
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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``ccs_from_labeled_image``
--------------------------

[object] **ccs_from_labeled_image** ()


:Operates on: ``Image`` [OneBit]
:Returns: [object]
:Category: Utility
:Defined in: image_utilities.py
:Author: Christoph Dalitz and Hasan Yildiz


Returns all ``Cc``'s represented by unique labels in the given
onebit image. The bounding boxes are computed as tight as possible.

This is mostly useful for reading manually labeled groundtruth
data from color PNG files in combination with the plugin
colors_to_labels_. Example:

.. code:: Python

  labeled = rgb.colors_to_labels()
  ccs = labeled.ccs_from_labeled_image()

.. _colors_to_labels: color.html#colors-to-labels


``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.


``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.


``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. When no pixel value is given, the value 
corresponding to the color *white* is used.

*top*
  Padding on the top.

*right*
  Padding on the right.

*bottom*
  Padding on the bottom.

*left*
  Padding on the left.

*value*
  An optional pixel value of the pixel type of the image.
  When omitted or set to ``None``, the color white is used for padding.

----------

**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



``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.


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

``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex] **subimage** (``Point`` *upper_left*, ``Point`` *lower_right*)


:Operates on: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
:Returns: ``Image`` [OneBit|GreyScale|Grey16|RGB|Float|Complex]
: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.


``trim_image``
--------------

``Image`` [OneBit|GreyScale|Grey16|Float|RGB] **trim_image** (Pixel *PixelValue* = None)


:Operates on: ``Image`` [OneBit|GreyScale|Grey16|Float|RGB]
:Returns: ``Image`` [OneBit|GreyScale|Grey16|Float|RGB]
:Category: Utility
:Defined in: image_utilities.py
:Author: Tobias Bolten


Returns minimal view so that outside of the view only Pixels with
*PixelValue* exists. When no *PixelValue* is given, white is used.


