
Utility
=======


NestedLists
-----------

``nested_list_to_image``
````````````````````````

``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex] **nested_list_to_image** (object *nested_list*, ``Choice`` [ONEBIT|GREYSCALE|GREY16|RGB|FLOAT] *image_type*)


:Returns: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
:Category: Utility/NestedLists
:Defined in: image_utilities.py
:Author: Michael Droettboom and Karl MacMillan


Converts a nested Python list to an Image.  Is the inverse of
``to_nested_list``.

*nested_list*
  A nested Python list in row-major order.  If the list is a flat list,
  an image with a single row will be created.

*image_type*
  The resulting image type.  Should be one of the integer Image type
  constants (ONEBIT, GREYSCALE, GREY16, RGB, FLOAT).  If image_type
  is not provided or less than 0, the image type will be determined
  by auto-detection from the list.  The following list shows the mapping
  from Python type to image type:

  - int -> GREYSCALE
  - float -> FLOAT
  - RGBPixel -> RGB

To obtain other image types, the type number must be explicitly passed.

NOTE: This will not scale very well and should only be used
for small images, such as convolution kernels.

Examples:

.. code:: Python

  # Sobel kernel (implicitly will be a FLOAT image)
  kernel = nested_list_to_image([[0.125, 0.0, -0.125],
                                 [0.25 , 0.0, -0.25 ],
                                 [0.125, 0.0, -0.125]])

  # Single row image (note that nesting is optional)
  image = nested_list_to_image([RGBPixel(255, 0, 0),
                                RGBPixel(0, 255, 0),
                                RGBPixel(0, 0, 255)])


``to_nested_list``
``````````````````

object **to_nested_list** ()


:Operates on: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
:Returns: object
:Category: Utility/NestedLists
:Defined in: image_utilities.py
:Author: Michael Droettboom and Karl MacMillan


Converts an image to a nested Python list.
This method is the inverse of ``nested_list_to_image``.

The following table describes how each image type is converted to
Python types:

  - ONEBIT -> int
  - GREYSCALE -> int
  - GREY16 -> int
  - RGB -> RGBPixel
  - FLOAT -> float

NOTE: This will not scale very well and should only be used for
small images, such as convolution kernels.

----------

**Example 1:** to_nested_list()

..  image:: images/OneBit_generic.png
   :height: 99
   :width: 69

*result* = [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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``clip_image``
--------------

``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex] **clip_image** (``Rect`` *other*)


:Operates on: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
:Returns: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
:Category: Utility
:Defined in: image_utilities.py
:Author: Michael Droettboom and Karl MacMillan


Crops an image so that the bounding box includes only the
intersection of it and another image.  Returns a zero-sized image
if the two images do not intersect.


``diff_images``
---------------

``Image`` [RGB] **diff_images** (``Image`` [OneBit] *None*)


:Operates on: ``Image`` [OneBit]
:Returns: ``Image`` [RGB]
:Category: Utility
:Defined in: image_utilities.py
:Author: Michael Droettboom and Karl MacMillan


Returns a color image representing the difference of two images
following the conventions of a number of Unix diff visualization
tools, such as CVS web.  Pixels in both images are black.  Pixels
in 'self' but not in the given image ("deleted" pixels) are red.
Pixels in the given image but not in self ("inserted" pixels)
are green.


``generate_features``
---------------------

**generate_features** (list *features*, ``bool`` *force*)


:Operates on: ``Image`` [OneBit]
:Category: Utility
:Defined in: features.py
:Author: Michael Droettboom and Karl MacMillan


Generates features for the image by calling a number of feature
functions and storing the results in the image's ``features``
member variable (a Python ``array``).

*features*
  Optional.  A list of feature function names.  If not given, the
  previously set feature functions will be used.  If none were
  previously given, all available feature functions will be used.
  Using all feature functions can also be forced by passing
  ``'all'``.

.. warning:: For efficiency, if the given feature functions match
   those that have been already generated for the image, the
   features are *not* recalculated.  If you want to force
   recalculation, pass the optional argument ``force=True``.


``image_copy``
--------------

``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex] **image_copy** (``Choice`` [DENSE|RLE] *storage_format*)


:Operates on: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
:Returns: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
:Category: Utility
:Defined in: image_utilities.py
:Author: Michael Droettboom and Karl MacMillan


Copies an image along with all of its underlying data.  Since the data is
copied, changes to the new image do not affect the original image.

*storage_format*
  specifies the compression type for the returned copy:

DENSE (0)
  no compression
RLE (1)
  run-length encoding compression


``image_save``
--------------

**image_save** (``FileSave`` *image_file_name*, ``Choice`` [TIFF|PNG] *File format*)


:Operates on: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
:Category: Utility
:Defined in: image_utilities.py
:Author: Michael Droettboom and Karl MacMillan


Saves an image to file with specified name and format.


``mirror_horizontal``
---------------------

**mirror_horizontal** ()


:Operates on: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
:Category: Utility
:Defined in: image_utilities.py
:Author: Michael Droettboom and Karl MacMillan


Flips the image across the horizontal (*x*) axis.

----------

**Example 1:** mirror_horizontal()

..  image:: images/RGB_generic.png
   :height: 129
   :width: 227

..  image:: images/mirror_horizontal_plugin_00.png
   :height: 129
   :width: 227



``mirror_vertical``
-------------------

**mirror_vertical** ()


:Operates on: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
:Category: Utility
:Defined in: image_utilities.py
:Author: Michael Droettboom and Karl MacMillan


Flips the image across the vertical (*y*) axis.

----------

**Example 1:** mirror_vertical()

..  image:: images/RGB_generic.png
   :height: 129
   :width: 227

..  image:: images/mirror_vertical_plugin_00.png
   :height: 129
   :width: 227



``mse``
-------

float **mse** (``Image`` [RGB] *None*)


:Operates on: ``Image`` [RGB]
:Returns: float
:Category: Utility
:Defined in: image_utilities.py
:Author: Michael Droettboom and Karl MacMillan


Calculates the mean square error between two images.


``pad_image``
-------------

``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex] **pad_image** (int *top*, int *right*, int *bottom*, int *left*, Pixel *value*)


:Operates on: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
:Returns: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
:Category: Utility
:Defined in: image_utilities.py
:Author: Michael Droettboom and Karl MacMillan


Pads an image with any value.

*top*
  Padding on the top.

*right*
  Padding on the right.

*bottom*
  Padding on the bottom.

*left*
  Padding on the left.

*value*
  A pixel value.  This value may be any value the pixel type can support.

----------

**Example 1:** pad_image(5, 10, 15, 20)

..  image:: images/RGB_generic.png
   :height: 129
   :width: 227

..  image:: images/pad_image_plugin_00.png
   :height: 149
   :width: 257



``pad_image_default``
---------------------

``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex] **pad_image_default** (``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex] *None*, int *top*, int *right*, int *bottom*, int *left*)


:Returns: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
:Category: Utility
:Defined in: image_utilities.py
:Author: Michael Droettboom and Karl MacMillan

.. warning:: No documentation written.



``reset_onebit_image``
----------------------

**reset_onebit_image** ()


:Operates on: ``Image`` [OneBit]
:Category: Utility
:Defined in: image_utilities.py
:Author: Christoph Dalitz


Resets all black pixel values in a onebit image to one.  This
can be necessary e.g. after a CC analysis which sets black
pixels to some other label value.


``resize``
----------

``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex] **resize** (``Dim`` *dim*, ``Choice`` [None|Linear|Spline] *interp_type*)


:Operates on: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
:Returns: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
:Category: Utility
:Defined in: image_utilities.py
:Author: Michael Droettboom and Karl MacMillan


Returns a resized copy of an image. In addition to size, the type
of interpolation can be specified, with a tradeoff between speed
and quality.

If you need to maintain the aspect ratio of the original image,
consider using scale_ instead.

*dim*
  The size of the resulting image.

*interp_type* [None|Linear|Spline]
  The type of interpolation used to resize the image.  Each option
  is progressively higher quality, yet slower.

.. _scale: #scale


``scale``
---------

``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex] **scale** (float *scaling*, ``Choice`` [None|Linear|Spline] *interp_type*)


:Operates on: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
:Returns: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
:Category: Utility
:Defined in: image_utilities.py
:Author: Michael Droettboom and Karl MacMillan


Returns a scaled copy of the image. In addition to scale, the type
of interpolation can be specified, with a tradeoff between speed
and quality.

If you need to change the aspect ratio of the original image,
consider using resize_ instead.

*scale*
  A scaling factor.  Values greater than 1 will result in a larger image.
  Values less than 1 will result in a smaller image.

*interp_type* [None|Linear|Spline]
  The type of interpolation used to resize the image.  Each option is
  progressively higher quality, yet slower.

.. _resize: #resize

----------

**Example 1:** scale(0.5, 2)

..  image:: images/RGB_generic.png
   :height: 129
   :width: 227

..  image:: images/scale_plugin_00.png
   :height: 64
   :width: 113

**Example 2:** scale(2.0, 2)

..  image:: images/RGB_generic.png
   :height: 129
   :width: 227

..  image:: images/scale_plugin_01.png
   :height: 259
   :width: 455



``subimage``
------------

``bool`` **subimage** (``Point`` *upper_left*, ``Point`` *lower_right*)


:Operates on: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
:Returns: ``bool``
:Category: Utility
:Defined in: plugin.py
:Author: Michael Droettboom and Karl MacMillan


Creates a new view on existing data.

There are a number of ways to create a subimage:

   - subimage(Point *upper_left*, Point *lower_right*)
      
   - subimage(Point *upper_left*, Size *size*)

   - subimage(Point *upper_left*, Dim *dim*)

   - subimage(Rect *rectangle*)

Changes to subimages will affect all other subimages viewing the same data.


