fits2hdf.io package¶

Submodules¶

fits2hdf.io.fitsio module¶

fitsio.py¶

FITS I/O for reading and writing to FITS files.

exception fits2hdf.io.fitsio.DeprecatedGroupsHDUWarning¶

Bases: astropy.io.fits.verify.VerifyWarning

Warning message when a deprecated ‘group HDU’ is found

fits2hdf.io.fitsio.create_column(col)¶

Create a astropy.io.fits column object from IdiColumn

This is a helper function that automatically computes a few things that should be obvious from the numpy data type and shape, but that the fits.column object needs to have set explicitly.

This fills in format, dim, and array keywords. Unit and null are left as keyword arguments. Bscale, bzero, disp, start, and ascii are NOT supported.

col: IdiColumn: IdiColumn object that contains the data array

fits_col: pf.Column: astropy.io.fits column

fits2hdf.io.fitsio.create_fits(hdul, verbosity=0)¶

Export HDU to FITS file in memory.

Returns an in-memory HDUlist, does not write to file.

hdul: IdiHduList: An IDI HDU list object to convert into a pyfits / astropy HDUlist() object in memory
verbosity: int: verbosity level, 0 (none) to 5 (all)

fits2hdf.io.fitsio.export_fits(hdul, outfile, verbosity=0)¶

Export HDU list to file

hdul: IdiHduList: HDU list to write to file
outfile: str: Filename of ourput file
verbosity: int: verbosity of output, 0 (none) to 5 (all)

fits2hdf.io.fitsio.fits_format_code_lookup(numpy_dtype, numpy_shape)¶

Return a FITS format code from a given numpy dtype

numpy_dtype: a numpy dtype object: Numpy dtype to lookup
numpy_shape: tuple: shape of data array to be converted into a FITS format

fmt_code: string: FITS format code, e.g. 8A for character string of length 8
fits_dim: string or None: Returns fits dimension for TDIM keyword

L logical (Boolean) 1 X bit * B Unsigned byte 1 I 16-bit integer 2 J 32-bit integer 4 K 64-bit integer 4 A character 1 E single precision floating point 4 D double precision floating point 8 C single precision complex 8 M double precision complex 16 P array descriptor 8 Q array descriptor 16

fits2hdf.io.fitsio.numpy_dtype_lookup(numpy_dtype)¶

Return the local OS datatype for a given dtype

This is added to workaround a bug in binary table writing, whereby an additional byteswap is done that is unnecessary.

numpy_dtype: numpy.dtype: Numpy datatype

numpy_local_dtype: numpy.dtype: Local numpy datatype

fits2hdf.io.fitsio.parse_fits_header(hdul)¶

Parse a FITS header into something less stupid.

hdul: HDUList: FITS HDUlist from which to parse the header

This function takes a fits HDU object and returns: header (dict): Dictionary of header values. Header comments

are written to [CARDNAME]_COMMENT

comment (list): Comment cards are parsed and then put into list: (order is important)

history (list): History cards also parsed into a list

fits2hdf.io.fitsio.read_fits(infile, verbosity=0)¶

Read and load contents of a FITS file

infile: str: File path of input file
verbosity: int: Verbosity level of output, 0 (none) to 5 (all)

fits2hdf.io.fitsio.write_headers(hduobj, idiobj)¶

copy headers over from idiobj to hduobj.

Need to skip values that refer to columns (TUNIT, TDISP), as these are necessarily generated by the table creation

hduobj: astropy FITS HDU (ImageHDU, BintableHDU): FITS HDU to which to write header values
idiobj: IdiImageHdu, IdiTableHdu, IdiPrimaryHdu: HDU object from which to copy headers from
verbosity: int: Level of verbosity, none (0) to all (5)

fits2hdf.io.hdfcompress module¶

hdfcompress.py¶

Helper functions for writing bitshuffled compressed datatsets

fits2hdf.io.hdfcompress.create_compressed(hgroup, name, data, **kwargs)¶

Add a compressed dataset to a given group.

Use bitshuffle compression and LZ4 to compress a dataset.

hgroup: h5py group in which to add dataset name: name of dataset data: data to write chunks: chunk size

fits2hdf.io.hdfcompress.create_dataset(hgroup, name, data, **kwargs)¶

Create dataset from data, will attempt to compress

Parameters:	hgroup – h5py group in which to add dataset name – name of dataset data – data to write

fits2hdf.io.hdfcompress.guess_chunk(shape)¶

Guess the optimal chunk size for a given shape :param shape: shape of dataset :return: chunk guess (tuple)

#TODO: Make this better

fits2hdf.io.hdfio module¶

hdfio.py¶

HDF I/O for reading and writing to HDF5 files.

fits2hdf.io.hdfio.export_hdf(idi_hdu, outfile, table_type='DATA_GROUP', **kwargs)¶

Export to HDF file

idi_hdu: IdiHduList: HDU list to write to file.
outfile: str: Name of output file

These are passed to h5py, and include:: compression=None, apply compression (lzf, bitshuffle, gzip) shuffle=False, apply shuffle precompression filter chunks=None, set chunk size

fits2hdf.io.hdfio.read_hdf(infile, mode='r+', verbosity=0)¶

Read and load contents of an HDF file

infile: str: file name of input file to read
mode: str: file read mode. Defaults to ‘r+’
verbosity: int: Level of verbosity, none (0) to all (5)

fits2hdf.io.hdfio.write_headers(hduobj, idiobj, verbosity=0)¶