topostats.plottingfuncs
=======================

.. py:module:: topostats.plottingfuncs

.. autoapi-nested-parse::

   Plotting data.

   ..
       !! processed by numpydoc !!


Attributes
----------

.. autoapisummary::

   topostats.plottingfuncs.LOGGER


Classes
-------

.. autoapisummary::

   topostats.plottingfuncs.Images


Functions
---------

.. autoapisummary::

   topostats.plottingfuncs.add_bounding_boxes_to_plot


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

.. py:data:: LOGGER

.. py:class:: Images(data: numpy.array, output_dir: Union[str, pathlib.Path], filename: str, pixel_to_nm_scaling: float = 1.0, masked_array: numpy.array = None, title: str = None, image_type: str = 'non-binary', image_set: str = 'core', core_set: bool = False, pixel_interpolation: Union[str, None] = None, cmap: str = 'nanoscope', mask_cmap: str = 'jet_r', region_properties: dict = None, zrange: list = [None, None], colorbar: bool = True, axes: bool = True, save: bool = True, save_format: str = 'png', histogram_log_axis: bool = True, histogram_bins: int = 200, dpi: Union[str, float] = 'figure')

   
   Plots image arrays
















   ..
       !! processed by numpydoc !!

   .. py:attribute:: data


   .. py:attribute:: output_dir


   .. py:attribute:: filename


   .. py:attribute:: pixel_to_nm_scaling


   .. py:attribute:: masked_array


   .. py:attribute:: title


   .. py:attribute:: image_type


   .. py:attribute:: image_set


   .. py:attribute:: core_set


   .. py:attribute:: interpolation


   .. py:attribute:: cmap


   .. py:attribute:: mask_cmap


   .. py:attribute:: region_properties


   .. py:attribute:: zrange


   .. py:attribute:: colorbar


   .. py:attribute:: axes


   .. py:attribute:: save


   .. py:attribute:: save_format


   .. py:attribute:: histogram_log_axis


   .. py:attribute:: histogram_bins


   .. py:attribute:: dpi


   .. py:method:: plot_histogram_and_save()

      
      Plot and save a histogram of the height map

      :returns: * **fig** (*plt.figure.Figure*) -- Matplotlib.pyplot figure object
                * **ax** (*plt.axes._subplots.AxesSubplot*) -- Matplotlib.pyplot axes object















      ..
          !! processed by numpydoc !!


   .. py:method:: plot_and_save()

      
      Plot and save the images with savefig or imsave depending on config file parameters.

      :returns: * **fig** (*plt.figure.Figure*) -- Matplotlib.pyplot figure object
                * **ax** (*plt.axes._subplots.AxesSubplot*) -- Matplotlib.pyplot axes object















      ..
          !! processed by numpydoc !!


   .. py:method:: save_figure()

      
      This function saves figures as plt.savefig objects.

      :returns: * **fig** (*plt.figure.Figure*) -- Matplotlib.pyplot figure object
                * **ax** (*plt.axes._subplots.AxesSubplot*) -- Matplotlib.pyplot axes object















      ..
          !! processed by numpydoc !!


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

      
      This function saves only the image array as an image using plt.imsave
















      ..
          !! processed by numpydoc !!


.. py:function:: add_bounding_boxes_to_plot(fig, ax, shape, region_properties: list, pixel_to_nm_scaling: float) -> None

   
   Add the bounding boxes to a plot.

   :param fig: Matplotlib.pyplot figure object
   :type fig: plt.figure.Figure
   :param ax: Matplotlib.pyplot axes object
   :type ax: plt.axes._subplots.AxesSubplot.
   :param shape: Tuple of the image-to-be-plot's shape.
   :type shape: tuple
   :param region_properties: Region properties to add bounding boxes from.
   :param pixel_to_nm_scaling: The scaling factor from px to nm.
   :type pixel_to_nm_scaling: float

   :returns: * **fig** (*plt.figure.Figure*) -- Matplotlib.pyplot figure object.
             * **ax** (*plt.axes._subplots.AxesSubplot*) -- Matplotlib.pyplot axes object.















   ..
       !! processed by numpydoc !!