Source code for astropy.io.fits.hdu.streaming

# Licensed under a 3-clause BSD style license - see PYFITS.rst

import gzip
import os

from .base import _BaseHDU, BITPIX2DTYPE
from .hdulist import HDUList
from .image import PrimaryHDU

from astropy.io.fits.file import _File
from astropy.io.fits.header import _pad_length
from astropy.io.fits.util import fileobj_name


[docs]class StreamingHDU: """ A class that provides the capability to stream data to a FITS file instead of requiring data to all be written at once. The following pseudocode illustrates its use:: header = astropy.io.fits.Header() for all the cards you need in the header: header[key] = (value, comment) shdu = astropy.io.fits.StreamingHDU('filename.fits', header) for each piece of data: shdu.write(data) shdu.close() """ def __init__(self, name, header): """ Construct a `StreamingHDU` object given a file name and a header. Parameters ---------- name : path-like or file-like The file to which the header and data will be streamed. If opened, the file object must be opened in a writeable binary mode such as 'wb' or 'ab+'. header : `Header` instance The header object associated with the data to be written to the file. Notes ----- The file will be opened and the header appended to the end of the file. If the file does not already exist, it will be created, and if the header represents a Primary header, it will be written to the beginning of the file. If the file does not exist and the provided header is not a Primary header, a default Primary HDU will be inserted at the beginning of the file and the provided header will be added as the first extension. If the file does already exist, but the provided header represents a Primary header, the header will be modified to an image extension header and appended to the end of the file. """ if isinstance(name, gzip.GzipFile): raise TypeError('StreamingHDU not supported for GzipFile objects.') self._header = header.copy() # handle a file object instead of a file name filename = fileobj_name(name) or '' # Check if the file already exists. If it does not, check to see # if we were provided with a Primary Header. If not we will need # to prepend a default PrimaryHDU to the file before writing the # given header. newfile = False if filename: if not os.path.exists(filename) or os.path.getsize(filename) == 0: newfile = True elif (hasattr(name, 'len') and name.len == 0): newfile = True if newfile: if 'SIMPLE' not in self._header: hdulist = HDUList([PrimaryHDU()]) hdulist.writeto(name, 'exception') else: # This will not be the first extension in the file so we # must change the Primary header provided into an image # extension header. if 'SIMPLE' in self._header: self._header.set('XTENSION', 'IMAGE', 'Image extension', after='SIMPLE') del self._header['SIMPLE'] if 'PCOUNT' not in self._header: dim = self._header['NAXIS'] if dim == 0: dim = '' else: dim = str(dim) self._header.set('PCOUNT', 0, 'number of parameters', after='NAXIS' + dim) if 'GCOUNT' not in self._header: self._header.set('GCOUNT', 1, 'number of groups', after='PCOUNT') self._ffo = _File(name, 'append') # TODO : Fix this once the HDU writing API is cleaned up tmp_hdu = _BaseHDU() # Passing self._header as an argument to _BaseHDU() will cause its # values to be modified in undesired ways...need to have a better way # of doing this tmp_hdu._header = self._header self._header_offset = tmp_hdu._writeheader(self._ffo)[0] self._data_offset = self._ffo.tell() self._size = self.size if self._size != 0: self.writecomplete = False else: self.writecomplete = True # Support the 'with' statement def __enter__(self): return self def __exit__(self, type, value, traceback): self.close()
[docs] def write(self, data): """ Write the given data to the stream. Parameters ---------- data : ndarray Data to stream to the file. Returns ------- writecomplete : int Flag that when `True` indicates that all of the required data has been written to the stream. Notes ----- Only the amount of data specified in the header provided to the class constructor may be written to the stream. If the provided data would cause the stream to overflow, an `OSError` exception is raised and the data is not written. Once sufficient data has been written to the stream to satisfy the amount specified in the header, the stream is padded to fill a complete FITS block and no more data will be accepted. An attempt to write more data after the stream has been filled will raise an `OSError` exception. If the dtype of the input data does not match what is expected by the header, a `TypeError` exception is raised. """ size = self._ffo.tell() - self._data_offset if self.writecomplete or size + data.nbytes > self._size: raise OSError('Attempt to write more data to the stream than the ' 'header specified.') if BITPIX2DTYPE[self._header['BITPIX']] != data.dtype.name: raise TypeError('Supplied data does not match the type specified ' 'in the header.') if data.dtype.str[0] != '>': # byteswap little endian arrays before writing output = data.byteswap() else: output = data self._ffo.writearray(output) if self._ffo.tell() - self._data_offset == self._size: # the stream is full so pad the data to the next FITS block self._ffo.write(_pad_length(self._size) * '\0') self.writecomplete = True self._ffo.flush() return self.writecomplete
@property def size(self): """ Return the size (in bytes) of the data portion of the HDU. """ size = 0 naxis = self._header.get('NAXIS', 0) if naxis > 0: simple = self._header.get('SIMPLE', 'F') random_groups = self._header.get('GROUPS', 'F') if simple == 'T' and random_groups == 'T': groups = 1 else: groups = 0 size = 1 for idx in range(groups, naxis): size = size * self._header['NAXIS' + str(idx + 1)] bitpix = self._header['BITPIX'] gcount = self._header.get('GCOUNT', 1) pcount = self._header.get('PCOUNT', 0) size = abs(bitpix) * gcount * (pcount + size) // 8 return size
[docs] def close(self): """ Close the physical FITS file. """ self._ffo.close()