;
end
end
end
end
for ii = 1 : numel( YAML.spatial)
if isfield( YAML.spatial{ii}, 'workflow' )
for jj = 1 : numel( YAML.spatial{ii}.workflow )
wf = fliplr( strtok( fliplr( YAML.spatial{ii}.workflow{jj}.native ), '/' ) );
if strcmp( wf, workflow )
YAML.spatial{ii}.workflow{jj}.dict = dictionary;
end
end
end
end
end
diff --git a/MATLAB/api/CreateDictionary.m b/MATLAB/api/CreateDictionary.m
new file mode 100644
index 0000000..c3b7bab
--- /dev/null
+++ b/MATLAB/api/CreateDictionary.m
...
function [dict] = createDictionary( YAML, workflow, dictionary )
% if workflow is empty then work on the raw
% dict goes in the top level of YAML
%
% if workflow has a value then look for the workflow name
% Dictionary needs to output a structure that can write YAML to make the
% dictionary
%
% You can loop over this function is you have heterogenous outputs.
persistent spatialvars aggregatevars
if numel( workflow ) == 0;
cc = {'output'};
israw = true;
else
cc = {'workflow', 'output'};
israw = false;
end
if numel( spatialvars ) == 0 spatialvars = cell(0); end
if numel( aggregatevars ) == 0 aggregatevars = cell(0); end
% read the native variable names from a YAML structure
%%
if israw
for ii = 1 : numel( YAML.aggregate )
for jj = 1 : numel( YAML.aggregate{ii}.output )
aggregatevars = union( aggregatevars, YAML.aggregate{ii}.output{jj}.native );
end
end
for ii = 1 : numel( YAML.spatial )
for jj = 1 : numel( YAML.spatial{ii}.output )
spatialvars = union( aggregatevars, YAML.spatial{ii}.output{jj}.native );
end
end
else
for ii = 1 : numel( YAML.aggregate )
if isfield( YAML.aggregate{ii}, 'workflow' )
for jj = 1 : numel( YAML.aggregate{ii}.workflow )
wf = fliplr( strtok( fliplr( YAML.aggregate{ii}.workflow{jj}.native ), '/' ) );
if strcmp( wf, workflow )
for kk = 1 : numel( YAML.aggregate{ii}.workflow{jj}.output )
aggregatevars = union( aggvars, YAML.aggregate{ii}.workflow{jj}.output{kk}.native );
end
end
end
end
end
if isfield( YAML.spatial{ii}, 'workflow' )
for jj = 1 : numel( YAML.spatial{ii}.workflow )
wf = fliplr( strtok( fliplr( YAML.spatial{ii}.workflow{jj}.native ), '/' ) );
if strcmp( wf, workflow )
for kk = 1 : numel( YAML.spatial{ii}.workflow{jj}.output )
spatialvars = union( spatialvars, YAML.spatial{ii}.workflow{jj}.output{kk}.native );
end
end
end
end
end
assignin( 'base','spatialvars',spatialvars);
assignin( 'base','aggregatevars',aggregatevars);
%%
% Create dictionary YAML Matlab Structure
if numel( aggregatevars ) > 0 | numel( spatialvars ) > 0
dict.name = dictionary;
dict.description = '';
end
if numel( aggregatevars ) > 0
% Create a default group
dict.aggregate{1}.group{1}=struct(...
'name','DEFAULT', ...
'description','',...
'links',struct( 'url','','name','') ...
);
for ii = 1 : numel( aggregatevars );
dict.aggregate{1}.group{1+ii} = struct(...
'pretty', aggregatevars{ii},...
'native', aggregatevars{ii},...
'units','undefined',...
'description','',...
'links',struct( 'url','','name','') ...
);
end
end
if numel( spatialvars ) > 0
% Create a default group
dict.spatial{1}.group{1}=struct(...
'name','DEFAULT', ...
'description','',...
'links',struct( 'url','','name','') ...
);
for ii = 1 : numel( spatialvars );
dict.spatial{1}.group{1+ii} = struct(...
'pretty', spatialvars{ii},...
'native', spatialvars{ii},...
'units','undefined',...
'description','',...
'links',struct( 'url','','name','') ...
);
end
end
diff --git a/MATLAB/api/createDataset.m b/MATLAB/api/createDataset.m
new file mode 100644
index 0000000..5a541c5
--- /dev/null
+++ b/MATLAB/api/createDataset.m
...
function YAML = createDataset( H5 );
% H5 is an output structure from h5info'
% YAML is an output structure from ReadYAML'
% Dictionary information is attached with a separate function
H5 = xx;
YAML = struct( 'layout','dataset');
[~,YAML.title,~] = fileparts(xx.Filename);
YAML.description = [];
cc = {'Groups' 'Groups'};
for ii = 1 : numel( H5.Groups)
% This loop indexes the datasets
dsetname = H5.Groups(ii).Name; %dataset name
for dd = 1 : numel( H5.Groups(ii).Datasets );
% Whether the dataset can be queried will be a file option in the
% converter
field = H5.Groups(ii).Datasets(dd).Name;
switch field
% The index is on the number of datasets
case {'aggregate','Aggregate'}
if ~isfield( YAML, 'aggregate' )
[ YAML.aggregate{ii}.name YAML.aggregate{ii}.native ] = ...
deal( dsetname(2:end) );
end
YAML.aggregate{ii}.description = [];
if numel( fieldnames(YAML.aggregate{ii}) )==0 dsetid = 0;
else dsetid = numel(YAML.aggregate{ii}); end
% Read the aggregate values here
data = h5read( hh,strjoin( {dsetname, field},'/'));
for mm = 1 : numel(H5.Groups(ii).Datasets(dd).Datatype.Type.Member);
YAML.aggregate{ii}.output{mm}.native = ...
H5.Groups(ii).Datasets(dd).Datatype.Type.Member(mm).Name;
YAML.aggregate{ii}.output{mm}.value = ...
getfield( data, YAML.aggregate{ii}.output{mm}.native );
end
case {'spatial','Spatial'}
if ~isfield( YAML, 'spatial' )
[ YAML.spatial{ii}.name YAML.spatial{ii}.native ] = ...
deal( dsetname(2:end) );
end
YAML.spatial{ii}.description = [];
for mm = 1 : numel(H5.Groups(ii).Datasets(dd).Datatype.Type.Member);
YAML.spatial{ii}.output{mm}.native = ...
H5.Groups(ii).Datasets(dd).Datatype.Type.Member(mm).Name;
end
end
end
% cycle through additional workflows
for gg = 1 : numel( H5.Groups(ii).Groups );
dsetname = H5.Groups(ii).Groups(gg).Name; %dataset name
for dd = 1 : numel( H5.Groups(ii).Groups(gg).Datasets );
% Whether the dataset can be queried will be a file option in the
% converter
field = H5.Groups(ii).Groups(gg).Datasets(dd).Name;
switch field
% The index is on the number of datasets
case {'aggregate','Aggregate'}
if ~isfield(YAML.aggregate{ii},'workflow') || ...
numel( fieldnames(YAML.aggregate{ii}.workflow{gg}) )==0 dsetid = 0;
else dsetid = numel(YAML.aggregate{ii}.workflow{gg}); end
dsetid = dsetid+1;
if ~isfield( YAML.aggregate{ii}, 'workflow' )
[ YAML.aggregate{ii}.workflow{dsetid}.name YAML.aggregate{ii}.workflow{dsetid}.native ] = ...
deal( dsetname(2:end) );
end
YAML.aggregate{ii}.workflow{dsetid}.description = [];
data = h5read( hh,strjoin( {dsetname, field},'/'));
for mm = 1 : numel(H5.Groups(ii).Groups(gg).Datasets(dd).Datatype.Type.Member);
YAML.aggregate{ii}.workflow{dsetid}.output{mm}.native = ...
H5.Groups(ii).Groups(gg).Datasets(dd).Datatype.Type.Member(mm).Name;
YAML.aggregate{ii}.workflow{dsetid}.output{mm}.value = ...
getfield( data, YAML.aggregate{ii}.workflow{dsetid}.output{mm}.native );
end
case {'spatial','Spatial'}
if ~isfield(YAML.spatial{ii},'workflow') || ...
numel( fieldnames(YAML.spatial{ii}.workflow{gg}) )==0 dsetid = 0;
else dsetid = numel(YAML.spatial{ii}.workflow{gg}); end
dsetid = dsetid+1;
if ~isfield( YAML.spatial{ii}, 'worflow' )
[ YAML.spatial{ii}.workflow{dsetid}.name YAML.spatial{ii}.workflow{dsetid}.native ] = ...
deal( dsetname(2:end) );
end
YAML.spatial{ii}.workflow{dsetid}.description = [];
if numel( fieldnames(YAML.spatial{ii}.workflow{dsetid}) )==0 dsetid = 0;
else dsetid = numel(YAML.spatial{ii}.workflow{dsetid}); end
for mm = 1 : numel(H5.Groups(ii).Datasets(dd).Datatype.Type.Member);
YAML.spatial{ii}.workflow{dsetid}.output{mm}.native = ...
H5.Groups(ii).Datasets(dd).Datatype.Type.Member(mm).Name;
end
end
end
end
for aa = 1 : numel( H5.Groups(2).Attributes )
field = H5.Groups(2).Attributes(aa).Name;
switch field
case 'location'
YAML.location = H5.Groups(2).Attributes(aa).Value;
end
end
end
diff --git a/Utilities/BatchWrite.m b/Utilities/BatchWrite.m
new file mode 100644
index 0000000..4236e59
--- /dev/null
+++ b/Utilities/BatchWrite.m
...
function h5nm = BatchWrite( fn, Data, writeloc )
% Write a structure generated from a single Polymer MD output to an HDF5
% using h5writecomposite
if ~exist( 'writeloc', 'var');
writeloc = '.';
end
stripnm = @(x)regexprep( fliplr(strtok(fliplr(x),'/')),'dump.','');
h5nm = fullfile( writeloc, horzcat( stripnm(fn), '.h5' ) )
assignin( 'base','h5nm',h5nm)
if ~exist( h5nm,'file' )
h5 = H5F.create( h5nm );
H5F.close( h5 );
end
h5 = H5F.open( h5nm,'H5F_ACC_RDWR','H5P_DEFAULT' );
h5writeattcompound( h5nm, '/', 'SHA', strtok(evalc( 'git log --pretty=oneline')) );
h5writeattcompound( h5nm, '/', 'origin_file', fliplr(strtok(fliplr(fn),'/')) );
H5O.set_comment_by_name( h5, '/', 'Tony Fast updated these datasets.','H5P_DEFAULT');
for ii = 1 : numel( Data.Aggregate )
try
gid = H5G.create( h5, ['/',num2str(ii)],'H5P_DEFAULT','H5P_DEFAULT','H5P_DEFAULT' );
H5G.close( gid );
catch
warning('The group name already exists.');
end
h5writecompound( h5nm, ['/',num2str(ii),'/Aggregate'], Data.Aggregate(ii));
if all ( structfun( @(x)numel(x), Data.Spatial(ii)) == Data.Aggregate(ii).Natoms )
h5writecompound( h5nm, ['/',num2str(ii),'/Spatial'], Data.Spatial(ii));
end
end
H5F.close( h5 );
diff --git a/Utilities/CreateThumbnails.m b/Utilities/CreateThumbnails.m
new file mode 100644
index 0000000..8c2f845
--- /dev/null
+++ b/Utilities/CreateThumbnails.m
...
function CreateThumbnails( vizdata,h5nm, postdir, imdir )
% Using the YAML portion of my Jekyll site, I am creating thumbnails based
% on the syntax given in the datapage viz.yml.
c = clock;
[p, f, ext] = fileparts( h5nm );
p = postdir
dataloc = sprintf( '%s/%i-%i-%i-%s.markdown',p,c(1),c(2),c(3),f);
vyml = ReadYaml(vizdata);
% Make it work right?
fo = fopen( dataloc );ct=0; while ~feof(fo) ct=ct+1;s{ct} = fgetl(fo);end; fclose(fo);
tfl = 'temp.yml';
fo = fopen( tfl,'w' ); for ii = 1 : numel( s) if ~all(s{ii}=='-') fprintf(fo,'%s\n',s{ii}); end;end;fclose(fo);
fo = fopen( tfl );ct=0; while ~feof(fo) ct=ct+1;s2{ct} = fgetl(fo);end; fclose(fo);
dyml = ReadYaml(tfl);
vars = {'X','Y','Z','C'};
lastim = 0;
for dd = 1 : numel(dyml.spatial)
imnm = sprintf('%s-*.png', f,lastim);
delete( fullfile( imdir, imnm ) );
for vv = 1 : numel( vyml )
sd = vyml{vv}.data{1};
nms = fieldnames( sd );
args = struct2cell(sd);
nargs = cellfun(@(x)numel(x), args );
cdid = find(cellfun( @(x)strcmp( x, 'Cdata'), nms )) ;
xyz = setdiff(1:numel(nms), cdid);
dims = max(2,sum(nargs(xyz)))
xyzi = xyz( nargs(xyz)>0 );
% if all the variable names are the same then it is gridded data
ispoint = numel( unique({args{xyzi}}) ) > 1;
isgridded = ~ispoint;
[ Xdata, Ydata, Zdata, Cdata ] = deal( [] );
for ii = xyzi
eval(sprintf('%s = struct2array(h5read( ''%s'', ''%s'', ''%s''));', nms{ii}, h5nm, dyml.spatial{dd}.native, args{ii} ));
end
if numel(args{cdid}) > 0
eval(sprintf('%s = struct2array(h5read( ''%s'', ''%s'', ''%s''));', 'Cdata', h5nm, dyml.spatial{dd}.native, args{cdid} ));
end
if numel(Cdata) > 0
xx = linspace( min(Cdata), max(Cdata), size(colormap,1));
co = colormap;
else
xx = [ 2 2];
co = 'c';
end
switch dims
case 2
if ispoint
for ii = 1 : (numel(xx)-1)
if numel(xx) == 2
b= ones(size(Xdata))==1;
else
b = Cdata>=xx(ii) & Cdata<=xx(ii+1);
end
plot( Xdata(b),Ydata(b),'ko','MarkerFaceColor',co(ii,:));
if ii == 1
hold on
end
end
hold off
else
pcolor( Cdata );
axis equal; axis tight;
end
case 3
if ispoint
for ii = 1 : (numel(xx)-1)
if numel(xx) == 2
b= ones(size(Xdata))==1;
else
b = Cdata>=xx(ii) & Cdata<=xx(ii+1);
end
plot3( Xdata(b),Ydata(b),Zdata(b),'ko','MarkerFaceColor',co(ii,:));
if ii == 1
hold on
end
end
hold off
end
otherwise
end
axis equal
if numel(Cdata) > 0
colorbar;
end
axis tight
set( gca,'Fontsize',14)
lastim = lastim + vv;
imnm = sprintf('%s-%i.png', f,lastim);
saveas(gcf,fullfile( imdir, imnm));
[IM ] = imread( fullfile( imdir, imnm) );
BIM = cat(3,all(IM == IM(1) ,3),all(IM == IM(end) ,3));
tr = find( ~all( BIM(:,:,1), 2), 1, 'first');
if numel( tr ) == 0 verttrim(1) = 1; else; verttrim(1) = tr; end
tr = find( ~all( BIM(:,:,2), 2), 1, 'last');
if numel( tr ) == 0 verttrim(2) = size(IM,1); else; verttrim(2) = tr; end
tr = find( ~all( BIM(:,:,1), 1), 1, 'first');
if numel( tr ) == 0 horztrim(1) = 1; else; horztrim(1) = tr; end
tr = find( ~all( BIM(:,:,2), 1), 1, 'last');
if numel( tr ) == 0 horztrim(2) = size(IM,2); else; horztrim(2) = tr; end
horztrim = [ 1 size(IM,2)];
verttrim = [ max( 1, verttrim(1)-20), min( size(IM,1), verttrim(2)+20)];
imwrite( IM( verttrim(1):verttrim(2), horztrim(1):horztrim(2),: ), fullfile( imdir, imnm));
dyml.spatial{dd}.viz{vv}.url= imnm;
dyml.spatial{dd}.viz{vv}.name= vyml{vv}.name;
dyml.spatial{dd}.viz{vv}.description= vyml{vv}.description;
% dyml.spatial{1}.viz{vv}.description = [];
end
lastim = lastim;
end
Struct2YMLMD( dyml, dataloc );
diff --git a/Utilities/H5toDict.m b/Utilities/H5toDict.m
new file mode 100644
index 0000000..3ebf4ed
--- /dev/null
+++ b/Utilities/H5toDict.m
...
function postout = H5toDict( h5nm, postout, source );
% From and HDF5 file, the native variables are stripped to make a metadata
% registry that can be dynamically changed.
if ~exist( 'postout','var')
postout = './_data/dictionary.yml';
end
% Initialize the file for writing
info = h5info( h5nm );
% Get root information
for rootid = 1 : numel( info.Groups ) % Iterate over the directories in the root
% Write Datasets
for dataid = 1 : numel( info.Groups( rootid ).Datasets )
T = info.Groups( rootid ).Datasets( dataid );
if strcmp( T.Name, 'Aggregate' )
% Get variable fields
if strcmp( T.Datatype.Class, 'H5T_COMPOUND' );
Agg.names = { T.Datatype.Type.Member.Name };
else
end
% Get attributes for fields
elseif strcmp( T.Name, 'Spatial' )
% Get variable fields
if strcmp( T.Datatype.Class, 'H5T_COMPOUND' );
Spa.names = { T.Datatype.Type.Member.Name };
else
end
% Get attributes for fields
% Get attibutes
% Get comment
else
end
end
for workid = 1 : info.Groups( rootid ).Groups
% Write Datasets
for dataid = 1 : numel( info.Groups( rootid ).Groups( workid ).Datasets )
end
end
end
c = clock;
[p, dnm, ext] = fileparts( postout );
dnm = 'A-Dictionary-Template';
dictout = fullfile( regexprep( p, 'data','posts'), sprintf( '%4i-%02i-%i-%s.markdown', c(1), c(2), c(3), dnm ));
[p, f, ext] = fileparts( h5nm );
% f = '~/my-awesome-site/_site/other';
fo = fopen( postout, 'w' );
fprintf(fo,'url: %s\n', sprintf( '%4i/%02i/%i/%s.html', c(1), c(2), c(3), dnm ) );
fprintf(fo,'short: %s\n', sprintf( '%s', dnm ) );
% Select the template
fprintf( fo, 'source : \n','');
fprintf( fo, ' - name: %s\n', source.name);
if isfield( source, 'url')
fprintf( fo, ' url: %s\n',source.url );
else
fprintf( fo, ' url: %s\n','');
end
fprintf( fo, 'converter : \n','');
fprintf( fo, ' - name: \n', mfilename);
fprintf( fo, ' sha: %s\n',strtok( evalc( 'git log --abbrev-commit --pretty=oneline' ) ));
if exist( 'Agg', 'var') & numel( Agg.names ) > 0
fprintf( fo, 'aggregate : \n','');
fprintf( fo, ' - group : \n');
fprintf( fo, ' - name : General\n');
fprintf( fo, ' description : \n');
for ii = 1 : numel( Agg.names )
fprintf( fo, ' - native : %s\n', Agg.names{ii});
fprintf( fo, ' pretty : %s\n', Agg.names{ii});
fprintf( fo, ' units : %s\n', '');
fprintf( fo, ' description : %s\n', '' );
fprintf( fo, ' links : %s\n', '' );
fprintf( fo, ' - url: %s\n', '' );
fprintf( fo, ' name: %s\n', '' );
end
end
if exist( 'Spa', 'var') & numel( Spa.names ) > 0
fprintf( fo, 'spatial : \n','');
fprintf( fo, ' - group : \n');
fprintf( fo, ' - name : General\n');
fprintf( fo, ' description : \n');
for ii = 1 : numel( Spa.names )
fprintf( fo, ' - native : %s\n', Spa.names{ii});
fprintf( fo, ' pretty : %s\n', Spa.names{ii});
fprintf( fo, ' units : %s\n', '');
fprintf( fo, ' description : %s\n', '' );
fprintf( fo, ' links : %s\n', '' );
fprintf( fo, ' - url: %s\n', '' );
fprintf( fo, ' name: %s\n', '' );
fprintf( fo, ' publish : %s\n', '' );
fprintf( fo, ' - isplot: %s\n', 'true' );
fprintf( fo, ' - isdisp: %s\n', 'true' );
end
end
fclose( fo );
fo = fopen( dictout, 'w' );
fprintf( fo,'---\nlayout: dictionary-template-final\ntitle: Dictionary Template\n---\n');
fclose(fo);
%%
diff --git a/Utilities/H5toDictMD.m b/Utilities/H5toDictMD.m
new file mode 100644
index 0000000..4d75d0d
--- /dev/null
+++ b/Utilities/H5toDictMD.m
...
function postout = H5toDict( h5nm, postout, source );
if ~exist( 'postout','var')
postout = './_data/dictionary.yml';
end
% Initialize the file for writing
info = h5info( h5nm );
% Get root information
for rootid = 1 : numel( info.Groups ) % Iterate over the directories in the root
% Write Datasets
for dataid = 1 : numel( info.Groups( rootid ).Datasets )
T = info.Groups( rootid ).Datasets( dataid );
if strcmp( T.Name, 'Aggregate' )
% Get variable fields
if strcmp( T.Datatype.Class, 'H5T_COMPOUND' );
Agg.names = { T.Datatype.Type.Member.Name };
else
end
% Get attributes for fields
elseif strcmp( T.Name, 'Spatial' )
% Get variable fields
if strcmp( T.Datatype.Class, 'H5T_COMPOUND' );
Spa.names = { T.Datatype.Type.Member.Name };
else
end
% Get attributes for fields
% Get attibutes
% Get comment
else
end
end
for workid = 1 : info.Groups( rootid ).Groups
% Write Datasets
for dataid = 1 : numel( info.Groups( rootid ).Groups( workid ).Datasets )
end
end
end
c = clock;
[p, dnm, ext] = fileparts( postout );
dnm = 'A-Dictionary-Template';
dictout = fullfile( regexprep( p, 'data','posts'), sprintf( '%4i-%02i-%i-%s.markdown', c(1), c(2), c(3), dnm ));
[p, f, ext] = fileparts( h5nm );
% f = '~/my-awesome-site/_site/other';
postout
fo = fopen( postout, 'w' );
fprintf(fo,'url: %s\n', sprintf( '%4i/%02i/%i/%s.html', c(1), c(2), c(3), dnm ) );
fprintf(fo,'short: %s\n', sprintf( '%s', dnm ) );
% Select the template
fprintf( fo, 'source : \n','');
fprintf( fo, ' - name: %s\n', source.name);
fprintf( fo, ' url: %s\n',source.url );
fprintf( fo, 'converter : \n','');
fprintf( fo, ' - name: \n', mfilename);
fprintf( fo, ' sha: %s\n',strtok( evalc( 'git log --abbrev-commit --pretty=oneline' ) ));
if exist( 'Agg','var') && numel( Agg.names ) > 0
fprintf( fo, 'aggregate : \n','');
fprintf( fo, ' - group : \n');
fprintf( fo, ' - name : General\n');
fprintf( fo, ' description : \n');
for ii = 1 : numel( Agg.names )
fprintf( fo, ' - native : %s\n', Agg.names{ii});
fprintf( fo, ' pretty : %s\n', Agg.names{ii});
fprintf( fo, ' units : %s\n', '');
fprintf( fo, ' description : %s\n', '' );
fprintf( fo, ' links : %s\n', '' );
fprintf( fo, ' - url: %s\n', '' );
fprintf( fo, ' name: %s\n', '' );
end
end
if exist( 'Spa','var') && numel( Spa.names ) > 0
fprintf( fo, 'spatial : \n','');
fprintf( fo, ' - group : \n');
fprintf( fo, ' - name : General\n');
fprintf( fo, ' description : \n');
for ii = 1 : numel( Spa.names )
fprintf( fo, ' - native : %s\n', Spa.names{ii});
fprintf( fo, ' pretty : %s\n', Spa.names{ii});
fprintf( fo, ' units : %s\n', '');
fprintf( fo, ' description : %s\n', '' );
fprintf( fo, ' links : %s\n', '' );
fprintf( fo, ' - url: %s\n', '' );
fprintf( fo, ' name: %s\n', '' );
fprintf( fo, ' publish : %s\n', '' );
fprintf( fo, ' - isplot: %s\n', 'true' );
fprintf( fo, ' - isdisp: %s\n', 'true' );
end
end
fclose( fo );
fo = fopen( dictout, 'w' );
fprintf( fo,'---\nlayout: dictionary-template-final\ntitle: Dictionary Template\n---\n');
fclose(fo)
%%
diff --git a/Utilities/H5toYAML.m b/Utilities/H5toYAML.m
new file mode 100644
index 0000000..f1a94b7
--- /dev/null
+++ b/Utilities/H5toYAML.m
...
function postout = H5toDict( h5nm, dictdata, to_dir, source );
if ~exist( 'to_dir','var')
to_dir = './';
end
% Initialize the file for writing
info = h5info( h5nm );
% Get root information
%% Scrape metadata from the HDF5 file. Don't access any data yet.
h5 = H5F.open( h5nm )
description = H5O.get_comment_by_name( h5, '/','H5P_DEFAULT');
for rootid = 1 : numel( info.Groups ) % Iterate over the directories in the root
% Write Datasets
for dataid = 1 : numel( info.Groups( rootid ).Datasets )
T = info.Groups( rootid ).Datasets( dataid );
if strcmp( T.Name, 'Aggregate' )
% Get variable fields
if strcmp( T.Datatype.Class, 'H5T_COMPOUND' );
Agg{rootid}.name = info.Groups( rootid ).Name;
Agg{rootid}.vars = { T.Datatype.Type.Member.Name };
else
end
% Get attributes for fields
elseif strcmp( T.Name, 'Spatial' )
% Get variable fields
if strcmp( T.Datatype.Class, 'H5T_COMPOUND' );
Spa{rootid}.name = info.Groups( rootid ).Name;
Spa{rootid}.vars = { T.Datatype.Type.Member.Name };
H5O.get_comment_by_name(h5,info.Groups( rootid ).Name,'H5P_DEFAULT');
else
end
% Get attributes for fields
% Get attibutes
% Get comment
else
end
end
for workid = 1 : info.Groups( rootid ).Groups
% Write Datasets
for dataid = 1 : numel( info.Groups( rootid ).Groups( workid ).Datasets )
end
end
end
H5F.close(h5);
%% Parse Metadata and Dictionary to the datapage
dyml = ReadYaml(dictdata);
[p, f, ext] = fileparts( h5nm );
% f = '~/my-awesome-site/_site/other';
c = clock;
p = to_dir
postout = sprintf( '%s/%i-%i-%i-%s.markdown',p,c(1),c(2),c(3),f)
fo = fopen( postout, 'w' );
fprintf( fo, '---\n');
fprintf( fo, 'layout: dataset-template-final\n');
fprintf( fo, 'description: %s\n',description);
fprintf( fo, 'aggregate: \n','');
if exist( 'Agg','var')
for dd = 1 : numel( Agg );
fprintf( fo, ' - name: %s\n',regexprep( Agg{dd}.name, '/','Dataset '));
native = [Agg{dd}.name,'/Aggregate'];
fprintf( fo, ' native: %s\n',native);
fprintf( fo, ' vars: \n');
for gg = 1 : numel(dyml.aggregate)
for jj = 1 : numel(dyml.aggregate{gg}.group)
data = h5read( h5nm, native );
if isfield( dyml.aggregate{gg}.group{jj}, 'native' )
dyml.aggregate{gg}.group{jj}.native
if any( ismember( dyml.aggregate{gg}.group{jj}.native, Agg{dd}.vars ));
fprintf( fo, ' - native: %s\n', dyml.aggregate{gg}.group{jj}.native);
fprintf( fo, ' value: %f\n', getfield( data,dyml.aggregate{gg}.group{jj}.native) );
end
end
end
end
end
end
h5 = H5F.open( h5nm );
fprintf( fo, 'spatial: \n','');
if exist( 'Spa','var')
for dd = 1 : numel( Spa );
fprintf( fo, ' - name: %s\n',regexprep( Spa{dd}.name, '/','Dataset '));
native = [Spa{dd}.name,'/Spatial'];
fprintf( fo, ' native: %s\n',native);
desc = H5O.get_comment_by_name( h5, Spa{dd}.name,'H5P_DEFAULT');
fprintf( fo, ' description: %s\n',desc);
fprintf( fo, ' vars: \n');
for gg = 1 : numel(dyml.spatial)
for jj = 1 : numel(dyml.spatial{gg}.group)
if isfield( dyml.spatial{gg}.group{jj}, 'native' )
dyml.spatial{gg}.group{jj}.native
if any( ismember( dyml.spatial{gg}.group{jj}.native, Spa{dd}.vars ));
fprintf( fo, ' - native: %s\n', dyml.spatial{gg}.group{jj}.native);
end
end
end
end
end
end
fprintf( fo, '---\n');
fclose(fo);
H5F.close(h5);
return
% Select the template
fprintf( fo, 'source : \n','');
fprintf( fo, ' - name: \n', source.name);
fprintf( fo, ' url: %s\n',source.url );
fprintf( fo, 'converter : \n','');
fprintf( fo, ' - name: \n', mfilename);
fprintf( fo, ' sha: %s\n',strtok( evalc( 'git log --abbrev-commit --pretty=oneline' ) ));
if numel( Agg.names ) > 0
fprintf( fo, 'aggregate : \n','');
fprintf( fo, ' - group : \n');
fprintf( fo, ' - name : General\n');
fprintf( fo, ' description : \n');
for ii = 1 : numel( Agg.names )
fprintf( fo, ' - native : %s\n', Agg.names{ii});
fprintf( fo, ' pretty : %s\n', Agg.names{ii});
fprintf( fo, ' units : %s\n', '');
fprintf( fo, ' description : %s\n', '' );
fprintf( fo, ' links : %s\n', '' );
fprintf( fo, ' - url: %s\n', '' );
fprintf( fo, ' name: %s\n', '' );
end
end
if numel( Spa.names ) > 0
fprintf( fo, 'spatial : \n','');
fprintf( fo, ' - group : \n');
fprintf( fo, ' - name : General\n');
fprintf( fo, ' description : \n');
for ii = 1 : numel( Spa.names )
fprintf( fo, ' - native : %s\n', Spa.names{ii});
fprintf( fo, ' pretty : %s\n', Spa.names{ii});
fprintf( fo, ' units : %s\n', '');
fprintf( fo, ' description : %s\n', '' );
fprintf( fo, ' links : %s\n', '' );
fprintf( fo, ' - url: %s\n', '' );
fprintf( fo, ' name: %s\n', '' );
fprintf( fo, ' publish : %s\n', '' );
fprintf( fo, ' - isplot: %s\n', 'true' );
fprintf( fo, ' - isdisp: %s\n', 'true' );
end
end
fclose( fo );
%%
diff --git a/Utilities/Struct2YMLMD.m b/Utilities/Struct2YMLMD.m
new file mode 100644
index 0000000..682a540
--- /dev/null
+++ b/Utilities/Struct2YMLMD.m
...
function fn = Stuct2YMLMD( D, fn)
fo = fopen( fn,'w');
fprintf( fo,'---\n');
fldsii = cellfun(@(x)char(x),fieldnames( D )','UniformOutput',false);
recurseii = [];
indent = '';
for ii = 1 : numel( fldsii )
data = getfield( D, fldsii{ii} );
if ~iscell( data )
if ischar( data )
fprintf( fo,'%s%s: %s\n',indent,char(fldsii{ii}),data);
else
fprintf( fo,'%s%s: %f\n',indent,char(fldsii{ii}),data);
end
else
%%
indent = '';
fprintf( fo,'%s%s: \n',indent,char(fldsii{ii}));
for dd = 1 : numel( data)
indent = ' - ';
flddata = getfield( D, fldsii{ii},{dd} );
fldsjj = cellfun(@(x)char(x),fieldnames( flddata{1} )','UniformOutput',false);
for jj = 1 : numel(fldsjj)
data = getfield( flddata{1}, fldsjj{jj});
if ~iscell( data )
if ischar( data )
fprintf( fo,'%s%s: %s\n',indent,char(fldsjj{jj}),data);
else
fprintf( fo,'%s%s: %f\n',indent,char(fldsjj{jj}),data);
end
indent = regexprep(indent, '-',' ');
else
indent = ' ';
%%
fprintf( fo,'%s%s: \n',indent,char(fldsjj{jj}));
for ee = 1 : numel( data)
indent = ' - ';
flddatajj = getfield( flddata{1}, fldsjj{jj},{ee} );
fldskk = cellfun(@(x)char(x),fieldnames( flddatajj{1} )','UniformOutput',false);
for kk = 1 : numel(fldskk)
data = getfield( flddatajj{1}, fldskk{kk});
%%
if ~iscell( data )
if ischar( data )
fprintf( fo,'%s%s: %s\n',indent,char(fldskk{kk}),data);
else
fprintf( fo,'%s%s: %f\n',indent,char(fldskk{kk}),data);
end
indent = regexprep(indent, '-',' ');
else
indent = ' ';
%%
fprintf( fo,'%s%s: \n',indent,char(fldskk{kk}));
for ff = 1 : numel( data)
indent = ' - ';
flddatakk = getfield( flddatajj{1}, fldskk{kk},{ff} );
fldsll = cellfun(@(x)char(x),fieldnames( flddatakk{1} )','UniformOutput',false);
for ll = 1 : numel(fldsll)
data = getfield( flddatakk{1}, fldsll{ll});
%%
if ~iscell( data )
if ischar( data )
fprintf( fo,'%s%s: %s\n',indent,char(fldsll{ll}),data);
else
fprintf( fo,'%s%s: %f\n',indent,char(fldsll{ll}),data);
end
indent = regexprep(indent, '-',' ');
else
indent = ' ';
%%
fprintf( fo,'%s%s: \n',indent,char(fldsll{ll}));
for gg = 1 : numel( data)
indent = ' - ';
flddatall = getfield( flddatakk{1}, fldsll{ll},{gg} );
fldsmm = cellfun(@(x)char(x),fieldnames( flddatall{1} )','UniformOutput',false);
for mm = 1 : numel(fldsmm)
data = getfield( flddatamm{1}, fldskk{mm});
%%
if ~iscell( data )
if ischar( data )
fprintf( fo,'%s%s: %s\n',indent,char(fldsmm{mm}),data);
else
fprintf( fo,'%s%s: %f\n',indent,char(fldsmm{mm}),data);
end
indent = regexprep(indent, '-',' ');
else
indent = ' ';
%%
%%
end
%%
end
end
%%
end
%%
end
end
%%
end
%%
end
end
%%
end
end
end
% fldsjj = cellfun(@(x)char(x),fieldnames( D )','UniformOutput',false);
recurseii = [ recurseii, ii];
indent = '';
%%
end
end
fprintf( fo,'---\n');
fclose(fo);
diff --git a/Utilities/h5read.m b/Utilities/h5read.m
new file mode 100644
index 0000000..25315d6
--- /dev/null
+++ b/Utilities/h5read.m
...
function DATA = h5read( fn, dset, FIELD )
% Reads from HDF5 filetypes. This function was specifically made to support partial reading of composite datatypes.
%
% INPUTS:
% fn - file name where the data is written to.
% dset - name of the dataset in the HDF5 that the data is being stored as
% FIELD - Name or Index of the composite field to be read from the datasset
% dset
fid = H5F.open( fn );
did = H5D.open(fid,dset);
tid = H5D.get_type(did);
tid2 = H5T.create('H5T_COMPOUND',H5T.get_size( tid ) );
N = H5T.get_nmembers(tid);
if nargin == 3
if isnumeric(FIELD)
index = FIELD;
index_on = true;
else
if ischar( FIELD)
FIELD = {FIELD};
end
nm = arrayfun(@(x)H5T.get_member_name(tid,x),[1:N]-1,'UniformOutput',false);
index = find( ismember( nm, FIELD) );
end
for ii = index-1
H5T.insert( tid2, nm{ii+1}, H5T.get_member_offset( tid, ii ),'H5T_NATIVE_DOUBLE');
end
else
index = 1:N;
tid2 = 'H5ML_DEFAULT';
end
%
DATA = H5D.read(did, tid2 , 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT' );
H5D.close( did )
H5T.close( tid )
if nargin == 3
H5T.close( tid2 )
end
H5F.close(fid);
diff --git a/Utilities/h5writeatt.m b/Utilities/h5writeatt.m
new file mode 100644
index 0000000..220abdb
--- /dev/null
+++ b/Utilities/h5writeatt.m
...
function h5writeattcompound( fn, dset, attname, DATA )
% An improved version of the matlab function h5write. Natively, h5write lacks the
% ability to write structures to HDF5 files.
%
% INPUTS:
% fn - file name where the data is written to.
% dset - name of the dataset in the HDF5 that the data is being stored as
% DATA - allows structures are all h5write native datatypes to be written.
% if DATA is a structure then the information is written as a
% compound datatype. The size of each field should be the same.
if isstruct( DATA )
if exist( fn, 'file')
fo = H5F.open(fn,'H5F_ACC_RDWR','H5P_DEFAULT');
else
fo = H5F.create(fn);
end
fields = fieldnames(DATA);
sz = size( getfield( DATA, fields{1}));
tid = H5T.create('H5T_COMPOUND',numel(fields)*8);
ii = 1;
H5T.insert(tid,fields{ii},(ii-1)*8,'H5T_NATIVE_DOUBLE');
ii = 2;
strType = H5T.copy( 'H5T_C_S1' );
H5T.set_size(strType, numel(getfield( DATA, fields{ii})) );
% DATA = setfield( DATA, fields{ii}, getfield( DATA, fields{ii} ) );
H5T.insert(tid,fields{ii},(ii-1)*8,strType);
sid = H5S.create_simple( numel(sz), fliplr(sz), fliplr(sz) );
% dset = horzcat(dset, num2str(round(rand(1)*1e5)));
did = H5D.open( fo, dset);
aid = H5A.create( did, attname, tid, sid, H5P.create('H5P_ATTRIBUTE_CREATE'));
H5A.write( aid, tid, DATA );
H5A.close(aid)
H5S.close(sid)
H5D.close(did)
H5T.close(tid)
H5F.close(fo);
else
h5writeatt( fn,dset, attname, DATA);
end
end
diff --git a/Utilities/h5writeattcompound.m b/Utilities/h5writeattcompound.m
new file mode 100644
index 0000000..94507f0
--- /dev/null
+++ b/Utilities/h5writeattcompound.m
...
function h5writeattcompound( fn, dset, attname, DATA )
% An improved version of the matlab function h5write. Natively, h5write lacks the
% ability to write structures to HDF5 files.
%
% INPUTS:
% fn - file name where the data is written to.
% dset - name of the dataset in the HDF5 that the data is being stored as
% DATA - allows structures are all h5write native datatypes to be written.
% if DATA is a structure then the information is written as a
% compound datatype. The size of each field should be the same.
if isstruct( DATA )
if exist( fn, 'file')
fo = H5F.open(fn,'H5F_ACC_RDWR','H5P_DEFAULT');
else
fo = H5F.create(fn);
end
fields = fieldnames(DATA);
sz = size( getfield( DATA, fields{1}));
tid = H5T.create('H5T_COMPOUND',numel(fields)*8);
ii = 1;
H5T.insert(tid,fields{ii},(ii-1)*8,'H5T_NATIVE_DOUBLE');
ii = 2;
strType = H5T.copy( 'H5T_C_S1' );
H5T.set_size(strType, numel(getfield( DATA, fields{ii})) );
% DATA = setfield( DATA, fields{ii}, getfield( DATA, fields{ii} ) );
H5T.insert(tid,fields{ii},(ii-1)*8,strType);
sid = H5S.create_simple( numel(sz), fliplr(sz), fliplr(sz) );
% dset = horzcat(dset, num2str(round(rand(1)*1e5)));
did = H5D.open( fo, dset);
aid = H5A.create( did, attname, tid, sid, H5P.create('H5P_ATTRIBUTE_CREATE'));
H5A.write( aid, tid, DATA );
H5A.close(aid)
H5S.close(sid)
H5D.close(did)
H5T.close(tid)
H5F.close(fo);
elseif ischar(DATA)
if exist( fn, 'file')
fo = H5F.open(fn,'H5F_ACC_RDWR','H5P_DEFAULT');
else
fo = H5F.create(fn);
end
SDIM = size(DATA,2);
filetype = H5T.copy ('H5T_FORTRAN_S1');
H5T.set_size (filetype, SDIM );
memtype = H5T.copy ('H5T_C_S1');
H5T.set_size (memtype, SDIM );
% Create dataspace. Setting maximum size to [] sets the maximum
% size to be the current size.
%
dims = size(DATA,1);
space = H5S.create_simple (1,fliplr( dims), []);
%
% Create the attribute and write the string data to it.
%
if strcmp( dset, '/');
attr = H5A.create (fo, attname, filetype, space, 'H5P_DEFAULT');
H5A.write (attr, memtype, DATA');
else
did = H5D.open( fo, dset );
attr = H5A.create (fo, attname, filetype, space, 'H5P_DEFAULT');
H5A.write (attr, memtype, DATA');
H5D.close (did);
end
%
% Close and release resources.
%
H5A.close (attr);
H5S.close (space);
H5T.close (filetype);
H5T.close (memtype);
H5F.close ( fo );
else
h5writeatt( fn,dset, attname, DATA);
end
end
diff --git a/Utilities/h5writecompound.m b/Utilities/h5writecompound.m
new file mode 100644
index 0000000..84b5b21
--- /dev/null
+++ b/Utilities/h5writecompound.m
...
function h5writecompound( fn, dset, DATA )
% An improved version of the matlab function h5write. Natively, h5write lacks the
% ability to write structures to HDF5 files.
%
% INPUTS:
% fn - file name where the data is written to.
% dset - name of the dataset in the HDF5 that the data is being stored as
% DATA - allows structures are all h5write native datatypes to be written.
% if DATA is a structure then the information is written as a
% compound datatype. The size of each field should be the same.
flds = fieldnames( DATA );
for ii = 1 : numel( flds )
switch class( getfield( DATA, flds{ii} ) )
case 'int8'
hdftype{ii} = 'H5T_STD_I8LE';
hdfbyte(ii) = 1;
case 'int16'
hdftype{ii} = 'H5T_STD_I16LE';
hdfbyte(ii) = 2;
case 'int32'
hdftype{ii} = 'H5T_STD_I32LE';
hdfbyte(ii) = 4;
case 'uint8'
hdftype{ii} = 'H5T_STD_I8LE';
hdfbyte(ii) = 1;
case 'int16'
hdftype{ii} = 'H5T_STD_I16LE';
hdfbyte(ii) = 2;
case 'uint32'
hdftype{ii} = 'H5T_STD_U32LE';
hdfbyte(ii) = 4;
otherwise
hdftype{ii} = 'H5T_NATIVE_DOUBLE';
hdfbyte(ii) = 8;
end
end
cumhdfbyte = [0 , cumsum(hdfbyte)];
if isstruct( DATA )
if exist( fn, 'file')
fo = H5F.open(fn,'H5F_ACC_RDWR','H5P_DEFAULT');
else
fo = H5F.create(fn);
end
fields = fieldnames(DATA);
sz = size( getfield( DATA, fields{1}));
tid = H5T.create('H5T_COMPOUND', sum(hdfbyte));
for ii = 1 : numel( fields )
H5T.insert(tid,fields{ii},cumhdfbyte(ii),hdftype{ii});
if ~all( sz == size( getfield( DATA, fields{ii})))
error('The size of the elements in the data structure must be the same. The data was not written.')
H5T.close(tid)
H5F.close(fo);
end
end
sid = H5S.create_simple( numel(sz), fliplr(sz), fliplr(sz) );
% dset = horzcat(dset, num2str(round(rand(1)*1e5)));
did = H5D.create( fo, dset, tid, sid, 'H5P_DEFAULT');
H5D.write( did, tid, 'H5S_ALL', 'H5S_ALL', 'H5P_DEFAULT', DATA );
H5D.close(did)
H5S.close(sid)
else
h5create( fn,dset, DATA, size(DATA) );
end
end
diff --git a/Utilities/h5writemeta.m b/Utilities/h5writemeta.m
new file mode 100644
index 0000000..8465c49
--- /dev/null
+++ b/Utilities/h5writemeta.m
...
function h5writemeta( fn, dset, attname, DATA )
% An improved version of the matlab function h5write. Natively, h5write lacks the
% ability to write structures to HDF5 files.
%
% INPUTS:
% fn - file name where the data is written to.
% dset - name of the dataset in the HDF5 that the data is being stored as
% DATA - allows structures are all h5write native datatypes to be written.
% if DATA is a structure then the information is written as a
% compound datatype. The size of each field should be the same.
if isstruct( DATA )
if exist( fn, 'file')
fo = H5F.open(fn,'H5F_ACC_RDWR','H5P_DEFAULT');
else
fo = H5F.create(fn);
end
fields = fieldnames(DATA);
sz = size( getfield( DATA, fields{1}));
nbytes = [ 8 50 128];
cnb = cumsum( nbytes );
tid = H5T.create('H5T_COMPOUND',cnb(end));
ii = 1;
H5T.insert(tid,fields{ii},0,'H5T_NATIVE_DOUBLE');
ii = 2;
strType = H5T.copy( 'H5T_C_S1' );
H5T.set_size(strType, cnb(ii-1) );
H5T.insert(tid,fields{ii},nbytes(ii),strType);
if numel( fields ) == 3
ii = 3;
strType = H5T.copy( 'H5T_C_S1' );
H5T.set_size(strType, cnb(ii-1) );
H5T.insert(tid,fields{ii},nbytes(ii),strType);
elseif numel(fields) > 3
error(sprintf('Invalid %s attribute.', attname ));
end
% DATA = setfield( DATA, fields{ii}, getfield( DATA, fields{ii} ) );
sid = H5S.create_simple( numel(sz), fliplr(sz), fliplr(sz) );
% dset = horzcat(dset, num2str(round(rand(1)*1e5)));
did = H5D.open( fo, dset);
aid = H5A.create( did, attname, tid, sid, H5P.create('H5P_ATTRIBUTE_CREATE'));
H5A.write( aid, tid, DATA );
H5A.close(aid)
H5S.close(sid)
H5D.close(did)
H5T.close(tid)
H5F.close(fo);
else
h5writeatt( fn,dset, attname, DATA);
end
end
