Simple XDMF reader

read_xdmf.py

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import xml.etree.ElementTree as ET

import numpy as np

###

def read_xml(fn):
    """Read XDMF XML descriptor file."""
    tree = ET.parse(fn)
    root = tree.getroot()
    grid = root[0][0]
    frames = []
    for frame in grid:
        frame_dict = {}
        frame_dict['_id'] = int(frame.attrib['Name'])
        for entry in frame:
            if entry.tag == 'Time':
                frame_dict['_time'] = float(entry.attrib['Value'])
            elif entry.tag == 'Attribute':
                data_dict = {}
                for data in entry:
                    data_dict['shape'] = tuple(int(dim) for dim in data.attrib['Dimensions'].split())
                    for raw_data in data:
                        shape = tuple(int(dim) for dim in raw_data.attrib['Dimensions'].split())
                        assert shape == data_dict['shape']
                        assert raw_data.attrib['Format'] == 'Binary'
                        data_dict['type'] = '<f'+raw_data.attrib['Precision']
                        data_dict['seek'] = int(raw_data.attrib['Seek'])
                        data_dict['filename'] = raw_data.text.strip()
                frame_dict[entry.attrib['Name']] = data_dict
        frames += [frame_dict]
    return frames

def read_frame(frame):
    """Read a single data frame."""
    data = {}
    for key, descr in frame.items():
        if not key.startswith('_'):
            with open(descr['filename'], 'rb') as f:
                f.seek(descr['seek'])
                data[key] = np.fromfile(f, dtype=np.dtype(descr['type']),
                                        count=np.prod(descr['shape'])).reshape(descr['shape'])
    return data