topostats.io
============

.. py:module:: topostats.io

.. autoapi-nested-parse::

   Functions for reading and writing data.

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Attributes
----------

.. autoapisummary::

   topostats.io.LOGGER


Classes
-------

.. autoapisummary::

   topostats.io.LoadScan


Functions
---------

.. autoapisummary::

   topostats.io.read_yaml
   topostats.io.write_yaml


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

.. py:data:: LOGGER

.. py:function:: read_yaml(filename: Union[str, pathlib.Path]) -> Dict

   
   Read a YAML file.

   :param filename: YAML file to read.
   :type filename: Union[str, Path]

   :returns: Dictionary of the file.
   :rtype: Dict















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.. py:function:: write_yaml(config: dict, output_dir: Union[str, pathlib.Path]) -> None

   
   Write a configuration (stored as a dictionary) to a YAML file.

   :param config: Configuration dictionary.
   :type config: dict
   :param output_dir: Path to save the dictionary to as a YAML file (it will be called 'config.yaml').
   :type output_dir: Union[str, Path]















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.. py:class:: LoadScan(img_path: Union[str, pathlib.Path], channel: str)

   
   Load the image and image parameters from a file path.
















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   .. py:attribute:: img_path


   .. py:attribute:: channel


   .. py:attribute:: channel_data
      :value: None



   .. py:attribute:: file_path


   .. py:attribute:: filename


   .. py:attribute:: suffix


   .. py:attribute:: image
      :value: None



   .. py:attribute:: pixel_to_nm_scaling
      :value: None



   .. py:method:: load_spm() -> tuple

      
      Extract image and pixel to nm scaling from the Bruker .spm file.
















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   .. py:method:: _spm_pixel_to_nm_scaling(channel_data) -> float

      
      Extract pixel to nm scaling from the SPM image metadata.

      :param channel_data: Channel data

      :returns: Pixel to nm scaling factor.
      :rtype: float















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   .. py:method:: load_ibw() -> tuple

      
      Loads image from Asylum Research (Igor) .ibw files
















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   .. py:method:: _ibw_pixel_to_nm_scaling(scan) -> float

      
      Extract pixel to nm scaling from the IBW image metadata.
















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   .. py:method:: load_jpk() -> None


   .. py:method:: _extract_jpk(jpk: afmformats.mod_creep_compliance.AFMCreepCompliance) -> numpy.ndarray
      :staticmethod:


      
      Extract data from jpk object.
















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   .. py:method:: get_data() -> None

      
      Method to extract image and pixel to nm scaling.
















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