dacapo.blockwise
================

.. py:module:: dacapo.blockwise


Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/dacapo/blockwise/argmax_worker/index
   /autoapi/dacapo/blockwise/blockwise_task/index
   /autoapi/dacapo/blockwise/empanada_function/index
   /autoapi/dacapo/blockwise/predict_worker/index
   /autoapi/dacapo/blockwise/relabel_worker/index
   /autoapi/dacapo/blockwise/scheduler/index
   /autoapi/dacapo/blockwise/segment_worker/index
   /autoapi/dacapo/blockwise/threshold_worker/index
   /autoapi/dacapo/blockwise/watershed_function/index


Classes
-------

.. autoapisummary::

   dacapo.blockwise.DaCapoBlockwiseTask


Functions
---------

.. autoapisummary::

   dacapo.blockwise.run_blockwise
   dacapo.blockwise.segment_blockwise


Package Contents
----------------

.. py:class:: DaCapoBlockwiseTask(worker_file: str | upath.UPath, total_roi: daisy.Roi, read_roi: daisy.Roi, write_roi: daisy.Roi, num_workers: int = 16, max_retries: int = 2, timeout=None, upstream_tasks=None, *args, **kwargs)



   A task to run a blockwise worker function. This task is used to run a
   blockwise worker function on a given ROI.

   .. attribute:: worker_file

      The path to the worker file.

      :type: str | Path

   .. attribute:: total_roi

      The ROI to process.

      :type: Roi

   .. attribute:: read_roi

      The ROI to read from for a block.

      :type: Roi

   .. attribute:: write_roi

      The ROI to write to for a block.

      :type: Roi

   .. attribute:: num_workers

      The number of workers to use.

      :type: int

   .. attribute:: max_retries

      The maximum number of times a task will be retried if failed
      (either due to failed post check or application crashes or network
      failure)

      :type: int

   .. attribute:: timeout

      The timeout for the task.

   .. attribute:: upstream_tasks

      The upstream tasks.

   .. attribute:: \*args

      Additional positional arguments to pass to ``worker_function``.

   .. attribute:: \*\*kwargs

      Additional keyword arguments to pass to ``worker_function``.

   .. method:: __init__

      
      Initialize the task.
      


   .. py:attribute:: worker_name


   .. py:attribute:: worker


   .. py:attribute:: timestamp


   .. py:attribute:: task_id


   .. py:attribute:: process_function


   .. py:attribute:: read_write_conflict


   .. py:attribute:: fit


   .. py:attribute:: kwargs


.. py:function:: run_blockwise(worker_file: str | upath.UPath, total_roi: funlib.geometry.Roi, read_roi: funlib.geometry.Roi, write_roi: funlib.geometry.Roi, num_workers: int = 16, max_retries: int = 1, timeout=None, upstream_tasks=None, *args, **kwargs)

   Run a function in parallel over a large volume.

   :param worker_file: The path to the file containing the necessary worker functions:
                       ``spawn_worker`` and ``start_worker``.
                       Optionally, the file can also contain a ``check_function`` and an ``init_callback_fn``.
   :type worker_file: ``str`` or ``Path``
   :param total_roi: The ROI to process.
   :type total_roi: ``Roi``
   :param read_roi: The ROI to read from for a block.
   :type read_roi: ``Roi``
   :param write_roi: The ROI to write to for a block.
   :type write_roi: ``Roi``
   :param num_workers: The number of workers to use.
   :type num_workers: ``int``
   :param max_retries: The maximum number of times a task will be retried if failed
                       (either due to failed post check or application crashes or network
                       failure)
   :type max_retries: ``int``
   :param \*args: Additional positional arguments to pass to ``worker_function``.
   :param \*\*kwargs: Additional keyword arguments to pass to ``worker_function``.

   :returns: ``Bool``.

   .. rubric:: Examples

   >>> run_blockwise(worker_file, total_roi, read_roi, write_roi, num_workers, max_retries, timeout, upstream_tasks)


.. py:function:: segment_blockwise(segment_function_file: str | upath.UPath, context: funlib.geometry.Coordinate, total_roi: funlib.geometry.Roi, read_roi: funlib.geometry.Roi, write_roi: funlib.geometry.Roi, num_workers: int = 16, max_retries: int = 2, timeout=None, upstream_tasks=None, keep_tmpdir=False, *args, **kwargs)

   Run a segmentation function in parallel over a large volume.

   :param segment_function_file: The path to the file containing the necessary worker functions:
                                 ``spawn_worker`` and ``start_worker``.
                                 Optionally, the file can also contain a ``check_function`` and an ``init_callback_fn``.
   :type segment_function_file: ``str`` or ``Path``
   :param context: The context to add to the read and write ROI.
   :type context: ``Coordinate``
   :param total_roi: The ROI to process.
   :type total_roi: ``Roi``
   :param read_roi: The ROI to read from for a block.
   :type read_roi: ``Roi``
   :param write_roi: The ROI to write to for a block.
   :type write_roi: ``Roi``
   :param num_workers: The number of workers to use.
   :type num_workers: ``int``
   :param max_retries: The maximum number of times a task will be retried if failed
                       (either due to failed post check or application crashes or network
                       failure)
   :type max_retries: ``int``
   :param timeout: The maximum time in seconds to wait for a worker to complete a task.
   :type timeout: ``int``
   :param upstream_tasks: List of upstream tasks.
   :type upstream_tasks: ``List``
   :param keep_tmpdir: Whether to keep the temporary directory.
   :type keep_tmpdir: ``bool``
   :param \*args: Additional positional arguments to pass to ``worker_function``.
   :param \*\*kwargs: Additional keyword arguments to pass to ``worker_function``.

   :returns: ``Bool``.

   .. rubric:: Examples

   >>> segment_blockwise(segment_function_file, context, total_roi, read_roi, write_roi, num_workers, max_retries, timeout, upstream_tasks)