ehtim (eht-imaging)
===================
.. image:: https://zenodo.org/badge/42943499.svg
:target: https://zenodo.org/badge/latestdoi/42943499
Python modules for simulating and manipulating VLBI data and producing images with regularized maximum likelihood methods. This version is an early release so please raise an issue, submit a pull request, or email achael@princeton.edu if you have trouble or need help for your application.
The package contains several primary classes for loading, simulating, and manipulating VLBI data. The main classes are the ``Image``, ``Movie``, ``Array``, ``Obsdata``, ``Imager``, and ``Caltable`` classes, which provide tools for loading images and data, producing simulated data from realistic u-v tracks, calibrating, inspecting, and plotting data, and producing images from data sets in various polarizations using various data terms and regularizing functions.
Installation
------------
The latest stable version (`1.2.8 <https://github.com/achael/eht-imaging/releases/tag/v1.2.7>`_) is available on `PyPi <https://pypi.org/project/ehtim/>`_. Simply install pip and run
.. code-block:: bash
pip install ehtim
Incremental updates are developed on the `dev branch <https://github.com/achael/eht-imaging/tree/dev>`_. To use the very latest (unstable) code, checkout the dev branch, change to the main eht-imaging directory, and run:
.. code-block:: bash
pip install .
Installing with pip will update most of the required libraries automatically (`numpy <http://www.numpy.org/>`_, `scipy <http://www.scipy.org/>`_, `matplotlib <http://www.matplotlib.org/>`_, `astropy <http://www.astropy.org/>`_, `ephem <http://pypi.python.org/pypi/pyephem/>`_, `future <http://pypi.python.org/pypi/future>`_, `h5py <http://www.h5py.org/>`_, and `pandas <http://www.pandas.pydata.org/>`_).
**If you want to use fast fourier transforms, you will also need to separately install** `NFFT <https://github.com/NFFT/nfft>`_ **and its** `pynfft wrapper <https://github.com/ghisvail/pyNFFT/>`__. The simplest way is to use `conda <https://anaconda.org/conda-forge/pynfft/>`__ to install both:
.. code-block:: bash
conda install -c conda-forge pynfft
Alternatively, first install NFFT manually following the instructions on the `readme <https://github.com/NFFT/nfft>`__, making sure to use the ``--enable-openmp`` flag in compilation. Then install `pynfft <https://github.com/ghisvail/pyNFFT/>`__, with pip, following the readme instructions to link the installation to where you installed NFFT. Finally, reinstall ehtim.
**For M1 Macs (OS >= v12.0)**, install the M1 Mac version of `pynfft <https://github.com/rohandahale/pyNFFT.git>`__ and follow the instructions on the `readme <https://github.com/rohandahale/pyNFFT.git>`__. It has the instructions to install `fftw <http://www.fftw.org>`_, `nfft <https://github.com/NFFT/nfft>`__ and then `pynfft <https://github.com/rohandahale/pyNFFT.git>`__.
**Certain eht-imaging functions require other external packages that are not automatically installed.** In addition to pynfft, these include `networkx <https://networkx.github.io/>`_ (for image comparison functions), `requests <http://docs.python-requests.org/en/master/>`_ (for dynamical imaging), and `scikit-image <https://scikit-image.org/>`_ (for a few image analysis functions). However, the vast majority of the code will work without these dependencies.
Documentation and Tutorials
---------------------------
Documentation is `here <https://achael.github.io/eht-imaging>`_.
A intro to imaging tutorial jupyter notebook can be found in the repo at `tutorials/ehtim_tutorial.ipynb <https://github.com/achael/eht-imaging/blob/main/tutorials/ehtim_tutorial.ipynb>`__
`Slides <https://docs.google.com/presentation/d/1A0y9omYI2ueSUa6_t5reylBhw6eiLwjqDzw-HUOk8Ac/edit?usp=sharing>`__ for the included tutorial walk through the basic steps of reconstructing EHT images with the code
Here are some other ways to learn to use the code:
- Start with the script examples/example.py, which contains a series of sample commands to load an image and array, generate data, and produce an image with various imaging algorithms.
- Older `Slides <https://www.dropbox.com/s/7533ucj8bt54yh7/Bouman_Chael.pdf?dl=0>`__ from the EHT2016 data generation and imaging workshop contain a tutorial on generating data with the VLBI imaging `website <http://vlbiimaging.csail.mit.edu>`_, loading into the library, and producing an image.
Citation
--------------------------------
If you use ehtim in your publication, please cite `Chael+ 2018 <http://adsabs.harvard.edu/abs/2018ApJ...857...23C>`_.
The latest version is also available as a static doi on `Zenodo <https://zenodo.org/badge/latestdoi/42943499>`_.
Selected publications that use ehtim
------------------------------------
Let us know if you use ehtim in your publication and we'll list it here!
- High-Resolution Linear Polarimetric Imaging for the Event Horizon Telescope, `Chael et al. 2016 <https://arxiv.org/abs/1605.06156>`_
- Computational Imaging for VLBI Image Reconstruction, `Bouman et al. 2016 <http://www.cv-foundation.org/openaccess/content_cvpr_2016/html/Bouman_Computational_Imaging_for_CVPR_2016_paper.html>`_
- Stochastic Optics: A Scattering Mitigation Framework for Radio Interferometric Imaging, `Johnson 2016 <https://arxiv.org/abs/1610.05326>`_
- Reconstructing Video from Interferometric Measurements of Time-Varying Sources, `Bouman et al. 2017 <https://arxiv.org/abs/1711.01357>`_
- Dynamical Imaging with Interferometry, `Johnson et al. 2017 <https://arxiv.org/abs/1711.01286>`_
- Interferometric Imaging Directly with Closure Phases and Closure Amplitudes, `Chael et al. 2018 <https://arxiv.org/abs/1803.07088>`_
- A Model for Anisotropic Interstellar Scattering and its Application to Sgr A*, `Psaltis et al. 2018 <https://arxiv.org/abs/1805.01242>`_
- The Currrent Ability to Test Theories of Gravity with Black Hole Shadows, `Mizuno et al. 2018 <https://arxiv.org/abs/1804.05812>`_
- The Scattering and Intrinsic Structure of Sagittarius A* at Radio Wavelengths, `Johnson et al. 2018 <https://arxiv.org/abs/18008.08966>`_
- Testing GR with the Black Hole Shadow Size and Asymmetry of Sagittarius A*: Limitations from Interstellar Scattering, `Zhu et al. 2018 <https://arxiv.org/abs/1811.02079>`_
- The Size, Shape, and Scattering of Sagittarius A* at 86 GHz: First VLBI with ALMA, `Issaoun et al. 2019a <https://arxiv.org/abs/1901.06226>`_
- First M87 Event Horizon Telescope Results IV: Imaging the Central Supermassive Black Hole, `EHTC et al. 2019 <https://arxiv.org/abs/1906.11241>`_
- EHT-HOPS Pipeline for Millimeter VLBI Data Reduction, `Blackburn et al. 2019 <https://arxiv.org/pdf/1903.08832>`_
- Discriminating Accretion States via Rotational Symmetry in Simulated Polarimetric Images of M87, `Palumbo et al. 2020 <https://arxiv.org/pdf/2004.01751.pdf>`_
- SYMBA: An end-to-end VLBI synthetic data generation pipeline, `Roelofs et al. 2020 <https://arxiv.org/pdf/2004.01161.pdf>`_
- Monitoring the Morphology of M87* in 2009-2017 with the Event Horizon Telescope, `Wielgus et al. 2020 <https://arxiv.org/pdf/2009.11842>`_
- EHT imaging of the archetypal blazar 3C 279 at extreme 20 microarcsecond resolution, `Kim et al. 2020 <https://www.aanda.org/articles/aa/pdf/2020/08/aa37493-20.pdf>`_
- Verification of Radiative Transfer Schemes for the EHT, `Gold et al. 2020 <https://iopscience.iop.org/article/10.3847/1538-4357/ab96c6/pdf>`_
- Closure Traces: Novel Calibration-insensitive Quantities for Radio Astronomy, `Broderick and Pesce. 2020 <https://iopscience.iop.org/article/10.3847/1538-4357/abbd9d/pdf>`_
- Evaluation of New Submillimeter VLBI Sites for the Event Horizon Telescope, `Raymond et al. 2021 <https://iopscience.iop.org/article/10.3847/1538-3881/abc3c3/pdf>`_
- Imaging VGOS Observations and Investigating Source Structure Effects, `Xu et al. 2021 <https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2020JB021238>`_
- A D-term Modeling Code (DMC) for Simultaneous Calibration and Full-Stokes Imaging of VLBI Data, `Pesce et al. 2021 <https://iopscience.iop.org/article/10.3847/1538-3881/abe3f8/pdf>`_
- Using space-VLBI to probe gravity around Sgr A*, `Fromm et al. 2021 <https://www.aanda.org/articles/aa/pdf/2021/05/aa37335-19.pdf>`_
- Persistent Non-Gaussian Structure in the Image of Sagittarius A* at 86 GHz, `Issaoun et al. 2021 <https://iopscience.iop.org/article/10.3847/1538-4357/ac00b0/pdf>`_
- First M87 Event Horizon Telescope Results. VII. Polarization of the Ring, `EHTC et al. 2021 <https://iopscience.iop.org/article/10.3847/2041-8213/abe71d/pdf>`_
- Event Horizon Telescope observations of the jet launching and collimation in Centaurus A, `Janssen et al. 2021 <https://www.nature.com/articles/s41550-021-01417-w.pdf>`_
- RadioAstron discovers a mini-cocoon around the restarted parsec-scale jet in 3C 84 `Savolainen et al. 2021 <https://arxiv.org/pdf/2111.04481.pdf>`_
- Unravelling the Innermost Jet Structure of OJ 287 with the First GMVA+ALMA Observations, `Zhao et al. 2022 <https://arxiv.org/pdf/2205.00554.pdf>`_
- First Sagittarius A* Event Horizon Telescope Results. III: Imaging of the Galactic Center Supermassive Black Hole, `EHTC et al. 2022 <https://arxiv.org/pdf/2311.09479.pdf>`_
- Resolving the Inner Parsec of the Blazar J1924-2914 with the Event Horizon Telescope, `Issaoun et al. 2022 <https://arxiv.org/pdf/2208.01662.pdf>`_
- The Event Horizon Telescope Image of the Quasar NRAO 530, `Jorstad et al. 2023 <https://arxiv.org/pdf/2302.04622.pdf>`_
- First M87 Event Horizon Telescope Results. IX. Detection of Near-horizon Circular Polarization, `EHTC et al. 2023 <https://arxiv.org/pdf/2311.10976.pdf>`_
- Filamentary structures as the origin of blazar jet radio variability, `Fuentes et al. 2023 <https://arxiv.org/pdf/2311.01861.pdf>`_
- The persistent shadow of the supermassive black hole of M 87. I. Observations, calibration, imaging, and analysis, `EHTC 2023 <https://www.aanda.org/articles/aa/pdf/2024/01/aa47932-23.pdf>`_
- Parsec-scale evolution of the gigahertz-peaked spectrum quasar PKS 0858-279, `Kosogorov et al. 2024 <https://arxiv.org/pdf/2401.03603.pdf>`_
oifits Documentation
--------------------
The oifits_new.py file used for reading/writing .oifits files is a slightly modified version of Paul Boley's package `oifits <http://astro.ins.urfu.ru/pages/~pboley/oifits/>`_.
The oifits read/write functionality in ehtim is still being developed and may not work with all versions of python or astropy.
The documentation is styled after `dfm's projects <https://github.com/dfm>`_
License
-------
ehtim is licensed under GPLv3. See LICENSE.txt for more details.
Raw data
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"description": "ehtim (eht-imaging)\n===================\n.. image:: https://zenodo.org/badge/42943499.svg\n :target: https://zenodo.org/badge/latestdoi/42943499\n\nPython modules for simulating and manipulating VLBI data and producing images with regularized maximum likelihood methods. This version is an early release so please raise an issue, submit a pull request, or email achael@princeton.edu if you have trouble or need help for your application.\n\nThe package contains several primary classes for loading, simulating, and manipulating VLBI data. The main classes are the ``Image``, ``Movie``, ``Array``, ``Obsdata``, ``Imager``, and ``Caltable`` classes, which provide tools for loading images and data, producing simulated data from realistic u-v tracks, calibrating, inspecting, and plotting data, and producing images from data sets in various polarizations using various data terms and regularizing functions.\n\nInstallation\n------------\n\nThe latest stable version (`1.2.8 <https://github.com/achael/eht-imaging/releases/tag/v1.2.7>`_) is available on `PyPi <https://pypi.org/project/ehtim/>`_. Simply install pip and run\n\n.. code-block:: bash\n\n pip install ehtim\n\nIncremental updates are developed on the `dev branch <https://github.com/achael/eht-imaging/tree/dev>`_. To use the very latest (unstable) code, checkout the dev branch, change to the main eht-imaging directory, and run:\n\n.. code-block:: bash\n\n pip install .\n\nInstalling with pip will update most of the required libraries automatically (`numpy <http://www.numpy.org/>`_, `scipy <http://www.scipy.org/>`_, `matplotlib <http://www.matplotlib.org/>`_, `astropy <http://www.astropy.org/>`_, `ephem <http://pypi.python.org/pypi/pyephem/>`_, `future <http://pypi.python.org/pypi/future>`_, `h5py <http://www.h5py.org/>`_, and `pandas <http://www.pandas.pydata.org/>`_).\n\n**If you want to use fast fourier transforms, you will also need to separately install** `NFFT <https://github.com/NFFT/nfft>`_ **and its** `pynfft wrapper <https://github.com/ghisvail/pyNFFT/>`__. The simplest way is to use `conda <https://anaconda.org/conda-forge/pynfft/>`__ to install both:\n\n\n.. code-block:: bash\n\n conda install -c conda-forge pynfft\n\nAlternatively, first install NFFT manually following the instructions on the `readme <https://github.com/NFFT/nfft>`__, making sure to use the ``--enable-openmp`` flag in compilation. Then install `pynfft <https://github.com/ghisvail/pyNFFT/>`__, with pip, following the readme instructions to link the installation to where you installed NFFT. Finally, reinstall ehtim.\n\n**For M1 Macs (OS >= v12.0)**, install the M1 Mac version of `pynfft <https://github.com/rohandahale/pyNFFT.git>`__ and follow the instructions on the `readme <https://github.com/rohandahale/pyNFFT.git>`__. It has the instructions to install `fftw <http://www.fftw.org>`_, `nfft <https://github.com/NFFT/nfft>`__ and then `pynfft <https://github.com/rohandahale/pyNFFT.git>`__.\n\n**Certain eht-imaging functions require other external packages that are not automatically installed.** In addition to pynfft, these include `networkx <https://networkx.github.io/>`_ (for image comparison functions), `requests <http://docs.python-requests.org/en/master/>`_ (for dynamical imaging), and `scikit-image <https://scikit-image.org/>`_ (for a few image analysis functions). However, the vast majority of the code will work without these dependencies.\n\nDocumentation and Tutorials\n---------------------------\nDocumentation is `here <https://achael.github.io/eht-imaging>`_.\n\nA intro to imaging tutorial jupyter notebook can be found in the repo at `tutorials/ehtim_tutorial.ipynb <https://github.com/achael/eht-imaging/blob/main/tutorials/ehtim_tutorial.ipynb>`__\n\n`Slides <https://docs.google.com/presentation/d/1A0y9omYI2ueSUa6_t5reylBhw6eiLwjqDzw-HUOk8Ac/edit?usp=sharing>`__ for the included tutorial walk through the basic steps of reconstructing EHT images with the code\n\nHere are some other ways to learn to use the code:\n\n- Start with the script examples/example.py, which contains a series of sample commands to load an image and array, generate data, and produce an image with various imaging algorithms.\n\n- Older `Slides <https://www.dropbox.com/s/7533ucj8bt54yh7/Bouman_Chael.pdf?dl=0>`__ from the EHT2016 data generation and imaging workshop contain a tutorial on generating data with the VLBI imaging `website <http://vlbiimaging.csail.mit.edu>`_, loading into the library, and producing an image.\n\nCitation\n--------------------------------\nIf you use ehtim in your publication, please cite `Chael+ 2018 <http://adsabs.harvard.edu/abs/2018ApJ...857...23C>`_.\n\nThe latest version is also available as a static doi on `Zenodo <https://zenodo.org/badge/latestdoi/42943499>`_.\n\nSelected publications that use ehtim\n------------------------------------\n\nLet us know if you use ehtim in your publication and we'll list it here!\n\n- High-Resolution Linear Polarimetric Imaging for the Event Horizon Telescope, `Chael et al. 2016 <https://arxiv.org/abs/1605.06156>`_ \n\n- Computational Imaging for VLBI Image Reconstruction, `Bouman et al. 2016 <http://www.cv-foundation.org/openaccess/content_cvpr_2016/html/Bouman_Computational_Imaging_for_CVPR_2016_paper.html>`_ \n\n- Stochastic Optics: A Scattering Mitigation Framework for Radio Interferometric Imaging, `Johnson 2016 <https://arxiv.org/abs/1610.05326>`_ \n\n- Reconstructing Video from Interferometric Measurements of Time-Varying Sources, `Bouman et al. 2017 <https://arxiv.org/abs/1711.01357>`_ \n\n- Dynamical Imaging with Interferometry, `Johnson et al. 2017 <https://arxiv.org/abs/1711.01286>`_ \n\n- Interferometric Imaging Directly with Closure Phases and Closure Amplitudes, `Chael et al. 2018 <https://arxiv.org/abs/1803.07088>`_\n\n- A Model for Anisotropic Interstellar Scattering and its Application to Sgr A*, `Psaltis et al. 2018 <https://arxiv.org/abs/1805.01242>`_\n\n- The Currrent Ability to Test Theories of Gravity with Black Hole Shadows, `Mizuno et al. 2018 <https://arxiv.org/abs/1804.05812>`_\n\n- The Scattering and Intrinsic Structure of Sagittarius A* at Radio Wavelengths, `Johnson et al. 2018 <https://arxiv.org/abs/18008.08966>`_\n\n- Testing GR with the Black Hole Shadow Size and Asymmetry of Sagittarius A*: Limitations from Interstellar Scattering, `Zhu et al. 2018 <https://arxiv.org/abs/1811.02079>`_\n\n- The Size, Shape, and Scattering of Sagittarius A* at 86 GHz: First VLBI with ALMA, `Issaoun et al. 2019a <https://arxiv.org/abs/1901.06226>`_\n\n- First M87 Event Horizon Telescope Results IV: Imaging the Central Supermassive Black Hole, `EHTC et al. 2019 <https://arxiv.org/abs/1906.11241>`_\n\n- EHT-HOPS Pipeline for Millimeter VLBI Data Reduction, `Blackburn et al. 2019 <https://arxiv.org/pdf/1903.08832>`_\n\n- Discriminating Accretion States via Rotational Symmetry in Simulated Polarimetric Images of M87, `Palumbo et al. 2020 <https://arxiv.org/pdf/2004.01751.pdf>`_\n\n- SYMBA: An end-to-end VLBI synthetic data generation pipeline, `Roelofs et al. 2020 <https://arxiv.org/pdf/2004.01161.pdf>`_\n\n- Monitoring the Morphology of M87* in 2009-2017 with the Event Horizon Telescope, `Wielgus et al. 2020 <https://arxiv.org/pdf/2009.11842>`_\n\n- EHT imaging of the archetypal blazar 3C 279 at extreme 20 microarcsecond resolution, `Kim et al. 2020 <https://www.aanda.org/articles/aa/pdf/2020/08/aa37493-20.pdf>`_\n\n- Verification of Radiative Transfer Schemes for the EHT, `Gold et al. 2020 <https://iopscience.iop.org/article/10.3847/1538-4357/ab96c6/pdf>`_\n\n- Closure Traces: Novel Calibration-insensitive Quantities for Radio Astronomy, `Broderick and Pesce. 2020 <https://iopscience.iop.org/article/10.3847/1538-4357/abbd9d/pdf>`_\n\n- Evaluation of New Submillimeter VLBI Sites for the Event Horizon Telescope, `Raymond et al. 2021 <https://iopscience.iop.org/article/10.3847/1538-3881/abc3c3/pdf>`_\n\n- Imaging VGOS Observations and Investigating Source Structure Effects, `Xu et al. 2021 <https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2020JB021238>`_\n\n- A D-term Modeling Code (DMC) for Simultaneous Calibration and Full-Stokes Imaging of VLBI Data, `Pesce et al. 2021 <https://iopscience.iop.org/article/10.3847/1538-3881/abe3f8/pdf>`_\n\n- Using space-VLBI to probe gravity around Sgr A*, `Fromm et 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VII. Polarization of the Ring, `EHTC et al. 2021 <https://iopscience.iop.org/article/10.3847/2041-8213/abe71d/pdf>`_\n\n- Event Horizon Telescope observations of the jet launching and collimation in Centaurus A, `Janssen et al. 2021 <https://www.nature.com/articles/s41550-021-01417-w.pdf>`_\n\n- RadioAstron discovers a mini-cocoon around the restarted parsec-scale jet in 3C 84 `Savolainen et al. 2021 <https://arxiv.org/pdf/2111.04481.pdf>`_\n\n- Unravelling the Innermost Jet Structure of OJ 287 with the First GMVA+ALMA Observations, `Zhao et al. 2022 <https://arxiv.org/pdf/2205.00554.pdf>`_\n\n- First Sagittarius A* Event Horizon Telescope Results. III: Imaging of the Galactic Center Supermassive Black Hole, `EHTC et al. 2022 <https://arxiv.org/pdf/2311.09479.pdf>`_\n\n- Resolving the Inner Parsec of the Blazar J1924-2914 with the Event Horizon Telescope, `Issaoun et al. 2022 <https://arxiv.org/pdf/2208.01662.pdf>`_\n\n- The Event Horizon Telescope Image of the Quasar NRAO 530, `Jorstad et al. 2023 <https://arxiv.org/pdf/2302.04622.pdf>`_\n\n- First M87 Event Horizon Telescope Results. IX. Detection of Near-horizon Circular Polarization, `EHTC et al. 2023 <https://arxiv.org/pdf/2311.10976.pdf>`_\n\n- Filamentary structures as the origin of blazar jet radio variability, `Fuentes et al. 2023 <https://arxiv.org/pdf/2311.01861.pdf>`_\n\n- The persistent shadow of the supermassive black hole of M 87. I. Observations, calibration, imaging, and analysis, `EHTC 2023 <https://www.aanda.org/articles/aa/pdf/2024/01/aa47932-23.pdf>`_\n\n- Parsec-scale evolution of the gigahertz-peaked spectrum quasar PKS 0858-279, `Kosogorov et al. 2024 <https://arxiv.org/pdf/2401.03603.pdf>`_\n\noifits Documentation\n--------------------\n\nThe oifits_new.py file used for reading/writing .oifits files is a slightly modified version of Paul Boley's package `oifits <http://astro.ins.urfu.ru/pages/~pboley/oifits/>`_. \nThe oifits read/write functionality in ehtim is still being developed and may not work with all versions of python or astropy.\n\nThe documentation is styled after `dfm's projects <https://github.com/dfm>`_ \n\nLicense\n-------\nehtim is licensed under GPLv3. See LICENSE.txt for more details.\n",
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