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AstroImage.py
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AstroImage.py
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#
# AstroImage.py -- Abstraction of an astronomical data image.
#
# This is open-source software licensed under a BSD license.
# Please see the file LICENSE.txt for details.
#
import sys
import traceback
import warnings
from collections import OrderedDict
import numpy as np
from ginga.util import wcs, wcsmod
from ginga.BaseImage import BaseImage, ImageError, Header
class AstroHeader(Header):
pass
class AstroImage(BaseImage):
"""
Abstraction of an astronomical data (image).
NOTE: this module is NOT thread-safe!
"""
# class variables for WCS and IO can be set
wcsClass = None
ioClass = None
@classmethod
def set_wcsClass(cls, klass):
cls.wcsClass = klass
@classmethod
def set_ioClass(cls, klass):
cls.ioClass = klass
def __init__(self, data_np=None, metadata=None, logger=None,
name=None, wcsclass=None, ioclass=None,
inherit_primary_header=False, save_primary_header=True):
BaseImage.__init__(self, data_np=data_np, metadata=metadata,
logger=logger, name=name)
# wcsclass specifies a pluggable WCS module
if wcsclass is None:
if self.wcsClass is None:
wcsclass = wcsmod.WCS
else:
wcsclass = self.wcsClass
self.wcs = wcsclass(self.logger)
# ioclass specifies a pluggable IO module
if ioclass is None:
if self.ioClass is None:
from ginga.util import io_fits
ioclass = io_fits.fitsLoaderClass
else:
ioclass = self.ioClass
self.io = ioclass(self.logger)
self.inherit_primary_header = inherit_primary_header
self.save_primary_header = inherit_primary_header or save_primary_header
if self.save_primary_header:
# User wants to save/inherit from primary header--this will hold it
self._primary_hdr = AstroHeader()
else:
self._primary_hdr = None
if metadata is not None:
header = self.get_header()
self.wcs.load_header(header)
# For navigating multidimensional data
self.naxispath = []
self.revnaxis = []
self._md_data = None
def setup_data(self, data, naxispath=None):
# initialize data attribute to something reasonable
if data is None:
data = np.zeros((0, 0))
elif not isinstance(data, np.ndarray):
data = np.zeros((0, 0))
elif 0 in data.shape:
data = np.zeros((0, 0))
# this is a handle to the full data array
self._md_data = data
self.axisdim = data.shape
# this will get reset in set_naxispath() if array is
# multidimensional
self._data = self._md_data
if naxispath is None:
naxispath = []
# Set naxispath to drill down to first 2D data slice
if len(naxispath) == 0:
naxispath = ([0] * (len(data.shape) - 2))
self.set_naxispath(naxispath)
def load_hdu(self, hdu, fobj=None, naxispath=None,
inherit_primary_header=None):
# this seems to be necessary now for some fits files...
try:
hdu.verify('fix')
except Exception as e:
# Let's hope for the best!
self.logger.warning("Problem verifying fits HDU: {}".format(e))
self.clear_metadata()
# collect HDU header
ahdr = self.get_header()
self._copy_hdu_header(hdu, ahdr)
# Set PRIMARY header
if inherit_primary_header is None:
inherit_primary_header = self.inherit_primary_header
else: # This ensures get_header() is consistent
self.inherit_primary_header = inherit_primary_header
save_primary_header = (self.save_primary_header or
inherit_primary_header)
if save_primary_header and (fobj is not None):
if self._primary_hdr is None:
self._primary_hdr = AstroHeader()
self._copy_hdu_header(fobj[0], self._primary_hdr)
self.setup_data(hdu.data, naxispath=naxispath)
# Try to make a wcs object on the header
if hasattr(self, 'wcs') and self.wcs is not None:
self.wcs.load_header(hdu.header, fobj=fobj)
def load_nddata(self, ndd, naxispath=None):
"""Load from an astropy.nddata.NDData object.
"""
self.clear_metadata()
# Make a header based on any NDData metadata
ahdr = self.get_header()
ahdr.update(ndd.meta)
self.setup_data(ndd.data, naxispath=naxispath)
if ndd.wcs is None:
# no wcs in ndd obj--let's try to make one from the header
self.wcs = wcsmod.WCS(logger=self.logger)
self.wcs.load_header(ahdr)
else:
# already have a valid wcs in the ndd object
# we assume it needs an astropy compatible wcs
wcsinfo = wcsmod.get_wcs_class('astropy')
self.wcs = wcsinfo.wrapper_class(logger=self.logger)
self.wcs.load_nddata(ndd)
def load_file(self, filespec, **kwargs):
if self.io is None:
raise ImageError("No IO loader defined")
self.io.load_file(filespec, dstobj=self, **kwargs)
def load_data(self, data_np, naxispath=None, metadata=None):
self.clear_metadata()
self.setup_data(data_np, naxispath=naxispath)
if metadata is not None:
self.update_metadata(metadata)
def load_buffer(self, buf, dims, dtype, byteswap=False,
naxispath=None, metadata=None):
data = np.fromstring(buf, dtype=dtype)
if byteswap:
data.byteswap(True)
data = data.reshape(dims)
self.load_data(data, naxispath=naxispath, metadata=metadata)
def get_mddata(self):
return self._md_data
def set_naxispath(self, naxispath):
"""Choose a slice out of multidimensional data.
"""
revnaxis = list(naxispath)
revnaxis.reverse()
# construct slice view and extract it
ndim = min(self.ndim, 2)
view = tuple(revnaxis + [slice(None)] * ndim)
data = self.get_mddata()[view]
if len(data.shape) not in (1, 2):
raise ImageError(
"naxispath does not lead to a 1D or 2D slice: {}".format(naxispath))
self.naxispath = naxispath
self.revnaxis = revnaxis
self.set_data(data)
def set_wcs(self, wcs):
self.wcs = wcs
def set_io(self, io):
self.io = io
def get_data_size(self):
return self.get_size()
def get_header(self, create=True, include_primary_header=None):
try:
# By convention, the fits header is stored in a dictionary
# under the metadata keyword 'header'
hdr = self.metadata['header']
if include_primary_header is None:
include_primary_header = self.inherit_primary_header
if include_primary_header and self._primary_hdr is not None:
# Inherit PRIMARY header for display but keep metadata intact
displayhdr = AstroHeader()
for key in hdr.keyorder:
card = hdr.get_card(key)
bnch = displayhdr.__setitem__(card.key, card.value)
bnch.comment = card.comment
for key in self._primary_hdr.keyorder:
if key not in hdr:
card = self._primary_hdr.get_card(key)
bnch = displayhdr.__setitem__(card.key, card.value)
bnch.comment = card.comment
else:
# Normal, separate header
displayhdr = hdr
except KeyError as e:
if not create:
raise e
hdr = AstroHeader()
self.metadata['header'] = hdr
displayhdr = hdr
return displayhdr
def get_keyword(self, kwd, *args):
"""Get an item from the fits header, if any."""
try:
kwds = self.get_header()
return kwds[kwd]
except KeyError:
# return a default if there is one
if len(args) > 0:
return args[0]
raise KeyError(kwd)
def get_keywords_list(self, *args):
return list(map(self.get_keyword, args))
def set_keyword(self, kwd, value, create=True):
kwds = self.get_header(create=create)
kwd = kwd.upper()
if not create:
prev = kwds[kwd] # noqa, this raises KeyError
kwds[kwd] = value
def update_keywords(self, keyDict):
hdr = self.get_header()
# Upcase all keywords
for kwd, val in keyDict.items():
hdr[kwd.upper()] = val
# Try to make a wcs object on the header
if hasattr(self, 'wcs') and self.wcs is not None:
self.wcs.load_header(hdr)
def set_keywords(self, **kwds):
"""Set an item in the fits header, if any."""
return self.update_keywords(kwds)
def update_data(self, data_np, metadata=None, astype=None):
"""DO NOT USE: this method will be deprecated!
"""
self.set_data(data_np.copy(), metadata=metadata,
astype=astype)
def update_metadata(self, key_dict):
for key, val in key_dict.items():
self.metadata[key] = val
# refresh the WCS
if hasattr(self, 'wcs') and self.wcs is not None:
header = self.get_header()
self.wcs.load_header(header)
def has_primary_header(self):
return self._primary_hdr is not None
def clear_all(self):
# clear metadata and data
super(AstroImage, self).clear_all()
# unreference full data array
self._md_data = self._data
def transfer(self, other, astype=None):
data = self._get_data()
other.update_data(data, astype=astype)
other.update_metadata(self.metadata)
def copy(self, astype=None):
data = self._get_data()
other = AstroImage(data, logger=self.logger)
self.transfer(other, astype=astype)
return other
def as_nddata(self, nddata_class=None):
"Return a version of ourself as an astropy.nddata.NDData object"
if nddata_class is None:
from astropy.nddata import NDData
nddata_class = NDData
# transfer header, preserving ordering
ahdr = self.get_header()
header = OrderedDict(ahdr.items())
data = self.get_mddata()
wcs = None
if hasattr(self, 'wcs') and self.wcs is not None:
# for now, assume self.wcs wraps an astropy wcs object
wcs = self.wcs.wcs
ndd = nddata_class(data, wcs=wcs, meta=header)
return ndd
def as_hdu(self):
"Return a version of ourself as an astropy.io.fits.PrimaryHDU object"
from astropy.io import fits
# transfer header, preserving ordering
ahdr = self.get_header()
header = fits.Header(ahdr.items())
data = self.get_mddata()
hdu = fits.PrimaryHDU(data=data, header=header)
return hdu
def _copy_hdu_header(self, hdu, ahdr):
"""Copy a FITS header from an astropy.io.fits.PrimaryHDU object
into a ginga.AstroImage.AstroHeader object.
"""
header = hdu.header
for card in header.cards:
if len(card.keyword) == 0:
continue
ahdr.set_card(card.keyword, card.value, comment=card.comment)
def astype(self, type_name):
"""Convert AstroImage object to some other kind of object.
"""
if type_name == 'nddata':
return self.as_nddata()
if type_name == 'hdu':
return self.as_hdu()
raise ValueError("Unrecognized conversion type '%s'" % (type_name))
def save_as_file(self, filepath, **kwdargs):
data = self._get_data()
header = self.get_header()
self.io.save_as_file(filepath, data, header, **kwdargs)
def pixtocoords(self, x, y, system=None, coords='data'):
args = [x, y] + self.revnaxis
return self.wcs.pixtocoords(args, system=system, coords=coords)
def spectral_coord(self, coords='data'):
args = [0, 0] + self.revnaxis
return self.wcs.spectral_coord(args, coords=coords)
def pixtoradec(self, x, y, format='deg', coords='data'):
args = [x, y] + self.revnaxis
ra_deg, dec_deg = self.wcs.pixtoradec(args, coords=coords)
if format == 'deg':
return ra_deg, dec_deg
return wcs.deg2fmt(ra_deg, dec_deg, format)
def radectopix(self, ra_deg, dec_deg, format='deg', coords='data'):
if format != 'deg':
# convert coordinates to degrees
ra_deg = wcs.lon_to_deg(ra_deg)
dec_deg = wcs.lat_to_deg(dec_deg)
return self.wcs.radectopix(ra_deg, dec_deg, coords=coords,
naxispath=self.revnaxis)
# -----> TODO:
# This section has been merged into ginga.util.wcs or
# ginga.util.mosaic . Deprecate it here.
#
def get_starsep_XY(self, x1, y1, x2, y2):
warnings.warn("This function has been deprecated--"
"use the version in ginga.util.wcs",
PendingDeprecationWarning)
return wcs.get_starsep_XY(self, x1, y1, x2, y2)
def calc_radius_xy(self, x, y, radius_deg):
warnings.warn("This function has been deprecated--"
"use the version in ginga.util.wcs",
PendingDeprecationWarning)
return wcs.calc_radius_xy(self, x, y, radius_deg)
def calc_radius_deg2pix(self, ra_deg, dec_deg, delta_deg,
equinox=None):
warnings.warn("This function has been deprecated--"
"use the version in ginga.util.wcs",
PendingDeprecationWarning)
return wcs.calc_radius_deg2pix(self, ra_deg, dec_deg, delta_deg,
equinox=equinox)
def add_offset_xy(self, x, y, delta_deg_x, delta_deg_y):
warnings.warn("This function has been deprecated--"
"use the version in ginga.util.wcs",
PendingDeprecationWarning)
return wcs.add_offset_xy(self, x, y, delta_deg_x, delta_deg_y)
def calc_radius_center(self, delta_deg):
warnings.warn("This function has been deprecated--"
"use the version in ginga.util.wcs",
PendingDeprecationWarning)
return wcs.calc_radius_center(self, delta_deg)
def calc_compass(self, x, y, len_deg_e, len_deg_n):
warnings.warn("This function has been deprecated--"
"use the version in ginga.util.wcs",
PendingDeprecationWarning)
return wcs.calc_compass(self, x, y, len_deg_e, len_deg_n)
def calc_compass_radius(self, x, y, radius_px):
warnings.warn("This function has been deprecated--"
"use the version in ginga.util.wcs",
PendingDeprecationWarning)
return wcs.calc_compass_radius(self, x, y, radius_px)
def calc_compass_center(self):
warnings.warn("This function has been deprecated--"
"use the version in ginga.util.wcs",
PendingDeprecationWarning)
return wcs.calc_compass_center(self)
def get_wcs_rotation_deg(self):
warnings.warn("This function has been deprecated--"
"use get_rotation_and_scale in ginga.util.wcs",
PendingDeprecationWarning)
header = self.get_header()
(rot, cdelt1, cdelt2) = wcs.get_rotation_and_scale(header)
return rot
def mosaic_inline(self, imagelist, bg_ref=None, trim_px=None,
merge=False, allow_expand=True, expand_pad_deg=0.01,
max_expand_pct=None,
update_minmax=True, suppress_callback=False):
warnings.warn("This function has been deprecated--"
"use the version in ginga.util.mosaic",
PendingDeprecationWarning)
from ginga.util import mosaic
return mosaic.mosaic_inline(self, imagelist, bg_ref=bg_ref,
trim_px=trim_px, merge=merge,
allow_expand=allow_expand,
expand_pad_deg=expand_pad_deg,
max_expand_pct=max_expand_pct,
update_minmax=update_minmax,
suppress_callback=suppress_callback)
#
# <----- TODO: deprecate
def info_xy(self, data_x, data_y, settings):
info = super(AstroImage, self).info_xy(data_x, data_y, settings)
system = settings.get('wcs_coords', None)
format = settings.get('wcs_display', 'sexagesimal')
ra_lbl, dec_lbl = chr(945), chr(948)
# Calculate WCS coords, if available
try:
if self.wcs is None:
self.logger.debug("No WCS for this image")
ra_txt = dec_txt = 'NO WCS'
elif self.wcs.coordsys == 'raw':
self.logger.debug("No coordinate system determined")
ra_txt = dec_txt = 'NO WCS'
elif self.wcs.coordsys == 'pixel':
args = [data_x, data_y] + self.revnaxis
x, y = self.wcs.pixtosystem(args, system=system, coords='data')
ra_txt = "%+.3f" % (x)
dec_txt = "%+.3f" % (y)
ra_lbl, dec_lbl = "X", "Y"
else:
args = [data_x, data_y] + self.revnaxis
lon_deg, lat_deg = self.wcs.pixtosystem(
args, system=system, coords='data')
if format == 'sexagesimal':
if system in ('galactic', 'ecliptic'):
sign, deg, min, sec = wcs.degToDms(lon_deg,
isLatitude=False)
ra_txt = '+%03d:%02d:%06.3f' % (deg, min, sec)
else:
deg, min, sec = wcs.degToHms(lon_deg)
ra_txt = '%02d:%02d:%06.3f' % (deg, min, sec)
sign, deg, min, sec = wcs.degToDms(lat_deg)
if sign < 0:
sign = '-'
else:
sign = '+'
dec_txt = '%s%02d:%02d:%06.3f' % (sign, deg, min, sec)
else:
ra_txt = '%+10.7f' % (lon_deg)
dec_txt = '%+10.7f' % (lat_deg)
if system == 'galactic':
ra_lbl, dec_lbl = "l", "b"
elif system == 'ecliptic':
ra_lbl, dec_lbl = chr(0x03BB), chr(0x03B2)
elif system == 'helioprojective':
ra_txt = "%+5.3f" % (lon_deg * 3600)
dec_txt = "%+5.3f" % (lat_deg * 3600)
ra_lbl, dec_lbl = "x-Solar", "y-Solar"
except Exception as e:
self.logger.warning("Bad coordinate conversion: %s" % (
str(e)))
ra_txt = dec_txt = 'BAD WCS'
try:
# log traceback, if possible
(type_, value_, tb) = sys.exc_info()
tb_str = "".join(traceback.format_tb(tb))
self.logger.error("Traceback:\n%s" % (tb_str))
except Exception:
tb_str = "Traceback information unavailable."
self.logger.error(tb_str)
info.update(dict(itype='astro', ra_txt=ra_txt, dec_txt=dec_txt,
ra_lbl=ra_lbl, dec_lbl=dec_lbl))
return info
# END