topostats
=========

.. py:module:: topostats

.. autoapi-nested-parse::

   
   Topostats.
















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Subpackages
-----------

.. toctree::
   :maxdepth: 1

   /autoapi/topostats/logs/index
   /autoapi/topostats/tracing/index


Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/topostats/__main__/index
   /autoapi/topostats/entry_point/index
   /autoapi/topostats/filters/index
   /autoapi/topostats/grains/index
   /autoapi/topostats/grainstats/index
   /autoapi/topostats/io/index
   /autoapi/topostats/plotting/index
   /autoapi/topostats/plottingfuncs/index
   /autoapi/topostats/processing/index
   /autoapi/topostats/run_topostats/index
   /autoapi/topostats/scars/index
   /autoapi/topostats/statistics/index
   /autoapi/topostats/theme/index
   /autoapi/topostats/thresholds/index
   /autoapi/topostats/unet_masking/index
   /autoapi/topostats/utils/index
   /autoapi/topostats/validation/index


Attributes
----------

.. autoapisummary::

   topostats.LOGGER
   topostats.release
   topostats.__version__


Classes
-------

.. autoapisummary::

   topostats.Colormap


Functions
---------

.. autoapisummary::

   topostats.setup_logger


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

.. py:function:: setup_logger(log_name: str = LOGGER_NAME) -> logging.Logger

   
   Logger setup.

   The logger for the module is initialised when the module is loaded (as this functions is called from
   __init__.py). This creates two stream handlers, one for general output and one for errors which are formatted
   differently (there is greater information in the error formatter). To use in modules import the 'LOGGER_NAME' and
   create a logger as shown in the Examples, it will inherit the formatting and direction of messages to the correct
   stream.

   :param log_name: Name under which logging information occurs.
   :type log_name: str

   :returns: Logger object.
   :rtype: logging.Logger

   .. rubric:: Examples

   To use the logger in (sub-)modules have the following.

       import logging
       from topostats.logs.logs import LOGGER_NAME

       LOGGER = logging.getLogger(LOGGER_NAME)

       LOGGER.info('This is a log message.')















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.. py:class:: Colormap(name: str = 'nanoscope')

   
   Class for setting the Colormap.

   :param name: Name of colormap to use.
   :type name: str















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   .. py:attribute:: name


   .. py:attribute:: cmap
      :value: None



   .. py:method:: __str__() -> str

      
      Return string representation of object.

      :returns: String detailing the colormap.
      :rtype: str















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   .. py:method:: set_cmap(name: str) -> None

      
      Set the ColorMap.

      :param name: Name of the colormap to return.
      :type name: str















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   .. py:method:: get_cmap() -> matplotlib.cm

      
      Return the matplotlib.cm colormap object.

      :returns: Matplotlib Color map object.
      :rtype: matplotlib.cm















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   .. py:method:: nanoscope() -> matplotlib.colors.LinearSegmentedColormap
      :staticmethod:


      
      Matplotlib compatible colormap that replicates the Bruker Nanoscope colorscale.

      The colormap is implemented in Gwyddion's GwyGradient via 'Nanoscope.txt'.

      :returns: MatplotLib LinearSegmentedColourmap that replicates Bruker Nanoscope colorscale.
      :rtype: LinearSegmentedColormap















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   .. py:method:: gwyddion() -> matplotlib.colors.LinearSegmentedColormap
      :staticmethod:


      
      Set RGBA colour map for the Gwyddion.net colour gradient.

      :returns: The 'gwyddion' colormap.
      :rtype: LinearSegmentedColormap















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   .. py:method:: blue() -> matplotlib.colors.ListedColormap
      :staticmethod:


      
      Set RGBA colour map of just the colour blue.

      :returns: The 'blue' colormap.
      :rtype: ListedColormap















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   .. py:method:: blue_purple_green() -> matplotlib.colors.ListedColormap
      :staticmethod:


      
      RGBA colour map of just the colour blue/purple/green.

      :returns: The 'blue/purple/green' colormap.
      :rtype: ListedColormap















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.. py:data:: LOGGER

.. py:data:: release

.. py:data:: __version__