some first matlab hdf5 read/plot

matlab/PlotHDF5FieldData.m

@@ -0,0 +1,60 @@
+function PlotHDF5FieldData(file, PlotArgs)
+
+plane = PlotArgs.plane;
+component = PlotArgs.component;
+
+if (isfield(PlotArgs,'pauseTime'))
+    pauseT = PlotArgs.pauseTime;
+else
+    pauseT = 0.01;
+end
+
+mesh = ReadHDF5Mesh(file);
+fields = ReadHDF5FieldData(file);
+
+max_amp = 0;
+
+if (strcmp(plane,'zx'))
+    [X1 X2] = meshgrid(mesh.lines{3}, mesh.lines{1});
+    
+    if (component>0)
+        for n=1:numel(fields.values)
+            Z{n} = squeeze(double(fields.values{n}(:,1,:,component)));
+        end
+    else 
+        for n=1:numel(fields.values)
+            fx = squeeze(double(fields.values{n}(:,1,:,1)));
+            fy = squeeze(double(fields.values{n}(:,1,:,2)));
+            fz = squeeze(double(fields.values{n}(:,1,:,3)));
+            Z{n} = sqrt(fx.^2 + fy.^2 + fz.^2);
+        end        
+    end
+end
+
+
+
+for n=1:numel(Z)
+    amp = max(max(abs(Z{n})));
+    if (amp>max_amp)
+        max_amp = amp;
+    end
+end
+if (max_amp==0)
+    disp('max found amplitude was 0 --> nothing to plot');
+    return
+end
+
+for n=1:numel(Z)
+    surf(X1,X2,Z{n})
+    title(fields.names{n});
+    
+    if (isfield(PlotArgs,'zlim'))
+        if ~ischar(PlotArgs.zlim)
+            zlim(PlotArgs.zlim);
+        elseif strcmp(PlotArgs.zlim,'auto')
+            zlim([-max_amp*(component>0) max_amp]);
+        end
+    end
+      
+    pause(pauseT)
+end

matlab/ReadHDF5FieldData.m

@@ -0,0 +1,16 @@
+function hdf_fielddata = ReadHDF5FieldData(file)
+
+info = hdf5info(file);
+
+for n=1:numel(info.GroupHierarchy.Groups)
+    if strcmp(info.GroupHierarchy.Groups(n).Name,'/FieldData')
+        for m=1:numel(info.GroupHierarchy.Groups(n).Datasets)
+            names{m} = info.GroupHierarchy.Groups(n).Datasets(m).Name;
+        end
+    end
+end
+
+hdf_fielddata.names = names;
+for n=1:numel(names)
+    hdf_fielddata.values{n} = hdf5read(file,names{n});
+end

matlab/ReadHDF5Mesh.m

@@ -0,0 +1,16 @@
+function hdf_mesh = ReadHDF5Mesh(file)
+
+info = hdf5info(file);
+
+for n=1:numel(info.GroupHierarchy.Groups)
+    if strcmp(info.GroupHierarchy.Groups(n).Name,'/Mesh')
+        for m=1:numel(info.GroupHierarchy.Groups(n).Datasets)
+            names{m} = info.GroupHierarchy.Groups(n).Datasets(m).Name;
+        end
+    end
+end
+
+hdf_mesh.names = names;
+for n=1:numel(names)
+    hdf_mesh.lines{n} = hdf5read(file,names{n});
+end

matlab/examples/PlaneWave.m

@@ -72,3 +72,11 @@ disp(command);
 system(command)
 cd(savePath);
 
+% plotting
+PlotArgs.plane='zx';
+PlotArgs.pauseTime=0.01;
+PlotArgs.component=1;
+PlotArgs.zlim='auto';
+
+PlotHDF5FieldData('tmp/Ht_.h5',PlotArgs)
+