diff --git a/Modules/Applications/AppImageUtils/app/otbConvert.cxx b/Modules/Applications/AppImageUtils/app/otbConvert.cxx
index 362cee272e0e41f3b0852b1281057e044b9b025e..9dc6b4d17559d141591f7c04707c846575743877 100644
--- a/Modules/Applications/AppImageUtils/app/otbConvert.cxx
+++ b/Modules/Applications/AppImageUtils/app/otbConvert.cxx
@@ -105,8 +105,8 @@ private:
SetDocAuthors("OTB-Team");
SetDocSeeAlso("Rescale");
- AddDocTag(Tags::Manip);
AddDocTag(Tags::Deprecated);
+ AddDocTag(Tags::Manip);
AddDocTag("Conversion");
AddDocTag("Image Dynamic");
diff --git a/Modules/Applications/AppImageUtils/app/otbDynamicConvert.cxx b/Modules/Applications/AppImageUtils/app/otbDynamicConvert.cxx
index a714194faf7c185f000bf0efa3390d1b5daec33e..08696439549ca1c0b15e66baffd3352ccee7d29b 100644
--- a/Modules/Applications/AppImageUtils/app/otbDynamicConvert.cxx
+++ b/Modules/Applications/AppImageUtils/app/otbDynamicConvert.cxx
@@ -70,36 +70,39 @@ public:
typedef itk::Statistics::ListSample<FloatVectorImageType::PixelType> ListSampleType;
typedef itk::Statistics::DenseFrequencyContainer2 DFContainerType;
typedef ListSampleToHistogramListGenerator<ListSampleType,
- FloatVectorImageType::InternalPixelType,
- DFContainerType> HistogramsGeneratorType;
+ FloatVectorImageType::InternalPixelType,
+ DFContainerType> HistogramsGeneratorType;
+
typedef StreamingShrinkImageFilter<FloatVectorImageType,
- FloatVectorImageType> ShrinkFilterType;
+ FloatVectorImageType> ShrinkFilterType;
+
typedef Functor::LogFunctor<FloatVectorImageType::InternalPixelType> TransferLogFunctor;
typedef UnaryImageFunctorWithVectorImageFilter<FloatVectorImageType,
- FloatVectorImageType,
- TransferLogFunctor> TransferLogType;
+ FloatVectorImageType,
+ TransferLogFunctor> TransferLogType;
private:
void DoInit() ITK_OVERRIDE
{
SetName("DynamicConvert");
- SetDescription("Convert an image to a different format and rescaling the dynamic ...");
+ SetDescription("Change the pixel type and rescale the image's 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.");
+ 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 between the 2nd to "
+ "the 98th percentile. 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");
@@ -121,29 +124,35 @@ private:
AddChoice("type.log2", "Log2");
SetParameterString("type", "linear", false);
- AddParameter(ParameterType_Float,"type.linear.gamma","Gamma correction factor");
- SetParameterDescription("type.linear.gamma","Gamma correction factor");
+ 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 "
+ 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");
+ 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 "
+ 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 "
+ 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);
@@ -154,11 +163,14 @@ private:
"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).");
+ 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");
+ 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);
@@ -205,7 +217,8 @@ private:
{
typedef otb::ImageMetadataInterfaceBase ImageMetadataInterfaceType;
ImageMetadataInterfaceType::Pointer metadataInterface =
- ImageMetadataInterfaceFactory::CreateIMI(GetParameterImage("in")->GetMetaDataDictionary());
+ ImageMetadataInterfaceFactory::CreateIMI(
+ GetParameterImage("in")->GetMetaDataDictionary());
int nbBand = GetParameterImage("in")->GetNumberOfComponentsPerPixel();
SetMaximumParameterIntValue("channels.grayscale.channel", nbBand);
@@ -243,14 +256,17 @@ private:
// Shrink factor is computed so as to load a quicklook of 1000
// pixels square at most
auto imageSize = tempImage->GetLargestPossibleRegion().GetSize();
- unsigned int shrinkFactor = std::max({int(imageSize[0])/1000, int(imageSize[1])/1000, 1});
+ unsigned int shrinkFactor = std::max({int(imageSize[0])/1000,
+ int(imageSize[1])/1000, 1});
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...");
+ shrinkFilter->GetStreamer()->
+ SetAutomaticAdaptativeStreaming(GetParameterInt("ram"));
+ AddProcess(shrinkFilter->GetStreamer(),
+ "Computing shrink Image for min/max estimation...");
if ( rescaleType == "log2")
{
@@ -272,10 +288,12 @@ private:
otbAppLogDEBUG( << "Evaluating input Min/Max..." );
itk::ImageRegionConstIterator<FloatVectorImageType>
- it(shrinkFilter->GetOutput(), shrinkFilter->GetOutput()->GetLargestPossibleRegion());
+ it(shrinkFilter->GetOutput(),
+ shrinkFilter->GetOutput()->GetLargestPossibleRegion());
typename ListSampleType::Pointer listSample = ListSampleType::New();
- listSample->SetMeasurementVectorSize(tempImage->GetNumberOfComponentsPerPixel());
+ listSample->SetMeasurementVectorSize(
+ tempImage->GetNumberOfComponentsPerPixel());
// Now we generate the list of samples
if (IsParameterEnabled("mask"))
@@ -284,10 +302,12 @@ private:
ShrinkFilterType::Pointer maskShrinkFilter = ShrinkFilterType::New();
maskShrinkFilter->SetShrinkFactor(shrinkFactor);
maskShrinkFilter->SetInput(mask);
- maskShrinkFilter->GetStreamer()->SetAutomaticAdaptativeStreaming(GetParameterInt("ram"));
+ maskShrinkFilter->GetStreamer()->
+ SetAutomaticAdaptativeStreaming(GetParameterInt("ram"));
maskShrinkFilter->Update();
- auto itMask = itk::ImageRegionConstIterator<FloatVectorImageType>(maskShrinkFilter->GetOutput(),
+ auto itMask = itk::ImageRegionConstIterator<FloatVectorImageType>(
+ maskShrinkFilter->GetOutput(),
maskShrinkFilter->GetOutput()->GetLargestPossibleRegion());
// Remove masked pixels
@@ -296,7 +316,7 @@ private:
for(; !it.IsAtEnd(); ++it, ++itMask)
{
// float values, so the threshold is set to 0.5
- if (itMask.Get()[0] < 0.5)
+ if (itMask.Get()[0] > 0.5)
{
listSample->PushBack(it.Get());
}
@@ -304,8 +324,8 @@ private:
// if listSample is empty
if (listSample->Size() == 0)
{
- otbAppLogINFO( << "All pixels were masked, the application assume a wrong mask "
- "and include all the image");
+ otbAppLogINFO( << "All pixels were masked, the application assume "
+ "a wrong mask and include all the image");
}
}
@@ -319,7 +339,8 @@ private:
}
// And then the histogram
- typename HistogramsGeneratorType::Pointer histogramsGenerator = HistogramsGeneratorType::New();
+ typename HistogramsGeneratorType::Pointer histogramsGenerator =
+ HistogramsGeneratorType::New();
histogramsGenerator->SetListSample(listSample);
histogramsGenerator->SetNumberOfBins(255);
// Samples with nodata values are ignored
@@ -334,11 +355,15 @@ private:
{
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"));
+ 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
+ otbAppLogDEBUG( << std::setprecision(5)
+ << "Min/Max computation done : min="
+ << inputMin
<< " max=" << inputMax );
rescaler->AutomaticInputMinMaxComputationOff();
@@ -364,6 +389,7 @@ private:
itkExceptionMacro("The outmax value at " << GetParameterFloat("outmax") <<
" is too high, select a value in "<< outmaxvalue <<" max.");
*/
+
maximum.Fill( GetParameterFloat("outmax") );
minimum.Fill( GetParameterFloat("outmin") );
@@ -407,7 +433,8 @@ private:
}
else
{
- itkExceptionMacro(<< "At least one needed channel has an invalid index");
+ itkExceptionMacro(<< "At least one needed channel has an invalid "
+ "index");
}
}
else if (channelMode == "all")
@@ -424,13 +451,14 @@ private:
typename TImageType::Pointer GetSelectedChannels()
{
typedef MultiToMonoChannelExtractROI<FloatVectorImageType::InternalPixelType,
- typename TImageType::InternalPixelType> ExtractROIFilterType;
- typedef otb::ImageList<otb::Image<typename TImageType::InternalPixelType> > ImageListType;
+ typename TImageType::InternalPixelType> ExtractROIFilterType;
+ typedef otb::ImageList<otb::Image<typename TImageType::InternalPixelType> > ImageListType;
typedef ImageListToVectorImageFilter<ImageListType,
- TImageType > ListConcatenerFilterType;
+ TImageType > ListConcatenerFilterType;
- typename ImageListType::Pointer imageList = ImageListType::New();
- typename ListConcatenerFilterType::Pointer concatener = ListConcatenerFilterType::New();
+ typename ImageListType::Pointer imageList = ImageListType::New();
+ typename ListConcatenerFilterType::Pointer concatener =
+ ListConcatenerFilterType::New();
//m_Filters.push_back(imageList.GetPointer());
m_Filters.push_back(concatener.GetPointer());
@@ -442,10 +470,13 @@ private:
for (auto && channel : channels)
{
- typename ExtractROIFilterType::Pointer extractROIFilter = ExtractROIFilterType::New();
+ typename ExtractROIFilterType::Pointer extractROIFilter =
+ ExtractROIFilterType::New();
m_Filters.push_back(extractROIFilter.GetPointer());
extractROIFilter->SetInput(GetParameterImage("in"));
- if (!monoChannel) extractROIFilter->SetChannel(channel);
+ if (!monoChannel)
+ extractROIFilter->SetChannel(channel);
+
extractROIFilter->UpdateOutputInformation();
imageList->PushBack(extractROIFilter->GetOutput());
}
@@ -483,7 +514,8 @@ private:
GenericDoExecute<DoubleVectorImageType>();
break;
default:
- itkExceptionMacro("Unknown pixel type "<<this->GetParameterOutputImagePixelType("out")<<".");
+ itkExceptionMacro("Unknown pixel type "
+ <<this->GetParameterOutputImagePixelType("out")<<".");
break;
}
}
diff --git a/Modules/Applications/AppImageUtils/app/otbRescale.cxx b/Modules/Applications/AppImageUtils/app/otbRescale.cxx
index fa807fbe7af52c68895a2b9259f0fc73235aa946..f5c08c80a24bed127fb76e1fbc93f13d54d40915 100644
--- a/Modules/Applications/AppImageUtils/app/otbRescale.cxx
+++ b/Modules/Applications/AppImageUtils/app/otbRescale.cxx
@@ -62,8 +62,8 @@ private:
SetDocAuthors("OTB-Team");
SetDocSeeAlso(" ");
- AddDocTag(Tags::Manip);
AddDocTag(Tags::Deprecated);
+ AddDocTag(Tags::Manip);
AddParameter(ParameterType_InputImage, "in", "Input Image");
SetParameterDescription( "in", "The image to scale." );
AddParameter(ParameterType_OutputImage, "out", "Output Image");