128 lines
4.7 KiB
Python
128 lines
4.7 KiB
Python
|
# -*- coding: utf-8 -*-
|
||
|
|
# imageio is distributed under the terms of the (new) BSD License.
|
||
|
|
|
||
|
|
""" Plugin for reading FITS files.
|
||
|
|
"""
|
||
|
|
|
||
|
|
from .. import formats
|
||
|
|
from ..core import Format
|
||
|
|
|
||
|
|
_fits = None # lazily loaded
|
||
|
|
|
||
|
|
|
||
|
|
def load_lib():
|
||
|
|
global _fits
|
||
|
|
try:
|
||
|
|
from astropy.io import fits as _fits
|
||
|
|
except ImportError:
|
||
|
|
raise ImportError(
|
||
|
|
"The FITS format relies on the astropy package."
|
||
|
|
"Please refer to http://www.astropy.org/ "
|
||
|
|
"for further instructions."
|
||
|
|
)
|
||
|
|
return _fits
|
||
|
|
|
||
|
|
|
||
|
|
class FitsFormat(Format):
|
||
|
|
|
||
|
|
""" Flexible Image Transport System (FITS) is an open standard defining a
|
||
|
|
digital file format useful for storage, transmission and processing of
|
||
|
|
scientific and other images. FITS is the most commonly used digital
|
||
|
|
file format in astronomy.
|
||
|
|
|
||
|
|
This format requires the ``astropy`` package.
|
||
|
|
|
||
|
|
Parameters for reading
|
||
|
|
----------------------
|
||
|
|
cache : bool
|
||
|
|
If the file name is a URL, `~astropy.utils.data.download_file` is used
|
||
|
|
to open the file. This specifies whether or not to save the file
|
||
|
|
locally in Astropy's download cache (default: `True`).
|
||
|
|
uint : bool
|
||
|
|
Interpret signed integer data where ``BZERO`` is the
|
||
|
|
central value and ``BSCALE == 1`` as unsigned integer
|
||
|
|
data. For example, ``int16`` data with ``BZERO = 32768``
|
||
|
|
and ``BSCALE = 1`` would be treated as ``uint16`` data.
|
||
|
|
|
||
|
|
Note, for backward compatibility, the kwarg **uint16** may
|
||
|
|
be used instead. The kwarg was renamed when support was
|
||
|
|
added for integers of any size.
|
||
|
|
ignore_missing_end : bool
|
||
|
|
Do not issue an exception when opening a file that is
|
||
|
|
missing an ``END`` card in the last header.
|
||
|
|
checksum : bool or str
|
||
|
|
If `True`, verifies that both ``DATASUM`` and
|
||
|
|
``CHECKSUM`` card values (when present in the HDU header)
|
||
|
|
match the header and data of all HDU's in the file. Updates to a
|
||
|
|
file that already has a checksum will preserve and update the
|
||
|
|
existing checksums unless this argument is given a value of
|
||
|
|
'remove', in which case the CHECKSUM and DATASUM values are not
|
||
|
|
checked, and are removed when saving changes to the file.
|
||
|
|
disable_image_compression : bool, optional
|
||
|
|
If `True`, treats compressed image HDU's like normal
|
||
|
|
binary table HDU's.
|
||
|
|
do_not_scale_image_data : bool
|
||
|
|
If `True`, image data is not scaled using BSCALE/BZERO values
|
||
|
|
when read.
|
||
|
|
ignore_blank : bool
|
||
|
|
If `True`, the BLANK keyword is ignored if present.
|
||
|
|
scale_back : bool
|
||
|
|
If `True`, when saving changes to a file that contained scaled
|
||
|
|
image data, restore the data to the original type and reapply the
|
||
|
|
original BSCALE/BZERO values. This could lead to loss of accuracy
|
||
|
|
if scaling back to integer values after performing floating point
|
||
|
|
operations on the data.
|
||
|
|
"""
|
||
|
|
|
||
|
|
def _can_read(self, request):
|
||
|
|
# We return True if ext matches, because this is the only plugin
|
||
|
|
# that can. If astropy is not installed, a useful error follows.
|
||
|
|
return request.extension in self.extensions
|
||
|
|
|
||
|
|
def _can_write(self, request):
|
||
|
|
# No write support
|
||
|
|
return False
|
||
|
|
|
||
|
|
# -- reader
|
||
|
|
|
||
|
|
class Reader(Format.Reader):
|
||
|
|
def _open(self, cache=False, **kwargs):
|
||
|
|
if not _fits:
|
||
|
|
load_lib()
|
||
|
|
hdulist = _fits.open(self.request.get_file(), cache=cache, **kwargs)
|
||
|
|
|
||
|
|
self._index = []
|
||
|
|
allowed_hdu_types = (_fits.ImageHDU, _fits.PrimaryHDU, _fits.CompImageHDU)
|
||
|
|
for n, hdu in zip(range(len(hdulist)), hdulist):
|
||
|
|
if isinstance(hdu, allowed_hdu_types):
|
||
|
|
# Ignore (primary) header units with no data (use '.size'
|
||
|
|
# rather than '.data' to avoid actually loading the image):
|
||
|
|
if hdu.size > 0:
|
||
|
|
self._index.append(n)
|
||
|
|
self._hdulist = hdulist
|
||
|
|
|
||
|
|
def _close(self):
|
||
|
|
self._hdulist.close()
|
||
|
|
|
||
|
|
def _get_length(self):
|
||
|
|
return len(self._index)
|
||
|
|
|
||
|
|
def _get_data(self, index):
|
||
|
|
# Get data
|
||
|
|
if index < 0 or index >= len(self._index):
|
||
|
|
raise IndexError("Index out of range while reading from fits")
|
||
|
|
im = self._hdulist[self._index[index]].data
|
||
|
|
# Return array and empty meta data
|
||
|
|
return im, {}
|
||
|
|
|
||
|
|
def _get_meta_data(self, index):
|
||
|
|
# Get the meta data for the given index
|
||
|
|
raise RuntimeError("The fits format does not support meta data.")
|
||
|
|
|
||
|
|
|
||
|
|
# Register
|
||
|
|
format = FitsFormat(
|
||
|
|
"fits", "Flexible Image Transport System (FITS) format", "fits fit fts fz", "iIvV"
|
||
|
|
)
|
||
|
|
formats.add_format(format)
|