From b10f60c06db3944d496bac0a1b7347269d54cd3f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?C=C3=A9dric=20Traizet?= <cedric.traizet@c-s.fr>
Date: Tue, 18 Dec 2018 11:06:45 +0100
Subject: [PATCH] ENH: removed deprecated app Convert
---
.../AppImageUtils/app/CMakeLists.txt | 6 -
.../AppImageUtils/app/otbConvert.cxx | 528 ------------------
2 files changed, 534 deletions(-)
delete mode 100644 Modules/Applications/AppImageUtils/app/otbConvert.cxx
diff --git a/Modules/Applications/AppImageUtils/app/CMakeLists.txt b/Modules/Applications/AppImageUtils/app/CMakeLists.txt
index e89f03ee6f..b3834d621c 100644
--- a/Modules/Applications/AppImageUtils/app/CMakeLists.txt
+++ b/Modules/Applications/AppImageUtils/app/CMakeLists.txt
@@ -23,12 +23,6 @@ otb_create_application(
SOURCES otbDownloadSRTMTiles.cxx
LINK_LIBRARIES ${${otb-module}_LIBRARIES})
-
-otb_create_application(
- NAME Convert
- SOURCES otbConvert.cxx
- LINK_LIBRARIES ${${otb-module}_LIBRARIES})
-
otb_create_application(
NAME PixelValue
SOURCES otbPixelValue.cxx
diff --git a/Modules/Applications/AppImageUtils/app/otbConvert.cxx b/Modules/Applications/AppImageUtils/app/otbConvert.cxx
deleted file mode 100644
index 41619d0991..0000000000
--- a/Modules/Applications/AppImageUtils/app/otbConvert.cxx
+++ /dev/null
@@ -1,528 +0,0 @@
-/*
- * Copyright (C) 2005-2017 Centre National d'Etudes Spatiales (CNES)
- *
- * This file is part of Orfeo Toolbox
- *
- * https://www.orfeo-toolbox.org/
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include <numeric>
-
-#include "otbWrapperApplication.h"
-#include "otbWrapperApplicationFactory.h"
-
-#include "otbVectorRescaleIntensityImageFilter.h"
-#include "otbUnaryImageFunctorWithVectorImageFilter.h"
-#include "otbStreamingShrinkImageFilter.h"
-#include "itkListSample.h"
-#include "otbListSampleToHistogramListGenerator.h"
-#include "itkImageRegionConstIterator.h"
-
-#include "otbImageListToVectorImageFilter.h"
-#include "otbMultiToMonoChannelExtractROI.h"
-#include "otbImageList.h"
-
-namespace otb
-{
-namespace Wrapper
-{
-
-namespace Functor
-{
-template< class TScalar >
-class ITK_EXPORT LogFunctor
-{
-public:
- LogFunctor(){};
- ~LogFunctor(){};
- TScalar operator() (const TScalar& v) const
- {
- return std::log(v);
- }
-};
-} // end namespace Functor
-
-
-class Convert : public Application
-{
-public:
- /** Standard class typedefs. */
- typedef Convert Self;
- typedef Application Superclass;
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
-
- /** Standard macro */
- itkNewMacro(Self);
-
- itkTypeMacro(Convert, otb::Application);
-
- /** Filters typedef */
- typedef itk::Statistics::ListSample<FloatVectorImageType::PixelType> ListSampleType;
- typedef itk::Statistics::DenseFrequencyContainer2 DFContainerType;
- typedef ListSampleToHistogramListGenerator<ListSampleType,
- FloatVectorImageType::InternalPixelType,
- DFContainerType> HistogramsGeneratorType;
- typedef StreamingShrinkImageFilter<FloatVectorImageType,
- FloatVectorImageType> ShrinkFilterType;
- typedef Functor::LogFunctor<FloatVectorImageType::InternalPixelType> TransferLogFunctor;
- typedef UnaryImageFunctorWithVectorImageFilter<FloatVectorImageType,
- FloatVectorImageType,
- TransferLogFunctor> TransferLogType;
-
-
-private:
-
- void DoInit() override
- {
- SetName("Convert");
- SetDescription("Convert an image to a different format, optionally rescaling the data"
- " and/or changing the pixel type.");
- // Documentation
- SetDocName("Image Conversion");
- SetDocLongDescription("This application performs an image pixel type conversion "
- "(short, ushort, uchar, int, uint, float and double types are handled). "
- "The output image is written in the specified format (ie. that corresponds "
- "to the given extension).\n The conversion can include a rescale of the data range, "
- "by default it's set from 2% to 98% of the data values. The rescale can be linear or log2. \n "
- "The choice of the output channels can be done with the extended filename, "
- "but less easy to handle. To do this, a 'channels' parameter allows you to select "
- "the desired bands at the output. There are 3 modes, the available choices are: \n"
- " * grayscale : to display mono image as standard color image \n"
- " * rgb : select 3 bands in the input image (multi-bands) \n"
- " * all : keep all bands.");
- SetDocLimitations("The application does not support complex pixel types as output.");
- SetDocAuthors("OTB-Team");
- SetDocSeeAlso("Rescale");
-
- AddDocTag(Tags::Deprecated);
- AddDocTag(Tags::Manip);
- AddDocTag("Conversion");
- AddDocTag("Image Dynamic");
-
- AddParameter(ParameterType_InputImage, "in", "Input image");
- SetParameterDescription("in", "Input image");
-
- AddParameter(ParameterType_Choice, "type", "Rescale type");
- SetParameterDescription("type", "Transfer function for the rescaling");
- AddChoice("type.none", "None");
- AddChoice("type.linear", "Linear");
- AddChoice("type.log2", "Log2");
- SetParameterString("type", "none");
-
- AddParameter(ParameterType_Float,"type.linear.gamma","Gamma correction factor");
- SetParameterDescription("type.linear.gamma","Gamma correction factor");
- SetDefaultParameterFloat("type.linear.gamma",1.0);
- MandatoryOff("type.linear.gamma");
-
- AddParameter(ParameterType_InputImage, "mask", "Input mask");
- SetParameterDescription("mask",
- "Optional mask to indicate which pixels are valid for computing the histogram quantiles. "
- "Only pixels where the mask is less than 0.5 will contribute to the histogram. "
- "The mask must have the same dimensions as the input image.");
- MandatoryOff("mask");
- DisableParameter("mask");
-
- AddParameter(ParameterType_Group,"hcp","Histogram Cutting Parameters");
- SetParameterDescription("hcp","Parameters to cut the histogram edges before rescaling");
-
- AddParameter(ParameterType_Float, "hcp.high", "High Cut Quantile");
- SetParameterDescription("hcp.high", "Quantiles to cut from histogram high values "
- "before computing min/max rescaling (in percent, 2 by default)");
- MandatoryOff("hcp.high");
- SetDefaultParameterFloat("hcp.high", 2.0);
- DisableParameter("hcp.high");
-
- AddParameter(ParameterType_Float, "hcp.low", "Low Cut Quantile");
- SetParameterDescription("hcp.low", "Quantiles to cut from histogram low values "
- "before computing min/max rescaling (in percent, 2 by default)");
- MandatoryOff("hcp.low");
- SetDefaultParameterFloat("hcp.low", 2.0);
- DisableParameter("hcp.low");
-
- AddParameter(ParameterType_OutputImage, "out", "Output Image");
- SetParameterDescription("out", "Output image");
- SetDefaultOutputPixelType("out",ImagePixelType_uint8);
-
- AddParameter(ParameterType_Choice, "channels", "Channels selection");
- SetParameterDescription("channels", "It's possible to select the channels "
- "of the output image. There are 3 modes, the available choices are:");
-
- AddChoice("channels.all", "Default mode");
- SetParameterDescription("channels.all", "Select all bands in the input image, (1,...,n).");
-
- AddChoice("channels.grayscale", "Grayscale mode");
- SetParameterDescription("channels.grayscale", "Display single channel as standard color image.");
- AddParameter(ParameterType_Int, "channels.grayscale.channel", "Grayscale channel");
- SetDefaultParameterInt("channels.grayscale.channel", 1);
- SetMinimumParameterIntValue("channels.grayscale.channel", 1);
-
- AddChoice("channels.rgb", "RGB composition");
- SetParameterDescription("channels.rgb", "Select 3 bands in the input image "
- "(multi-bands), by default (1,2,3).");
-
- AddParameter(ParameterType_Int, "channels.rgb.red", "Red Channel");
- SetParameterDescription("channels.rgb.red", "Red channel index.");
- SetMinimumParameterIntValue("channels.rgb.red", 1);
- AddParameter(ParameterType_Int, "channels.rgb.green", "Green Channel");
- SetParameterDescription("channels.rgb.green", "Green channel index.");
- SetMinimumParameterIntValue("channels.rgb.green", 1);
- AddParameter(ParameterType_Int, "channels.rgb.blue", "Blue Channel");
- SetParameterDescription("channels.rgb.blue", "Blue channel index.");
- SetMinimumParameterIntValue("channels.rgb.blue", 1);
-
- AddRAMParameter();
-
- // Doc example parameter settings
- SetDocExampleParameterValue("in", "QB_Toulouse_Ortho_XS.tif");
- SetDocExampleParameterValue("out", "otbConvertWithScalingOutput.png");
- SetDocExampleParameterValue("type", "linear");
- SetDocExampleParameterValue("channels", "rgb");
-
- SetOfficialDocLink();
- }
-
- void DoUpdateParameters() override
- {
- // Read information
- if ( HasValue("in") )
- {
- typedef otb::ImageMetadataInterfaceBase ImageMetadataInterfaceType;
- ImageMetadataInterfaceType::Pointer metadataInterface =
- ImageMetadataInterfaceFactory::CreateIMI(GetParameterImage("in")->GetMetaDataDictionary());
-
- int nbBand = GetParameterImage("in")->GetNumberOfComponentsPerPixel();
- SetMaximumParameterIntValue("channels.grayscale.channel", nbBand);
- SetMaximumParameterIntValue("channels.rgb.red", nbBand);
- SetMaximumParameterIntValue("channels.rgb.green", nbBand);
- SetMaximumParameterIntValue("channels.rgb.blue", nbBand);
-
- if (nbBand > 1)
- {
- // get band index : Red/Green/Blue
- int bandRed = metadataInterface->GetDefaultDisplay()[0] + 1;
- int bandGreen = metadataInterface->GetDefaultDisplay()[1] + 1;
- int bandBlue = metadataInterface->GetDefaultDisplay()[2] + 1;
- SetDefaultParameterInt("channels.rgb.red", bandRed);
- SetDefaultParameterInt("channels.rgb.green", bandGreen);
- SetDefaultParameterInt("channels.rgb.blue", bandBlue);
- }
- }
-
-
- }
-
- template<class TImageType>
- void GenericDoExecute()
- {
-
- // Clear previously registered filters
- m_Filters.clear();
-
- std::string rescaleType = this->GetParameterString("type");
-
- if( (rescaleType != "none") && (rescaleType != "linear") && (rescaleType != "log2") )
- {
- itkExceptionMacro("Unknown rescale type "<<rescaleType<<".");
- }
-
- if( rescaleType == "none" )
- {
- // selected channel
- typename TImageType::Pointer tempImage;
- tempImage = GetSelectedChannels<TImageType>();
-
- SetParameterOutputImage<TImageType>("out", tempImage);
-
- }
- else // linear or log2
- {
- FloatVectorImageType::Pointer mask;
-
- if (IsParameterEnabled("mask")) mask = this->GetParameterImage("mask");
-
- // selected channel
- typename FloatVectorImageType::Pointer tempImage;
- tempImage = GetSelectedChannels<FloatVectorImageType>();
-
- const unsigned int nbComp(tempImage->GetNumberOfComponentsPerPixel());
-
- typedef otb::VectorRescaleIntensityImageFilter<FloatVectorImageType, TImageType> RescalerType;
- typename TImageType::PixelType minimum;
- typename TImageType::PixelType maximum;
- minimum.SetSize(nbComp);
- maximum.SetSize(nbComp);
- minimum.Fill( itk::NumericTraits<typename TImageType::InternalPixelType>::min() );
- maximum.Fill( itk::NumericTraits<typename TImageType::InternalPixelType>::max() );
-
- typename RescalerType::Pointer rescaler = RescalerType::New();
-
- rescaler->SetOutputMinimum(minimum);
- rescaler->SetOutputMaximum(maximum);
-
- // We need to subsample the input image in order to estimate its
- // histogram
-
- typename ShrinkFilterType::Pointer shrinkFilter = ShrinkFilterType::New();
-
- // Shrink factor is computed so as to load a quicklook of 1000
- // pixels square at most
- typename FloatVectorImageType::SizeType imageSize = tempImage->GetLargestPossibleRegion().GetSize();
- unsigned int shrinkFactor =
- std::max(imageSize[0], imageSize[1]) < 1000 ? 1 : std::max(imageSize[0], imageSize[1])/1000;
-
- otbAppLogDEBUG( << "Shrink factor used to compute Min/Max: "<<shrinkFactor );
-
- otbAppLogDEBUG( << "Shrink starts..." );
-
- shrinkFilter->SetShrinkFactor(shrinkFactor);
- shrinkFilter->GetStreamer()->SetAutomaticAdaptativeStreaming(GetParameterInt("ram"));
- AddProcess(shrinkFilter->GetStreamer(), "Computing shrink Image for min/max estimation...");
-
- if ( rescaleType == "log2")
- {
- //define the transfer log
- m_TransferLog = TransferLogType::New();
- m_TransferLog->SetInput(tempImage);
- m_TransferLog->UpdateOutputInformation();
-
- shrinkFilter->SetInput(m_TransferLog->GetOutput());
- rescaler->SetInput(m_TransferLog->GetOutput());
- shrinkFilter->Update();
- }
- else
- {
- shrinkFilter->SetInput(tempImage);
- rescaler->SetInput(tempImage);
- shrinkFilter->Update();
- }
-
- ShrinkFilterType::Pointer maskShrinkFilter = ShrinkFilterType::New();
-
- otbAppLogDEBUG( << "Evaluating input Min/Max..." );
- itk::ImageRegionConstIterator<FloatVectorImageType>
- it(shrinkFilter->GetOutput(), shrinkFilter->GetOutput()->GetLargestPossibleRegion());
- itk::ImageRegionConstIterator<FloatVectorImageType> itMask;
-
- typename ListSampleType::Pointer listSample = ListSampleType::New();
- listSample->SetMeasurementVectorSize(tempImage->GetNumberOfComponentsPerPixel());
-
- // Now we generate the list of samples
- if (IsParameterEnabled("mask"))
- {
- maskShrinkFilter->SetShrinkFactor(shrinkFactor);
- maskShrinkFilter->SetInput(mask);
- maskShrinkFilter->GetStreamer()->SetAutomaticAdaptativeStreaming(GetParameterInt("ram"));
- maskShrinkFilter->Update();
-
- itMask = itk::ImageRegionConstIterator<FloatVectorImageType>(
- maskShrinkFilter->GetOutput(),maskShrinkFilter->GetOutput()->GetLargestPossibleRegion());
-
- // Remove masked pixels
- it.GoToBegin();
- itMask.GoToBegin();
- while (!it.IsAtEnd())
- {
- // float values, so the threshold is set to 0.5
- if (itMask.Get()[0] < 0.5)
- {
- listSample->PushBack(it.Get());
- }
- ++it;
- ++itMask;
- }
- if (listSample->Size() == 0)
- {
- otbAppLogINFO( << "All pixels were masked, the application assume a wrong mask "
- "and include all the image");
- }
- }
-
- // if mask is disable and all pixels were masked
- if ((!IsParameterEnabled("mask")) || (listSample->Size() == 0))
- {
- for(it.GoToBegin(); !it.IsAtEnd(); ++it)
- {
- listSample->PushBack(it.Get());
- }
- }
-
- // And then the histogram
- typename HistogramsGeneratorType::Pointer histogramsGenerator = HistogramsGeneratorType::New();
- histogramsGenerator->SetListSample(listSample);
- histogramsGenerator->SetNumberOfBins(255);
- histogramsGenerator->NoDataFlagOn();
- histogramsGenerator->Update();
-
- // And extract the lower and upper quantile
- typename FloatVectorImageType::PixelType inputMin(nbComp), inputMax(nbComp);
-
- auto histOutput = histogramsGenerator->GetOutput();
- assert(histOutput);
-
- for(unsigned int i = 0; i < nbComp; ++i)
- {
- auto && elm = histOutput->GetNthElement(i);
- assert(elm);
- inputMin[i] = elm->Quantile(0, 0.01 * GetParameterFloat("hcp.low"));
- inputMax[i] = elm->Quantile(0, 1.0 - 0.01 * GetParameterFloat("hcp.high"));
- }
-
- otbAppLogDEBUG( << std::setprecision(5) << "Min/Max computation done : min=" << inputMin
- << " max=" << inputMax );
-
- rescaler->AutomaticInputMinMaxComputationOff();
- rescaler->SetInputMinimum(inputMin);
- rescaler->SetInputMaximum(inputMax);
-
- if ( rescaleType == "linear")
- {
- rescaler->SetGamma(GetParameterFloat("type.linear.gamma"));
- }
-
- m_Filters.push_back(rescaler.GetPointer());
-
- SetParameterOutputImage<TImageType>("out", rescaler->GetOutput());
- }
- }
-
- // Get the bands order
- std::vector<int> GetChannels()
- {
- std::vector<int> channels;
-
- int nbChan = GetParameterImage("in")->GetNumberOfComponentsPerPixel();
- std::string channelMode = GetParameterString("channels");
-
- if(channelMode == "grayscale")
- {
- if (GetParameterInt("channels.grayscale.channel") <= nbChan)
- {
- channels = {GetParameterInt("channels.grayscale.channel"),
- GetParameterInt("channels.grayscale.channel"),
- GetParameterInt("channels.grayscale.channel")};
- }
- else
- {
- itkExceptionMacro(<< "The channel has an invalid index");
- }
- }
- else if (channelMode == "rgb")
- {
- if ((GetParameterInt("channels.rgb.red") <= nbChan)
- && ( GetParameterInt("channels.rgb.green") <= nbChan)
- && ( GetParameterInt("channels.rgb.blue") <= nbChan))
- {
- channels = {GetParameterInt("channels.rgb.red"),
- GetParameterInt("channels.rgb.green"),
- GetParameterInt("channels.rgb.blue")};
- }
- else
- {
- itkExceptionMacro(<< "At least one needed channel has an invalid index");
- }
- }
- else if (channelMode == "all")
- {
- // take all bands
- channels.resize(nbChan);
- std::iota(channels.begin(), channels.end(), 1);
- }
- return channels;
- }
-
- // return an image with the bands order modified of the input image
- template<class TImageType>
- typename TImageType::Pointer GetSelectedChannels()
- {
- typedef MultiToMonoChannelExtractROI<FloatVectorImageType::InternalPixelType,
- typename TImageType::InternalPixelType> ExtractROIFilterType;
- typedef otb::ImageList<otb::Image<typename TImageType::InternalPixelType> > ImageListType;
- typedef ImageListToVectorImageFilter<ImageListType,
- TImageType > ListConcatenerFilterType;
-
- typename ImageListType::Pointer imageList;
- typename ListConcatenerFilterType::Pointer concatener;
-
- imageList = ImageListType::New();
- concatener = ListConcatenerFilterType::New();
-
- //m_Filters.push_back(imageList.GetPointer());
- m_Filters.push_back(concatener.GetPointer());
-
- const bool monoChannel = IsParameterEnabled("channels.grayscale");
-
- // get band order
- std::vector<int> channels = GetChannels();
-
- for (auto && channel : channels)
- {
- typename ExtractROIFilterType::Pointer extractROIFilter = ExtractROIFilterType::New();
- m_Filters.push_back(extractROIFilter.GetPointer());
- extractROIFilter->SetInput(GetParameterImage("in"));
- if (!monoChannel) extractROIFilter->SetChannel(channel);
- extractROIFilter->UpdateOutputInformation();
- imageList->PushBack(extractROIFilter->GetOutput());
- }
-
- concatener->SetInput(imageList);
- concatener->UpdateOutputInformation();
-
- return concatener->GetOutput();
- }
-
-
- void DoExecute() override
- {
- switch ( this->GetParameterOutputImagePixelType("out") )
- {
- case ImagePixelType_uint8:
- GenericDoExecute<UInt8VectorImageType>();
- break;
- case ImagePixelType_int16:
- GenericDoExecute<Int16VectorImageType>();
- break;
- case ImagePixelType_uint16:
- GenericDoExecute<UInt16VectorImageType>();
- break;
- case ImagePixelType_int32:
- GenericDoExecute<Int32VectorImageType>();
- break;
- case ImagePixelType_uint32:
- GenericDoExecute<UInt32VectorImageType>();
- break;
- case ImagePixelType_float:
- GenericDoExecute<FloatVectorImageType>();
- break;
- case ImagePixelType_double:
- GenericDoExecute<DoubleVectorImageType>();
- break;
- default:
- itkExceptionMacro("Unknown pixel type " << this->GetParameterOutputImagePixelType("out") <<"." << std::endl
- << "The Convert application does not support complex pixel type as output." << std::endl
- << "You can use instead the ExtractROI application to perform complex image conversion.");
- break;
- }
- }
-
- TransferLogType::Pointer m_TransferLog;
- std::vector<itk::LightObject::Pointer> m_Filters;
-};
-
-}
-}
-
-OTB_APPLICATION_EXPORT(otb::Wrapper::Convert)
-
--
GitLab