def test_kplr10417986():
"""Integration test"""
filename = download_file(
'https://archive.stsci.edu/missions/kepler/lightcurves/0104/010417986/kplr010417986-2010174085026_llc.fits',
cache=True) # noqa
period = .0737309 * u.day
epoch_mbjd = 55000.027476 * u.day
duration = 1 * u.hour
target_name = "KPLR 010417986"
event_name = "False Positive"
epoch_bkjd = epoch_mbjd - exo_const.mbjd + exo_const.bkjd
tce = Tce(period=period,
epoch=epoch_bkjd,
epoch_offset=exo_const.bkjd,
duration=duration,
depth=0 * exo_const.frac_amp,
target_name=target_name,
event_name=event_name)
lc = lightkurve.read(filename, flux_column="pdcsap_flux")
sweet_vetter = Sweet()
res = sweet_vetter.run(tce, lc)
amp = res['amp']
assert np.allclose(amp[0, 0], 637, atol=30) # Amplitude
assert np.allclose(amp[0, 2], 106.94, atol=10) # SNR
def test_contaminante():
tpfc = lk.read(fname)
period = 0.700606
t0 = 131.59767
duration = 0.993 / 24
res = contaminante.calculate_contamination(tpfc,
period,
t0,
duration,
plot=False,
cbvs=False)
assert res[0]["delta_transit_depth[sigma]"] > 5
assert res[0]["centroid_shift"][0].value > 5
res = contaminante.calculate_contamination(tpfc,
period,
t0,
duration,
plot=False,
cbvs=True)
assert res[0]["delta_transit_depth[sigma]"] > 5
assert res[0]["centroid_shift"][0].value > 5
res = contaminante.calculate_contamination(tpfc,
period,
t0,
duration,
plot=False,
cbvs=True,
spline=False)
assert res[0]["delta_transit_depth[sigma]"] > 5
assert res[0]["centroid_shift"][0].value > 5
res = contaminante.calculate_contamination(tpfc,
period,
t0,
duration,
plot=False,
cbvs=True,
sff=True)
assert res[0]["delta_transit_depth[sigma]"] > 5
assert res[0]["centroid_shift"][0].value > 5
res = contaminante.calculate_contamination(tpfc,
1000,
t0,
duration,
plot=False,
cbvs=True,
sff=True)
assert (res[0]["transit_depth"] == 0).all()
def _from_path_AltaiPony(path):
# rhdul = fits.open(path)
# attrs = dict()
# for k, v in rhdul[0].header.items():
# if str.lower(k) not in ['simple', 'bitpix', 'naxis', 'extend']:
# if str.lower(k) == "keplerid": #rename keplerid if it appears
# k = "targetid"
# attrs[str.lower(k)] = v
#
# for k in ['time', 'flux', 'flux_err', 'centroid_col',
# 'centroid_row', 'quality', 'cadenceno',
# 'detrended_flux', 'detrended_flux_err',
# 'quality_bitmask', 'saturation']:
# try:
# attrs[k] = rhdul[1].data[k].byteswap().newbyteorder()
# except KeyError:
# LOG.info("Warning: Keyword {} not in file.".format(k))
# continue
lc = read(path)
lc = lc[np.isfinite(lc.time.value) & np.isfinite(lc.flux.value)
& np.isfinite(lc.cadenceno.value)]
# keys = dict([(key, lc[key].value) for key in lc.colnames[:3]])
# print(keys)
# flc = lc.FlareLightCurve(**keys, time_format=lc.time.format, meta=lc.meta)
# flc = FlareLightCurve(time=lc.time.value,
# flux=lc.flux.value,
# flux_err=lc.flux_err.value,
# pos_corr1=
# meta=lc.meta)
lc["detrended_flux"] = np.nan
lc["detrended_flux_err"] = np.nan
lc.__class__ = FlareLightCurve
lc._init_flare_table()
return lc
def xmkpy3_finder_chart_tpf_overlay_v6():
import matplotlib.pyplot as plt
import astropy.units as u
import sys
import os
import ntpath
import argparse
import ast
import lightkurve as lk # ignore PEP8 warning of redefinition
lk.log.setLevel('INFO')
import mkpy3
#
# argparse: BEGIN =========================================================
#
parser = argparse.ArgumentParser()
#
parser.add_argument(
'--tpf_filename',
action="store",
type=str,
default=None,
help="Filename of the Target Pixel File (TPF) [default: None]")
parser.add_argument('--frame',
action="store",
type=int,
default=0,
help='Frame number (integer) [default: 0]')
parser.add_argument('--survey',
action="store",
type=str,
default='2MASS-J',
help="Survey name (str) [default: '2MASS-J']")
parser.add_argument(
'--width_height_arcmin',
action="store",
type=float,
default=2.0,
help='Width and height size in arcmin (float) [default: 2.0]')
parser.add_argument('--show_plot',
type=mkpy3.mkpy3_util_str2bool,
default=True,
help='If True, show the plot [default=True]')
parser.add_argument(
'--plotfile',
action="store",
type=str,
default='mkpy3_plot.png',
help="Filename of the output plotfile [default: 'mkpy3_plot.png']")
parser.add_argument(
'--overwrite',
type=mkpy3.mkpy3_util_str2bool,
default=False,
help='If True, overwrite ("clobber") an existing output file '
'[default: False.')
parser.add_argument(
'--figsize',
action="store",
type=ast.literal_eval,
default="[9,9]",
help="2-item list of figure width and height [Matplotlib] (str) "
"[default: \"[9,9]\"")
parser.add_argument('--title',
action="store",
type=str,
default=None,
help='Title of the finder chart (str) [default: None]')
parser.add_argument(
'--percentile',
action="store",
type=float,
default=99.0,
help='Percentile [percentage of pixels to keep: 0.0 to 100.0] '
'(float) [default: 99.0]')
parser.add_argument(
'--cmap',
action="store",
type=str,
default=None,
help="Colormap name [Matplotlib] (str) [default: 'gray']")
parser.add_argument(
'--colors',
action="store",
type=ast.literal_eval,
default="[None,'cornflowerblue','red']",
help="3-item list of overlay color names [Matplotlib] (str) "
"[default: \"['None','cornflowerblue','red']\"")
parser.add_argument(
'--lws',
action="store",
type=ast.literal_eval,
default="[0,3,4]",
help="3-item list of overlay line widths [Matplotlib] (str) "
"[default: \"[0,3,4]\"")
parser.add_argument(
'--zorders',
action="store",
type=ast.literal_eval,
default="[0,1,2]",
help="3-item list of overlay zorder values [Matplotlib] (str) "
"[default: \"[0,1,2]\"")
parser.add_argument(
'--marker_dict',
action="store",
type=ast.literal_eval,
default="{'edgecolor':'yellow', 's':600, 'facecolor':'None', 'lw':3, "
"'zorder':10}",
help="marker kwargs (dictonary string) for ax.scatter() [Matplotlib] "
"(str) [default: \"{'edgecolor':'yellow', 's':600, 'facecolor':'None',"
" 'lw':3, 'zorder':10}\"")
parser.add_argument(
'--verbose',
type=mkpy3.mkpy3_util_str2bool,
default=False,
help='Print extra information if True (bool) [default=False]')
#
args = parser.parse_args()
tpf_filename = args.tpf_filename
frame = args.frame
survey = args.survey
width_height_arcmin = args.width_height_arcmin
show_plot = args.show_plot
plotfile = args.plotfile
overwrite = args.overwrite
figsize = args.figsize
title_ = args.title
percentile = args.percentile
cmap = args.cmap
colors = args.colors
lws = args.lws
zorders = args.zorders
marker_dict = args.marker_dict
verbose = args.verbose
#
if (verbose):
print('%s =args.tpf_filename' % (args.tpf_filename))
print('%s =args.frame' % (args.frame))
print("'%s' =args.survey" % (args.survey))
print('%s =args.width_height_arcmin' % (args.width_height_arcmin))
print('%s =args.show_plot' % (args.show_plot))
print("'%s' =args.plotfile" % (args.plotfile))
print('%s =args.overwrite' % (args.overwrite))
print('%s =args.figsize' % (args.figsize))
print('%s =args.title' % (args.title))
print('%s =args.percentile' % (args.percentile))
print('%s =args.cmap' % (args.cmap))
print('%s =args.colors' % (args.colors))
print('%s =args.lws' % (args.lws))
print('%s =args.zorders' % (args.zorders))
print('%s =args.marker_dict' % (args.marker_dict))
print('%s =args.verbose' % (args.verbose))
print()
# pass:if
#
# argparse: END ===========================================================
#
ok = (type(marker_dict) is dict) or (marker_dict is None)
if (not ok):
print()
print('**** ERROR ***** BAD ARGUMENT VALUE *****')
print()
print('marker_dict must be a dictionary or None:')
print(marker_dict, '=marker_dict')
print()
sys.exit(1)
# pass:if
if (tpf_filename is not None):
mkpy3.mkpy3_util_check_file_exists(tpf_filename, True)
tpf = lk.read(tpf_filename)
else:
tpf = lk.search_targetpixelfile(target='kepler-138b',
mission='kepler',
cadence='long',
quarter=10).download(quality_bitmask=0)
# 6--- exoplanet Kelper-138b is "KIC 7603200"
print()
print('No TargetPixelFile (TPF) filename given.')
print()
print('Using default TPF [Kepler Q10 observations of exoplanet Kepler-'
'138b (KIC 760320)]:')
# pass#if
print()
print('TPF filename:', ntpath.basename(tpf.path))
print('TPF dirname: ', os.path.dirname(tpf.path))
print()
ra_deg = tpf.ra
dec_deg = tpf.dec
if (verbose):
print()
print(ra_deg, '=ra_deg')
print(dec_deg, '=dec_deg')
# pass#if
print()
# get survey image data
# survey = '2MASS-J' # hard-wired option
survey_hdu, survey_hdr, survey_data, survey_wcs, survey_cframe = \
mkpy3.mkpy3_finder_chart_survey_fits_image_get_v1(
ra_deg, dec_deg, radius_arcmin=width_height_arcmin,
survey=survey, verbose=verbose)
# create a matplotlib figure object
fig = plt.figure(figsize=figsize)
# create a matplotlib axis object with right ascension and declination axes
ax = plt.subplot(projection=survey_wcs)
# show the survey image
mkpy3.mkpy3_finder_chart_image_show_v1(ax=ax,
image_data=survey_data,
percentile=percentile,
cmap=cmap,
verbose=verbose)
# show the TPF overlay
mkpy3_finder_chart_tpf_overlay_v6(ax=ax,
survey_wcs=survey_wcs,
tpf=tpf,
frame=frame,
colors=colors,
lws=lws,
zorders=zorders,
verbose=verbose)
# add title
if (title_ is None):
title_ = tpf.hdu[0].header['object']
# pass:if
plt.suptitle(title_, size=25)
# put a yellow circle at the target position
if (type(marker_dict) is dict):
ax.scatter(ra_deg * u.deg,
dec_deg * u.deg,
transform=ax.get_transform(survey_cframe),
**marker_dict)
# adjust the plot margins
plt.subplots_adjust(left=0.2, right=0.9, top=0.9, bottom=0.2)
if (plotfile != ''):
if (plotfile != 'mkpy3_plot.png'):
mkpy3.mkpy3_util_check_file_exists(plotfile, overwrite)
plt.savefig(plotfile, dpi=300) # , bbox_inches = "tight")
print('\n%s <--- plotfile written :-)\n' % (plotfile))
# pass:if
if (show_plot):
plt.ioff()
plt.show()
# pass:if
plt.close()
#
ok = (type(marker_dict) is dict) or (marker_dict is None)
if (not ok):
print()
print('**** ERROR ***** BAD ARGUMENT VALUE *****')
print()
print('marker_dict must be a dictionary or None:')
print(marker_dict, '=marker_dict')
print()
sys.exit(1)
# pass:if
if (tpf_filename is not None):
check_file_exists(tpf_filename, True)
tpf = lk.read(tpf_filename)
else:
tpf = lk.search_targetpixelfile(target='kepler-138b',
mission='kepler',
quarter=10).download(quality_bitmask=0)
# 6--- exoplanet Kelper-138b is "KIC 7603200"
print()
print('No TargetPixelFile (TPF) filename given.')
print()
print('Using default TPF [Kepler Q10 observations of exoplanet Kepler-'
'138b (KIC 760320)]:')
# pass#if
print()
print('TPF filename:', ntpath.basename(tpf.path))
print('TPF dirname: ', os.path.dirname(tpf.path))
print()
"""
This contains a collection of functions to test the Machine API
"""
import numpy as np
from scipy import sparse
import pytest
import lightkurve as lk
from astropy.utils.data import get_pkg_data_filename
from psfmachine import TPFMachine
tpfs = []
for idx in range(10):
tpfs.append(lk.read(get_pkg_data_filename(f"data/tpf_test_{idx:02}.fits")))
tpfs = lk.collections.TargetPixelFileCollection(tpfs)
@pytest.mark.remote_data
def test_create_delta_sparse_arrays():
machine = TPFMachine.from_TPFs(tpfs)
# create numpy arrays
machine._create_delta_arrays()
non_sparse_arr = machine.__dict__.copy()
# check for main attrs shape
assert non_sparse_arr["time"].shape == (10, )
assert non_sparse_arr["flux"].shape == (10, 285)
assert non_sparse_arr["flux_err"].shape == (10, 285)
assert non_sparse_arr["column"].shape == (285, )
assert non_sparse_arr["row"].shape == (285, )
assert non_sparse_arr["ra"].shape == (285, )