add h5create_group()

Author: scivision

+stdlib/+hdf5nc/h5create_group.m

@@ -0,0 +1,53 @@
+function fid = h5create_group(file, hpath)
+%% create HDF5 group
+%
+% file: HDF5 file name or handle
+% hpath: HDF5 group/dataset -- ensure final character is "/" if hpath is only a group
+
+arguments
+  file
+  hpath (1,1) string {mustBeNonzeroLengthText}
+end
+
+import stdlib.fileio.expanduser
+
+%% polymorphic fid/filename
+if isa(file, 'H5ML.id')
+  fid = file;
+else
+  file = expanduser(file);
+  if isfile(file)
+    dcpl = 'H5P_DEFAULT';
+    fid = H5F.open(file, 'H5F_ACC_RDWR', dcpl);
+  else
+    fid = H5F.create(file);
+  end
+end
+
+%% are there any groups
+grps = split(hpath, "/");
+if length(grps) < 3
+  return
+end
+
+%% recursively create groups as needed
+plist = 'H5P_DEFAULT';
+groot = H5G.open(fid, "/");
+
+for i = 0:length(grps) - 3
+  n = join(grps(1:i+2), "/");
+
+  if ~H5L.exists(groot, n, plist)
+    gid = H5G.create(fid, n, plist, plist, plist);
+    H5G.close(gid)
+  end
+end % for
+
+H5G.close(groot)
+
+if nargout == 0
+  H5F.close(fid);
+  clear('fid')
+end
+
+end

+stdlib/+hdf5nc/h5exists.m

@@ -1,10 +1,10 @@
 function exists = h5exists(file, varnames)
-% check if variable(s) exists in HDF5 file
+% check if object(s) exists in HDF5 file
 %
 % parameters
 % ----------
 % file: HDF5 filename
-% varname: name of variable inside HDF5 file
+% varname: name of variable in file
 %
 % returns
 % -------

+stdlib/+hdf5nc/h5ndims.m

@@ -13,8 +13,6 @@
 
 file = expanduser(file);
 
-assert(isfile(file), "%s not found", file)
-
 dsi = h5info(file, variable).Dataspace;
 if dsi.Type == "scalar"
   frank = 0;

+stdlib/+hdf5nc/h5size.m

@@ -14,8 +14,6 @@
 
 file = expanduser(file);
 
-assert(isfile(file), "%s not found", file)
-
 dsi = h5info(file, variable).Dataspace;
 if dsi.Type == "scalar"
   fsize = [];

+stdlib/+hdf5nc/h5variables.m

@@ -1,6 +1,6 @@
-function [names, groups] = h5variables(file, group)
-% get dataset names in a file
-% Optionally, get first level of groups in a file.
+function names = h5variables(file, group)
+%% get dataset names in a file under group
+% default is datasets under "/", optionally under "/group"
 %
 % parameters
 % ----------
@@ -10,7 +10,6 @@
 % returns
 % -------
 % names: variable names
-% groups: file groups
 
 arguments
   file (1,1) string {mustBeNonzeroLengthText}
@@ -22,9 +21,6 @@
 file = expanduser(file);
 
 names = string.empty;
-groups = string.empty;
-
-assert(isfile(file), "%s not found", file)
 
 if isempty(group)
   finf = h5info(file);
@@ -33,14 +29,11 @@
 end
 
 ds = finf.Datasets;
-gs = finf.Groups;
 
-if ~isempty(ds)
-  names = string({ds.Name});
+if isempty(ds)
+  return
 end
 
-if nargout > 1 && ~isempty(gs)
-  groups = string({gs.Name});
-end
+names = string({ds.Name});
 
 end % function

+stdlib/+hdf5nc/ncndims.m

@@ -13,8 +13,6 @@
 
 file = expanduser(file);
 
-assert(isfile(file), "%s not found", file)
-
 dsi = ncinfo(file, variable);
 if isempty(dsi.Dimensions)
   frank = 0;

+stdlib/+hdf5nc/ncsize.m

@@ -14,8 +14,6 @@
 
 file = expanduser(file);
 
-assert(isfile(file), "%s not found", file)
-
 dsi = ncinfo(file, variable);
 if isempty(dsi.Dimensions)
   fsize = [];

+stdlib/+hdf5nc/ncvariables.m

@@ -17,8 +17,6 @@
 
 file = expanduser(file);
 
-assert(isfile(file), "%s not found", file)
-
 finf = ncinfo(file);
 ds = finf.Variables(:);
 names = string({ds(:).Name});

+stdlib/+hdf5nc/private/create_hdf5_group.m

@@ -1,21 +1,17 @@
-function h5_write_scalar(filename, varname, A)
+function h5_write_scalar(file, hpath, A)
 %% write HDF5 scalar as a scalar
 %  h5create doesn't support scalars
 arguments
-  filename (1,1) string {mustBeNonzeroLengthText}
-  varname (1,1) string {mustBeNonzeroLengthText}
+  file (1,1)
+  hpath (1,1) string {mustBeNonzeroLengthText}
   A (1,1)
 end
 
-dcpl = 'H5P_DEFAULT';
+import stdlib.hdf5nc.h5create_group
 
-if isfile(filename)
-  fid = H5F.open(filename, 'H5F_ACC_RDWR', dcpl);
-else
-  fid = H5F.create(filename);
-end
+dcpl = 'H5P_DEFAULT';
 
-create_hdf5_group(fid, varname);
+fid = h5create_group(file, hpath);
 
 space_id = H5S.create('H5S_SCALAR');
 if isstring(A)
@@ -30,7 +26,7 @@ function h5_write_scalar(filename, varname, A)
   type_id = H5T.copy(class2h5t(A));
 end
 
-dset_id = H5D.create(fid, varname, type_id, space_id, dcpl);
+dset_id = H5D.create(fid, hpath, type_id, space_id, dcpl);
 
 H5D.write(dset_id,'H5ML_DEFAULT','H5S_ALL','H5S_ALL', dcpl, A);