Hello Kyle,
coordinates are not normally explicitly stored in hdf5 files.
However if you asked for output of the coordinates grid functions (those defined in CartGrid3D) then you will have output files name like this:
x.file_0.h5 ... y.file_0.h5 ... z.file_0.h5
and those datasets do indeed contain the coordinates (and the datasets correspond to the datasets in vx.file_0.h etc.). See eg
https://bitbucket.org/einsteintoolkit/einsteinexamples/raw/master/par/GW1509...
If you do not have the CartGrid3D files (they may be large after all and change only rarely) then you can also construct coordinates (at least Cartesian ones, this does not work for curvilinear coordinates from Llama) using the attributes.
Each dataset (assuming you use the "standard" vertex centered mesh refinement scheme and use no staggering) has attributes:
origin delta
and the hdf5 shape of the dataset.
origin is the coordinate of the upper/left/front coordinate of the grid patch that the dataset corresponds to (in order x,y,z) while delta is the grid spacing (dx,dy,dz).
shape is the hdf5 shape of the patch in order z,y,z (since HDF5 wants C ordering but Cactus normally uses Fortran ordering).
If you are using h5py then you can construct coordinates like so (I hope I got the ordering all right, you may have to try a bit in case the order should be x,y,z instead of z,y,z):
z,y,x = numpy.meshgrid(\ numpy.arange(origin[0],origin[0]+shape[2]*delta[0],delta[0]), numpy.arange(origin[1],origin[1]+shape[1]*delta[1],delta[1]), numpy.arange(origin[2],origin[2]+shape[0]*delta[2],delta[2]), indexing='ij')
Yours, Roland
Hello,
I have vector data in the form of h5 files as such
vx.file_0.h5 vy.file_0.h5 vz.file_0.h5 vx.file_1.h5 vy.file_1.h5 vz.file_1.h5
and so on. I am trying to use a python script to access the actual position of each data point so I can use it in a calculation but I'm not sure how to access it. I imagine it is buried somewhere in the attributes of each refinement level of the dataset, but I'm not sure where.
Much appreciated, Kyle Nelli