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ehtim (eht-imaging) | ||
=================== | ||
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Python modules for simulating and manipulating VLBI data and producing images with regularized gradient descent methods. | ||
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The code can be found `GitHub <https://github.com/achael/eht-imaging>`_ | ||
Python modules for simulating and manipulating VLBI data and producing images with regularized maximum likelihood methods. This version is an early release so please submit a pull request or email achael@cfa.harvard.edu if you have trouble or need help for your application. | ||
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The package contains several primary classes for loading, simulating, and manipulating VLBI data. The main classes are the :class:`Image`, :class:`Array`, and :class:`Obsdata`. :class:`Movie` and :class:`Vex` provide tools for producing time-variable simulated data and observing with real VLBI tracks from .vex files. :class:`imager` is a generic Stokes I imager class that can produce images from data sets using various data terms and regularizers. | ||
The package contains several primary classes for loading, simulating, and manipulating VLBI data. The main classes are the :class:`Image`, :class:`Array`, and :class:`Obsdata`, which provide tools for manipulating images, simulating interferometric data from images, and plotting and analyzing these data. :class:`Movie` and :class:`Vex` provide tools for producing time-variable simulated data and observing with real VLBI tracks from .vex files. :class:`imager` is a generic imager class that can produce images from data sets in various polarizationsusing various data terms and regularizers. | ||
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.. note:: | ||
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If you have a problem please submit a pull request on the git repository and/or email [email protected] | ||
This is a pre-release of ehtim. If you have a problem please submit a pull request on the git repository and/or email [email protected] | ||
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Installation | ||
------------ | ||
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pip install . | ||
It should install the depended libraries `astropy <http://www.astropy.org/>`_, `ephem <http://pypi.python.org/pypi/pyephem/>`_, `future <http://pypi.python.org/pypi/future>`_, `matplotlib <http://www.matplotlib.org/>`_, `numpy <http://www.numpy.org/>`_, `scipy <http://www.scipy.org/>`_, `pandas <http://www.pandas.pydata.org/>`_ automatically. | ||
If you want to use fast fourier transforms, you will also need to install `NFFT <https://github.com/NFFT/nfft>`_ and the `pynnft wrapper <https://github.com/ghisvail/pyNFFT/>`_ before installing ehtim. The simplest way is to use `conda <https://anaconda.org/conda-forge/pynfft/>`__ to to install both NFFT and the pynfft wrapper. | ||
It should install most of the required libraries automatically (`astropy <http://www.astropy.org/>`_, `ephem <http://pypi.python.org/pypi/pyephem/>`_, `future <http://pypi.python.org/pypi/future>`_, `h5py <http://www.h5py.org/>`_ ,`html <https://www.decalage.info/python/html>`_, `networkx <https://networkx.github.io/>`_, `numpy <http://www.numpy.org/>`_, `pandas <http://www.pandas.pydata.org/>`_ , `matplotlib <http://www.matplotlib.org/>`_, `requests <http://docs.python-requests.org/en/master/>`_, `scipy <http://www.scipy.org/>`_, `skimage <https://scikit-image.org/>`_). | ||
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**If you want to use fast fourier transforms, you will also need to separately install** `**NFFT** <https://github.com/NFFT/nfft>`_ **and its** `**pynnft wrapper** <https://github.com/ghisvail/pyNFFT/>`_. The simplest way is to use `conda <https://anaconda.org/conda-forge/pynfft/>`__ to to install both: | ||
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.. code-block:: bash | ||
conda install -c conda-forge pynfft | ||
Alternatively, first install NFFT following the instructions on the `github readme <https://github.com/NFFT/nfft>`_, making sure to use the --enable-openmp flag in compilation. Then install `pynnft <https://github.com/ghisvail/pyNFFT/>`_, with pip, following the readme instructions to link the installation to where you installed NFFT. | ||
Alternatively, first install NFFT manually following the instructions on the `readme <https://github.com/NFFT/nfft>`_, making sure to use the :code:`--enable-openmp` flag in compilation. Then install `pynft <https://github.com/ghisvail/pyNFFT/>`_, with pip, following the readme instructions to link the installation to where you installed NFFT. Finally, reinstall ehtim. | ||
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Documentation | ||
Tutorials | ||
------------- | ||
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Tutorials are in progress, but here are some ways to learn the code | ||
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- The script in `examples/example.py <https://github.com/achael/eht-imaging/blob/master/examples/example.py>`_ has a series of sample commands to load an image and array, generate data, and produce an image with regularized maximum likelihood on closure quantities. | ||
- `Slides <https://www.dropbox.com/s/7533ucj8bt54yh7/Bouman_Chael.pdf?dl=0>`_ from the EHT 2016 conference data generation and imaging workshop contain a tutorial on generating data externally with the vlbi imaging `website <http://vlbiimaging.csail.mit.edu>`_, loading into the library, and producing an image. | ||
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Documentation | ||
------------- | ||
.. toctree:: | ||
:maxdepth: 2 | ||
:caption: Contents: | ||
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statistics | ||
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The documentation is in progress, but here are some other ways to learn to use the code: | ||
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- The file examples/example.py has a series of sample commands to load an image and array, generate data, and produce an image. | ||
- `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. | ||
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Acknowledgements | ||
---------------- | ||
The oifits_new code used for reading/writing .oifits files is a slightly modified version of Paul Boley's package at `<http://astro.ins.urfu.ru/pages/~pboley/oifits>`_. The oifits read/write functionality is still being tested and may not work with all versions of python or astropy.io.fits. | ||
The :code:`oifits_new` code used for reading/writing .oifits files is a slightly modified version of Paul Boley's package at `<http://astro.ins.urfu.ru/pages/~pboley/oifits>`_. The oifits read/write functionality is still being tested and may not work with all versions of python. | ||
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This documentation is styled after `dfm's projects <https://github.com/dfm>`_ and the documentation for `scatterbrane <https://github.com/krosenfeld/scatterbrane>`_ | ||
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