├── .github └── workflows │ ├── build-wheels.sh │ └── test.yml ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.rst ├── commit_www.bash ├── cosmolopy ├── EH │ ├── LISCENSE │ ├── README │ ├── __init__.py │ ├── power.c │ ├── power.i │ ├── tests │ │ ├── test_power.py │ │ └── test_tf_fit.py │ ├── tf_fit.c │ └── tf_fit.i ├── __init__.py ├── __version__.py ├── constants.py ├── density.py ├── distance.py ├── luminosityfunction.py ├── magnitudes.py ├── parameters.py ├── perturbation.py ├── reionization.py ├── saveable.py └── utils.py ├── examples └── plot_2d_distances.py ├── make_docs.bash ├── pypi_notes.txt ├── requirements.txt ├── setup.cfg ├── setup.py ├── tests ├── icosmo_testdata │ ├── distances.txt │ ├── growth.txt │ ├── h_z.txt │ ├── power_z0.1_nb.txt │ ├── power_z0.5_nb.txt │ ├── power_z0.txt │ ├── power_z0_b.txt │ ├── power_z0_nb.txt │ ├── power_z1_nb.txt │ ├── power_z3_nb.txt │ ├── power_z4.9.txt │ ├── power_z4.9_b.txt │ └── power_z4.9_nb.txt ├── test_BrokenPowerlawSED.py ├── test_SFR_from_L_nu.py ├── test_age.py ├── test_distances.py ├── test_growth.py ├── test_plot_BKP.py ├── test_plot_HH.py ├── test_plot_Hogg.py ├── test_plot_clumping_factor_Chary.py ├── test_plot_optical_depth.py ├── test_plot_reionization.py ├── test_plot_reionization_BH.py ├── test_utils.py ├── test_wmap.py └── testingutils.py └── www ├── astrobetter.html ├── astrobetter_example.py ├── astropy.html ├── cosmolopy.css ├── docAPI ├── _tf_fit'-module.html ├── api-objects.txt ├── class-tree.html ├── cosmolopy-module.html ├── cosmolopy-pysrc.html ├── cosmolopy.EH-module.html ├── cosmolopy.EH-pysrc.html ├── cosmolopy.EH._power-module.html ├── cosmolopy.EH.download_EH_power-module.html ├── cosmolopy.EH.download_EH_power-pysrc.html ├── cosmolopy.EH.power-module.html ├── cosmolopy.EH.power-pysrc.html ├── cosmolopy.EH.tf_fit-module.html ├── cosmolopy.EH.tf_fit-pysrc.html ├── cosmolopy.constants-module.html ├── cosmolopy.constants-pysrc.html ├── cosmolopy.density-module.html ├── cosmolopy.density-pysrc.html ├── cosmolopy.distance-module.html ├── cosmolopy.distance-pysrc.html ├── cosmolopy.luminosityfunction-module.html ├── cosmolopy.luminosityfunction-pysrc.html ├── cosmolopy.luminosityfunction.BrokenPowerlawSED-class.html ├── cosmolopy.luminosityfunction.LFHistory-class.html ├── cosmolopy.magnitudes-module.html ├── cosmolopy.magnitudes-pysrc.html ├── cosmolopy.parameters-module.html ├── cosmolopy.parameters-pysrc.html ├── cosmolopy.perturbation-module.html ├── cosmolopy.perturbation-pysrc.html ├── cosmolopy.reionization-module.html ├── cosmolopy.reionization-pysrc.html ├── cosmolopy.saveable-module.html ├── cosmolopy.saveable-pysrc.html ├── cosmolopy.saveable.NullWriter-class.html ├── cosmolopy.saveable.Saveable-class.html ├── cosmolopy.utils-module.html ├── cosmolopy.utils-pysrc.html ├── cosmolopy.utils.AgeSpacedRedshift-class.html ├── cosmolopy.utils.Extrapolate1d-class.html ├── cosmolopy.utils.Normalize-class.html ├── cosmolopy.utils.PiecewisePowerlaw-class.html ├── crarr.png ├── epydoc.css ├── epydoc.js ├── frames.html ├── help.html ├── identifier-index.html ├── index.html ├── module-tree.html ├── redirect.html ├── toc-cosmolopy-module.html ├── toc-cosmolopy.EH-module.html ├── toc-cosmolopy.EH._power-module.html ├── toc-cosmolopy.EH.download_EH_power-module.html ├── toc-cosmolopy.EH.power-module.html ├── toc-cosmolopy.constants-module.html ├── toc-cosmolopy.density-module.html ├── toc-cosmolopy.distance-module.html ├── toc-cosmolopy.luminosityfunction-module.html ├── toc-cosmolopy.magnitudes-module.html ├── toc-cosmolopy.parameters-module.html ├── toc-cosmolopy.perturbation-module.html ├── toc-cosmolopy.reionization-module.html ├── toc-cosmolopy.saveable-module.html ├── toc-cosmolopy.utils-module.html ├── toc-everything.html ├── toc.html ├── uml_class_diagram_for_cosmolop.gif ├── uml_class_diagram_for_cosmolop_2.gif ├── uml_class_diagram_for_cosmolop_3.gif ├── uml_class_diagram_for_cosmolop_4.gif └── uml_class_diagram_for_cosmolop_5.gif ├── figs ├── dist2d_D_A.png ├── dist2d_D_A_ony.png ├── dist2d_D_A_ony_small.png ├── dist2d_D_A_small.png ├── dist2d_D_M.png ├── dist2d_D_M_ony.png ├── dist2d_D_M_ony_small.png ├── dist2d_D_M_small.png └── makefigs.bash ├── index.html ├── others.html └── others.txt /.github/workflows/build-wheels.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -e -x 3 | 4 | # Install swig3 5 | yum localinstall -y http://springdale.math.ias.edu/data/puias/computational/6/x86_64//swig3012-3.0.12-3.sdl6.x86_64.rpm 6 | ln /usr/local/swig/3.0.12/bin/swig /usr/bin/swig --symbolic 7 | ln /usr/local/swig/3.0.12/bin/ccache-swig /usr/bin/ccache-swig --symbolic 8 | 9 | # Compile wheels 10 | for PYBIN in /opt/python/*[3][678]*/bin; do 11 | "${PYBIN}/pip" install -r /io/requirements.txt 12 | "${PYBIN}/pip" wheel /io/ -w wheelhouse/ 13 | done 14 | 15 | # Bundle external shared libraries into the wheels 16 | for whl in wheelhouse/cosmolopy*.whl; do 17 | auditwheel repair "$whl" --plat $PLAT -w /io/wheelhouse/ 18 | done 19 | 20 | # Install packages and test 21 | for PYBIN in /opt/python/*[3][678]*/bin/; do 22 | "${PYBIN}/pip" install cosmolopy --no-index -f /io/wheelhouse 23 | "${PYBIN}/python" -c "import cosmolopy; import cosmolopy.EH.power" 24 | done 25 | -------------------------------------------------------------------------------- /.github/workflows/test.yml: -------------------------------------------------------------------------------- 1 | # This workflow will install Python dependencies, run tests and lint with a variety of Python versions 2 | # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions 3 | 4 | name: Test 5 | 6 | on: [push, pull_request] 7 | 8 | jobs: 9 | ubuntu: 10 | name: ubuntu-latest 11 | runs-on: ubuntu-latest 12 | strategy: 13 | matrix: 14 | docker_image: [quay.io/pypa/manylinux2010_x86_64] 15 | platform: [manylinux2010_x86_64] 16 | fail-fast: false 17 | 18 | steps: 19 | - uses: actions/checkout@v2 20 | - name: Pull Docker image 21 | run: | 22 | docker pull ${{ matrix.docker_image }} 23 | - name: Run Docker image 24 | run: | 25 | docker run --rm -e PLAT=${{ matrix.platform }} -v `pwd`:/io ${{ matrix.docker_image }} $PRE_CMD /io/.github/workflows/build-wheels.sh 26 | - name: Deploy package 27 | if: ${{ success() && github.event_name == 'push' && github.ref == 'refs/heads/master' }} 28 | env: 29 | TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }} 30 | TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }} 31 | run: | 32 | pip install twine 33 | twine upload --skip-existing wheelhouse/cosmolopy* 34 | 35 | macosx: 36 | name: ${{ matrix.os }} ${{ matrix.architecture }}, Python ${{ matrix.python-version }} 37 | runs-on: ${{ matrix.os }} 38 | strategy: 39 | matrix: 40 | architecture: [x64] 41 | os: [macos-latest] 42 | python-version: [3.6, 3.7, 3.8] 43 | fail-fast: false 44 | 45 | steps: 46 | - uses: actions/checkout@v2 47 | - name: Set up Python ${{ matrix.python-version }} ${{ matrix.architecture }} 48 | uses: actions/setup-python@v2 49 | with: 50 | python-version: ${{ matrix.python-version }} 51 | architecture: ${{ matrix.architecture }} 52 | - name: Install dependencies 53 | run: | 54 | brew install swig@3 55 | brew link swig@3 56 | python -m pip install --upgrade pip setuptools wheel 57 | pip install -r requirements.txt 58 | - name: Create wheels 59 | run: | 60 | python setup.py sdist -d wheelhouse 61 | pip wheel . -w wheelhouse 62 | cd wheelhouse 63 | pip install cosmolopy --no-index -f . 64 | python -c "import cosmolopy; import cosmolopy.EH.power" 65 | cd .. 66 | - name: Deploy package 67 | if: ${{ success() && github.event_name == 'push' && github.ref == 'refs/heads/master' }} 68 | env: 69 | TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }} 70 | TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }} 71 | run: | 72 | pip install twine 73 | twine upload --skip-existing wheelhouse/cosmolopy* 74 | 75 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | *~ 2 | .coverage 3 | *.pyc 4 | cosmolopy/EH/*.o 5 | cosmolopy/EH/*.so 6 | CosmoloPy.egg-info/ 7 | build/ 8 | dist/ -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | The MIT License 2 | 3 | Copyright (c) 2009-2010 Roban Hultman Kramer and contributors 4 | http://roban.github.com/CosmoloPy/ 5 | 6 | Permission is hereby granted, free of charge, to any person obtaining a copy 7 | of this software and associated documentation files (the "Software"), to deal 8 | in the Software without restriction, including without limitation the rights 9 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 | copies of the Software, and to permit persons to whom the Software is 11 | furnished to do so, subject to the following conditions: 12 | 13 | The above copyright notice and this permission notice shall be included in 14 | all copies or substantial portions of the Software. 15 | 16 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 22 | THE SOFTWARE. 23 | 24 | -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include LISCENSE 2 | include README.rst 3 | include MANIFEST.in 4 | include requirements*.txt 5 | include conftest.py 6 | 7 | exclude travis www 8 | recursive-exclude travis * 9 | recursive-exclude www * 10 | exclude *.yml 11 | exclude *.bash 12 | exclude pypi_notes.txt 13 | recursive-exclude * __pycache__ 14 | recursive-exclude * *.py[co] 15 | -------------------------------------------------------------------------------- /README.rst: -------------------------------------------------------------------------------- 1 | ========= 2 | CosmoloPy 3 | ========= 4 | 5 | A cosmology package for Python. 6 | 7 | For documentation and installation instructions, see 8 | http://roban.github.io/CosmoloPy/ 9 | 10 | CosmoloPy is released under the MIT software liscense (see LISCENSE). 11 | 12 | Example 13 | ------- 14 | 15 | Calculate the comoving distance to redshift 6. 16 | 17 | >>> import cosmolopy.distance as cd 18 | >>> cosmo = {'omega_M_0':0.3, 'omega_lambda_0':0.7, 'omega_k_0':0.0, 'h':0.72} 19 | >>> d_co = cd.comoving_distance(6., **cosmo) 20 | >>> print "Comoving distance to z=6 is %.1f Mpc" % (d_co) 21 | Comoving distance to z=6 is 8017.8 Mpc 22 | 23 | 24 | Prerequisites 25 | ============= 26 | 27 | Python 28 | NumPy 29 | SciPy 30 | 31 | For tests (optional): 32 | nose 33 | matplotlib 34 | 35 | For power spectrum calculation (needed for most of perturbation module): 36 | python-dev 37 | 38 | Installation from PyPI 39 | ====================== 40 | 41 | You can easily install the package directly from the Python Package 42 | Index with pip. 43 | 44 | Run with: 45 | 46 | > pip install cosmolopy 47 | 48 | Installation from Source 49 | ======================== 50 | 51 | To install from source, you first need to install `SWIG `_ v3 or later. 52 | Then, download the CosmoloPy source and install it by running (in CosmoloPy folder) 53 | 54 | > pip install . 55 | 56 | Testing 57 | ======= 58 | 59 | Note that currently the _udot integration appears to be failing in nosetests. 60 | The prefered way to run all tests is: 61 | 62 | > python setup.py nosetests --with-doctest 63 | 64 | Or if you don't want to run the doctests: 65 | 66 | > python setup.py nosetests 67 | 68 | If you don't have nose: 69 | 70 | > python setup.py test 71 | > python -m doctest cosmolopy/*.py 72 | 73 | Contributors 74 | ============ 75 | 76 | - Python 3 implementation by @JohannesBuchner and @1313e 77 | - Automated PyPI deployment on GitHub Actions by @1313e 78 | -------------------------------------------------------------------------------- /commit_www.bash: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | #From http://happygiraffe.net/blog/tag/git/ 4 | 5 | parent_sha=$(git show-ref -s refs/heads/gh-pages) 6 | doc_sha=$(git ls-tree -d HEAD www | awk '{print $3}') 7 | new_commit=$(echo "Auto-update docs." | git commit-tree $doc_sha -p $parent_sha) 8 | git update-ref refs/heads/gh-pages $new_commit -------------------------------------------------------------------------------- /cosmolopy/EH/LISCENSE: -------------------------------------------------------------------------------- 1 | power.c and tf_fit.f are redistributed under the MIT License with the permission of 2 | Wayne Hu 3 | 4 | http://background.uchicago.edu/~whu/transfer/transferpage.html 5 | 6 | and are described in Eisenstein, D. J., & Hu, W. "Power Spectra for 7 | Cold Dark Matter and Its Variants," 1999, ApJ, 511, 5 8 | [astro-ph/9710252], and Ibid. "Baryonic Features in 9 | the Matter Transfer Function," 1998, ApJ, 496, 605 10 | [astro-ph/9709112]. 11 | 12 | Please cite these papers to acknowledge use of power spectrum calculations. 13 | 14 | The MIT License 15 | 16 | power.c is copyright (c) 1997 Wayne Hu and Daniel Eisenstein 17 | tf_fit.f is copyright (c) 1997 Wayne Hu and Daniel Eisenstein 18 | 19 | Permission is hereby granted, free of charge, to any person obtaining a copy 20 | of this software and associated documentation files (the "Software"), to deal 21 | in the Software without restriction, including without limitation the rights 22 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 23 | copies of the Software, and to permit persons to whom the Software is 24 | furnished to do so, subject to the following conditions: 25 | 26 | The above copyright notice and this permission notice shall be included in 27 | all copies or substantial portions of the Software. 28 | 29 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 30 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 31 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 32 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 33 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 34 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 35 | THE SOFTWARE. 36 | 37 | -------------------------------------------------------------------------------- /cosmolopy/EH/README: -------------------------------------------------------------------------------- 1 | ================================= 2 | Eisenstein & Hu Fitting functions 3 | ================================= 4 | 5 | Power spectra for CDM variants without baryonic effects 6 | ======================================================= 7 | 8 | Original c code 9 | --------------- 10 | 11 | power.c is redistributed under the MIT License with the permission of 12 | Wayne Hu 13 | 14 | http://background.uchicago.edu/~whu/transfer/transferpage.html 15 | 16 | and is described in Eisenstein, D. J., & Hu, W. "Power Spectra for 17 | Cold Dark Matter and Its Variants," 1999, ApJ, 511, 5 18 | [astro-ph/9710252]. Please cite this paper to acknowledge use of power 19 | spectrum calculations. 20 | 21 | See LISCENSE file. 22 | 23 | Python Interface 24 | ---------------- 25 | 26 | These notes are by Roban Kramer. 27 | 28 | I use swig to generate the python interface to `power.c`. 29 | 30 | `power_wrap.c` and `power.py` are created from `power.i` and `power.c` 31 | by runing: 32 | 33 | > swig -python power.i 34 | 35 | I used to let distutils run swig, but that stopped working for some 36 | reason. The code was: 37 | 38 | power_module = Extension('cosmolopy.EH._power', 39 | sources=[os.path.join(eh_dir, 'power.i'), os.path.join(eh_dir, 40 | 'power.c')]) 41 | 42 | I still let distutils do the compiling to create `_power.so`. This has 43 | the advantage of not requiring the user to install swig. 44 | 45 | Power spectra with baryonic effects 46 | =================================== 47 | 48 | Original C code 49 | --------------------- 50 | 51 | tf_fit.c is redistributed under the MIT License 52 | 53 | http://background.uchicago.edu/~whu/transfer/transferpage.html 54 | 55 | and is described in Eisenstein, D. J., & Hu, W. "Baryonic Features in 56 | the Matter Transfer Function," 1998, ApJ, 496, 605 57 | [astro-ph/9709112]. Please cite this paper to acknowledge use of power 58 | spectrum calculations. 59 | 60 | See LISCENSE file. 61 | 62 | Python interface 63 | ---------------- 64 | 65 | These notes are by Berian James. 66 | 67 | I use SWIG to generate the python interface to `tf_fit.c`, following 68 | Roban's method with a few modifications. 69 | 70 | `tf_fit_wrap.c` and `tf_fit.py` are created from `tf_fit.i` and `tf_fit.c` 71 | by running: 72 | 73 | > swig -python tf_fit.i 74 | 75 | As with power.c, these files will be preserved in distribution, so that the 76 | user does not need SWIG. I have added an analogous Extension object to 77 | setup.py which will compile the library during the cosmolopy build. 78 | 79 | Some modifications to the source code of tf_fit.c were required. In particular, 80 | tf_fit.TFfit_onek originally took several pointers among its arguments, which I 81 | have removed. I have also made the returned variable from that function a global. 82 | In all cases, I have left the original lines in the source code, commented with //. -------------------------------------------------------------------------------- /cosmolopy/EH/__init__.py: -------------------------------------------------------------------------------- 1 | """See `cosmolopy.perturbation.transfer_function_EH` 2 | 3 | Eisenstein & Hu power spectrum transfer function used in 4 | `cosmolopy.perturbation.transfer_function_EH`. 5 | 6 | This package contains two modules: 7 | 8 | i. `power` (or `cosmolopy.EH.power`), which is a python wrapper of power.c 9 | from Eisenstein & Hu (1999 ApJ 511 5) 10 | 11 | ii. `tf_fit` (or `cosmolopy.EH.tf_fit`), which is a python wrapper of 12 | tf_fit.c from Eisenstein & Hu (1998 ApJ 496 605) 13 | 14 | The first module contains no baryonic features in the transfer function, but 15 | applies to wider range of CDM variants (e.g. including neutrinos). The second 16 | module applies more narrowly but possesses effects including the baryonic 17 | acoustic osciallations. 18 | 19 | See also: http://background.uchicago.edu/~whu/transfer/transferpage.html 20 | 21 | power.c is redistributed under the MIT License with the permission of 22 | Wayne Hu, and is described in Eisenstein, D. J., & Hu, W. "Power 23 | Spectra for Cold Dark Matter and Its Variants," 1999, ApJ, 511, 5 24 | [astro-ph/9710252]. Please cite this paper to acknowledge use of power 25 | spectrum calculations. 26 | 27 | See LISCENSE for additional information. 28 | 29 | """ 30 | 31 | from __future__ import absolute_import, division, print_function 32 | -------------------------------------------------------------------------------- /cosmolopy/EH/power.i: -------------------------------------------------------------------------------- 1 | /* power.i */ 2 | %module power 3 | %{ 4 | /* Put header files here or function declarations like below */ 5 | extern int TFmdm_set_cosm(float omega_matter, float omega_baryon, float omega_hdm, 6 | int degen_hdm, float omega_lambda, float hubble, 7 | float redshift); 8 | extern float TFmdm_onek_mpc(float kk); 9 | extern float TFmdm_onek_hmpc(float kk ); 10 | extern float tf_cbnu; 11 | %} 12 | 13 | extern int TFmdm_set_cosm(float omega_matter, float omega_baryon, float omega_hdm, 14 | int degen_hdm, float omega_lambda, float hubble, 15 | float redshift); 16 | extern float TFmdm_onek_mpc(float kk); 17 | extern float TFmdm_onek_hmpc(float kk ); 18 | 19 | extern float tf_cbnu; 20 | -------------------------------------------------------------------------------- /cosmolopy/EH/tests/test_power.py: -------------------------------------------------------------------------------- 1 | """Check that the power module is working.""" 2 | 3 | from __future__ import absolute_import, division, print_function 4 | 5 | import numpy.testing.utils as ntest 6 | 7 | def test_power(): 8 | """Check that the power module is working.""" 9 | import cosmolopy.EH.power as power 10 | power.TFmdm_set_cosm(0.3, 0.04, 0.0, 0, 0.7, 0.72, 0.0) 11 | ntest.assert_approx_equal(power.TFmdm_onek_hmpc(100.0), 12 | 1.48236347286e-06) 13 | -------------------------------------------------------------------------------- /cosmolopy/EH/tests/test_tf_fit.py: -------------------------------------------------------------------------------- 1 | """Check that the tf_fit module is working.""" 2 | 3 | from __future__ import absolute_import, division, print_function 4 | 5 | import numpy.testing.utils as ntest 6 | 7 | def test_tf_fit(): 8 | """Check that the tf_fit module is working.""" 9 | import cosmolopy.EH.tf_fit as tf_fit 10 | tf_fit.TFset_parameters(0.136, 0.2, 2.728) 11 | ntest.assert_approx_equal( tf_fit.TFfit_onek(10.0), 12 | 3.69328954548e-05) 13 | -------------------------------------------------------------------------------- /cosmolopy/EH/tf_fit.i: -------------------------------------------------------------------------------- 1 | /* tf_fit.i */ 2 | %module tf_fit 3 | %{ 4 | /* Put header files here or function declarations like below */ 5 | extern void TFset_parameters(float omega0hh, float f_baryon, float Tcmb); 6 | extern float TFfit_onek(float k); 7 | extern float T_full; 8 | %} 9 | 10 | extern void TFset_parameters(float omega0hh, float f_baryon, float Tcmb); 11 | extern float TFfit_onek(float k); 12 | extern float T_full; 13 | -------------------------------------------------------------------------------- /cosmolopy/__init__.py: -------------------------------------------------------------------------------- 1 | """CosmoloPy is a package of cosmology routines built on NumPy/SciPy. 2 | 3 | Capabilities include 4 | -------------------- 5 | 6 | `cosmolopy.density` 7 | Various cosmological densities. 8 | 9 | `cosmolopy.distance` 10 | Various cosmological distance measures. 11 | 12 | `cosmolopy.luminosityfunction` 13 | Galaxy luminosity functions (Schecter functions). 14 | 15 | `cosmolopy.magnitudes` 16 | Conversion in and out of the AB magnitude system. 17 | 18 | `cosmolopy.parameters` 19 | Pre-defined sets of cosmological parameters (e.g. from WMAP). 20 | 21 | `cosmolopy.perturbation` 22 | Perturbation theory and the power spectrum. 23 | 24 | `cosmolopy.reionization` 25 | The reionization of the IGM. 26 | 27 | Functions take cosmological parameters (which can be numpy arrays) 28 | as keywords, and ignore any extra keywords. This means you can make a 29 | dictionary of all of your cosmological parameters and pass it to any 30 | function. 31 | 32 | The `parameters` module supplies some convenient pre-defined parameter sets. 33 | 34 | Usage 35 | ----- 36 | 37 | The easiest way to use CosmoloPy is to create a dictionary of the 38 | cosmology parameters and pass it to each function using the ** syntax. 39 | 40 | >>> import cosmolopy.distance as cd 41 | >>> cosmo = {'omega_M_0':0.3, 'omega_lambda_0':0.7, 'omega_k_0':0.0, 'h':0.72} 42 | >>> d_co = cd.comoving_distance(6., **cosmo) 43 | >>> print "Comoving distance to z=6 is %.1f Mpc" % (d_co) 44 | Comoving distance to z=6 is 8017.8 Mpc 45 | 46 | The cosmolopy package also defines some convenient shortcuts, 47 | including a fiducial cosmology (currently the WMAP7+BAO+H0 mean), so 48 | you can just do this: 49 | 50 | >>> from cosmolopy import * 51 | >>> d_a = cd.angular_diameter_distance(6, **fidcosmo) 52 | >>> print "Angluar-diameter distance to z=6 is %.1f Mpc" % (d_a) 53 | Angluar-diameter distance to z=6 is 1209.9 Mpc 54 | >>> d_light = cd.light_travel_distance(6, **fidcosmo) 55 | >>> print "Light-travel distance to z=6 is %.1f Mpc" % (d_light) 56 | Light-travel distance to z=6 is 3922.9 Mpc 57 | 58 | Calculate the mass of a halo with Virial temperature of 10^4 kelvin, 59 | then verify the Virial temperature for a halo of that mass: 60 | 61 | >>> import cosmolopy.perturbation as cp 62 | >>> cosmo = {'omega_M_0' : 0.27, 63 | ... 'omega_lambda_0' : 1-0.27, 64 | ... 'omega_b_0' : 0.045, 65 | ... 'omega_n_0' : 0.0, 66 | ... 'N_nu' : 0, 67 | ... 'h' : 0.72, 68 | ... 'n' : 1.0, 69 | ... 'sigma_8' : 0.9 70 | ... } 71 | >>> mass = cp.virial_mass(1e4, 6.0, **cosmo) 72 | >>> temp = cp.virial_temp(mass, 6.0, **cosmo) 73 | >>> print "Mass = %.3g M_sun" % mass 74 | Mass = 1.68e+08 M_sun 75 | >>> print round(temp, 4) 76 | 10000.0 77 | 78 | Calculate the critical and matter densities: 79 | 80 | >>> from cosmolopy import * 81 | >>> 'rho_crit=%.3g Msun/Mpc^3, rho_0=%.3g Msun/Mpc^3' % cden.cosmo_densities(**fidcosmo) 82 | 'rho_crit=1.38e+11 Msun/Mpc^3, rho_0=3.75e+10 Msun/Mpc^3' 83 | 84 | Look in the tests/ and examples/ directories for more examples. 85 | 86 | """ 87 | 88 | from __future__ import absolute_import, division, print_function 89 | 90 | from .__version__ import __version__ 91 | from . import constants as cc 92 | from . import density as cden 93 | from . import distance as cd 94 | from . import perturbation as cp 95 | from . import reionization as cr 96 | from . import parameters as cparam 97 | from . import magnitudes as cmag 98 | from . import luminosityfunction as cl 99 | 100 | fidcosmo = cparam.WMAP7_BAO_H0_mean(flat=True, extras=True) 101 | -------------------------------------------------------------------------------- /cosmolopy/__version__.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | 3 | # %% VERSIONS 4 | # Default/Latest/Current version 5 | __version__ = '0.4.1' 6 | -------------------------------------------------------------------------------- /cosmolopy/constants.py: -------------------------------------------------------------------------------- 1 | """Various constants used by CosmoloPy code. 2 | 3 | Unit abreviations are appended to the name, but powers are not 4 | specified. For instance, the gravitational constant has units "Mpc^3 5 | msun^-1 s^-2", but is called "G_const_Mpc_Msun_s". 6 | 7 | Most of these numbers are from google calculator. 8 | 9 | Constants are: 10 | 11 | :: 12 | 13 | """ 14 | 15 | from __future__ import absolute_import, division, print_function 16 | 17 | ### If you add a constant, make sure to add a description too. ### 18 | 19 | doc = "" 20 | 21 | doc += " pc_cm: Parsec in cm\n" 22 | pc_cm = 3.08568025e18 #cm 23 | 24 | doc += " Mpc_cm: Megaparsec in cm\n" 25 | Mpc_cm = 3.08568025e24 # cm 26 | 27 | doc += " Mpc_km: Megaparsec in km\n" 28 | Mpc_km = Mpc_cm * 1.0e-5 # km 29 | 30 | doc += " angstrom_cm: Angstrom in cm\n" 31 | angstrom_cm = 1e-8 #cm 32 | 33 | doc += " yr_s: a year in s\n" 34 | yr_s = 365. * 24. * 60. * 60. 35 | 36 | doc += " Myr_s: Megayear in s\n" 37 | Myr_s = 1.e6 * yr_s 38 | 39 | doc += " Gyr_s: Gigayear in s\n" 40 | Gyr_s = 1.e9 * yr_s 41 | 42 | doc += " amu_g: atomic mass unit in g\n" 43 | amu_g = 1.66053886e-24 #g 44 | 45 | doc += " m_p_g: mass of a proton in g\n" 46 | m_p_g = 1.67262158e-24 # g 47 | 48 | doc += " m_H_g: mass of a hydrogen atom in g\n" 49 | m_H_g = 1.00794 * amu_g # g 50 | 51 | doc += " m_He_g: mass of a helium atom in g\n" 52 | m_He_g = 4.002602 * amu_g # g 53 | 54 | doc += " M_sun_g: Solar mass in grams.\n" 55 | M_sun_g = 1.98892e33 # g 56 | 57 | doc += " c_light_cm_s: Speed of light in Mpc/s (from google calculator)\n" 58 | c_light_cm_s = 29979245800. # cm/s 59 | 60 | doc += " c_light_Mpc_s: Speed of light in Mpc/s\n" 61 | c_light_Mpc_s = c_light_cm_s / Mpc_cm # Mpc / s 62 | 63 | doc += " c_light_Mpc_Gyr: Speed of light in Mpc/Gyr \n" 64 | c_light_Mpc_Gyr = Gyr_s * c_light_cm_s / Mpc_cm # Mpc / Gyr 65 | 66 | doc += " H100_s: 100 km s^-1 Mpc^-1 in s^-1\n" 67 | H100_s = 100. / Mpc_km # s^-1 68 | 69 | doc += " G_const_Mpc_Msun_s: Gravitational constant in Mpc^3 msun^-1 s^-2\n" 70 | G_const_Mpc_Msun_s = M_sun_g * (6.673e-8) / Mpc_cm**3. # Mpc^3 msun^-1 s^-2 71 | 72 | doc += " lambda_Lya_0: Central wavelength of H Lyman-alpha in Angstroms\n" 73 | lambda_Lya_0 = 1215.67 # Ang 74 | 75 | doc += " lambda_NY_0: Central wavelength of an NV doublet in Angstroms\n" 76 | lambda_NV_0 = 1240.81 # Ang 77 | 78 | doc += " alpha_B_cm_s_1e4: hydrogen recombination coefficient at T=10^4 K\n" 79 | alpha_B_cm_s_1e4 = 2.59e-13 # cm^3 s^-1 80 | 81 | doc += " sigma_T_cm: Thomson cross section in cm^2\n" 82 | sigma_T_cm = 6.6524586e-25 # cm^2 83 | 84 | doc += " sigma_T_cm: Thomson cross section in Mpc^2\n" 85 | sigma_T_Mpc = sigma_T_cm / (Mpc_cm ** 2.) # Mpc^2 86 | 87 | __doc__ += "\n".join(sorted(doc.split("\n"))) 88 | 89 | 90 | -------------------------------------------------------------------------------- /cosmolopy/density.py: -------------------------------------------------------------------------------- 1 | """Cosmological densities like matter density, baryon density, etc. 2 | """ 3 | 4 | from __future__ import absolute_import, division, print_function 5 | 6 | import math 7 | 8 | import numpy 9 | import scipy 10 | import scipy.special 11 | import scipy.integrate as si 12 | 13 | from . import constants as cc 14 | from . import distance as cd 15 | from .distance import get_omega_k_0, set_omega_k_0 16 | 17 | def omega_M_z(z, **cosmo): 18 | """Matter density omega_M as a function of redshift z. 19 | 20 | Notes 21 | ----- 22 | 23 | From Lahav et al. (1991, MNRAS 251, 128) equations 11b-c. This is 24 | equivalent to equation 10 of Eisenstein & Hu (1999 ApJ 511 5). 25 | 26 | """ 27 | if get_omega_k_0(**cosmo) == 0: 28 | return 1.0 / (1. + (1. - cosmo['omega_M_0'])/ 29 | (cosmo['omega_M_0'] * (1. + z)**3.)) 30 | else: 31 | return (cosmo['omega_M_0'] * (1. + z)**3. / 32 | cd.e_z(z, **cosmo)**2.) 33 | 34 | def cosmo_densities(**cosmo): 35 | """The critical and mean densities of the universe. 36 | 37 | Returns 38 | ------- 39 | rho_crit and rho_0 in solar masses per cubic Megaparsec. 40 | 41 | """ 42 | 43 | omega_M_0 = cosmo['omega_M_0'] 44 | h = cosmo['h'] 45 | 46 | rho_crit = 3. * (h * cc.H100_s)**2. / (8. * math.pi * cc.G_const_Mpc_Msun_s) 47 | rho_0 = omega_M_0 * rho_crit 48 | 49 | #print " Critical density rho_crit = %.3g Msun/Mpc^3" % rho_crit 50 | #print " Matter density rho_0 = %.3g Msun/Mpc^3" % rho_0 51 | 52 | return rho_crit, rho_0 53 | 54 | def get_X_Y(**cosmo): 55 | """The fraction of baryonic mass in hydrogen and helium. 56 | 57 | Assumes X_H + Y_He = 1. 58 | 59 | You must specify either 'X_H', or 'Y_He', or both. 60 | """ 61 | if 'X_H' in cosmo and 'Y_He' not in cosmo: 62 | X_H = cosmo['X_H'] 63 | Y_He = 1. - X_H 64 | elif 'Y_He' in cosmo and 'X_H' not in cosmo: 65 | Y_He = cosmo['Y_He'] 66 | X_H = 1. - Y_He 67 | else: 68 | X_H = cosmo['X_H'] 69 | Y_He = cosmo['Y_He'] 70 | return X_H, Y_He 71 | 72 | def baryon_densities(**cosmo): 73 | """Hydrogen number density at z=0. 74 | 75 | Parameters 76 | ---------- 77 | 78 | cosmo: cosmological parameters 79 | 80 | parameters used: 'omega_b_0', 'X_H' and/or 'Y_He', plus those 81 | needed by cosmo_densities. 82 | 83 | 84 | Returns 85 | ------- 86 | 87 | rho_crit, rho_0, n_He_0, n_H_0 88 | 89 | The first two are in units of solar masses per cubic 90 | Megaparsec. The later two are in number per cubic Megaparsec. 91 | 92 | """ 93 | 94 | X_H, Y_He = get_X_Y(**cosmo) 95 | 96 | rho_crit, rho_0 = cosmo_densities(**cosmo) 97 | 98 | n_H_0 = (rho_crit * cosmo['omega_b_0'] * X_H * cc.M_sun_g / 99 | cc.m_H_g) 100 | n_He_0 = (rho_crit * cosmo['omega_b_0'] * Y_He * cc.M_sun_g / 101 | cc.m_He_g) 102 | # print " Hydrogen number density n_H_0 = %.4g (Mpc^-3)" % n_H_0 103 | return rho_crit, rho_0, n_He_0, n_H_0 104 | -------------------------------------------------------------------------------- /cosmolopy/saveable.py: -------------------------------------------------------------------------------- 1 | """A Saveable class with methods to save and restore. 2 | 3 | Saveable is designed to be subclassed to create new types of objects 4 | that can easily be pickled and reloaded. 5 | """ 6 | 7 | from __future__ import absolute_import, division, print_function 8 | 9 | import pickle 10 | 11 | class NullWriter: 12 | """Dummy file-like object that does nothing. 13 | 14 | From 15 | http://stackoverflow.com/questions/1809958/hide-stderr-output-in-unit-tests 16 | 17 | Used in Saveable. 18 | """ 19 | def write(self, s): 20 | pass 21 | 22 | 23 | def loadSaveable(filename): 24 | """Return an instance of an object unpickled from a file. 25 | """ 26 | picfile = open(filename) 27 | loaded = pickle.load(picfile) 28 | picfile.close() 29 | return loaded 30 | 31 | class Saveable(object): 32 | """An object with methods to save and restore. 33 | 34 | Unpickleable attributes will simply be deleted from the object. 35 | """ 36 | 37 | def __init__(self, filename=None): 38 | if filename is not None: 39 | self.load(filename) 40 | 41 | def save(self, filename): 42 | """Save object to a file.""" 43 | picfile = open(filename, 'w') 44 | pickle.dump(self, picfile) 45 | picfile.close() 46 | 47 | def load(self, filename): 48 | """Return an instance of an object unpickled from a file. 49 | """ 50 | picfile = open(filename) 51 | loaded = pickle.load(picfile) 52 | picfile.close() 53 | self.__dict__.update(loaded.__dict__) 54 | return self 55 | 56 | def dumb_pickle_filter(self): 57 | """Filter out attributes that can't be pickled. 58 | 59 | Returns a copy of dict with 60 | """ 61 | picfile = NullWriter() 62 | sdict = self.__dict__.copy() 63 | for k, v in list(sdict.items()): 64 | # Avoid self references (and thereby infinite recurion). 65 | if v is self: 66 | del sdict[k] 67 | continue 68 | # Remove any attributes that can't be pickled. 69 | try: 70 | pickle.dump(v, picfile) 71 | except (TypeError, pickle.PicklingError) as err: 72 | if hasattr(self, 'verbose') and self.verbose: 73 | print("Won't pickle", k, type(v), ": ") 74 | print("'", err, "'") 75 | del sdict[k] 76 | return sdict 77 | def __getstate__(self): 78 | """Prepare a state of pickling.""" 79 | return self.dumb_pickle_filter() 80 | 81 | def __setstate__(self, dict): 82 | """Unpickle.""" 83 | self.__dict__.update(dict) 84 | -------------------------------------------------------------------------------- /examples/plot_2d_distances.py: -------------------------------------------------------------------------------- 1 | """Plot some distance measures versus redshift and omega_M. 2 | 3 | """ 4 | from __future__ import absolute_import, division, print_function 5 | 6 | import sys 7 | import getopt 8 | 9 | import numpy 10 | import matplotlib.pyplot as pylab 11 | import matplotlib.cm as cm 12 | 13 | import cosmolopy.distance as cd 14 | import cosmolopy.constants as cc 15 | 16 | def plot_DM(filename): 17 | """The dimensionless proper motion distance DM/DH. 18 | """ 19 | 20 | # Set up an array of redshift values. 21 | dz = 0.1 22 | z = numpy.arange(0., 10. + 1.1 * dz, dz) 23 | 24 | # Set up a cosmology dictionary, with an array of matter density values. 25 | cosmo = {} 26 | dom = 0.01 27 | om = numpy.atleast_2d(numpy.linspace(0.1, 1.0, (1.-0.1)/dom)).transpose() 28 | cosmo['omega_M_0'] = om 29 | cosmo['omega_lambda_0'] = 1. - cosmo['omega_M_0'] 30 | cosmo['h'] = 0.701 31 | cosmo['omega_k_0'] = 0.0 32 | 33 | # Calculate the hubble distance. 34 | dh = cd.hubble_distance_z(0, **cosmo) 35 | # Calculate the comoving distance. 36 | dm = cd.comoving_distance_transverse(z, **cosmo) 37 | 38 | # Make plots. 39 | plot_dist(z, dz, om, dom, dm, dh, 'proper motion distance', r'D_M', 40 | filename) 41 | plot_dist_ony(z, dz, om, dom, dm, dh, 'proper motion distance', r'D_M', 42 | filename) 43 | 44 | def plot_DA(filename): 45 | """The dimensionless angular diameter distance DA/DH. 46 | """ 47 | 48 | # Set up an array of redshift values. 49 | dz = 0.1 50 | z = numpy.arange(0., 10. + dz, dz) 51 | 52 | # Set up a cosmology dictionary, with an array of matter density values. 53 | cosmo = {} 54 | dom = 0.01 55 | om = numpy.atleast_2d(numpy.linspace(0.1, 1.0, (1.-0.1)/dom)).transpose() 56 | cosmo['omega_M_0'] = om 57 | cosmo['omega_lambda_0'] = 1. - cosmo['omega_M_0'] 58 | cosmo['h'] = 0.701 59 | cosmo['omega_k_0'] = 0.0 60 | 61 | # Calculate the hubble distance. 62 | dh = cd.hubble_distance_z(0, **cosmo) 63 | # Calculate the angular diameter distance. 64 | da = cd.angular_diameter_distance(z, **cosmo) 65 | 66 | # Make plots. 67 | plot_dist(z, dz, om, dom, da, dh, 'angular diameter distance', r'D_A', 68 | filename) 69 | plot_dist_ony(z, dz, om, dom, da, dh, 'angular diameter distance', r'D_A', 70 | filename) 71 | 72 | def plot_dist(z, dz, om, dom, dist, dh, name, mathname, filename=None): 73 | """Make a 2-D plot of a distance versus redshift (x) and matter density (y). 74 | """ 75 | # Grid of redshift and matter density values. 76 | x, y = numpy.meshgrid(z, om) 77 | pylab.figure(figsize=(5.5,4.5)) 78 | pylab.imshow(dist/dh, 79 | extent=(z.min() - dz/2., 80 | z.max() + dz/2., 81 | om.max() + dom/2., 82 | om.min() - dom/2., 83 | ), 84 | interpolation='nearest', 85 | aspect = z.max()/om.max(), 86 | cmap = cm.Spectral, 87 | ) 88 | cb = pylab.colorbar() 89 | cb.ax.set_ylabel(r'$' + mathname + '/D_H$') 90 | 91 | pylab.contour(x, y, dist/dh, 10, colors='k') 92 | pylab.xlim(z.min(), z.max()) 93 | pylab.ylim(om.min(), om.max()) 94 | pylab.xlabel("redshift z") 95 | pylab.ylabel(r"$\Omega_M = 1 - \Omega_\lambda$") 96 | pylab.title(name) 97 | if filename is not None: 98 | prefix, extension = filename.split('.') 99 | pylab.savefig(prefix + '_' + mathname + '.' + extension, 100 | bbox_inches="tight") 101 | 102 | 103 | def plot_dist_ony(z, dz, om, dom, dist, dh, name, mathname, filename=None): 104 | """Make a 2-D plot of matter density versus redshift (x) and distance (y) 105 | """ 106 | 107 | 108 | dist = dist/dh 109 | z = z * numpy.ones(dist.shape) 110 | om = om * numpy.ones(dist.shape) 111 | 112 | pylab.figure(figsize=(5.5,4.5)) 113 | 114 | 115 | pylab.contour(z, dist, om, 50) 116 | cb = pylab.colorbar() 117 | cb.ax.set_ylabel(r'$\Omega_M = 1 - \Omega_\lambda$') 118 | 119 | pylab.xlim(z.min(), z.max()) 120 | pylab.ylim(dist.min(), dist.max()) 121 | pylab.xlabel("redshift z") 122 | pylab.ylabel(name + r': $'+mathname+'/D_H$') 123 | pylab.title(name) 124 | if filename is not None: 125 | prefix, extension = filename.split('.') 126 | pylab.savefig(prefix + '_' + mathname + '_ony.' + extension, 127 | bbox_inches="tight") 128 | 129 | if __name__ == "__main__": 130 | if len(sys.argv)==1: 131 | print "Run with a filename argument to produce image files, e.g.:" 132 | print " python plot_2d_distances.py dist2d.png" 133 | print " python plot_2d_distances.py dist2d.eps" 134 | if len(sys.argv) > 1: 135 | filename = sys.argv[1] 136 | else: 137 | filename = None 138 | 139 | plot_DM(filename) 140 | plot_DA(filename) 141 | 142 | if filename is None: 143 | pylab.show() 144 | 145 | -------------------------------------------------------------------------------- /make_docs.bash: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | epydoc --exclude='cosmolopy.EH._power' --exclude='cosmolopy.EH._tf_fit' --exclude='cosmolopy.EH.power' --exclude='cosmolopy.EH.tf_fit' -v --no-private --no-frames --html --docformat restructuredtext cosmolopy/ -o www/docAPI/ -------------------------------------------------------------------------------- /pypi_notes.txt: -------------------------------------------------------------------------------- 1 | To upload to PyPI: 2 | 3 | > python setup.py sdist upload 4 | > python setup.py bdist_egg upload 5 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | numpy>=1.12.0 2 | scipy>=1.0.0 3 | 4 | -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [bdist_wheel] 2 | universal = 0 3 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # Future imports 3 | 4 | from __future__ import absolute_import, division, print_function 5 | 6 | import re 7 | import subprocess 8 | from setuptools import setup, find_packages, Extension 9 | from os import path 10 | import sys 11 | 12 | dirpath = path.abspath(path.dirname(__file__)) 13 | 14 | eh_dir = path.join(dirpath,'cosmolopy','EH') 15 | 16 | ext_names = ['power', 'tf_fit'] 17 | 18 | def generate_swig(): 19 | print("Swigging sources") 20 | for d in ext_names: 21 | filename = path.join(eh_dir, d+'.i') 22 | p = subprocess.call(['swig', '-python', filename], 23 | cwd=dirpath) 24 | if p != 0: 25 | raise RuntimeError("Running swig failed!") 26 | 27 | # Generate swig if build is requested 28 | for command in ['develop', 'build', 'bdist_wheel', 'build_ext', 'build_src']: 29 | if command in sys.argv[1:]: 30 | generate_swig() 31 | break 32 | 33 | # Generate dict of all data files to include 34 | EH_files = [] 35 | if 'sdist' in sys.argv[1:]: 36 | for name in ext_names: 37 | EH_files.extend(['%s.c' % (name), '%s.i' % (name)]) 38 | package_data = { 39 | '': ['*.txt', '*.rst', 'LISCENSE'], 40 | 'cosmolopy.EH': EH_files} 41 | 42 | # Create extension modules 43 | ext_mods = [] 44 | for name in ext_names: 45 | mod = Extension('cosmolopy.EH._%s' % (name), 46 | sources=[path.join(eh_dir, '%s_wrap.c' % (name)), 47 | path.join(eh_dir, '%s.c' % (name))]) 48 | ext_mods.append(mod) 49 | 50 | # Get the requirements list 51 | with open(path.join(dirpath, 'requirements.txt'), 'r') as f: 52 | requirements = f.read().splitlines() 53 | 54 | # Read the __version__.py file 55 | with open(path.join(dirpath, 'cosmolopy/__version__.py'), 'r') as f: 56 | vf = f.read() 57 | 58 | # Obtain version from read-in __version__.py file 59 | version = re.search(r"^_*version_* = ['\"]([^'\"]*)['\"]", vf, re.M).group(1) 60 | 61 | setup( 62 | name = "cosmolopy", 63 | version = version, 64 | packages = find_packages(), 65 | install_requires = requirements, 66 | 67 | ext_modules = ext_mods, 68 | 69 | tests_require = ['nose', 'matplotlib'], 70 | test_suite = 'nose.collector', 71 | platforms=["Windows", "Linux", "Unix"], 72 | 73 | # metadata for upload to PyPI 74 | author = "Roban Hultman Kramer", 75 | author_email = "robanhk@gmail.com", 76 | description = "a cosmology package for Python.", 77 | url = "http://roban.github.com/CosmoloPy/", # project home page 78 | keywords = ("astronomy cosmology cosmological distance density galaxy" + 79 | "luminosity magnitude reionization Press-Schechter Schecter"), 80 | license = "MIT", 81 | python_requires = ">=3.6, <4", 82 | package_data=package_data, 83 | long_description = \ 84 | """CosmoloPy is a package of cosmology routines built on NumPy/SciPy. 85 | 86 | Capabilities include 87 | -------------------- 88 | 89 | `cosmolopy.density` 90 | Various cosmological densities. 91 | 92 | `cosmolopy.distance` 93 | Various cosmological distance measures. 94 | 95 | `cosmolopy.luminosityfunction` 96 | Galaxy luminosity functions (Schecter functions). 97 | 98 | `cosmolopy.magnitudes` 99 | Conversion in and out of the AB magnitude system. 100 | 101 | `cosmolopy.parameters` 102 | Pre-defined sets of cosmological parameters (e.g. from WMAP). 103 | 104 | `cosmolopy.perturbation` 105 | Perturbation theory and the power spectrum. 106 | 107 | `cosmolopy.reionization` 108 | The reionization of the IGM. 109 | 110 | """, 111 | classifiers = ['License :: OSI Approved :: MIT License', 112 | 'Programming Language :: Python', 113 | 'Programming Language :: Python :: 3', 114 | 'Programming Language :: Python :: 3.6', 115 | 'Programming Language :: Python :: 3.7', 116 | 'Programming Language :: Python :: 3.8', 117 | 'Topic :: Scientific/Engineering :: Astronomy', 118 | 'Operating System :: OS Independent' 119 | ] 120 | ) 121 | -------------------------------------------------------------------------------- /tests/test_BrokenPowerlawSED.py: -------------------------------------------------------------------------------- 1 | 2 | from __future__ import absolute_import, division, print_function 3 | 4 | import numpy 5 | 6 | import cosmolopy.utils as utils 7 | from cosmolopy.luminosityfunction import BrokenPowerlawSED 8 | 9 | def test_BrokenPowerlawSED(plot=False): 10 | """Test that the BrokenPowerlawSED has the right break and normalization. 11 | """ 12 | if plot: import pylab 13 | runtest_BrokenPowerlawSED(BrokenPowerlawSED(), plot=plot) 14 | runtest_BrokenPowerlawSED(BrokenPowerlawSED(s_ion=-2., s_red=-0.5), plot=plot) 15 | if plot: pylab.show() 16 | 17 | def runtest_BrokenPowerlawSED(sed, plot=False): 18 | 19 | nu_912 = sed.lambdanu(912.) 20 | 21 | ratio_1500_L_num = (sed(sed.lambdanu(1500.))/ 22 | sed(sed.lambdanu(912. - 1e-10)))[0] 23 | 24 | # Test the magnitude of the break. 25 | assert numpy.abs(ratio_1500_L_num - sed.break_factor) < 1e-9 26 | 27 | # Test the normalization of the integral. 28 | numintegral = utils.logquad(sed, sed.lambdanu(3000.), sed.lambdanu(1e-6))[0] 29 | assert numpy.abs(numintegral - 1.) < 1e-6 30 | 31 | if plot: 32 | import pylab 33 | wav = numpy.arange(100.,2000.,1.0) 34 | nu = sed.lambdanu(wav) 35 | pylab.subplot(121) 36 | #norm = sed(nu_912 + 1e10) 37 | norm = 1.0 38 | pylab.plot(wav, sed(nu)/norm) 39 | #pylab.axhline(y=6, ls=':') 40 | #pylab.axvline(x=1500, ls=':') 41 | pylab.subplot(122) 42 | pylab.plot(nu, sed(nu)/norm) 43 | 44 | if __name__ == '__main__': 45 | test_BrokenPowerlawSED(True) 46 | -------------------------------------------------------------------------------- /tests/test_SFR_from_L_nu.py: -------------------------------------------------------------------------------- 1 | """Test SFR - UV luminosity conversion. 2 | """ 3 | 4 | from __future__ import absolute_import, division, print_function 5 | 6 | import numpy 7 | 8 | import cosmolopy.parameters as cparam 9 | 10 | import cosmolopy.magnitudes as magnitudes 11 | import cosmolopy.luminosityfunction as luminosityfunction 12 | 13 | 14 | def test_sfr(): 15 | """Check that M = -18 -> SFR ~ 1 Msun/yr. 16 | 17 | From Oesch et al (2009 ApJ 690 1350). 18 | """ 19 | 20 | mag = -18 21 | lum = magnitudes.L_nu_from_magAB(mag) 22 | sfr = luminosityfunction.sfr_from_L_nu(lum) 23 | 24 | print("M = %.3g -> L_nu = %.3g erg/s/Hz -> SFR = %.3g Msun/yr" % (mag, 25 | lum, 26 | sfr)) 27 | assert numpy.round(sfr) == 1 28 | 29 | def test_sfrd(): 30 | """ Check conversion of Lmin -> SFRD. 31 | 32 | At z=7: 33 | Lmin = 0.2 L*z=6 -> Mmin=-18.5 -> log(rho/erg/s/Hz/Mpc^3)=25.5 -> 34 | SFRD = 10^-2.32 Msun/yr^-1/Mpc^-3. 35 | 36 | From Oesch et al (2009 ApJ 690 1350). 37 | """ 38 | 39 | cosmo = cparam.WMAP7_BAO_H0_mean(flat=True) 40 | 41 | 42 | # # From Bouwens 2008ApJ...686..230B 43 | # lfhist = luminosityfunction.LFHistory(params=luminosityfunction.B2008, 44 | # **cosmo) 45 | 46 | # mStarz6 = lfhist.params_z(6.0)['MStar'] 47 | 48 | alpha = -1.74 49 | mStarz6 = -20.24 50 | mStarz7 = -19.7 51 | phiStar = 1.4e-3 52 | 53 | lStarz6 = magnitudes.L_nu_from_magAB(mStarz6) 54 | lmin = 0.2 * lStarz6 55 | magmin = magnitudes.magnitude_AB_from_L_nu(lmin) 56 | ltot = luminosityfunction.schechterCumuLM(magnitudeAB=magmin, 57 | MStar=mStarz7, 58 | phiStar=phiStar, 59 | alpha=alpha) 60 | sfrd = luminosityfunction.sfr_from_L_nu(ltot) 61 | 62 | print("""Lmin = 0.2 L*z=6 -> Lmin/erg/s/Hz = %.3g -> Mmin = %.3g -> 63 | log(rho/(erg/s/Hz/Mpc^3)) = %.3g -> log(SFRD/(MSun/yr)) = %.3g""" 64 | % (lmin, magmin, numpy.log10(ltot), numpy.log10(sfrd))) 65 | 66 | ltotz6 = luminosityfunction.schechterCumuLM(magnitudeAB=magmin, 67 | MStar=mStarz6, 68 | phiStar=phiStar, 69 | alpha=alpha) 70 | 71 | print("luminosity density increase from z=7 to z=6 is %.2g percent." 72 | % (100 * (1. - ltot/ltotz6))) 73 | 74 | 75 | assert numpy.abs(numpy.round(1. - ltot/ltotz6, 1) - 0.5) < 0.1 76 | assert numpy.round(magmin, 1) == -18.5 77 | assert numpy.abs(numpy.round(numpy.log10(ltot), 1) - 25.5) < 0.2 78 | assert numpy.abs(numpy.round(numpy.log10(sfrd), 1) - -2.32) < 0.05 79 | 80 | if __name__ == '__main__': 81 | test_sfr() 82 | test_sfrd() 83 | 84 | 85 | -------------------------------------------------------------------------------- /tests/test_age.py: -------------------------------------------------------------------------------- 1 | """Test integrated age against analytical age.""" 2 | 3 | from __future__ import absolute_import, division, print_function 4 | 5 | import numpy 6 | import numpy.testing.utils as ntest 7 | import matplotlib as mpl 8 | mpl.use('Agg') 9 | 10 | import matplotlib.pyplot as pylab 11 | 12 | import cosmolopy.distance as cd 13 | import cosmolopy.constants as cc 14 | 15 | 16 | def test_age(): 17 | """Test integrated age against analytical age.""" 18 | z = numpy.arange(0, 10.0, 0.05) 19 | 20 | cosmo = {} 21 | cosmo['omega_M_0'] = numpy.array([[0.99],[0.01],[0.3]]) 22 | cosmo['omega_lambda_0'] = 1. - cosmo['omega_M_0'] 23 | cosmo['h'] = 0.7 24 | cd.set_omega_k_0(cosmo) 25 | 26 | linestyle = ['-', ':', '--'] 27 | 28 | gyr = 1e9 * cc.yr_s 29 | 30 | tl = cd.lookback_time(z, **cosmo) 31 | age = cd.age(z, **cosmo) 32 | age_ana = cd.age_flat(z, **cosmo) 33 | 34 | pylab.figure(figsize=(6,6)) 35 | for i in range(len(linestyle)): 36 | pylab.plot(z, (tl/gyr)[i], ls=linestyle[i], color='0.5') 37 | pylab.plot(z, (age/gyr)[i], ls=linestyle[i], color='r') 38 | pylab.plot(z, (age_ana/gyr)[i], ls=linestyle[i], color='k') 39 | pylab.xlabel("redshift z") 40 | pylab.ylabel(r"age $t_L/$Gyr") 41 | 42 | pylab.figure(figsize=(6,6)) 43 | for i in range(len(linestyle)): 44 | pylab.plot(z, ((age - age_ana)/age_ana)[i], ls=linestyle[i], 45 | color='k') 46 | # Make sure errors are small: 47 | ntest.assert_array_less((numpy.abs((age - age_ana)/age_ana)[i]), 48 | 3e-13) 49 | pylab.xlabel("redshift z") 50 | pylab.ylabel(r"age: (integral - analytical)/analytical") 51 | 52 | if __name__ == "__main__": 53 | test_age() 54 | pylab.show() 55 | -------------------------------------------------------------------------------- /tests/test_distances.py: -------------------------------------------------------------------------------- 1 | 2 | from __future__ import absolute_import, division, print_function 3 | 4 | import os 5 | import numpy 6 | import numpy.testing.utils as ntest 7 | import cosmolopy.distance as cd 8 | import cosmolopy.constants as cc 9 | 10 | import matplotlib.pyplot as pylab 11 | 12 | def cosmo_wmap_5(): 13 | """Cosmology from Komatsu et al. 2008 (arXiv:0803.0547v1)""" 14 | cosmo = {} 15 | omega_c = 0.233 #+-0.013, 16 | cosmo['omega_b_0'] = 0.0462 #+-0.0015, 17 | cosmo['omega_M_0'] = omega_c + cosmo['omega_b_0'] # 0.2792 18 | cosmo['omega_k_0'] = 0.0 19 | cosmo['omega_lambda_0'] = (1. - cosmo['omega_M_0'] - cosmo['omega_k_0']) 20 | #cosmo['omega_lambda_0'] = 0.721 #+-0.015 21 | cosmo['h'] = 0.701 #+-0.0013 22 | cosmo['n'] = 0.960 #+0.014-0.013 23 | cosmo['sigma_8'] = 0.817 #+-0.026 24 | y_p = 0.240 # +- 0.006: the observed helium abundance 25 | cosmo['X_H'] = 1. / (1. + 1. / (4. * ((1. / y_p) - 1.))) 26 | 27 | cosmo['omega_n_0'] = 0.0 28 | cosmo['N_nu'] = 0 29 | 30 | return cosmo 31 | 32 | def test_distances(threshold = 1e-3): 33 | """Compare distance measures with calculations from http://icosmo.org/""" 34 | cosmo = cosmo_wmap_5() 35 | 36 | print("Comparing distances with calculations from http://icosmo.org/") 37 | 38 | # load external distance calculations 39 | # z DA(z) DT(z) DL(z) 40 | distance_file = os.path.dirname(os.path.abspath(__file__)) 41 | distance_file = os.path.join(distance_file, 'icosmo_testdata', 42 | 'distances.txt') 43 | ic_dists = numpy.loadtxt(distance_file) 44 | 45 | z = ic_dists[:,0] 46 | 47 | cd_da = cd.angular_diameter_distance(z, **cosmo) 48 | cd_dt = cd.light_travel_distance(z, **cosmo) 49 | cd_dl = cd.luminosity_distance(z, **cosmo) 50 | cd_dm = cd.comoving_distance_transverse(z, **cosmo) 51 | 52 | cd_dists = numpy.vstack((cd_dm, cd_da, cd_dt, cd_dl)) 53 | 54 | labels = [ r'$D_M$', r'$D_A$', r'$D_T$', r'$D_L$'] 55 | threshold = [1e-7, 1e-7, 1e-3, 1e-7 ] 56 | 57 | pylab.figure() 58 | for i in range(len(labels)): 59 | pylab.plot(ic_dists[:,0], ic_dists[:,i+1], 60 | label=labels[i] +' IC', ls=':') 61 | pylab.plot(z, cd_dists[i], label=labels[i] +' distance.py', ls='-') 62 | pylab.legend(loc='best') 63 | 64 | pylab.figure() 65 | 66 | for i in range(len(labels)): 67 | diff = (cd_dists[i] - ic_dists[:,i+1]) / ic_dists[:,i+1] 68 | maxdiff = numpy.max(numpy.abs(diff[ic_dists[:,i+1] > 0])) 69 | print("Maximum fraction difference in %s is %e." % (labels[i], 70 | maxdiff)) 71 | assert(numpy.all(maxdiff < threshold[i])) 72 | pylab.plot(ic_dists[:,0], 73 | diff, 74 | label=labels[i], ls='-') 75 | 76 | #pylab.plot(z, err2, label=labels[1] + ' err.', ls=':') 77 | #pylab.plot(z, err3, label=labels[2] + ' err.', ls=':') 78 | #pylab.plot(z, err5, label=labels[3] + ' err.', ls=':') 79 | #pylab.plot(z, err6, label=labels[0] + ' err.', ls=':') 80 | 81 | pylab.legend(loc='best') 82 | 83 | def test_hubble(threshold = 1e-7): 84 | cosmo = cosmo_wmap_5() 85 | print("Comparing hubble constant with calculations from " 86 | "http://icosmo.org/") 87 | 88 | # load external distance calculations 89 | # z H(z) 90 | hz_file = os.path.dirname(os.path.abspath(__file__)) 91 | hz_file = os.path.join(hz_file, 'icosmo_testdata', 92 | 'h_z.txt') 93 | ic_hz = numpy.loadtxt(hz_file) 94 | 95 | z = ic_hz[:,0] 96 | 97 | cd_hz = cd.hubble_z(z, **cosmo) * cc.Mpc_km 98 | 99 | label = r"$H(z)$" 100 | pylab.figure() 101 | pylab.plot(z, ic_hz[:,1], 102 | label=label + ' IC', ls=':') 103 | pylab.plot(z, cd_hz, label=label + ' distance.py', ls='-') 104 | pylab.legend(loc='best') 105 | 106 | pylab.figure() 107 | diff = (ic_hz[:,1] - cd_hz) / ic_hz[:,1] 108 | 109 | maxdiff = numpy.max(numpy.abs(diff)) 110 | print("Maximum fraction difference in %s is %e." % (label, 111 | maxdiff)) 112 | if maxdiff > threshold: 113 | print("Warning: difference exceeds threshold %e !!!" % threshold) 114 | assert(maxdiff < threshold) 115 | 116 | pylab.plot(z, 117 | diff, 118 | label=label, ls='-') 119 | pylab.legend(loc='best') 120 | 121 | 122 | if __name__ == "__main__": 123 | test_distances() 124 | test_hubble() 125 | pylab.show() 126 | 127 | 128 | 129 | -------------------------------------------------------------------------------- /tests/test_growth.py: -------------------------------------------------------------------------------- 1 | 2 | from __future__ import absolute_import, division, print_function 3 | 4 | import os 5 | import numpy 6 | import numpy.testing.utils as ntest 7 | import cosmolopy.perturbation as cp 8 | import cosmolopy.constants as cc 9 | 10 | import matplotlib.pyplot as pylab 11 | 12 | def cosmo_wmap_5(): 13 | """Cosmology from Komatsu et al. 2008 (arXiv:0803.0547v1)""" 14 | cosmo = {} 15 | omega_c = 0.233 #+-0.013, 16 | cosmo['omega_b_0'] = 0.0462 #+-0.0015, 17 | cosmo['omega_M_0'] = omega_c + cosmo['omega_b_0'] # 0.2792 18 | cosmo['omega_k_0'] = 0.0 19 | cosmo['omega_lambda_0'] = (1. - cosmo['omega_M_0'] - cosmo['omega_k_0']) 20 | #cosmo['omega_lambda_0'] = 0.721 #+-0.015 21 | cosmo['h'] = 0.701 #+-0.0013 22 | cosmo['n'] = 0.960 #+0.014-0.013 23 | cosmo['sigma_8'] = 0.817 #+-0.026 24 | y_p = 0.240 # +- 0.006: the observed helium abundance 25 | cosmo['X_H'] = 1. / (1. + 1. / (4. * ((1. / y_p) - 1.))) 26 | 27 | cosmo['omega_n_0'] = 0.0 28 | cosmo['N_nu'] = 0 29 | 30 | return cosmo 31 | 32 | def test_growth(cosmo=None): 33 | if cosmo is None: 34 | cosmo = cosmo_wmap_5() 35 | print("Comparing growth factor with calculations from http://icosmo.org/") 36 | 37 | # load external distance calculations 38 | # z D 39 | growth_file = os.path.dirname(os.path.abspath(__file__)) 40 | growth_file = os.path.join(growth_file, 'icosmo_testdata', 'growth.txt') 41 | ic_growth = numpy.loadtxt(growth_file) 42 | 43 | z = ic_growth[:,0] 44 | 45 | cp_growth = cp.fgrowth(z, cosmo['omega_M_0']) 46 | 47 | label = r"$D(z)$" 48 | pylab.figure() 49 | pylab.plot(z, ic_growth[:,1], 50 | label=label + ' IC', ls=':') 51 | pylab.plot(z, cp_growth, label=label + ' perturbation.py', ls='-') 52 | pylab.legend(loc='best') 53 | 54 | pylab.figure() 55 | diff = (ic_growth[:,1] - cp_growth) / ic_growth[:,1] 56 | 57 | maxdiff = numpy.max(numpy.abs(diff)) 58 | print("Maximum fraction difference in %s is %e." % (label, 59 | maxdiff)) 60 | pylab.plot(z, 61 | diff, 62 | label=label, ls='-') 63 | pylab.legend(loc='best') 64 | 65 | ntest.assert_array_less(numpy.abs(diff), 5e-3) 66 | 67 | if __name__ == "__main__": 68 | test_growth() 69 | pylab.show() 70 | 71 | 72 | 73 | -------------------------------------------------------------------------------- /tests/test_plot_BKP.py: -------------------------------------------------------------------------------- 1 | """Reionization consistency check with BK&P 2009MNRAS.397..971B""" 2 | 3 | from __future__ import absolute_import, division, print_function 4 | 5 | import numpy 6 | import numpy.testing.utils as ntest 7 | import matplotlib.pyplot as pylab 8 | 9 | import cosmolopy.perturbation as cp 10 | import cosmolopy.distance as cd 11 | import cosmolopy.density as cden 12 | import cosmolopy.reionization as cr 13 | import cosmolopy.constants as cc 14 | import cosmolopy.parameters as cparam 15 | 16 | def test_tau_BKP(): 17 | """Reionization consistency check with BK&P 2009MNRAS.397..971B 18 | 19 | Bagla J.~S., Kulkarni G., Padmanabhan T., 2009 (2009MNRAS.397..971B). 20 | 21 | Take their cannonical set of cosmological parameters and ionization 22 | coefficients and make sure I get the same optical depth value. 23 | 24 | The first figure demonstrates the calculation of the ionization 25 | fraction and the optical depth (not shown in the paper). 26 | 27 | The second figure shows dependence of the f_* f_esc,gamma values on 28 | tau (actually calculated the other way around, f_* f_esc,gamma -> 29 | tau). The plotted point (x) marks the value from the paper. The 30 | agreement between the calculated optical depth and the WMAP tau value 31 | is printed in the text output. 32 | 33 | """ 34 | N_gamma = 6804. 35 | 36 | # f_* f_esc N_gamma 37 | f_ion = numpy.transpose(numpy.atleast_2d(numpy.arange(10., 200., 10.))) 38 | 39 | alpha_B = 1e-13 # cm^3 s^-1 40 | m_min = 1e8 # M_sun 41 | 42 | x_ionHe = 2.0 43 | 44 | dz = 0.1 45 | z = numpy.arange(20., 6. - 1.5 * dz, -1. * dz) 46 | #z = numpy.arange(6., 20. + 1.5 * dz, dz) 47 | 48 | cosmos = [cparam.WMAP5_ML(flat=True), 49 | cparam.WMAP5_mean(flat=True)] 50 | 51 | pylab.figure(figsize=(8,8)) 52 | colors=['r', 'k'] 53 | names = ["WMAP5 ML", "WMAP5 mean"] 54 | i = -1 55 | for cosmo in cosmos: 56 | i += 1 57 | 58 | print("\n%s" % (names[i])) 59 | # calculate ionized fraction, including recombinations 60 | x_rec, w_rec, t = cr.integrate_ion_recomb_collapse(z, f_ion, 61 | m_min, 62 | passed_min_mass=True, 63 | alpha_B=alpha_B, 64 | **cosmo) 65 | # calculate the optical depth in this scenario 66 | tau_z0 = cr.optical_depth_instant(z[-1], 67 | x_ionH=1.0, 68 | x_ionHe=2.0, 69 | **cosmo) 70 | 71 | tau_later = cr.integrate_optical_depth(x_rec, x_ionHe * x_rec, 72 | z, **cosmo) 73 | tau_0 = tau_later[:, -1] + tau_z0 74 | 75 | tau = tau_later 76 | 77 | print("tau(WMAP) = %.3f" % (cosmo['tau'])) 78 | for j in range(len(f_ion.flat)): 79 | if round(f_ion[j],1) != 50.0: 80 | continue 81 | print("with f_* f_esc_gamma N_gamma = %.1f:" % (f_ion[j])) 82 | pylab.plot(z, x_rec[j], ls='-', color=colors[i]) 83 | pylab.plot(z, w_rec[j], ls=':', color=colors[i]) 84 | #pylab.plot(z, 10. * tau[j], ls='--', color=colors[i]) 85 | pylab.plot(z, 10. * (tau_0[j] - tau[j]), ls='--', color=colors[i]) 86 | pylab.axhline(y=10. * tau_0[j], ls='--', color=colors[i]) 87 | print("tau(z=0) = %.4f" % (tau_0[j])) 88 | print("fractional diff. = %.3g" % ((tau_0[j] - cosmo['tau']) / 89 | cosmo['tau'])) 90 | if i==1: 91 | # Make sure we recover the WMAP value. 92 | ntest.assert_approx_equal(tau_0[j], cosmo['tau'], 2) 93 | 94 | pylab.ylim(0,1.01) 95 | pylab.xlabel("redshift z") 96 | pylab.ylabel(r"ionized fraction or optical depth $\tau \times 10$") 97 | 98 | pylab.figure(figsize=(8,8)) 99 | pylab.plot(tau_0, f_ion / N_gamma, '-', color='k') 100 | pylab.plot([cosmo['tau']], [50.0 / N_gamma], 'x', color='b') 101 | pylab.xlim(0.06, 0.12) 102 | pylab.ylim(0., 0.022) 103 | pylab.xlabel(r'$\tau$') 104 | pylab.ylabel(r'$f_* f_{esc,\gamma}$') 105 | 106 | if __name__ == "__main__": 107 | test_tau_BKP() 108 | pylab.show() 109 | 110 | -------------------------------------------------------------------------------- /tests/test_plot_HH.py: -------------------------------------------------------------------------------- 1 | """Reproduce collapse fraction plot from Haiman and Holder (2003) 2 | 3 | Haiman and Holder 2003ApJ...595....1H. 4 | 5 | """ 6 | 7 | from __future__ import absolute_import, division, print_function 8 | 9 | import inspect 10 | 11 | import numpy 12 | import matplotlib.pyplot as pylab 13 | 14 | import cosmolopy.distance as cd 15 | import cosmolopy.constants as cc 16 | import cosmolopy.perturbation as cp 17 | import cosmolopy.reionization as cr 18 | import cosmolopy.parameters as cparams 19 | 20 | def hh_cosmo(flat=True, extras=True): 21 | """Cosmological parameters used in HH2003.""" 22 | cosmo = {'omega_b_0' : 0.047, 23 | 'omega_M_0' : 0.29, 24 | 'omega_lambda_0' : 0.71, 25 | 'h' : 0.72, 26 | 'n' : 0.99, 27 | 'sigma_8' : 0.9 28 | } 29 | if flat: 30 | cosmo['omega_lambda_0'] = 1. - cosmo['omega_M_0'] 31 | cosmo['omega_k_0'] = 0.0 32 | if extras: 33 | cparams.add_extras(cosmo) 34 | return cosmo 35 | 36 | def test_figure1(): 37 | """Plot HH fig. 1: Evolution of the collapsed fraction (no quant. tests). 38 | 39 | "Evolution of the collapsed fraction of all baryons in halos in 40 | three different virial temperature ranges." 41 | 42 | Haiman and Holder 2003ApJ...595....1H. 43 | 44 | """ 45 | 46 | dz = 1. 47 | z = numpy.arange(45., 0.0, -1. * dz) 48 | 49 | cosmo = hh_cosmo() 50 | 51 | T_min = numpy.array([[1.0e2], 52 | [1.0e4], 53 | [2.0e5]]) 54 | 55 | linestyle = ['-', ':', '--'] 56 | 57 | # Collapse fraction with the various minimum Virial temps. 58 | fc = cp.collapse_fraction(*cp.sig_del(T_min, z, **cosmo)) 59 | 60 | # Calculate fraction of mass in halos in the ranges of min T. 61 | fc_diff = numpy.empty((T_min.shape[0], z.shape[0])) 62 | fc_diff[0:-1] = fc[0:-1] - fc[1:] 63 | fc_diff[-1] = fc[-1] 64 | 65 | pylab.figure(figsize=(6,6)) 66 | for i in range(len(linestyle)): 67 | pylab.plot(z, fc_diff[i], ls=linestyle[i]) 68 | 69 | pylab.xlabel(r"$\mathrm{z}$") 70 | pylab.ylabel(r"$\mathrm{F_{coll}}$") 71 | 72 | pylab.yscale('log') 73 | pylab.ylim(1e-5, 1.0) 74 | pylab.xlim(45.,0.) 75 | 76 | pylab.title("compare to " + inspect.stack()[0][3].replace('test_', '') + 77 | " H&H (2003ApJ...595....1H).") 78 | 79 | if __name__ == '__main__': 80 | test_figure1() 81 | pylab.show() 82 | 83 | 84 | -------------------------------------------------------------------------------- /tests/test_plot_Hogg.py: -------------------------------------------------------------------------------- 1 | """Reproduce some plots from David Hogg's arXiv:astro-ph/9905116v4 2 | 3 | """ 4 | 5 | from __future__ import absolute_import, division, print_function 6 | 7 | import inspect 8 | 9 | import numpy 10 | import matplotlib.pyplot as pylab 11 | 12 | import cosmolopy.distance as cd 13 | import cosmolopy.constants as cc 14 | 15 | def test_figure1(): 16 | """Plot Hogg fig. 1: The dimensionless proper motion distance DM/DH. 17 | 18 | The three curves are for the three world models, Einstein-de 19 | Sitter (omega_M, omega_lambda) = (1, 0), solid; low-density, 20 | (0.05, 0), dotted; and high lambda, (0.2, 0.8), dashed. 21 | 22 | Hubble distance DH = c / H0 23 | 24 | z from 0--5 25 | DM / DH from 0--3 26 | 27 | """ 28 | 29 | z = numpy.arange(0, 5.05, 0.05) 30 | 31 | cosmo = {} 32 | cosmo['omega_M_0'] = numpy.array([[1.0],[0.05],[0.2]]) 33 | cosmo['omega_lambda_0'] = numpy.array([[0.0],[0.0],[0.8]]) 34 | cosmo['h'] = 0.5 35 | cd.set_omega_k_0(cosmo) 36 | 37 | linestyle = ['-', ':', '--'] 38 | 39 | dh = cd.hubble_distance_z(0, **cosmo) 40 | dm = cd.comoving_distance_transverse(z, **cosmo) 41 | 42 | pylab.figure(figsize=(6,6)) 43 | for i in range(len(linestyle)): 44 | pylab.plot(z, (dm/dh)[i], ls=linestyle[i]) 45 | #pylab.plot(z, (dm_err/dh)[i], ls=linestyle[i]) 46 | pylab.xlim(0,5) 47 | pylab.ylim(0,3) 48 | pylab.xlabel("redshift z") 49 | pylab.ylabel(r"proper motion distance $D_M/D_H$") 50 | pylab.title("compare to " + inspect.stack()[0][3].replace('test_', '') + 51 | " (astro-ph/9905116v4)") 52 | 53 | def test_figure2(): 54 | """Plot Hogg fig. 2: The dimensionless angular diameter distance DA/DH. 55 | 56 | The three curves are for the three world models, 57 | 58 | - Einstein-de Sitter (omega_M, omega_lambda) = (1, 0) [solid] 59 | 60 | : Low-density (0.05, 0) [dotted] 61 | 62 | -- High lambda, (0.2, 0.8) [dashed] 63 | 64 | Hubble distance DH = c / H0 65 | 66 | z from 0--5 67 | DA / DH from 0--0.5 68 | 69 | """ 70 | 71 | z = numpy.arange(0, 5.05, 0.05) 72 | 73 | cosmo = {} 74 | cosmo['omega_M_0'] = numpy.array([[1.0],[0.05],[0.2]]) 75 | cosmo['omega_lambda_0'] = numpy.array([[0.0],[0.0],[0.8]]) 76 | cosmo['h'] = 0.5 77 | cd.set_omega_k_0(cosmo) 78 | 79 | linestyle = ['-', ':', '--'] 80 | 81 | dh = cd.hubble_distance_z(0, **cosmo) 82 | da = cd.angular_diameter_distance(z, **cosmo) 83 | 84 | # Also test the pathway with non-zero z0 85 | da2 = cd.angular_diameter_distance(z, z0=1e-8, **cosmo) 86 | 87 | pylab.figure(figsize=(6,6)) 88 | for i in range(len(linestyle)): 89 | pylab.plot(z, (da/dh)[i], ls=linestyle[i]) 90 | pylab.plot(z, (da2/dh)[i], ls=linestyle[i]) 91 | pylab.xlim(0,5) 92 | pylab.ylim(0,0.5) 93 | pylab.xlabel("redshift z") 94 | pylab.ylabel(r"angular diameter distance $D_A/D_H$") 95 | pylab.title("compare to " + inspect.stack()[0][3].replace('test_', '') + 96 | " (astro-ph/9905116v4)") 97 | 98 | def test_figure3(): 99 | """Plot Hogg fig. 3: The dimensionless luminosity distance DL/DH 100 | 101 | The three curves are for the three world models, 102 | 103 | - Einstein-de Sitter (omega_M, omega_lambda) = (1, 0) [solid] 104 | 105 | : Low-density (0.05, 0) [dotted] 106 | 107 | -- High lambda, (0.2, 0.8) [dashed] 108 | 109 | Hubble distance DH = c / H0 110 | 111 | z from 0--5 112 | DL / DH from 0--16 113 | 114 | """ 115 | 116 | z = numpy.arange(0, 5.05, 0.05) 117 | 118 | cosmo = {} 119 | cosmo['omega_M_0'] = numpy.array([[1.0],[0.05],[0.2]]) 120 | cosmo['omega_lambda_0'] = numpy.array([[0.0],[0.0],[0.8]]) 121 | cosmo['h'] = 0.5 122 | cd.set_omega_k_0(cosmo) 123 | 124 | linestyle = ['-', ':', '--'] 125 | 126 | dh = cd.hubble_distance_z(0, **cosmo) 127 | dl = cd.luminosity_distance(z, **cosmo) 128 | 129 | pylab.figure(figsize=(6,6)) 130 | for i in range(len(linestyle)): 131 | pylab.plot(z, (dl/dh)[i], ls=linestyle[i]) 132 | pylab.xlim(0,5) 133 | pylab.ylim(0,16) 134 | pylab.xlabel("redshift z") 135 | pylab.ylabel(r"luminosity distance $D_L/D_H$") 136 | pylab.title("compare to " + inspect.stack()[0][3].replace('test_', '') + 137 | " (astro-ph/9905116v4)") 138 | 139 | 140 | def test_figure5(): 141 | """Plot Hogg fig. 5: The dimensionless comoving volume element (1/DH)^3(dVC/dz). 142 | 143 | The three curves are for the three world models, (omega_M, omega_lambda) = 144 | (1, 0), solid; (0.05, 0), dotted; and (0.2, 0.8), dashed. 145 | 146 | """ 147 | z = numpy.arange(0, 5.05, 0.05) 148 | 149 | cosmo = {} 150 | cosmo['omega_M_0'] = numpy.array([[1.0],[0.05],[0.2]]) 151 | cosmo['omega_lambda_0'] = numpy.array([[0.0],[0.0],[0.8]]) 152 | cosmo['h'] = 0.5 153 | cd.set_omega_k_0(cosmo) 154 | 155 | linestyle = ['-', ':', '--'] 156 | 157 | dh = cd.hubble_distance_z(0, **cosmo) 158 | 159 | dVc = cd.diff_comoving_volume(z, **cosmo) 160 | dVc_normed = dVc/(dh**3.) 161 | 162 | Vc = cd.comoving_volume(z, **cosmo) 163 | dz = z[1:] - z[:-1] 164 | dVc_numerical = (Vc[:,1:] - Vc[:,:-1])/dz/(4. * numpy.pi) 165 | dVc_numerical_normed = dVc_numerical/(dh**3.) 166 | 167 | pylab.figure(figsize=(6,6)) 168 | for i in range(len(linestyle)): 169 | pylab.plot(z, dVc_normed[i], ls=linestyle[i], lw=2.) 170 | pylab.plot(z[:-1], dVc_numerical_normed[i], ls=linestyle[i], 171 | c='k', alpha=0.1) 172 | pylab.xlim(0,5) 173 | pylab.ylim(0,1.1) 174 | pylab.xlabel("redshift z") 175 | pylab.ylabel(r"comoving volume element $[1/D_H^3]$ $dV_c/dz/d\Omega$") 176 | pylab.title("compare to " + inspect.stack()[0][3].replace('test_', '') + 177 | " (astro-ph/9905116v4)") 178 | 179 | def test_figure6(): 180 | """Plot Hogg fig. 6: The dimensionless lookback time t_L/t_H and age t/t_H. 181 | 182 | The three curves are for the three world models, 183 | 184 | - Einstein-de Sitter (omega_M, omega_lambda) = (1, 0) [solid] 185 | 186 | : Low-density (0.05, 0) [dotted] 187 | 188 | -- High lambda, (0.2, 0.8) [dashed] 189 | 190 | Hubble distance DH = c / H0 191 | 192 | z from 0--5 193 | t/th from 0--1.2 194 | 195 | """ 196 | 197 | z = numpy.arange(0, 5.05, 0.05) 198 | 199 | cosmo = {} 200 | cosmo['omega_M_0'] = numpy.array([[1.0],[0.05],[0.2]]) 201 | cosmo['omega_lambda_0'] = numpy.array([[0.0],[0.0],[0.8]]) 202 | cosmo['h'] = 0.5 203 | cd.set_omega_k_0(cosmo) 204 | 205 | linestyle = ['-', ':', '--'] 206 | 207 | th = 1/ cd.hubble_z(0, **cosmo) 208 | 209 | tl = cd.lookback_time(z, **cosmo) 210 | age = cd.age(z, **cosmo) 211 | 212 | pylab.figure(figsize=(6,6)) 213 | for i in range(len(linestyle)): 214 | pylab.plot(z, (tl/th)[i], ls=linestyle[i]) 215 | pylab.plot(z, (age/th)[i], ls=linestyle[i]) 216 | pylab.xlim(0,5) 217 | pylab.ylim(0,1.2) 218 | pylab.xlabel("redshift z") 219 | pylab.ylabel(r"lookback timne $t_L/t_H$") 220 | pylab.title("compare to " + inspect.stack()[0][3].replace('test_', '') + 221 | " (astro-ph/9905116v4)") 222 | 223 | if __name__ == "__main__": 224 | 225 | test_figure1() 226 | test_figure2() 227 | test_figure3() 228 | test_figure5() 229 | test_figure6() 230 | pylab.show() 231 | 232 | -------------------------------------------------------------------------------- /tests/test_plot_clumping_factor_Chary.py: -------------------------------------------------------------------------------- 1 | 2 | from __future__ import absolute_import, division, print_function 3 | 4 | import sys 5 | 6 | import numpy 7 | import pylab 8 | 9 | import cosmolopy.reionization as cr 10 | 11 | def plot_clumping_factor_Chary(): 12 | """Plot clumping factor from Chary paper. 13 | """ 14 | z = numpy.linspace(5,15,500) 15 | cf = cr.clumping_factor_Chary(z) 16 | 17 | pylab.plot(z,cf) 18 | pylab.yscale('log') 19 | pylab.xlim(5,15) 20 | pylab.ylim(1,100) 21 | 22 | if __name__ == "__main__": 23 | if len(sys.argv)==1: 24 | print("Run with a filename argument to produce image files, e.g.:") 25 | if len(sys.argv) > 1: 26 | filename = sys.argv[1] 27 | else: 28 | filename = None 29 | 30 | plot_clumping_factor_Chary() 31 | 32 | ### Plot output code. ### 33 | if filename is None: 34 | pylab.show() 35 | else: 36 | from matplotlib import _pylab_helpers 37 | for manager in _pylab_helpers.Gcf.get_all_fig_managers(): 38 | fig = manager.canvas.figure 39 | if len(fig.get_label()) > 0: 40 | label = fig.get_label() 41 | else: 42 | label = 'clumpFig' + str(manager.num) 43 | newfilename = prefix + '_' + label + extension 44 | fig.savefig(newfilename, bbox_inches="tight") 45 | -------------------------------------------------------------------------------- /tests/test_plot_optical_depth.py: -------------------------------------------------------------------------------- 1 | """Test that analytical and numerical optical depth calculations agree. 2 | 3 | Also reproduces a figure from Griffiths et al. astro-ph/9812125v3 4 | (don't use the published version, which contains errors). 5 | """ 6 | 7 | from __future__ import absolute_import, division, print_function 8 | 9 | import math 10 | 11 | import numpy 12 | import numpy.testing.utils as ntest 13 | import matplotlib.pyplot as pylab 14 | 15 | import cosmolopy.distance as cd 16 | import cosmolopy.constants as cc 17 | import cosmolopy.density as cden 18 | import cosmolopy.reionization as cr 19 | 20 | 21 | def test_GBL_tau_star(): 22 | """Test tau_* against GB&L astro-ph/9812125v3. 23 | 24 | tau_* is a quantity used in optical_depth_instant. 25 | """ 26 | z = 1.0 27 | 28 | # Fully ionized H and He 29 | x_ionH = 1.0 30 | x_ionHe = 2.0 31 | 32 | cosmo = {} 33 | cosmo['omega_M_0'] = numpy.array([[0.3],[0.6],[1.0]]) 34 | cosmo['omega_lambda_0'] = 1. - cosmo['omega_M_0'] 35 | cosmo['h'] = 0.65 36 | cosmo['omega_b_0'] = 0.02 / cosmo['h']**2. 37 | cosmo['Y_He'] = 0.24 38 | cd.set_omega_k_0(cosmo) 39 | 40 | tau_inst, tau_star = cr.optical_depth_instant(z, 41 | x_ionH=x_ionH, 42 | x_ionHe=x_ionHe, 43 | return_tau_star=True, 44 | **cosmo) 45 | print("tau_star = %.7f" % (tau_star)) 46 | print("tau_star/(h Omega_b) = %.7f =? 0.061" % 47 | (tau_star / (cosmo['h'] * cosmo['omega_b_0']))) 48 | 49 | ntest.assert_approx_equal(tau_star / (cosmo['h'] * cosmo['omega_b_0']), 50 | 0.061, 51 | 2) 52 | 53 | print("(1 - Y_He/2) = %.3f =? 0.88" % (1. - (cosmo['Y_He']/2.))) 54 | ntest.assert_approx_equal((1. - (cosmo['Y_He']/2.)), 55 | 0.88, 56 | 7) 57 | 58 | H_0 = cc.H100_s * cosmo['h'] 59 | 60 | # s^-1 * Mpc s^-1 * Mpc^2 / Mpc^3 msun^-1 s^-2 / Msun -> 61 | tau_star_explicit = ((1. - (cosmo['Y_He']/2.)) * 62 | ((3. * H_0 * cosmo['omega_b_0'] * cc.c_light_Mpc_s * 63 | cc.sigma_T_Mpc) / 64 | (8. * math.pi * cc.G_const_Mpc_Msun_s * 65 | (cc.m_p_g/cc.M_sun_g)))) 66 | 67 | print("tau_star_explicit = %.7f =? tau_star" % (tau_star_explicit)) 68 | ntest.assert_approx_equal(tau_star, tau_star_explicit, 3) 69 | 70 | def test_GBL_tau_inst(): 71 | """Test match between analytical and numerical tau with instant 72 | reionization. 73 | 74 | Also makes a plot reproducing figure 1 of arXiv:astro-ph/9812125v3. 75 | """ 76 | dz = 0.05 77 | z = numpy.arange(0., 80. + 1.5*dz, dz) 78 | 79 | # Fully ionized H and He 80 | x_ionH = 1.0 81 | x_ionHe = 2.0 82 | 83 | cosmo = {} 84 | cosmo['omega_M_0'] = numpy.array([[0.3],[0.6],[1.0]]) 85 | cosmo['omega_lambda_0'] = 1. - cosmo['omega_M_0'] 86 | cosmo['h'] = 0.65 87 | cosmo['omega_b_0'] = 0.02 / cosmo['h']**2. 88 | cosmo['Y_He'] = 0.24 89 | cd.set_omega_k_0(cosmo) 90 | 91 | tau_inst = cr.optical_depth_instant(z, x_ionH=x_ionH, x_ionHe=x_ionHe, 92 | **cosmo) 93 | tau_int = cr.integrate_optical_depth(x_ionH, x_ionHe, z, **cosmo) 94 | 95 | linestyle = ['-', ':', '--'] 96 | 97 | pylab.figure() 98 | pylab.subplot(2,1,1) 99 | pylab.title("Compare to GB&L fig. 1 (astro-ph/9812125v3.)") 100 | for i in range(len(linestyle)): 101 | pylab.plot(z, tau_inst[i], ls=linestyle[i], color='b') 102 | pylab.plot(z, tau_int[i], ls=linestyle[i], color='r') 103 | 104 | pylab.xlim(0,80) 105 | pylab.ylim(0,1) 106 | pylab.xlabel(r"$\mathrm{z_{ion}}$") 107 | pylab.ylabel(r"$\tau$") 108 | 109 | pylab.subplot(2,1,2) 110 | for i in range(len(linestyle)): 111 | pylab.plot(z, 112 | 1.e4 * (tau_int[i] - tau_inst[i])/tau_inst[i], 113 | ls=linestyle[i], color='k') 114 | diff = (tau_int[i] - tau_inst[i]) / tau_inst[i] 115 | diff[numpy.isnan(diff)] = 0.0 116 | print("max fractional error in num. int. = %.3g" % 117 | numpy.max(numpy.abs(diff)) 118 | ) 119 | ntest.assert_array_less(numpy.abs(diff), 120 | numpy.zeros(diff.shape) + 2.e-4) 121 | 122 | pylab.xlim(0,40) 123 | pylab.xlabel(r"$\mathrm{z_{ion}}$") 124 | pylab.ylabel(r"$\mathrm{10^4 \times (num.\tau - ana.\tau)/ana.\tau}$") 125 | 126 | if __name__ == "__main__": 127 | test_GBL_tau_star() 128 | test_GBL_tau_inst() 129 | pylab.show() 130 | 131 | -------------------------------------------------------------------------------- /tests/test_plot_reionization.py: -------------------------------------------------------------------------------- 1 | """Plot IGM ionized fraction. 2 | 3 | Note that there are no actual quantitative tests here. Just checks 4 | that it runs without errors. 5 | 6 | """ 7 | 8 | from __future__ import absolute_import, division, print_function 9 | 10 | import numpy 11 | import numpy.testing.utils as ntest 12 | import matplotlib.pyplot as pylab 13 | 14 | import cosmolopy.perturbation as cp 15 | import cosmolopy.distance as cd 16 | import cosmolopy.density as cden 17 | import cosmolopy.reionization as cr 18 | import cosmolopy.constants as cc 19 | import cosmolopy.parameters as cparam 20 | 21 | import testingutils as tu 22 | 23 | def test_plot_FZH(): 24 | """Plot figure 3 from FZH (2004ApJ...613....1F) (no quantitative tests). 25 | """ 26 | 27 | cosmo = {} 28 | cosmo['omega_M_0'] = 0.3 29 | cosmo['omega_k_0'] = 0.0 30 | cosmo['omega_lambda_0'] = 0.7 31 | cosmo['h'] = 0.7 32 | cosmo['n'] = 1.0 33 | cosmo['sigma_8'] = 0.9 34 | 35 | cosmo['omega_b_0'] = 0.0462 # not specified in paper 36 | cosmo['omega_n_0'] = 0.0 # not specified in paper 37 | cosmo['N_nu'] = 0 # not specified in paper 38 | cosmo['Y_He'] = 0.24 # not specified in paper 39 | cosmo['baryonic_effects'] = False 40 | dz = 0.1 41 | z = numpy.arange(25., 8. - 1.5 * dz, -1. * dz) 42 | 43 | T_min = 1e4 #K 44 | c_ion = numpy.array([[500.], [40.], [12.]]) 45 | 46 | # calculate ionized fraction from collapse fraction 47 | x_fcol = cr.ionization_from_collapse(z, 48 | c_ion, 49 | T_min, 50 | **cosmo) 51 | #linestyle = ['-', ':', '--'] 52 | color = ['r', 'g', 'b'] 53 | pylab.figure() 54 | pylab.subplot(2,1,1) 55 | for i in range(len(color)): 56 | pylab.plot(z, x_fcol[i], ls='--', color=color[i]) 57 | pylab.axhline(y=0.75) 58 | pylab.yscale('log') 59 | pylab.xlim(8,25) 60 | pylab.ylim(1e-4, 1) 61 | pylab.title("Compare to figure 3 from FZH (2004ApJ...613....1F)") 62 | 63 | pylab.subplot(2,1,2) 64 | for i in range(len(color)): 65 | pylab.plot(z, x_fcol[i], ls='--', color=color[i]) 66 | pylab.axhline(y=0.75) 67 | pylab.xlim(8,25) 68 | pylab.ylim(0, 1) 69 | 70 | def test_plot_integrate_ion_recomb_collapse(): 71 | """Plot results of integrate_ion_recomb_collapse (no quantitative tests). 72 | """ 73 | 74 | cosmo = cparam.WMAP5_mean(flat=True) 75 | 76 | dz = 0.5 77 | z = numpy.arange(25., 8. - 1.5 * dz, -1. * dz) 78 | 79 | T_min = 1e4 #K 80 | c_ion = numpy.array([[500.], [40.], [12.]]) 81 | 82 | # calculate ionized fraction from collapse fraction 83 | x_fcol = cr.ionization_from_collapse(z, 84 | c_ion, 85 | T_min, 86 | **cosmo) 87 | 88 | x_rec = numpy.empty(x_fcol.shape) 89 | w_rec = numpy.empty(x_fcol.shape) 90 | for i in range(x_fcol.shape[0]): 91 | # calculate ionized fraction, including recombinations 92 | x_rec[i], w_rec[i], t = cr.integrate_ion_recomb_collapse(z, c_ion[i,0], 93 | temp_min = T_min, 94 | **cosmo) 95 | 96 | #linestyle = ['-', ':', '--'] 97 | color = ['r', 'g', 'b'] 98 | pylab.figure() 99 | pylab.subplot(2,1,1) 100 | for i in range(len(color)): 101 | pylab.plot(z, x_fcol[i], ls='--', color=color[i]) 102 | pylab.plot(z, x_rec[i], ls='-', color=color[i]) 103 | pylab.plot(z, w_rec[i], ls=':', color=color[i]) 104 | pylab.axhline(y=0.75) 105 | pylab.yscale('log') 106 | pylab.xlim(8,25) 107 | pylab.ylim(1e-4, 1) 108 | 109 | pylab.subplot(2,1,2) 110 | for i in range(len(color)): 111 | pylab.plot(z, x_fcol[i], ls='--', color=color[i]) 112 | pylab.plot(z, x_rec[i], ls='-', color=color[i]) 113 | pylab.plot(z, w_rec[i], ls=':', color=color[i]) 114 | pylab.axhline(y=0.75) 115 | pylab.xlim(8,25) 116 | pylab.ylim(0, 1) 117 | 118 | if __name__ == "__main__": 119 | test_plot_FZH() 120 | test_plot_integrate_ion_recomb_collapse() 121 | pylab.show() 122 | 123 | -------------------------------------------------------------------------------- /tests/test_plot_reionization_BH.py: -------------------------------------------------------------------------------- 1 | """Reproduce some results from Bolton and Haehnelt (2007MNRAS.382..325B). 2 | """ 3 | 4 | from __future__ import absolute_import, division, print_function 5 | 6 | import pylab 7 | 8 | import numpy 9 | import scipy.interpolate 10 | 11 | import cosmolopy.distance as cd 12 | import cosmolopy.reionization as cr 13 | import cosmolopy.perturbation as cp 14 | 15 | def nIonDotLowz(z): 16 | """Ionizations per second per Mpc^3 from BH2007 for z < 6 17 | """ 18 | return 10.**(50.5 - 0.06 * (z - 6.0)) 19 | 20 | def nIonDotBHmodel2(z): 21 | """Ionization model 2 from BH2007: constant above z=6. 22 | """ 23 | return ((z < 6) * nIonDotLowz(z) + 24 | (z >= 6) * nIonDotLowz(6)) 25 | 26 | def test_plot_nIonDotBH(): 27 | """Compare with BH2007 figure 7.""" 28 | z = numpy.linspace(1.75, 15., 100) 29 | n2 = nIonDotBHmodel2(z) 30 | 31 | pylab.figure() 32 | pylab.plot(z, numpy.log10(n2), label='Model 2') 33 | pylab.xlim(1.75, 15.) 34 | pylab.ylim(48.9, 51.8) 35 | pylab.legend(loc='best') 36 | 37 | def test_plot_integrate_ionization_recomb_BH(xHe=0.0): 38 | 39 | cosmo = {'omega_b_0' : 0.0463, 40 | 'omega_M_0' : 0.26, 41 | 'omega_lambda_0' : 1.-0.26, 42 | 'omega_k_0' : 0.0, 43 | 'h' : 0.72, 44 | 'n' : 0.95, 45 | 'sigma_8' : 0.85, 46 | #'tau' : 0.09, 47 | #'tau_err' : 0.03, 48 | 'omega_n_0' : 0.0, 49 | 'N_nu': 0, 50 | 'Y_He': 0.24, 51 | 'baryonic_effects' : False, 52 | } 53 | 54 | nIonDot2 = lambda z1: cr.ionization_from_luminosity(z1, 55 | nIonDotBHmodel2, 56 | xHe=xHe, 57 | **cosmo) 58 | 59 | zi = numpy.linspace(3.,15.,500.) 60 | w2i = nIonDot2(zi) 61 | ifunc2 = scipy.interpolate.interp1d(zi, w2i) 62 | ifunc2b = scipy.interpolate.interp1d(zi, w2i * 2.0) 63 | 64 | clump_fact_func = lambda z1: 2.0 65 | 66 | z = numpy.linspace(15,4,100.) 67 | fIon2, w2, t2 = cr.integrate_ion_recomb(z, 68 | ifunc2, 69 | clump_fact_func, 70 | xHe=xHe, 71 | **cosmo) 72 | fIon2b, w2b, t2b = cr.integrate_ion_recomb(z, 73 | ifunc2b, 74 | clump_fact_func, 75 | xHe=xHe, 76 | **cosmo) 77 | 78 | pylab.plot(z, fIon2, "--", label='Model 2') 79 | pylab.plot(z, fIon2b, "-", label='Model 2b') 80 | pylab.plot(z, w2, "0.75", label='M2 no rec.') 81 | 82 | pylab.xlim(4,15) 83 | pylab.ylim(0,1.0) 84 | pylab.legend(loc='best') 85 | 86 | if __name__ == '__main__': 87 | test_plot_nIonDotBH() 88 | pylab.figure() 89 | test_plot_integrate_ionization_recomb_BH() 90 | pylab.show() 91 | 92 | -------------------------------------------------------------------------------- /tests/test_utils.py: -------------------------------------------------------------------------------- 1 | 2 | from __future__ import absolute_import, division, print_function 3 | 4 | import numpy 5 | 6 | from cosmolopy.utils import * 7 | from cosmolopy.saveable import Saveable 8 | 9 | 10 | ######### Testing ############ 11 | 12 | def test_integrate_piecewise(pieces=2, method='quad'): 13 | # Test modified from scipy test_quadrature.py. 14 | n = 2 15 | z = 1.8 16 | def func(x): # Bessel function integrand 17 | return numpy.cos(n*x-z*numpy.sin(x))/numpy.pi 18 | x = numpy.linspace(0, numpy.pi, pieces) 19 | val = integrate_piecewise(func,x, method=method) 20 | table_val = 0.30614353532540296487 21 | diff = val[-1] - table_val 22 | print("Error with %i %s pieces = %.3g" % (pieces, method, diff)) 23 | numpy.testing.assert_almost_equal(val[-1], table_val, decimal=7) 24 | 25 | def test_PiecewisePowerlaw(n=4, plot=False): 26 | 27 | powers = 1.5 * (0.5 - numpy.random.rand(n)) 28 | limits = 10. * numpy.cumsum(numpy.random.rand(n+1)) 29 | 30 | pfunc = PiecewisePowerlaw(limits, powers, externalval=0) 31 | x = numpy.linspace(limits[0] - 0.1, limits[-1] + 0.1, 20.) 32 | #x = numpy.linspace(limits[0], limits[-1], 20.) 33 | y = pfunc(x) 34 | 35 | integral = pfunc.integrate(0, x) 36 | numintegral = integrate_piecewise(pfunc, x, method='quad') 37 | 38 | integral2 = pfunc.integrate(x, x[-1]) 39 | numintegral2 = numintegral[-1] - numintegral 40 | 41 | # Weighted integral 42 | integral3 = pfunc.integrate(0, x, weight_power=1.5) 43 | weightedfunc = lambda x: (x**1.5) * pfunc(x) 44 | numintegral3 = integrate_piecewise(weightedfunc, x, method='quad') 45 | 46 | if plot: 47 | import pylab 48 | 49 | pylab.subplot(221) 50 | pylab.title('x vs. y') 51 | pylab.plot(x,y) 52 | pylab.xlim(min(x), max(x)) 53 | for xlim in pfunc._limits.flat: 54 | pylab.axvline(x=xlim) 55 | 56 | pylab.subplot(223) 57 | pylab.title('x vs. forward/reverse integral') 58 | pylab.plot(x, integral) 59 | pylab.plot(x, numintegral) 60 | pylab.plot(x, integral2) 61 | pylab.plot(x, numintegral2) 62 | pylab.plot(pfunc._limits.flat[1:], numpy.cumsum(pfunc._integrals), '.') 63 | pylab.xlim(min(x), max(x)) 64 | 65 | pylab.subplot(222) 66 | pylab.title('frac. diffs (num - ana)/ana') 67 | pylab.plot(x, (integral - numintegral)/integral) 68 | pylab.plot(x, (integral2 - numintegral2)/integral2) 69 | pylab.plot(x, (integral3 - numintegral3)/integral3) 70 | 71 | pylab.subplot(224) 72 | pylab.title('weighted integrals') 73 | pylab.plot(x, integral3) 74 | pylab.plot(x, numintegral3) 75 | 76 | pylab.show() 77 | assert numpy.all(numpy.abs(integral - numintegral) < 1e-4) 78 | assert numpy.all(numpy.abs(integral2 - numintegral2) < 1e-4) 79 | assert numpy.all(numpy.abs(integral3[integral3>0] - 80 | numintegral3[integral3>0]) / 81 | integral3[integral3>0] < 1e-3) 82 | assert numpy.abs(integral[-1] - 1.) < 1e-4 83 | assert numpy.abs(integral2[0] - 1.) < 1e-4 84 | 85 | 86 | def test_Extrapolate1d(): 87 | 88 | slope = 2. * (0.5 - numpy.random.rand(1)) 89 | intercept = 20. * (0.5 - numpy.random.rand(1)) 90 | x = numpy.array([3., 4., 91 | 5., 6., 7., 92 | 8., 9.]) 93 | y = slope * x + intercept 94 | 95 | # Random deviations in the midde. 96 | y[2:5] = y[2:5] + (5. * (0.5 - numpy.random.rand(3))) 97 | x1 = numpy.linspace(0., 15., 100.) 98 | 99 | extrap = Extrapolate1d(x,y) 100 | print(extrap.extrap_string()) 101 | y1 = extrap(x1) 102 | ytrue = slope * x1 + intercept 103 | 104 | # Test extrapolation with a fixed slope. 105 | newslopes = [3.0, 2.0] 106 | extrap2 = Extrapolate1d(x, y, slopes=newslopes) 107 | print(extrap2.extrap_string()) 108 | y2 = extrap2(x1) 109 | 110 | mask = numpy.logical_or(x1 >= x[5], 111 | x1 <= x[1]) 112 | 113 | assert numpy.all(numpy.abs((y1 - ytrue)[mask]) < 1e-10) 114 | 115 | import pylab 116 | pylab.plot(x, y, 'o') 117 | pylab.plot(x1, y1, '-') 118 | pylab.plot(x1, ytrue, ':') 119 | pylab.plot(x1, y2, '--') 120 | 121 | if __name__ == '__main__': 122 | 123 | import pylab 124 | pylab.figure() 125 | for i in range(4): 126 | test_Extrapolate1d() 127 | pylab.show() 128 | 129 | 130 | test_PiecewisePowerlaw(plot=True) 131 | 132 | import numpy.testing 133 | for method in ['quad', 'romberg']: 134 | for pieces in range(2,1000,300): 135 | test_integrate_piecewise(pieces, method) 136 | -------------------------------------------------------------------------------- /tests/test_wmap.py: -------------------------------------------------------------------------------- 1 | """Optical depth and cosmic age consistency check against WMAP parameters. 2 | 3 | Take various sets of WMAP parameters and see if I derive values for 4 | instant reionization optical depth and age of universe that agree with 5 | them. 6 | 7 | """ 8 | 9 | from __future__ import absolute_import, division, print_function 10 | 11 | import numpy 12 | import numpy.testing.utils as ntest 13 | import matplotlib.pyplot as pylab 14 | 15 | import cosmolopy.perturbation as cp 16 | import cosmolopy.distance as cd 17 | import cosmolopy.density as cden 18 | import cosmolopy.reionization as cr 19 | #import reionization as cr 20 | import cosmolopy.constants as cc 21 | import cosmolopy.parameters as cparam 22 | #import parameters as cparam 23 | 24 | import testingutils as tu 25 | 26 | def test_tau_instant(): 27 | """Check the optical depth we get using the WMAP z_reion. 28 | """ 29 | dz = 0.1 30 | z = numpy.arange(80., 0. - 1.5 * dz, -1. * dz) 31 | 32 | # Can't match WMAP7 optical depths exactly. Need to look into new 33 | # treatment in CAMB as mentioned in the WMAP7 paper (see 34 | # parameters.py). 35 | cosmos = [cparam.WMAP7_BAO_H0_mean(flat=True), 36 | cparam.WMAP7_ML(flat=True), 37 | cparam.WMAP5_BAO_SN_mean(flat=True), 38 | cparam.WMAP5_ML(flat=True), 39 | cparam.WMAP5_mean(flat=True)] 40 | 41 | # The WMAP5 numbers apparently assume He is neutral, while WMAP7 42 | # includes simultaneous singly ionized He plus Helium (double) 43 | # reionization at z=3.5. 44 | x_ionHe_list = [1.0, 1.0, 0, 0, 0] 45 | z_rHe_list = [3.5, 3.5, None, None, None] #[3.5, None, None, None] 46 | for cosmo in cosmos: 47 | # Fully ionized H 48 | x_ionH = 1.0 49 | 50 | # He ionization with H? 51 | x_ionHe = x_ionHe_list.pop(0) 52 | 53 | # Redshift for Helium double reionization? 54 | z_rHe = z_rHe_list.pop(0) 55 | 56 | zr = cosmo['z_reion'] 57 | tau_zr = cosmo['tau'] 58 | tau_calc = cr.optical_depth_instant(zr, 59 | x_ionH=x_ionH, 60 | x_ionHe=x_ionHe, 61 | z_rHe=z_rHe, 62 | verbose = 1, 63 | **cosmo) 64 | 65 | print("z_r = %f, testing tau:" % (zr)) 66 | print(tu.fractional_diff_string(tau_zr, tau_calc, 3)) 67 | 68 | ntest.assert_approx_equal(tau_calc, tau_zr, significant=2, 69 | err_msg="Optical depth doesn't match WMAP") 70 | 71 | 72 | def test_t_0(): 73 | """Check the age of the universe we get using WMAP cosmologies. 74 | 75 | We only find agreement to 3 sig figs, not the 4 specified in the 76 | WMAP paper. 77 | 78 | The results of test_age.py show that we're doing the integral 79 | correctly, so I think the problem is that we're not taking into 80 | account some of the higher-order effects included in the WMAP 81 | numbers. 82 | 83 | """ 84 | 85 | dz = 0.1 86 | z = numpy.arange(80., 0. - 1.5 * dz, -1. * dz) 87 | 88 | flat = True 89 | cosmos = [cparam.WMAP7_BAO_H0_mean(flat=True), 90 | cparam.WMAP7_ML(flat=True), 91 | cparam.WMAP5_BAO_SN_mean(flat=True), 92 | cparam.WMAP5_ML(flat=True), 93 | cparam.WMAP5_mean(flat=True)] 94 | 95 | for cosmo in cosmos: 96 | age = cd.age(0.0, **cosmo) 97 | age_flat = cd.age_flat(0.0, **cosmo) 98 | gyr = 1e9 * cc.yr_s 99 | age /= gyr 100 | age_flat /= gyr 101 | 102 | print("integrated age: ") 103 | print(tu.fractional_diff_string(age, cosmo['t_0'], 4)) 104 | ntest.assert_approx_equal(age, cosmo['t_0'], significant=3, 105 | err_msg="Integrated age doesn't match WMAP") 106 | 107 | print("analytical age: ") 108 | print(tu.fractional_diff_string(age_flat, cosmo['t_0'], 4)) 109 | ntest.assert_approx_equal(age_flat, cosmo['t_0'], significant=3, 110 | err_msg="Analytical age doesn't match WMAP") 111 | 112 | if __name__ == "__main__": 113 | test_tau_instant() 114 | test_t_0() 115 | -------------------------------------------------------------------------------- /tests/testingutils.py: -------------------------------------------------------------------------------- 1 | from __future__ import absolute_import, division, print_function 2 | 3 | import numpy 4 | 5 | def fractional_diff_string(actual, desired, places=3): 6 | formats = "% ." + ("%i" % places) + "g" 7 | template = "frac. diff. of "+formats+" and "+formats+" = "+formats 8 | return template % (actual, desired, (desired - actual)/desired) 9 | 10 | 11 | -------------------------------------------------------------------------------- /www/astrobetter.html: -------------------------------------------------------------------------------- 1 | angular diameter distance calculated with CosmoloPy 2 | 3 | Sample blurb about me, feel free to modify or delete: This is 4 | a guest post by Roban 5 | Hultman Kramer, who is currently an astronomy grad student at 6 | Columbia University, but will be starting as a Zwicky Fellow at ETH 7 | Zurich in January. 8 | 9 |

CosmoloPy is a 10 | package of basic cosmology routines for Python, designed for use with 11 | NumPy and SciPy. Features currently 12 | include: calculation of cosmological distance measures, 13 | perturbation-theory-based calculation of the matter power spectrum and 14 | halo collapse fraction (courtesy of Eisenstein & Hu's transfer 15 | function code), and integration of simple reionization models and the 16 | resulting electron scattering optical depth due to reionization. I 17 | hope it will prove useful to the increasing number of astronomers 18 | turning to Python.

19 | 20 | Using CosmoloPy is as simple as setting up a dictionary of 21 | cosmological parameters (some WMAP5 parameters are provided for 22 | convenience in cosmolopy.parameters) and passing it to 23 | the functions you want to use. For instance, we could quickly calculate the comoving distance to redshift 6 like this: 24 | 
25 | >>> import cosmolopy.distance as cd
26 | >>> cosmo = {'omega_M_0' : 0.3,
27 | ...          'omega_lambda_0' : 0.7, 
28 | ...          'h' : 0.72}
29 | >>> d_co, err = cd.comoving_distance(z=6., **cosmo)
30 | >>> print "Comoving distance to z=6 is %.1f Mpc" % (d_co)
31 | Comoving distance to z=6 is 8017.8 Mpc
32 |
33 | A few more lines 34 | of code, 35 | and you can produce a plot like the one shown above. 36 | 37 |

CosmoloPy is released under 38 | the MIT 39 | software license, which allows it to be freely used and 40 | modified. So 41 | please download 42 | it, use it, and request or add features you'd like to see included 43 | (and point out bugs we need to fix). Anyone can 44 | access the git 45 | repository, so please edit the code and send in useful changes and 46 | additions. All questions about use or development can be posted to 47 | the developer 48 | discussion group.

49 | -------------------------------------------------------------------------------- /www/astrobetter_example.py: -------------------------------------------------------------------------------- 1 | 2 | from __future__ import absolute_import, division, print_function 3 | 4 | import numpy 5 | import cosmolopy.perturbation as cp 6 | import cosmolopy.parameters as cparam 7 | import pylab 8 | 9 | # Get WMAP5 cosmological parameters. 10 | cosmo = cparam.WMAP5_BAO_SN_mean() 11 | 12 | # Set up an array of z values. 13 | z = numpy.arange(6.0, 20.0, 0.1) 14 | 15 | # Calculate collapse fraction. 16 | f_col = cp.collapse_fraction(*cp.sig_del(1e4, z, **cosmo)) 17 | 18 | pylab.figure(figsize=(8,6)) 19 | pylab.plot(z, f_col) 20 | pylab.xlabel('z') 21 | pylab.ylabel(r'$f_\mathrm{col}$') 22 | pylab.show() 23 | -------------------------------------------------------------------------------- /www/astropy.html: -------------------------------------------------------------------------------- 1 | CosmoloPy
2 | Description: a cosmology package for Python
3 | Homepage URL: http://roban.github.com/CosmoloPy/
4 | Version: 0.1.001
5 | 6 |

7 | CosmoloPy is a package of cosmology routines for Python, designed for 8 | use with NumPy and SciPy. Reionization is a particular focus. See 9 | below for a longer list of capabilities. 10 | 11 | 12 |

Functions take cosmological parameters (which can be numpy arrays) 13 | as keywords, and ignore any extra keywords. This means you can make a 14 | dictionary of all of your cosmological parameters and pass it to any 15 | function. 16 | 17 |

Example 18 | 19 |

20 | Calculate the comoving distance to redshift 6. 21 | 

22 | >>> import cosmolopy.distance as cd
23 | >>> cosmo = {'omega_M_0':0.3, 'omega_lambda_0':0.7, 'omega_k_0':0.0, 'h':0.72}
24 | >>> d_co, err = cd.comoving_distance(6., **cosmo)
25 | >>> print "Comoving distance to z=6 is %.1f Mpc" % (d_co)
26 | Comoving distance to z=6 is 8017.8 Mpc
27 |
28 | 29 |

30 | Look 31 | in tests/ 32 | and examples/ 33 | for more examples. 34 | 35 |

36 | Capabilities 37 |

See the API 38 | docs for a full listing. 39 |

40 |
cosmolopy.reionization
41 |
Routines related to the reionization of the IGM.
42 |
cosmolopy.distance
43 |
Calculate various cosmological distance measures.
44 |
cosmolopy.luminosityfunction
45 |
Routines related to galaxy luminosity functions (Schechter 46 | functions).
47 |
cosmolopy.perturbation
48 |
Routines related to perturbation theory and the power 49 | spectrum.
50 | 51 |
52 |

53 | 54 | angular diameter distance versus redshift and Omega_M 55 | 56 | propper motion distance vs. redshift and Omega_M 57 | 58 | 59 | 60 | 61 | 62 | 63 | -------------------------------------------------------------------------------- /www/cosmolopy.css: -------------------------------------------------------------------------------- 1 | body { 2 | background-color: #FFFFFF; 3 | font-family: "Veradana,sans-serif"; 4 | color: #000000; 5 | } 6 | h1 { font-size: 1.5em; color: #AA0000; margin-bottom: 0.5em; 7 | font-family: "sans-serif"; } 8 | h2 { font-size: 1.3em; color: #AA0000; 9 | font-family: "sans-serif"; background: #FFE0E0;} 10 | h3 { font-size: 1.0em; color: #AA0000; 11 | font-family: "sans-serif";} 12 | a { color: #3030AA; 13 | text-decoration:none 14 | } 15 | a:hover { text-decoration:underline } 16 | pre { font-size: 1.1em; 17 | background: #D0D0FF; color: #000000; padding: 2ex; width:90ex} 18 | img{border-style: none;} 19 | p{ max-width: 90ex } 20 | ul{ max-width: 90ex } 21 | .container { align: center; 22 | width:90%; 23 | max-width:150ex; 24 | margin: 0 5%; 25 | } 26 | .description { font-size: 1.1em; margin-bottom: 0.5em; margin-top: 0;} 27 | .linkstoc { font-size: 0.9em; margin-bottom: 0; margin-top: 0; 28 | background: #E0E0FF;} 29 | .fig { float: right; margin: 0px; border:1px solid #000000; background: #FFFFFF} 30 | .news { float: right; margin: 0 0px; min-width:244px; 31 | padding: 0; text-align: center; min-height:8em; 32 | background: #FFFFFF; border:1px solid #000000} 33 | .news h2 { margin-bottom: 1ex; margin-top: 0.0ex } 34 | .news ul { 35 | marker-offset: 0px; 36 | list-style-image: none; 37 | list-style-type: none; 38 | padding: 0px; 39 | margin: 0px; 40 | font-size: 80%; 41 | } 42 | .news li { 43 | padding: 0.75ex 0em; 44 | } 45 | .footer { text-align:center; padding-top:1em; } 46 | 47 | .note {font-size: 0.9em; font-style:italic} -------------------------------------------------------------------------------- /www/docAPI/_tf_fit'-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | _tf_fit' 7 | 8 | 9 | 10 | 11 | 13 | 14 | 16 | 17 | 18 | 19 | 21 | 22 | 23 | 25 | 26 | 27 | 29 | 30 | 31 | 32 |
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36 | 37 | Module _tf_fit' 38 | 39 | 41 | 42 | 43 |
44 |
47 | 48 |

Module _tf_fit'

49 | 50 | 51 | 53 | 54 | 56 | 57 | 58 | 72 | 73 | 74 | 88 | 89 | 90 | 104 | 105 |
55 | Functions
59 |   60 | 61 | 62 | 63 | 64 | 68 | 69 |
SWIG_PyInstanceMethod_New(...) 65 | 66 | 67 |
70 | 71 |
75 |   76 | 77 | 78 | 79 | 80 | 84 | 85 |
TFfit_onek(...) 81 | 82 | 83 |
86 | 87 |
91 |   92 | 93 | 94 | 95 | 96 | 100 | 101 |
TFset_parameters(...) 97 | 98 | 99 |
102 | 103 |
106 | 107 | 108 | 110 | 111 | 113 | 114 | 115 | 120 | 121 | 122 | 127 | 128 |
112 | Variables
116 |   117 | 118 | __package__ = None 119 |
123 |   124 | 125 | cvar = <Swig global variables> 126 |
129 | 130 | 132 | 133 | 134 | 135 | 137 | 138 | 139 | 141 | 142 | 143 | 145 | 146 | 147 | 148 |
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152 | Generated by Epydoc 3.0.1 on Tue Mar 27 20:37:58 2012 153 | 155 | http://epydoc.sourceforge.net 157 |
160 | 161 | 170 | 171 | 172 | -------------------------------------------------------------------------------- /www/docAPI/class-tree.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | Class Hierarchy 7 | 8 | 9 | 10 | 11 | 13 | 14 | 16 | 17 | 18 | 20 | 21 | 22 | 24 | 25 | 26 | 28 | 29 | 30 | 32 | 33 | 34 | 35 |
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43 |
46 |
47 | [ Module Hierarchy 48 | | Class Hierarchy ] 49 |

50 |

Class Hierarchy

51 | 85 | 86 | 88 | 89 | 90 | 92 | 93 | 94 | 96 | 97 | 98 | 100 | 101 | 102 | 104 | 105 | 106 | 107 |
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119 | 120 | 129 | 130 | 131 | -------------------------------------------------------------------------------- /www/docAPI/cosmolopy.EH-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | cosmolopy.EH 7 | 8 | 9 | 10 | 11 | 13 | 14 | 16 | 17 | 18 | 20 | 21 | 22 | 24 | 25 | 26 | 28 | 29 | 30 | 32 | 33 | 34 | 35 |
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36 | 37 | 38 | 44 | 49 | 50 |
39 | 40 | Package cosmolopy :: 41 | Package EH 42 | 43 | 45 | 46 | 47 |
48 |
51 | 52 |

Package EH

source code

53 |

See cosmolopy.perturbation.transfer_function_EH

54 |

Eisenstein & Hu power spectrum transfer function used in 55 | cosmolopy.perturbation.transfer_function_EH.

56 |

This package contains two modules:

57 |
    58 |
  1. 59 |
    power (or cosmolopy.EH.power), which is a python wrapper of power.c
    60 |

    from Eisenstein & Hu (1999 ApJ 511 5)

    61 |
    62 |
    63 |
    2. 64 |
  2. 65 |
    tf_fit (or cosmolopy.EH.tf_fit), which is a python wrapper of
    66 |

    tf_fit.c from Eisenstein & Hu (1998 ApJ 496 605)

    67 |
    68 |
    69 |
    3. 70 |
71 |

The first module contains no baryonic features in the transfer function, but 72 | applies to wider range of CDM variants (e.g. including neutrinos). The second 73 | module applies more narrowly but possesses effects including the baryonic 74 | acoustic osciallations.

75 |

See also: http://background.uchicago.edu/~whu/transfer/transferpage.html

76 |

power.c is redistributed under the MIT License with the permission of 77 | Wayne Hu, and is described in Eisenstein, D. J., & Hu, W. "Power 78 | Spectra for Cold Dark Matter and Its Variants," 1999, ApJ, 511, 5 79 | [astro-ph/9710252]. Please cite this paper to acknowledge use of power 80 | spectrum calculations.

81 |

See LISCENSE for additional information.

82 | 83 | 84 | 85 | 87 | 88 | 90 | 91 | 92 | 97 | 98 |
89 | Variables
93 |   94 | 95 | __package__ = None 96 |
99 | 100 | 102 | 103 | 104 | 106 | 107 | 108 | 110 | 111 | 112 | 114 | 115 | 116 | 118 | 119 | 120 | 121 |
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122 | 123 | 124 | 127 | 131 | 132 |
125 | Generated by Epydoc 3.0.1 on Tue Mar 27 20:49:14 2012 126 | 128 | http://epydoc.sourceforge.net 130 |
133 | 134 | 143 | 144 | 145 | -------------------------------------------------------------------------------- /www/docAPI/cosmolopy.EH-pysrc.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | cosmolopy.EH 7 | 8 | 9 | 10 | 11 | 13 | 14 | 16 | 17 | 18 | 20 | 21 | 22 | 24 | 25 | 26 | 28 | 29 | 30 | 32 | 33 | 34 | 35 |
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36 | 37 | 38 | 44 | 49 | 50 |
39 | 40 | Package cosmolopy :: 41 | Package EH 42 | 43 | 45 | 46 | 47 |
48 |
51 |

Source Code for Package cosmolopy.EH

52 | 
 53 |  1  """See `cosmolopy.perturbation.transfer_function_EH` 
 54 |  2   
 55 |  3  Eisenstein & Hu power spectrum transfer function used in 
 56 |  4  `cosmolopy.perturbation.transfer_function_EH`. 
 57 |  5   
 58 |  6  This package contains two modules: 
 59 |  7   
 60 |  8  i. `power` (or `cosmolopy.EH.power`), which is a python wrapper of power.c  
 61 |  9      from Eisenstein & Hu (1999 ApJ 511 5) 
 62 | 10   
 63 | 11  ii. `tf_fit` (or `cosmolopy.EH.tf_fit`), which is a python wrapper of 
 64 | 12       tf_fit.c from Eisenstein & Hu (1998 ApJ 496 605) 
 65 | 13   
 66 | 14  The first module contains no baryonic features in the transfer function, but  
 67 | 15  applies to wider range of CDM variants (e.g. including neutrinos). The second 
 68 | 16  module applies more narrowly but possesses effects including the baryonic 
 69 | 17  acoustic osciallations. 
 70 | 18   
 71 | 19  See also: http://background.uchicago.edu/~whu/transfer/transferpage.html 
 72 | 20   
 73 | 21  power.c is redistributed under the MIT License with the permission of 
 74 | 22  Wayne Hu, and is described in Eisenstein, D. J., & Hu, W. "Power 
 75 | 23  Spectra for Cold Dark Matter and Its Variants," 1999, ApJ, 511, 5 
 76 | 24  [astro-ph/9710252]. Please cite this paper to acknowledge use of power 
 77 | 25  spectrum calculations. 
 78 | 26   
 79 | 27  See LISCENSE for additional information. 
 80 | 28   
 81 | 29  """ 
 82 | 30   
 87 |
88 |
89 | 90 | 92 | 93 | 94 | 96 | 97 | 98 | 100 | 101 | 102 | 104 | 105 | 106 | 108 | 109 | 110 | 111 |
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123 | 124 | 133 | 134 | 135 | -------------------------------------------------------------------------------- /www/docAPI/cosmolopy.EH._power-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | cosmolopy.EH._power 7 | 8 | 9 | 10 | 11 | 13 | 14 | 16 | 17 | 18 | 20 | 21 | 22 | 24 | 25 | 26 | 28 | 29 | 30 | 32 | 33 | 34 | 35 |
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36 | 37 | 38 | 45 | 50 | 51 |
39 | 40 | Package cosmolopy :: 41 | Package EH :: 42 | Module _power 43 | 44 | 46 | 47 | 48 |
49 |
52 | 53 |

Module _power

54 | 55 | 56 | 58 | 59 | 61 | 62 | 63 | 77 | 78 | 79 | 93 | 94 | 95 | 109 | 110 |
60 | Functions
64 |   65 | 66 | 67 | 68 | 69 | 73 | 74 |
TFmdm_onek_hmpc(...) 70 | 71 | 72 |
75 | 76 |
80 |   81 | 82 | 83 | 84 | 85 | 89 | 90 |
TFmdm_onek_mpc(...) 86 | 87 | 88 |
91 | 92 |
96 |   97 | 98 | 99 | 100 | 101 | 105 | 106 |
TFmdm_set_cosm(...) 102 | 103 | 104 |
107 | 108 |
111 | 112 | 113 | 115 | 116 | 118 | 119 | 120 | 125 | 126 | 127 | 132 | 133 |
117 | Variables
121 |   122 | 123 | __package__ = None 124 |
128 |   129 | 130 | cvar = <Swig global variables> 131 |
134 | 135 | 137 | 138 | 139 | 141 | 142 | 143 | 145 | 146 | 147 | 149 | 150 | 151 | 153 | 154 | 155 | 156 |
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168 | 169 | 178 | 179 | 180 | -------------------------------------------------------------------------------- /www/docAPI/cosmolopy.EH.download_EH_power-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | cosmolopy.EH.download_EH_power 7 | 8 | 9 | 10 | 11 | 13 | 14 | 16 | 17 | 18 | 20 | 21 | 22 | 24 | 25 | 26 | 28 | 29 | 30 | 32 | 33 | 34 | 35 |
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36 | 37 | 38 | 45 | 52 | 53 |
39 | 40 | Package cosmolopy :: 41 | Package EH :: 42 | Module download_EH_power 43 | 44 | 46 | 47 | 48 | 50 |
[hide private]
51 |
54 | 55 |

Module download_EH_power

source code

56 |

Download the power.c power spectrum code from Wayne Hu's website.

57 |

For more information see:

58 |
59 |

http://background.uchicago.edu/~whu/transfer/transferpage.html

60 |

Eisenstein & Hu (1999ApJ...511....5E, or astro-ph/9710252)

61 |
62 |

The url for the code is:

63 |
64 | http://background.uchicago.edu/~whu/transfer/power.c
65 | 66 | 67 | 68 | 70 | 71 | 82 | 83 | 84 | 98 | 99 |
72 | 73 | 74 | 75 | 79 | 80 |
Functions[hide private]
81 |
85 |   86 | 87 | 88 | 89 | 90 | 94 | 95 |
download_power() 91 | source code 92 | 93 |
96 | 97 |
100 | 101 | 102 | 104 | 105 | 116 | 117 | 118 | 123 | 124 |
106 | 107 | 108 | 109 | 113 | 114 |
Variables[hide private]
115 |
119 |   120 | 121 | __package__ = 'cosmolopy.EH' 122 |
125 | 126 | 128 | 129 | 130 | 132 | 133 | 134 | 136 | 137 | 138 | 140 | 141 | 142 | 144 | 145 | 146 | 147 |
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159 | 160 | 169 | 170 | 171 | -------------------------------------------------------------------------------- /www/docAPI/cosmolopy.EH.power-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | cosmolopy.EH.power 7 | 8 | 9 | 10 | 11 | 13 | 14 | 16 | 17 | 18 | 20 | 21 | 22 | 24 | 25 | 26 | 28 | 29 | 30 | 32 | 33 | 34 | 35 |
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36 | 37 | 38 | 45 | 50 | 51 |
39 | 40 | Package cosmolopy :: 41 | Package EH :: 42 | Module power 43 | 44 | 46 | 47 | 48 |
49 |
52 | 53 |

Module power

source code

54 | 55 | 56 | 58 | 59 | 61 | 62 | 63 | 68 | 69 | 70 | 75 | 76 |
60 | Variables
64 |   65 | 66 | cvar = <Swig global variables> 67 |
71 |   72 | 73 | __package__ = 'cosmolopy.EH' 74 |
77 | 78 | 80 | 81 | 82 | 84 | 85 | 86 | 88 | 89 | 90 | 92 | 93 | 94 | 96 | 97 | 98 | 99 |
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103 | Generated by Epydoc 3.0.1 on Fri Jul 23 14:13:52 2010 104 | 106 | http://epydoc.sourceforge.net 108 |
111 | 112 | 121 | 122 | 123 | -------------------------------------------------------------------------------- /www/docAPI/cosmolopy.EH.tf_fit-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | cosmolopy.EH.tf_fit 7 | 8 | 9 | 10 | 11 | 13 | 14 | 16 | 17 | 18 | 19 | 21 | 22 | 23 | 25 | 26 | 27 | 29 | 30 | 31 | 32 |
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33 | 34 | 35 | 42 | 47 | 48 |
36 | 37 | Package cosmolopy :: 38 | Package EH :: 39 | Module tf_fit 40 | 41 | 43 | 44 | 45 |
46 |
49 | 50 |

Module tf_fit

source code

51 | 52 | 53 | 55 | 56 | 58 | 59 | 60 | 65 | 66 | 67 | 72 | 73 |
57 | Variables
61 |   62 | 63 | cvar = <Swig global variables> 64 |
68 |   69 | 70 | __package__ = 'cosmolopy.EH' 71 |
74 | 75 | 77 | 78 | 79 | 80 | 82 | 83 | 84 | 86 | 87 | 88 | 90 | 91 | 92 | 93 |
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105 | 106 | 115 | 116 | 117 | -------------------------------------------------------------------------------- /www/docAPI/cosmolopy.saveable-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | cosmolopy.saveable 7 | 8 | 9 | 10 | 11 | 13 | 14 | 16 | 17 | 18 | 20 | 21 | 22 | 24 | 25 | 26 | 28 | 29 | 30 | 32 | 33 | 34 | 35 |
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36 | 37 | 38 | 44 | 49 | 50 |
39 | 40 | Package cosmolopy :: 41 | Module saveable 42 | 43 | 45 | 46 | 47 |
48 |
51 | 52 |

Module saveable

source code

53 |

A Saveable class with methods to save and restore.

54 |

Saveable is designed to be subclassed to create new types of objects 55 | that can easily be pickled and reloaded.

56 | 57 | 58 | 59 | 61 | 62 | 64 | 65 | 66 | 72 | 73 | 74 | 80 | 81 |
63 | Classes
67 |   68 | 69 | NullWriter
70 | Dummy file-like object that does nothing. 71 |
75 |   76 | 77 | Saveable
78 | An object with methods to save and restore. 79 |
82 | 83 | 84 | 86 | 87 | 89 | 90 | 91 | 106 | 107 |
88 | Functions
92 |   93 | 94 | 95 | 96 | 98 | 102 | 103 |
loadSaveable(filename)
97 | Return an instance of an object unpickled from a file.		 99 | source code 100 | 101 |
104 | 105 |
108 | 109 | 110 | 112 | 113 | 115 | 116 | 117 | 122 | 123 |
114 | Variables
118 |   119 | 120 | __package__ = 'cosmolopy' 121 |
124 | 125 | 127 | 128 | 129 | 131 | 132 | 133 | 135 | 136 | 137 | 139 | 140 | 141 | 143 | 144 | 145 | 146 |
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150 | Generated by Epydoc 3.0.1 on Tue Mar 27 20:49:15 2012 151 | 153 | http://epydoc.sourceforge.net 155 |
158 | 159 | 168 | 169 | 170 | -------------------------------------------------------------------------------- /www/docAPI/cosmolopy.saveable.NullWriter-class.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | cosmolopy.saveable.NullWriter 7 | 8 | 9 | 10 | 11 | 13 | 14 | 16 | 17 | 18 | 20 | 21 | 22 | 24 | 25 | 26 | 28 | 29 | 30 | 32 | 33 | 34 | 35 |
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36 | 37 | 38 | 45 | 50 | 51 |
39 | 40 | Package cosmolopy :: 41 | Module saveable :: 42 | Class NullWriter 43 | 44 | 46 | 47 | 48 |
49 |
52 | 53 |

Class NullWriter

source code

54 |

Dummy file-like object that does nothing.

55 |

From 56 | http://stackoverflow.com/questions/1809958/hide-stderr-output-in-unit-tests

57 |

Used in Saveable.

58 | 59 | 60 | 61 | 63 | 64 | 66 | 67 | 68 | 83 | 84 |
65 | Instance Methods
69 |   70 | 71 | 72 | 73 | 75 | 79 | 80 |
write(self, 74 | s) 76 | source code 77 | 78 |
81 | 82 |
85 | 86 | 88 | 89 | 90 | 92 | 93 | 94 | 96 | 97 | 98 | 100 | 101 | 102 | 104 | 105 | 106 | 107 |
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119 | 120 | 129 | 130 | 131 | -------------------------------------------------------------------------------- /www/docAPI/cosmolopy.utils.Normalize-class.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | cosmolopy.utils.Normalize 7 | 8 | 9 | 10 | 11 | 13 | 14 | 16 | 17 | 18 | 20 | 21 | 22 | 24 | 25 | 26 | 28 | 29 | 30 | 32 | 33 | 34 | 35 |
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36 | 37 | 38 | 45 | 50 | 51 |
39 | 40 | Package cosmolopy :: 41 | Module utils :: 42 | Class Normalize 43 | 44 | 46 | 47 | 48 |
49 |
52 | 53 |

Class Normalize

source code

54 |

A decorator that normalizes a function.

55 |

Only works for functions of a single variable.

56 |

The new function is normalized over the interval from min to max, 57 | i.e. the integral of the new function from low to high is one.

58 | 59 | 60 | 61 | 63 | 64 | 66 | 67 | 68 | 86 | 87 | 88 | 103 | 104 |
65 | Instance Methods
69 |   70 | 71 | 72 | 73 | 78 | 82 | 83 |
__init__(self, 74 | min, 75 | max, 76 | quiet=False, 77 | **kwargs) 79 | source code 80 | 81 |
84 | 85 |
89 |   90 | 91 | 92 | 93 | 95 | 99 | 100 |
__call__(self, 94 | function) 96 | source code 97 | 98 |
101 | 102 |
105 | 106 | 108 | 109 | 110 | 112 | 113 | 114 | 116 | 117 | 118 | 120 | 121 | 122 | 124 | 125 | 126 | 127 |
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131 | Generated by Epydoc 3.0.1 on Tue Mar 27 20:49:15 2012 132 | 134 | http://epydoc.sourceforge.net 136 |
139 | 140 | 149 | 150 | 151 | -------------------------------------------------------------------------------- /www/docAPI/crarr.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roban/CosmoloPy/fca8bcd244a9e689e19a1337a90d0f594048d17e/www/docAPI/crarr.png -------------------------------------------------------------------------------- /www/docAPI/frames.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | API Documentation 7 | 8 | 9 | 10 | 12 | 14 | 15 | 16 | 17 | 18 | -------------------------------------------------------------------------------- /www/docAPI/module-tree.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | Module Hierarchy 7 | 8 | 9 | 10 | 11 | 13 | 14 | 16 | 17 | 18 | 20 | 21 | 22 | 24 | 25 | 26 | 28 | 29 | 30 | 32 | 33 | 34 | 35 |
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36 | 37 | 38 | 39 | 44 | 45 |
  40 | 41 | 42 |
43 |
46 |
47 | [ Module Hierarchy 48 | | Class Hierarchy ] 49 |

50 |

Module Hierarchy

51 | 68 | 69 | 71 | 72 | 73 | 75 | 76 | 77 | 79 | 80 | 81 | 83 | 84 | 85 | 87 | 88 | 89 | 90 |
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91 | 92 | 93 | 96 | 100 | 101 |
94 | Generated by Epydoc 3.0.1 on Tue Mar 27 20:49:14 2012 95 | 97 | http://epydoc.sourceforge.net 99 |
102 | 103 | 112 | 113 | 114 | -------------------------------------------------------------------------------- /www/docAPI/redirect.html: -------------------------------------------------------------------------------- 1 | Epydoc Redirect Page 2 | 3 | 4 | 5 | 6 | 7 | 8 | 18 | 19 |

Epydoc Auto-redirect page

20 | 21 |

When javascript is enabled, this page will redirect URLs of 22 | the form redirect.html#dotted.name to the 23 | documentation for the object with the given fully-qualified 24 | dotted name.

25 |

 

26 | 27 | 36 | 37 | 38 | 39 | -------------------------------------------------------------------------------- /www/docAPI/toc-cosmolopy-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | cosmolopy 7 | 8 | 9 | 10 | 11 | 13 |

Module cosmolopy

14 |
15 |

Variables

16 | __package__
fidcosmo
19 | [hide private] 21 | 22 | 31 | 32 | 33 | -------------------------------------------------------------------------------- /www/docAPI/toc-cosmolopy.EH-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | EH 7 | 8 | 9 | 10 | 11 | 13 |

Module EH

14 |
15 |

Variables

16 | __package__
18 | [hide private] 20 | 21 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /www/docAPI/toc-cosmolopy.EH._power-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | _power 7 | 8 | 9 | 10 | 11 | 13 |

Module _power

14 |
15 |

Functions

16 |
17 | TFmdm_onek_hmpc
19 |
20 | TFmdm_onek_mpc
22 |
23 | TFmdm_set_cosm
25 |

Variables

26 |
27 | __package__
29 |
30 | cvar
32 |
33 | [hide private] 35 | 36 | 45 | 46 | 47 | -------------------------------------------------------------------------------- /www/docAPI/toc-cosmolopy.EH.download_EH_power-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | download_EH_power 7 | 8 | 9 | 10 | 11 | 13 |

Module download_EH_power

14 |
15 |

Functions

16 | download_power

Variables

18 | __package__
20 | [hide private] 22 | 23 | 32 | 33 | 34 | -------------------------------------------------------------------------------- /www/docAPI/toc-cosmolopy.EH.power-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | power 7 | 8 | 9 | 10 | 11 | 13 |

Module power

14 |
15 |

Functions

16 |
17 | _swig_getattr
19 |
20 | _swig_repr
22 |
23 | _swig_setattr
25 |
26 | _swig_setattr_nondynamic
28 |

Variables

29 | __package__
31 | _newclass
33 | cvar
35 | [hide private] 37 | 38 | 47 | 48 | 49 | -------------------------------------------------------------------------------- /www/docAPI/toc-cosmolopy.constants-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | constants 7 | 8 | 9 | 10 | 11 | 13 |

Module constants

14 |
15 |

Variables

16 | G_const_Mpc_Msun_s
Gyr_s
H100_s
M_sun_g
Mpc_cm
Mpc_km
Myr_s
__package__
alpha_B_cm_s_1e4
amu_g
angstrom_cm
c_light_Mpc_s
c_light_cm_s
doc
lambda_Lya_0
lambda_NV_0
m_H_g
m_He_g
m_p_g
pc_cm
sigma_T_Mpc
sigma_T_cm
yr_s
40 | [hide private] 42 | 43 | 52 | 53 | 54 | -------------------------------------------------------------------------------- /www/docAPI/toc-cosmolopy.density-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | density 7 | 8 | 9 | 10 | 11 | 13 |

Module density

14 |
15 |

Functions

16 | baryon_densities
cosmo_densities
get_X_Y
omega_M_z

Variables

21 | __package__
23 | [hide private] 25 | 26 | 35 | 36 | 37 | -------------------------------------------------------------------------------- /www/docAPI/toc-cosmolopy.distance-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | distance 7 | 8 | 9 | 10 | 11 | 13 |

Module distance

14 |
15 |

Functions

16 |
17 | _comoving_integral
19 |
20 | _lookback_integral
22 | age
age_flat
angular_diameter_distance
comoving_distance
comoving_distance_transverse
e_z
get_omega_k_0
hubble_distance_z
hubble_z
light_travel_distance
lookback_time
luminosity_distance
propper_motion_distance
quick_age_function
quick_redshift_age_function
redshift_d_light
set_omega_k_0

Variables

40 | __package__
42 | [hide private] 44 | 45 | 54 | 55 | 56 | -------------------------------------------------------------------------------- /www/docAPI/toc-cosmolopy.luminosityfunction-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | luminosityfunction 7 | 8 | 9 | 10 | 11 | 13 |

Module luminosityfunction

14 |
15 |

Classes

16 | BrokenPowerlawSED
LFHistory

Functions

19 | L_nu_from_sfr
iPhotonRateDensity
magnitudeAB_from_sfr
mass_from_sfr
plotLFevo
schechterCumuLL
schechterCumuLM
schechterL
schechterM
schechterTotLL
schechterTotLM
sfr_from_L_nu
sfr_from_mass
test_plot_schechter

Variables

34 | B2007_z4
B2007_z5
B2007_z6
B2007_z7
B2008
B2008_fixed
B2008_linear_z5
O2010_z7
T2010ICLF
__package__
zlinear
46 | [hide private] 48 | 49 | 58 | 59 | 60 | -------------------------------------------------------------------------------- /www/docAPI/toc-cosmolopy.magnitudes-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | magnitudes 7 | 8 | 9 | 10 | 11 | 13 |

Module magnitudes

14 |
15 |

Functions

16 | L_nu_from_magAB
f_nu_from_magAB
magnitude_AB
magnitude_AB1450
magnitude_AB_from_L_nu

Variables

22 | __package__
24 | [hide private] 26 | 27 | 36 | 37 | 38 | -------------------------------------------------------------------------------- /www/docAPI/toc-cosmolopy.parameters-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | parameters 7 | 8 | 9 | 10 | 11 | 13 |

Module parameters

14 |
15 |

Functions

16 | WMAP5_BAO_SN_mean
WMAP5_ML
WMAP5_mean
WMAP7_BAO_H0_mean
WMAP7_ML
add_extras

Variables

23 | __package__
25 | [hide private] 27 | 28 | 37 | 38 | 39 | -------------------------------------------------------------------------------- /www/docAPI/toc-cosmolopy.perturbation-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | perturbation 7 | 8 | 9 | 10 | 11 | 13 |

Module perturbation

14 |
15 |

Functions

16 |
17 | _klims
19 |
20 | _sigmasq_integrand_log
22 |
23 | _sigmasq_r_scalar
25 | collapse_fraction
fgrowth
mass_to_radius
norm_power
power_spectrum
radius_to_mass
sig_del
sigma_r
transfer_function_EH
virial_mass
virial_mass_HB
virial_temp
virial_temp_HB
volume_radius_dmdr
w_tophat

Variables

41 | __package__
43 | _sigmasq_r_vec
45 |
46 | _vec_transfer_func
48 |
49 | [hide private] 51 | 52 | 61 | 62 | 63 | -------------------------------------------------------------------------------- /www/docAPI/toc-cosmolopy.reionization-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | reionization 7 | 8 | 9 | 10 | 11 | 13 |

Module reionization

14 |
15 |

Functions

16 |
17 | _udot
19 | clumping_factor_BKP
clumping_factor_Chary
clumping_factor_HB
delta_lambda_delta_dl
integrate_ion_recomb
integrate_ion_recomb_collapse
integrate_optical_depth
ionization_from_collapse
ionization_from_luminosity
nDotRecMHR
optical_depth_instant
quick_ion_col_function
recomb_rate_coeff_HG

Variables

33 | __package__
35 | [hide private] 37 | 38 | 47 | 48 | 49 | -------------------------------------------------------------------------------- /www/docAPI/toc-cosmolopy.saveable-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | saveable 7 | 8 | 9 | 10 | 11 | 13 |

Module saveable

14 |
15 |

Classes

16 | Saveable

Functions

18 | loadSaveable

Variables

20 | __package__
22 | [hide private] 24 | 25 | 34 | 35 | 36 | -------------------------------------------------------------------------------- /www/docAPI/toc-cosmolopy.utils-module.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | utils 7 | 8 | 9 | 10 | 11 | 13 |

Module utils

14 |
15 |

Classes

16 | AgeSpacedRedshift
Extrapolate1d
Normalize
PiecewisePowerlaw

Functions

21 | ccumulate
integrate_piecewise

Variables

24 | __package__
logquad
vecquad
28 | [hide private] 30 | 31 | 40 | 41 | 42 | -------------------------------------------------------------------------------- /www/docAPI/toc.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | Table of Contents 7 | 8 | 9 | 10 | 11 | 13 |

Table of Contents

14 |
15 | Everything 16 |
17 |

Modules

18 | cosmolopy
cosmolopy.EH
21 | cosmolopy.EH._power
23 | cosmolopy.EH.download_EH_power
cosmolopy.EH.power
cosmolopy.constants
cosmolopy.density
cosmolopy.distance
cosmolopy.luminosityfunction
cosmolopy.magnitudes
cosmolopy.parameters
cosmolopy.perturbation
cosmolopy.reionization
cosmolopy.saveable
cosmolopy.utils
36 | [hide private] 38 | 39 | 48 | 49 | 50 | -------------------------------------------------------------------------------- /www/docAPI/uml_class_diagram_for_cosmolop.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roban/CosmoloPy/fca8bcd244a9e689e19a1337a90d0f594048d17e/www/docAPI/uml_class_diagram_for_cosmolop.gif -------------------------------------------------------------------------------- /www/docAPI/uml_class_diagram_for_cosmolop_2.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roban/CosmoloPy/fca8bcd244a9e689e19a1337a90d0f594048d17e/www/docAPI/uml_class_diagram_for_cosmolop_2.gif -------------------------------------------------------------------------------- /www/docAPI/uml_class_diagram_for_cosmolop_3.gif: -------------------------------------------------------------------------------- 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-scale 244 dist2d_D_M.png dist2d_D_M_small.png 9 | 10 | -------------------------------------------------------------------------------- /www/others.txt: -------------------------------------------------------------------------------- 1 | Python astronomy resources 2 | --------------------------- 3 | 4 | See http://www.astropython.org/resources for a nice up-to-date list of 5 | python astronomy resources. 6 | 7 | Other python cosmology resources 8 | -------------------------------- 9 | 10 | Below is a (no-doubt incomplete) list of cosmology-specific resources 11 | I've come across. 12 | 13 | CosmoFisher by David Ventimiglia 14 | 15 | http://dventimi.github.com/CosmoFisher/ 16 | 17 | "Python code 'to help create, manipulate, visualize, and gain value 18 | from Fisher information matrices' 19 | 20 | cosmology module in esutil 21 | 22 | http://code.google.com/p/esutil/ 23 | 24 | Mostly distance measures. 25 | 26 | James Schombert's version of Ned Wright's Cosmology Calculator 27 | 28 | http://www.astro.ucla.edu/~wright/CC.python 29 | 30 | cosmocalc by Tom Aldcroft 31 | 32 | http://cxc.harvard.edu/contrib/cosmocalc 33 | 34 | Improved version of CC.py with programmatic interface. Not designed 35 | for use with numpy. 36 | 37 | CosmoPy 38 | 39 | http://www.ifa.hawaii.edu/cosmopy/ 40 | 41 | Interface to the powerful CAMB software for CMB anisotropy 42 | calculations. 43 | 44 | PyCos 45 | 46 | http://www.astro.princeton.edu/~msshin/science/code/index.html 47 | 48 | Source not posted. 49 | 50 | Andrew Becker's cosmology-1.1.py 51 | 52 | http://www.astro.washington.edu/users/becker/python_software.html 53 | 54 | OO interface to distance measure calculations. 55 | 56 | Taro Sato's Python version of kcorrect by Michael Blanton 57 | 58 | http://nomo17k.wordpress.com/2009/08/02/kcorrect-kcorrect-python-port-project/ 59 | 60 | k correction and photometric redshifts. 61 | 62 | Miscellaneous non-python projects 63 | --------------------------------- 64 | 65 | Ned Wright's Cosmology Calculator 66 | 67 | http://www.astro.ucla.edu/~wright/CosmoCalc.html 68 | 69 | CAMB: Code for Anisotropies in the Microwave Background 70 | 71 | http://camb.info/ 72 | 73 | INITIATIVE FOR COSMOLOGY 74 | 75 | http://icosmo.org/cgi-bin/Interactive_Step1.cgi 76 | 77 | Online and IDL calculator 78 | --------------------------------------------------------------------------------