Source code for pyspeckit.spectrum.readers.hdf5_reader

"""
==========================
PySpecKit HDF5 Reader
==========================

Routines for reading in spectra from HDF5 files.

Note: Current no routines for parsing HDF5 headers in classes.py.

.. moduleauthor:: Adam Ginsburg <adam.g.ginsburg@gmail.com>
.. moduleauthor:: Jordan Mirocha <mirochaj@gmail.com>
"""
import numpy as np
from .. import units

try:
    import astropy.io.fits as pyfits
except ImportError:
    import pyfits

def open_hdf5(filename, xaxkey = 'xarr', datakey = 'data', errkey = 'error'):
    """
    This reader expects three datasets to exist in the hdf5 file 'filename': 
    'xarr', 'data', and 'error', by default.  Can specify other dataset names.
    """
    import h5py

    f = h5py.File(filename, 'r')
    
    try: xarr = f[xaxkey].value
    except KeyError: print('Dataset \'%s\' not found.' % xaxkey)
    
    try: data = f[datakey].value
    except KeyError: print('Dataset \'%s\' not found.' % datakey)

    try: error = f[errkey].value
    except KeyError: 
        print('Dataset \'%s\' not found.  Assuming uniform errors.' % errkey)
        error = np.ones_like(data)
        
    try: 
        xunits = f[xaxkey].attrs['units']
        if xunits == '': 
            xunits = 'unknown'
    except KeyError: 
        xunits = 'unknown'    
    
    try: 
        yunits = f[datakey].attrs['units']
        if yunits == '': 
            yunits = 'unknown'
    except KeyError: 
        yunits = 'unknown'    
        
    try: 
        xtype = f[xaxkey].attrs['type']
        if xtype == '': 
            xtype = xaxkey
    except KeyError: 
        xtype = xaxkey
    
    try: 
        ytype = f[datakey].attrs['type']
        if ytype == '': 
            ytype = datakey
    except KeyError: 
        ytype = datakey            
        
    XAxis = units.SpectroscopicAxis(xarr, xunits)    

    header = {'xunits': xunits, 'xtype': xtype, 'yunits': yunits, 'ytype': ytype}
    
    return data, error, XAxis, header