:py:mod:`diamond_utils`
=======================

.. py:module:: diamond_utils

.. autodoc2-docstring:: diamond_utils
   :allowtitles:

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

Classes
~~~~~~~

.. list-table::
   :class: autosummary longtable
   :align: left

   * - :py:obj:`ProcessArgs <diamond_utils.ProcessArgs>`
     - .. autodoc2-docstring:: diamond_utils.ProcessArgs
          :summary:

Functions
~~~~~~~~~

.. list-table::
   :class: autosummary longtable
   :align: left

   * - :py:obj:`get_im_path <diamond_utils.get_im_path>`
     - .. autodoc2-docstring:: diamond_utils.get_im_path
          :summary:
   * - :py:obj:`setup_processing <diamond_utils.setup_processing>`
     - .. autodoc2-docstring:: diamond_utils.setup_processing
          :summary:
   * - :py:obj:`create_process_config <diamond_utils.create_process_config>`
     - .. autodoc2-docstring:: diamond_utils.create_process_config
          :summary:
   * - :py:obj:`check_folder <diamond_utils.check_folder>`
     - .. autodoc2-docstring:: diamond_utils.check_folder
          :summary:
   * - :py:obj:`check_folder_corruption <diamond_utils.check_folder_corruption>`
     - .. autodoc2-docstring:: diamond_utils.check_folder_corruption
          :summary:
   * - :py:obj:`get_good_paths <diamond_utils.get_good_paths>`
     - .. autodoc2-docstring:: diamond_utils.get_good_paths
          :summary:
   * - :py:obj:`colour_text <diamond_utils.colour_text>`
     - .. autodoc2-docstring:: diamond_utils.colour_text
          :summary:
   * - :py:obj:`data_corruption_warning <diamond_utils.data_corruption_warning>`
     - .. autodoc2-docstring:: diamond_utils.data_corruption_warning
          :summary:
   * - :py:obj:`create_experiment <diamond_utils.create_experiment>`
     - .. autodoc2-docstring:: diamond_utils.create_experiment
          :summary:
   * - :py:obj:`initial_value_checks <diamond_utils.initial_value_checks>`
     - .. autodoc2-docstring:: diamond_utils.initial_value_checks
          :summary:
   * - :py:obj:`setup_dps <diamond_utils.setup_dps>`
     - .. autodoc2-docstring:: diamond_utils.setup_dps
          :summary:
   * - :py:obj:`standard_adjustments <diamond_utils.standard_adjustments>`
     - .. autodoc2-docstring:: diamond_utils.standard_adjustments
          :summary:
   * - :py:obj:`make_mask_lists <diamond_utils.make_mask_lists>`
     - .. autodoc2-docstring:: diamond_utils.make_mask_lists
          :summary:
   * - :py:obj:`make_new_hdf5 <diamond_utils.make_new_hdf5>`
     - .. autodoc2-docstring:: diamond_utils.make_new_hdf5
          :summary:
   * - :py:obj:`run_one_scan_process <diamond_utils.run_one_scan_process>`
     - .. autodoc2-docstring:: diamond_utils.run_one_scan_process
          :summary:
   * - :py:obj:`run_scanlist_loop <diamond_utils.run_scanlist_loop>`
     - .. autodoc2-docstring:: diamond_utils.run_scanlist_loop
          :summary:
   * - :py:obj:`run_scanlist_combined <diamond_utils.run_scanlist_combined>`
     - .. autodoc2-docstring:: diamond_utils.run_scanlist_combined
          :summary:
   * - :py:obj:`get_run_function <diamond_utils.get_run_function>`
     - .. autodoc2-docstring:: diamond_utils.get_run_function
          :summary:
   * - :py:obj:`run_process_list <diamond_utils.run_process_list>`
     - .. autodoc2-docstring:: diamond_utils.run_process_list
          :summary:
   * - :py:obj:`run_full_map_process <diamond_utils.run_full_map_process>`
     - .. autodoc2-docstring:: diamond_utils.run_full_map_process
          :summary:
   * - :py:obj:`save_binoviewer_hdf5 <diamond_utils.save_binoviewer_hdf5>`
     - .. autodoc2-docstring:: diamond_utils.save_binoviewer_hdf5
          :summary:
   * - :py:obj:`get_volume_and_bounds <diamond_utils.get_volume_and_bounds>`
     - .. autodoc2-docstring:: diamond_utils.get_volume_and_bounds
          :summary:

API
~~~

.. py:function:: get_im_path(directorypath: str, scan_number: int, image_number: int = 0)
   :canonical: diamond_utils.get_im_path

   .. autodoc2-docstring:: diamond_utils.get_im_path

.. py:function:: setup_processing(exp_setup_file: pathlib.Path, job_file_path: str, scan_numbers: list, debuglogging: bool)
   :canonical: diamond_utils.setup_processing

   .. autodoc2-docstring:: diamond_utils.setup_processing

.. py:function:: create_process_config(exp_setup_file: pathlib.Path, job_file_path: str, scan_numbers: list, debuglogging: bool)
   :canonical: diamond_utils.create_process_config

   .. autodoc2-docstring:: diamond_utils.create_process_config

.. py:function:: check_folder(folder)
   :canonical: diamond_utils.check_folder

   .. autodoc2-docstring:: diamond_utils.check_folder

.. py:function:: check_folder_corruption(folderpath: pathlib.Path)
   :canonical: diamond_utils.check_folder_corruption

   .. autodoc2-docstring:: diamond_utils.check_folder_corruption

.. py:function:: get_good_paths(process_config: types.SimpleNamespace)
   :canonical: diamond_utils.get_good_paths

   .. autodoc2-docstring:: diamond_utils.get_good_paths

.. py:function:: colour_text(colour, string)
   :canonical: diamond_utils.colour_text

   .. autodoc2-docstring:: diamond_utils.colour_text

.. py:function:: data_corruption_warning(cfg: types.SimpleNamespace)
   :canonical: diamond_utils.data_corruption_warning

   .. autodoc2-docstring:: diamond_utils.data_corruption_warning

.. py:function:: create_experiment(process_config: types.SimpleNamespace)
   :canonical: diamond_utils.create_experiment

   .. autodoc2-docstring:: diamond_utils.create_experiment

.. py:function:: initial_value_checks(dps_centres, cylinder_axis, setup, output_file_size)
   :canonical: diamond_utils.initial_value_checks

   .. autodoc2-docstring:: diamond_utils.initial_value_checks

.. py:function:: setup_dps(scan, process_config)
   :canonical: diamond_utils.setup_dps

   .. autodoc2-docstring:: diamond_utils.setup_dps

.. py:function:: standard_adjustments(experiment, process_config)
   :canonical: diamond_utils.standard_adjustments

   .. autodoc2-docstring:: diamond_utils.standard_adjustments

.. py:function:: make_mask_lists(specific_pixels, mask_regions)
   :canonical: diamond_utils.make_mask_lists

   .. autodoc2-docstring:: diamond_utils.make_mask_lists

.. py:function:: make_new_hdf5(cfg: types.SimpleNamespace, scan_index: int, name_start: str, experiment: fast_rsm.experiment.Experiment)
   :canonical: diamond_utils.make_new_hdf5

   .. autodoc2-docstring:: diamond_utils.make_new_hdf5

.. py:function:: run_one_scan_process(cfg, i, experiment, inputscan, runoptions)
   :canonical: diamond_utils.run_one_scan_process

   .. autodoc2-docstring:: diamond_utils.run_one_scan_process

.. py:function:: run_scanlist_loop(cfg, experiment, runoptions)
   :canonical: diamond_utils.run_scanlist_loop

   .. autodoc2-docstring:: diamond_utils.run_scanlist_loop

.. py:function:: run_scanlist_combined(cfg, experiment, runoptions)
   :canonical: diamond_utils.run_scanlist_combined

   .. autodoc2-docstring:: diamond_utils.run_scanlist_combined

.. py:function:: get_run_function(map_per_image)
   :canonical: diamond_utils.get_run_function

   .. autodoc2-docstring:: diamond_utils.get_run_function

.. py:function:: run_process_list(experiment, process_config)
   :canonical: diamond_utils.run_process_list

   .. autodoc2-docstring:: diamond_utils.run_process_list

.. py:function:: run_full_map_process(experiment, cfg)
   :canonical: diamond_utils.run_full_map_process

   .. autodoc2-docstring:: diamond_utils.run_full_map_process

.. py:function:: save_binoviewer_hdf5(output_path: str, process_config: types.SimpleNamespace)
   :canonical: diamond_utils.save_binoviewer_hdf5

   .. autodoc2-docstring:: diamond_utils.save_binoviewer_hdf5

.. py:function:: get_volume_and_bounds(path_to_npy: str) -> typing.Tuple[numpy.ndarray]
   :canonical: diamond_utils.get_volume_and_bounds

   .. autodoc2-docstring:: diamond_utils.get_volume_and_bounds

.. py:class:: ProcessArgs
   :canonical: diamond_utils.ProcessArgs

   .. autodoc2-docstring:: diamond_utils.ProcessArgs

   .. py:attribute:: exp_path
      :canonical: diamond_utils.ProcessArgs.exp_path
      :type: str
      :value: None

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.exp_path

   .. py:attribute:: calc_path
      :canonical: diamond_utils.ProcessArgs.calc_path
      :type: str
      :value: None

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.calc_path

   .. py:attribute:: version_path
      :canonical: diamond_utils.ProcessArgs.version_path
      :type: str
      :value: None

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.version_path

   .. py:attribute:: python_version
      :canonical: diamond_utils.ProcessArgs.python_version
      :type: str
      :value: None

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.python_version

   .. py:attribute:: scan_nums
      :canonical: diamond_utils.ProcessArgs.scan_nums
      :type: list[int] | None
      :value: None

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.scan_nums

   .. py:attribute:: scan_range
      :canonical: diamond_utils.ProcessArgs.scan_range
      :type: list[int] | None
      :value: None

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.scan_range

   .. py:attribute:: out_path
      :canonical: diamond_utils.ProcessArgs.out_path
      :type: str | None
      :value: None

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.out_path

   .. py:attribute:: debuglogging
      :canonical: diamond_utils.ProcessArgs.debuglogging
      :type: bool
      :value: 0

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.debuglogging

   .. py:attribute:: local
      :canonical: diamond_utils.ProcessArgs.local
      :type: bool
      :value: 0

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.local

   .. py:attribute:: dev
      :canonical: diamond_utils.ProcessArgs.dev
      :type: bool
      :value: 0

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.dev

   .. py:method:: start_loggers()
      :canonical: diamond_utils.ProcessArgs.start_loggers

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.start_loggers

   .. py:method:: parse_setup()
      :canonical: diamond_utils.ProcessArgs.parse_setup

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.parse_setup

   .. py:method:: parse_scans()
      :canonical: diamond_utils.ProcessArgs.parse_scans

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.parse_scans

   .. py:method:: create_job_name()
      :canonical: diamond_utils.ProcessArgs.create_job_name

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.create_job_name

   .. py:method:: create_jobscript()
      :canonical: diamond_utils.ProcessArgs.create_jobscript

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.create_jobscript

   .. py:method:: create_jobfile()
      :canonical: diamond_utils.ProcessArgs.create_jobfile

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.create_jobfile

   .. py:method:: check_slurmfiles()
      :canonical: diamond_utils.ProcessArgs.check_slurmfiles

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.check_slurmfiles

   .. py:method:: print_exp_lines()
      :canonical: diamond_utils.ProcessArgs.print_exp_lines

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.print_exp_lines

   .. py:method:: print_calc_lines()
      :canonical: diamond_utils.ProcessArgs.print_calc_lines

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.print_calc_lines

   .. py:method:: run_cluster_job()
      :canonical: diamond_utils.ProcessArgs.run_cluster_job

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.run_cluster_job

   .. py:method:: parse_and_reduce()
      :canonical: diamond_utils.ProcessArgs.parse_and_reduce

      .. autodoc2-docstring:: diamond_utils.ProcessArgs.parse_and_reduce