repo stringlengths 2 99 | file stringlengths 13 225 | code stringlengths 0 18.3M | file_length int64 0 18.3M | avg_line_length float64 0 1.36M | max_line_length int64 0 4.26M | extension_type stringclasses 1
value |
|---|---|---|---|---|---|---|
PROTES | PROTES-main/calc/opti/opti_optimatt.py | import numpy as np
from opti import Opti
try:
import teneva
with_teneva = True
except Exception as e:
with_teneva = False
class OptiOptimatt(Opti):
def __init__(self, name='optimatt', *args, **kwargs):
super().__init__(name, *args, **kwargs)
def opts(self, dr_max=2):
self.opts_d... | 763 | 22.875 | 65 | py |
PROTES | PROTES-main/calc/opti/opti_opo.py | import numpy as np
from opti import Opti
try:
import nevergrad as ng
with_ng = True
except Exception as e:
with_ng = False
class OptiOPO(Opti):
def __init__(self, name='opo', *args, **kwargs):
super().__init__(name, *args, **kwargs)
def _init(self):
if not with_ng:
s... | 453 | 18.73913 | 52 | py |
PROTES | PROTES-main/calc/opti/__init__.py | from .opti import Opti
from .opti_nb import OptiNB
from .opti_opo import OptiOPO
from .opti_optimatt import OptiOptimatt
from .opti_portfolio import OptiPortfolio
from .opti_pso import OptiPSO
from .opti_protes import OptiProtes
from .opti_spsa import OptiSPSA
from .opti_ttopt import OptiTTOpt
| 295 | 28.6 | 41 | py |
PROTES | PROTES-main/calc/opti/opti_spsa.py | import numpy as np
from opti import Opti
try:
import nevergrad as ng
with_ng = True
except Exception as e:
with_ng = False
class OptiSPSA(Opti):
def __init__(self, name='spsa', *args, **kwargs):
super().__init__(name, *args, **kwargs)
def _init(self):
if not with_ng:
... | 449 | 18.565217 | 53 | py |
PROTES | PROTES-main/animation/animate.py | import numpy as np
import os
import sys
from protes import animation
def func_build_ackley(n):
"""Ackley function. See https://www.sfu.ca/~ssurjano/ackley.html."""
d = 2 # Dimension
a = -32.768 # Grid lower bound
b = +32.768 # Grid upper bound
par_a = 20. #... | 3,182 | 29.028302 | 79 | py |
DeblendingStarfields | DeblendingStarfields-master/setup.py | import setuptools
setuptools.setup(
name='DeblendingStarfieldsDevRunjingLiu120',
version='0.0.1',
author='Runjing Liu',
author_email='[email protected]',
packages=['deblending_runjingdev'],
url='https://github.com/Runjing-Liu120/DeblendingStarfields',
description='A package to reprod... | 486 | 33.785714 | 95 | py |
DeblendingStarfields | DeblendingStarfields-master/deblending_runjingdev/flux_utils.py | import torch
import numpy as np
from torch import nn
from torch import optim
import deblending_runjingdev.utils as utils
from deblending_runjingdev.simulated_datasets_lib import plot_one_star
from deblending_runjingdev.wake_lib import PlanarBackground
class FluxEstimator(nn.Module):
def __init__(self, observed_i... | 6,185 | 34.348571 | 104 | py |
DeblendingStarfields | DeblendingStarfields-master/deblending_runjingdev/image_utils.py | import torch
from torch import nn
import deblending_runjingdev.utils as utils
from deblending_runjingdev.which_device import device
# This function copied from
# https://gist.github.com/dem123456789/23f18fd78ac8da9615c347905e64fc78
def _extract_patches_2d(img,patch_shape,step=[1.0,1.0],batch_first=False):
patch... | 8,377 | 42.409326 | 126 | py |
DeblendingStarfields | DeblendingStarfields-master/deblending_runjingdev/daophot_catalog_lib.py | import torch
import numpy as np
from deblending_runjingdev.which_device import device
from deblending_runjingdev.sdss_dataset_lib import convert_mag_to_nmgy
from deblending_runjingdev.image_statistics_lib import get_locs_error
def load_daophot_results(data_file,
nelec_per_nmgy,
... | 2,859 | 38.178082 | 96 | py |
DeblendingStarfields | DeblendingStarfields-master/deblending_runjingdev/utils.py | import torch
import numpy as np
from torch.distributions import normal, categorical
from deblending_runjingdev.which_device import device
# Functions to work with n_stars
def get_is_on_from_n_stars(n_stars, max_stars):
assert len(n_stars.shape) == 1
batchsize = len(n_stars)
is_on_array = torch.zeros((ba... | 2,374 | 29.448718 | 95 | py |
DeblendingStarfields | DeblendingStarfields-master/deblending_runjingdev/starnet_lib.py | import torch
import torch.nn as nn
import numpy as np
import deblending_runjingdev.image_utils as image_utils
import deblending_runjingdev.utils as utils
from deblending_runjingdev.which_device import device
from itertools import product
from torch.distributions import poisson
class Flatten(nn.Module):
def fo... | 18,839 | 40.045752 | 130 | py |
DeblendingStarfields | DeblendingStarfields-master/deblending_runjingdev/elbo_lib.py | import torch
import numpy as np
import time
from torch import nn
import deblending_runjingdev.starnet_lib as starnet_lib
from deblending_runjingdev.which_device import device
def get_neg_elbo(simulator, full_image, locs, fluxes, n_stars, \
log_q_locs, log_q_fluxes, log_q_n_stars,
... | 8,194 | 40.180905 | 107 | py |
DeblendingStarfields | DeblendingStarfields-master/deblending_runjingdev/wake_lib.py | import torch
import torch.nn as nn
from torch import optim
import numpy as np
from deblending_runjingdev.simulated_datasets_lib import _get_mgrid, plot_multiple_stars
from deblending_runjingdev.psf_transform_lib import PowerLawPSF
import deblending_runjingdev.utils
from deblending_runjingdev.which_device import devic... | 18,610 | 36.147705 | 109 | py |
DeblendingStarfields | DeblendingStarfields-master/deblending_runjingdev/plotting_utils.py | import matplotlib.pyplot as plt
import torch
import numpy as np
import deblending_runjingdev.image_utils as image_utils
from deblending_runjingdev.which_device import device
def plot_image(fig, image,
true_locs = None, estimated_locs = None,
vmin = None, vmax = None,
a... | 4,500 | 35.593496 | 84 | py |
DeblendingStarfields | DeblendingStarfields-master/deblending_runjingdev/sdss_dataset_lib.py | import pathlib
import os
import pickle
import numpy as np
from scipy.interpolate import RegularGridInterpolator
import scipy.stats as stats
import torch
from torch.utils.data import Dataset
from astropy.io import fits
from astropy.wcs import WCS
import matplotlib.pyplot as plt
from deblending_runjingdev.simulated_d... | 10,043 | 37.482759 | 110 | py |
DeblendingStarfields | DeblendingStarfields-master/deblending_runjingdev/psf_transform_lib.py | import torch
import torch.nn as nn
from torch.nn.functional import unfold, softmax, pad
from astropy.io import fits
import deblending_runjingdev.image_utils as image_utils
from deblending_runjingdev.utils import eval_normal_logprob
from deblending_runjingdev.simulated_datasets_lib import _get_mgrid, plot_multiple_st... | 6,346 | 32.582011 | 101 | py |
DeblendingStarfields | DeblendingStarfields-master/deblending_runjingdev/simulated_datasets_lib.py | import numpy as np
import scipy.stats as stats
import torch
from torch.utils.data import Dataset, DataLoader
import torch
import torch.nn.functional as F
import deblending_runjingdev.utils as utils
from deblending_runjingdev.which_device import device
def _trim_psf(psf, slen):
# crop the psf to length slen x sl... | 10,604 | 30.751497 | 98 | py |
DeblendingStarfields | DeblendingStarfields-master/deblending_runjingdev/image_statistics_lib.py | import torch
import numpy as np
from deblending_runjingdev.sdss_dataset_lib import convert_nmgy_to_mag
from deblending_runjingdev.which_device import device
def filter_params(locs, fluxes, slen, pad = 5):
assert len(locs.shape) == 2
if fluxes is not None:
assert len(fluxes.shape) == 1
assert ... | 5,243 | 35.416667 | 97 | py |
DeblendingStarfields | DeblendingStarfields-master/deblending_runjingdev/sleep_lib.py | import torch
import numpy as np
import math
import time
from torch.distributions import normal
from torch.nn import CrossEntropyLoss
import deblending_runjingdev.utils as utils
import deblending_runjingdev.elbo_lib as elbo_lib
from deblending_runjingdev.which_device import device
from itertools import permutations... | 9,800 | 37.136187 | 127 | py |
DeblendingStarfields | DeblendingStarfields-master/deblending_runjingdev/__init__.py | 0 | 0 | 0 | py | |
DeblendingStarfields | DeblendingStarfields-master/deblending_runjingdev/which_device.py | import torch
device = torch.device("cuda:6" if torch.cuda.is_available() else "cpu")
# device = 'cpu'
| 102 | 24.75 | 71 | py |
DeblendingStarfields | DeblendingStarfields-master/experiments_sparse_field/sparse_field_lib.py | import numpy as np
import torch
import fitsio
from astropy.io import fits
from astropy.wcs import WCS
import deblending_runjingdev.sdss_dataset_lib as sdss_dataset_lib
from deblending_runjingdev.sdss_dataset_lib import _get_mgrid2
def load_data(catalog_file = '../coadd_field_catalog_runjing_liu.fit',
... | 2,936 | 33.151163 | 90 | py |
DeblendingStarfields | DeblendingStarfields-master/experiments_sparse_field/train_sleep-sparse_field.py | import numpy as np
import torch
import torch.optim as optim
from deblending_runjingdev import simulated_datasets_lib
from deblending_runjingdev import starnet_lib
from deblending_runjingdev import sleep_lib
from deblending_runjingdev import psf_transform_lib
from deblending_runjingdev import wake_lib
import json
im... | 4,469 | 29.827586 | 87 | py |
DeblendingStarfields | DeblendingStarfields-master/experiments_m2/train_wake_sleep.py | import numpy as np
import torch
import torch.optim as optim
import deblending_runjingdev.sdss_dataset_lib as sdss_dataset_lib
import deblending_runjingdev.simulated_datasets_lib as simulated_datasets_lib
import deblending_runjingdev.starnet_lib as starnet_lib
import deblending_runjingdev.sleep_lib as sleep_lib
from d... | 7,431 | 33.567442 | 112 | py |
DeblendingStarfields | DeblendingStarfields-master/experiments_m2/train_sleep.py | import numpy as np
import torch
import torch.optim as optim
import deblending_runjingdev.simulated_datasets_lib as simulated_datasets_lib
import deblending_runjingdev.sdss_dataset_lib as sdss_dataset_lib
import deblending_runjingdev.starnet_lib as starnet_lib
import deblending_runjingdev.sleep_lib as sleep_lib
import... | 3,978 | 28.474074 | 89 | py |
DeblendingStarfields | DeblendingStarfields-master/experiments_deblending/train_encoder.py | import numpy as np
import torch
import torch.optim as optim
import deblending_runjingdev.simulated_datasets_lib as simulated_datasets_lib
import deblending_runjingdev.starnet_lib as starnet_lib
import deblending_runjingdev.sleep_lib as sleep_lib
import deblending_runjingdev.psf_transform_lib as psf_transform_lib
imp... | 3,330 | 25.862903 | 89 | py |
DeblendingStarfields | DeblendingStarfields-master/experiments_elbo_vs_sleep/train_elbo.py | import numpy as np
import torch
import torch.optim as optim
import deblending_runjingdev.elbo_lib as elbo_lib
import deblending_runjingdev.simulated_datasets_lib as simulated_datasets_lib
import deblending_runjingdev.starnet_lib as starnet_lib
import deblending_runjingdev.psf_transform_lib as psf_transform_lib
impor... | 5,869 | 30.55914 | 90 | py |
DeblendingStarfields | DeblendingStarfields-master/experiments_elbo_vs_sleep/train_elbo-Copy1.py | import numpy as np
import torch
import torch.optim as optim
import deblending_runjingdev.elbo_lib as elbo_lib
import deblending_runjingdev.simulated_datasets_lib as simulated_datasets_lib
import deblending_runjingdev.starnet_lib as starnet_lib
import deblending_runjingdev.psf_transform_lib as psf_transform_lib
impor... | 5,279 | 33.509804 | 100 | py |
DeblendingStarfields | DeblendingStarfields-master/experiments_elbo_vs_sleep/simulate_test_images.py | import numpy as np
import torch
import json
import matplotlib.pyplot as plt
import deblending_runjingdev.simulated_datasets_lib as simulated_datasets_lib
import deblending_runjingdev.psf_transform_lib as psf_transform_lib
from deblending_runjingdev.which_device import device
np.random.seed(65765)
_ = torch.manual_... | 3,256 | 29.439252 | 97 | py |
DeblendingStarfields | DeblendingStarfields-master/experiments_elbo_vs_sleep/train_sleep.py | import numpy as np
import torch
import torch.optim as optim
import deblending_runjingdev.simulated_datasets_lib as simulated_datasets_lib
import deblending_runjingdev.starnet_lib as starnet_lib
import deblending_runjingdev.sleep_lib as sleep_lib
import deblending_runjingdev.psf_transform_lib as psf_transform_lib
impo... | 4,752 | 26.316092 | 89 | py |
DeblendingStarfields | DeblendingStarfields-master/blip_wrapper/performance_eval.py | import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as patches
mag_vec = np.concatenate((np.array([15]),
np.arange(19, 22.2, 0.4),
np.array([100])))
MAG_CONST = 2.5
def convert_nmgy_to_mag(nmgy):
return 22.5 - MAG_CONST * np.log10(nmgy)
def filter_params(locs, fluxes, sle... | 8,448 | 23.923304 | 93 | py |
lightkurve | lightkurve-main/src/lightkurve/utils.py | """This module provides various helper functions."""
import logging
import sys
import os
import warnings
from functools import wraps
import matplotlib.pyplot as plt
from matplotlib.colors import LogNorm
import numpy as np
from tqdm import tqdm
import astropy
from astropy.utils.data import download_file
from astropy.u... | 26,156 | 31.292593 | 106 | py |
lightkurve | lightkurve-main/src/lightkurve/lightcurve.py | """Defines LightCurve, KeplerLightCurve, and TessLightCurve."""
import os
import datetime
import logging
import warnings
import collections
from collections.abc import Sequence
import numpy as np
from scipy.signal import savgol_filter
from scipy.interpolate import interp1d
import matplotlib
from matplotlib import pypl... | 138,768 | 39.754479 | 140 | py |
lightkurve | lightkurve-main/src/lightkurve/units.py | """Define custom AstroPy units commonly used by the Kepler/TESS community."""
from astropy import units as u
__all__ = ["ppt", "ppm"]
ppt = u.def_unit(["ppt", "parts per thousand"], u.Unit(1e-3))
ppm = u.def_unit(["ppm", "parts per million"], u.Unit(1e-6))
u.add_enabled_units([ppt, ppm])
| 291 | 31.444444 | 77 | py |
lightkurve | lightkurve-main/src/lightkurve/interact.py | """Provides tools for interactive visualizations.
Example use
-----------
The functions in this module are used to create Bokeh-based visualization
widgets. For example, the following code will create an interactive
visualization widget showing the pixel data and a lightcurve::
# SN 2018 oh Supernova example
... | 53,474 | 37.471223 | 145 | py |
lightkurve | lightkurve-main/src/lightkurve/lightcurvefile.py | """DEPRECATED: `LightCurveFile` classes were removed in Lightkurve v2.0 in
favor of only having `LightCurve` classes. To minimize breaking code, we
retain the `LightCurveFile` classes here as wrappers around the new
`LightCurve` objects, but will remove these wrappers in a future version..
"""
from . import LightCurve... | 470 | 41.818182 | 74 | py |
lightkurve | lightkurve-main/src/lightkurve/time.py | """Adds the BKJD and BTJD time format for use by Astropy's `Time` object.
Caution: AstroPy time objects make a distinction between a time's format
(e.g. ISO, JD, MJD) and its scale (e.g. UTC, TDB). This can be confusing
because the acronym "BTJD" refers both to a format (TJD) and to a scale (TDB).
Note: the classes ... | 1,509 | 31.12766 | 82 | py |
lightkurve | lightkurve-main/src/lightkurve/version.py | # It is important to store the version number in a separate file
# so that we can read it from setup.py without importing the package
__version__ = "2.4.1dev"
| 159 | 39 | 68 | py |
lightkurve | lightkurve-main/src/lightkurve/interact_bls.py | """This module provides helper functions for the `LightCurve.interact_bls()` feature."""
import logging
import warnings
import numpy as np
from astropy.convolution import convolve, Box1DKernel
from astropy.time import Time, TimeDelta
from astropy.timeseries import BoxLeastSquares
import astropy.units as u
from .utils... | 37,534 | 36.348259 | 202 | py |
lightkurve | lightkurve-main/src/lightkurve/targetpixelfile.py | """Defines TargetPixelFile, KeplerTargetPixelFile, and TessTargetPixelFile."""
from __future__ import division
import datetime
import os
import warnings
import logging
import collections
from astropy.io import fits
from astropy.io.fits import Undefined, BinTableHDU
from astropy.nddata import Cutout2D
from astropy.ta... | 115,945 | 38.981379 | 143 | py |
lightkurve | lightkurve-main/src/lightkurve/periodogram.py | """Defines the Periodogram class and associated tools."""
from __future__ import division, print_function
import copy
import logging
import math
import re
import warnings
import numpy as np
from matplotlib import pyplot as plt
import astropy
from astropy.table import Table
from astropy import units as u
from astropy... | 53,767 | 39.487952 | 106 | py |
lightkurve | lightkurve-main/src/lightkurve/__init__.py | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import os
PACKAGEDIR = os.path.abspath(os.path.dirname(__file__))
MPLSTYLE = "{}/data/lightkurve.mplstyle".format(PACKAGEDIR)
"""Lightkurve's stylesheet for matplotlib.
It is useful for users who create their own figures and want th... | 3,896 | 31.747899 | 117 | py |
lightkurve | lightkurve-main/src/lightkurve/search.py | """Defines tools to retrieve Kepler data from the archive at MAST."""
from __future__ import division
import glob
import logging
import os
import re
import warnings
import numpy as np
from astropy import units as u
from astropy.coordinates import SkyCoord
from astropy.io import ascii
from astropy.table import Row, Ta... | 56,015 | 39.328294 | 185 | py |
lightkurve | lightkurve-main/src/lightkurve/collections.py | """Defines collections of data products."""
import warnings
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
from astropy.table import vstack
from astropy.utils.decorators import deprecated
from . import MPLSTYLE
from .targetpixelfile import TargetPixelFile
from .utils import LightkurveWarning, L... | 11,762 | 36.945161 | 136 | py |
lightkurve | lightkurve-main/src/lightkurve/convenience.py | from __future__ import division, print_function
import numpy as np
from .lightcurve import LightCurve
__all__ = ["estimate_cdpp"]
def estimate_cdpp(flux, **kwargs):
"""A convenience function which wraps LightCurve.estimate_cdpp().
For details on the algorithm used to compute the Combined Differential
... | 818 | 25.419355 | 83 | py |
lightkurve | lightkurve-main/src/lightkurve/io/tasoc.py | """TESS Asteroseismic Science Operations Center - https://tasoc.dk
TESS Data For Asteroseismology Lightcurves - https://archive.stsci.edu/hlsp/tasoc
Data provided with this release have been extracted using the TASOC Photometry pipeline. The TASOC
pipeline used to generate the data is open source and available... | 1,421 | 38.5 | 103 | py |
lightkurve | lightkurve-main/src/lightkurve/io/tglc.py | """Reader for TGLC light curve files.
Details can be found at https://archive.stsci.edu/hlsp/tglc
"""
import numpy as np
from astropy import units as u
from ..lightcurve import TessLightCurve
from ..utils import TessQualityFlags
from .generic import read_generic_lightcurve
def read_tglc_lightcurve(
filename, flu... | 3,971 | 39.948454 | 122 | py |
lightkurve | lightkurve-main/src/lightkurve/io/kepseismic.py | """Reader function for KEPSEISMIC community light curve products."""
from ..lightcurve import KeplerLightCurve
from .generic import read_generic_lightcurve
def read_kepseismic_lightcurve(filename, **kwargs):
"""Read a KEPSEISMIC light curve file.
More information: https://archive.stsci.edu/prepds/kepseismic
... | 832 | 24.242424 | 68 | py |
lightkurve | lightkurve-main/src/lightkurve/io/k2sff.py | """Reader function for K2SFF community light curve products."""
from ..lightcurve import KeplerLightCurve
from ..utils import validate_method
from .generic import read_generic_lightcurve
def read_k2sff_lightcurve(filename, ext="BESTAPER", **kwargs):
"""Read a K2SFF light curve file.
More information: https:... | 965 | 27.411765 | 79 | py |
lightkurve | lightkurve-main/src/lightkurve/io/detect.py | """Provides a function to automatically detect Kepler/TESS file types."""
from astropy.io import fits
from astropy.io.fits import HDUList
__all__ = ["detect_filetype"]
def detect_filetype(hdulist: HDUList) -> str:
"""Returns Kepler and TESS file types given a FITS object.
This function will detect the file ... | 5,304 | 32.575949 | 82 | py |
lightkurve | lightkurve-main/src/lightkurve/io/everest.py | """Reader for K2 EVEREST light curves."""
from ..lightcurve import KeplerLightCurve
from ..utils import KeplerQualityFlags
from .generic import read_generic_lightcurve
def read_everest_lightcurve(
filename, flux_column="flux", quality_bitmask="default", **kwargs
):
"""Read an EVEREST light curve file.
M... | 2,316 | 35.203125 | 79 | py |
lightkurve | lightkurve-main/src/lightkurve/io/qlp.py | """Reader for MIT Quicklook Pipeline (QLP) light curve files.
Website: http://archive.stsci.edu/hlsp/qlp
Product description: https://archive.stsci.edu/hlsps/qlp/hlsp_qlp_tess_ffi_all_tess_v1_data-prod-desc.pdf
"""
from ..lightcurve import TessLightCurve
from ..utils import TessQualityFlags
from .generic import read_... | 2,872 | 43.890625 | 123 | py |
lightkurve | lightkurve-main/src/lightkurve/io/generic.py | """Read a generic FITS table containing a light curve."""
import logging
import warnings
from copy import deepcopy
from astropy.io import fits
from astropy.table import Table
from astropy.time import Time
from astropy.units import UnitsWarning
import numpy as np
from ..utils import validate_method
from ..lightcurve i... | 5,192 | 38.340909 | 85 | py |
lightkurve | lightkurve-main/src/lightkurve/io/cdips.py | """Reader for A PSF-Based Approach to TESS Cluster Difference Imaging Photometric Survey (CDIPS) light curves
Website: https://archive.stsci.edu/hlsp/cdips
Product Description: https://archive.stsci.edu/hlsps/cdips/hlsp_cdips_tess_ffi_all_tess_v01_readme.md
"""
import logging
from ..lightcurve import TessLightCurve
f... | 3,389 | 39.843373 | 109 | py |
lightkurve | lightkurve-main/src/lightkurve/io/eleanor.py | """Reader for GSFC-ELEANOR-LITE light curve files.
Details can be found at https://archive.stsci.edu/hlsp/eleanor and https://archive.stsci.edu/hlsp/gsfc-eleanor-lite
"""
from ..lightcurve import TessLightCurve
from ..utils import TessQualityFlags
from astropy import units as u
from .generic import read_generic_lightc... | 6,004 | 43.481481 | 132 | py |
lightkurve | lightkurve-main/src/lightkurve/io/pathos.py | """Reader for A PSF-Based Approach to TESS High Quality Data Of Stellar Clusters (PATHOS) light curve files.
Website: https://archive.stsci.edu/hlsp/pathos
A product description file wasn't obvious on the MAST website
"""
from ..lightcurve import TessLightCurve
from ..utils import TessQualityFlags
from .generic impor... | 2,439 | 36.538462 | 108 | py |
lightkurve | lightkurve-main/src/lightkurve/io/__init__.py | """The .io sub-package provides functions for reading data."""
from astropy.io import registry
from .. import LightCurve
from . import (
cdips,
eleanor,
everest,
k2sff,
kepler,
kepseismic,
pathos,
qlp,
tasoc,
tess,
tglc,
)
from .detect import *
from .read import *
__all__ =... | 1,462 | 33.833333 | 84 | py |
lightkurve | lightkurve-main/src/lightkurve/io/tess.py | """Reader for official TESS light curve FITS files produced by the Ames SPOC pipeline."""
from ..lightcurve import TessLightCurve
from ..utils import TessQualityFlags
from .generic import read_generic_lightcurve
def read_tess_lightcurve(
filename, flux_column="pdcsap_flux", quality_bitmask="default"
):
"""Re... | 1,985 | 39.530612 | 89 | py |
lightkurve | lightkurve-main/src/lightkurve/io/read.py | """Functions for reading light curve data."""
import logging
from astropy.io import fits
from astropy.utils import deprecated
from ..lightcurve import KeplerLightCurve, TessLightCurve
from ..utils import LightkurveDeprecationWarning, LightkurveError
from .detect import detect_filetype
log = logging.getLogger(__name_... | 5,788 | 40.35 | 181 | py |
lightkurve | lightkurve-main/src/lightkurve/io/kepler.py | """Reader for official Kepler light curve FITS files produced by the Ames pipeline."""
from ..lightcurve import KeplerLightCurve
from ..utils import KeplerQualityFlags
from .generic import read_generic_lightcurve
def read_kepler_lightcurve(
filename, flux_column="pdcsap_flux", quality_bitmask="default"
):
""... | 2,196 | 38.945455 | 89 | py |
lightkurve | lightkurve-main/src/lightkurve/config/__init__.py | import os
import warnings
import astropy.config as astropyconfig
ROOTNAME = 'lightkurve'
class ConfigNamespace(astropyconfig.ConfigNamespace):
rootname = ROOTNAME
class ConfigItem(astropyconfig.ConfigItem):
rootname = ROOTNAME
def get_config_dir():
"""
Determines the package configuration direc... | 4,091 | 31.47619 | 116 | py |
lightkurve | lightkurve-main/src/lightkurve/correctors/pldcorrector.py | """Defines a `PLDCorrector` class which provides a simple way to correct a
light curve by utilizing the pixel time series data contained within the
target's own Target Pixel File.
`PLDCorrector` builds upon `RegressionCorrector` by correlating the light curve
against a design matrix composed of the following elements:... | 22,759 | 38.929825 | 134 | py |
lightkurve | lightkurve-main/src/lightkurve/correctors/sffcorrector.py | """Defines the `SFFCorrector` class.
`SFFCorrector` enables systematics to be removed from light curves using the
Self Flat-Fielding (SFF) method described in Vanderburg and Johnson (2014).
"""
import logging
import warnings
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
from astropy.modeling... | 18,054 | 34.471513 | 112 | py |
lightkurve | lightkurve-main/src/lightkurve/correctors/cbvcorrector.py | """Defines Corrector classes that utilize Kepler/K2/TESS Cotrending Basis Vectors.
"""
import logging
import copy
import requests
import urllib.request
import glob
import os
import warnings
from astropy.io import fits as pyfits
from astropy.table import Table
from astropy.time import Time
from astropy.timeseries impor... | 79,354 | 39.281726 | 112 | py |
lightkurve | lightkurve-main/src/lightkurve/correctors/metrics.py | """Metrics to assess under- and over-fitting of systematic noise.
This module provides two metrics, `overfit_metric_lombscargle` and `underfit_metric_neighbors`,
which enable users to assess whether the noise in a systematics-corrected light curve has been
under- or over-fitted. These features were contributed by Jef... | 18,295 | 38.010661 | 141 | py |
lightkurve | lightkurve-main/src/lightkurve/correctors/__init__.py | """This sub-package defines classes which help remove instrument systematics
or variability from time series photometry data.
Classes provided by this package should inherit from an abstract `Corrector`
class, which provides three key methods::
Corrector(**data_required):
.correct(**options) -> Returns a ... | 762 | 35.333333 | 85 | py |
lightkurve | lightkurve-main/src/lightkurve/correctors/regressioncorrector.py | """Defines `RegressionCorrector` to solve large linear regression problems
with user-defined Gaussian priors in a fast, analytical way.
"""
import logging
import warnings
from astropy.stats import sigma_clip
from astropy import units as u
from astropy.utils.exceptions import AstropyUserWarning
from astropy.utils.maske... | 16,667 | 38.035129 | 169 | py |
lightkurve | lightkurve-main/src/lightkurve/correctors/corrector.py | """Implements the abstract `Corrector` base class.
"""
from abc import ABC, abstractmethod
import matplotlib
import numpy as np
from .. import LightCurve
from .metrics import overfit_metric_lombscargle, underfit_metric_neighbors
class Corrector(ABC):
"""Abstract base class documenting the required structure of ... | 5,460 | 34.461039 | 96 | py |
lightkurve | lightkurve-main/src/lightkurve/correctors/designmatrix.py | """Defines design matrix objects to aid linear regression problems.
Specifically, this module adds the `DesignMatrix`, `DesignMatrixCollection`,
`SparseDesignMatrix`, and `SparseDesignMatrixCollection` classes which
are design to work with the `RegressionCorrector` class.
"""
from copy import deepcopy
import warnings
... | 34,995 | 34.207243 | 118 | py |
lightkurve | lightkurve-main/src/lightkurve/prf/tpfmodel.py | """Provides tools to model a Kepler image for PRF photometry fitting.
Examples
--------
%matplotlib inline
import numpy as np
from lightkurve import KeplerTargetPixelFile, LightCurve
from lightkurve.prf import StarPrior, BackgroundPrior, FocusPrior, MotionPrior, TPFModel, PRFPhotometry
from oktopus import GaussianPrio... | 29,717 | 33.880282 | 106 | py |
lightkurve | lightkurve-main/src/lightkurve/prf/prfmodel.py | """Provides callable models of the Kepler Pixel Response Function (PRF)."""
from __future__ import division, print_function
import math
from astropy.io import fits as pyfits
import numpy as np
import scipy
import scipy.interpolate
from ..utils import channel_to_module_output, plot_image
__all__ = ["KeplerPRF", "Si... | 12,737 | 33.334232 | 97 | py |
lightkurve | lightkurve-main/src/lightkurve/prf/__init__.py | from .prfmodel import *
from .tpfmodel import *
| 48 | 15.333333 | 23 | py |
lightkurve | lightkurve-main/src/lightkurve/seismology/stellar_estimators.py | """Functions to estimate stellar parameters (radius, mass, logg) using
asteroseismic scaling relations.
"""
from uncertainties import ufloat, umath
from astropy import units as u
from astropy import constants as const
from .utils import SeismologyQuantity
__all__ = ["estimate_radius", "estimate_mass", "estimate_logg... | 10,895 | 39.962406 | 89 | py |
lightkurve | lightkurve-main/src/lightkurve/seismology/deltanu_estimators.py | """Helper functions for estimating deltanu from periodograms."""
from __future__ import division, print_function
import numpy as np
from scipy.signal import find_peaks
from matplotlib import pyplot as plt
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
from astropy import units as u
from .utils import S... | 10,981 | 34.086262 | 88 | py |
lightkurve | lightkurve-main/src/lightkurve/seismology/core.py | """Defines the Seismology class."""
import logging
import warnings
import numpy as np
from matplotlib import pyplot as plt
from scipy.signal import find_peaks
from astropy import units as u
from astropy.units import cds
from .. import MPLSTYLE
from . import utils, stellar_estimators
from ..periodogram import SNRPeri... | 38,459 | 40.533477 | 124 | py |
lightkurve | lightkurve-main/src/lightkurve/seismology/utils.py | """Generic classes and functions which aid the asteroseismology features."""
import numpy as np
import copy
from astropy import units as u
from astropy.units import Quantity
__all__ = ["SeismologyQuantity"]
class SeismologyQuantity(Quantity):
"""Holds an asteroseismic value including its unit, error, and estimat... | 5,796 | 36.4 | 93 | py |
lightkurve | lightkurve-main/src/lightkurve/seismology/numax_estimators.py | """Helper functions for estimating numax from periodograms."""
import numpy as np
from matplotlib import pyplot as plt
from astropy.convolution import convolve, Gaussian1DKernel
from astropy import units as u
from .. import MPLSTYLE
from . import utils
from .utils import SeismologyQuantity
__all__ = ["estimate_numax... | 12,338 | 36.966154 | 88 | py |
lightkurve | lightkurve-main/src/lightkurve/seismology/__init__.py | """The `lightkurve.seismology` sub-package provides classes and functions for
quick-look asteroseismic analyses."""
# Do not export the modules in this subpackage to the root namespace, important
# because `lightkurve.utils` collides with `lightkurve.seismology.utils`.
__all__ = [
"Seismology",
"SeismologyQuan... | 653 | 26.25 | 79 | py |
lightkurve | lightkurve-main/tests/test_interact_bls.py | """Tests the features of the lightkurve.interact_bls module."""
import pytest
from astropy.timeseries import BoxLeastSquares
import astropy.units as u
import numpy as np
from lightkurve.lightcurve import KeplerLightCurve, TessLightCurve
from .test_lightcurve import KEPLER10, TESS_SIM
bad_optional_imports = False
try... | 4,603 | 35.539683 | 114 | py |
lightkurve | lightkurve-main/tests/test_targetpixelfile.py | import collections
import os
import tempfile
import warnings
import matplotlib.pyplot as plt
import numpy as np
from numpy.testing import assert_array_equal
import pytest
from astropy.utils.data import get_pkg_data_filename
from astropy.io.fits.verify import VerifyWarning
from astropy.coordinates import SkyCoord
from... | 33,035 | 36.583618 | 159 | py |
lightkurve | lightkurve-main/tests/conftest.py | import os
import tempfile
import pytest
def pytest_runtest_setup(item):
r"""Our tests will often run in headless virtual environments. For this
reason, we enforce the use of matplotlib's robust Agg backend, because it
does not require a graphical display.
This avoids errors such as:
c:\hoste... | 2,138 | 33.5 | 100 | py |
lightkurve | lightkurve-main/tests/test_interact.py | """Tests the features of the lightkurve.interact module."""
import warnings
from astropy.utils.data import get_pkg_data_filename
import numpy as np
from numpy.testing import assert_array_equal
import pytest
from lightkurve import LightkurveWarning, LightkurveError
from lightkurve.search import search_targetpixelfile
... | 12,240 | 39.39934 | 121 | py |
lightkurve | lightkurve-main/tests/test_correctors.py | import pytest
@pytest.mark.remote_data
def test_to_corrector():
"""Does the tpf.to_corrector('pld') convenience method work?"""
from lightkurve import KeplerTargetPixelFile
from .test_targetpixelfile import TABBY_TPF
tpf = KeplerTargetPixelFile(TABBY_TPF)
lc = tpf.to_corrector("pld").correct()
... | 359 | 26.692308 | 67 | py |
lightkurve | lightkurve-main/tests/test_lightcurve.py | from astropy.io import fits as pyfits
from astropy.utils.data import get_pkg_data_filename
from astropy.utils.masked import Masked
from astropy import units as u
from astropy.table import Table, Column, MaskedColumn
from astropy.time import Time, TimeDelta
from astropy.timeseries import aggregate_downsample
import mat... | 74,521 | 37.021429 | 117 | py |
lightkurve | lightkurve-main/tests/test_synthetic_data.py | """Use synthetic data to verify lightkurve detrending and signal recovery.
"""
from __future__ import division, print_function
from astropy.utils.data import get_pkg_data_filename
from astropy.stats.bls import BoxLeastSquares
import numpy as np
import pytest
from scipy import stats
from lightkurve.targetpixelfile im... | 8,818 | 32.660305 | 87 | py |
lightkurve | lightkurve-main/tests/test_search.py | """Test features of lightkurve that interact with the data archive at MAST.
Note: if you have the `pytest-remotedata` package installed, then tests flagged
with the `@pytest.mark.remote_data` decorator below will only run if the
`--remote-data` argument is passed to py.test. This allows tests to pass
if no internet c... | 24,606 | 38.817152 | 119 | py |
lightkurve | lightkurve-main/tests/test_conf.py | from astropy.utils.data import get_pkg_data_filename
import os
from pathlib import Path
import shutil
import tempfile
import lightkurve as lk
def test_read_conf_from_file():
"""Sanity test to ensure lightkurve per-user config is in the expected location."""
# assert the default config
assert [] == lk.c... | 2,226 | 34.349206 | 98 | py |
lightkurve | lightkurve-main/tests/test_collections.py | import warnings
import pytest
from astropy import units as u
from astropy.utils.data import get_pkg_data_filename
from astropy.utils.masked import Masked
import matplotlib.pyplot as plt
import numpy as np
from numpy.testing import assert_array_equal
from lightkurve.lightcurve import LightCurve, KeplerLightCurve, Tess... | 13,286 | 31.328467 | 99 | py |
lightkurve | lightkurve-main/tests/__init__.py | import os
# Where is the test data located?
TESTROOT = os.path.abspath(os.path.dirname(__file__))
TESTDATA = os.path.join(TESTROOT, "data")
| 141 | 22.666667 | 53 | py |
lightkurve | lightkurve-main/tests/test_time.py | from astropy.time import Time
import numpy as np
def test_bkjd():
"""Tests for the Barycentric Kepler Julian Date (BKJD) time format."""
# Sanity checks
t0 = Time(0, format="bkjd")
assert t0.format == "bkjd"
assert t0.scale == "tdb"
assert t0.iso == "2009-01-01 12:00:00.000"
def test_btjd():... | 1,239 | 39 | 109 | py |
lightkurve | lightkurve-main/tests/test_periodogram.py | import sys
import pytest
import numpy as np
import matplotlib.pyplot as plt
from numpy.testing import assert_almost_equal, assert_array_equal
from astropy import units as u
from astropy.time import Time
from astropy.stats.bls import BoxLeastSquares
from astropy.utils.masked import Masked
from lightkurve.lightcurve i... | 15,371 | 32.933775 | 145 | py |
lightkurve | lightkurve-main/tests/test_units.py | import pytest
import lightkurve as lk # necessary to enable the units tested below
from astropy import units as u
from .io.test_tasoc import TEST_TIC_ID
def test_custom_units():
"""Are ppt, ppm, and percent enabled AstroPy units?"""
u.Unit("ppt") # custom unit defined in lightkurve.units
u.Unit("ppm... | 699 | 30.818182 | 78 | py |
lightkurve | lightkurve-main/tests/test_utils.py | import pytest
import warnings
import numpy as np
from numpy.testing import assert_almost_equal, assert_array_equal
from lightkurve.utils import KeplerQualityFlags, TessQualityFlags
from lightkurve.utils import module_output_to_channel, channel_to_module_output
from lightkurve.utils import LightkurveWarning
from light... | 6,830 | 34.952632 | 86 | py |
lightkurve | lightkurve-main/tests/test_convenience.py | from __future__ import division, print_function
import numpy as np
from numpy.testing import assert_almost_equal
from lightkurve.lightcurve import LightCurve
from lightkurve.convenience import estimate_cdpp
def test_cdpp():
"""Tests the estimate_cdpp() convenience function which wraps
`LightCurve.estimate_c... | 510 | 30.9375 | 65 | py |
lightkurve | lightkurve-main/tests/io/test_detect.py | import os
from astropy.io import fits
from lightkurve import PACKAGEDIR
from lightkurve.io import detect_filetype
from .. import TESTDATA
def test_detect_filetype():
"""Can we detect the correct filetype?"""
k2_path = os.path.join(TESTDATA, "test-tpf-star.fits")
tess_path = os.path.join(TESTDATA, "tess... | 506 | 28.823529 | 81 | py |
lightkurve | lightkurve-main/tests/io/test_everest.py | import pytest
from lightkurve import search_lightcurve
@pytest.mark.remote_data
def test_search_everest():
"""Can we search and download an EVEREST light curve?"""
search = search_lightcurve("GJ 9827", author="EVEREST", campaign=12)
assert len(search) == 1
assert search.table["author"][0] == "EVEREST... | 429 | 27.666667 | 72 | py |
lightkurve | lightkurve-main/tests/io/test_k2sff.py | import pytest
from astropy.io import fits
import numpy as np
from numpy.testing import assert_array_equal
from lightkurve.io.k2sff import read_k2sff_lightcurve
from lightkurve import search_lightcurve
@pytest.mark.remote_data
def test_read_k2sff():
"""Can we read K2SFF files?"""
url = "http://archive.stsci.... | 1,568 | 34.659091 | 126 | py |
lightkurve | lightkurve-main/tests/io/test_kepseismic.py | import pytest
from astropy.io import fits
import numpy as np
from lightkurve.io.kepseismic import read_kepseismic_lightcurve
from lightkurve.io.detect import detect_filetype
@pytest.mark.remote_data
def test_detect_kepseismic():
"""Can we detect the correct format for KEPSEISMIC files?"""
url = "https://arch... | 1,014 | 31.741935 | 155 | py |
lightkurve | lightkurve-main/tests/io/test_cdips.py | import pytest
from astropy.io import fits
import numpy as np
from numpy.testing import assert_array_equal
from lightkurve import search_lightcurve
from lightkurve.io.cdips import read_cdips_lightcurve
from lightkurve.io.detect import detect_filetype
TEST_TIC_ID = 104669918
TEST_FIT_URL = "https://mast.stsci.edu/api/... | 2,117 | 33.16129 | 182 | py |
lightkurve | lightkurve-main/tests/io/test_tglc.py | import numpy as np
import pytest
from astropy.io import fits
from numpy.testing import assert_array_equal
from lightkurve import search_lightcurve
from lightkurve.io.detect import detect_filetype
from lightkurve.io.tglc import read_tglc_lightcurve
@pytest.mark.remote_data
def test_tglc():
"""Can we read in TGLC ... | 1,499 | 37.461538 | 191 | py |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.