diff --git a/app/cbDimensionalityReduction.cxx b/app/cbDimensionalityReduction.cxx
index 106f609d48078a1e5cee94ed5276571dd589e61c..bc9a5754fec14e92c50e394ccc781d8b211bcf5b 100644
--- a/app/cbDimensionalityReduction.cxx
+++ b/app/cbDimensionalityReduction.cxx
@@ -222,7 +222,7 @@ private:
}
// Rescale vector image
- m_Rescaler->SetScale(stddevMeasurementVector);
+ m_Rescaler->SetScale(stddevMeasurementVector*3);
m_Rescaler->SetShift(meanMeasurementVector);
m_Rescaler->SetInput(inImage);
diff --git a/app/cbDimensionalityReductionTrainer.cxx b/app/cbDimensionalityReductionTrainer.cxx
index aee6fb3ed966fb657980b5063ef4b35efdaa5e4e..55232ef871b527a00e5e3664737eb2bb4c9bdb1f 100644
--- a/app/cbDimensionalityReductionTrainer.cxx
+++ b/app/cbDimensionalityReductionTrainer.cxx
@@ -37,7 +37,7 @@ public:
typedef Superclass::ListSampleType ListSampleType;
typedef Superclass::SampleImageType SampleImageType;
- typedef double ValueType;
+ typedef float ValueType;
typedef itk::VariableLengthVector<ValueType> MeasurementType;
typedef otb::StatisticsXMLFileReader<SampleType> StatisticsReader;
@@ -81,8 +81,6 @@ private:
void DoExecute()
{
- std::cout << "Appli Training!" << std::endl;
-
std::string shapefile = GetParameterString("io.vd");
otb::ogr::DataSource::Pointer source = otb::ogr::DataSource::New(shapefile, otb::ogr::DataSource::Modes::Read);
@@ -103,7 +101,7 @@ private:
}
input->PushBack(mv);
}
-
+
MeasurementType meanMeasurementVector;
MeasurementType stddevMeasurementVector;
@@ -126,7 +124,7 @@ private:
ShiftScaleFilterType::Pointer trainingShiftScaleFilter = ShiftScaleFilterType::New();
trainingShiftScaleFilter->SetInput(input);
trainingShiftScaleFilter->SetShifts(meanMeasurementVector);
- trainingShiftScaleFilter->SetScales(stddevMeasurementVector);
+ trainingShiftScaleFilter->SetScales(stddevMeasurementVector*3);
trainingShiftScaleFilter->Update();
ListSampleType::Pointer trainingListSample= trainingShiftScaleFilter->GetOutput();
diff --git a/app/cbDimensionalityReductionVector.cxx b/app/cbDimensionalityReductionVector.cxx
index ce4e1fa1ca35437a92762a8bab2297faba3fe3b3..cf2caed54850b84703a3a5d34670438f9c5c3a5f 100644
--- a/app/cbDimensionalityReductionVector.cxx
+++ b/app/cbDimensionalityReductionVector.cxx
@@ -57,7 +57,7 @@ class CbDimensionalityReductionVector : public Application
/** Filters typedef */
- typedef double ValueType;
+ typedef float ValueType;
typedef itk::VariableLengthVector<ValueType> InputSampleType;
typedef itk::Statistics::ListSample<InputSampleType> ListSampleType;
typedef MachineLearningModel<itk::VariableLengthVector<ValueType>, itk::VariableLengthVector<ValueType>> DimensionalityReductionModelType;
@@ -136,6 +136,7 @@ class CbDimensionalityReductionVector : public Application
if ( HasValue("in") )
{
+
std::string shapefile = GetParameterString("in");
otb::ogr::DataSource::Pointer ogrDS;
OGRSpatialReference oSRS("");
@@ -150,29 +151,29 @@ class CbDimensionalityReductionVector : public Application
{
std::string item = layerDefn.GetFieldDefn(iField)->GetNameRef();
std::string key(item);
+ std::string::iterator end = std::remove_if( key.begin(), key.end(), IsNotAlphaNum );
+ std::transform( key.begin(), end, key.begin(), tolower );
+ /*
key.erase( std::remove_if(key.begin(),key.end(),IsNotAlphaNum), key.end());
- std::transform(key.begin(), key.end(), key.begin(), tolower);
+ std::transform(key.begin(), key.end(), key.begin(), tolower);*/
OGRFieldType fieldType = layerDefn.GetFieldDefn(iField)->GetType();
-
- if(fieldType == OFTInteger || ogr::version_proxy::IsOFTInteger64(fieldType) || fieldType == OFTReal)
- {
- std::string tmpKey="feat."+key;
- AddChoice(tmpKey,item);
- }
- /*
- if(fieldType == OFTInteger || ogr::version_proxy::IsOFTInteger64(fieldType) || fieldType == OFTReal)
- {
- std::string tmpKey="featout."+key;
+ /* if(fieldType == OFTInteger || ogr::version_proxy::IsOFTInteger64(fieldType) || fieldType == OFTReal)
+ {*/
+ //std::string tmpKey="feat."+key;
+ std::string tmpKey = "feat." + key.substr( 0, static_cast<unsigned long>( end - key.begin() ) );
AddChoice(tmpKey,item);
- }*/
+ //} // this is the same as in otbVectorClassifier, but it doesnt work
}
+
}
+
}
void DoExecute() ITK_OVERRIDE
{
clock_t tic = clock();
+
std::string shapefile = GetParameterString("in");
otb::ogr::DataSource::Pointer source = otb::ogr::DataSource::New(shapefile, otb::ogr::DataSource::Modes::Read);
otb::ogr::Layer layer = source->GetLayer(0);
@@ -187,12 +188,16 @@ class CbDimensionalityReductionVector : public Application
{
MeasurementType mv;
mv.SetSize(nbFeatures);
+
for(int idx=0; idx < nbFeatures; ++idx)
{
- mv[idx] = (*it)[GetSelectedItems("feat")[idx]].GetValue<double>();
+ mv[idx] = static_cast<float>( (*it)[GetSelectedItems("feat")[idx]].GetValue<double>() );
+
}
input->PushBack(mv);
+
}
+
/** Statistics for shift/scale */
@@ -218,7 +223,7 @@ class CbDimensionalityReductionVector : public Application
ShiftScaleFilterType::Pointer trainingShiftScaleFilter = ShiftScaleFilterType::New();
trainingShiftScaleFilter->SetInput(input);
trainingShiftScaleFilter->SetShifts(meanMeasurementVector);
- trainingShiftScaleFilter->SetScales(stddevMeasurementVector);
+ trainingShiftScaleFilter->SetScales(stddevMeasurementVector*3);
trainingShiftScaleFilter->Update();
otbAppLogINFO("mean used: " << meanMeasurementVector);
otbAppLogINFO("standard deviation used: " << stddevMeasurementVector);
@@ -246,9 +251,7 @@ class CbDimensionalityReductionVector : public Application
/** Perform Dimensionality Reduction */
ListSampleType::Pointer listSample = trainingShiftScaleFilter->GetOutput();
- ListSampleType::Pointer target;
- target = m_Model->PredictBatch(listSample);
-
+ ListSampleType::Pointer target = m_Model->PredictBatch(listSample);
/** Create/Update Output Shape file */
@@ -276,8 +279,8 @@ class CbDimensionalityReductionVector : public Application
OGRFeatureDefn &inLayerDefn = layer.GetLayerDefn();
for (int k=0 ; k<inLayerDefn.GetFieldCount()-nbBands ; k++) // we don't copy the original bands
{
- OGRFieldDefn fieldDefn(inLayerDefn.GetFieldDefn(k));
- newLayer.CreateField(fieldDefn);
+ OGRFieldDefn fieldDefn(inLayerDefn.GetFieldDefn(k));
+ newLayer.CreateField(fieldDefn);
}
}
else if (GetParameterString("mode")=="update")
@@ -306,20 +309,7 @@ class CbDimensionalityReductionVector : public Application
}
- /*
- else
- {
- // Update mode
- updateMode = true;
- otbAppLogINFO("Update input vector data.");
- // fill temporary buffer for the transfer
- otb::ogr::Layer inputLayer = layer;
- layer = buffer->CopyLayer(inputLayer, std::string("Buffer"));
- // close input data source
- source->Clear();
- // Re-open input data source in update mode
- output = otb::ogr::DataSource::New(shapefile, otb::ogr::DataSource::Modes::Update_LayerUpdate);
- }*/
+
otb::ogr::Layer outLayer = output->GetLayer(0);
@@ -351,34 +341,26 @@ class CbDimensionalityReductionVector : public Application
}
}
- // Add an ID field. (The ID already contained in the layer refers to the polygon)
- /*
- OGRFieldDefn IDField("ID_point", OFTInteger);
- ogr::FieldDefn IDFieldDef(IDField);
- outLayer.CreateField(IDFieldDef);
- */
+
// Fill output layer
unsigned int count=0;
auto classfieldname = GetParameterStringList("featout");
it = layer.cbegin();
itEnd = layer.cend();
- int id=0;
+
for( ; it!=itEnd ; ++it, ++count)
{
ogr::Feature dstFeature(outLayer.GetLayerDefn());
- /*
- if (GetParameterString("mode")=="overwrite")
- {*/
- dstFeature.SetFrom( *it , TRUE);
- dstFeature.SetFID(it->GetFID());
- //}
+
+ dstFeature.SetFrom( *it , TRUE);
+ dstFeature.SetFID(it->GetFID());
+
for (std::size_t i=0; i<classfieldname.size(); ++i){
- dstFeature[classfieldname[i]].SetValue<ValueType>(target->GetMeasurementVector(count)[i]);
+ dstFeature[classfieldname[i]].SetValue<double>(target->GetMeasurementVector(count)[i]);
}
- //dstFeature["ID_point"].SetValue<int>(id);
if (updateMode)
{
outLayer.SetFeature(dstFeature);
@@ -387,7 +369,6 @@ class CbDimensionalityReductionVector : public Application
{
outLayer.CreateFeature(dstFeature);
}
- id++;
}
if(outLayer.ogr().TestCapability("Transactions"))
diff --git a/include/ImageDimensionalityReductionFilter.txx b/include/ImageDimensionalityReductionFilter.txx
index 53a1739bd28fed73fe3f0623f1018dd12e124d56..e98a0b79f753624246d732d01e60a47b43f2595a 100644
--- a/include/ImageDimensionalityReductionFilter.txx
+++ b/include/ImageDimensionalityReductionFilter.txx
@@ -189,7 +189,7 @@ ImageDimensionalityReductionFilter<TInputImage, TOutputImage, TMaskImage>
// This call is threadsafe
labels = m_Model->PredictBatch(samples);
-
+
// Set the output values
typename TargetListSampleType::ConstIterator labIt = labels->Begin();
diff --git a/include/PCAModel.txx b/include/PCAModel.txx
index e9ea1e2a2b94d3cc1331b65a2123f340087943f6..364dd8def35fa51373f3b0cf30e927622044d736 100644
--- a/include/PCAModel.txx
+++ b/include/PCAModel.txx
@@ -43,7 +43,6 @@ void PCAModel<TInputValue>::Train()
shark::Data<shark::RealVector> inputSamples = shark::createDataFromRange( features );
m_pca.setData(inputSamples);
m_pca.encoder(m_encoder, this->m_Dimension);
- std::cout << m_encoder.matrix() << std::endl;
m_pca.decoder(m_decoder, this->m_Dimension);
}
@@ -175,8 +174,6 @@ void PCAModel<TInputValue>
//target[a]=1;
//target.SetElement(a,p[a]);
-
-
}
//std::cout << p << std::endl;
targets->SetMeasurementVector(id,target);