Matlab: major updates/fixes for Octave support handling hdf5 field dumps

Octave: to setup the full octave hdf5 support
run setup.m to build all necessary octave files.
Repeat this process any time you update openEMS or octave.

Signed-off-by: Thorsten Liebig <Thorsten.Liebig@gmx.de>

matlab/AnalyzeNF2FF.m

@@ -40,11 +40,11 @@ end
 
 % read time domain field data and transform into frequency domain
 for n=find(nf2ff.directions==1)
-    [Ef{n}, E_mesh{n}] = ReadHDF5Dump( [Sim_Path '/' filenames_E{n}], 'Frequency', f );
+    [Ef{n}, E_mesh{n}] = ReadHDF5Dump( [Sim_Path '/' filenames_E{n} '.h5'], 'Frequency', f );
     %clear out time domain data
     Ef{n} = rmfield(Ef{n},'TD');
 
-    [Hf{n}, H_mesh{n}] = ReadHDF5Dump( [Sim_Path '/' filenames_H{n}], 'Frequency', f );
+    [Hf{n}, H_mesh{n}] = ReadHDF5Dump( [Sim_Path '/' filenames_H{n} '.h5'], 'Frequency', f );
     %clear out time domain data
     Hf{n} = rmfield(Hf{n},'TD');
 

matlab/ReadHDF5FieldData.m

@@ -2,15 +2,21 @@ function hdf_fielddata = ReadHDF5FieldData(file)
 % function hdf_fielddata = ReadHDF5FieldData(file)
 %
 % returns:
-% hdf_fielddata.time
-% hdf_fielddata.names
-% hdf_fielddata.values
+% % time domain data (if exist)
+% hdf_fielddata.TD.time
+% hdf_fielddata.TD.names
+% hdf_fielddata.TD.values
+%
+% % frequency domain data (if exist)
+% hdf_fielddata.FD.time
+% hdf_fielddata.FD.names
+% hdf_fielddata.FD.values
 %
 % example: values of timestep 12:
-% hdf_fielddata.values{12}: array (x,y,z,polarization)
+% hdf_fielddata.TD.values{12}: array (x,y,z,polarization)
 %
 % plot z-field component along y-direction for timestep 12:
-% plot( hdf_fielddata.values{12}(1,:,1,3) )
+% plot( hdf_fielddata.TD.values{12}(1,:,1,3) )
 %
 % openEMS matlab interface
 % -----------------------
@@ -81,11 +87,26 @@ if (numel(FD.names)>0)
     end
 end
 
-
 function hdf_fielddata = ReadHDF5FieldData_octave(file)
 hdf = load( '-hdf5', file );
-hdf_fielddata.names = fieldnames(hdf.FieldData);
-for n=1:numel(hdf_fielddata.names)
-    hdf_fielddata.time(n) = str2double(hdf_fielddata.names{n}(2:end));
-    hdf_fielddata.values{n} = hdf.FieldData.(hdf_fielddata.names{n});
+if ~isfield(hdf,'FieldData')
+    error('no field data found')
+end
+if isfield(hdf.FieldData,'TD')
+    %read TD data
+    hdf_fielddata_names = fieldnames(hdf.FieldData.TD);
+    for n=1:numel(hdf_fielddata_names)
+        hdf_fielddata.TD.values{n} = hdf.FieldData.TD.(hdf_fielddata_names{n});
+        hdf_fielddata.TD.names{n} = ['/FieldData/TD/' hdf_fielddata_names{n}(2:end)];
+        hdf_fielddata.TD.time(n) = h5readatt_octave(file, hdf_fielddata.TD.names{n},'time');
+    end
+end
+if isfield(hdf.FieldData,'FD')
+    %read FD data
+    hdf_fielddata_names = fieldnames(hdf.FieldData.FD);
+    for n=1:numel(hdf_fielddata_names)/2
+        hdf_fielddata.FD.values{n} = hdf.FieldData.FD.(hdf_fielddata_names{2*n}) + 1j*hdf.FieldData.FD.(hdf_fielddata_names{2*n-1});
+        hdf_fielddata.FD.names{n} = ['/FieldData/FD/' hdf_fielddata_names{2*n-1}(1:end-5)];
+        hdf_fielddata.FD.freq(n) = h5readatt_octave(file,['/FieldData/FD/' hdf_fielddata_names{2*n}],'frequency');
+    end
 end

matlab/ReadHDF5Mesh.m

@@ -57,3 +57,9 @@ for n=1:numel(hdf_mesh.names)
         hdf_mesh.type = 1; % cylindrical mesh
     end
 end
+
+if (hdf_mesh.type==1)
+    % alpha and rho are in the wrong order, flip to have rho, alpha, z
+    hdf_mesh.names(1:2) = fliplr(hdf_mesh.names(1:2));
+    hdf_mesh.lines(1:2) = fliplr(hdf_mesh.lines(1:2));
+end

matlab/h5readatt_octave.cc

@@ -0,0 +1,57 @@
+#include <octave/oct.h>
+#include <octave/ov-struct.h>
+#include "hdf5.h"
+
+DEFUN_DLD (h5readatt_octave, args, nargout, "h5readatt_octave(<File_Name>,<DataSet_Name>,<Attribute_Name>)")
+{
+	octave_value retval;
+	int nargin = args.length();
+	if (nargin != 3)
+	{
+		print_usage();
+		return retval;
+	}
+	if ((args(0).is_string()==false) || (args(1).is_string()==false) || (args(2).is_string()==false))
+	{
+		print_usage();
+		return retval;
+	}
+
+	//suppress hdf5 error output
+	H5Eset_auto(NULL, NULL);
+
+	hid_t file = H5Fopen( args(0).string_value().c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
+	if (file==-1)
+	{
+	  error("h5readatt_octave: opening the given File failed");
+	  return retval;
+	}
+
+	hid_t ds = H5Dopen(file, args(1).string_value().c_str());
+	if (ds==-1)
+	{
+	  error("h5readatt_octave: opening the given DataSet failed");
+	  return retval;
+	}
+
+	hid_t attr = H5Aopen_name(ds, args(2).string_value().c_str());
+	if (attr==-1)
+	{
+	  error("h5readatt_octave: opening the given Attribute failed");
+	  return retval;
+	}
+
+	float value;
+	if (H5Aread(attr, H5T_NATIVE_FLOAT, &value)<0)
+	{
+	  error("h5readatt_octave: reading the given Attribute failed");
+	  return retval;
+	}
+
+	H5Aclose(attr);
+	H5Dclose(ds);
+	H5Fclose(file);
+	retval = octave_value(value);
+	return retval;
+}
+

matlab/setup.m

@@ -0,0 +1,23 @@
+function setup()
+% function setup()
+%
+% setup openEMS Matlab/octave interface
+%
+% openEMS matlab/octave interface
+% -----------------------
+% author: Thorsten Liebig (2011)
+
+disp('setting up openEMS matlab/octave interface')
+
+% cd to directory of this file and restore current path at the end
+current_path = pwd;
+dir  = fileparts( mfilename('fullpath') );
+cd(dir);
+
+if isOctave()
+    disp('compiling oct files')
+    mkoctfile -lhdf5 h5readatt_octave.cc
+else
+end
+
+cd(current_path);