An example of writing 3D time series data to an XMF file which references data in an accompanying HDF5 file (output.h5)

XMF_3D_timeseries.py

from xml.etree.ElementTree import Element, SubElement
from xml.etree import ElementTree
from xml.dom import minidom

def prettify(elem):
    """Return a pretty-printed XML string for the Element.
    """
    rough_string = ElementTree.tostring(elem, 'utf-8')
    reparsed = minidom.parseString(rough_string)
    return reparsed.toprettyxml(indent="  ")

def write_xdmf(self, filename='output.xdmf', timesteps=[0]):
    """Write an XDMF file to accompany the HDF5 data file.
    """

    # Get the size of the datasets to write
    dims_x = str(self.density.shape[0])
    dims_y = str(self.density.shape[1])
    dims_z = str(self.density.shape[2])
    dims_t = str(self.density.shape[3])
    
    dims = np.transpose(self.density).shape
    # Topology dimensions do not include time dimension
    dims_topol = "{0} {1} {2}".format(dims_z, dims_y, dims_x)
    # The full dimensions of the data
    dims_data =  "{0} {1} {2} {3}".format(dims_t, dims_z, dims_y, dims_x)
    # The dimensions of a single slab
    dims_slab = "1 " + dims_topol
    
    # Create the basic structure
    root = Element('Xdmf')
    root.set('version', '2.2')
    domain = SubElement(root, 'Domain')
    
    # The geometry. This will be referenced by each timestep, rather
    # than inserting it into each one
    geometry        = SubElement(root, 'Geometry',       {'GeometryType':"VXVYVZ"})
    x_data = SubElement(geometry, 'DataItem', {'Dimensions':dims_x,
                                               "NumberType":"Float",
                                               "Precision":"8",
                                               "Format":"HDF5"})
    x_data.text = "output.h5:/data/3D/fields/x"
    y_data = SubElement(geometry, 'DataItem', {'Dimensions':dims_y,
                                               "NumberType":"Float",
                                               "Precision":"8",
                                               "Format":"HDF5"})
    y_data.text = "output.h5:/data/3D/fields/y"
    z_data = SubElement(geometry, 'DataItem', {'Dimensions':dims_z,
                                               "NumberType":"Float",
                                               "Precision":"8",
                                               "Format":"HDF5"})
    z_data.text = "output.h5:/data/3D/fields/z"
    
    # Create the temporal collection and insert the time data
    # Future: use hyperslab?
    # Number of timesteps to write
    time_dims = str(len(timesteps))
    time_grid = SubElement(domain, 'Grid',    {'Name':'DensityGrid',
                                               'GridType':'Collection',
                                               'CollectionType':'Temporal'})
    time      = SubElement(time_grid, 'Time', {'TimeType':'List',
                                               'Dimensions':time_dims})
    time_data = SubElement(time, 'DataItem',  {'NumberType':'Float',
                                               'Dimensions':time_dims,
                                               'Format':'XML'})
    time_data.text = np.array_str(self.T[timesteps]).strip('[]').replace(",","")
    
    # Add all the timesteps
    for step in timesteps:
        grid  =          SubElement(time_grid, 'Grid',
                                    {'Name':'Structred Grid',
                                     'GridType':'Uniform'})
        topology =       SubElement(grid, 'Topology',
                                    {'TopologyType':'3DRECTMesh',
                                     'Dimensions':dims_topol})
        geometry =       SubElement(grid, 'Geometry',
                                    {"Reference":"/Xdmf/Geometry[1]"})
        density =        SubElement(grid, "Attribute",
                                    {"Name":"density",
                                     "AttributeType":"Scalar",
                                     "Center":"Node"})
        density_slab =   SubElement(density, "DataItem",
                                    {"ItemType":"HyperSlab",
                                     "Dimensions":dims_slab,
                                     "Type":"HyperSlab"})
        density_extent = SubElement(density_slab, "DataItem",
                                    {"Dimensions":"3 4",
                                     "Format":"XML"})
        density_extent.text = str(step) + " 0 0 0\n1 1 1 1\n" + dims_slab
        density_data =   SubElement(density_slab, "DataItem",
                                    {"Format":"HDF",
                                     "NumberType":"Float",
                                     "Precision":"8",
                                     "Dimensions":dims_data})
        density_data.text = "output.h5:/data/3D/fields/density"
        
        self.root = root
        
        with open(filename,'w') as f:
            f.write(prettify(self.root))