ascl_id stringclasses 752
values | repo_url stringclasses 737
values | file_path stringlengths 4 194 | content large_stringlengths 1 1M | language stringclasses 29
values | license_type stringclasses 24
values | size int64 1 1M |
|---|---|---|---|---|---|---|
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | src/Parallel_Framework/reports/read_4dc.pro | PRO read_4d, file,data
OPENU, 13,file, /f77_unformatted
n1 = 0L
n2 = 0L
n3 = 0L
n4 = 0L
readu,13, n1
readu,13, n2
readu,13, n3
readu,13, n4
data = dcomplexarr(n1,n2,n3,n4)
readu,13, data
close, 13
END
| IDL | Unknown | 214 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | src/Parallel_Framework/reports/assemble_cube.pro | spawn, 'ls workspace/*initial', ifiles
ni = N_ELEMENTS(ifles)
cube = dblarr(64,100,32,1)
for i = 0, ni -1 DO BEGIN
read_4d,dat,ifiles[i], lims = lims
rstart = lims.rstart
rend = lims.rend
tstart = lims.tstart
tend = lims.tend
cube[*,istart:iend,tstart:tend,0] = dat
endfor
end
| IDL | Unknown | 284 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | src/Parallel_Framework/reports/read_sr.pro | PRO read_sr, file,res
OPENU, 13,file, /f77_unformatted
np = 0L
readu,13, np
sc = lonarr(np)
sd = lonarr(np)
rc = lonarr(np)
rd = lonarr(np)
readu,13, sc
readu,13, sd
readu,13, rc
readu,13, rd
close, 13
res = {np:np, scount:sc,sdisp:sd,rcount:rc,rdisp:rd}
END
| IDL | Unknown | 274 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | src/Test_Suite/TestSuite.F90 | !
! Copyright (C) 2018 by the authors of the RAYLEIGH code.
!
! This file is part of RAYLEIGH.
!
! RAYLEIGH is free software; you can redistribute it and/or modify
! it under the terms of the GNU General Public License as published by
! the Free Software Foundation; either version 3, or (at your option)
! any lat... | Fortran | Unknown | 1,490 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | src/Test_Suite/Test_Cheby.F90 | !
! Copyright (C) 2018 by the authors of the RAYLEIGH code.
!
! This file is part of RAYLEIGH.
!
! RAYLEIGH is free software; you can redistribute it and/or modify
! it under the terms of the GNU General Public License as published by
! the Free Software Foundation; either version 3, or (at your option)
! any lat... | Fortran | Unknown | 13,793 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | src/Test_Suite/Test_SHT.F90 | !
! Copyright (C) 2018 by the authors of the RAYLEIGH code.
!
! This file is part of RAYLEIGH.
!
! RAYLEIGH is free software; you can redistribute it and/or modify
! it under the terms of the GNU General Public License as published by
! the Free Software Foundation; either version 3, or (at your option)
! any lat... | Fortran | Unknown | 22,972 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | job_scripts/NASA_Pleiades/pleiades_script.sh | #PBS -S /bin/bash
#PBS -q long # 'long' queue allows jobs up to 5 days (use 'normal' for 8 hours or less).
#PBS -j oe
#PBS -W group_list=s1234 # account number
#PBS -m e
#PBS -N nrho5_ff_5 # job name
#PBS -l walltime=120:00:00 # run for 120 hours
#PBS -l select=74:ncpus=28:mpiprocs=28:model=... | Shell | Unknown | 2,320 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | job_scripts/TACC_Stampede3/stampede3_jobscript.sh | #!/bin/bash
#SBATCH -J geodynamo-test # Job name
#SBATCH -o log.o%j # Name of stdout output file
#SBATCH -e error.e%j # Name of stderr error file
#SBATCH -p skx-dev # Queue (partition) name; skx-dev for testing; skx, icx, or spr for production.
#SBATCH -N 1 # Total # of nodes. 1-4 f... | Shell | Unknown | 964 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | .github/dependabot.yml | # Set update schedule for GitHub Actions
version: 2
updates:
- package-ecosystem: "github-actions"
directory: "/"
schedule:
# Check for updates to GitHub Actions every week
interval: "weekly"
| YAML | Unknown | 216 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | .github/workflows/main.yml | name: continuous-integration
on: pull_request
concurrency:
group: ${{ github.actor }}-${{ github.ref }}
cancel-in-progress: true
env:
OMPI_MCA_btl_base_warn_component_unused: 0
OMPI_MCA_mpi_yield_when_idle: 1
OMPI_MCA_rmaps_base_oversubscribe: 1
OMPI_ALLOW_RUN_AS_ROOT: 1
OMPI_ALLOW_RUN_AS_ROOT_CONFIRM:... | YAML | Unknown | 4,357 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | .github/workflows/docker.yml | name: github-docker
on:
push:
branches:
- 'main'
release:
types: [created]
concurrency:
group: docker-build
cancel-in-progress: true
permissions:
contents: read
packages: write
jobs:
build-docker:
runs-on: ubuntu-latest
if: github.repository == 'geodynamics/rayleigh'
steps:... | YAML | Unknown | 3,100 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | .github/workflows/black.yml | name: Lint
on: [push, pull_request]
jobs:
lint:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: psf/black@stable
with:
src: "./post_processing/rayleigh.py"
| YAML | Unknown | 216 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | spack-repo/repo.yaml | repo:
namespace: rayleigh
| YAML | Unknown | 28 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | spack-repo/packages/rayleigh/package.py | # Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
from spack import *
class Rayleigh(MakefilePackage):
__doc__ = 'Rayleigh is a 3-D convection code designed ... | Python | Unknown | 2,550 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | docker/rayleigh-tacc/Readme.md | This is a docker container that can be used to run Rayleigh on the set of TACC
supercomputers, in particular Frontera and Stampede3, without having to manually
compile the code.
Steps to use this container on Stampede3/Frontera are described on
https://rayleigh-documentation.readthedocs.io/en/latest/doc/source/User_Gu... | Markdown | Unknown | 346 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | docker/rayleigh-tacc/build.sh | #!/bin/bash
# This script generates a docker image from the latest Rayleigh development version.
# It requires a docker installation on the local machine, and the ability to
# communicate with the docker daemon without root user privileges (see the docker
# webpage for an explanation).
# Note: This container is build ... | Shell | Unknown | 546 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | docker/rayleigh/README.md | This container hosts a built version of Rayleigh.
| Markdown | Unknown | 50 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | docker/rayleigh-devel-jammy/entrypoint.sh | #!/bin/sh
export HOME=/work
cd "$HOME"
if [ -n "$HOSTGID" -a -n "$HOSTUSER" -a -n "$HOSTUID" ]
then
# only create user if all options are provided
# This only creates the group if a group with that GID does not already exist.
getent group $HOSTGID > /dev/null || groupadd -g $HOSTGID $HOSTUSER
useradd -u $HOSTUID... | Shell | Unknown | 1,094 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | docker/rayleigh-buildenv-jammy/README.md | Build environment for Rayleigh using the Ubuntu Jammy Docker container.
| Markdown | Unknown | 72 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | tests/chi_scalar/test_output.py | #!/usr/bin/env python3
from rayleigh_diagnostics import G_Avgs, build_file_list
import numpy as np
import os
import sys
vals = {
"kesgav" : 401,
"Tsgav" : 501,
"Tpsgav" : 503,
"Tmsgav" : 505,
"Tdrsgav" : 507,
"Tpdrsgav" : 509,
"... | Python | Unknown | 3,109 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | tests/chi_scalar/run_test.sh | #!/usr/bin/env bash
cd tests/chi_scalar
#cd bench
#mpirun -np 4 $RAYLEIGH_TEST_MPI_PARAMS ../../../bin/rayleigh.dbg
#cd ..
# generate initial conditions
../../pre_processing/rayleigh_spectral_input.py -ar 0.35 -sd 1.0 -nt 64 -nr 48 -o bench_t_init \
-e 'import numpy as np; x = 2*radius - rmin - rmax; rmax*rmin/ra... | Shell | Unknown | 970 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | tests/coupled_bcs/test_output.py | #!/usr/bin/env python3
from rayleigh_diagnostics import Shell_Slices, main_input
import numpy as np
import sys, os
error = False
def test_bcs(case):
"""
For a given case check if the values contained in the shell slices match the expected values based on the coefficients in
main_input
"""
error = False
... | Python | Unknown | 3,146 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | tests/coupled_bcs/run_test.sh | #!/usr/bin/env bash
cd tests/coupled_bcs
# we run a const case, where the bcs on the field that everything is coupled to are just constant
cd const
PYTHONPATH=../../../pre_processing:$PYTHONPATH python3 generate_input.py
mpirun -np 4 $RAYLEIGH_TEST_MPI_PARAMS ../../../bin/rayleigh.dbg
cd ..
# after running, we test ... | Shell | Unknown | 432 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | tests/coupled_bcs/const/generate_input.py | ### Use rayleigh_spectral_input.py to generate generic input.
from rayleigh_spectral_input import *
rmin = 0.5; rmax = 1.0
si = SpectralInput(n_theta=1,n_r=48)
si.transform_from_rtp_function(lambda radius: 2.0 - (rmax/radius)*(radius - rmin)/(rmax - rmin), rmin=rmin, rmax=rmax)
si.write('radial_prof_init')
si = Spe... | Python | Unknown | 390 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | tests/custom_reference/run_test.sh | #!/usr/bin/env bash
cd tests/custom_reference
# Run a test where the full reference state is specified
cd basic
cp ../../../post_processing/reference_tools.py .
python3 gen_case0.py
mpirun -np 4 ../../../bin/rayleigh.dbg
# Augment the usual case 0 with heating and higher Ra
cd ..
cd augment
cp ../../../post_process... | Shell | Unknown | 403 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | tests/custom_reference/augment/augment.py | import reference_tools as rt
import numpy
# Grid Parameters
nr = 128 # Number of radial points
#aspect ratio
#beta=ri/ro
beta = 0.35e0
# shell depth
d=1.e0
#outer radial boundary
ro=d/(1-beta)
#inner radial boundary
ri=beta*ro
#radial grid
radius=numpy.linspace(ri,ro,nr)
# Initialize an equation_coeffi... | Python | Unknown | 1,071 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | tests/custom_reference/basic/gen_case0.py | import reference_tools as rt
import numpy
# Grid Parameters
nr = 128 # Number of radial points
#aspect ratio
#beta=ri/ro
beta = 0.35e0
# shell depth
d=1.e0
#outer radial boundary
ro=d/(1-beta)
#inner radial boundary
ri=beta*ro
#radial grid
radius=numpy.linspace(ri,ro,nr)
# Initialize an equation_coeffi... | Python | Unknown | 1,711 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | tests/generic_input/run_test.sh | #!/usr/bin/env bash
cd tests/generic_input
# first we run the "base" case, this just sets up and runs Rayleigh for one time-step with hard-coded initial conditions
# for the Christensen et al., 2001 benchmark case 1
cd base
mpirun -np 4 $RAYLEIGH_TEST_MPI_PARAMS ../../../bin/rayleigh.dbg
../../../post_processing/con... | Shell | Unknown | 2,966 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | tests/generic_input/test_output.py | #!/usr/bin/env python3
from rayleigh_diagnostics import Spherical_3D_multi, Shell_Slices
from rayleigh_spectral_input import SpectralInput, radial_extents
import numpy as np
import sys
import vtk
error = False
# test using the raw data imported from the output files
base = Spherical_3D_multi('00000001_0501', path='b... | Python | Unknown | 5,494 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | tests/generic_input/script/generate_magnetic_input.py | ### Use rayleigh_spectral_input.py to generate generic input.
### Christensen Benchmark case 1.
from rayleigh_spectral_input import *
ar = 0.35; sd=1.0
rmin, rmax = radial_extents(aspect_ratio=ar, shell_depth=sd)
### Poloidal magnetic potential BC.
si_BC = SpectralInput(n_theta=64,n_r=48)
def func_BC(theta,phi,radiu... | Python | Unknown | 1,393 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | tests/generic_input/radial_sparse/generate_input.py | ### Use rayleigh_spectral_input.py to generate generic input.
### Christensen Benchmark case 1.
from rayleigh_spectral_input import *
rmin = 0.5; rmax = 1.0
si = SpectralInput(n_theta=1,n_r=48)
si.transform_from_rtp_function(lambda radius: 1.0 - (rmax/radius)*(radius - rmin)/(rmax - rmin), rmin=rmin, rmax=rmax)
si.w... | Python | Unknown | 342 |
[ascl:2401.002] | https://github.com/geodynamics/Rayleigh | tests/generic_input/radial_dense/generate_input.py | ### Use rayleigh_spectral_input.py to generate generic input.
### Christensen Benchmark case 1.
from rayleigh_spectral_input import *
rmin = 0.5; rmax = 1.0
si = SpectralInput(n_theta=64,n_r=48)
si.transform_from_rtp_function(lambda radius: 1.0 - (rmax/radius)*(radius - rmin)/(rmax - rmin), rmin=rmin, rmax=rmax)
si.... | Python | Unknown | 343 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | DESCRIPTION.rst | A parallel nested sampler
(C) 2023-2025 Walter Del Pozzo, John Veitch
| reStructuredText | MIT | 76 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | README.rst | raynest
======
Parallel nested sampling in python
----
© 2015-2021 Walter Del Pozzo, John Veitch
.. image:: https://img.shields.io/badge/license-MIT-blue.svg
:alt: MIT license
:target: https://github.com/wdpozzo/raynest/blob/master/LICENSE
walter.delpozzo@ligo.org,
john.veitch@ligo.org
raynest is a python m... | reStructuredText | MIT | 899 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | INSTALL.txt |
The simplest way to install cpnest is via pip
pip install raynest
It is also available from conda-forge
conda install -c conda-forge cpnest
--
Install this package from source using setuptools:
python3 setup.py install
Tests can be run with:
python3 setup.py test
For developers, local install with:
pyth... | Text | MIT | 438 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | setup.py | import os
import platform
import numpy
from setuptools import setup, Extension, find_packages
from Cython.Build import cythonize
WINDOWS = platform.system().lower() == "windows"
# set extension
libraries = [] if WINDOWS else ["m"]
ext_modules = [Extension("raynest.parameter",
sources=[os.path... | Python | MIT | 1,035 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | pyproject.toml | [build-system]
requires = [
"setuptools>=61.0",
"wheel",
"cython",
"numpy"
]
build-backend = "setuptools.build_meta"
[project]
name = "raynest"
description = "raynest: Parallel nested sampling based on ray"
version = "1.1.2"
requires-python = ">=3.9"
readme = {file = "README.rst", content-type = "text/plain"}
... | TOML | MIT | 780 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | examples/ackley.py | import unittest
import numpy as np
import raynest.model
from numpy import log
class AckleyModel(raynest.model.Model):
"""
Ackley problem from https://en.wikipedia.org/wiki/Test_functions_for_optimization
"""
names=['x','y']
bounds=[[-5,5],[-5,5]]
data = None
def log_likelihood(self,x):
... | Python | MIT | 1,062 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | examples/gaussianmixture.py | import warnings
import numpy as np
import raynest.model
from scipy.stats import norm
from scipy.special import logsumexp
def hypertriangulate(x, bounds=(0, 1)):
"""
Transform a vector of numbers from the hypercube to the hypertriangle.
The hypercube is the space the samplers usually work in; the
comp... | Python | MIT | 10,942 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | examples/profiling.py | import pstats, cProfile
s = pstats.Stats("prof_sampler.prof")
s.strip_dirs().sort_stats("time").print_stats()
s = pstats.Stats("prof_nested_sampling.prof")
s.strip_dirs().sort_stats("cumulative").print_stats()
| Python | MIT | 212 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | examples/test_50d.py | import unittest
import numpy as np
import raynest.model
from scipy import stats
class GaussianModel(raynest.model.Model):
"""
An n-dimensional gaussian
"""
def __init__(self,dim=50):
self.distr = stats.norm(loc=0,scale=1.0)
self.dim=dim
self.names=['{0}'.format(i) for i in range... | Python | MIT | 2,259 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | examples/diagnose_trajectory.py | import numpy as np
import matplotlib.cm as cm
import matplotlib.pyplot as plt
import sys, os
np.seterr(all='raise')
def log_likelihood(x):
return np.sum([-0.5*x[n]**2-0.5*np.log(2.0*np.pi) for n in range(x.shape[0])])
mode = sys.argv[1]
if mode == 'delete':
allfiles = os.listdir('.')
toremove = [a for a ... | Python | MIT | 1,089 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | examples/rosenbrock.py | #!/bin/usr/env python
import numpy as np
import raynest.model
class RosenbrockModel(raynest.model.Model):
"""
The n-dimensional Rosenbrock function
See: https://arxiv.org/pdf/1903.09556.pdf
"""
def __init__(self, ndims=2):
self.ndims = ndims
self.names = ['x' + str(i) for i in ran... | Python | MIT | 1,260 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | examples/burst.py | import numpy as np
import raynest.model
def sine_gaussian(x,t):
e = (t-x['t0'])/x['tau']
return x['A']*np.exp(-e**2)*np.cos(2*np.pi*x['f']*t + x['phi'])
class BurstModel(raynest.model.Model):
"""
A Burst like search model
"""
def __init__(self, time, data, sigma = 1.0):
self.time = t... | Python | MIT | 2,057 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | examples/eggbox.py | import unittest
import numpy as np
import raynest.model
class EggboxModel(raynest.model.Model):
"""
Eggbox problem from https://arxiv.org/pdf/0809.3437v1.pdf
"""
names=['1','2','3','4','5']
bounds=[[0,10.0*np.pi],[0,10.0*np.pi],[0,10.0*np.pi],[0,10.0*np.pi],[0,10.0*np.pi]]
data = None
... | Python | MIT | 729 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | examples/memory_footprint.py | from __future__ import print_function
from sys import getsizeof, stderr
from itertools import chain
from collections import deque
try:
from reprlib import repr
except ImportError:
pass
def total_size(o, handlers={}, verbose=False):
""" Returns the approximate memory footprint an object and all of its conte... | Python | MIT | 2,293 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | examples/eggbox_profile.py | import unittest
import numpy as np
import raynest.model
"""
Once run this example, use
pyprof2calltree -i <profile report file> -k
for detail call tree information
"""
from eggbox import EggboxModel
if __name__=='__main__':
work=raynest.raynest(EggboxModel(),verbose=2,nthreads=4,nlive=1000,maxmcmc=5000)
wo... | Python | MIT | 365 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | docs/index.rst | .. CPNest documentation master file, created by
sphinx-quickstart on Thu Dec 7 13:57:03 2017.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
.. toctree::
:maxdepth: 2
:caption: Contents:
Welcome to CPNest's documentation!
===============... | reStructuredText | MIT | 4,077 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | docs/conf.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# CPNest documentation build configuration file, created by
# sphinx-quickstart on Thu Dec 7 13:57:03 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# aut... | Python | MIT | 5,836 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/model.py | from abc import ABCMeta,abstractmethod,abstractproperty
from numpy import inf
import numpy as np
from .parameter import LivePoint
import logging
LOGGER = logging.getLogger('raynest.model') # <--- for module-level logging
class Model(object):
"""
Base class for user's model. User should subclass this
and... | Python | MIT | 4,886 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/proposal.py | from __future__ import division
from functools import reduce
import numpy as np
from math import log,sqrt,fabs,exp
from abc import ABCMeta,abstractmethod
from scipy.stats import multivariate_normal
from scipy.special import logsumexp
from .nest2pos import acl
import ray
def update_mean_covariance(ensemble):
"""
... | Python | MIT | 30,702 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/NestedSampling.py | from __future__ import division, print_function
from asyncio import tasks
import sys
import os
import pickle
import time
import logging
import bisect
import numpy as np
from numpy import logaddexp
from numpy import inf
from scipy.stats import kstest
from math import isnan
from . import nest2pos
from .nest2pos import lo... | Python | MIT | 21,565 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/plot.py | import os
import matplotlib as mpl
from matplotlib import pyplot as plt
import numpy as np
def init_plotting():
"""
utility function to set up the
plotting environment
"""
plt.rcParams['figure.figsize'] = (3.4, 3.4)
plt.rcParams['font.size'] = 11
plt.rcParams['font.family'] = 'DejaVu Sans'
... | Python | MIT | 4,826 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/sampler.py | from __future__ import division
import sys
import os
import logging
import numpy as np
from math import log
from collections import deque
from . import parameter
from .proposal import DefaultProposalCycle, EnsembleProposal, update_mean_covariance
import numpy.lib.recfunctions as rfn
import array
from .nest2pos import ... | Python | MIT | 14,049 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/utils.py | import os
import gc
import logging
import psutil
# Default formats and level names
FORMATTER = logging.Formatter(
'%(asctime)s - %(name)-38s: %(message)s',
datefmt='%Y-%m-%d, %H:%M:%S'
)
LEVELS = ['CRITICAL', 'WARNING', 'INFO', 'DEBUG']
LOGGER = logging.getLogger('raynest.utils')
class _Handler(logging.Handl... | Python | MIT | 3,178 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/raynest.py | # coding: utf-8
import numpy as np
import os
import sys
import signal
import logging
import dill
from .utils import LogFile
# module logger takes name according to its path
LOGGER = logging.getLogger('raynest.raynest')
import ray
from ray.util import ActorPool
from ray.util.scheduling_strategies import PlacementGrou... | Python | MIT | 21,721 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/__init__.py | import logging
from .utils import StreamHandler, LEVELS
# Configure base logger for the raynest package - inherited by all loggers with
# names prefixed by 'raynest'
logger = logging.getLogger('raynest')
logger.setLevel(LEVELS[-1]) # maximum verbosity recorded to base logger
logger.addHandler(logging.NullHandler())
c... | Python | MIT | 1,048 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/figaro_gradient.py | try:
from figaro.mixture import DPGMM
from figaro._likelihood import log_norm
except:
print("FIGARO not available! Hamiltonian Monte Carlo sampling not supported!")
pass
import numpy as np
from tqdm import tqdm
from scipy.stats import multivariate_normal as mn
class ADPGMM(DPGMM):
def __init__(sel... | Python | MIT | 1,878 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/nest2pos.py | import logging
import numpy as np
from numpy import logaddexp, vstack
from numpy.random import uniform
from functools import reduce
from scipy.signal import correlate
# if not logging.Logger.manager.loggerDict:
# LOGGER = logging.getLogger('raynest.nest2pos')
# else:
# LOGGER = logging.getLogger('raynest.raynes... | Python | MIT | 8,031 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/tests/test_gaussian.py | import unittest
import numpy as np
import raynest.model
class GaussianModel(raynest.model.Model):
"""
A simple gaussian model with parameters mean and sigma
"""
names=['mean','sigma']
bounds=[[-5,5],[0.05,1]]
data = np.array([x for x in np.random.normal(0.5,0.5,size=10)])
analyticZ = np.log... | Python | MIT | 1,183 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/tests/test_half_gaussian.py | import sys
import unittest
import numpy as np
from scipy import integrate,stats
import raynest
import raynest.model
import matplotlib as mpl
mpl.use('Agg')
from matplotlib import pyplot as plt
class HalfGaussianModel(raynest.model.Model):
"""
A simple gaussian model with parameters mean and sigma
"""
d... | Python | MIT | 2,122 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/tests/test_ring_slice.py | import unittest
import numpy as np
import raynest.model
class RingModel(raynest.model.Model):
"""
A circular ring in parameter space
logZ ~ -2.31836
"""
names=['x','y']
bounds=[[-2,2],[-2,2]]
data = None
analytic_log_Z = -2.31836
@staticmethod
def log_likelihood(x):
retu... | Python | MIT | 1,526 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/tests/test_verbosity.py | import unittest
import numpy as np
import raynest.model
class GaussianModel(raynest.model.Model):
"""
A simple gaussian model with parameters mean and sigma
"""
names=['mean','sigma']
bounds=[[-5,5],[0.05,1]]
data = np.array([x for x in np.random.normal(0.5,0.5,size=10)])
analyticZ = np.log... | Python | MIT | 1,299 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/tests/test_2d_slice.py | import unittest
import numpy as np
import raynest.model
class GaussianModel(raynest.model.Model):
"""
A simple 2 dimensional gaussian
"""
def __init__(self):
pass
names=['x','y']
bounds=[[-10,10],[-10,10]]
analytic_log_Z=0.0 - np.log(bounds[0][1]-bounds[0][0]) - np.log(bounds[1][1]-... | Python | MIT | 1,334 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/tests/test_2d_hmc.py | import unittest
import numpy as np
import raynest.model
class GaussianModel(raynest.model.Model):
"""
A simple 2 dimensional gaussian
"""
def __init__(self):
pass
names=['x','y']
bounds=[[-10,10],[-10,10]]
analytic_log_Z=0.0 - np.log(bounds[0][1]-bounds[0][0]) - np.log(bounds[1][1]-... | Python | MIT | 1,439 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/tests/test_ring.py | import unittest
import numpy as np
import raynest.model
class RingModel(raynest.model.Model):
"""
A circular ring in parameter space
logZ ~ -2.31836
"""
names=['x','y']
bounds=[[-2,2],[-2,2]]
data = None
analytic_log_Z = -2.31836
@staticmethod
def log_likelihood(x):
retu... | Python | MIT | 1,537 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/tests/test_1d.py | import unittest
import numpy as np
from scipy import integrate,stats
import raynest
import raynest.model
import matplotlib as mpl
mpl.use('Agg')
from matplotlib import pyplot as plt
class GaussianModel(raynest.model.Model):
"""
A simple gaussian model with parameters mean and sigma
"""
def __init__(sel... | Python | MIT | 2,354 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/tests/test_2d.py | import unittest
import numpy as np
import raynest.model
class GaussianModel(raynest.model.Model):
"""
A simple 2 dimensional gaussian
"""
def __init__(self):
pass
names=['x','y']
bounds=[[-5,5],[-5,5]]
analytic_log_Z=0.0 - np.log(bounds[0][1]-bounds[0][0]) - np.log(bounds[1][1]-boun... | Python | MIT | 1,508 |
[ascl:2405.003] | https://github.com/wdpozzo/raynest | raynest/tests/__init__.py | __all__=['test_1d','test_2d','test_gaussian']
| Python | MIT | 46 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | README.md | # Creating updated, scientifically-calibrated mosaics for the RC3 Catalogue
The Third Reference Catalogue of Bright Galaxies (RC3) is a reasonably complete listing of 23,010 large, bright galaxies. Using the latest Sloan Digital Sky Survey’s Data Release 10 (SDSS DR10) data, we provide color composite images and scient... | Markdown | null | 3,052 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | database/database.py | import sqlite3
def create_table(db_name,table_name,sql): #sql statement that you want to take
with sqlite3.connect(db_name) as db: #open db and do stuff within function. If crashes then connection automatically closed.
cursor = db.cursor() #give latest info about navigate around database
cursor.exec... | Python | null | 1,421 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | database/rc3_database.py | # Remember to remove rc3.db everytime you rerun this. Database files (.db) can only be instantiated once.
import sqlite3
conn = sqlite3.connect("rc3.db")
c = conn.cursor()
def tableCreate():
#this can only be done once
# create table and specify column, primary key is auto incremnting ID number
c.execute("CREATE TAB... | Python | null | 4,776 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | script/list_rc3_in_sdss.sh | for i in */
do
if [ -d $i/sdss/ ]; then
echo $i
echo $i | cut -f1 -d'/'>> rc3_in_sdss.txt
fi
done
| Shell | null | 117 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | script/rename.py | # Script for renaming all the data poduct (FITS and TIFF)
import glob
import os
# print [f for f in os.listdir('.') if os.path.isfile(f)]
for i in os.walk('.').next()[1]:
print ("Working on PGC {} ".format(i))
os.chdir("{}/sdss".format(i))
#directory name is pgc number
try:
os.rename(glob.glob... | Python | null | 1,351 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | script/SCcount.py | import numpy as np
ra= []
dec = []
radius=[]
pgc=[]
rc3= {}
with open("rc3_ra_dec_diameter_pgc.txt",'r') as f:
for line in f:
a = str(line)[0]
if a[0] =="@":
start=True
continue
if (start):
rai = float(line.split()[0])
deci=float(line.split()[1])
radi=float(line.split()[2])/2.
ra.append(rai)
... | Python | null | 931 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | script/readfile.py | #Run in Python2
output = open("rc3_ra_dec_only(Final).txt", "w")
#output.write("ra |")
#output.write("dec |")
#output.write("radius \n")
for line in file('rc3.txt'):
x = float(line[0:2])
y = float(line[2:4])
z = float(line[4:8])
sign = line[9]
decval = float(line[10:12])... | Python | null | 1,088 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | script/ipython_log.py | # IPython log file
get_ipython().magic(u'logon ')
get_ipython().magic(u'logstart ')
ra = []
for i in rc3.values():
ra.append(i[1])
ra
for i in rc3.values():
ra.append(i[1])
a = [1,2]
a.indexOf()
a.indexOf(2)
a.index(2)
| Python | null | 238 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | script/list_pgc.sh | for i in RUN*
do
echo "Working on $i"
cd $i
rm -r r/
ls -d */ | cut -f1 -d'/' >> ../pgc_done.txt
cd ..
done
| Shell | null | 132 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | script/thumbnail_process.py | #Keep only BEST images and convert all TIFF color images to .gif
import os
import glob
os.chdir("Mosaic")
bests = glob.glob("*_BEST.tiff")
for i in bests:
print (i)
os.system("gm convert -resize 128x128\! {} {}.gif".format(i,i[:-5]))
os.system("rm *.tiff")
os.chdir("..")
os.rename("Mosaic", "img")
| Python | null | 302 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | script/survey_merge.py | '''
This script merges the data product output
[pgc_number]-->[files] from each survey
to the general catalog format
[pgc_number]-->dss,sdss,2mass..etc-->[files]
'''
import os
import glob
import shutil
ADDITIONAL_NUM_DSS_COUNT = 0
# for i in os.listdir("dss_data/"):
# eliminate weird files like .DSStore and other php a... | Python | null | 1,907 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | script/other_rc3.py | import sqlcl
import numpy as np
with open("rc3_ra_dec_diameter_pgc.txt",'r') as f:
for line in f:
ra = float(line.split()[0])
dec = float(line.split()[1])
radius = float(line.split()[2])/2. #radius = diameter/2'
margin = 3*radius
pgc=str(line.split()[3]).replace(' ', '')
... | Python | null | 1,818 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | script/nersc/qsub_everything.sh | for i in $( ls -d RUN* );do qsub $i/run.pbs ;done
| Shell | null | 50 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | script/nersc/insert_start.py | import sys
print sys.argv
n=int(sys.argv[1])
linenumber=int(sys.argv[2])
print n
print linenumber
f = open("rc3_ra_dec_diameter_pgc.txt".format(n),'r')
contents = f.readlines()
contents.insert(linenumber, "@ \n")
contents = "".join(contents)
#print contents
f.close()
f = open("rc3_ra_dec_diameter_pgc.txt".format(n),'... | Python | null | 352 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | script/nersc/getserialscript.py | import sys
#nproc is not npric here, it is a dummy for just the number of run counts
for arg in sys.argv:
nproc=arg
nproc = int(nproc)
#print "#PBS -q thruput"
print "#PBS -q serial"
print "#PBS -l walltime=48:00:00"
print "#PBS -N RC3_RUN{}".format(nproc)
print "#PBS -e test.$PBS_JOBID.err"
print "#PBS -o test.$P... | Python | null | 592 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | script/nersc/serial_submit.sh | source /project/projectdirs/cmb/modules/hpcports_NERSC.sh
hpcports shared_gnu
module load astromatic-hpcp
module load python
line=2612 #starting from line 2612
step=730 #Estimated number of lines that the pipeline goes thorugh in 48 hour runs (!= to # of galaxy mosaiced!)
for (( i=1; i <=28; i++ ))
do
line=$[$line... | Shell | null | 699 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | pipeline/mosaic.sh | mImgtbl projdir images.tbl
mOverlaps images.tbl diffs.tbl
mDiffExec -p projdir diffs.tbl template.hdr diffdir
mFitExec diffs.tbl fits.tbl diffdir
mBgModel images.tbl fits.tbl corrections.tbl
mBgExec -p projdir images.tbl corrections.tbl corrdir
mAdd -p corrdir images.tbl template.hdr mosaic.fits
mJPEG -gray mosaic.fits... | Shell | null | 356 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | pipeline/sdss.py | from survey import *
class SDSS(Survey):
def __init__(self):
self.name='SDSS'
self.bands=['u','g','r','i','z']
self.color_bands=['g','r','i']
self.best_band='r'
self.data_server=Survey._initServer(self)
self.pixel_scale = 0.396 #(arcsec/pix)
# Mosaic Program ... | Python | null | 677 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | pipeline/bulk_run_dss.py | from rc3Catalog import RC3Catalog
from dss import DSS
from rc3 import RC3
rc3cat = RC3Catalog()
dss = DSS()
rc3cat.mosaicAll(dss) | Python | null | 130 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | pipeline/dss.py | # Survey Class for the Digitized Sky Survey (Digitized Palomar Observatory Sky Survey)
from survey import *
class DSS(Survey):
def __init__(self):
self.name = 'DSS'
self.bands=['1b','1r','2b','2r','2ir']
self.color_bands=['2b','2r','2ir']
self.best_band ='2r'
self.data_server... | Python | null | 1,088 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | pipeline/catalog.py |
from abc import ABCMeta , abstractmethod
class Catalog(object):
'''
Class for Catalog objects
'''
__metaclass__= ABCMeta
def __init__(self):
self.name= 'Catalog'
self.frame= 'fk5'
self.equinox = 'J2000'
self.allObj=_initAllObj()
@abstractmethod
def _initAllObj(self):
'''
Create a list of all obje... | Python | null | 667 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | pipeline/rc3.py | #!PATH=/usr/bin/:/data/small/des/montage/montage/Montage_v3.3/bin/:/bin
from rc3Catalog import RC3Catalog
from sdss import SDSS
from twoMass import TwoMass
import montage_wrapper as montage
from astropy.io import fits as pyfits
import os
import shutil
from math import trunc
import glob
import sqlcl
import sys
import f... | Python | null | 24,293 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | pipeline/bulk_run.py | from rc3Catalog import RC3Catalog
from sdss import SDSS
from rc3 import RC3
rc3cat = RC3Catalog()
sloan = SDSS()
rc3cat.mosaicAll(sloan)
| Python | null | 138 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | pipeline/survey.py | from dssServer import DSSServer
from gator import Gator
from skyserver import SkyServer
from server import Server
class Survey(object):
def __init__(self):
self.name=name
# Preset defaults for the specific survey
self.bands = []
self.color_bands= []
self.best_band='@'
... | Python | null | 1,025 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | pipeline/skyserver.py | # Class for interacting with SDSS's SkyServer
from server import Server
import sqlcl
import abc
import os
import time
DEBUG = False
class SkyServer(Server):
#Default constructor
def __init__ (self):
if (DEBUG):print("SkyServer constructor")
super(SkyServer,self).__init__()
self.name = 'SkyServe... | Python | null | 2,941 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | pipeline/server.py | '''
The Server object is an abstract class for accessing raw data from survey and feeds it into program in the appropraite format.
'''
import astropy.units as u
from astroquery.vizier import *
#from astropy.coordinates import SkyCoord
from astropy.coordinates import FK5
from astropy import coordinates
from abc import ... | Python | null | 2,827 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | pipeline/rc3Catalog.py | import os
from catalog import Catalog
class RC3Catalog(Catalog):
'''
Class for RC3 Catalog objects
'''
def __init__(self):
self.name= 'RC3 Catalog'
self.frame= 'fk5'
self.equinox = 'J2000'
self.allObj=self._initAllObj()
def _initAllObj(self):
'''
Create a list of all objects inside the catalog
'''
... | Python | null | 3,025 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | pipeline/bulk_run_twoMass.py | from rc3Catalog import RC3Catalog
from twoMass import TwoMass
from rc3 import RC3
rc3cat = RC3Catalog()
tm = TwoMass()
rc3cat.mosaicAll(tm) | Python | null | 140 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | pipeline/__init__.py | Python | null | 1 | |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | pipeline/gator.py | # Class for interacting with IPAC's Gator API
from astropy import *
from astroquery.vizier import *
from astroquery.irsa import Irsa
import astropy.units as u
from astropy import coordinates
from astropy.coordinates import FK5
#from astropy.coordinates import SkyCoord
from server import Server
import abc
import re
i... | Python | null | 3,775 |
[ascl:1411.006] | https://github.com/ProfessorBrunner/rc3-pipeline | pipeline/catalogSubset.txt | ID PGC_number ra dec radius new_ra new_dec new_radius in_SDSS_footprint clean error
9295 28630 148.889583333 69.0666666667 0.22951905907 148.888495 69.0654192 0.0897604255636 1 1 0
11134 34697 170.067916667 13.5894444444 0.123259032594 170.0670631 13.59372 0.0872663485941 1 1 0
12812 39346 184.180833333 69.4655555556 0... | Text | null | 1,509 |
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