:mod:`neuron_morphology.snap_polygons.image_outputter`
======================================================

.. py:module:: neuron_morphology.snap_polygons.image_outputter

.. autoapi-nested-parse::

   Utilites for writing diagnostic overlay images

   ..
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Module Contents
---------------

Classes
~~~~~~~

.. autoapisummary::

   neuron_morphology.snap_polygons.image_outputter.ImageOutputter



Functions
~~~~~~~~~

.. autoapisummary::

   neuron_morphology.snap_polygons.image_outputter.write_figure
   neuron_morphology.snap_polygons.image_outputter.read_image
   neuron_morphology.snap_polygons.image_outputter.read_with_ndimage
   neuron_morphology.snap_polygons.image_outputter.read_jp2
   neuron_morphology.snap_polygons.image_outputter.fname_suffix
   neuron_morphology.snap_polygons.image_outputter.make_pathpatch


.. py:class:: ImageOutputter(native_geo: Geometries, result_geo: Geometries, image_specs: Optional[Sequence[Dict]], alpha: float = 0.4, color_cycle: Optional[Sequence] = None, savefig_kwargs: Optional[Dict] = None)

   Overlays polygons and surfaces on provided images. Writes the 
   results to files.


   :Parameters:

       **native_geo** : Layer geometries before gaps are filled
           ..

       **result_geo** : Layer geometries after gaps are filled
           ..

       **image_specs** : Each is a dictionary defining a single image. Must
           provide string keys:
               - input_path : read from here
               - output_path : write to (siblings of) this path
               - downsample : the image will be scaled by this factor in each 
                   dimension
               - overlay_types : produce these kinds of overlay for this image

       **alpha** : of the transparent overlays
           ..

       **color_cycle** : as polygon fills are drawn, cycle through these colors
           ..

       **savefig_kwargs** : Passed directly to pyplot's savefig, use to specify
           e.g dpi.














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   .. attribute:: DEFAULT_COLOR_CYCLE
      :annotation: = ['c', 'm', 'y', 'k', 'r', 'g', 'b']

      

   .. attribute:: OVERLAY_TYPES
      

      

   .. method:: _draw_geometries(self, geometries: Geometries, image: np.ndarray)

      Utility for overlaying polygons and surfaces on an image. See 
      draw_before and draw_after for more details.
















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   .. method:: draw_before(self, image: np.ndarray, scale: float = 1.0)

      Display the pre-fill polygons and surfaces overlaid on an image.


      :Parameters:

          **image** : onto which objects will be drawn
              ..

          **scale** : required to transform from object space to image space
              ..

      :Returns:

          A matplotlib figure containing the overlay
              ..













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   .. method:: draw_after(self, image: np.ndarray, scale: float = 1.0)

      Display the post-fill polygons and surfaces overlaid on an image.


      :Parameters:

          **image** : onto which objects will be drawn
              ..

          **scale** : required to transform from object space to image space
              ..

      :Returns:

          A matplotlib figure containing the overlay
              ..













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   .. method:: write_images(self)

      For each image specified in this outputter and each overlay type
      requested for that image, produce and save an overlay.
















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.. function:: write_figure(fig: plt.Figure, *args, **kwargs)

   Write a matplotlib figure without respect to the current figure.


   :Parameters:

       **fig** : the figure to be writter
           ..

       **\*args, **kwargs** : passed to plt.savefig
           ..














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.. function:: read_image(path: str, decimate: int = 1)

   Read an image. Dispatch to an appropriate library based on that 
   image's extension.


   :Parameters:

       **path** : to the image
           ..

       **decimate** : apply a decimation of this factor along each axis of the image
           ..














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.. function:: read_with_ndimage(path: str, decimate: int)

   Read (and symmetrically decimate) an image file into a numpy array
















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.. function:: read_jp2(path: str, decimate: int)

   Read (and symmetrically decimate) a jp2 file into a numpy array 
















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.. function:: fname_suffix(path: str, suffix: str)

   Utility for adding a suffix to a path string. The suffix will be 
   inserted before the extension.
















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.. function:: make_pathpatch(vertices: Sequence[Tuple[float, float]], **patch_kwargs) -> mpl.patches.PathPatch

   Utility for building a matplotlib pathpatch from an array of vertices


   :Parameters:

       **vertices** : Defines the path. May be closed or open
           ..

       **\*\*patch_kwargs** : passed directly to pathpatch constructor
           ..














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