From cb788786043e8967c5de63a195b29c9cc14bc02f Mon Sep 17 00:00:00 2001
From: Thorsten Liebig <Thorsten.Liebig@gmx.de>
Date: Mon, 30 Jul 2012 11:13:36 +0200
Subject: [PATCH] matlab: some fixes and updates handling hdf5 files

---
 matlab/ReadHDF5FieldData.m | 49 ++++++++++----------------------------
 matlab/WriteHDF5.m         | 17 +++++++------
 2 files changed, 21 insertions(+), 45 deletions(-)

diff --git a/matlab/ReadHDF5FieldData.m b/matlab/ReadHDF5FieldData.m
index 2d49c41..b10cadf 100644
--- a/matlab/ReadHDF5FieldData.m
+++ b/matlab/ReadHDF5FieldData.m
@@ -8,8 +8,7 @@ function hdf_fielddata = ReadHDF5FieldData(file)
 % hdf_fielddata.TD.values
 %
 % % frequency domain data (if exist)
-% hdf_fielddata.FD.time
-% hdf_fielddata.FD.names
+% hdf_fielddata.FD.frequency
 % hdf_fielddata.FD.values
 %
 % example: values of timestep 12:
@@ -32,7 +31,6 @@ end
 
 info = hdf5info(file);
 TD.names = {};
-FD.names = {};
 hdf_fielddata = [];
 
 for n=1:numel(info.GroupHierarchy.Groups)
@@ -49,16 +47,6 @@ for n=1:numel(info.GroupHierarchy.Groups)
                     end
                 end
             end
-            %search and read FD data
-            if strcmp(info.GroupHierarchy.Groups(n).Groups(nGroup).Name,'/FieldData/FD')
-                for m=1:numel(info.GroupHierarchy.Groups(n).Groups(nGroup).Datasets)
-                    FD.names{m} = info.GroupHierarchy.Groups(n).Groups(nGroup).Datasets(m).Name;
-                    for a = 1:numel(info.GroupHierarchy.Groups(n).Groups(nGroup).Datasets(m).Attributes)
-                        str = regexp(info.GroupHierarchy.Groups(n).Groups(nGroup).Datasets(m).Attributes(a).Name,'\w/*\w*','match');
-                        FD.(str{end})(m) = double(info.GroupHierarchy.Groups(n).Groups(nGroup).Datasets(m).Attributes(a).Value);
-                    end
-                end
-            end
         end
         
     end
@@ -71,24 +59,15 @@ if (numel(TD.names)>0)
     end
 end
 
-if (numel(FD.names)>0)
-    hdf_fielddata.FD=FD;
-    Nr_freq = numel(FD.names);
-    for n=1:Nr_freq
-        name = ['/FieldData/FD/f' int2str(n-1) '_real'];
-        ind = find(strcmp(FD.names,name));
-        if isempty(ind)
-            ind = find(strcmp(FD.names,['/FieldData/FD/f' int2str(n-1)]));
-            if ~isempty(ind)
-                hdf_fielddata.FD.values{n} = double(hdf5read(file,FD.names{ind}));
-            end
-        else
-            hdf_fielddata.FD.values{n} = double(hdf5read(file,FD.names{ind}));
-            name = ['/FieldData/FD/f' int2str(n-1) '_imag'];
-            ind = find(strcmp(FD.names,name));
-            hdf_fielddata.FD.values{n} = hdf_fielddata.FD.values{n} + 1j*double(hdf5read(file,FD.names{ind}));
-        end
-    end
+% extract FD data
+try
+    hdf_fielddata.FD.frequency = double(hdf5read(file,'/FieldData/FD','frequency'));
+catch err
+    disp(err)
+    return
+end
+for n=1:numel(hdf_fielddata.FD.frequency)
+   hdf_fielddata.FD.values{n} = double(hdf5read(file,['/FieldData/FD/f' int2str(n-1) '_real']) + 1i*hdf5read(file,['/FieldData/FD/f' int2str(n-1) '_imag']));
 end
 
 function hdf_fielddata = ReadHDF5FieldData_octave(file)
@@ -107,10 +86,8 @@ if isfield(hdf.FieldData,'TD')
 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.frequencies(n) = h5readatt_octave(file,['/FieldData/FD/' hdf_fielddata_names{2*n}],'frequency');
+    hdf_fielddata.FD.frequency = h5readatt_octave(file,'/FieldData/FD/','frequency');
+    for n=1:numel(hdf_fielddata.FD.frequency)
+        hdf_fielddata.FD.values{n} = double(hdf.FieldData.FD.(['f' int2str(n-1) '_real']) +1i*hdf.FieldData.FD.(['f' int2str(n-1) '_imag']) );
     end
 end
diff --git a/matlab/WriteHDF5.m b/matlab/WriteHDF5.m
index 130e7ca..df6a8d7 100644
--- a/matlab/WriteHDF5.m
+++ b/matlab/WriteHDF5.m
@@ -38,26 +38,25 @@ if isfield( hdf_fielddata, 'TD' )
 end
 if isfield( hdf_fielddata, 'FD' )
     % this is a frequency domain data set
-    freq = hdf_fielddata.FD.freq;
+    freq = hdf_fielddata.FD.frequency;
     for n=1:numel(freq)
         name = ['/FieldData/FD/f' int2str(n-1) '_real'];
         [details.Location, details.Name] = fileparts(name);
-        attribute_details.AttachedTo = name;
-        attribute_details.AttachType = 'dataset';
-        attribute_details.Name = 'freq';
         hdf5write( filename, details, real(hdf_fielddata.FD.values{n}), ...
-                   attribute_details, freq(n), ...
                    'WriteMode', writemode );
         name = ['/FieldData/FD/f' int2str(n-1) '_imag'];
         [details.Location, details.Name] = fileparts(name);
-        attribute_details.AttachedTo = name;
-        attribute_details.AttachType = 'dataset';
-        attribute_details.Name = 'freq';
         hdf5write( filename, details, imag(hdf_fielddata.FD.values{n}), ...
-                   attribute_details, freq(n), ...
                    'WriteMode', 'append' );
         writemode = 'append';
     end
+    name = '/FieldData/FD';
+    [details.Location, details.Name] = fileparts(name);
+    attribute_details.AttachedTo = name;
+    attribute_details.AttachType = 'group';
+    attribute_details.Name = 'frequency';
+    hdf5write( filename, attribute_details, freq, ...
+                   'WriteMode', 'append' );
 end
 
 names = hdf_mesh.names; % names is a cell array