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