MorphologicalProfilesAnalysis - Morphological Profiles Analysis
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Performs morphological profiles analysis on an input image channel.

Detailed description
--------------------

This algorithm is derived from the following publication:

Martino Pesaresi and Jon Alti Benediktsson, Member, IEEE: A new approach
for the morphological segmentation of high resolution satellite imagery.
IEEE Transactions on geoscience and remote sensing, vol. 39, NO. 2,
February 2001, p. 309-320.

Depending of the profile selection, the application provides::

- The multi scale geodesic morphological opening or closing profile of the input image.
- The multi scale derivative of the opening or closing profile.
- The parameter (called characteristic) of the maximum derivative value of the multi scale closing or opening profile for which this maxima occurs.
- The labeled classification of the input image.

The behavior of the classification is :

Given :math:`x_1` and :math:`x_2` two membership values,
:math:`L_1, L_2` two labels associated, and :math:`\sigma` a tolerance
value, the following decision rule is applied:

:math:`L = \begin{cases}  L_{1} & : x_{1}>x_{2} \quad and \quad x_{1}>\sigma \\ L_{2} & : x_{2}>x_{1} \quad and \quad x_{2}>\sigma \\ 0   & : otherwise. \end{cases}` 

The output image can be :- A :math:`N` multi band image for the opening/closing normal or derivative profiles.
- A mono band image for the opening/closing characteristics.
- A labeled image for the classification.

Parameters
----------

This section describes in details the parameters available for this application. Table [#]_ presents a summary of these parameters and the parameters keys to be used in command-line and programming languages. Application key is *MorphologicalProfilesAnalysis* .

.. [#] Table: Parameters table for Morphological Profiles Analysis.

+------------------------------+----------------------------------+--------------------------+
|Parameter Key                 |Parameter Name                    |Parameter Type            |
+==============================+==================================+==========================+
|in                            |Input Image                       |Input image               |
+------------------------------+----------------------------------+--------------------------+
|out                           |Output Image                      |Output image              |
+------------------------------+----------------------------------+--------------------------+
|channel                       |Selected Channel                  |Int                       |
+------------------------------+----------------------------------+--------------------------+
|ram                           |Available RAM (Mb)                |Int                       |
+------------------------------+----------------------------------+--------------------------+
|structype                     |Structuring Element Type          |Choices                   |
+------------------------------+----------------------------------+--------------------------+
|structype ball                |Ball                              | *Choice*                 |
+------------------------------+----------------------------------+--------------------------+
|structype cross               |Cross                             | *Choice*                 |
+------------------------------+----------------------------------+--------------------------+
|size                          |Profile Size                      |Int                       |
+------------------------------+----------------------------------+--------------------------+
|radius                        |Initial radius                    |Int                       |
+------------------------------+----------------------------------+--------------------------+
|step                          |Radius step.                      |Int                       |
+------------------------------+----------------------------------+--------------------------+
|profile                       |Profile                           |Choices                   |
+------------------------------+----------------------------------+--------------------------+
|profile opening               |opening                           | *Choice*                 |
+------------------------------+----------------------------------+--------------------------+
|profile closing               |closing                           | *Choice*                 |
+------------------------------+----------------------------------+--------------------------+
|profile derivativeopening     |derivativeopening                 | *Choice*                 |
+------------------------------+----------------------------------+--------------------------+
|profile derivativeclosing     |derivativeclosing                 | *Choice*                 |
+------------------------------+----------------------------------+--------------------------+
|profile openingcharacteristics|openingcharacteristics            | *Choice*                 |
+------------------------------+----------------------------------+--------------------------+
|profile closingcharacteristics|closingcharacteristics            | *Choice*                 |
+------------------------------+----------------------------------+--------------------------+
|profile classification        |classification                    | *Choice*                 |
+------------------------------+----------------------------------+--------------------------+
|profile.classification.sigma  |Sigma value for leveling tolerance|Float                     |
+------------------------------+----------------------------------+--------------------------+
|inxml                         |Load otb application from xml file|XML input parameters file |
+------------------------------+----------------------------------+--------------------------+
|outxml                        |Save otb application to xml file  |XML output parameters file|
+------------------------------+----------------------------------+--------------------------+

**Input Image**: The input image.

**Output Image**: The output image.

**Selected Channel**: The selected channel index for input image.

**Available RAM (Mb)**: Available memory for processing (in MB).

**Structuring Element Type**: Choice of the structuring element type. Available choices are: 

- **Ball**
- **Cross**

**Profile Size**: Size of the profiles.

**Initial radius**: Initial radius of the structuring element (in pixels).

**Radius step.**: Radius step along the profile (in pixels).

**Profile** Available choices are: 

- **opening**
- **closing**
- **derivativeopening**
- **derivativeclosing**
- **openingcharacteristics**
- **closingcharacteristics**
- **classification**

 * **Sigma value for leveling tolerance**: Sigma value for leveling tolerance.


**Load otb application from xml file**: Load otb application from xml file.

**Save otb application to xml file**: Save otb application to xml file.



Example
-------

To run this example in command-line, use the following: 
::

	otbcli_MorphologicalProfilesAnalysis -in ROI_IKO_PAN_LesHalles.tif -channel 1 -structype ball -profile classification -size 5 -radius 1 -step 1 -profile.classification.sigma 1 -out output.tif

To run this example from Python, use the following code snippet: 

::

	#!/usr/bin/python

	# Import the otb applications package
	import otbApplication

	# The following line creates an instance of the MorphologicalProfilesAnalysis application 
	MorphologicalProfilesAnalysis = otbApplication.Registry.CreateApplication("MorphologicalProfilesAnalysis")

	# The following lines set all the application parameters:
	MorphologicalProfilesAnalysis.SetParameterString("in", "ROI_IKO_PAN_LesHalles.tif")

	MorphologicalProfilesAnalysis.SetParameterInt("channel", 1)

	MorphologicalProfilesAnalysis.SetParameterString("structype","ball")

	MorphologicalProfilesAnalysis.SetParameterString("profile","classification")

	MorphologicalProfilesAnalysis.SetParameterInt("size", 5)

	MorphologicalProfilesAnalysis.SetParameterInt("radius", 1)

	MorphologicalProfilesAnalysis.SetParameterInt("step", 1)

	MorphologicalProfilesAnalysis.SetParameterFloat("profile.classification.sigma", 1)

	MorphologicalProfilesAnalysis.SetParameterString("out", "output.tif")

	# The following line execute the application
	MorphologicalProfilesAnalysis.ExecuteAndWriteOutput()

Limitations
~~~~~~~~~~~

Generation of the morphological profile is not streamable, pay attention to this fact when setting the radius initial size and step of the structuring element.

Authors
~~~~~~~

This application has been written by OTB-Team.

See Also
~~~~~~~~

These additional resources can be useful for further information: 
  | otbMorphologicalOpeningProfileFilter, otbMorphologicalClosingProfileFilter, otbProfileToProfileDerivativeFilter, otbProfileDerivativeToMultiScaleCharacteristicsFilter, otbMultiScaleConvexOrConcaveClassificationFilter, classes