View source for Request for Changes-1: Read, Write and manage no-data flags in Orfeo ToolBox

=== Status === 

* Author: Julien Michel
* Additional Contributors: Guillaume Pasero
* Submitted on 17.09.2015
* Proposed target release: 5.2
<!-- * Adopted (if voted for), Rejected (if voted against), Merged in OTB x.y (if merged) -->
* Git branch: https://git.orfeo-toolbox.org/otb.git/shortlog/refs/heads/rfc-7-backend

=== Summary ===

This Request for Changes implements reading no data flags to the Image MetaDataDictionary and write them back if the driver supports it. Some low-level helper functions are provided to manipulate those flags, as well as filters to build a no-data mask and update the no-data value. An application allows to perform both operations.

=== Rationale ===

This will improve OTB support of no-data flags, which was very poor until now. See [http://wiki.orfeo-toolbox.org/index.php/Requests_for_Comments-7_Better_support_of_no_data_in_Orfeo_ToolBox Request for Comments 7].

=== Implementation details ===

Note that gdal no-data flags consist in, for each channel:
* A boolean flag to tell if a no-data value exists for this channel
* A value to be used as no-data

Implementation proposed in this Request for Changes reflects this (support setup for each channel separately). Internally, flags are managed through a std::vector<bool> and values through a std::vector<double>.

Note that filters and applications also have an option to consider NaN values as no-data as well.

==== Classes and files ====

* Module Adapters/OSSIMAdapters:
** otb::MetaDataKey: Add key for no-data available and no-data values MetaData
* Module IO/IOGDAL:
** GdalImageIO: Read/Write no-data values and flags from/to MetaDataDictionary.
* Module Core/Metadata:
** Adding NoDataHelper.cxx and .h files containing functions to help no-data flag manipulation (import/export flags from/to MetaDataDictionary, test a pixel for no-data, update no-data in a pixel)
** Add a method ot ImageMetadataInterfaceBase to get the no-data flags
* Filtering/ImageManipulation:
** Add a ImageToNoDataMaskFilter, which outputs a mask of pixel containg no-data
** Add a ChangeNoDataValueFilter, which allows to change the no-data value in an image (update MetaDataDictionary and Image content)

==== Applications ==== 

* In Applications/AppImageUtils, the ReadImageInfo application has been modified to output no-data flags and values
* In Applications/AppImageUtils, the ManageNoData application has been created. It allows to :
** Create a mask of pixels containing no-data values using the ImageToNoDataMaskFilter
** Update the no-data value (only a single value is supported for all channels) using the ChangeNoDataValueFilter

==== Tests ====
[http://dash.orfeo-toolbox.org/buildSummary.php?buildid=200392 Branch is tested on the dashboard]

The following tests have been added:
* Core/Metadata/test/otbNoDataHelperTest.cxx
** Tests the funcions in otbNoDataHelper.h
** Does not require any input or baseline data
** [http://dash.orfeo-toolbox.org/testSummary.php?project=3&name=coreMetaDataNoDataHelperTest&date=2015-09-17 Test passes as of today]
* ImageManipulation/test/otbImageToNoDataMaskFilter.cxx
** Tests the ImageToNoDataMaskFilter class
** Does not require any input or baseline data
** [http://dash.orfeo-toolbox.org/testSummary.php?project=3&name=filteringImageManipulationImageToNoDataMaskFilter&date=2015-09-17 Test passes as of today]
* Filtering/ImageManipulation/test/otbChangeNoDataValueFilter.cxx
** Test the ChangeNoDataValueFilter class
** Does not require any input or baseline data
** [http://dash.orfeo-toolbox.org/testSummary.php?project=3&name=filteringImageManipulationChangeNoDataValueFilter&date=2015-09-17 Test passes as of today]

==== Documentation ====
* Doxygen documentation added for ChangeNoDataValueFilter, ImageToNoDataMaskFilter, new methods in ImageMetadataInterfaceBase, functions in otbNoDataHelper.h
* Application documentation completed.

=== Additional notes ===

Application ManageNoData is not tested per se. Testing it would require to add an image with no-data flags in OTB-Data/Input.