diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 00000000..188c487d --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,65 @@ +name: ExoCTK CI + +on: [push, pull_request] + +jobs: + + ExoCTK-CI: + + name: Python - ${{ matrix.python-version }} + runs-on: ${{ matrix.os }} + strategy: + max-parallel: 5 + matrix: + os: [ubuntu-latest, macos-latest] + python-version: [3.7, 3.8, 3.9] + + steps: + - uses: actions/checkout@v2 + + - uses: conda-incubator/setup-miniconda@v2 + with: + activate-environment: exoctk-${{ matrix.python-version }} + + - name: Build exoctk conda environment and run tests + shell: bash -l {0} + run: | + + echo "Setting useful environment variables:" + echo " " + export PYTHONVERSION=${{ matrix.python-version }} + echo "PYTHONVERSION: $PYTHONVERSION" + export EXOCTK_DATA=$RUNNER_WORKSPACE/exoctk/exoctk/data/ + echo $EXOCTK_DATA + + echo " " + echo "Installing exoctk conda environment" + echo " " + cd $RUNNER_WORKSPACE/ + cd exoctk/ + $CONDA/bin/conda env update -f env/environment-${{ matrix.python-version }}.yml -n exoctk-${{ matrix.python-version }} + + echo " " + echo "Installing exoctk package" + echo " " + python setup.py develop + + echo " " + echo "Testing package installation" + echo " " + python -c "import exoctk; print('Version: ' + exoctk.__version__); print('Path: ' + exoctk.__path__[0])" + + # echo " " + # echo "Reinstall numpy to fix numpy.core.multiarray error" + # echo " " + pip install -U numpy + + echo " " + echo "The conda environment being used:" + echo " " + $CONDA/bin/conda env export + + echo " " + echo "Running pytests" + echo " " + pytest exoctk/tests/ diff --git a/.pyup.yml b/.pyup.yml index 75357de1..0a8a67c3 100644 --- a/.pyup.yml +++ b/.pyup.yml @@ -13,7 +13,7 @@ pin: True # set the default branch # default: empty, the default branch on GitHub -branch: master +branch: develop # update schedule # default: empty diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index ef6440fe..00000000 --- a/.travis.yml +++ /dev/null @@ -1,35 +0,0 @@ -language: generic - -sudo: false - -cache: - directories: - - $HOME/miniconda3 - -before_cache: - - rm -rf $HOME/miniconda3/pkgs/cache - - rm -rf $HOME/miniconda3/envs/exoctk-3.6 - - rm -rf $HOME/miniconda3/envs/exoctk-3.7 - -os: - - linux - - osx - -env: - - PYTHON_VERSION="3.6" - - PYTHON_VERSION="3.7" - -before_install: - - export PATH="$HOME/miniconda3/bin:$PATH" - - export EXOCTK_DATA="$HOME/exoctk_data/" - - chmod +x ci/install_conda.sh - - chmod +x ci/setup_conda_env.sh - -install: - - ci/install_conda.sh - - ci/setup_conda_env.sh - - python setup.py install - -script: - - export PATH="$HOME/miniconda3/envs/exoctk-$PYTHON_VERSION/bin:$PATH" - - travis_wait 30 pytest \ No newline at end of file diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 00000000..7c931a02 --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,147 @@ +# Changelog + +This file tracks all major changes in each `exoctk` release. + +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), +and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + +## [1.2.0] - 2021-05-10 + +### Added + +- Citation information in the `README` file (see PR #472). +- Contribution guide on the project's wiki (https://github.com/ExoCTK/exoctk/wiki/Git-Workflow). +- Procedures for ExoCTK release (https://github.com/ExoCTK/exoctk/wiki/Release-Procedure). +- Support for installation via PyPI (see PR #385). +- JWST instrument throughputs for limb-darkening calculations (see PR #458). + +### Fixed + +- Dropped support for `python3.6` (see PR #471). +- Installation problem with Python 3.8 (see issue #465 and PR #469). +- Pip & asteval enviornment issues (see PR #468). + +### Changed + +- Missing links to JDox on contamination tool (see PR #433). +- ExoCTK data is now downloaded as-needed for individual tools (see PR #488). + +## [1.1.1] - 2021-05-10 + +### Added + +- Added `CHANGELOG.md` (this file!) to repo + +### Fixed + +- WFC3_IR.G102 filter in LDC + +### Changed + +- Updated readthedocs/JDox links +- `pyup` updates to several packages + +## [1.1.0] - 2020-10-12 + +### Added + +- Added Jupyter notebook for Phase Constraint tool +- Added ACES and ATLAS9 model grids as child classes for Limb Darkening tool + +### Fixed + +- Fixed MIRI trace shape in Contamination and Visibility tool +- Fixed table truncation in Limb Darkening Calculator results table + +## [1.0.0] - 2019-12-31 + +### Added + +- Added Amazon AWS cloud computing support +- Added Contamination and Visibility Tool support for all JWST instruments +- Added Phase Constraint Tool + +## [0.4.0] - 2019-08-09 + +### Added + +- Added tests for atmospheric retrieval code +- Added form validation to Web app with `flask_wtf` +- Added Lightcurve Fitting tool +- Added generic model grid to forward models +- Added `jwst_gtvt` package dependency for Contamination and Visibility tool +- Added planetary parameter support with `exomast` +- Added `platon` support to forward models +- Added dependency support with `pyup` + +### Removed + +- Package data in favor of package data download + +## [0.2.0] - 2018-11-11 + +### Added + +- PEP257 and PEP8 compliance for all tools +- Updated LDC plotting and notebook +- Documentation support with `sphinx-build` + +### Changed + +- Changed `ldc` function to `LDC` class +- Renamed top level directory `exoctk` from `ExoCTK` +- Major `README` updates + +### Removed + +- Built-in filter support removed in favor of `svo_filters` package dependency +- Removed `astropy_helpers` support since it was not helping + +## [0.1.4] - 2017-07-10 + +### Added + +- Added Contmination and Visibility tool +- Added additional filter support to LDC including NIRISS GR700XD and custom filter profile + +## [0.1.3] - 2017-07-07 + +### Added + +- Line Forward Models support with `chimera` + +## [0.1.2] - 2017-06-30 + +### Added + +- Added precomputed pickle file of bandpass throughputs for speedier LDC calculations + +## [0.1.1] - 2017-06-29 + +### Fixed + +- Minor bug fixes to initial release + +## [0.1.0] - 2017-06-28 + +### Added + +- Limb darkening calculator (LDC) +- Forward modeling with exotransmit (PAL) +- Transit observation tools using PandExo (TOT) +- Groups and integrations calculator (TOR) +- Model grid handling +- References tracking +- Jupyter notebooks for LDC, PAL, and TOT modules +- SVO Filter Profile Service for photometric bandpasses + +[1.1.1]: https://github.com/ExoCTK/exoctk/compare/v1.1.0...HEAD +[1.1.0]: https://github.com/ExoCTK/exoctk/compare/v1.0.0...v1.1.0 +[1.0.0]: https://github.com/ExoCTK/exoctk/compare/v0.4.0...v1.0.0 +[0.4.0]: https://github.com/ExoCTK/exoctk/compare/v0.2.0...v0.4.0 +[0.2.0]: https://github.com/ExoCTK/exoctk/compare/v0.1.4...v0.2.0 +[0.1.4]: https://github.com/ExoCTK/exoctk/compare/v0.1.3...v0.1.4 +[0.1.3]: https://github.com/ExoCTK/exoctk/compare/v0.1.2...v0.1.3 +[0.1.2]: https://github.com/ExoCTK/exoctk/compare/v0.1.1...v0.1.2 +[0.1.1]: https://github.com/ExoCTK/exoctk/compare/v0.1.0...v0.1.1 +[0.1.0]: https://github.com/ExoCTK/exoctk/releases/tag/v0.1.0 diff --git a/README.rst b/README.rst index 7701991d..03cd8e24 100644 --- a/README.rst +++ b/README.rst @@ -1,8 +1,19 @@ .. image:: /exoctk/data/images/ExoCTK_logo.png :alt: ExoCTK Logo - :scale: 10% - -|build-status| |docs| + :scale: 5% + +.. image:: https://img.shields.io/github/release/ExoCTK/exoctk.svg + :target: https://github.com/ExoCTK/exoctk/releases/latest/ +.. image:: https://img.shields.io/pypi/l/Django.svg + :target: https://github.com/ExoCTK/exoctk/blob/master/LICENSE.rst +.. image:: https://travis-ci.org/ExoCTK/exoctk.svg?branch=master + :target: https://travis-ci.org/ExoCTK/exoctk +.. image:: https://readthedocs.org/projects/exoctk/badge/?version=latest + :target: https://exoctk.readthedocs.io/en/latest/?badge=latest +.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4556063.svg + :target: https://doi.org/10.5281/zenodo.4556063 +.. image:: https://img.shields.io/badge/powered%20by-STScI-blue.svg?colorA=707170&colorB=3e8ddd&style=flat + :target: http://www.stsci.edu Introduction @@ -70,7 +81,7 @@ Next, one can create the ``exoctk`` ``conda`` environment via the appropriate `` conda env create -f environment-.yml -where ```` is the version of python you are using (e.g. ``environment-3.6.yml``) +where ```` is the version of python you are using (e.g. ``environment-3.8.yml``) Lastly, one can activate the newly-created environment with: @@ -78,7 +89,7 @@ Lastly, one can activate the newly-created environment with: conda activate exoctk- -where again, ```` is the version of python you are using (e.g. ``exoctk-3.6``) +where again, ```` is the version of python you are using (e.g. ``exoctk-3.8``) Package Installation @@ -120,7 +131,42 @@ Missing Dependencies? If you find that the `exoctk` `conda` is missing a required dependency, please feel free to `submit a GitHub Issue `_ detailing the problem. +Citation +-------- + +If you use ExoCTK for work/research presented in a publication (whether directly, or as a dependency to another package), we recommend and encourage the following acknowledgment: + +:: + + This research made use of the open source Python package exoctk, the Exoplanet Characterization Toolkit (Espinoza et al, 2021). + +where (Espinoza et al, 2021) is a citation of the Zenodo record, e.g.: + +:: + + @software{nestor_espinoza_2021_4556063, + author = {Néstor Espinoza and + Matthew Bourque and + Joseph Filippazzo and + Michael Fox and + Jules Fowler and + Teagan King and + Catherine Martlin and + Jennifer Medina and + Mees Fix and + Kevin Stevenson and + Jeff Valenti}, + title = {The Exoplanet Characterization Toolkit (ExoCTK)}, + month = feb, + year = 2021, + publisher = {Zenodo}, + version = {1.0.0}, + doi = {10.5281/zenodo.4556063}, + url = {https://doi.org/10.5281/zenodo.4556063} + } + + Want to stay up-to-date with our releases and updates? -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +------------------------------------------------------ Subscribe to our newsletter by sending an email with a blank body and subject to ``exoctk-news-subscribe-request@maillist.stsci.edu`` from the email you want to enroll. You should then receive a confirmation email with instructions on how to confirm your subscription, please be sure to do so within 48 hours. diff --git a/ci/install_conda.sh b/ci/install_conda.sh index d402e115..e6e16b5d 100755 --- a/ci/install_conda.sh +++ b/ci/install_conda.sh @@ -23,10 +23,4 @@ conda config --set always_yes true --set changeps1 false || exit 1 echo "Updating Miniconda" conda update conda conda update --all -conda info -a || exit 1 - -echo "Installing numpy" -conda install numpy -pip install Flask -pip install sphinx -pip install python-dateutil==2.8.0 \ No newline at end of file +conda info -a || exit 1 \ No newline at end of file diff --git a/ci/setup_conda_env.sh b/ci/setup_conda_env.sh index a7c08990..fab31ae1 100755 --- a/ci/setup_conda_env.sh +++ b/ci/setup_conda_env.sh @@ -1,5 +1,13 @@ #!/bin/bash -echo "Creating conda environment for Python $PYTHON_VERSION" -conda env create -f "env/environment-${PYTHON_VERSION}.yml" || exit 1 +echo "Creating base conda environment for Python $PYTHON_VERSION" +conda create --yes --prefix /home/travis/envs python=$PYTHON_VERSION +conda activate /home/travis/envs +conda install sphinx numpy flask + +echo "Creating ExoCTK conda environment for Python $PYTHON_VERSION" +conda env update -f "env/environment-${PYTHON_VERSION}.yml" || exit 1 export CONDA_ENV=exoctk-$PYTHON_VERSION -source activate $CONDA_ENV \ No newline at end of file +source activate $CONDA_ENV + +echo "The installed environment:" +conda env export \ No newline at end of file diff --git a/docs/tutorials/exoctk.AtmosphericRetrivals.rst b/docs/tutorials/exoctk.AtmosphericRetrivals.rst index 5075cef1..f2c3dcb2 100644 --- a/docs/tutorials/exoctk.AtmosphericRetrivals.rst +++ b/docs/tutorials/exoctk.AtmosphericRetrivals.rst @@ -356,23 +356,23 @@ Below are instructions for installing/configuring the software environment neede export EXOCTK_DATA='' // Create base CONDA - conda create --yes -n exoctk-3.6 python=3.6 git numpy flask pytest + conda create --yes -n exoctk-3.8 python=3.8 git numpy flask pytest conda init bash source ~/.bashrc - conda activate exoctk-3.6 + conda activate exoctk-3.8 // Install ExoCTK package and conda environment git clone https://github.com/ExoCTK/exoctk.git cd exoctk/ - conda env update -f env/environment-3.6.yml + conda env update -f env/environment-3.8.yml conda init bash source ~/.bashrc - conda activate exoctk-3.6 + conda activate exoctk-3.8 python setup.py develop cd ../ // Install jwst_gtvt - rm -fr /home/ec2-user/miniconda3/envs/exoctk-3.6/lib/python3.6/site-packages/jwst_gtvt + rm -fr /home/ec2-user/miniconda3/envs/exoctk-3.8/lib/python3.8/site-packages/jwst_gtvt git clone https://github.com/spacetelescope/jwst_gtvt.git cd jwst_gtvt git checkout cd6bc76f66f478eafbcc71834d3e735c73e03ed5 diff --git a/docs/tutorials/exoctk.GroupsandIntegrationsCalculator.rst b/docs/tutorials/exoctk.GroupsandIntegrationsCalculator.rst index a7bf3011..23622d1b 100644 --- a/docs/tutorials/exoctk.GroupsandIntegrationsCalculator.rst +++ b/docs/tutorials/exoctk.GroupsandIntegrationsCalculator.rst @@ -5,7 +5,7 @@ Groups & Integrations Calculator .. contents:: -This is a quick demo for the Groups and Integrations Calculator (i.e. the `exoctk.groups_integrations` subpackage). This demo can run with the `exoctk-3.6` `conda` environment and a proper installation of the `exoctk` software package and the `EXOCTK_DATA` data package. For instructions on how to download and install these things, see the `installation instructions `_. +This is a quick demo for the Groups and Integrations Calculator (i.e. the `exoctk.groups_integrations` subpackage). This demo can run with the `exoctk-3.8` `conda` environment and a proper installation of the `exoctk` software package and the `EXOCTK_DATA` data package. For instructions on how to download and install these things, see the `installation instructions `_. The Groups and Integrations Calculator was written as an exoplanet-focused alternative to the JWST ETC (also known as `pandeia`). It's power comes from: diff --git a/env/environment-3.6.yml b/env/environment-3.6.yml deleted file mode 100644 index c1ced648..00000000 --- a/env/environment-3.6.yml +++ /dev/null @@ -1,48 +0,0 @@ -name: exoctk-3.6 -channels: - - defaults - - http://ssb.stsci.edu/astroconda -dependencies: - - astropy=4.0.2 - - bokeh=2.2.1 - - boto3 - - cython=0.29.17 - - docopt=0.6.2 - - docutils=0.15.2 - - flake8=3.8.4 - - flask=1.1.2 - - gunicorn=20.0.4 - - h5py=2.10.0 - - ipython=7.16.1 - - jupyter=1.0.0 - - matplotlib=3.1.3 - - numpy=1.19.2 - - numpydoc=1.1.0 - - pandas=1.1.3 - - paramiko=2.7.2 - - pytest=6.2.1 - - python=3.6.7 - - scipy=1.5.2 - - scp=0.13.2 - - sphinx=3.4.3 - - sqlalchemy=1.3.20 - - wtforms=2.3.1 - - pip: - - asteval==0.9.16 - - astroquery==0.4.1 - - awscli - - bandit==1.7.0 - - batman-package==2.4.6 - - bibtexparser==1.2.0 - - corner==2.1.0 - - flask_wtf==0.14.3 - - lmfit==1.0.1 - - platon==5.1.2 - - pysiaf==0.10.0 - - pysynphot==1.0 - - pyyaml - - sphinx_astropy==1.3 - - sphinx-automodapi==0.11 - - svo-filters==0.2.19 - - werkzeug==0.16.1 - - git+https://github.com/spacetelescope/jwst_gtvt.git@cd6bc76f66f478eafbcc71834d3e735c73e03ed5 diff --git a/env/environment-3.7.yml b/env/environment-3.7.yml index 5bd72a41..e8f4eed6 100644 --- a/env/environment-3.7.yml +++ b/env/environment-3.7.yml @@ -3,45 +3,48 @@ channels: - defaults - http://ssb.stsci.edu/astroconda dependencies: - - astropy=4.2 - - bokeh=2.1.1 + - astropy<4.1 + - bokeh=2.3.0 - boto3 - - cython=0.29.17 + - cython=0.29.22 - docopt=0.6.2 - - docutils=0.15.2 - - flake8=3.8.4 + - docutils=0.16 + - flake8=3.9.0 - flask=1.1.2 - - gunicorn=19.9.0 + - gunicorn=20.1.0 - h5py=2.10.0 - - ipython=7.19.0 + - ipython=7.22.0 - jupyter=1.0.0 - matplotlib=3.1.3 - numpy=1.19.2 - numpydoc=1.1.0 - - pandas=1.2.0 + - pandas=1.2.3 - paramiko=2.7.2 - - pytest=6.2.1 + - pip=20.3.3 + - pytest=6.2.3 - python=3.7.1 - - scipy=1.5.2 - - scp=0.13.2 - - sphinx=3.4.3 - - sqlalchemy=1.3.20 - - wtforms=2.3.1 + - pyyaml + - scipy=1.6.2 + - scp=0.13.3 + - sphinx=3.5.1 + - sqlalchemy=1.3.23 + - wtforms=2.3.3 - pip: - asteval==0.9.16 - - astroquery==0.4.1 - awscli - bandit==1.7.0 - batman-package==2.4.6 - bibtexparser==1.2.0 - - corner==2.1.0 + - corner==2.2.1 + - ddtrace==0.48.2 - flask_wtf==0.14.3 - lmfit==1.0.1 - platon==5.1.2 - pysiaf==0.10.0 - pysynphot==1.0 - - pyyaml + - PyYAML>=5.4 - sphinx_astropy==1.3 - - svo-filters==0.2.16 + - svo-filters==0.4.1 - werkzeug==0.16.1 - git+https://github.com/spacetelescope/jwst_gtvt.git@cd6bc76f66f478eafbcc71834d3e735c73e03ed5 + - git+https://github.com/astropy/astroquery.git@ccc96185beeff86f3a12a31a00a801afcebe1dbe \ No newline at end of file diff --git a/env/environment-3.8.yml b/env/environment-3.8.yml new file mode 100644 index 00000000..56f90dee --- /dev/null +++ b/env/environment-3.8.yml @@ -0,0 +1,49 @@ +name: exoctk-3.8 +channels: + - defaults + - http://ssb.stsci.edu/astroconda +dependencies: + - astropy<4.1 + - bokeh=2.3.0 + - boto3 + - cython=0.29.22 + - docopt=0.6.2 + - docutils=0.16 + - flake8=3.9.0 + - flask=1.1.2 + - gunicorn=20.1.0 + - h5py=2.10.0 + - ipython=7.22.0 + - jupyter=1.0.0 + - matplotlib=3.3.4 + - numpy=1.19.2 + - numpydoc=1.1.0 + - pandas=1.2.3 + - paramiko=2.7.2 + - pip=20.3.3 + - pytest=6.2.3 + - python=3.8.5 + - pyyaml + - scipy=1.6.2 + - scp=0.13.3 + - sphinx=3.5.3 + - sqlalchemy=1.3.23 + - wtforms=2.3.3 + - pip: + - asteval==0.9.22 + - awscli + - bandit==1.7.0 + - batman-package==2.4.6 + - bibtexparser==1.2.0 + - corner==2.2.1 + - ddtrace==0.48.2 + - flask_wtf==0.14.3 + - lmfit==1.0.2 + - platon==5.1.2 + - pysiaf==0.10.0 + - pysynphot==1.0.0 + - sphinx_astropy==1.3 + - svo-filters==0.4.1 + - werkzeug==0.16.1 + - git+https://github.com/spacetelescope/jwst_gtvt.git@cd6bc76f66f478eafbcc71834d3e735c73e03ed5 + - git+https://github.com/astropy/astroquery.git@ccc96185beeff86f3a12a31a00a801afcebe1dbe \ No newline at end of file diff --git a/env/environment-3.9.yml b/env/environment-3.9.yml new file mode 100644 index 00000000..bf7a618a --- /dev/null +++ b/env/environment-3.9.yml @@ -0,0 +1,49 @@ +name: exoctk-3.9 +channels: + - defaults + - http://ssb.stsci.edu/astroconda +dependencies: + - astropy=4.2 + - bokeh=2.3.0 + - boto3 + - cython=0.29.22 + - docopt=0.6.2 + - flake8=3.9.0 + - flask=1.1.2 + - h5py=2.10.0 + - ipython=7.22.0 + - jupyter=1.0.0 + - matplotlib=3.3.4 + - numpy=1.19.2 + - numpydoc=1.1.0 + - pandas=1.2.3 + - paramiko=2.7.2 + - pip=20.3.3 + - pytest=6.2.3 + - python=3.9.1 + - pyyaml + - scipy=1.6.2 + - scp=0.13.3 + - sphinx=3.5.3 + - sqlalchemy=1.3.23 + - wtforms=2.3.3 + - pip: + - asteval==0.9.22 + - awscli + - bandit==1.7.0 + - batman-package==2.4.6 + - bibtexparser==1.2.0 + - corner==2.2.1 + - ddtrace==0.48.2 + - docutils==0.15.2 + - flask_wtf==0.14.3 + - gunicorn==20.0.4 + - lmfit==1.0.2 + - platon==5.1.2 + - pysiaf==0.10.0 + - pysynphot==1.0.0 + - sphinx_astropy==1.3 + - svo-filters==0.4.1 + - werkzeug==0.16.1 + - git+https://github.com/spacetelescope/jwst_gtvt.git@cd6bc76f66f478eafbcc71834d3e735c73e03ed5 + - git+https://github.com/astropy/astroquery.git@ccc96185beeff86f3a12a31a00a801afcebe1dbe \ No newline at end of file diff --git a/exoctk/__init__.py b/exoctk/__init__.py index 9e0acfb1..22eb2794 100644 --- a/exoctk/__init__.py +++ b/exoctk/__init__.py @@ -1,7 +1,8 @@ # !/usr/bin/python -# -*- coding: latin-1 -*- + """ -The Exoplanet Characterization Tool Kit is a collection of packages used to reduce and analyze observations of transiting exoplanets +The Exoplanet Characterization Tool Kit is a collection of packages +used to reduce and analyze observations of transiting exoplanets. """ import os @@ -14,6 +15,7 @@ from . import limb_darkening from . import phase_constraint_overlap from . import lightcurve_fitting +from . import log_exoctk try: setup_file = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'setup.py') diff --git a/exoctk/contam_visibility/_fieldSim.py b/exoctk/contam_visibility/_fieldSim.py deleted file mode 100644 index 3d7f4063..00000000 --- a/exoctk/contam_visibility/_fieldSim.py +++ /dev/null @@ -1,50 +0,0 @@ -"""UNDER CONSTRUCTION""" - -import glob -import os -import pysiaf - -import astropy.coordinates as crd -import astropy.units as u -import matplotlib.pyplot as plt -import numpy as np -from astroquery.irsa import Irsa -from matplotlib import cm -from scipy.io import readsav -from astropy.io import fits -from exoctk.utils import get_env_variables - -EXOCTK_DATA = os.environ.get('EXOCTK_DATA') -if not EXOCTK_DATA: - print('WARNING: The $EXOCTK_DATA environment variable is not set. ' - 'Contamination overlap will not work. Please set the ' - 'value of this variable to point to the location of the exoctk_data ' - 'download folder. Users may retreive this folder by clicking the ' - '"ExoCTK Data Download" button on the ExoCTK website, or by using ' - 'the exoctk.utils.download_exoctk_data() function.' - ) - TRACES_PATH = None -else: - TRACES_PATH = os.path.join(EXOCTK_DATA, 'exoctk_contam', 'traces') - - -class fieldSim: - def __init__(self, RA, DEC, INSTRUMENT): - self.ra = RA - self.dec = DEC - self.instrument = INSTRUMENT - - if 'NIRCam' in self.instrument: - siaf = pysiaf.Siaf('NIRCam') - dimX, dimY = 51, 1343 - rad = 2.5 - pixel_scale = siaf. - xSweet, ySweet = siaf. , siaf. - elif 'MIRI' in self.instrument: - siaf = pysiaf.Siaf('MIRI') - dimX, dimY = 51, 1343 - rad = 2.5 - pixel_scale = siaf. - xSweet, ySweet = siaf. , siaf. - - def getStars(self, ): diff --git a/exoctk/contam_visibility/field_simulator.py b/exoctk/contam_visibility/field_simulator.py index 82ad2c43..28087694 100755 --- a/exoctk/contam_visibility/field_simulator.py +++ b/exoctk/contam_visibility/field_simulator.py @@ -10,22 +10,11 @@ from matplotlib import cm from scipy.io import readsav from astropy.io import fits +from exoctk import utils from exoctk.utils import get_env_variables from pysiaf.utils import rotations -EXOCTK_DATA = os.environ.get('EXOCTK_DATA') -if not EXOCTK_DATA: - print('WARNING: The $EXOCTK_DATA environment variable is not set. ' - 'Contamination overlap will not work. Please set the ' - 'value of this variable to point to the location of the exoctk_data ' - 'download folder. Users may retreive this folder by clicking the ' - '"ExoCTK Data Download" button on the ExoCTK website, or by using ' - 'the exoctk.utils.download_exoctk_data() function.' - ) - TRACES_PATH = None -else: - TRACES_PATH = os.path.join(EXOCTK_DATA, 'exoctk_contam', 'traces') - +TRACES_PATH = os.path.join(os.environ.get('EXOCTK_DATA'), 'exoctk_contam', 'traces') def sossFieldSim(ra, dec, binComp='', dimX=256): """ Produce a SOSS field simulation for a target. @@ -77,6 +66,8 @@ def sossFieldSim(ra, dec, binComp='', dimX=256): # Add any missing companion if binComp != '': + binComp = [float(i) for i in binComp.split(',')] + deg2rad = np.pi / 180 bb = binComp[0] / 3600 / np.cos(allDEC[targetIndex] * deg2rad) allRA = np.append(allRA, (allRA[targetIndex] + bb)) @@ -760,6 +751,7 @@ def fieldSim(ra, dec, instrument, binComp='', testing=False): plt.plot() : matplotlib object A plot. Only if `testing` parameter is set to True. """ + utils.check_for_data('exoctk_contam') # Calling the variables which depend on what instrument you use if instrument == 'NIRISS': diff --git a/exoctk/contam_visibility/visibilityPA.py b/exoctk/contam_visibility/visibilityPA.py index c0d9b2ba..39c22f0e 100755 --- a/exoctk/contam_visibility/visibilityPA.py +++ b/exoctk/contam_visibility/visibilityPA.py @@ -172,7 +172,11 @@ def checkVisPA(ra, dec, targetName=None, ephFileName=None, fig=None): # Draw the curve and error try: - fig.line(gdMaskednum, paMasked, legend_label='cutoff', line_color=color) + fig.line( + gdMaskednum, + paMasked, + legend_label='cutoff', + line_color=color) except AttributeError: fig.line(gdMaskednum, paMasked, legend='cutoff', line_color=color) @@ -321,7 +325,7 @@ def using_gtvt( legend='Nominal Aperture PA', alpha=.5, source=SOURCE) - + fig.circle('date', 'pamin', color=COLOR, size=1, source=SOURCE) fig.circle('date', 'pamax', color=COLOR, size=1, source=SOURCE) @@ -405,17 +409,22 @@ def using_gtvt( # (sossContamFig.py) # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ badPAs = np.sort(badPAs) - grouped_badPAs = [[badPAs[0]]] - for idx in range(1, len(badPAs)): + if len(badPAs > 0): + grouped_badPAs = [[badPAs[0]]] + + for idx in range(1, len(badPAs)): + + if ((badPAs[idx - 1] + 1) == badPAs[idx]): - if ((badPAs[idx - 1] + 1) == badPAs[idx]): + grouped_badPAs[len(grouped_badPAs) - 1].append(badPAs[idx]) - grouped_badPAs[len(grouped_badPAs) - 1].append(badPAs[idx]) + elif ((badPAs[idx - 1] + 1) < badPAs[idx]): + grouped_badPAs.append([badPAs[idx]]) - elif ((badPAs[idx - 1] + 1) < badPAs[idx]): - grouped_badPAs.append([badPAs[idx]]) + grouped_badPAs = np.asarray(grouped_badPAs) - grouped_badPAs = np.asarray(grouped_badPAs) + else: # Accounting for targets with 100% visibility + grouped_badPAs = np.asarray([]) return paMin, paMax, gd, fig, table, grouped_badPAs diff --git a/exoctk/data/throughputs/MIRI.CLEAR.LONG.CH1.txt 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a/exoctk/data/throughputs/NIRCam.F210M.CLEARP.WLP8__TSGRISM.txt b/exoctk/data/throughputs/NIRCam.F210M.CLEARP.WLP8__TSGRISM.txt new file mode 100644 index 00000000..12450fc5 --- /dev/null +++ b/exoctk/data/throughputs/NIRCam.F210M.CLEARP.WLP8__TSGRISM.txt @@ -0,0 +1,500 @@ +1.929589999999999916e+00 8.959451974843193856e-05 +1.930265390781563006e+00 9.402568467485062362e-05 +1.930940781563126096e+00 1.001925611537524585e-04 +1.931616172344689186e+00 1.081700374297574435e-04 +1.932291563126252498e+00 1.175456116684057316e-04 +1.932966953907815588e+00 1.271344733790803934e-04 +1.933642344689378678e+00 1.371589880859449770e-04 +1.934317735470941768e+00 1.510774936043288283e-04 +1.934993126252504858e+00 1.630581295181332210e-04 +1.935668517034067948e+00 1.741813417236411424e-04 +1.936343907815631260e+00 1.899876065068552863e-04 +1.937019298597194350e+00 2.066015989588042355e-04 +1.937694689378757440e+00 2.238239844174142856e-04 +1.938370080160320530e+00 2.417999901218264398e-04 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6.229901445352686515e-03 +5.038116232464929567e+00 5.905753635489501864e-03 +5.039058116232465245e+00 5.599381540578455760e-03 +5.040000000000000036e+00 5.311891800652134878e-03 diff --git a/exoctk/exoctk_app/__init__.py b/exoctk/exoctk_app/__init__.py index 236c1030..7d826af5 100644 --- a/exoctk/exoctk_app/__init__.py +++ b/exoctk/exoctk_app/__init__.py @@ -1,3 +1,3 @@ from . import app_exoctk -from . import log_exoctk +from .. import log_exoctk from . import form_validation \ No newline at end of file diff --git a/exoctk/exoctk_app/app_exoctk.py b/exoctk/exoctk_app/app_exoctk.py index a976c749..c4f8ac80 100644 --- a/exoctk/exoctk_app/app_exoctk.py +++ b/exoctk/exoctk_app/app_exoctk.py @@ -1,15 +1,14 @@ from functools import wraps import os import json +import io from pkg_resources import resource_filename from astropy.coordinates import SkyCoord -from astropy.extern.six.moves import StringIO import astropy.table as at from astropy.time import Time import astropy.units as u from bokeh.resources import INLINE -from bokeh.util.string import encode_utf8 from bokeh.embed import components import flask from flask import Flask, Response, send_from_directory @@ -27,10 +26,11 @@ from exoctk.utils import filter_table, get_env_variables, get_target_data, get_canonical_name from exoctk.modelgrid import ModelGrid from exoctk.phase_constraint_overlap.phase_constraint_overlap import phase_overlap_constraint, calculate_pre_duration +from exoctk import log_exoctk +from exoctk.throughputs import Throughput from matplotlib.backends.backend_pdf import PdfPages -import log_exoctk from svo_filters import svo # FLASK SET UP @@ -58,13 +58,27 @@ @app_exoctk.route('/') @app_exoctk.route('/index') def index(): - """The Index page""" + """Returns the rendered index page + + Returns + ------- + ``flask.render_template`` obj + The rendered template for the index page. + + """ return render_template('index.html') @app_exoctk.route('/limb_darkening', methods=['GET', 'POST']) def limb_darkening(): - """The limb darkening form page. """ + """Returns the rendered limb darkening form page. + + Returns + ------- + ``flask.render_template`` obj + The rendered template for the limb-darkening page. + + """ # Load default form form = fv.LimbDarkeningForm() @@ -103,7 +117,7 @@ def limb_darkening(): kwargs['wave_max'] = 2 * u.um # Get the filter - bandpass = svo.Filter(form.bandpass.data, **kwargs) + bandpass = Throughput(form.bandpass.data, **kwargs) # Update the form data form.wave_min.data = bandpass.wave_min.value @@ -138,15 +152,12 @@ def limb_darkening(): # Validate form and submit for results if form.validate_on_submit() and form.calculate_submit.data: + # Form inputs for logging + form_input = dict(request.form) + # Get the stellar parameters star_params = [float(form.teff.data), float(form.logg.data), float(form.feh.data)] - # Log the form inputs - try: - log_exoctk.log_form_input(request.form, 'limb_darkening', DB) - except Exception: - pass - # Load the model grid model_grid = ModelGrid(form.modeldir.data, resolution=500) form.modeldir.data = [j for i, j in form.modeldir.choices if i == form.modeldir.data][0] @@ -155,8 +166,7 @@ def limb_darkening(): kwargs = {'n_bins': form.n_bins.data, 'wave_min': form.wave_min.data * u.um, 'wave_max': form.wave_max.data * u.um} # Make filter object and plot - bandpass = svo.Filter(form.bandpass.data, **kwargs) - # bp_name = bandpass.name + bandpass = Throughput(form.bandpass.data, **kwargs) bk_plot = bandpass.plot(draw=False) bk_plot.plot_width = 580 bk_plot.plot_height = 280 @@ -209,6 +219,12 @@ def limb_darkening(): profile_tables.append(html_table) + # Add the profile to the form inputs + form_input[profile] = 'true' + + # Log the successful form inputs + log_exoctk.log_form_input(form_input, 'limb_darkening', DB) + return render_template('limb_darkening_results.html', form=form, table=profile_tables, script=script, plot=div, file_as_string=repr(file_as_string), @@ -220,14 +236,27 @@ def limb_darkening(): @app_exoctk.route('/limb_darkening_error', methods=['GET', 'POST']) def limb_darkening_error(): - """The limb darkening error page""" + """The limb darkening error page + + Returns + ------- + ``flask.render_template`` obj + The rendered template for the limb-darkening error page. + + """ return render_template('limb_darkening_error.html') @app_exoctk.route('/groups_integrations', methods=['GET', 'POST']) def groups_integrations(): - """The groups and integrations calculator form page""" + """The groups and integrations calculator form page + + Returns + ------- + ``flask.render_template`` obj + The rendered template for the Groups & Integrations calculator page. + """ # Print out pandeia sat values with open(resource_filename('exoctk', 'data/groups_integrations/groups_integrations_input_data.json')) as f: @@ -350,11 +379,11 @@ def groups_integrations(): zero_group_error = 'Be careful! This oversaturated the TA in the minimum groups. Consider a different TA setup.' if results_dict['max_ta_groups'] == -1: zero_group_error = 'This object is too faint to reach the required TA SNR in this filter. Consider a different TA setup.' - results_dict['min_sat_ta'] = 0 - results_dict['t_duration_ta_max'] = 0 - results_dict['max_sat_ta'] = 0 - results_dict['t_duration_ta_max'] = 0 - if results_dict['max_sat_prediction'] > results_dict['sat_max']: + results_dict['min_saturation_ta'] = 0 + results_dict['duration_time_ta_max'] = 0 + results_dict['max_saturation_ta'] = 0 + results_dict['duration_time_ta_max'] = 0 + if results_dict['max_saturation_prediction'] > results_dict['sat_max']: one_group_error = 'This many groups will oversaturate the detector! Proceed with caution!' # Do some formatting for a prettier end product results_dict['filt'] = results_dict['filt'].upper() @@ -372,6 +401,12 @@ def groups_integrations(): form_dict = {'miri': 'MIRI', 'nircam': 'NIRCam', 'nirspec': 'NIRSpec', 'niriss': 'NIRISS'} results_dict['ins'] = form_dict[results_dict['ins']] + # Log the successful form inputs + params['kmag'] = form.kmag.data + params['targname'] = form.targname.data + params['num_groups'] = form.n_group.data + log_exoctk.log_form_input(params, 'groups_integrations', DB) + return render_template('groups_integrations_results.html', results_dict=results_dict, one_group_error=one_group_error, @@ -386,7 +421,14 @@ def groups_integrations(): @app_exoctk.route('/contam_visibility', methods=['GET', 'POST']) def contam_visibility(): - """The contamination and visibility form page""" + """The contamination and visibility form page + + Returns + ------- + ``flask.render_template`` obj + The rendered template for the contamination and visibility page. + + """ # Load default form form = fv.ContamVisForm() form.calculate_contam_submit.disabled = False @@ -448,10 +490,7 @@ def contam_visibility(): try: # Log the form inputs - try: - log_exoctk.log_form_input(request.form, 'contam_visibility', DB) - except Exception: - pass + log_exoctk.log_form_input(request.form, 'contam_visibility', DB) # Make plot title = form.targname.data or ', '.join([str(form.ra.data), str(form.dec.data)]) @@ -461,7 +500,7 @@ def contam_visibility(): targetName=str(title)) # Make output table - fh = StringIO() + fh = io.StringIO() table.write(fh, format='csv', delimiter=',') visib_table = fh.getvalue() @@ -510,7 +549,14 @@ def contam_visibility(): @app_exoctk.route('/visib_result', methods=['POST']) def save_visib_result(): - """Save the results of the Visibility Only calculation""" + """Save the results of the Visibility Only calculation + + Returns + ------- + ``flask.Response`` obj + flask.Response object with the results of the visibility only calculation. + + """ visib_table = flask.request.form['data_file'] targname = flask.request.form['targetname'] @@ -522,7 +568,13 @@ def save_visib_result(): @app_exoctk.route('/contam_verify', methods=['GET', 'POST']) def save_contam_pdf(): - """Save the results of the Contamination Science FOV """ + """Save the results of the Contamination Science FOV + + Returns + ------- + ``flask.render_template`` obj + The rendered template (and attachment) for the Contamination FOV. + """ RA, DEC = '19:50:50.2400', '+48:04:51.00' contam_pdf = contamVerify(RA, DEC, 'NIRISS', [1,2], binComp=[], PDF='', web=True) @@ -537,7 +589,14 @@ def save_contam_pdf(): @app_exoctk.route('/download', methods=['POST']) def exoctk_savefile(): - """Save results to file""" + """Save results to file + + Returns + ------- + ``flask.make_response`` obj + Returns response including results in txt form. + + """ file_as_string = eval(request.form['file_as_string']) @@ -548,7 +607,13 @@ def exoctk_savefile(): def _param_fort_validation(args): - """Validates the input parameters for the forward models""" + """Validates the input parameters for the forward models + + Returns + ------- + input_args : dict + Dictionary with the input parameters for the forward models. + """ temp = args.get('ptemp', 1000) chem = args.get('pchem', 'noTiO') @@ -571,6 +636,12 @@ def _param_fort_validation(args): def fortney(): """ Pull up Forntey Grid plot the results and download + + Returns + ------- + html : ``flask.render_template`` obj + The rendered template for the Fortney results. + """ # Grab the inputs arguments from the URL @@ -594,13 +665,24 @@ def fortney(): temp=temp_out, table_string=table_string ) - return encode_utf8(html) + + # Log the form inputs + if len(args) > 0: + log_exoctk.log_form_input(args, 'fortney', DB) + + return html @app_exoctk.route('/generic', methods=['GET', 'POST']) def generic(): """ Pull up Generic Grid plot the results and download + + Returns + ------- + html: ``flask.render_template`` obj + The rendered template for the generic grid page. + """ # Grab the inputs arguments from the URL @@ -626,12 +708,17 @@ def generic(): js_resources=js_resources, css_resources=css_resources, ) - return encode_utf8(html) + + # Log the form inputs + if len(args) > 0: + log_exoctk.log_form_input(args, 'generic', DB) + + return html @app_exoctk.route('/fortney_result', methods=['POST']) def save_fortney_result(): - """SAve the results of the Fortney grid""" + """Save the results of the Fortney grid""" table_string = flask.request.form['data_file'] return flask.Response(table_string, mimetype="text/dat", headers={"Content-disposition": "attachment; filename=fortney.dat"}) @@ -709,7 +796,14 @@ def decorated(*args, **kwargs): @app_exoctk.route('/admin') @requires_auth def secret_page(): - """Shhhhh! This is a secret page of admin stuff""" + """Shhhhh! This is a secret page of admin stuff + + Returns + ------- + ``flask.render_template`` obj + The rendered template for the admin page. + + """ tables = [i[0] for i in DB.execute("SELECT name FROM sqlite_master WHERE type='table'").fetchall()] @@ -750,6 +844,13 @@ def atmospheric_retrievals(): @app_exoctk.route('/phase_constraint', methods=['GET', 'POST']) def phase_constraint(transit_type='primary'): + """Render page for the phase-constraint calculator + + Returns + ------- + ``flask.render_template`` obj + The rendered template for the phase-constraint calculator. + """ # Load default form form = fv.PhaseConstraint() @@ -792,6 +893,10 @@ def phase_constraint(transit_type='primary'): # Extract transit type: transit_type = form.transit_type.data if form.validate_on_submit() and form.calculate_submit.data: + + # Log the form inputs + log_exoctk.log_form_input(request.form, 'phase_constraint', DB) + if transit_type == 'primary': minphase, maxphase = phase_overlap_constraint(target_name=form.targname.data, period=form.orbital_period.data, diff --git a/exoctk/exoctk_app/form_validation.py b/exoctk/exoctk_app/form_validation.py index 0320f91a..0b3f5868 100644 --- a/exoctk/exoctk_app/form_validation.py +++ b/exoctk/exoctk_app/form_validation.py @@ -7,7 +7,7 @@ from wtforms.widgets import ListWidget, CheckboxInput from exoctk.modelgrid import ModelGrid -from exoctk.utils import get_env_variables, FILTERS, PROFILES +from exoctk.utils import get_env_variables, FILTERS_LIST, PROFILES from svo_filters import svo @@ -67,7 +67,7 @@ class LimbDarkeningForm(BaseForm): # Bandpass default_filter = 'Kepler.K' defilt = svo.Filter(default_filter) - bandpass = SelectField('bandpass', default=default_filter, choices=[('tophat', 'Top Hat')]+[(filt, filt) for filt in sorted(FILTERS['Band'])], validators=[InputRequired('A filter is required!')]) + bandpass = SelectField('bandpass', default=default_filter, choices=[('tophat', 'Top Hat')] + [(filt, filt) for filt in FILTERS_LIST], validators=[InputRequired('A filter is required!')]) wave_min = DecimalField('wave_min', default=defilt.wave_min.value, validators=[NumberRange(min=0, max=30, message='Minimum wavelength must be between 0 and 30 microns!')]) wave_max = DecimalField('wave_max', default=defilt.wave_max.value, validators=[NumberRange(min=0, max=30, message='Maximum wavelength must be between 0 and 30 microns!')]) n_bins = IntegerField('n_bins', default=1) @@ -138,6 +138,7 @@ class ContamVisForm(BaseForm): class PhaseConstraint(BaseForm): + """Form validation for the phase-constraint tool""" calculate_submit = SubmitField('Calculate Phase Constraint') diff --git a/exoctk/exoctk_app/log_exoctk.py b/exoctk/exoctk_app/log_exoctk.py deleted file mode 100644 index ca652ad0..00000000 --- a/exoctk/exoctk_app/log_exoctk.py +++ /dev/null @@ -1,152 +0,0 @@ -""" -This module creates and manages a SQL database as a log for all jobs submitted -via the exoctk web app -""" -import os -import sqlite3 -import datetime - -import astropy.table as at -import numpy as np -from pathlib import Path - - -def create_db(dbpath, overwrite=True): - """ - Create a new database at the given dbpath - - Parameters - ---------- - dbpath: str - The full path for the new database, including the filename and .db - file extension. - schema: str - The path to the .sql schema for the database - overwrite: bool - Overwrite dbpath if it already exists - """ - if dbpath != ':memory:': - # Make sure the path is valid - if not os.path.exists(os.path.dirname(dbpath)): - raise IOError('Not a valid path:', dbpath) - - # Make sure the file is a .db - if not dbpath.endswith('.db'): - raise IOError('Please provide a path with a .db file extension') - - # Use pathlib.Path to become compliant with bandit. - p = Path(dbpath) - - # Remove existing file if overwriting - if os.path.isfile(dbpath) and overwrite: - p.unlink() - - # Make the new file - p.touch() - - # Generate the tables - conn = sqlite3.connect(dbpath) - cur = conn.cursor() - - # Table for groups_integrations - cur.execute("CREATE TABLE 'groups_integrations' ('id' INTEGER NOT NULL UNIQUE, 'date' TEXT NOT NULL, 'ins' TEXT, 'mag' REAL, 'groups' TEXT, 'amps' INTEGER, 'subarray' TEXT, 'sat_lvl' REAL, 'sat' TEXT, 'T' REAL, 'n_reset' INTEGER, 'band' TEXT, 'filt' TEXT, PRIMARY KEY(id));") - - # Table for limb_darkening - cur.execute("CREATE TABLE 'limb_darkening' ('id' INTEGER NOT NULL UNIQUE, 'date' TEXT NOT NULL, 'n_bins' INTEGER, 'teff' REAL, 'logg' REAL, 'feh' REAL, 'bandpass' TEXT, 'modeldir' TEXT, 'wave_min' REAL, 'mu_min' REAL, 'wave_max' REAL, 'local_files' TEXT, 'pixels_per_bin' INTEGER, 'uniform' TEXT, 'linear' TEXT, 'quadratic' TEXT, 'squareroot' TEXT, 'logarithmic' TEXT, 'exponential' TEXT, 'three_parameter' TEXT, 'four_parameter' TEXT, PRIMARY KEY(id));") - - # Tale for contam_visibility - cur.execute("CREATE TABLE 'contam_visibility' ('id' INTEGER NOT NULL UNIQUE, 'date' TEXT NOT NULL, 'targetname' TEXT, 'ra' REAL, 'dec' REAL, 'pamax' REAL, 'pamin' REAL, 'bininfo' TEXT, PRIMARY KEY(id));") - - # Commit and close the connection - conn.commit() - conn.close() - - if os.path.isfile(dbpath): - print("ExoCTK database created at {}".format(dbpath)) - - -def load_db(dbpath): - """ - Load a database - - Parameters - ---------- - dbpath: str - The path to the .db database file - """ - if os.path.isfile(dbpath) or dbpath == ':memory:': - - con = sqlite3.connect(dbpath, isolation_level=None, detect_types=sqlite3.PARSE_DECLTYPES, check_same_thread=False) - cur = con.cursor() - - return cur - - else: - print("Sorry, could not find the file '{}'".format(dbpath)) - - -def log_form_input(form_dict, table, database): - """ - A function to store the form inputs of any page GET requests in a database - - Parameters - ---------- - form_dict: dict - The dictionary of form inputs - table: str - The table name to INSERT on - database: sqlite.connection.cursor - The database cursor object - """ - try: - # Convert hyphens to underscores and leading numerics to letters for - # db column names - inpt = {k.replace('-', '_').replace('3', 'three').replace('4', 'four'): v[0] for k, v in dict(form_dict).items()} - except TypeError: - inpt = form_dict - - # Add a timestamp - inpt['date'] = datetime.datetime.now().strftime("%Y-%m-%d %H:%M") - - # Insert the form valsues - qmarks = ', '.join('?' * len(inpt)) - cols = ', '.join(inpt.keys()) - qry = "Insert Into {} ({}) Values ({})".format(table, cols, qmarks) - - database.execute(qry, list(inpt.values())) - - -def view_log(database, table): - """ - Visually inspect the job log - - Parameters - ---------- - database: str, sqlite3.connection.cursor - The database cursor object - table: str - The table name - """ - if isinstance(database, str): - DB = load_db(database) - elif isinstance(database, sqlite3.Cursor): - DB = database - else: - print("Please enter the path to a .db file or a sqlite.Cursor object.") - - # Query the database - table = scrub(table) - colnames = np.array(DB.execute("PRAGMA table_info('{}')".format(table)).fetchall()).T[1] - results = DB.execute("SELECT * FROM {}".format(table)).fetchall() - - results = at.Table(list(np.array(results).T), names=colnames) - - # Print them - return results - - -def scrub(table_name): - """ - Snippet to prevent SQL injection attcks! PEW PEW PEW! - """ - return ''.join(chr for chr in table_name if chr.isalnum()) diff --git a/exoctk/exoctk_app/static/images/._ExoCTK_logo.gif b/exoctk/exoctk_app/static/images/._ExoCTK_logo.gif deleted file mode 100644 index 9bdb30af..00000000 Binary files a/exoctk/exoctk_app/static/images/._ExoCTK_logo.gif and /dev/null differ diff --git a/exoctk/exoctk_app/static/images/._STScI_logo.png b/exoctk/exoctk_app/static/images/._STScI_logo.png deleted file mode 100644 index 85c3bdf0..00000000 Binary files a/exoctk/exoctk_app/static/images/._STScI_logo.png and /dev/null differ diff --git a/exoctk/exoctk_app/static/images/._favicon.png b/exoctk/exoctk_app/static/images/._favicon.png deleted file mode 100644 index 474e54c1..00000000 Binary files a/exoctk/exoctk_app/static/images/._favicon.png and /dev/null differ diff --git a/exoctk/exoctk_app/static/images/._ldc_results.png b/exoctk/exoctk_app/static/images/._ldc_results.png deleted file mode 100644 index 5f029a72..00000000 Binary files a/exoctk/exoctk_app/static/images/._ldc_results.png and /dev/null differ diff --git a/exoctk/exoctk_app/templates/base.html b/exoctk/exoctk_app/templates/base.html index ebc35d0f..a9f44a2f 100644 --- a/exoctk/exoctk_app/templates/base.html +++ b/exoctk/exoctk_app/templates/base.html @@ -146,7 +146,7 @@

Running
- exoctk v1.1.0{{version|safe}} + exoctk v1.2.0{{version|safe}}

Admin Area diff --git a/exoctk/exoctk_app/templates/groups_integrations_results.html b/exoctk/exoctk_app/templates/groups_integrations_results.html index 44889d6d..4865c92b 100644 --- a/exoctk/exoctk_app/templates/groups_integrations_results.html +++ b/exoctk/exoctk_app/templates/groups_integrations_results.html @@ -10,7 +10,7 @@

Groups & Integrations Calculator

Please know that at present this tool is likely to overestimate saturation on direct comparison to the ETC. (This means we may predict less groups -- and put you in LESS danger of - oversaturating your observation.)

+ oversaturating your observation.)

Source Specifics

@@ -33,9 +33,9 @@

Source Specifics

Target Acquisition

- +

Input and Instrument Parameters

- +
@@ -48,7 +48,7 @@

Input and Instrument Parameters

- +
{{ results_dict['ins'] }} {{ results_dict['filt_ta'] }} {{ results_dict['subarray_ta'] }}{{ results_dict['ta_t_frame'] }}{{ results_dict['ta_frame_time'] }}
@@ -57,7 +57,7 @@

Input and Instrument Parameters

APT Ready Outputs and Useful Tidbits

{{ zero_group_error }} - +
@@ -73,22 +73,22 @@

APT Ready Outputs and Useful Tidbits

- - - - + + + +
1 (fixed for target acquisition) {{ results_dict['max_ta_groups'] }} {{ results_dict['min_ta_groups'] }}{{ results_dict['t_duration_ta_max'] }}{{ results_dict['t_duration_ta_min'] }}{{ results_dict['max_sat_ta'] }}{{ results_dict['min_sat_ta'] }}{{ results_dict['duration_time_ta_max'] }}{{ results_dict['duration_time_ta_min'] }}{{ results_dict['max_saturation_ta'] }}{{ results_dict['min_saturation_ta'] }}
- +

Science Observation

-
- +
+

Input and Instrument Parameters

- +
@@ -103,7 +103,7 @@

Input and Instrument Parameters

- +
{{ results_dict['filt'] }} {{ results_dict['subarray'] }} {{ results_dict['sat_max']}}{{ results_dict['t_frame'] }}{{ results_dict['frame_time'] }}
@@ -121,23 +121,23 @@

APT Ready Outputs and Useful Tidbits

Photon Collection Time (hours) Observation Duration (hours) Observation Efficiency - Maximum Sat Reached + Maximum Sat Reached - {{ results_dict['n_int'] }} + {{ results_dict['num_integrations'] }} {{ results_dict['n_group'] }} - {{ results_dict['t_int'] }} - {{ results_dict['t_exp'] }} - {{ results_dict['t_duration'] }} - {{ results_dict['obs_eff'] }} - {{ results_dict['max_sat_prediction'] }} + {{ results_dict['integration_time'] }} + {{ results_dict['exposure_time'] }} + {{ results_dict['duration_time'] }} + {{ results_dict['observation_efficiency'] }} + {{ results_dict['max_saturation_prediction'] }} - +
- +
diff --git a/exoctk/forward_models/forward_models.py b/exoctk/forward_models/forward_models.py index 689c2bc9..0e865def 100644 --- a/exoctk/forward_models/forward_models.py +++ b/exoctk/forward_models/forward_models.py @@ -19,13 +19,12 @@ ## -- IMPORTS import os +import io import astropy.constants as constants -from astropy.extern.six.moves import StringIO import astropy.table as at import astropy.units as u from bokeh.resources import INLINE -from bokeh.util.string import encode_utf8 from bokeh.embed import components from bokeh.models import Range1d from bokeh.models.widgets import Panel, Tabs @@ -70,6 +69,7 @@ def fortney_grid(args, write_plot=False, write_table=False): temp_out : list of str of int The list of temperatures in the model grid. """ + utils.check_for_data('fortney') # Check for Fortney Grid database print(os.path.join(get_env_variables()['exoctk_data'], 'fortney/fortney_models.db')) @@ -150,7 +150,7 @@ def fortney_grid(args, write_plot=False, write_table=False): x, y = df['wavelength'], df['radius']**2.0 / 7e5**2.0 tab = at.Table(data=[x, y]) - fh = StringIO() + fh = io.StringIO() tab.write(fh, format='ascii.no_header') if write_table: @@ -206,6 +206,7 @@ def generic_grid(input_args, write_plot=False, write_table=False): error_message : str An error message, or lack therof. """ + utils.check_for_data('generic') # Find path to the database. database_path = os.path.join(get_env_variables()['exoctk_data'], 'generic/generic_grid_db.hdf5') @@ -215,7 +216,7 @@ def generic_grid(input_args, write_plot=False, write_table=False): # Build file out tab = at.Table(data=[solution['wv'], solution['spectra']]) - fh = StringIO() + fh = io.StringIO() tab.write(fh, format='ascii.no_header') if write_table: diff --git a/exoctk/groups_integrations/groups_integrations.py b/exoctk/groups_integrations/groups_integrations.py index 805d8777..ff8e6cf7 100644 --- a/exoctk/groups_integrations/groups_integrations.py +++ b/exoctk/groups_integrations/groups_integrations.py @@ -1,556 +1,578 @@ -""" -This is a module for calcuating groups and integrations with JWST on the fly. -the main function (perform_calculation) takes a dictionary of inputs -(modeled around how the web tool takes inputs) which must include : -obs_time, n_group, mag, mod, band, filt, filt_ta, ins, subarray, subarray_ta, -sat_mode, sat_max, and infile. It produces and dictionary of outputs that includes -all of the original information as well as groups, integrations, saturation levels, -and observation time estimates for target acquisition and science observations -with JWST. - +"""This is a module for calcuating groups and integrations with JWST on +the fly. The main function (``perform_calculation``) takes a dictionary +of inputs (modeled around how the web tool takes inputs) which must +include: ``observation_time``, ``num_groups``, ``magnitude``, +``model``, ``band``, ``filt``, ``filt_ta``, ``instrument``, +``subarray``, ``subarray_ta``, ``saturation_mode``, ``max_saturation``, +and ``infile``. It produces and dictionary of outputs that includes all +of the original information as well as groups, integrations, saturation +levels, and observation time estimates for target acquisition and +science observations with JWST. Authors ------- + Jules Fowler, April 2017 + Matthew Bourque, February 2021 Use --- - This is mostly a module to be used by ExoCTKWeb -- but the main function - can be run standalone. + This is mostly a module to be used by the ExoCTK web application, + but the main function can be run standalone as such: + :: + + from exoctk.groups_integrations.groups_integrations import perform_calculation + perform_calculation() + +Dependencies +------------ + + - ``astropy`` + - ``numpy`` + - ``scipy`` """ -## -- IMPORTS import json import math -import os -from decimal import Decimal -from astropy.io import ascii import numpy as np from scipy import interpolate -from scipy.integrate import quad -## -- FUNCTIONS -def calc_groups_from_exp_time(max_exptime_per_int, t_frame): - """ - Given the maximum saturation time, calculates the number - of frames per group. +def calc_duration_time(num_groups, num_integrations, num_reset_frames, frame_time, frames_per_group=1): + """Calculates duration time (or exposure duration as told by APT) Parameters ---------- - max_exptime_per_int : float - The maximum number of seconds an integration can last - before it's oversaturated. - t_frame : float - The time per frame. + num_groups : int + Groups per integration + num_integrations : int + Integrations per exposure + num_reset_frames : int + Reset frames per integration + frame_time : float + Frame time (in seconds) + frames_per_group : int, optional + Frames per group -- always one except brown dwarves Returns ------- - groups : int - The required number of groups. + duration_time : float + Duration time (in seconds). """ - groups = max_exptime_per_int/t_frame - return np.floor(groups) + duration_time = frame_time * (num_groups * frames_per_group + num_reset_frames) * num_integrations + return duration_time -def calc_n_int(transit_time, n_group, n_reset, t_frame, n_frame): - """Calculates number of integrations required. + +def calc_exposure_time(num_integrations, ramp_time): + """Calculates exposure time (or photon collection duration as told + by APT.) Parameters ---------- - transit_time : float - The time of your planeting transit (in hours.) - n_group : int - Groups per integration. - n_reset : int - Reset frames per integration. - t_frame : float - The frame time (in seconds). - n_frame : int - Frames per group -- always 1 except maybe brown dwarves. + num_integrations : int + Integrations per exposure. + ramp_time : float + Ramp time (in seconds). Returns ------- - n_ints : float - The required number of integraitions. + exposure_time : float + Exposure time (in seconds). """ - hour = 3600 - n_ints = (float(transit_time)*hour)/(t_frame*(n_group*n_frame+n_reset)) - - return math.ceil(n_ints) + exposure_time = num_integrations * ramp_time + return exposure_time -def calc_obs_efficiency(t_exp, t_duration): - """Calculates the observation efficiency. + +def calc_frame_time(num_columns, num_rows, num_amps, instrument): + """Calculates the frame time for a given instrument/readmode/subarray. Parameters ---------- - t_exp : float - Exposure time (in seconds). - t_duration : float - Duration time (in seconds). - + num_columns : int + Number of columns + num_rows : int + Number of rows + num_amps : int + Amplifiers reading data + instrument : str + The instrument + Returns ------- - obs_eff : float - Observation efficiency. + frame_time : float + The frame time (in seconds) """ - obs_eff = t_exp/t_duration - return obs_eff + num_columns, num_amps, num_rows = int(num_columns), int(num_amps), int(num_rows) + + if instrument == 'nirspec': + n = 2 + if instrument in ['nircam', 'niriss']: + n = 1 + + frame_time = (num_columns / num_amps + 12) * (num_rows + n) * (1e-5) + return frame_time -def calc_t_duration(n_group, n_int, n_reset, t_frame, n_frame=1): - """Calculates duration time (or exposure duration as told by APT.) + +def calc_groups_from_exp_time(max_exptime_per_int, frame_time): + """Given the maximum saturation time, calculates the number of + frames per group. Parameters ---------- - n_group : int - Groups per integration. - n_int : int - Integrations per exposure. - n_reset : int - Reset frames per integration. - t_frame : float - Frame time (in seconds). - n_frame : int, optional - Frames per group -- always one except brown dwarves. + max_exptime_per_int : float + The maximum number of seconds an integration can last before + it's oversaturated + frame_time : float + The time per frame Returns ------- - t_duration : float - Duration time (in seconds). + groups : int + The required number of groups. """ - - t_duration = t_frame*(n_group*n_frame + n_reset)*n_int - return t_duration + groups = np.floor(max_exptime_per_int / frame_time) + + return groups -def calc_t_exp(n_int, t_ramp): - """Calculates exposure time (or photon collection duration as told by APT.) + +def calc_integration_time(num_groups, frame_time, frames_per_group, num_skips): + """Calculates the integration time. Parameters ---------- - n_int : int - Integrations per exposure. - t_ramp : float - Ramp time (in seconds). + num_groups : int + Groups per integration.] + frame_time : float + Frame time (in seconds) + frames_per_group : int + Frames per group -- always 1 except maybe brown dwarves + num_skips : int + Skips per integration -- always 0 except maybe brown dwarves Returns ------- - t_exp : float - Exposure time (in seconds). + integration_time : float + Integration time (in seconds) """ - t_exp = n_int*t_ramp - return t_exp + integration_time = (num_groups * (frames_per_group + num_skips) - num_skips) * frame_time + + return integration_time -def calc_t_frame(n_col, n_row, n_amp, ins): - """Calculates the frame time for a given ins/readmode/subarray. +def calc_num_integrations(transit_time, num_groups, num_reset_frames, frame_time, frames_per_group): + """Calculates number of integrations required. Parameters ---------- - n_col : int - Number of columns. - n_row : int - Number of rows. - n_amp : int - Amplifiers reading data. - ins : str - The instrument key. - - Returns: - t_frame : float - The frame time (in seconds). + transit_time : float + The time of the transit (in hours) + num_groups : int + Groups per integration + num_reset_frames : int + Number of reset frames per integration + frame_time : float + The frame time (in seconds) + frames_per_group : int + Frames per group -- always 1 except maybe for brown dwarves + + Returns + ------- + num_integrations : float + The required number of integraitions. """ - n_col, n_amp, n_row = int(n_col), int(n_amp), int(n_row) - - if ins == 'nirspec': - n = 2 - if ins in ['nircam', 'niriss']: - n = 1 - t_frame = (n_col/n_amp + 12)*(n_row + n)*(1e-5) - - return t_frame + num_integrations = math.ceil((float(transit_time) * 3600) / (frame_time * (num_groups * frames_per_group + num_reset_frames))) + return num_integrations + + +def calc_observation_efficiency(exposure_time, duration_time): + """Calculates the observation efficiency. -def calc_t_int(n_group, t_frame, n_frame, n_skip): - """Calculates the integration time. - Parameters ---------- - n_group : int - Groups per integration. - t_frame : float - Frame time (in seconds). - n_frame : int - Frames per group -- always 1 except maybe brown dwarves. - n_skip : int - Skips per integration -- always 0 except maybe brown dwarves. + exposure_time : float + Exposure time (in seconds). + duration_time : float + Duration time (in seconds). Returns ------- - t_int : float - Integration time (in seconds). + observation_efficiency : float + Observation efficiency. """ - - t_int = (n_group*(n_frame + n_skip) - n_skip)*t_frame - return t_int + observation_efficiency = exposure_time / duration_time + + return observation_efficiency -def calc_t_ramp(t_int, n_reset, t_frame): + +def calc_ramp_time(integration_time, num_reset_frames, frame_time): """Calculates the ramp time -- or the integration time plus overhead for resets. Parameters ---------- - t_int : float - Integration time (in seconds). - n_reset : int + integration_time : float + Integration time (in seconds) + num_reset_frames : int Rest frames per integration - t_frame : float - Frame time (in seconds). + frame_time : float + Frame time (in seconds) Returns ------- - t_ramp : float + ramp_time : float Ramp time (in seconds). """ - t_ramp = t_int + (n_reset - 1)*t_frame - return t_ramp + ramp_time = integration_time + (num_reset_frames - 1) * frame_time + + return ramp_time -def convert_sat(sat_max, sat_mode, ins, infile, ta=False): - """ Converts full well fraction to a saturation in counts OR provides the - max fullwell for TA mode. +def convert_saturation(max_saturation, saturation_mode, instrument, infile, target_acq_mode=False): + """Converts full well fraction to a saturation in counts OR + provides the max fullwell for TA mode. Parameters ---------- - sat_max : float - Either a full well fraction or counts. - sat_mode : str - 'well' or 'counts'. - ins : str - The instrument. + max_saturation : float + Either a full well fraction or counts + saturation_mode : str + ``well`` or ``counts`` + instrument : str + The instrument infile : str - The path to the data file. - ta : bool, optional - Whether or not it's TA mode. - + The path to the data file + target_acq_mode : bool, optional + Whether or not it's TA mode + Returns ------- - sat_max : float + max_saturation : float The fullwell to use in counts. """ with open(infile) as f: - dat = json.load(f) - - ins_dict = dat['fullwell'] - - if sat_mode == 'well': - sat_max = float(sat_max)*float(ins_dict[ins]) - - if ta: - sat_max = ins_dict[ins] - - return sat_max - - -def interpolate_from_dat(mag, ins, filt, sub, mod, band, t_frame, sat_lvl, infile, ta=False): - """ - Interpolates the precalculated pandeia data to estimate the saturation limit. + data = json.load(f) + + instrument_dict = data['fullwell'] + + if saturation_mode == 'well': + max_saturation = float(max_saturation) * float(instrument_dict[instrument]) + + if target_acq_mode: + max_saturation = instrument_dict[instrument] + + return max_saturation + + +def interpolate_from_pandeia(magnitude, instrument, filt, subarray, model, band, frame_time, saturation_level, infile, target_acq_mode=False): + """Interpolates the precalculated ``pandeia`` data to estimate the + saturation limit. Parameters ---------- - mag : float + magnitude : float The magnitude of the source. (Takes between 4.5-12.5) - ins : str - The instrument, allowable "miri", "niriss", "nirspec", "nircam". + instrument : str + The instrument, allowable ``miri``, ``niriss``, ``nirspec``, + ``nircam`` filt : str - Filter. - sub : str - Subarray. - mod : str - Phoenix model key. + The filter + subarray : str + The subarray + model : str + Phoenix model key band : str - Magnitude band -- unsed rn. - t_frame : float - Frame time. - sat_lvl : float - The maximum fullwell saturation we'll allow. + Magnitude band + frame_time : float + Frame time + saturation_level : float + The maximum fullwell saturation we'll allow infile : str - The data file to use. - ta : bool, optional - Whether or not we're running this for TA. + The data file to use + target_acq_mode : bool, optional + Whether or not we're running this for TA Returns ------- - n_group : int - The number of groups that won't oversaturate the detector. + num_groups : int + The number of groups that won't oversaturate the detector max_sat : int - The maximum saturation level reached by that number of groups. + The maximum saturation level reached by that number of groups """ + # Create the dictionaries for each filter and select out the prerun data with open(infile) as f: - dat = json.load(f) + data = json.load(f) ta_or_sci = 'sci_sat' - if ta: + if target_acq_mode: ta_or_sci = 'ta_sat' # The data - mags = np.array(dat['mags']) - sat = dat[ta_or_sci][ins][filt][sub][mod] - log_sat = np.log10(sat) + magnitudes = np.array(data['mags']) + saturation = data[ta_or_sci][instrument][filt][subarray][model] + log_saturation = np.log10(saturation) # Interpolate the given magnitude - func_log = interpolate.interp1d(mags, log_sat) - max_log_sat = func_log(float(mag)) - max_sat = 10**(max_log_sat) + func_log = interpolate.interp1d(magnitudes, log_saturation) + max_log_saturation = func_log(float(magnitude)) + max_saturation = 10**(max_log_saturation) - # Figure out what it means in wake of the given sat lvl - max_exptime = float(sat_lvl)/max_sat + # Figure out what it means in wake of the given saturation lvl + max_exptime = float(saturation_level) / max_saturation # Calculate the nearest number of groups - n_group = calc_groups_from_exp_time(max_exptime, t_frame) + num_groups = calc_groups_from_exp_time(max_exptime, frame_time) # Can't have zero groups - n_group = n_group or 1 + num_groups = num_groups or 1 - return n_group, max_sat + return num_groups, max_saturation -def map_to_ta_modes(ins, max_group, min_group): - """Turns the min/max groups into the closest allowable - TA group mode. +def map_to_ta_modes(instrument, max_num_groups, min_num_groups): + """Turns the min/max groups into the closest allowable TA group + mode. Parameters ---------- - ins : str - Instrument. - max_group : int - The maximum number of groups without oversaturating. - - min_group : int - The groups needed to hit the target SNR. - + instrument : str + The instrument + max_num_groups : int + The maximum number of groups without oversaturating + min_num_groups : int + The groups needed to hit the target SNR + Returns ------- min_ta_groups : int - The min possible groups to hit target SNR. + The min possible groups to hit target SNR max_ta_groups : int - The max possible groups before saturation. + The max possible groups before saturation """ - # Allowable group modes for each ins + # Allowable group modes for each instrument groups = {'miri': [3, 5, 9, 15, 23, 33, 45, 59, 75, 93, 113, 135, 159, 185, 243, 275, 513], 'niriss': [3, 5, 7, 9, 1, 13, 15, 17, 19], - 'nirspec': [3], - 'nircam': [3, 5, 9, 17, 33, 65] - } - - # Match the literal min and max groups to the nearest mode. - allowable_groups = groups[ins] - min_ta_groups = min(allowable_groups, key=lambda x:abs(x-min_group)) - max_ta_groups = min(allowable_groups, key=lambda x:abs(x-max_group)) - + 'nirspec': [3], + 'nircam': [3, 5, 9, 17, 33, 65]} + + # Match the literal min and max groups to the nearest mode. + allowable_groups = groups[instrument] + min_ta_groups = min(allowable_groups, key=lambda x: abs(x - min_num_groups)) + max_ta_groups = min(allowable_groups, key=lambda x: abs(x - max_num_groups)) + # Unless it was oversaturated from the get-go OR there aren't enough groups # for SNR - if min_group == 0: + if min_num_groups == 0: min_ta_groups = 0 max_ta_groups = 0 - if min_group > max(allowable_groups): + if min_num_groups > max(allowable_groups): min_ta_groups = -1 max_ta_groups = 0 - - # BOTH ARE FLIPPED RN -- I WILL FLIP BOTH BACK SOON... + return max_ta_groups, min_ta_groups -def min_groups(mag, ins, filt, sub, mod, band, infile): - """Estimates the minimum number of groups to reach - target acq sat requirements. +def min_num_groups_for_sat(magnitude, instrument, filt, subarray, model, band, infile): + """Estimates the minimum number of groups to reach target acq + saturation requirements. Parameters ---------- - mag : float + magnitude : float Magnitude of star. - ins : str + instrument : str Instrument. filt : str Filter. - sub : str + subarray : str Subarray. - mod : str + model : str Phoenix model key. band : str, currently unused? The band -- right now only k sooo? infile : str The file with the pandeia data. - + Returns ------- - min_groups : int + min_num_groups_for_sat : int The minimum number of groups to reach target snr. """ with open(infile) as f: - dat = json.load(f) + data = json.load(f) # Match to closest magnitude - mags = [float(i) for i in dat['mags']] - closest_mag = min(mags, key=lambda x:abs(x-float(mag))) - index = mags.index(closest_mag) + magnitudes = [float(i) for i in data['mags']] + closest_magnitude = min(magnitudes, key=lambda x: abs(x - float(magnitude))) + index = magnitudes.index(closest_magnitude) - # Match to data - min_groups = dat['ta_snr'][ins][filt][sub][mod][index] + # Match to data + minimum_num_groups_for_sat = data['ta_snr'][instrument][filt][subarray][model][index] - return min_groups + return minimum_num_groups_for_sat -def perform_calculation(params, n_frame=1, n_skip=0): - """Calculates all of the outputs and puts them in a dictionary for easy access. +def perform_calculation(params, frames_per_group=1, num_skips=0): + """Calculates all of the outputs and puts them in a dictionary for + easy access. Parameters ---------- params : dict Dictionary of all the needed parameters. Must include: - obs_time, n_group, mag, mod, band, filt, filt_ta, - ins, subarray, subarray_ta, sat_mode, sat_max, infile - n_frame :int, optional - The number of frames -- almost always 1. - n_skip: int, optional + ``obs_time``, ``n_group``, ``mag``, ``mod``, ``band``, + ``filt``, ``filt_ta``, ``ins``, ``subarray``, ``subarray_ta``, + ``sat_mode``, ``max_sat``, ``infile`` + frames_per_group : int, optional + The number of frames -- almost always 1 + num_skips: int, optional Number of skips -- almost always 0 - + Returns ------- params : dict, str - Dictionary of outputs and inputs. If - the calculation throws an error it will return a string - error message instead. + Dictionary of outputs and inputs. If the calculation throws an + error it will return a string error message instead """ - - ## -- TARGET ACQ - ta_frame_time = set_t_frame(params['infile'], params['ins'], params['subarray_ta'], ta=True) - - max_sat_ta_lvl = convert_sat(params['sat_max'], params['sat_mode'], - params['ins'], params['infile'], ta=True) - - max_group, sat_rate_ta = interpolate_from_dat(params['mag'], params['ins'], params['filt_ta'], - params['subarray_ta'], params['mod'], params['band'], - ta_frame_time, max_sat_ta_lvl, params['infile'], ta=True) - min_group = min_groups(params['mag'], params['ins'], params['filt_ta'], params['subarray_ta'], - params['mod'], params['band'], params['infile']) - min_ta_groups, max_ta_groups = map_to_ta_modes(params['ins'], max_group, min_group) - t_duration_ta_min = calc_t_duration(min_ta_groups, 1, 1, ta_frame_time) - t_duration_ta_max = calc_t_duration(max_ta_groups, 1, 1, ta_frame_time) - - ## -- Science obs - - # Figure out the rows/cols/amps/px_size and sat - ins_params = set_params_from_ins(params['ins'], params['subarray']) - frame_time = set_t_frame(params['infile'], params['ins'], params['subarray']) + + # TARGET ACQ + ta_frame_time = set_frame_time( + params['infile'], params['ins'], params['subarray_ta'], target_acq_mode=True) + + max_saturation_ta_level = convert_saturation( + params['sat_max'], params['sat_mode'], params['ins'], params['infile'], target_acq_mode=True) + + max_num_groups, saturation_rate_ta = interpolate_from_pandeia( + params['mag'], params['ins'], params['filt_ta'], params['subarray_ta'], params['mod'], params['band'], + ta_frame_time, max_saturation_ta_level, params['infile'], target_acq_mode=True) + + min_num_groups = min_num_groups_for_sat( + params['mag'], params['ins'], params['filt_ta'], params['subarray_ta'], params['mod'], params['band'], params['infile']) + + min_ta_groups, max_ta_groups = map_to_ta_modes(params['ins'], max_num_groups, min_num_groups) + + duration_time_ta_min = calc_duration_time(min_ta_groups, 1, 1, ta_frame_time) + + duration_time_ta_max = calc_duration_time(max_ta_groups, 1, 1, ta_frame_time) + + # Science obs + # Figure out the rows/cols/amps/pixel_size and saturation + instrument_params = set_params_from_instrument(params['ins'], params['subarray']) + frame_time = set_frame_time(params['infile'], params['ins'], params['subarray']) # Run all the calculations - n_row, n_col, n_amp, px_size, t_frame, n_reset = ins_params - band_ins = '{0}_{1}'.format(params['band'], params['filt']) - - params['sat_max'] = convert_sat(params['sat_max'], params['sat_mode'], params['ins'], params['infile']) + num_rows, num_columns, num_amps, pixel_size, frame_time, num_reset_frames = instrument_params + params['sat_max'] = convert_saturation(params['sat_max'], params['sat_mode'], params['ins'], params['infile']) # Calculate countrate and n_groups if it isn't supplied - n_group, sat_rate = interpolate_from_dat(params['mag'], - params['ins'], params['filt'], params['subarray'], params['mod'], - params['band'], frame_time, params['sat_max'], params['infile']) - + num_groups, saturation_rate = interpolate_from_pandeia( + params['mag'], params['ins'], params['filt'], params['subarray'], params['mod'], params['band'], + frame_time, params['sat_max'], params['infile']) if str(params['n_group']) == 'optimize': - params['n_group'] = int(n_group) + params['n_group'] = int(num_groups) else: params['n_group'] = int(float(params['n_group'])) - - ## -- Aditional helpful params + # Aditional helpful params # Calculate times/ramps/etc - t_int = calc_t_int(params['n_group'], frame_time, n_frame, n_skip) - t_ramp = calc_t_ramp(t_int, n_reset, frame_time) - + integration_time = calc_integration_time(params['n_group'], frame_time, frames_per_group, num_skips) + ramp_time = calc_ramp_time(integration_time, num_reset_frames, frame_time) + # Calculate nubmer of integrations (THE MEAT) - n_int = calc_n_int(params['obs_time'], params['n_group'], n_reset, frame_time, n_frame) - + num_integrations = calc_num_integrations(params['obs_time'], params['n_group'], num_reset_frames, frame_time, frames_per_group) + # Other things that may come in handy who knows? - t_exp = calc_t_exp(n_int, t_ramp) - t_duration = calc_t_duration(params['n_group'], n_int, n_reset, frame_time, n_frame) - obs_eff = calc_obs_efficiency(t_exp, t_duration) - - # Update params with new friends - params['n_col'] = n_col - params['n_row'] = n_row - params['n_amp'] = n_amp - params['n_reset'] = n_reset - params['n_frame'] = n_frame - params['n_skip'] = n_skip - params['t_frame'] = round(frame_time, 3) - params['t_int'] = round(t_int, 3) - params['t_ramp'] = round(t_ramp, 3) - params['n_int'] = n_int - params['t_exp'] = round(t_exp/3600, 3) - params['t_duration'] = round(t_duration/3600, 3) - params['obs_eff'] = round(obs_eff, 3) - params['ta_t_frame'] = ta_frame_time - params['min_ta_groups'] = int(min_ta_groups) + exposure_time = calc_exposure_time(num_integrations, ramp_time) + duration_time = calc_duration_time(params['n_group'], num_integrations, num_reset_frames, frame_time, frames_per_group) + observation_efficiency = calc_observation_efficiency(exposure_time, duration_time) + + # Update params with new information + params['duration_time'] = round(duration_time / 3600, 3) + params['duration_time_ta_max'] = duration_time_ta_max + params['duration_time_ta_min'] = duration_time_ta_min + params['exposure_time'] = round(exposure_time / 3600, 3) + params['frames_per_group'] = frames_per_group + params['frame_time'] = round(frame_time, 3) + params['integration_time'] = round(integration_time, 3) + params['max_saturation_prediction'] = round(saturation_rate * frame_time * params['n_group'], 3) + params['max_saturation_ta'] = round(saturation_rate_ta * ta_frame_time * max_ta_groups, 3) + params['min_saturation_ta'] = round(saturation_rate_ta * ta_frame_time * min_ta_groups, 3) params['max_ta_groups'] = int(max_ta_groups) - params['t_duration_ta_min'] = t_duration_ta_min - params['t_duration_ta_max'] = t_duration_ta_max - params['max_sat_prediction'] = round(sat_rate*frame_time*params['n_group'], 3) - params['max_sat_ta'] = round(sat_rate_ta*ta_frame_time*max_ta_groups, 3) - params['min_sat_ta'] = round(sat_rate_ta*ta_frame_time*min_ta_groups, 3) - - return params + params['min_ta_groups'] = int(min_ta_groups) + params['num_amps'] = num_amps + params['num_columns'] = num_columns + params['num_integrations'] = num_integrations + params['num_reset_frames'] = num_reset_frames + params['num_rows'] = num_rows + params['num_skips'] = num_skips + params['observation_efficiency'] = round(observation_efficiency, 3) + params['ramp_time'] = round(ramp_time, 3) + params['ta_frame_time'] = ta_frame_time + return params -def set_params_from_ins(ins, subarray): + +def set_params_from_instrument(instrument, subarray): """Sets/collects the running parameters from the instrument. - + Parameters ---------- - ins : str - Instrument, options are nircam, niriss, nirpec, and miri. + instrument : str + Instrument, options are ``nircam``, ``niriss``, ``nirpec``, and + ``miri`` subarray : str - Subarray mode. + Subarray mode Returns ------- - rows : int + rows : int The number of pixels per row. cols : int The number of columns per row. + amps : int + The number of amplifiers. + pixel_size : int + The pixel size. + frame_time : float + The frame time. + num_reset_frames : int + The number of reset frames. """ - - n_reset = 1 - - if ins == 'nirspec': - px_size = (40e-4)**2 + num_reset_frames = 1 + + if instrument == 'nirspec': + + pixel_size = (40e-4)**2 if subarray == 'sub2048': rows, cols = 2048, 32 elif subarray in ['sub1024a', 'sub1024b']: rows, cols = 1024, 32 elif subarray == 'sub512': rows, cols = 512, 32 - - amps = 1 # 4 if not NRSRAPID???? - ft = calc_t_frame(cols, rows, amps, ins) - - elif ins == 'nircam': - px_size = (18e-4)**2 - + amps = 1 # 4 if not NRSRAPID???? + frame_time = calc_frame_time(cols, rows, amps, instrument) + + elif instrument == 'nircam': + + pixel_size = (18e-4)**2 if subarray == 'full': rows, cols, amps = 2048, 2048, 4 elif subarray == 'subgrism256': @@ -559,68 +581,57 @@ def set_params_from_ins(ins, subarray): rows, cols, amps = 128, 2048, 1 elif subarray == 'subgrism64': rows, cols, amps = 64, 2048, 1 - - ft = calc_t_frame(cols, rows, amps, ins) - - elif ins == 'miri': - px_size = (25e-4)**2 - + frame_time = calc_frame_time(cols, rows, amps, instrument) + + elif instrument == 'miri': + + pixel_size = (25e-4)**2 if subarray == 'slitlessprism': - rows, cols, ft = 416, 72, .159 - + rows, cols, frame_time = 416, 72, .159 amps = 4 - n_reset = 0 - - elif ins == 'niriss': - px_size = (40e-4)**2 - + num_reset_frames = 0 + + elif instrument == 'niriss': + pixel_size = (40e-4)**2 if subarray == 'substrip96': rows, cols = 2048, 96 elif subarray == 'substrip256': rows, cols = 2048, 256 - amps = 1 - ft = calc_t_frame(cols, rows, amps, ins) - - return rows, cols, amps, px_size, ft, n_reset - + frame_time = calc_frame_time(cols, rows, amps, instrument) + + return rows, cols, amps, pixel_size, frame_time, num_reset_frames -def set_t_frame(infile, ins, sub, ta=False): - """ Assign the appropriate frame time based on the ins - and subarray. For now, modes are implied. + +def set_frame_time(infile, instrument, subarray, target_acq_mode=False): + """Assign the appropriate frame time based on the instrument and + subarray. For now, modes are implied. Parameters ---------- infile: str The path to the data file. - ins : str - The instrument : 'miri', 'niriss', 'nirspec', or - 'nircam'. - sub : str - The subarray -- too lazy to write out the options - here. - ta : bool + instrument : str + The instrument : ``miri``, ``niriss``, ``nirspec``, or + ``nircam`` + subarray : str + The subarray + target_acq_mode : bool Whether this is for TA or not. Returns ------- - t_frame : float - The frame time for this ins/sub combo. + frame_time : float + The frame time for this instrument/subarray combo. """ - + # Read in dict with frame times with open(infile) as f: frame_time = json.load(f)['frame_time'] - if ta: - t_frame = frame_time[ins]['ta'][sub] + if target_acq_mode: + frame_time = frame_time[instrument]['ta'][subarray] else: - t_frame = frame_time[ins][sub] - - return t_frame - - -## -- RUN + frame_time = frame_time[instrument][subarray] -# There's no function call right now because these inputs are ornery. -# I can add one if someone feels strongly. + return frame_time diff --git a/exoctk/helpers.py b/exoctk/helpers.py index ee3ce784..703b8408 100755 --- a/exoctk/helpers.py +++ b/exoctk/helpers.py @@ -1,22 +1,50 @@ #!/usr/bin/python -# -*- coding: latin-1 -*- -""" -A module for helpful code snippets + +"""A module for helpful code snippets. + +Authors +------- + + - Joe Filippazzo + +Use +--- + + This module is intended to be imported and used by other python + modules/scripts, e.g. + + :: + + from exoctk import helpers + helpers.convert_ATLAS9() + +Dependencies +------------ + + - ``astropy`` + - ``numpy`` """ + from glob import glob import os from pkg_resources import resource_filename from shutil import copyfile -from astropy.io import fits, ascii import astropy.constants as ac +from astropy.io import fits, ascii import astropy.units as q import numpy as np + def external_files(): - """ - A snippet to propagate the external files directory + """A snippet to propagate the external files directory to the to the submodules + + + Returns + ------- + ext_files : str + The external files directory """ try: from ConfigParser import ConfigParser @@ -26,10 +54,12 @@ def external_files(): conf = ConfigParser() conf.read(['../setup.cfg']) metadata = dict(conf.items('metadata')) + ext_files = metadata.get('external_files') - return metadata.get('external_files') + return ext_files -def convert_ATLAS9(filepath, destination='', template=resource_filename('ExoCTK', 'data/core/ModelGrid_tmp.fits')): + +def convert_ATLAS9(filepath, destination='', template=resource_filename('exoctk', 'data/core/ModelGrid_tmp.fits')): """ Split ATLAS9 FITS files into separate files containing one Teff, log(g), and Fe/H @@ -37,29 +67,28 @@ def convert_ATLAS9(filepath, destination='', template=resource_filename('ExoCTK' Parameters ---------- - filepath: str - The path to the ATLAS9 FITS file to convert - feh: float - The metallicity for the grid - destination: str + filepath : str + The path to the ``ATLAS9`` FITS file to convert + destination : str The destination for the split files - template: str + template : str The path to the FITS template file to use - """ + """ + # Get all the data L = open(filepath, encoding='utf-8').readlines() - + # Get the indexes of each log(g) chunk start = [] for idx,l in enumerate(L): if l.startswith('TEFF'): start.append(idx) - + # Break up into chunks for n,idx in enumerate(start): - + try: - + # Get the parameters h = L[idx].strip().split() teff = int(h[1].split('.')[0]) @@ -67,58 +96,58 @@ def convert_ATLAS9(filepath, destination='', template=resource_filename('ExoCTK' vturb = float(h[8]) xlen = float(h[11]) feh = float(h[6].replace('[','').replace(']','')) - + # Parse the data try: end = start[n+1] except: end = -1 data = L[idx+3:end-4] - + # Fix column spacing for n,l in enumerate(data): data[n] = l[:19]+' '+' '.join([l[idx:idx+6] for idx in np.arange(19,len(l),6)]) - + # Get cols and data cols = ['wl']+L[idx+2].strip().split() data = ascii.read(data, names=cols) - + # Put intensity array for increasing mu values in a cube data_cube = np.array([data[cols][n] for n in cols[1:]])[::-1] - + # Scale the flux values by the flux(mu=1) value data_cube[:-1] *= data_cube[-1] data_cube[-1] *= 1E5 - + # Apply units data_cube = data_cube*q.erg/q.cm**2/q.s/q.steradian/q.Hz - + # mu values mu = list(map(float,cols[1:]))[::-1] - + # Get the wavelength and convert from nm to A wave = np.array(data['wl'])*q.nm.to(q.AA) - + # Convert the flux from [erg/cm2/s/hz/ster] to [erg*m/cm**2/Hz/s**2/sr] # by multiplying by c/lambda**2 data_cube = data_cube*ac.c/(wave**2) - + # Convert [m/sr] to [cm-1] data_cube = data_cube*q.steradian/q.cm**2 - + # Convert to [erg/s/cm2/cm] data_cube = data_cube.to(q.erg/q.s/q.cm**3)*1E16 - + # Copy the old HDU list logg_txt = str(abs(int(logg*10.))).zfill(2) feh_txt = '{}{}'.format('m' if feh<0 else 'p', str(abs(int(feh*10.))).zfill(2)) new_file = destination+'ATLAS9_{}_{}_{}.fits'.format(teff,logg_txt,feh_txt) HDU = fits.open(template) - + # Write the new data HDU[0].data = data_cube.value HDU[1].data = mu - + # Write the new key/values HDU[0].header['PHXTEFF'] = teff HDU[0].header['PHXLOGG'] = logg @@ -136,16 +165,16 @@ def convert_ATLAS9(filepath, destination='', template=resource_filename('ExoCTK' HDU[0].header['PHXLUM'] = '-' HDU[0].header['CRVAL1'] = '-' HDU[0].header['CDELT1'] = '-' - + # Create a WAVELENGTH extension ext = fits.ImageHDU(wave) ext.update_ext_name('WAVELENGTH') HDU.append(ext) - + # Write the new file fits.HDUList(HDU).writeto(new_file, clobber=True) - + HDU.close() - + except: pass diff --git a/exoctk/limb_darkening/limb_darkening_fit.py b/exoctk/limb_darkening/limb_darkening_fit.py index aa2938b8..18efeb59 100755 --- a/exoctk/limb_darkening/limb_darkening_fit.py +++ b/exoctk/limb_darkening/limb_darkening_fit.py @@ -294,11 +294,14 @@ def calculate(self, Teff, logg, FeH, profile, mu_min=0.05, ld_min=0.01, imu, = np.where(mu > mu_min) scaled_mu, scaled_ld = mu[imu], ld[:, imu] + # Get effective wavelengths + wave_effs = np.mean(bandpass.wave, axis=1) + # Fit limb darkening coefficients for each wavelength bin for n, ldarr in enumerate(scaled_ld): # Get effective wavelength of bin - wave_eff = bandpass.centers[0, n].round(5) + wave_eff = wave_effs[n] try: @@ -314,8 +317,9 @@ def calculate(self, Teff, logg, FeH, profile, mu_min=0.05, ld_min=0.01, # Check the count result['name'] = name or 'Calculation {}'.format(self.count) self.count += 1 - if len(bandpass.centers[0]) == len(scaled_ld) and name is None: - result['name'] = '{} {}'.format(str(round(bandpass.centers[0][n], 2)), self.model_grid.wave_units) + + if bandpass.wave.shape[0] == len(scaled_ld) and name is None: + result['name'] = '{:.3f}'.format(wave_eff) # Set a color if possible result['color'] = color or self.ld_color[profile] diff --git a/exoctk/log_exoctk.py b/exoctk/log_exoctk.py new file mode 100644 index 00000000..2b4bbbea --- /dev/null +++ b/exoctk/log_exoctk.py @@ -0,0 +1,208 @@ +"""This module creates and manages a SQL database as a log for all jobs +submitted via the exoctk web app. + +Authors +------- + + - Joe Filippazzo + +Use +--- + + This module is intended to be imported and used within a separate + python environment, e.g. + + :: + + from exoctk import log_exoctk + log_exoctk.create_db() + +Dependencies +------------ + + - ``astropy`` + - ``numpy`` + - ``pathlib`` + - ``sqlite3`` +""" + +import os +import datetime + +import astropy.table as at +import numpy as np +from pathlib import Path +import sqlite3 + + +def create_db(dbpath, overwrite=True): + """Create a new database at the given ``dbpath`` + + Parameters + ---------- + dbpath : str + The full path for the new database, including the filename + and ``.db`` file extension. + schema : str + The path to the ``.sql`` schema for the database + overwrite : bool + Overwrite dbpath if it already exists + """ + + if dbpath != ':memory:': + + # Make sure the path is valid + if not os.path.exists(os.path.dirname(dbpath)): + raise IOError('Not a valid path:', dbpath) + + # Make sure the file is a .db + if not dbpath.endswith('.db'): + raise IOError('Please provide a path with a .db file extension') + + # Use pathlib.Path to become compliant with bandit. + p = Path(dbpath) + + # Remove existing file if overwriting + if os.path.isfile(dbpath) and overwrite: + p.unlink() + + # Make the new file + p.touch() + + # Generate the tables + conn = sqlite3.connect(dbpath) + cur = conn.cursor() + + # Table for groups_integrations + cur.execute("CREATE TABLE 'groups_integrations' ('id' INTEGER NOT NULL UNIQUE, 'date' TEXT NOT NULL, 'targname' TEXT, 'kmag' REAL, 'mod' TEXT, 'obs_time' REAL, 'n_group' REAL, 'ins' TEXT, 'filt' TEXT, 'filt_ta' TEXT, 'subarray' TEXT, 'subarray_ta' TEXT, 'sat_mode' TEXT, 'sat_max' REAL, PRIMARY KEY(id));") + + # Table for limb_darkening + cur.execute("CREATE TABLE 'limb_darkening' ('id' INTEGER NOT NULL UNIQUE, 'date' TEXT NOT NULL, 'n_bins' INTEGER, 'teff' REAL, 'logg' REAL, 'feh' REAL, 'bandpass' TEXT, 'modeldir' TEXT, 'wave_min' REAL, 'mu_min' REAL, 'wave_max' REAL, 'local_files' TEXT, 'pixels_per_bin' INTEGER, 'uniform' TEXT, 'linear' TEXT, 'quadratic' TEXT, 'squareroot' TEXT, 'logarithmic' TEXT, 'exponential' TEXT, 'three_parameter' TEXT, 'four_parameter' TEXT, PRIMARY KEY(id));") + + # Table for contam_visibility + cur.execute("CREATE TABLE 'contam_visibility' ('id' INTEGER NOT NULL UNIQUE, 'date' TEXT NOT NULL, 'targname' TEXT, 'ra' REAL, 'dec' REAL, 'inst' TEXT, 'companion' TEXT, PRIMARY KEY(id));") + + # Table for phase_constraint + cur.execute("CREATE TABLE 'phase_constraint' ('id' INTEGER NOT NULL UNIQUE, 'date' TEXT NOT NULL, 'targname' TEXT, 'orbital_period' REAL, 'eccentricity' REAL, 'transit_type' TEXT, 'omega' REAL, 'inclination' REAL, 'transit_time' REAL, 'window_size' REAL, 'observation_duration' REAL, 'minimum_phase' REAL, 'maximum_phase' REAL, PRIMARY KEY(id));") + + # Table for fortney grid + cur.execute("CREATE TABLE 'fortney' ('id' INTEGER NOT NULL UNIQUE, 'date' TEXT NOT NULL, 'ptemp' REAL, 'pchem' TEXT, 'cloud' TEXT, 'pmass' REAL, 'm_unit' TEXT, 'refrad' REAL, 'r_unit' TEXT, 'rstar' REAL, 'rstar_unit' TEXT, PRIMARY KEY(id));") + + # Table for generic grid + cur.execute("CREATE TABLE 'generic' ('id' INTEGER NOT NULL UNIQUE, 'date' TEXT NOT NULL, 'temperature' REAL, 'gravity' REAL, 'r_planet' REAL, 'r_star' REAL, 'condensation' TEXT, 'metallicity' REAL, 'c_o' REAL, 'haze' REAL, 'cloud' REAL, PRIMARY KEY(id));") + + # Commit and close the connection + conn.commit() + conn.close() + + if os.path.isfile(dbpath): + print("ExoCTK database created at {}".format(dbpath)) + + +def load_db(dbpath): + """Load a database + + Parameters + ---------- + dbpath : str + The path to the ``.db`` database file + + + Returns + ------- + cur : ``sqlite.connection.cursor`` obj + An SQLite3 Cursor object if dbpath is found. + """ + + if os.path.isfile(dbpath) or dbpath == ':memory:': + + con = sqlite3.connect(dbpath, isolation_level=None, detect_types=sqlite3.PARSE_DECLTYPES, check_same_thread=False) + cur = con.cursor() + + print('Database loaded: {}'.format(dbpath)) + + return cur + + else: + print("Sorry, could not find the file '{}'".format(dbpath)) + + +def log_form_input(form_dict, table, database): + """A function to store the form inputs of any page ``GET`` requests + in a database. + + Parameters + ---------- + form_dict : dict + The dictionary of form inputs + table : str + The table name to INSERT on + database : ``sqlite.connection.cursor`` obj + The database cursor object + """ + try: + + # Get the column names + colnames = np.array(database.execute("PRAGMA table_info('{}')".format(table)).fetchall()).T[1] + + # Convert hyphens to underscores and leading numerics to letters for db column names + inpt = {k.replace('-', '_').replace('3', 'three').replace('4', 'four'): v for k, v in form_dict.items()} + + # Add a timestamp + inpt['date'] = datetime.datetime.now().strftime("%Y-%m-%d %H:%M") + + # Insert the form values that are valid column names + cols = [col for col in inpt.keys() if col in colnames] + vals = [str(inpt.get(col, 'none')) for col in cols] + qry = "Insert Into {} ({}) Values ({})".format(table, ', '.join(cols), ', '.join('?' * len(cols))) + database.execute(qry, vals) + + except Exception as e: + print('Could not log form submission.') + print(e) + + +def view_log(database, table, limit=50): + """Visually inspect the job log. + + Parameters + ---------- + database : str or ``sqlite3.connection.cursor`` obj + The database cursor object + table : str + The table name + limit : int + The number of records to show + + Returns + ------- + table : ``astropy.Table`` obj + An astropy.table object containing the results. + + """ + + if isinstance(database, str): + DB = load_db(database) + elif isinstance(database, sqlite3.Cursor): + DB = database + else: + print("Please enter the path to a .db file or a sqlite.Cursor object.") + + # Query the database + colnames = np.array(DB.execute("PRAGMA table_info('{}')".format(table)).fetchall()).T[1] + results = DB.execute("SELECT * FROM {} LIMIT {}".format(table, limit)).fetchall() + + # Empty table + table = at.Table(names=colnames, dtype=['O'] * len(colnames)) + + # Add the results + if len(results) > 0: + for row in results: + table.add_row(row) + + return table + + +def scrub(table_name): + """Snippet to prevent SQL injection attcks! PEW PEW PEW!""" + return ''.join(chr for chr in table_name if chr.isalnum()) diff --git a/exoctk/modelgrid.py b/exoctk/modelgrid.py index f21e627d..1af6f614 100644 --- a/exoctk/modelgrid.py +++ b/exoctk/modelgrid.py @@ -26,6 +26,8 @@ warnings.simplefilter('ignore', category=AstropyWarning) warnings.simplefilter('ignore', category=FutureWarning) +ON_GITHUB_ACTIONS = os.path.expanduser('~') in ['/home/runner', '/Users/runner'] + class ModelGrid(object): """ @@ -77,6 +79,10 @@ def __init__(self, model_directory, bibcode='2013A & A...553A...6H', of the grid spectra wave_units: astropy.units.quantity """ + + if not ON_GITHUB_ACTIONS: + utils.check_for_data('modelgrid') + # Make sure we can use glob if a directory # is given without a wildcard if '*' not in model_directory: diff --git a/exoctk/notebooks/figures/._binCompsField.png b/exoctk/notebooks/figures/._binCompsField.png deleted file mode 100644 index 56ec00f3..00000000 Binary files a/exoctk/notebooks/figures/._binCompsField.png and /dev/null differ diff --git a/exoctk/tests/__init__.py b/exoctk/tests/__init__.py index b777aea0..662bf4bd 100644 --- a/exoctk/tests/__init__.py +++ b/exoctk/tests/__init__.py @@ -7,3 +7,4 @@ from . import test_lightcurve_fitting from . import test_limb_darkening from . import test_modelgrid +from . import test_visibilityPA diff --git a/exoctk/tests/test_atmospheric_retrievals.py b/exoctk/tests/test_atmospheric_retrievals.py index 5cc74d80..860eb529 100755 --- a/exoctk/tests/test_atmospheric_retrievals.py +++ b/exoctk/tests/test_atmospheric_retrievals.py @@ -26,7 +26,7 @@ from ..atmospheric_retrievals.platon_wrapper import _apply_factors from ..atmospheric_retrievals.platon_wrapper import PlatonWrapper -ON_TRAVIS = os.path.expanduser('~') in ['/Users/travis', '/home/travis'] +ON_GITHUB_ACTIONS = os.path.expanduser('~') in ['/home/runner', '/Users/runner'] def initialize_platon_wrapper_object(): @@ -103,7 +103,7 @@ def test_get_config(): assert 'ssh_file' in settings -@pytest.mark.skipif(ON_TRAVIS, reason='Test takes too long on Travis server. Try testing locally.') +@pytest.mark.skipif(ON_GITHUB_ACTIONS, reason='Test takes too long on Travis server. Try testing locally.') def test_retrieve_emcee(): """Test that the ``emcee`` method of ``platon_wrapper`` produces results for a small example. @@ -115,7 +115,7 @@ def test_retrieve_emcee(): assert pw.result -@pytest.mark.skipif(ON_TRAVIS, reason='Test takes too long on Travis server. Try testing locally.') +@pytest.mark.skipif(ON_GITHUB_ACTIONS, reason='Test takes too long on Travis server. Try testing locally.') def test_retrieve_multinest(): """Test that the ``multinest`` method of ``platon_wrapper`` produces results for a small example. diff --git a/exoctk/tests/test_visibilityPA.py b/exoctk/tests/test_visibilityPA.py new file mode 100644 index 00000000..d5bb72d0 --- /dev/null +++ b/exoctk/tests/test_visibilityPA.py @@ -0,0 +1,28 @@ +import sys + +import pytest + +from exoctk.contam_visibility import visibilityPA + + +@pytest.mark.skipif(sys.version_info > (3, 9), reason='jwst_gtvt does not currently support python>=3.9.') +def test_using_gtvt(): + instrument = 'NIRISS' + + # this ra/dec has bad PAs + ra = "-66" + dec = "44" + paMin, paMax, gd, fig, table, grouped_badPAs = visibilityPA.using_gtvt(ra, dec, instrument, targetName="Target", output="bokeh") + assert grouped_badPAs is not None + + # this ra/dec has 100% coverage (no bad PAs) + ra = '88' + dec = '-64' + output = visibilityPA.using_gtvt(ra, dec, instrument, targetName="Target", output="bokeh") + + assert output is not None + assert len(output) == 6 + + paMin, paMax, gd, fig, table, grouped_badPAs = output + + assert len(grouped_badPAs) == 0 diff --git a/exoctk/throughputs.py b/exoctk/throughputs.py new file mode 100644 index 00000000..a4b9c69e --- /dev/null +++ b/exoctk/throughputs.py @@ -0,0 +1,150 @@ +# !/usr/bin/python +# -*- coding: latin-1 -*- +""" +A module for creating and managing grids of model spectra +""" +from glob import glob +import json +import os +from pkg_resources import resource_filename +import warnings + +import numpy as np +from svo_filters.svo import Filter + +try: + from pandeia.engine.instrument_factory import InstrumentFactory +except ImportError: + print("pandeia not installed. Functionality limited.") + +FILT_DIR = resource_filename('exoctk', 'data/throughputs/') +JWST_THROUGHPUTS = [os.path.basename(file).replace('.txt', '') for file in glob(FILT_DIR + '*')] + + +class Throughput(Filter): + def __init__(self, name, **kwargs): + """ + Initialize the Throughput object as a child class of svo_filters.svo.Filter + + Parameters + ---------- + name: str + The [instrument.element_name] of the filter or disperser + """ + # Check if JWST instrument + if name in JWST_THROUGHPUTS: + + # Change throughput directory + super().__init__(name, filter_directory=FILT_DIR, **kwargs) + + # Otherwise, just use svo_filters default + else: + super().__init__(name, **kwargs) + + +def get_pce(instrument='niriss', mode='soss', filter='clear', disperser='gr700xd', aperture='soss'): + """ + Use pandeia to generate the JWST throughputs + + Parameters + ---------- + instrument: str + The JWST instrument to use, ['niriss', 'nirspec', 'miri', 'nircam'] + mode: str + The observing mode to use, ['soss', 'wfss', 'ami', etc.] + filter: str + The filter wheel element to use + disperser: str + The dispersion element to use + aperture: str + The aperture to use + + Returns + ------- + wave, pce + The wavelength and throughput + """ + # Get optical element configuration + obsmode = {'instrument': instrument, 'mode': mode, 'filter': filter, 'aperture': aperture, 'disperser': disperser} + conf = {'instrument': obsmode} + i = InstrumentFactory(config=conf) + + # Determine wavelength range + wr = i.get_wave_range() + wave = np.linspace(wr['wmin'], wr['wmax'], num=500) + + # Evaluate the throughput + pce = i.get_total_eff(wave) + + return wave, pce + + +def generate_JWST_throughputs(path=None, data_dir=None): + """ + Function to generate .txt filte of all JWST filter and grism throughputs + """ + # Check if environment variable exists + path = path or os.environ.get('pandeia_refdata') + data_dir = data_dir or resource_filename('exoctk', 'data/throughputs/') + + if path is None: + raise IOError("No path to pandeia_refdata directory provided!") + + else: + + # Iterate over science instruments + for inst in ['niriss', 'nircam', 'nirspec', 'miri']: + + # Get all valid configurations from pandeia config file + cfgfile = open(os.path.join(path, 'jwst/{}/config.json'.format(inst))) + cfg = json.load(cfgfile) + cfgfile.close() + + # Iterate over list of modes + for mode, params in cfg['mode_config'].items(): + + # Only interested in science modes + if mode != 'target_acq': + + # Get aperture and filter lists + aper_list = params['apertures'] + filt_list = params['filters'] or ['CLEAR'] + + # Split disperser into orders if necessary + disp_list = [] + try: + for dis in params['dispersers']: + orders = cfg['disperser_config'][dis].get('orders', [1]) + if len(orders) == 1: + disp_list.append(dis) + else: + for order in orders: + disp_list.append('{}_{}'.format(dis, order)) + except KeyError: + disp_list = None + disp_list = disp_list or ['CLEARP'] + + # Make a list of all aperture, dispersion, and filter combinations + combinations = [[[[a, d, f] for f in filt_list] for d in disp_list] for a in aper_list] + combinations = [k for l in [i for j in combinations for i in j] for k in l] + + for conf in combinations: + + try: + + # Get the configuration + aper, disp, filt = conf + + # Generate throughput + wave, thru = get_pce(inst, mode, filt, disp, aper) + name = '.'.join([inst.upper().replace('CAM', 'Cam').replace('SPEC', 'Spec'), filt.upper(), disp.upper(), aper.upper()]) + + # Save to txt file + data = np.array([wave, thru]).T + datafile_path = os.path.join(data_dir, '{}.txt'.format(name)) + with open(datafile_path, 'w+') as datafile_id: + np.savetxt(datafile_id, data) + print("{} file created!".format(datafile_path)) + + except KeyError: + print("Could not produce throughput for {}".format(conf)) \ No newline at end of file diff --git a/exoctk/utils.py b/exoctk/utils.py index 58062309..ef29412c 100755 --- a/exoctk/utils.py +++ b/exoctk/utils.py @@ -15,10 +15,11 @@ from astropy.io import fits import bokeh.palettes as bpal from scipy.interpolate import RegularGridInterpolator -import matplotlib.pyplot as plt import numpy as np from svo_filters import svo +from .throughputs import JWST_THROUGHPUTS + # Supported profiles PROFILES = ['uniform', 'linear', 'quadratic', 'square-root', 'logarithmic', 'exponential', @@ -26,19 +27,38 @@ # Supported filters FILTERS = svo.filters() - -# Get the location of EXOCTK_DATA environvment variable and check that it is valid -EXOCTK_DATA = os.environ.get('EXOCTK_DATA') +NON_JWST = [filt for filt in FILTERS if not filt.startswith('NIRISS') and not filt.startswith('NIRCam') and not filt.startswith('NIRSpec') and not filt.startswith('MIRI')] +FILTERS_LIST = sorted(NON_JWST + JWST_THROUGHPUTS) + +DATA_URLS = { + 'exoctk_contam': ['https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/exoctk_contam.tar.gz'], + 'groups_integrations': ['https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/groups_integrations.tar.gz'], + 'fortney': ['https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/fortney.tar.gz'], + 'generic': ['https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/generic.tar.gz'], + 'exoctk_log': ['https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/exoctk_log.tar.gz'], + 'modelgrid': ['https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/modelgrid_ATLAS9.tar.gz', + 'https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/modelgrid_ACES_1.tar.gz', + 'https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/modelgrid_ACES_2.tar.gz'], + 'all': ['https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/modelgrid_ATLAS9.tar.gz', + 'https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/modelgrid_ACES_1.tar.gz', + 'https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/modelgrid_ACES_2.tar.gz', + 'https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/generic.tar.gz', + 'https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/fortney.tar.gz', + 'https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/groups_integrations.tar.gz', + 'https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/groups_integrations.tar.gz', + 'https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/exoctk_contam.tar.gz'] + } # If the variable is blank or doesn't exist HOME_DIR = os.path.expanduser('~') -ON_TRAVIS_OR_RTD = HOME_DIR == '/home/travis' or HOME_DIR == '/Users/travis' or HOME_DIR == '/home/docs' -if not ON_TRAVIS_OR_RTD: +EXOCTK_DATA = os.environ.get('EXOCTK_DATA', os.path.join(HOME_DIR, 'exoctk_data')) +ON_GITHUB_ACTIONS_OR_RTD = HOME_DIR == '/home/runner' or HOME_DIR == '/Users/runner' or HOME_DIR == '/home/docs' +if not ON_GITHUB_ACTIONS_OR_RTD: if not EXOCTK_DATA: print( 'WARNING: The $EXOCTK_DATA environment variable is not set. Please set the ' 'value of this variable to point to the location of the exoctk_data ' - 'download folder. Users may retreive this folder by clicking the ' + 'download folder. Users may retrieve this folder by clicking the ' '"ExoCTK Data Download" button on the ExoCTK website, or by using ' 'the exoctk.utils.download_exoctk_data() function.') else: @@ -49,13 +69,9 @@ 'cannot be accessed.') # If the variable exists, points to a real location, but is missing contents - for item in ['exoctk_contam', 'exoctk_log', 'fortney', 'generic', 'groups_integrations', 'modelgrid']: + for item in DATA_URLS.keys(): if item not in [os.path.basename(item) for item in glob.glob(os.path.join(EXOCTK_DATA, '*'))]: - print( - 'WARNING: Missing {}/ directory from {}. Please ensure that the ExoCTK data package has been ' - 'downloaded. Users may retrieve this package by clicking the "ExoCTK Data Download" ' - 'button on the ExoCTK website, or by using the exoctk.utils.download_exoctk_data() ' - 'function'.format(item, EXOCTK_DATA)) + os.makedirs(os.path.join(EXOCTK_DATA, item)) EXOCTK_CONTAM_DIR = os.path.join(EXOCTK_DATA, 'exoctk_contam/') EXOCTKLOG_DIR = os.path.join(EXOCTK_DATA, 'exoctk_log/') @@ -65,38 +81,57 @@ MODELGRID_DIR = os.path.join(EXOCTK_DATA, 'modelgrid/') -def download_exoctk_data(download_location=os.path.expanduser('~')): +def check_for_data(tool): + """Checks to see if the necessary data has been downloaded for the given tool + + Parameters + ---------- + tool: str + The tool to check for + """ + # Validate tool + if tool not in DATA_URLS: + raise ValueError("'{}' not a supported tool. Try {}".format(tool, list(DATA_URLS.keys()))) + + # Make a path and glob the files + path = os.path.join(EXOCTK_DATA, tool) + files = glob.glob(os.path.join(path, '*')) + print(path, files) + + if len(files) == 0: + raise IOError("This tool requires the '{0}' data. Try downloading with exoctk.utils.download_exoctk_data('{0}')".format(tool)) + + +def download_exoctk_data(tool='all', exoctk_data_dir=EXOCTK_DATA): """Retrieves the ``exoctk_data`` materials from Box, downloads them to the user's local machine, uncompresses the files, and arranges them into an ``exoctk_data`` directory. Parameters ---------- - download_location : string + tool: str + The ExoCTK tool data to download + exoctk_data_dir : string The path to where the ExoCTK data package will be downloaded. The default setting is the user's $HOME directory. """ + # Validate tool + if tool not in DATA_URLS: + raise ValueError("'{}' not a supported tool. Try {}".format(tool, list(DATA_URLS.keys()))) print('\nDownloading ExoCTK data package. This may take a few minutes.') - print('Materials will be downloaded to {}/exoctk_data/\n'.format(download_location)) + print('Materials will be downloaded to {}/\n'.format(exoctk_data_dir)) # Ensure the exoctk_data/ directory exists in user's home directory - exoctk_data_dir = os.path.join(download_location, 'exoctk_data') try: if not os.path.exists(exoctk_data_dir): os.makedirs(exoctk_data_dir) except PermissionError: - print('Data download failed. Unable to create {}. Please check permissions.') + print('Data download failed. Unable to create {}. Please check permissions.'.format(exoctk_data_dir)) - # URLs to download contents - urls = ['https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/exoctk_contam.tar.gz', - 'https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/exoctk_log.tar.gz', - 'https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/groups_integrations.tar.gz', - 'https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/fortney.tar.gz', - 'https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/generic.tar.gz', - 'https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/modelgrid_ATLAS9.tar.gz', - 'https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/modelgrid_ACES_1.tar.gz', - 'https://data.science.stsci.edu/redirect/JWST/ExoCTK/compressed/modelgrid_ACES_2.tar.gz'] + # Select the URLs and always include the log files + urls = DATA_URLS[tool] + urls += DATA_URLS['exoctk_log'] # Build landing paths for downloads download_paths = [os.path.join(exoctk_data_dir, os.path.basename(url)) for url in urls] @@ -104,7 +139,7 @@ def download_exoctk_data(download_location=os.path.expanduser('~')): # Perform the downloads for i, url in enumerate(urls): landing_path = os.path.join(exoctk_data_dir, os.path.basename(url)) - print('({}/{}) Downloading data to {} from {}'.format(i+1, len(urls), landing_path, url)) + print('({}/{}) Downloading data to {} from {}'.format(i + 1, len(urls), landing_path, url)) with requests.get(url, stream=True) as response: with open(landing_path, 'wb') as f: for chunk in response.iter_content(chunk_size=2048): @@ -138,9 +173,11 @@ def download_exoctk_data(download_location=os.path.expanduser('~')): shutil.move(src, dst) except shutil.Error: print('Unable to organize modelgrid/ directory') - shutil.rmtree(os.path.join(exoctk_data_dir, 'modelgrid.ATLAS9')) - shutil.rmtree(os.path.join(exoctk_data_dir, 'modelgrid.ACES_1')) - shutil.rmtree(os.path.join(exoctk_data_dir, 'modelgrid.ACES_2')) + + for dir in ['modelgrid.ATLAS9', 'modelgrid.ACES_1', 'modelgrid.ACES_2']: + path = os.path.join(exoctk_data_dir, dir) + if os.path.exists(path): + shutil.rmtree(path) print('Completed!') @@ -233,13 +270,13 @@ def calc_zoom(R_f, arr): The array to zoom """ # Get initial resolution - lam = arr[-1]-arr[0] + lam = arr[-1] - arr[0] d_lam_i = np.nanmean(np.diff(arr)) # R_i = lam/d_lam_i # Calculate zoom - d_lam_f = lam/R_f - z = d_lam_i/d_lam_f + d_lam_f = lam / R_f + z = d_lam_i / d_lam_f return z @@ -265,23 +302,19 @@ def rebin_spec(spec, wavnew, oversamp=100, plot=False): wave, flux = spec nlam = len(wave) x0 = np.arange(nlam, dtype=float) - x0int = np.arange((nlam-1.) * oversamp + 1., dtype=float)/oversamp + x0int = np.arange((nlam - 1.) * oversamp + 1., dtype=float) / oversamp w0int = np.interp(x0int, x0, wave) - spec0int = np.interp(w0int, wave, flux)/oversamp + spec0int = np.interp(w0int, wave, flux) / oversamp # Set up the bin edges for down-binning maxdiffw1 = np.diff(wavnew).max() - w1bins = np.concatenate(([wavnew[0]-maxdiffw1], - .5*(wavnew[1::]+wavnew[0: -1]), - [wavnew[-1]+maxdiffw1])) + w1bins = np.concatenate(([wavnew[0] - maxdiffw1], .5 * (wavnew[1::] + wavnew[0: -1]), [wavnew[-1] + maxdiffw1])) # Bin down the interpolated spectrum: w1bins = np.sort(w1bins) - nbins = len(w1bins)-1 + nbins = len(w1bins) - 1 specnew = np.zeros(nbins) - inds2 = [[w0int.searchsorted(w1bins[ii], side='left'), - w0int.searchsorted(w1bins[ii+1], side='left')] - for ii in range(nbins)] + inds2 = [[w0int.searchsorted(w1bins[ii], side='left'), w0int.searchsorted(w1bins[ii + 1], side='left')] for ii in range(nbins)] for ii in range(nbins): specnew[ii] = np.sum(spec0int[inds2[ii][0]: inds2[ii][1]]) @@ -367,17 +400,16 @@ def smooth(x, window_len=10, window='hanning'): raise ValueError("Window is one of 'flat', 'hanning', 'hamming',\ 'bartlett', 'blackman'") - s = np.r_[2*np.median(x[0: window_len/5])-x[window_len: 1: -1], x, - 2*np.median(x[-window_len/5:])-x[-1: -window_len: -1]] + s = np.r_[2 * np.median(x[0: window_len / 5]) - x[window_len: 1: -1], x, 2 * np.median(x[-window_len / 5:]) - x[-1: -window_len: -1]] if window == 'flat': w = np.ones(window_len, 'd') else: - w = eval('np.'+window+'(window_len)') + w = eval('np.' + window + '(window_len)') - y = np.convolve(w/w.sum(), s, mode='same') + y = np.convolve(w / w.sum(), s, mode='same') - return y[window_len-1: -window_len+1] + return y[window_len - 1: -window_len + 1] def medfilt(x, window_len): @@ -401,12 +433,11 @@ def medfilt(x, window_len): if window_len % 2 == 0: s1 = "Median filter length (" s2 = ") must be odd. Adding 1." - print(s1+str(window_len)+s2) + print(s1 + str(window_len) + s2) window_len += 1 window_len = int(window_len) - k2 = int((window_len - 1)//2) - s = np.r_[2*np.median(x[0: int(window_len/5)])-x[window_len: 1: -1], - x, 2*np.median(x[int(-window_len/5):])-x[-1: -window_len: -1]] + k2 = int((window_len - 1) // 2) + s = np.r_[2 * np.median(x[0: int(window_len / 5)]) - x[window_len: 1: -1], x, 2 * np.median(x[int(-window_len / 5):]) - x[-1: -window_len: -1]] y = np.zeros((len(s), window_len), dtype=s.dtype) y[:, k2] = s @@ -414,9 +445,9 @@ def medfilt(x, window_len): j = k2 - i y[j:, i] = s[:-j] y[: j, i] = s[0] - y[: -j, -(i+1)] = s[j:] - y[-j:, -(i+1)] = s[-1] - return np.median(y[window_len-1: -window_len+1], axis=1) + y[: -j, -(i + 1)] = s[j:] + y[-j:, -(i + 1)] = s[-1] + return np.median(y[window_len - 1: -window_len + 1], axis=1) def filter_table(table, **kwargs): @@ -452,14 +483,12 @@ def filter_table(table, **kwargs): data = list(map(str, table[param])) if not value.startswith('*'): - value = '^'+value + value = '^' + value if not value.endswith('*'): - value = value+'$' + value = value + '$' # Strip double quotes and decod - value = value.replace("'", '')\ - .replace('"', '')\ - .replace('*', '(.*)') + value = value.replace("'", '').replace('"', '').replace('*', '(.*)') # Regex reg = re.compile(value, re.IGNORECASE) @@ -482,7 +511,7 @@ def filter_table(table, **kwargs): # Assume eqality if no operator else: - value = ['=='+value] + value = ['==' + value] # Turn numbers into strings if isinstance(value, (int, float, np.float16)): @@ -494,7 +523,7 @@ def filter_table(table, **kwargs): # Equality if cond.startswith('='): v = cond.replace('=', '') - if v.replace('.','',1).isdigit(): + if v.replace('.', '', 1).isdigit(): table = table[table[param] == eval(v)] else: table = table[table[param] == v] @@ -550,8 +579,8 @@ def find_closest(axes, points, n=1, values=False): for i, (axis, point) in enumerate(zip(axes, points)): if point >= min(axis) and point <= max(axis): axis = np.asarray(axis) - idx = np.clip(axis.searchsorted(point), 1, len(axis)-1) - slc = slice(max(0, idx-n), min(idx+n, len(axis))) + idx = np.clip(axis.searchsorted(point), 1, len(axis) - 1) + slc = slice(max(0, idx - n), min(idx + n, len(axis))) if values: result = axis[slc] @@ -566,6 +595,7 @@ def find_closest(axes, points, n=1, values=False): return results + def build_target_url(target_name): '''Build restful api url based on target name. @@ -584,6 +614,7 @@ def build_target_url(target_name): return target_url + def get_canonical_name(target_name): '''Get ExoMAST prefered name for exoplanet. @@ -600,7 +631,7 @@ def get_canonical_name(target_name): target_url = "https://exo.mast.stsci.edu/api/v0.1/exoplanets/identifiers/" # Create params dict for url parsing. Easier than trying to format yourself. - params = {"name":target_name} + params = {"name": target_name} r = requests.get(target_url, params=params) planetnames = r.json() @@ -608,6 +639,7 @@ def get_canonical_name(target_name): return canonical_name + def get_env_variables(): """Returns a dictionary containing various environment variable information. @@ -624,8 +656,8 @@ def get_env_variables(): env_variables['exoctk_data'] = os.environ.get('EXOCTK_DATA') # If the variable is blank or doesn't exist - ON_TRAVIS = os.path.expanduser('~') == '/home/travis' or os.path.expanduser('~') == '/Users/travis' - if not ON_TRAVIS: + ON_GITHUB_ACTIONS = os.path.expanduser('~') == '/home/runner' or os.path.expanduser('~') == '/Users/runner' + if not ON_GITHUB_ACTIONS: if not env_variables['exoctk_data']: raise ValueError( 'The $EXOCTK_DATA environment variable is not set. Please set the ' diff --git a/pip_requirements.txt b/pip_requirements.txt index aad10577..c586d2fa 100644 --- a/pip_requirements.txt +++ b/pip_requirements.txt @@ -1,38 +1,39 @@ asteval==0.9.16 -astropy==4.2 -astroquery==0.4.1 +astropy==4.0.2 bandit==1.7.0 batman-package==2.4.6 bibtexparser==1.2.0 -bokeh==2.2.3 -boto3==1.16.47 -corner==2.1.0 -cython==0.29.21 +bokeh==2.3.0 +boto3==1.17.42 +corner==2.2.1 +cython==0.29.22 +ddtrace==0.48.2 docopt==0.6.2 docutils==0.16 -flake8==3.8.4 +flake8==3.9.0 flask==1.1.2 flask_wtf==0.14.3 -gunicorn==20.0.4 -h5py==3.1.0 -ipython==7.19.0 +gunicorn==20.1.0 +h5py==3.2.1 +ipython==7.22.0 lmfit==1.0.1 -matplotlib==3.3.3 -numpy==1.19.4 +matplotlib==3.4.1 +numpy==1.20.2 numpydoc==1.1.0 -pandas==1.2.0 +pandas==1.2.3 paramiko==2.7.2 platon==5.1.2 pysiaf==0.10.0 pysynphot==1.0.0 -pytest==6.2.1 -pyyaml==5.3.1 -scipy==1.6.0 +pytest==6.2.2 +pyyaml==5.4.1 +scipy==1.6.2 scp==0.13.3 -sphinx==3.4.1 +sphinx==3.5.3 sphinx_astropy==1.3 sphinx-automodapi==0.13 -sqlalchemy==1.3.22 -svo_filters==0.3.0 +svo_filters==0.4.1 +sqlalchemy==1.4.4 wtforms==2.3.3 git+https://github.com/spacetelescope/jwst_gtvt.git@cd6bc76f66f478eafbcc71834d3e735c73e03ed5 +git+https://github.com/astropy/astroquery.git@ccc96185beeff86f3a12a31a00a801afcebe1dbe diff --git a/setup.py b/setup.py index d640198b..a92fa003 100755 --- a/setup.py +++ b/setup.py @@ -3,7 +3,7 @@ from setuptools import setup, find_packages REQUIRES = ['asteval', - 'astropy', + 'astropy<4.1', 'astroquery', 'bandit', 'bibtexparser', @@ -11,8 +11,9 @@ 'boto3', 'corner', 'cython', + 'ddtrace', 'docopt', - 'docutils==0.14', + 'docutils==0.15.2', 'flake8', 'flask', 'flask_wtf', @@ -37,27 +38,28 @@ 'sqlalchemy', 'svo_filters', 'wtforms', - 'werkzeug==0.16.1'] - -DEPENDENCY_LINKS = ['git+https://github.com/spacetelescope/jwst_gtvt.git@cd6bc76f66f478eafbcc71834d3e735c73e03ed5'] + 'werkzeug==0.16.1', + 'jwst_gtvt @ git+https://github.com/spacetelescope/jwst_gtvt.git@cd6bc76f66f478eafbcc71834d3e735c73e03ed5'] FILES = [] for root, _, files in os.walk("exoctk"): - FILES += [os.path.join(root.replace("exoctk/", ""), fname) \ - for fname in files if not fname.endswith(".py") and not fname.endswith(".pyc")] + FILES += [os.path.join(root.replace("exoctk/", ""), fname) + for fname in files if not fname.endswith(".py") and not fname.endswith(".pyc")] -setup(name='exoctk', - version='1.1.0', - description='Observation reduction and planning tools for exoplanet science', - packages=find_packages(".", exclude=["*.tests"]), - package_data={'exoctk': FILES}, - install_requires=REQUIRES, - dependency_links=DEPENDENCY_LINKS, - author='The ExoCTK Group', - author_email='exoctk@gmail.com', - license='MIT', - url='https://github.com/ExoCTK/exoctk', - long_description='', - zip_safe=True, - use_2to3=False -) +setup( + name='exoctk', + version='1.2.0', + description='Observation reduction and planning tools for exoplanet science', + packages=find_packages( + ".", + exclude=["*.tests"]), + package_data={ + 'exoctk': FILES}, + install_requires=REQUIRES, + author='The ExoCTK Group', + author_email='exoctk@gmail.com', + license='MIT', + url='https://github.com/ExoCTK/exoctk', + long_description='', + zip_safe=True, + use_2to3=False)