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/*
* Copyright (C) 2005-2022 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 "otbWrapperApplication.h"
#include "otbWrapperApplicationFactory.h"
#include "otbOGRDataSourceWrapper.h"
#include "otbOGRFeatureWrapper.h"
#include "otbStatisticsXMLFileWriter.h"
#include "itkVariableLengthVector.h"
#include <time.h>
namespace otb
{
namespace Wrapper
{
class ComputeOGRLayersFeaturesStatistics : public Application
{
public:
typedef ComputeOGRLayersFeaturesStatistics Self;
typedef Application Superclass;
typedef itk::SmartPointer<Self> Pointer;
typedef itk::SmartPointer<const Self> ConstPointer;
itkNewMacro(Self);
itkTypeMacro(ComputeOGRLayersFeaturesStatistics, otb::Application);
private:
void DoInit() override
{
SetName("ComputeOGRLayersFeaturesStatistics");
SetDescription("Compute statistics of the features in a set of OGR Layers");
SetDocLongDescription(
"Compute statistics (mean and standard deviation) of the features in a set of OGR Layers, and write them in an XML file. The resulting XML file can "
"then be used by the training application.");
SetDocLimitations("Experimental. For now only shapefiles are supported.");
SetDocAuthors("David Youssefi during internship at CNES");
SetDocSeeAlso("OGRLayerClassifier,TrainVectorClassifier");
AddDocTag(Tags::Segmentation);
AddParameter(ParameterType_InputVectorData, "inshp", "Vector Data");
SetParameterDescription("inshp", "Name of the input shapefile");
AddParameter(ParameterType_OutputFilename, "outstats", "Output XML file");
SetParameterDescription("outstats", "XML file containing mean and variance of each feature.");
AddParameter(ParameterType_Field, "feat", "Feature");
SetParameterDescription("feat", "List of features to consider for statistics.");
SetVectorData("feat", "inshp");
// Doc example parameter settings
SetDocExampleParameterValue("inshp", "vectorData.shp");
SetDocExampleParameterValue("outstats", "results.xml");
SetDocExampleParameterValue("feat", "perimeter");
SetOfficialDocLink();
}
void DoUpdateParameters() override
{
if (HasValue("inshp"))
{
std::string shapefile = GetParameterString("inshp");
otb::ogr::DataSource::Pointer ogrDS;
otb::ogr::Layer layer(nullptr, false);
OGRSpatialReference oSRS("");
std::vector<std::string> options;
ogrDS = otb::ogr::DataSource::New(shapefile, otb::ogr::DataSource::Modes::Read);
std::string layername = itksys::SystemTools::GetFilenameName(shapefile);
layername = layername.substr(0, layername.size() - 4);
layer = ogrDS->GetLayer(0);
otb::ogr::Feature feature = layer.ogr().GetNextFeature();
ClearChoices("feat");
std::vector<std::string> choiceKeys;
for (int iField = 0; iField < feature.ogr().GetFieldCount(); iField++)
{
std::string key, item = feature.ogr().GetFieldDefnRef(iField)->GetNameRef();
key = item;
// Transform chain : lowercase and alphanumerical
key.erase(std::remove_if(key.begin(), key.end(), std::not1(std::ptr_fun(::isalnum))), key.end());
std::transform(key.begin(), key.end(), key.begin(), tolower);
// Key must be unique
choiceKeys = GetChoiceKeys("feat");
while (choiceKeys.end() != std::find(choiceKeys.begin(), choiceKeys.end(), key))
key.append("0");
key = "feat." + key;
AddChoice(key, item);
}
}
}
void DoExecute() override
{
clock_t tic = clock();
std::string shapefile = GetParameterString("inshp");
std::string XMLfile = GetParameterString("outstats");
otb::ogr::DataSource::Pointer source = otb::ogr::DataSource::New(shapefile, otb::ogr::DataSource::Modes::Read);
otb::ogr::Layer layer = source->GetLayer(0);
bool goesOn = true;
otb::ogr::Feature feature = layer.ogr().GetNextFeature();
typedef double ValueType;
typedef itk::VariableLengthVector<ValueType> MeasurementType;
std::vector<MeasurementType> featValue;
const std::vector<int>::size_type nbFeatures = GetSelectedItems("feat").size();
if (feature.addr())
while (goesOn)
{
MeasurementType mv;
mv.SetSize(nbFeatures);
for (unsigned int idx = 0; idx < nbFeatures; ++idx)
mv[idx] = feature.ogr().GetFieldAsDouble(GetSelectedItems("feat")[idx]);
featValue.push_back(mv);
feature = layer.ogr().GetNextFeature();
goesOn = feature.addr() != nullptr;
}
MeasurementType mean;
mean.SetSize(nbFeatures);
MeasurementType stddev;
stddev.SetSize(nbFeatures);
for (unsigned int featIt = 0; featIt < nbFeatures; featIt++)
{
double sum = 0.0;
for (unsigned add = 0; add < featValue.size(); add++)
sum += featValue[add][featIt];
mean[featIt] = sum / featValue.size();
double accum = 0.0;
for (unsigned add = 0; add < featValue.size(); add++)
accum += (featValue[add][featIt] - mean[featIt]) * (featValue[add][featIt] - mean[featIt]);
stddev[featIt] = sqrt(accum / (featValue.size() - 1));
}
typedef otb::StatisticsXMLFileWriter<MeasurementType> StatisticsWriter;
StatisticsWriter::Pointer writer = StatisticsWriter::New();
writer->SetFileName(XMLfile);
writer->AddInput("mean", mean);
writer->AddInput("stddev", stddev);
writer->Update();
clock_t toc = clock();
otbAppLogINFO("Elapsed: " << ((double)(toc - tic) / CLOCKS_PER_SEC) << " seconds.");
}
};
}
}
OTB_APPLICATION_EXPORT(otb::Wrapper::ComputeOGRLayersFeaturesStatistics)
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