Number of endmember estimation application

Summary

Application for number of endmembers estimation in hyperspectral images.

Rationale

There are two classes in OTB for estimating the number of endmembers in hyperspectral images, one implementing the virtual dimensionality algorithm and the other using the Eigenvalue Likelihood Maximization algorithm, but there are no application corresponding to these algorithm.

This MR adds an application for the endmember number estimation. The application will first compute the covariance and correlation matrices of the input image using a otb::StreamingStatisticsVectorImageFilter and then use a EigenvalueLikelihoodMaximisation or a VirtualDimensionality object with the computed statistics to output an estimation of the number of endmembers.

Implementation Details

Classes and files

New file otbEndmemberNumberEstimation.cxx where the new application is implemented.

Applications

A new application has been created : EndmemberNumberEstimation, it has the following parameters :

• in : input multi-channel image
• number: number of endmembers
• algo : chosen algorithm
  • elm : eigenvalue likelihood maximization
  • vd : virtual dimensionality
• algo.vd.far : false alarm rate for the virtual dimensionality algorithm.
• ram : ram parameter

Tests

New validation tests for both algorithms.

Copyright

The copyright owner is CNES and has signed the ORFEO ToolBox Contributor License Agreement.

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Check before merging:

• All discussions are resolved
• At least 2 votes from core developers, no vote.
• The feature branch is (reasonably) up-to-date with the base branch
• Dashboard is green
• Copyright owner has signed the ORFEO ToolBox Contributor License Agreement

changed the description

Suggestions:

• Better explain that the output is made with the parameter "number" in the documentation.

• Display the "number" value in the log. (Otherwise the application is unusable from the command line).

• Move the "number" parameter to be the second parameter (so it shows up on top in otbgui).

I agree with @poughov. You have my +1.

added 1 commit

• fd887393 - DOC: improve doc of EndmemberNumberEstimation

Compare with previous version

I pushed a commit with a few improvements to the documentation directly to the branch.

added 50 commits

• fd887393...734a0d16 - 47 commits from branch develop
• 59cd64eb - Merge branch 'develop' into number_of_endmember_estimation
• 43a93438 - ENH: added progress reporting to the statistic estimation step
• fa5f216a - DOC: updated doc for output number parameter

Compare with previous version

added 1 commit

• c4ff6702 - DOC: moved the output parameter up in the app so it shows up on top in otbgui

Compare with previous version

I added progress reporting for the stat computation step.

@poughov I don't think we need to print the output number of endmembers, as it is done automatically when we declare a parameter as "output" ( SetParameterRole("number", Role_Output) ), this is the log from the application :

cedric@PO16088LX:~/Documents/OTB/develop_build$ bin/otbcli_EndmemberNumberEstimation -in ../otb-data/Input/Hyperspectral/synthetic/hsi_cube.tif
2019-01-14 15:12:29 (INFO): Default RAM limit for OTB is 128 MB
2019-01-14 15:12:29 (INFO): GDAL maximum cache size is 794 MB
2019-01-14 15:12:29 (INFO): OTB will use at most 12 threads
2019-01-14 15:12:29 (INFO): No kwl metadata found in file ../otb-data/Input/Hyperspectral/synthetic/hsi_cube.tif
2019-01-14 15:12:29 (INFO): Computing statistics on input image...
2019-01-14 15:12:29 (INFO): Estimated memory for full processing: 17.0898MB (avail.: 128 MB), optimal image partitioning: 1 blocks
2019-01-14 15:12:29 (INFO): Estimation will be performed in 1 blocks of 100x100 pixels
Statistic estimation step: 100% [**************************************************] (1s)
2019-01-14 15:12:31 (INFO): Estimation algorithm: Eigenvalue Likelihood Maximization.
Output parameters value:
number: 5

ok!

This can be merged because:

• Cookbuild error is fixed by !346 (merged)
• SIFTKeyPoint test is irrelevant !345 (merged)

mentioned in commit 73406694

merged