diff --git a/Modules/Applications/AppImageUtils/app/otbDynamicConvert.cxx b/Modules/Applications/AppImageUtils/app/otbDynamicConvert.cxx
index 0a6fb3bd0de6e1260e2296c6dbc3982acec99cf6..2db1ffdb004cb6ae17b6f28a9bdb233c705d80c0 100644
--- a/Modules/Applications/AppImageUtils/app/otbDynamicConvert.cxx
+++ b/Modules/Applications/AppImageUtils/app/otbDynamicConvert.cxx
@@ -57,451 +57,451 @@ class ITK_EXPORT LogFunctor
class DynamicConvert : public Application
{
public:
- /** Standard class typedefs. */
- typedef DynamicConvert Self;
- typedef Application Superclass;
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
-
- /** Standard macro */
- itkNewMacro(Self);
-
- itkTypeMacro(DynamicConvert, 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() ITK_OVERRIDE
+ /** Standard class typedefs. */
+ typedef DynamicConvert Self;
+ typedef Application Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ /** Standard macro */
+ itkNewMacro(Self);
+
+ itkTypeMacro(DynamicConvert, 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() ITK_OVERRIDE
+ {
+ SetName("DynamicConvert");
+ SetDescription("Convert an image to a different format and rescaling the dynamic ...");
+
+ // Documentation
+ SetDocName("Dynamic Conversion");
+ // TODO
+ 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("None");
+ SetDocAuthors("OTB-Team");
+ SetDocSeeAlso("Convert, Rescale");
+
+ AddDocTag(Tags::Manip);
+ AddDocTag("Conversion");
+ AddDocTag("Image Dynamic");
+
+ AddParameter(ParameterType_InputImage, "in", "Input image");
+ SetParameterDescription("in", "Input image");
+
+ AddParameter(ParameterType_OutputImage, "out", "Output Image");
+ SetParameterDescription("out", "Output image");
+ SetDefaultOutputPixelType("out",ImagePixelType_uint8);
+
+ AddParameter(ParameterType_Choice, "type", "Rescale type");
+ SetParameterDescription("type", "Transfer function for the rescaling");
+ AddChoice("type.linear", "Linear");
+ AddChoice("type.log2", "Log2");
+ SetParameterString("type", "linear", false);
+
+ 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", "The masked pixels won't be used to adapt the dynamic "
+ "(the mask must have the same dimensions as the input image)");
+ MandatoryOff("mask");
+ DisableParameter("mask");
+
+ AddParameter(ParameterType_Group,"quantile","Histogram quantile cutting");
+ SetParameterDescription("quantile","Cut the histogram edges before rescaling");
+
+ AddParameter(ParameterType_Float, "quantile.high", "High cut quantile");
+ SetParameterDescription("quantile.high", "Quantiles to cut from histogram high values "
+ "before computing min/max rescaling (in percent, 2 by default)");
+ MandatoryOff("quantile.high");
+ SetDefaultParameterFloat("quantile.high", 2.0);
+ DisableParameter("quantile.high");
+
+ AddParameter(ParameterType_Float, "quantile.low", "Low cut quantile");
+ SetParameterDescription("quantile.low", "Quantiles to cut from histogram low values "
+ "before computing min/max rescaling (in percent, 2 by default)");
+ MandatoryOff("quantile.low");
+ SetDefaultParameterFloat("quantile.low", 2.0);
+ DisableParameter("quantile.low");
+
+ 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);
+
+ AddParameter(ParameterType_Float, "outmin", "Output min value");
+ SetDefaultParameterFloat("outmin", 0.0);
+ SetParameterDescription( "outmin", "Minimum value of the output image." );
+ AddParameter(ParameterType_Float, "outmax", "Output max value");
+ SetDefaultParameterFloat("outmax", 255.0);
+ SetParameterDescription( "outmax", "Maximum value of the output image." );
+ MandatoryOff("outmin");
+ MandatoryOff("outmax");
+
+ AddRAMParameter();
+
+ // Doc example parameter settings
+ SetDocExampleParameterValue("in", "QB_Toulouse_Ortho_XS.tif");
+ SetDocExampleParameterValue("out", "otbConvertWithScalingOutput.png");
+ SetDocExampleParameterValue("type", "linear");
+ SetDocExampleParameterValue("channels", "rgb");
+ SetDocExampleParameterValue("outmin", "0");
+ SetDocExampleParameterValue("outmax", "255");
+
+ SetOfficialDocLink();
+ }
+
+ void DoUpdateParameters() ITK_OVERRIDE
+ {
+ // Read information
+ if ( HasValue("in") )
{
- SetName("DynamicConvert");
- SetDescription("Convert an image to a different format and rescaling the dynamic ...");
-
- // Documentation
- SetDocName("Dynamic Conversion");
- // TODO
- 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("None");
- SetDocAuthors("OTB-Team");
- SetDocSeeAlso("Convert, Rescale");
-
- AddDocTag(Tags::Manip);
- AddDocTag("Conversion");
- AddDocTag("Image Dynamic");
-
- AddParameter(ParameterType_InputImage, "in", "Input image");
- SetParameterDescription("in", "Input image");
-
- AddParameter(ParameterType_OutputImage, "out", "Output Image");
- SetParameterDescription("out", "Output image");
- SetDefaultOutputPixelType("out",ImagePixelType_uint8);
-
- AddParameter(ParameterType_Choice, "type", "Rescale type");
- SetParameterDescription("type", "Transfer function for the rescaling");
- AddChoice("type.linear", "Linear");
- AddChoice("type.log2", "Log2");
- SetParameterString("type", "linear", false);
-
- 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", "The masked pixels won't be used to adapt the dynamic "
- "(the mask must have the same dimensions as the input image)");
- MandatoryOff("mask");
- DisableParameter("mask");
-
- AddParameter(ParameterType_Group,"quantile","Histogram quantile cutting");
- SetParameterDescription("quantile","Cut the histogram edges before rescaling");
-
- AddParameter(ParameterType_Float, "quantile.high", "High cut quantile");
- SetParameterDescription("quantile.high", "Quantiles to cut from histogram high values "
- "before computing min/max rescaling (in percent, 2 by default)");
- MandatoryOff("quantile.high");
- SetDefaultParameterFloat("quantile.high", 2.0);
- DisableParameter("quantile.high");
-
- AddParameter(ParameterType_Float, "quantile.low", "Low cut quantile");
- SetParameterDescription("quantile.low", "Quantiles to cut from histogram low values "
- "before computing min/max rescaling (in percent, 2 by default)");
- MandatoryOff("quantile.low");
- SetDefaultParameterFloat("quantile.low", 2.0);
- DisableParameter("quantile.low");
-
- 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);
-
- AddParameter(ParameterType_Float, "outmin", "Output min value");
- SetDefaultParameterFloat("outmin", 0.0);
- SetParameterDescription( "outmin", "Minimum value of the output image." );
- AddParameter(ParameterType_Float, "outmax", "Output max value");
- SetDefaultParameterFloat("outmax", 255.0);
- SetParameterDescription( "outmax", "Maximum value of the output image." );
- MandatoryOff("outmin");
- MandatoryOff("outmax");
-
- AddRAMParameter();
-
- // Doc example parameter settings
- SetDocExampleParameterValue("in", "QB_Toulouse_Ortho_XS.tif");
- SetDocExampleParameterValue("out", "otbConvertWithScalingOutput.png");
- SetDocExampleParameterValue("type", "linear");
- SetDocExampleParameterValue("channels", "rgb");
- SetDocExampleParameterValue("outmin", "0");
- SetDocExampleParameterValue("outmax", "255");
-
- SetOfficialDocLink();
+ 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, in depending on the sensor
+ 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);
+ }
}
+ }
- void DoUpdateParameters() ITK_OVERRIDE
+ template<class TImageType>
+ void GenericDoExecute()
+ {
+ // Clear previously registered filters
+ m_Filters.clear();
+
+ std::string rescaleType = this->GetParameterString("type");
+ typedef otb::VectorRescaleIntensityImageFilter<FloatVectorImageType, TImageType> RescalerType;
+ typename RescalerType::Pointer rescaler = RescalerType::New();
+
+ // selected channel
+ typename FloatVectorImageType::Pointer tempImage;
+ tempImage = GetSelectedChannels<FloatVectorImageType>();
+
+ const unsigned int nbComp(tempImage->GetNumberOfComponentsPerPixel());
+
+ // We need to subsample the input image in order to estimate its histogram
+ // 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..." );
+ typename ShrinkFilterType::Pointer shrinkFilter = ShrinkFilterType::New();
+ 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
{
- // 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, in depending on the sensor
- 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);
- }
- }
+ shrinkFilter->SetInput(tempImage);
+ rescaler->SetInput(tempImage);
+ shrinkFilter->Update();
}
- template<class TImageType>
- void GenericDoExecute()
+ 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"))
{
- // Clear previously registered filters
- m_Filters.clear();
-
- std::string rescaleType = this->GetParameterString("type");
- typedef otb::VectorRescaleIntensityImageFilter<FloatVectorImageType, TImageType> RescalerType;
- typename RescalerType::Pointer rescaler = RescalerType::New();
-
- // selected channel
- typename FloatVectorImageType::Pointer tempImage;
- tempImage = GetSelectedChannels<FloatVectorImageType>();
-
- const unsigned int nbComp(tempImage->GetNumberOfComponentsPerPixel());
-
- // We need to subsample the input image in order to estimate its histogram
- // 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..." );
- typename ShrinkFilterType::Pointer shrinkFilter = ShrinkFilterType::New();
- 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();
- }
-
- 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"))
- {
- FloatVectorImageType::Pointer mask;
- mask = this->GetParameterImage("mask");
- ShrinkFilterType::Pointer maskShrinkFilter = ShrinkFilterType::New();
- 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");
- }
- }
-
- // get all pixels : if mask is disable or 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);
- // Samples with nodata values are ignored
- histogramsGenerator->NoDataFlagOn();
- histogramsGenerator->Update();
- auto histOutput = histogramsGenerator->GetOutput();
- assert(histOutput);
-
- // And extract the lower and upper quantile
- typename FloatVectorImageType::PixelType inputMin(nbComp), inputMax(nbComp);
- for(unsigned int i = 0; i < nbComp; ++i)
- {
- auto && elm = histOutput->GetNthElement(i);
- assert(elm);
- inputMin[i] = elm->Quantile(0, 0.01 * GetParameterFloat("quantile.low"));
- inputMax[i] = elm->Quantile(0, 1.0 - 0.01 * GetParameterFloat("quantile.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"));
- }
-
- typename TImageType::PixelType minimum(nbComp);
- typename TImageType::PixelType maximum(nbComp);
-
- float outminvalue = itk::NumericTraits<typename TImageType::InternalPixelType>::min();
- float outmaxvalue = itk::NumericTraits<typename TImageType::InternalPixelType>::max();
- // TODO test outmin/outmax values
- if (outminvalue > GetParameterFloat("outmin"))
- itkExceptionMacro("The outmin value at " << GetParameterFloat("outmin") <<
- " is too low, select a value in "<< outminvalue <<" min.");
- if ( outmaxvalue < GetParameterFloat("outmax") )
- itkExceptionMacro("The outmax value at " << GetParameterFloat("outmax") <<
- " is too high, select a value in "<< outmaxvalue <<" max.");
- maximum.Fill( GetParameterFloat("outmax") );
- minimum.Fill( GetParameterFloat("outmin") );
-
- rescaler->SetOutputMinimum(minimum);
- rescaler->SetOutputMaximum(maximum);
-
- m_Filters.push_back(rescaler.GetPointer());
- SetParameterOutputImage<TImageType>("out", rescaler->GetOutput());
+ FloatVectorImageType::Pointer mask;
+ mask = this->GetParameterImage("mask");
+ ShrinkFilterType::Pointer maskShrinkFilter = ShrinkFilterType::New();
+ 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");
+ }
}
- // Get the bands order
- std::vector<int> GetChannels()
+ // get all pixels : if mask is disable or all pixels were masked
+ if ((!IsParameterEnabled("mask")) || (listSample->Size() == 0))
{
- 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()
+ 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);
+ // Samples with nodata values are ignored
+ histogramsGenerator->NoDataFlagOn();
+ histogramsGenerator->Update();
+ auto histOutput = histogramsGenerator->GetOutput();
+ assert(histOutput);
+
+ // And extract the lower and upper quantile
+ typename FloatVectorImageType::PixelType inputMin(nbComp), inputMax(nbComp);
+ for(unsigned int i = 0; i < nbComp; ++i)
{
- typedef MultiToMonoChannelExtractROI<FloatVectorImageType::InternalPixelType,
- typename TImageType::InternalPixelType> ExtractROIFilterType;
- typedef otb::ImageList<otb::Image<typename TImageType::InternalPixelType> > ImageListType;
- typedef ImageListToVectorImageFilter<ImageListType,
- TImageType > ListConcatenerFilterType;
+ auto && elm = histOutput->GetNthElement(i);
+ assert(elm);
+ inputMin[i] = elm->Quantile(0, 0.01 * GetParameterFloat("quantile.low"));
+ inputMax[i] = elm->Quantile(0, 1.0 - 0.01 * GetParameterFloat("quantile.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"));
+ }
- typename ImageListType::Pointer imageList;
- typename ListConcatenerFilterType::Pointer concatener;
+ typename TImageType::PixelType minimum(nbComp);
+ typename TImageType::PixelType maximum(nbComp);
+
+ float outminvalue = itk::NumericTraits<typename TImageType::InternalPixelType>::min();
+ float outmaxvalue = itk::NumericTraits<typename TImageType::InternalPixelType>::max();
+ // TODO test outmin/outmax values
+ if (outminvalue > GetParameterFloat("outmin"))
+ itkExceptionMacro("The outmin value at " << GetParameterFloat("outmin") <<
+ " is too low, select a value in "<< outminvalue <<" min.");
+ if ( outmaxvalue < GetParameterFloat("outmax") )
+ itkExceptionMacro("The outmax value at " << GetParameterFloat("outmax") <<
+ " is too high, select a value in "<< outmaxvalue <<" max.");
+ maximum.Fill( GetParameterFloat("outmax") );
+ minimum.Fill( GetParameterFloat("outmin") );
+
+ rescaler->SetOutputMinimum(minimum);
+ rescaler->SetOutputMaximum(maximum);
+
+ m_Filters.push_back(rescaler.GetPointer());
+ SetParameterOutputImage<TImageType>("out", rescaler->GetOutput());
+ }
+
+ // Get the bands order
+ std::vector<int> GetChannels()
+ {
+ std::vector<int> channels;
- imageList = ImageListType::New();
- concatener = ListConcatenerFilterType::New();
+ int nbChan = GetParameterImage("in")->GetNumberOfComponentsPerPixel();
+ std::string channelMode = GetParameterString("channels");
- //m_Filters.push_back(imageList.GetPointer());
- m_Filters.push_back(concatener.GetPointer());
+ 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;
+ }
- const bool monoChannel = IsParameterEnabled("channels.grayscale");
+ // 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;
- // get band order
- std::vector<int> channels = GetChannels();
+ typename ImageListType::Pointer imageList;
+ typename ListConcatenerFilterType::Pointer concatener;
- 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());
- }
+ imageList = ImageListType::New();
+ concatener = ListConcatenerFilterType::New();
- concatener->SetInput(imageList);
- concatener->UpdateOutputInformation();
+ //m_Filters.push_back(imageList.GetPointer());
+ m_Filters.push_back(concatener.GetPointer());
- return concatener->GetOutput();
+ 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() ITK_OVERRIDE
+
+ void DoExecute() ITK_OVERRIDE
+ {
+ switch ( this->GetParameterOutputImagePixelType("out") )
{
- 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")<<".");
- break;
- }
+ 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")<<".");
+ break;
}
+ }
- itk::ProcessObject::Pointer m_TmpFilter;
- TransferLogType::Pointer m_TransferLog;
- std::vector<itk::LightObject::Pointer> m_Filters;
- };
+ itk::ProcessObject::Pointer m_TmpFilter;
+ TransferLogType::Pointer m_TransferLog;
+ std::vector<itk::LightObject::Pointer> m_Filters;
+};
}
}