/
targetpixelfile.py
1325 lines (1173 loc) · 54.7 KB
/
targetpixelfile.py
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from __future__ import division
import datetime
import os
import warnings
import logging
from astropy.io import fits
from astropy.nddata import Cutout2D
from astropy.table import Table
from astropy.wcs import WCS
from matplotlib import patches
import matplotlib.pyplot as plt
import numpy as np
from tqdm import tqdm
from astropy.coordinates import SkyCoord
from astropy.io.fits.card import Undefined
from . import PACKAGEDIR, MPLSTYLE
from .lightcurve import KeplerLightCurve, TessLightCurve
from .prf import KeplerPRF
from .utils import KeplerQualityFlags, TessQualityFlags, \
plot_image, bkjd_to_astropy_time, btjd_to_astropy_time
from .mast import download_kepler_products
__all__ = ['KeplerTargetPixelFile', 'TessTargetPixelFile']
log = logging.getLogger(__name__)
class TargetPixelFile(object):
"""
Generic TargetPixelFile class for Kepler, K2, and TESS data.
See `KeplerTargetPixelFile` and `TessTargetPixelFile` for constructor
documentation.
"""
def __init__(self, path, quality_bitmask='default', targetid=None, **kwargs):
self.path = path
if isinstance(path, fits.HDUList):
self.hdu = path
else:
self.hdu = fits.open(self.path, **kwargs)
self.quality_bitmask = quality_bitmask
self.targetid = targetid
@property
def hdu(self):
return self._hdu
@hdu.setter
def hdu(self, value, keys=['FLUX', 'QUALITY']):
'''Raises a ValueError exception if value does not appear to be a Target Pixel File.
'''
for key in keys:
if ~(np.any([value[1].header[ttype] == key
for ttype in value[1].header['TTYPE*']])):
raise ValueError("File {} does not have a {} column, "
"is this a target pixel file?".format(self.path, key))
else:
self._hdu = value
@property
def header(self):
"""Returns the header of the primary extension."""
return self.hdu[0].header
@property
def ra(self):
"""Right Ascension of target ('RA_OBJ' header keyword)."""
try:
return self.header['RA_OBJ']
except KeyError:
return None
@property
def dec(self):
"""Declination of target ('DEC_OBJ' header keyword)."""
try:
return self.header['DEC_OBJ']
except KeyError:
return None
@property
def column(self):
try:
out = self.hdu[1].header['1CRV5P']
except KeyError:
out = 0
return out
@property
def row(self):
try:
out = self.hdu[1].header['2CRV5P']
except KeyError:
out = 0
return out
@property
def pos_corr1(self):
"""Returns the column position correction."""
return self.hdu[1].data['POS_CORR1'][self.quality_mask]
@property
def pos_corr2(self):
"""Returns the row position correction."""
return self.hdu[1].data['POS_CORR2'][self.quality_mask]
@property
def pipeline_mask(self):
"""Returns the aperture mask used by the pipeline"""
return self.hdu[2].data > 2
@property
def shape(self):
"""Return the cube dimension shape."""
return self.flux.shape
@property
def time(self):
"""Returns the time for all good-quality cadences."""
return self.hdu[1].data['TIME'][self.quality_mask]
@property
def cadenceno(self):
"""Return the cadence number for all good-quality cadences."""
return self.hdu[1].data['CADENCENO'][self.quality_mask]
@property
def nan_time_mask(self):
"""Returns a boolean mask flagging cadences whose time is `nan`."""
return ~np.isfinite(self.time)
@property
def flux(self):
"""Returns the flux for all good-quality cadences."""
return self.hdu[1].data['FLUX'][self.quality_mask]
@property
def flux_err(self):
"""Returns the flux uncertainty for all good-quality cadences."""
return self.hdu[1].data['FLUX_ERR'][self.quality_mask]
@property
def flux_bkg(self):
"""Returns the background flux for all good-quality cadences."""
return self.hdu[1].data['FLUX_BKG'][self.quality_mask]
@property
def flux_bkg_err(self):
return self.hdu[1].data['FLUX_BKG_ERR'][self.quality_mask]
@property
def quality(self):
"""Returns the quality flag integer of every good cadence."""
return self.hdu[1].data['QUALITY'][self.quality_mask]
@property
def wcs(self):
"""Returns an astropy.wcs.WCS object with the World Coordinate System
solution for the target pixel file.
Returns
-------
w : astropy.wcs.WCS object
WCS solution
"""
# Use WCS keywords of the 5th column (FLUX)
wcs_keywords = {'1CTYP5': 'CTYPE1',
'2CTYP5': 'CTYPE2',
'1CRPX5': 'CRPIX1',
'2CRPX5': 'CRPIX2',
'1CRVL5': 'CRVAL1',
'2CRVL5': 'CRVAL2',
'1CUNI5': 'CUNIT1',
'2CUNI5': 'CUNIT2',
'1CDLT5': 'CDELT1',
'2CDLT5': 'CDELT2',
'11PC5': 'PC1_1',
'12PC5': 'PC1_2',
'21PC5': 'PC2_1',
'22PC5': 'PC2_2',
'NAXIS1': 'NAXIS1',
'NAXIS2': 'NAXIS2'}
mywcs = {}
for oldkey, newkey in wcs_keywords.items():
mywcs[newkey] = self.hdu[1].header[oldkey]
return WCS(mywcs)
@classmethod
def from_fits(cls, path_or_url, **kwargs):
"""Open a Target Pixel File using the path or url of a FITS file.
This is identical to opening a Target Pixel File via the constructor.
This method was added because many tutorials use the `from_archive`
method, therefore users may expect a `from_fits` equivalent.
Parameters
----------
path_or_url : str
Path or URL of a FITS file.
**kwargs : dict
Keyword arguments that will be passed to the constructor.
Returns
-------
tpf : TargetPixelFile object
The loaded target pixel file.
"""
return cls(path_or_url, **kwargs)
def get_coordinates(self, cadence='all'):
"""Returns two 3D arrays of RA and Dec values in decimal degrees.
If cadence number is given, returns 2D arrays for that cadence. If
cadence is 'all' returns one RA, Dec value for each pixel in every cadence.
Uses the WCS solution and the POS_CORR data from TPF header.
Parameters
----------
cadence : 'all' or int
Which cadences to return the RA Dec coordinates for.
Returns
-------
ra : numpy array, same shape as tpf.flux[cadence]
Array containing RA values for every pixel, for every cadence.
dec : numpy array, same shape as tpf.flux[cadence]
Array containing Dec values for every pixel, for every cadence.
"""
w = self.wcs
X, Y = np.meshgrid(np.arange(self.shape[2]), np.arange(self.shape[1]))
pos_corr1_pix = np.copy(self.hdu[1].data['POS_CORR1'])
pos_corr2_pix = np.copy(self.hdu[1].data['POS_CORR2'])
# We zero POS_CORR* when the values are NaN or make no sense (>50px)
with warnings.catch_warnings(): # Comparing NaNs to numbers is OK here
warnings.simplefilter("ignore", RuntimeWarning)
bad = np.any([~np.isfinite(pos_corr1_pix),
~np.isfinite(pos_corr2_pix),
np.abs(pos_corr1_pix - np.nanmedian(pos_corr1_pix)) > 50,
np.abs(pos_corr2_pix - np.nanmedian(pos_corr2_pix)) > 50], axis=0)
pos_corr1_pix[bad], pos_corr2_pix[bad] = 0, 0
# Add in POSCORRs
X = (np.atleast_3d(X).transpose([2, 0, 1]) +
np.atleast_3d(pos_corr1_pix).transpose([1, 2, 0]))
Y = (np.atleast_3d(Y).transpose([2, 0, 1]) +
np.atleast_3d(pos_corr2_pix).transpose([1, 2, 0]))
# Pass through WCS
ra, dec = w.wcs_pix2world(X.ravel(), Y.ravel(), 1)
ra = ra.reshape((pos_corr1_pix.shape[0], self.shape[1], self.shape[2]))
dec = dec.reshape((pos_corr2_pix.shape[0], self.shape[1], self.shape[2]))
ra, dec = ra[self.quality_mask], dec[self.quality_mask]
if cadence is not 'all':
return ra[cadence], dec[cadence]
return ra, dec
def show_properties(self):
'''Print out a description of each of the non-callable attributes of a
TargetPixelFile object.
Prints in order of type (ints, strings, lists, arrays and others)
Prints in alphabetical order.'''
attrs = {}
for attr in dir(self):
if not attr.startswith('_'):
res = getattr(self, attr)
if callable(res):
continue
if attr == 'hdu':
attrs[attr] = {'res': res, 'type': 'list'}
for idx, r in enumerate(res):
if idx == 0:
attrs[attr]['print'] = '{}'.format(r.header['EXTNAME'])
else:
attrs[attr]['print'] = '{}, {}'.format(attrs[attr]['print'],
'{}'.format(r.header['EXTNAME']))
continue
else:
attrs[attr] = {'res': res}
if isinstance(res, int):
attrs[attr]['print'] = '{}'.format(res)
attrs[attr]['type'] = 'int'
elif isinstance(res, np.ndarray):
attrs[attr]['print'] = 'array {}'.format(res.shape)
attrs[attr]['type'] = 'array'
elif isinstance(res, list):
attrs[attr]['print'] = 'list length {}'.format(len(res))
attrs[attr]['type'] = 'list'
elif isinstance(res, str):
if res == '':
attrs[attr]['print'] = '{}'.format('None')
else:
attrs[attr]['print'] = '{}'.format(res)
attrs[attr]['type'] = 'str'
elif attr == 'wcs':
attrs[attr]['print'] = 'astropy.wcs.wcs.WCS'.format(attr)
attrs[attr]['type'] = 'other'
else:
attrs[attr]['print'] = '{}'.format(type(res))
attrs[attr]['type'] = 'other'
output = Table(names=['Attribute', 'Description'], dtype=[object, object])
idx = 0
types = ['int', 'str', 'list', 'array', 'other']
for typ in types:
for attr, dic in attrs.items():
if dic['type'] == typ:
output.add_row([attr, dic['print']])
idx += 1
output.pprint(max_lines=-1, max_width=-1)
def to_lightcurve(self, method='aperture', **kwargs):
"""Performs photometry.
See the docstring of `aperture_photometry()` for valid
arguments if the method is 'aperture'. Otherwise, see the docstring
of `prf_photometry()` for valid arguments if the method is 'prf'.
Parameters
----------
method : 'aperture' or 'prf'.
Photometry method to use.
**kwargs : dict
Extra arguments to be passed to the `aperture_photometry` or the
`prf_photometry` method of this class.
Returns
-------
lc : LightCurve object
Object containing the resulting lightcurve.
"""
if method == 'aperture':
return self.extract_aperture_photometry(**kwargs)
elif method == 'prf':
return self.prf_lightcurve(**kwargs)
else:
raise ValueError("Photometry method must be 'aperture' or 'prf'.")
def _parse_aperture_mask(self, aperture_mask):
"""Parse the `aperture_mask` parameter as given by a user.
The `aperture_mask` parameter is accepted by a number of methods.
This method ensures that the parameter is always parsed in the same way.
Parameters
----------
aperture_mask : array-like, 'pipeline', 'all', or None
A boolean array describing the aperture such that `False` means
that the pixel will be masked out.
If None or 'all' are passed, a mask that is `True` everywhere will
be returned.
If 'pipeline' is passed, the mask suggested by the pipeline
will be returned.
Returns
-------
aperture_mask : ndarray
2D boolean numpy array containing `True` for selected pixels.
"""
with warnings.catch_warnings():
# `aperture_mask` supports both arrays and string values; these yield
# uninteresting FutureWarnings when compared, so let's ignore that.
warnings.simplefilter(action='ignore', category=FutureWarning)
if aperture_mask is None or aperture_mask == 'all':
aperture_mask = np.ones((self.shape[1], self.shape[2]), dtype=bool)
elif aperture_mask == 'pipeline':
aperture_mask = self.pipeline_mask
self._last_aperture_mask = aperture_mask
return aperture_mask
def centroids(self, **kwargs):
"""DEPRECATED: use `estimate_cdpp()` instead."""
log.warning("WARNING: centroids() is deprecated and will be removed in v1.0.0; "
"please use estimate_centroids() instead.")
return self.estimate_centroids(**kwargs)
def estimate_centroids(self, aperture_mask='pipeline'):
"""Returns centroid positions estimated using sample moments.
Parameters
----------
aperture_mask : array-like, 'pipeline', or 'all'
A boolean array describing the aperture such that `False` means
that the pixel will be masked out.
If the string 'all' is passed, all pixels will be used.
The default behaviour is to use the Kepler pipeline mask.
Returns
-------
col_centr, row_centr : tuple
Arrays containing centroids for column and row at each cadence
"""
aperture_mask = self._parse_aperture_mask(aperture_mask)
yy, xx = np.indices(self.shape[1:]) + 0.5
yy = self.row + yy
xx = self.column + xx
total_flux = np.nansum(self.flux[:, aperture_mask], axis=1)
with warnings.catch_warnings():
# RuntimeWarnings may occur below if total_flux contains zeros
warnings.simplefilter("ignore", RuntimeWarning)
col_centr = np.nansum(xx * aperture_mask * self.flux, axis=(1, 2)) / total_flux
row_centr = np.nansum(yy * aperture_mask * self.flux, axis=(1, 2)) / total_flux
return col_centr, row_centr
def plot(self, ax=None, frame=0, cadenceno=None, bkg=False, aperture_mask=None,
show_colorbar=True, mask_color='pink', style='lightkurve', **kwargs):
"""
Plot a target pixel file at a given frame (index) or cadence number.
Parameters
----------
ax : matplotlib.axes._subplots.AxesSubplot
A matplotlib axes object to plot into. If no axes is provided,
a new one will be generated.
frame : int
Frame number. The default is 0, i.e. the first frame.
cadenceno : int, optional
Alternatively, a cadence number can be provided.
This argument has priority over frame number.
bkg : bool
If True, background will be added to the pixel values.
aperture_mask : ndarray
Highlight pixels selected by aperture_mask.
show_colorbar : bool
Whether or not to show the colorbar
mask_color : str
Color to show the aperture mask
style : str
Path or URL to a matplotlib style file, or name of one of
matplotlib's built-in stylesheets (e.g. 'ggplot').
Lightkurve's custom stylesheet is used by default.
kwargs : dict
Keywords arguments passed to `lightkurve.utils.plot_image`.
Returns
-------
ax : matplotlib.axes._subplots.AxesSubplot
The matplotlib axes object.
"""
if style == 'lightkurve' or style is None:
style = MPLSTYLE
if cadenceno is not None:
try:
frame = np.argwhere(cadenceno == self.cadenceno)[0][0]
except IndexError:
raise ValueError("cadenceno {} is out of bounds, "
"must be in the range {}-{}.".format(
cadenceno, self.cadenceno[0], self.cadenceno[-1]))
try:
if bkg and np.any(np.isfinite(self.flux_bkg[frame])):
pflux = self.flux[frame] + self.flux_bkg[frame]
else:
pflux = self.flux[frame]
except IndexError:
raise ValueError("frame {} is out of bounds, must be in the range "
"0-{}.".format(frame, self.shape[0]))
with plt.style.context(style):
img_title = 'Target ID: {}'.format(self.targetid)
img_extent = (self.column, self.column + self.shape[2],
self.row, self.row + self.shape[1])
ax = plot_image(pflux, ax=ax, title=img_title, extent=img_extent,
show_colorbar=show_colorbar, **kwargs)
ax.grid(False)
if aperture_mask is not None:
aperture_mask = self._parse_aperture_mask(aperture_mask)
for i in range(self.shape[1]):
for j in range(self.shape[2]):
if aperture_mask[i, j]:
ax.add_patch(patches.Rectangle((j+self.column, i+self.row),
1, 1, color=mask_color, fill=True,
alpha=.6))
return ax
def to_fits(self, output_fn=None, overwrite=False):
"""Writes the TPF to a FITS file on disk."""
if output_fn is None:
output_fn = "{}-targ.fits".format(self.targetid)
self.hdu.writeto(output_fn, overwrite=overwrite, checksum=True)
def interact(self, lc=None, notebook_url='localhost:8888', max_cadences=30000):
"""Display an interactive Jupyter Notebook widget to inspect the pixel data.
The widget will show both the lightcurve and pixel data. By default,
the lightcurve shown is obtained by calling the `to_lightcurve()` method,
unless the user supplies a custom `LightCurve` object.
This feature requires an optional dependency, bokeh (v0.12.15 or later).
This dependency can be installed using e.g. `conda install bokeh`.
At this time, this feature only works inside an active Jupyter
Notebook, and tends to be too slow when more than ~30,000 cadences
are contained in the TPF (e.g. short cadence data).
Parameters
----------
lc : LightCurve object
An optional pre-processed lightcurve object to show.
notebook_url: str
Location of the Jupyter notebook page (default: "localhost:8888")
When showing Bokeh applications, the Bokeh server must be
explicitly configured to allow connections originating from
different URLs. This parameter defaults to the standard notebook
host and port. If you are running on a different location, you
will need to supply this value for the application to display
properly. If no protocol is supplied in the URL, e.g. if it is
of the form "localhost:8888", then "http" will be used.
max_cadences : int
Raise a RuntimeError if the number of cadences shown is larger than
this value. This limit helps keep browsers from becoming unresponsive.
"""
from .interact import show_interact_widget
return show_interact_widget(self, lc=lc, notebook_url=notebook_url,
max_cadences=max_cadences)
class KeplerTargetPixelFile(TargetPixelFile):
"""
Defines a TargetPixelFile class for the Kepler/K2 Mission.
Enables extraction of raw lightcurves and centroid positions.
Parameters
----------
path : str or `astropy.io.fits.HDUList`
Path to a Kepler Target Pixel (FITS) File or a `HDUList` object.
quality_bitmask : str or int
Bitmask (integer) which identifies the quality flag bitmask that should
be used to mask out bad cadences. If a string is passed, it has the
following meaning:
* "none": no cadences will be ignored (`quality_bitmask=0`).
* "default": cadences with severe quality issues will be ignored
(`quality_bitmask=1130799`).
* "hard": more conservative choice of flags to ignore
(`quality_bitmask=1664431`). This is known to remove good data.
* "hardest": removes all data that has been flagged
(`quality_bitmask=2096639`). This mask is not recommended.
See the :class:`KeplerQualityFlags` class for details on the bitmasks.
kwargs : dict
Keyword arguments passed to `astropy.io.fits.open()`.
References
----------
.. [1] Kepler: A Search for Terrestrial Planets. Kepler Archive Manual.
http://archive.stsci.edu/kepler/manuals/archive_manual.pdf
"""
def __init__(self, path, quality_bitmask='default', **kwargs):
super(KeplerTargetPixelFile, self).__init__(path,
quality_bitmask=quality_bitmask,
**kwargs)
self.quality_mask = KeplerQualityFlags.create_quality_mask(
quality_array=self.hdu[1].data['QUALITY'],
bitmask=quality_bitmask)
if self.targetid is None:
try:
self.targetid = self.header['KEPLERID']
except KeyError:
pass
@staticmethod
def from_archive(target, cadence='long', quarter=None, month=None,
campaign=None, radius=1., targetlimit=1,
quality_bitmask='default', **kwargs):
"""Fetch a Target Pixel File from the Kepler/K2 data archive at MAST.
See the :class:`KeplerQualityFlags` class for details on the bitmasks.
Raises an `ArchiveError` if a unique TPF cannot be found. For example,
this is the case if a target was observed in multiple Quarters and the
quarter parameter is unspecified.
Parameters
----------
target : str or int
KIC/EPIC ID or object name.
cadence : str
'long' or 'short'.
quarter, campaign : int, list of ints, or 'all'
Kepler Quarter or K2 Campaign number.
month : 1, 2, 3, list or 'all'
For Kepler's prime mission, there are three short-cadence
Target Pixel Files for each quarter, each covering one month.
Hence, if cadence='short' you need to specify month=1, 2, or 3.
radius : float
Search radius in arcseconds. Default is 1 arcsecond.
targetlimit : None or int
If multiple targets are present within `radius`, limit the number
of returned TargetPixelFile objects to `targetlimit`.
If `None`, no limit is applied.
quality_bitmask : str or int
Bitmask (integer) which identifies the quality flag bitmask that should
be used to mask out bad cadences. If a string is passed, it has the
following meaning:
* "none": no cadences will be ignored (`quality_bitmask=0`).
* "default": cadences with severe quality issues will be ignored
(`quality_bitmask=1130799`).
* "hard": more conservative choice of flags to ignore
(`quality_bitmask=1664431`). This is known to remove good data.
* "hardest": removes all data that has been flagged
(`quality_bitmask=2096639`). This mask is not recommended.
See the :class:`KeplerQualityFlags` class for details on the bitmasks.
kwargs : dict
Keywords arguments passed to the constructor of
:class:`KeplerTargetPixelFile`.
Returns
-------
tpf : :class:`KeplerTargetPixelFile` object.
"""
if os.path.exists(str(target)) or str(target).startswith('http'):
log.warning('Warning: from_archive() is not intended to accept a '
'direct path, use KeplerTargetPixelFile(path) instead.')
path = [target]
else:
path = download_kepler_products(
target=target, filetype='Target Pixel', cadence=cadence,
quarter=quarter, campaign=campaign, month=month,
radius=radius, targetlimit=targetlimit)
if len(path) == 1:
return KeplerTargetPixelFile(path[0],
quality_bitmask=quality_bitmask,
**kwargs)
return [KeplerTargetPixelFile(p, quality_bitmask=quality_bitmask, **kwargs)
for p in path]
def __repr__(self):
return('KeplerTargetPixelFile Object (ID: {})'.format(self.targetid))
def get_prf_model(self):
"""Returns an object of KeplerPRF initialized using the
necessary metadata in the tpf object.
Returns
-------
prf : instance of SimpleKeplerPRF
"""
return KeplerPRF(channel=self.channel, shape=self.shape[1:],
column=self.column, row=self.row)
@property
def obsmode(self):
"""'short cadence' or 'long cadence'. ('OBSMODE' header keyword)"""
return self.header['OBSMODE']
@property
def module(self):
"""Kepler CCD module number. ('MODULE' header keyword)"""
return self.header['MODULE']
@property
def output(self):
"""Kepler CCD module output number. ('OUTPUT' header keyword)"""
return self.header['OUTPUT']
@property
def channel(self):
"""Kepler CCD channel number. ('CHANNEL' header keyword)"""
return self.header['CHANNEL']
@property
def astropy_time(self):
"""Returns an AstroPy Time object for all good-quality cadences."""
return bkjd_to_astropy_time(bkjd=self.time)
@property
def quarter(self):
"""Kepler quarter number. ('QUARTER' header keyword)"""
try:
return self.header['QUARTER']
except KeyError:
return None
@property
def campaign(self):
"""K2 Campaign number. ('CAMPAIGN' header keyword)"""
try:
return self.header['CAMPAIGN']
except KeyError:
return None
@property
def mission(self):
"""'Kepler' or 'K2'. ('MISSION' header keyword)"""
try:
return self.header['MISSION']
except KeyError:
return None
def extract_aperture_photometry(self, aperture_mask='pipeline'):
"""Returns a LightCurve obtained using aperture photometry.
Parameters
----------
aperture_mask : array-like, 'pipeline', or 'all'
A boolean array describing the aperture such that `False` means
that the pixel will be masked out.
If the string 'all' is passed, all pixels will be used.
The default behaviour is to use the Kepler pipeline mask.
Returns
-------
lc : KeplerLightCurve object
Array containing the summed flux within the aperture for each
cadence.
"""
aperture_mask = self._parse_aperture_mask(aperture_mask)
if aperture_mask.sum() == 0:
log.warning('Warning: aperture mask contains zero pixels.')
centroid_col, centroid_row = self.estimate_centroids(aperture_mask)
# Ignore warnings related to zero or negative errors
with warnings.catch_warnings():
warnings.simplefilter("ignore", RuntimeWarning)
flux_err = np.nansum(self.flux_err[:, aperture_mask]**2, axis=1)**0.5
keys = {'centroid_col': centroid_col,
'centroid_row': centroid_row,
'quality': self.quality,
'channel': self.channel,
'campaign': self.campaign,
'quarter': self.quarter,
'mission': self.mission,
'cadenceno': self.cadenceno,
'ra': self.ra,
'dec': self.dec,
'label': self.header['OBJECT'],
'targetid': self.targetid}
return KeplerLightCurve(time=self.time,
time_format='bkjd',
time_scale='tdb',
flux=np.nansum(self.flux[:, aperture_mask], axis=1),
flux_err=flux_err,
**keys)
def get_bkg_lightcurve(self, aperture_mask=None):
aperture_mask = self._parse_aperture_mask(aperture_mask)
# Ignore warnings related to zero or negative errors
with warnings.catch_warnings():
warnings.simplefilter("ignore", RuntimeWarning)
flux_bkg_err = np.nansum(self.flux_bkg_err[:, aperture_mask]**2, axis=1)**0.5
keys = {'quality': self.quality,
'channel': self.channel,
'campaign': self.campaign,
'quarter': self.quarter,
'mission': self.mission,
'cadenceno': self.cadenceno,
'ra': self.ra,
'dec': self.dec,
'label': self.header['OBJECT'],
'targetid': self.targetid}
return KeplerLightCurve(time=self.time,
time_format='bkjd',
time_scale='tdb',
flux=np.nansum(self.flux_bkg[:, aperture_mask], axis=1),
flux_err=flux_bkg_err,
**keys)
def get_model(self, star_priors=None, **kwargs):
"""Returns a default `TPFModel` object for PRF fitting.
The default model only includes one star and only allows its flux
and position to change. A different set of stars can be added using
the `star_priors` parameter.
Parameters
----------
**kwargs : dict
Arguments to be passed to the `TPFModel` constructor, e.g.
`star_priors`.
Returns
-------
model : TPFModel object
Model with appropriate defaults for this Target Pixel File.
"""
from .prf import TPFModel, StarPrior, BackgroundPrior
from .prf import UniformPrior, GaussianPrior
# Set up the model
if 'star_priors' not in kwargs:
centr_col, centr_row = self.estimate_centroids()
star_priors = [StarPrior(col=GaussianPrior(mean=np.nanmedian(centr_col),
var=np.nanstd(centr_col)**2),
row=GaussianPrior(mean=np.nanmedian(centr_row),
var=np.nanstd(centr_row)**2),
flux=UniformPrior(lb=0.5*np.nanmax(self.flux[0]),
ub=2*np.nansum(self.flux[0]) + 1e-10),
targetid=self.targetid)]
kwargs['star_priors'] = star_priors
if 'prfmodel' not in kwargs:
kwargs['prfmodel'] = self.get_prf_model()
if 'background_prior' not in kwargs:
if np.all(np.isnan(self.flux_bkg)): # If TargetPixelFile has no background flux data
# Use the median of the lower half of flux as an estimate for flux_bkg
clipped_flux = np.ma.masked_where(self.flux > np.percentile(self.flux, 50),
self.flux)
flux_prior = GaussianPrior(mean=np.ma.median(clipped_flux),
var=np.ma.std(clipped_flux)**2)
else:
flux_prior = GaussianPrior(mean=np.nanmedian(self.flux_bkg),
var=np.nanstd(self.flux_bkg)**2)
kwargs['background_prior'] = BackgroundPrior(flux=flux_prior)
return TPFModel(**kwargs)
def extract_prf_photometry(self, cadences=None, parallel=True, **kwargs):
"""Returns the results of PRF photometry applied to the pixel file.
Parameters
----------
cadences : list of int
Cadences to fit. If `None` (default) then all cadences will be fit.
parallel : bool
If `True`, fitting cadences will be distributed across multiple
cores using Python's `multiprocessing` module.
**kwargs : dict
Keywords to be passed to `tpf.get_model()` to create the
`TPFModel` object that will be fit.
Returns
-------
results : PRFPhotometry object
Object that provides access to PRF-fitting photometry results and
various diagnostics.
"""
from .prf import PRFPhotometry
log.warning('Warning: PRF-fitting photometry is experimental '
'in this version of lightkurve.')
prfphot = PRFPhotometry(model=self.get_model(**kwargs))
prfphot.run(self.flux + self.flux_bkg, cadences=cadences, parallel=parallel,
pos_corr1=self.pos_corr1, pos_corr2=self.pos_corr2)
return prfphot
def prf_lightcurve(self, **kwargs):
lc = self.extract_prf_photometry(**kwargs).lightcurves[0]
keys = {'quality': self.quality,
'channel': self.channel,
'campaign': self.campaign,
'quarter': self.quarter,
'mission': self.mission,
'cadenceno': self.cadenceno,
'ra': self.ra,
'dec': self.dec,
'targetid': self.targetid}
return KeplerLightCurve(time=self.time,
flux=lc.flux,
time_format='bkjd',
time_scale='tdb',
**keys)
@staticmethod
def from_fits_images(images, position=None, size=(11, 11), extension=1,
target_id="unnamed-target", hdu0_keywords={}, **kwargs):
"""Creates a new Target Pixel File from a set of images.
This method is intended to make it easy to cut out targets from
Kepler/K2 "superstamp" regions or TESS FFI images.
Parameters
----------
images : list of str, or list of fits.ImageHDU objects
Sorted list of FITS filename paths or ImageHDU objects to get
the data from.
position : astropy.SkyCoord
Position around which to cut out pixels.
size : (int, int)
Dimensions (cols, rows) to cut out around `position`.
extension : int or str
If `images` is a list of filenames, provide the extension number
or name to use. Default: 0.
target_id : int or str
Unique identifier of the target to be recorded in the TPF.
hdu0_keywords : dict
Additional keywords to add to the first header file.
**kwargs : dict
Extra arguments to be passed to the `KeplerTargetPixelFile` constructor.
Returns
-------
tpf : KeplerTargetPixelFile
A new Target Pixel File assembled from the images.
"""
basic_keywords = ['MISSION', 'TELESCOP', 'INSTRUME', 'QUARTER',
'CAMPAIGN', 'CHANNEL', 'MODULE', 'OUTPUT']
carry_keywords = {}
if not isinstance(position, SkyCoord):
raise FactoryError('Position must be an astropy.coordinates.SkyCoord.')
# Define a helper function to accept images in a flexible way
def _open_image(img, extension):
if isinstance(img, fits.ImageHDU):
hdu = img
elif isinstance(img, fits.HDUList):
hdu = img[extension]
else:
hdu = fits.open(img)[extension]
return hdu
# Set the default extension if unspecified
if extension is None:
extension = 0
if isinstance(images[0], str) and images[0].endswith("ffic.fits"):
extension = 1 # TESS FFIs have the image data in extension #1
# If no position is given, ensure the cut-out size matches the image size
if position is None:
size = _open_image(images[0], extension).data.shape
# Find middle image to use as a WCS reference
try:
mid_hdu = _open_image(images[int(len(images) / 2) - 1], extension)
wcs_ref = WCS(mid_hdu)
column, row = wcs_ref.wcs_world2pix(
np.asarray([[position.ra.deg], [position.dec.deg]]).T,
0)[0]
column, row = int(column), int(row)
except Exception:
raise FactoryError("Images must have a valid WCS astrometric solution.")
return None
# Create a factory and set default keyword values based on the middle image
factory = KeplerTargetPixelFileFactory(n_cadences=len(images),
n_rows=size[0],
n_cols=size[1],
target_id=target_id)
# Get some basic keywords
for kw in basic_keywords:
if kw in mid_hdu.header:
if not isinstance(mid_hdu.header[kw], Undefined):
carry_keywords[kw] = mid_hdu.header[kw]
if ('MISSION' not in carry_keywords) and ('TELESCOP' in carry_keywords):
carry_keywords['MISSION'] = carry_keywords['TELESCOP']
allkeys = hdu0_keywords.copy()
allkeys.update(carry_keywords)
ext_info = {'1CRV5P': column, '2CRV5P': row}
for idx, img in tqdm(enumerate(images), total=len(images)):
hdu = _open_image(img, extension)
if idx == 0: # Get default keyword values from the first image
factory.keywords = hdu.header
if position is None:
cutout = hdu
else:
cutout = Cutout2D(hdu.data, position, wcs=WCS(hdu.header),
size=size, mode='partial')
factory.add_cadence(frameno=idx, flux=cutout.data, header=hdu.header)
return factory.get_tpf(hdu0_keywords=allkeys, ext_info=ext_info, **kwargs)
class FactoryError(Exception):
"""Raised if there is a problem creating a TPF."""
pass
class KeplerTargetPixelFileFactory(object):
"""Class to create a KeplerTargetPixelFile."""
def __init__(self, n_cadences, n_rows, n_cols, target_id="unnamed-target",
keywords={}):
self.n_cadences = n_cadences
self.n_rows = n_rows
self.n_cols = n_cols
self.target_id = target_id
self.keywords = keywords
# Initialize the 3D data structures
self.raw_cnts = np.empty((n_cadences, n_rows, n_cols), dtype='int')
self.flux = np.empty((n_cadences, n_rows, n_cols), dtype='float32')
self.flux_err = np.empty((n_cadences, n_rows, n_cols), dtype='float32')
self.flux_bkg = np.empty((n_cadences, n_rows, n_cols), dtype='float32')
self.flux_bkg_err = np.empty((n_cadences, n_rows, n_cols), dtype='float32')
self.cosmic_rays = np.empty((n_cadences, n_rows, n_cols), dtype='float32')
# Set 3D data defaults
self.raw_cnts[:, :, :] = -1
self.flux[:, :, :] = np.nan
self.flux_err[:, :, :] = np.nan
self.flux_bkg[:, :, :] = np.nan
self.flux_bkg_err[:, :, :] = np.nan
self.cosmic_rays[:, :, :] = np.nan
# Initialize the 1D data structures
self.mjd = np.zeros(n_cadences, dtype='float64')
self.time = np.zeros(n_cadences, dtype='float64')
self.timecorr = np.zeros(n_cadences, dtype='float32')
self.cadenceno = np.zeros(n_cadences, dtype='int')
self.quality = np.zeros(n_cadences, dtype='int')
self.pos_corr1 = np.zeros(n_cadences, dtype='float32')
self.pos_corr2 = np.zeros(n_cadences, dtype='float32')
def add_cadence(self, frameno, wcs=None, raw_cnts=None, flux=None, flux_err=None,
flux_bkg=None, flux_bkg_err=None, cosmic_rays=None,
header={}):
"""Populate the data for a single cadence."""
if frameno >= self.n_cadences: