arrakis.linmos
==============

.. py:module:: arrakis.linmos

.. autoapi-nested-parse::

   Run LINMOS on cutouts in parallel

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Attributes
----------

.. autoapisummary::

   arrakis.linmos.TQDM_OUT


Classes
-------

.. autoapisummary::

   arrakis.linmos.ImagePaths


Functions
---------

.. autoapisummary::

   arrakis.linmos.cli
   arrakis.linmos.find_images
   arrakis.linmos.genparset
   arrakis.linmos.get_yanda
   arrakis.linmos.linmos
   arrakis.linmos.linmos_parser
   arrakis.linmos.main
   arrakis.linmos.serial_loop
   arrakis.linmos.smooth_images


Module Contents
---------------

.. py:class:: ImagePaths

   Bases: :py:obj:`NamedTuple`


   
   Class to hold image paths
















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   .. py:attribute:: images
      :type:  list[pathlib.Path]

      
      List of image paths
















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   .. py:attribute:: weights
      :type:  list[pathlib.Path]

      
      List of weight paths
















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.. py:function:: cli()

   
   Command-line interface
















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.. py:function:: find_images(field: str, beams_row: tuple[int, pandas.Series], stoke: str, datadir: pathlib.Path) -> ImagePaths

   
   Find the images and weights for a given field and stokes parameter

   :Parameters: * **field** (*str*) -- Field name.
                * **beams** (*dict*) -- Beam information.
                * **stoke** (*str*) -- Stokes parameter.
                * **datadir** (*Path*) -- Data directory.

   :raises Exception: If no files are found.

   :returns: List of images and weights.
   :rtype: ImagePaths















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.. py:function:: genparset(image_paths: ImagePaths, stoke: str, datadir: pathlib.Path, holofile: pathlib.Path | None = None) -> str

   
   Generate parset for LINMOS

   :Parameters: * **image_paths** (*ImagePaths*) -- List of images and weights.
                * **stoke** (*str*) -- Stokes parameter.
                * **datadir** (*Path*) -- Data directory.
                * **holofile** (*Path, optional*) -- Path to the holography file to include in the bind list. Defaults to None.

   :raises Exception: If no files are found.

   :returns: Path to parset file.
   :rtype: str















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.. py:function:: get_yanda(version='1.3.0') -> str

   
   Pull yandasoft image from dockerhub.

   :Parameters: **version** (*str, optional*) -- Yandasoft version. Defaults to "1.3.0".

   :returns: Path to yandasoft image.
   :rtype: str















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.. py:function:: linmos(parset: str | None, fieldname: str, image: str, holofile: pathlib.Path) -> pymongo.UpdateOne | None

   
   Run linmos

   :Parameters: * **parset** (*str*) -- Path to parset file.
                * **fieldname** (*str*) -- Name of RACS field.
                * **image** (*str*) -- Name of Yandasoft image.
                * **holofile** (*Path*) -- Path to the holography file to include in the bind list.

   :raises Exception: If LINMOS fails.
   :raises Exception: LINMOS output not found.

   :returns: Mongo update object.
   :rtype: pymongo.UpdateOne















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.. py:function:: linmos_parser(parent_parser: bool = False) -> argparse.ArgumentParser

.. py:function:: main(field: str, datadir: pathlib.Path, host: str, epoch: int, sbid: int | None = None, holofile: pathlib.Path | None = None, username: str | None = None, password: str | None = None, yanda: str = '1.3.0', yanda_img: pathlib.Path | None = None, stokeslist: list[str] | None = None, limit: int | None = None) -> None

   
   LINMOS flow

   :Parameters: * **field** (*str*) -- RACS field name.
                * **datadir** (*str*) -- Data directory.
                * **host** (*str*) -- MongoDB host IP.
                * **holofile** (*str*) -- Path to primary beam file.
                * **username** (*str, optional*) -- Mongo username. Defaults to None.
                * **password** (*str, optional*) -- Mongo password. Defaults to None.
                * **yanda** (*str, optional*) -- Yandasoft version. Defaults to "1.3.0".
                * **yanda_img** (*Path, optional*) -- Path to a yandasoft singularirt image. If `None`, the container version `yanda` will be downloaded. Defaults to None.
                * **stokeslist** (*List[str], optional*) -- Stokes parameters to process. Defaults to None.
                * **limit** (*int, optional*) -- Limit the number of islands to process. Defaults to None.















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.. py:function:: serial_loop(field: str, beams_row: tuple[int, pandas.Series], stokeslist: list[str], cutdir: pathlib.Path, holofile: pathlib.Path, image: pathlib.Path) -> list[pymongo.UpdateOne | None]

.. py:function:: smooth_images(image_dict: dict[str, ImagePaths]) -> dict[str, ImagePaths]

   
   Smooth cubelets to a common resolution

   :Parameters: **image_list** (*ImagePaths*) -- List of cubelets to smooth.

   :returns: Smoothed cubelets.
   :rtype: ImagePaths















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.. py:data:: TQDM_OUT