Cannot find CompositePreprocessing in the list of OTB Apps #1
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Hi, Thanks for trying out WASP - And sorry for causing problems :) I will try to help. And if not, could you please try to open a terminal, and run: Kind regards, |
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Hello Thanks for your quick answer. Do not worry, I tend to stumble with anything. Is true that in the VM might be another installation of OTB, as is the one I use to run MAJA. However, when I run
When I run
In case it was useful, I also ran Kind regards, |
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Hi Ignacio, I was able to reproduce the error when using another VM. I updated both the source code and the archive (now v1.1). Could you please try re-installing? Kind regards, |
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The version available on the CNES site is still v1.0, I am missing something? |
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Only the french version was updated apparently. Now the english one should be available as well. Peter |
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Hello Sorry for the delay. I made a quick test with the ubuntu subsystem. In first place I deleted the old folder , and re-created it Afterwards I performed the installation And re-run the command, obtaining the following output To try and make sure the $PATH was not part of the problem I also ran Ignacio |
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Hi Ignacio, The variable |
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Hello Peter I created and tested the script as instructed (the path is ok), getting the following output; The contents of the applications folder are: The contents of the lib folder are: Thanks a lot for your help |
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Same output as from python - This didn't help unfortuntely. If you append In any case, sorry for not being able to solve the problem with the binary package until now and for bearing with me! I will still try to solve this issue, but if you want to advance in the meantime with WASP you can compile it yourself. Kind regards, |
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Hello modified the script to read the following: When executed, it produces the following output The other command produces the following output: I am using the ubuntu subsystem of windows, mostly because VMs do weird things when a script tries to create symlinks in the host machine. However I also have a Ubuntu and a CentOS VM, so I can try and see what happens in those. Thanks a lot for your help, I whish I could help more. I do not know if I will able to compile it (I have very little experience compiling things) Kind regards, PD: to make sure there was nothing weird happening in the previous run I also tried on the centos VM, ntaining the following results: |
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Thanks again for the info. I forgot to specify that the EDIT And the path should be now appended and not reset, so all in all the script will be: Kind regards, |
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Hello Sorry for the dumb mistake. I made the changes and re-ran: Kind regards, |
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Now this is finally a trace. You seem to be missing Please run EDIT And the script containing the ldd-commands as well :) Peter |
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Hello Running the script after the installation ( For the moment it seems to work, so far it has produced the following output It has finished okay (It has artifacts, but I guess it is because I used a shorter time interval)
Kind regards, |
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Congratulations first of all, WASP technically runs ;) To follow up on your output: Maybe @olivierhagolle would like to comment on the artifacts as well. Kind regards, |
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Hi, nice, we have our first stand alone user ! Thanks Peter and Ignacio ! Most artefacts must be flagged as clouds, there is a cloud mask with the synthesis Here, a thin cirrus cloud seems to have been missed by MAJA. Using a longer period should blend it with the other cloud free dates. By the way, which version of MAJA did you use ? As said by Peter, our recommendation is a total synthesis period of 46 days. Maybe a bit longer for very cloudy regions. |
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Hello, Re-did the experiment with the recommended period and the artifacts where aminorated. There are some "haze" left, but I do not know if it is even possible to elliminate it completely... maybe I should examine a longer period than 8 days when using MAJA? (I am using version
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Hi Ignacio, I hope it's okay that I closed the issue already due to the fact that the original technical problem was resolved. Peter |
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Hello Peter Sorry for the off-topic comment, I wanted to answer to Olivier’s comment. I am aware that mountains are one the most difficult places to try this (in fact, this is from September, one of the “easy” months where there is no snow). I wanted to create monthly mosaics to characterize phenology in the context of forest type classification, so I am not sure how the classifier will cope with the cloudy pixels. I guess I will make some tests with WASP and with the algorithm of presented by Griffiths et al., 2019 to see which one fares better (they use the Haze-Optimized Transformation by Zhang et al., 2002 to identify haze and thin clouds). Yesterday I thought to try and incorporate the HOT in WASP… What do you think?. Thanks a lot for your help, |
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Hi Ignacio, That's a nice landscape you are working on ! The issue with mountains is that the cirrus detection is not as efficient as in plains, because high elevation pixels can also be seen in the 1.38 µm band, so you have to increase the detection threshold in order to avoid classifying mountains as clouds all year long. However, I have introduced a multi-temporal version of the HOT transform, and worked on a better cirrus detection in next MAJA. As MAJA 3.3 should be a bug-fix version, it will be introduced in MAJA 3.4. But something puzzles me, the fact that you want to use composites (with inaccurate observation dates), to characterize phenology, which needs accurate dates. I would recommend keeping L2A for that. Best regards, |
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Hello Olivier I guess I will try and make some tests when MAJA 3.4 comes out. Regarding the composites, I wanted to create composites to reduce a the data volume, creating 12 synthetic images to capture how forest changes along the year. The other reason was that I am also supposed to fuse S1 and S2 images. However SAR data has its own problems, like geometric distortions, 'specke' and a huge influence of the terrain or humidity, so its time series are quite noisy. David Small proposed some methods to solve these problems, one of which is creating composites, aminorating these effects, obtaining a less 'spiky' time series (if you are curious here is an example). My idea was to do something similar with S2... but, there is a better alternative? Kind regards, |
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For Land cover, syntheses should be OK, but to study phenology, I would use L2A to keep all info about phenology. This means your method will have to handle data gaps due to clouds, which can be complicated. Regarding Sentinel-1, did you try this tool ? |
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Hello Olivier Yes, In fact my supervisor already had processed the images using that program before I came to Romania:
The main problem is that what it does not consider the effect of the scattering area, nor it does mask the areas that suffer foreshortening, so the effect of the slopes is huge. However, If the effect of the slope is considered, I get something like this:
As you can see, the foreshortened areas are masked (in this case the white is NODATA), and the illumination pattern has been greatly diminished. I wish I could use it, but, as far as I know, it lacks some features that are necessary in my study area. |
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Hello Peter, Olivier, FROM centos:7 Actually, I have exactly the same error : "NameError: Cannot find CompositePreprocessing in the list of OTB Apps". As you can see in Dockerfile, mesa-libGLU-devel library is installed. EnvWasp.sh : YOUR_WASP_INSTALL_PATH=/wasp export PATH=$YOUR_WASP_INSTALL_PATH/bin:$PATH ldd $YOUR_WASP_INSTALL_PATH/lib/otbapp_CompositePreprocessing.so Thanks for your help. |
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Hi Nicolas, Thank you for your feedback. Given that this issue is related to a different environment, I propose that you create a new one indicating in the title that this is a docker issue. Other than that, the info you provided seems sufficient for me to try and recreate the problem. Once I know more, I will respond in the new issue. Kind regards, |
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Hi Peter, If you want more informations, don't hesitate. Thanks you ! Nicolas |
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Good morning
I have started making some tests with WASP by running the pre-compiled binaries in Ubuntu and in CentOS:
The content of the inputs is the following
Seeing that WASP.py was being called, I digged around a bit, adding some prints... when print(availableApplications) is called within the function "checkApplicationAvailability", it produces the following output:
['BandMath', 'BandMathX', 'BinaryMorphologicalOperation', 'BlockMatching', 'BundleToPerfectSensor', 'ClassificationMapRegularization', 'ColorMapping', 'CompareImages', 'ComputeConfusionMatrix', 'ComputeImagesStatistics', 'ComputeModulusAndPhase', 'ComputeOGRLayersFeaturesStatistics', 'ComputePolylineFeatureFromImage', 'ConcatenateImages', 'ConcatenateVectorData', 'ConnectedComponentSegmentation', 'Convert', 'ConvertCartoToGeoPoint', 'ConvertSensorToGeoPoint', 'DEMConvert', 'DSFuzzyModelEstimation', 'Despeckle', 'DimensionalityReduction', 'DisparityMapToElevationMap', 'DomainTransform', 'DownloadSRTMTiles', 'EdgeExtraction', 'ExtractROI', 'FineRegistration', 'FusionOfClassifications', 'GeneratePlyFile', 'GenerateRPCSensorModel', 'GrayScaleMorphologicalOperation', 'GridBasedImageResampling', 'HaralickTextureExtraction', 'HomologousPointsExtraction', 'HooverCompareSegmentation', 'HyperspectralUnmixing', 'ImageClassifier', 'ImageEnvelope', 'KMeansClassification', 'KmzExport', 'LSMSSegmentation', 'LSMSSmallRegionsMerging', 'LSMSVectorization', 'LargeScaleMeanShift', 'LineSegmentDetection', 'LocalStatisticExtraction', 'ManageNoData', 'MeanShiftSmoothing', 'MorphologicalClassification', 'MorphologicalMultiScaleDecomposition', 'MorphologicalProfilesAnalysis', 'MultiImageSamplingRate', 'MultiResolutionPyramid', 'MultivariateAlterationDetector', 'OGRLayerClassifier', 'OSMDownloader', 'ObtainUTMZoneFromGeoPoint', 'OpticalCalibration', 'OrthoRectification', 'Pansharpening', 'PixelValue', 'PolygonClassStatistics', 'PredictRegression', 'Quicklook', 'RadiometricIndices', 'Rasterization', 'ReadImageInfo', 'RefineSensorModel', 'Rescale', 'RigidTransformResample', 'SARCalibration', 'SARDeburst', 'SARDecompositions', 'SARPolarMatrixConvert', 'SARPolarSynth', 'SFSTextureExtraction', 'SOMClassification', 'SampleExtraction', 'SampleSelection', 'Segmentation', 'Smoothing', 'SplitImage', 'StereoFramework', 'StereoRectificationGridGenerator', 'Superimpose', 'TestApplication', 'TileFusion', 'TrainImagesClassifier', 'TrainRegression', 'TrainVectorClassifier', 'VectorClassifier', 'VectorDataDSValidation', 'VectorDataExtractROI', 'VectorDataReprojection', 'VectorDataSetField', 'VectorDataTransform', 'VertexComponentAnalysis']Where the applications that "checkApplicationAvailability" is looking for do not appear
Sorry for the inconvenience
Kind regards,
Ignacio
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