An error occurred while loading the file. Please try again.
-
Cresson Remi authoredae88ab51
/*========================================================================= Copyright (c) 2018-2019 IRSTEA Copyright (c) 2020-2021 INRAE This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information.=========================================================================*/#include "itkFixedArray.h"#include "itkObjectFactory.h"#include "otbWrapperApplicationFactory.h"// Application engine#include "otbStandardFilterWatcher.h"#include "itkFixedArray.h"// Filter#include "otbTensorflowSampler.h"// Stack#include "otbTensorflowSource.h"namespace otb{namespace Wrapper{class PatchesExtraction : public Application{public: /** Standard class typedefs. */ typedef PatchesExtraction Self; typedef Application Superclass; typedef itk::SmartPointer<Self> Pointer; typedef itk::SmartPointer<const Self> ConstPointer; /** Standard macro */ itkNewMacro(Self); itkTypeMacro(PatchesExtraction, Application); /** Filter typedef */ typedef otb::TensorflowSampler<FloatVectorImageType, VectorDataType> SamplerType; /** Typedefs for image concatenation */ typedef TensorflowSource<FloatVectorImageType> TFSourceType; // // Store stuff related to one source // struct SourceBundle { TFSourceType m_ImageSource; // Image source FloatVectorImageType::SizeType m_PatchSize; // Patch size std::string m_KeyIn; // Key of input image list std::string m_KeyOut; // Key of output samples image std::string m_KeyPszX; // Key for samples sizes X std::string m_KeyPszY; // Key for samples sizes Y std::string m_KeyNoData; // Key for no-data value FloatVectorImageType::InternalPixelType m_NoDataValue; // No data value }; // // Add an input source, which includes:7172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140
// -an input image list
// -an output image (samples)
// -an input patchsize (dimensions of samples)
//
void AddAnInputImage()
{
// Number of source
unsigned int inputNumber = m_Bundles.size() + 1;
// Create keys and descriptions
std::stringstream ss_group_key, ss_desc_group, ss_key_in, ss_key_out, ss_desc_in,
ss_desc_out, ss_key_dims_x, ss_desc_dims_x, ss_key_dims_y, ss_desc_dims_y, ss_key_nodata, ss_desc_nodata;
ss_group_key << "source" << inputNumber;
ss_desc_group << "Parameters for source " << inputNumber;
ss_key_out << ss_group_key.str() << ".out";
ss_desc_out << "Output patches for image " << inputNumber;
ss_key_in << ss_group_key.str() << ".il";
ss_desc_in << "Input image(s) " << inputNumber;
ss_key_dims_x << ss_group_key.str() << ".patchsizex";
ss_desc_dims_x << "X patch size for image " << inputNumber;
ss_key_dims_y << ss_group_key.str() << ".patchsizey";
ss_desc_dims_y << "Y patch size for image " << inputNumber;
ss_key_nodata << ss_group_key.str() << ".nodata";
ss_desc_nodata << "No-data value for image " << inputNumber;
// Populate group
AddParameter(ParameterType_Group, ss_group_key.str(), ss_desc_group.str());
AddParameter(ParameterType_InputImageList, ss_key_in.str(), ss_desc_in.str() );
AddParameter(ParameterType_OutputImage, ss_key_out.str(), ss_desc_out.str());
AddParameter(ParameterType_Int, ss_key_dims_x.str(), ss_desc_dims_x.str());
SetMinimumParameterIntValue (ss_key_dims_x.str(), 1);
AddParameter(ParameterType_Int, ss_key_dims_y.str(), ss_desc_dims_y.str());
SetMinimumParameterIntValue (ss_key_dims_y.str(), 1);
AddParameter(ParameterType_Float, ss_key_nodata.str(), ss_desc_nodata.str());
MandatoryOff (ss_key_nodata.str());
// Add a new bundle
SourceBundle bundle;
bundle.m_KeyIn = ss_key_in.str();
bundle.m_KeyOut = ss_key_out.str();
bundle.m_KeyPszX = ss_key_dims_x.str();
bundle.m_KeyPszY = ss_key_dims_y.str();
bundle.m_KeyNoData = ss_key_nodata.str();
m_Bundles.push_back(bundle);
}
//
// Prepare bundles from the number of points
//
void PrepareInputs()
{
for (auto& bundle: m_Bundles)
{
// Create a stack of input images
FloatVectorImageListType::Pointer list = GetParameterImageList(bundle.m_KeyIn);
bundle.m_ImageSource.Set(list);
// Patch size
bundle.m_PatchSize[0] = GetParameterInt(bundle.m_KeyPszX);
bundle.m_PatchSize[1] = GetParameterInt(bundle.m_KeyPszY);
// No data value
if (HasValue(bundle.m_KeyNoData))
{
bundle.m_NoDataValue = GetParameterFloat(bundle.m_KeyNoData);
}
}
141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210
}
void DoInit()
{
// Documentation
SetName("PatchesExtraction");
SetDescription("This application extracts patches in multiple input images. Change "
"the " + tf::ENV_VAR_NAME_NSOURCES + " environment variable to set the number of "
"sources.");
SetDocLongDescription("The application takes an input vector layer which is a set of "
"points, typically the output of the \"SampleSelection\" or the \"LabelImageSampleSelection\" "
"application to sample patches in the input images (samples are centered on the points). "
"A \"source\" parameters group is composed of (i) an input image list (can be "
"one image e.g. high res. image, or multiple e.g. time series), (ii) the size "
"of the patches to sample, and (iii) the output images of patches which will "
"be generated at the end of the process. The example below show how to "
"set the samples sizes. For a SPOT6 image for instance, the patch size can "
"be 64x64 and for an input Sentinel-2 time series the patch size could be "
"1x1. Note that if a dimension size is not defined, the largest one will "
"be used (i.e. input image dimensions. The number of input sources can be changed "
"at runtime by setting the system environment variable " + tf::ENV_VAR_NAME_NSOURCES);
SetDocAuthors("Remi Cresson");
AddDocTag(Tags::Learning);
// Input/output images
AddAnInputImage();
for (int i = 1; i < tf::GetNumberOfSources() ; i++)
AddAnInputImage();
// Input vector data
AddParameter(ParameterType_InputVectorData, "vec", "Positions of the samples (must be in the same projection as input image)");
// Output label
AddParameter(ParameterType_OutputImage, "outlabels", "output labels");
SetDefaultOutputPixelType ("outlabels", ImagePixelType_uint8);
MandatoryOff ("outlabels");
// Class field
AddParameter(ParameterType_String, "field", "field of class in the vector data");
// Examples values
SetDocExampleParameterValue("vec", "points.sqlite");
SetDocExampleParameterValue("source1.il", "$s2_list");
SetDocExampleParameterValue("source1.patchsizex", "16");
SetDocExampleParameterValue("source1.patchsizey", "16");
SetDocExampleParameterValue("field", "class");
SetDocExampleParameterValue("source1.out", "outpatches_16x16.tif");
SetDocExampleParameterValue("outlabels", "outlabels.tif");
}
void DoExecute()
{
PrepareInputs();
// Setup the filter
SamplerType::Pointer sampler = SamplerType::New();
sampler->SetInputVectorData(GetParameterVectorData("vec"));
sampler->SetField(GetParameterAsString("field"));
for (auto& bundle: m_Bundles)
{
if (HasValue(bundle.m_KeyNoData))
{
otbAppLogINFO("Rejecting samples that have at least one no-data value");
sampler->PushBackInputWithPatchSize(bundle.m_ImageSource.Get(), bundle.m_PatchSize, bundle.m_NoDataValue);
211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262
}
else
{
sampler->PushBackInputWithPatchSize(bundle.m_ImageSource.Get(), bundle.m_PatchSize);
}
}
// Run the filter
AddProcess(sampler, "Sampling patches");
sampler->Update();
// Show numbers
otbAppLogINFO("Number of samples collected: " << sampler->GetNumberOfAcceptedSamples());
otbAppLogINFO("Number of samples rejected : " << sampler->GetNumberOfRejectedSamples());
// Save patches image
if (sampler->GetNumberOfAcceptedSamples()>0)
{
for (unsigned int i = 0 ; i < m_Bundles.size() ; i++)
{
SetParameterOutputImage(m_Bundles[i].m_KeyOut, sampler->GetOutputPatchImages()[i]);
}
}
else
{
otbAppLogFATAL("No patch to sample. Please check that your vector data falls inside your images, and no-data values.");
}
// Save label image (if needed)
if (HasValue("outlabels"))
{
SetParameterOutputImage("outlabels", sampler->GetOutputLabelImage());
}
}
void DoUpdateParameters()
{
}
private:
std::vector<SourceBundle> m_Bundles;
}; // end of class
} // end namespace wrapper
} // end namespace otb
OTB_APPLICATION_EXPORT(otb::Wrapper::PatchesExtraction)