def _draw_members(self, map, **kwargs):
"""
Draw individual extensions in members.
Useful for debugging.
Parameters
----------
map : Basemap axes object
**kwargs : Any plot arguments to pass to basemap
"""
wcs_list = self._indv_mem_wcslist()
for wcs in wcs_list:
poly = SphericalPolygon.from_wcs(wcs)
poly.draw(map, **kwargs)
def _draw_members(self, map, **kwargs):
"""
Draw individual extensions in members.
Useful for debugging.
Parameters
----------
map : Basemap axes object
**kwargs : Any plot arguments to pass to basemap
"""
wcs_list = self._indv_mem_wcslist()
for wcs in wcs_list:
poly = SphericalPolygon.from_wcs(wcs)
poly.draw(map, **kwargs)
def __init__(self, image, ext, dq_bits=0, dqimage=None, dqext=None,
usermask=None, usermask_ext=None):
"""
Parameters
----------
image : ImageRef
An :py:class:`~stsci.skypac.utils.ImageRef` object that refers
to an open FITS file
ext : tuple, int, str
Extension specification in the `image` the `SkyLineMember`
object will be associated with.
An int `ext` specifies extension number. A tuple in the form
(str, int) specifies extension name and number. A string `ext`
specifies extension name and the extension version is assumed
to be 1. See documentation for `astropy.io.fits.getData`
for examples.
dq_bits : int, None (Default = 0)
Integer sum of all the DQ bit values from the
input `image`'s DQ array that should be considered "good"
when building masks for sky computations. For example,
if pixels in the DQ array can be combinations of 1, 2, 4,
and 8 flags and one wants to consider DQ "defects" having
flags 2 and 4 as being acceptable for sky computations,
then `dq_bits` should be set to 2+4=6. Then a DQ pixel
having values 2,4, or 6 will be considered a good pixel,
while a DQ pixel with a value, e.g., 1+2=3, 4+8=12, etc.
will be flagged as a "bad" pixel.
| Default value (0) will make *all* non-zero
pixels in the DQ mask to be considered "bad" pixels,
and the corresponding image pixels will not be used
for sky computations.
| Set `dq_bits` to `None` to turn off the use of
image's DQ array for sky computations.
.. note::
DQ masks (if used), *will be* combined with user masks
specified by the `usermask` parameter.
dqimage : ImageRef
An :py:class:`~stsci.skypac.utils.ImageRef` object that refers
to an open FITS file that has DQ data of the input `image`.
.. note::
When DQ data are located in the same FITS file as the
science image data (e.g., HST/ACS, HST/WFC3, etc.),
`dqimage` may point to the
same :py:class:`~stsci.skypac.utils.ImageRef` object.
In this case the reference count of the
\ :py:class:`~stsci.skypac.utils.ImageRef` object must be
increased adequately.
dqext : tuple, int, str
Extension specification of the `dqimage` that contains
`image`'s DQ information. See help for `ext` for more
details on acceptable formats for this parameter.
usermask : ImageRef
An :py:class:`~stsci.skypac.utils.ImageRef` object that refers
to an open FITS file that has user mask data that indicate
what pixels in the input `image` should be used for sky
computations (``1``) and which pixels should **not** be used
for sky computations (``0``).
usermask_ext : tuple, int, str
Extension specification of the `usermask` mask file that
contains user's mask data that should be associated with
the input `image` and `ext`. See help for `ext` for more
details on acceptable formats for this parameter.
"""
assert(hasattr(self.__class__, '_initialized') and \
self.__class__._initialized)
self._reset()
# check that input images and extensions are valid --
# either integers or tuples of strings and integers, e.g., ('sci',1):
_check_valid_imgext(image, 'image', ext, 'ext', can_img_be_None=False)
if dq_bits is not None:
if dqimage is None:
dq_bits = 0
else:
_check_valid_imgext(dqimage, 'dqimage', dqext, 'dqext')
_check_valid_imgext(usermask, 'usermask', usermask_ext,'usermask_ext')
# get telescope, instrument, and detector info:
self.telescope, self.instrument, self.detector = get_instrument_info(
image, ext)
# check dq_bits:
if dq_bits is not None and not isinstance(dq_bits,int):
if image: dqimage.release()
if usermask: usermask.release()
if dqimage: dqimage.release()
raise TypeError("Argument 'dq_bits' must be either an integer or None.")
# buld mask:
self._buildMask(image.original_fname, ext, dq_bits,
dqimage, dqext, usermask, usermask_ext)
if dqimage: dqimage.release()
if usermask: usermask.release()
# save file, user mask, and DQ extension info:
self._fname = image.original_fname
self._basefname = basename(self._fname)
self._image = image
self._ext = ext
self._can_free_image = image.can_reload_data and self.optimize != 'speed'
# check extension and create a string representation:
try:
extstr = ext2str(ext)
except ValueError:
raise ValueError("Unexpected extension type \'{}\' for file {}.".\
format(ext,self._basefname))
self._id = "{:s}[{:s}]".format(self._basefname, extstr)
# extract WCS for bounding-box computation
try:
if hasattr(image.hdu[ext], 'wcs'):
self._wcs = image.hdu[ext].wcs
else:
if self.telescope in supported_telescopes:
self._wcs = wcsutil.HSTWCS(image.hdu, ext)
else:
self._wcs = pywcs.WCS(image.hdu[ext].header, image.hdu)
if self._wcs is None:
raise Exception("Invalid WCS.")
except:
msg = "Unable to obtain WCS information for the file {:s}." \
.format(self._id)
self._ml.error(msg)
self._ml.flush()
self._release_all()
raise
# determine pixel scale:
self._get_pixel_scale()
# see if image data are in counts or count-rate
# and compute count(-rate) to flux (per arcsec^2) conversion factor:
self._brightness_conv_from_hdu(image.hdu, self._idcscale)
# process Sky user's keyword and its value:
self._init_skyuser(image.hdu[ext].header)
# Set polygon to be the bounding box of the chip:
self._polygon = SphericalPolygon.from_wcs(self.wcs, steps=1)
def __init__(self,
image,
ext,
dq_bits=0,
dqimage=None,
dqext=None,
usermask=None,
usermask_ext=None):
"""
Parameters
----------
image : ImageRef
An :py:class:`~stsci.skypac.utils.ImageRef` object that refers
to an open FITS file
ext : tuple, int, str
Extension specification in the `image` the `SkyLineMember`
object will be associated with.
An int `ext` specifies extension number. A tuple in the form
(str, int) specifies extension name and number. A string `ext`
specifies extension name and the extension version is assumed
to be 1. See documentation for `astropy.io.fits.getData`
for examples.
dq_bits : int, None (Default = 0)
Integer sum of all the DQ bit values from the
input `image`'s DQ array that should be considered "good"
when building masks for sky computations. For example,
if pixels in the DQ array can be combinations of 1, 2, 4,
and 8 flags and one wants to consider DQ "defects" having
flags 2 and 4 as being acceptable for sky computations,
then `dq_bits` should be set to 2+4=6. Then a DQ pixel
having values 2,4, or 6 will be considered a good pixel,
while a DQ pixel with a value, e.g., 1+2=3, 4+8=12, etc.
will be flagged as a "bad" pixel.
| Default value (0) will make *all* non-zero
pixels in the DQ mask to be considered "bad" pixels,
and the corresponding image pixels will not be used
for sky computations.
| Set `dq_bits` to `None` to turn off the use of
image's DQ array for sky computations.
.. note::
DQ masks (if used), *will be* combined with user masks
specified by the `usermask` parameter.
dqimage : ImageRef
An :py:class:`~stsci.skypac.utils.ImageRef` object that refers
to an open FITS file that has DQ data of the input `image`.
.. note::
When DQ data are located in the same FITS file as the
science image data (e.g., HST/ACS, HST/WFC3, etc.),
`dqimage` may point to the
same :py:class:`~stsci.skypac.utils.ImageRef` object.
In this case the reference count of the
\ :py:class:`~stsci.skypac.utils.ImageRef` object must be
increased adequately.
dqext : tuple, int, str
Extension specification of the `dqimage` that contains
`image`'s DQ information. See help for `ext` for more
details on acceptable formats for this parameter.
usermask : ImageRef
An :py:class:`~stsci.skypac.utils.ImageRef` object that refers
to an open FITS file that has user mask data that indicate
what pixels in the input `image` should be used for sky
computations (``1``) and which pixels should **not** be used
for sky computations (``0``).
usermask_ext : tuple, int, str
Extension specification of the `usermask` mask file that
contains user's mask data that should be associated with
the input `image` and `ext`. See help for `ext` for more
details on acceptable formats for this parameter.
"""
assert(hasattr(self.__class__, '_initialized') and \
self.__class__._initialized)
self._reset()
# check that input images and extensions are valid --
# either integers or tuples of strings and integers, e.g., ('sci',1):
_check_valid_imgext(image, 'image', ext, 'ext', can_img_be_None=False)
if dq_bits is not None:
if dqimage is None:
dq_bits = 0
else:
_check_valid_imgext(dqimage, 'dqimage', dqext, 'dqext')
_check_valid_imgext(usermask, 'usermask', usermask_ext, 'usermask_ext')
# get telescope, instrument, and detector info:
self.telescope, self.instrument, self.detector = get_instrument_info(
image, ext)
# check dq_bits:
if dq_bits is not None and not isinstance(dq_bits, int):
if image: dqimage.release()
if usermask: usermask.release()
if dqimage: dqimage.release()
raise TypeError(
"Argument 'dq_bits' must be either an integer or None.")
# buld mask:
self._buildMask(image.original_fname, ext, dq_bits, dqimage, dqext,
usermask, usermask_ext)
if dqimage: dqimage.release()
if usermask: usermask.release()
# save file, user mask, and DQ extension info:
self._fname = image.original_fname
self._basefname = basename(self._fname)
self._image = image
self._ext = ext
self._can_free_image = image.can_reload_data and self.optimize != 'speed'
# check extension and create a string representation:
try:
extstr = ext2str(ext)
except ValueError:
raise ValueError("Unexpected extension type \'{}\' for file {}.".\
format(ext,self._basefname))
self._id = "{:s}[{:s}]".format(self._basefname, extstr)
# extract WCS for bounding-box computation
try:
if hasattr(image.hdu[ext], 'wcs'):
self._wcs = image.hdu[ext].wcs
else:
if self.telescope in supported_telescopes:
self._wcs = wcsutil.HSTWCS(image.hdu, ext)
else:
self._wcs = pywcs.WCS(image.hdu[ext].header, image.hdu)
if self._wcs is None:
raise Exception("Invalid WCS.")
except:
msg = "Unable to obtain WCS information for the file {:s}." \
.format(self._id)
self._ml.error(msg)
self._ml.flush()
self._release_all()
raise
# determine pixel scale:
self._get_pixel_scale()
# see if image data are in counts or count-rate
# and compute count(-rate) to flux (per arcsec^2) conversion factor:
self._brightness_conv_from_hdu(image.hdu, self._idcscale)
# process Sky user's keyword and its value:
self._init_skyuser(image.hdu[ext].header)
# Set polygon to be the bounding box of the chip:
self._polygon = SphericalPolygon.from_wcs(self.wcs, steps=1)
