diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f0de6bfcd81f02792a9521b220cd7a30a5695ac2..290f211737b44a302e5f2a2c703c7c26da2375ac 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -24,7 +24,7 @@ before_script:
# Provision efficiently the local LFS cache before checkout
- git lfs fetch origin $CI_COMMIT_SHA
# Checkout the expected branch
- - git checkout $CI_COMMIT_REF_NAME
+ - git checkout -f -q $CI_COMMIT_SHA
after_script:
- python3 CI/cdash_handler.py $CI_COMMIT_SHA $CI_PROJECT_ID $CI_PROJECT_DIR $K8S_SECRET_CDASH
diff --git a/Data/Baseline/OTB-Applications/Files/apTvClTrainVectorRegressionModel.1.txt b/Data/Baseline/OTB-Applications/Files/apTvClTrainVectorRegressionModel.1.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20e589ba2a9407e406e8511baf12a44bc63c2a43
--- /dev/null
+++ b/Data/Baseline/OTB-Applications/Files/apTvClTrainVectorRegressionModel.1.txt
@@ -0,0 +1 @@
+io.mse: 0.003289417131
diff --git a/Data/Baseline/OTB-Applications/Files/apTvClTrainVectorRegressionModel.txt b/Data/Baseline/OTB-Applications/Files/apTvClTrainVectorRegressionModel.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aec10cefd80236745402a3c392cbc9590a666de6
--- /dev/null
+++ b/Data/Baseline/OTB-Applications/Files/apTvClTrainVectorRegressionModel.txt
@@ -0,0 +1 @@
+io.mse: 0.001359587419
diff --git a/Documentation/Cookbook/Scripts/otbGenerateWrappersRstDoc.py b/Documentation/Cookbook/Scripts/otbGenerateWrappersRstDoc.py
index 8cd9ab8ed70e204d915e32c25ebb4944f52b4a9b..77d197f07a7f759cdd194eedd8713a9e884e1c67 100755
--- a/Documentation/Cookbook/Scripts/otbGenerateWrappersRstDoc.py
+++ b/Documentation/Cookbook/Scripts/otbGenerateWrappersRstDoc.py
@@ -356,10 +356,17 @@ def make_links(text, allapps):
rep = {appname: ":ref:`{}`".format(appname) for appname in allapps}
return multireplace(text, rep)
+def render_deprecation_string(app):
+ if app.IsDeprecated():
+ return "This application is deprecated and will be removed in a future release."
+ else:
+ return ""
+
def render_application(appname, allapps):
"Render app to rst"
- app = otbApplication.Registry.CreateApplication(appname)
+ # Create the application without logger to avoid the deprecation warning log
+ app = otbApplication.Registry.CreateApplicationWithoutLogger(appname)
# TODO: remove this when bug 440 is fixed
app.Init()
@@ -368,6 +375,7 @@ def render_application(appname, allapps):
output = template_application.format(
label=appname,
+ deprecation_string=render_deprecation_string(app),
heading=rst_section(app.GetName(), '='),
description=app.GetDescription(),
longdescription=make_links(app.GetDocLongDescription(), allapps),
@@ -381,8 +389,9 @@ def render_application(appname, allapps):
return output
def GetApplicationTags(appname):
- app = otbApplication.Registry.CreateApplication(appname)
- return app.GetDocTags()
+ # Create the application without logger to avoid the deprecation warning log
+ app = otbApplication.Registry.CreateApplicationWithoutLogger(appname)
+ return app.GetDocTags()
def GenerateRstForApplications(rst_dir):
"Generate .rst files for all applications"
@@ -404,9 +413,12 @@ def GenerateRstForApplications(rst_dir):
for appName in appNames:
# Get application first tag
- tags = GetApplicationTags(appName)
+ tags = list(GetApplicationTags(appName))
+ if "Deprecated" in tags:
+ tags.remove("Deprecated")
if not tags or len(tags) == 0:
raise RuntimeError("No tags for application: " + appName)
+
tag = tags[0]
tag_ = tag.replace(" ", "_")
diff --git a/Documentation/Cookbook/rst/templates/application.rst b/Documentation/Cookbook/rst/templates/application.rst
index 68db4a8b3cc9c224fcdc107d8c4e3f9f21f97329..bbe15bceff737e5f165a2bdea7d4ea17771fcaab 100644
--- a/Documentation/Cookbook/rst/templates/application.rst
+++ b/Documentation/Cookbook/rst/templates/application.rst
@@ -1,6 +1,9 @@
.. _{label}:
{heading}
+
+{deprecation_string}
+
{description}
Description
diff --git a/Modules/Applications/AppClassification/app/CMakeLists.txt b/Modules/Applications/AppClassification/app/CMakeLists.txt
index 50ac00ea1619c068da99774d0010ee532a5b7fd1..6fc42a4ee2c73a284a379f9763b170fac9b50093 100644
--- a/Modules/Applications/AppClassification/app/CMakeLists.txt
+++ b/Modules/Applications/AppClassification/app/CMakeLists.txt
@@ -65,6 +65,11 @@ otb_create_application(
SOURCES otbTrainRegression.cxx
LINK_LIBRARIES ${${otb-module}_LIBRARIES})
+otb_create_application(
+ NAME TrainVectorRegression
+ SOURCES otbTrainVectorRegression.cxx
+ LINK_LIBRARIES ${${otb-module}_LIBRARIES})
+
otb_create_application(
NAME PredictRegression
SOURCES otbPredictRegression.cxx
diff --git a/Modules/Applications/AppClassification/app/otbTrainRegression.cxx b/Modules/Applications/AppClassification/app/otbTrainRegression.cxx
index c4ac059fe4bd9fcd3ab758f94c4122999b42caf2..a93c8b5439d65e670fa92e52ee889933d45f3d61 100644
--- a/Modules/Applications/AppClassification/app/otbTrainRegression.cxx
+++ b/Modules/Applications/AppClassification/app/otbTrainRegression.cxx
@@ -271,8 +271,7 @@ void ParseCSVPredictors(std::string path, ListSampleType* outputList)
elem.Fill(0.0);
for (unsigned int i=0 ; i<nbCols ; ++i)
{
- iss.str(words[i]);
- iss >> elem[i];
+ elem[i] = std::stod(words[i]);
}
outputList->PushBack(elem);
}
diff --git a/Modules/Applications/AppClassification/app/otbTrainVectorClassifier.cxx b/Modules/Applications/AppClassification/app/otbTrainVectorClassifier.cxx
index 5d10533448e7a08e6141963f98ccc73d15eea063..fbd04d4a4b5c0fa213d5266d3588b1f8de7202cb 100644
--- a/Modules/Applications/AppClassification/app/otbTrainVectorClassifier.cxx
+++ b/Modules/Applications/AppClassification/app/otbTrainVectorClassifier.cxx
@@ -29,11 +29,11 @@ namespace otb
namespace Wrapper
{
-class TrainVectorClassifier : public TrainVectorBase
+class TrainVectorClassifier : public TrainVectorBase<float, int>
{
public:
typedef TrainVectorClassifier Self;
- typedef TrainVectorBase Superclass;
+ typedef TrainVectorBase<float, int> Superclass;
typedef itk::SmartPointer<Self> Pointer;
typedef itk::SmartPointer<const Self> ConstPointer;
itkNewMacro( Self )
@@ -66,13 +66,20 @@ protected:
"Learning (2.3.1 and later), and Shark ML The output of this application "
"is a text model file, whose format corresponds to the ML model type "
"chosen. There is no image nor vector data output.");
- SetDocLimitations("");
+ SetDocLimitations("None");
SetDocAuthors( "OTB Team" );
SetDocSeeAlso( " " );
SetOfficialDocLink();
Superclass::DoInit();
+
+ // Add a new parameter to compute confusion matrix / contingency table
+ this->AddParameter(ParameterType_OutputFilename, "io.confmatout", "Output confusion matrix or contingency table");
+ this->SetParameterDescription("io.confmatout",
+ "Output file containing the confusion matrix or contingency table (.csv format)."
+ "The contingency table is output when we unsupervised algorithms is used otherwise the confusion matrix is output.");
+ this->MandatoryOff("io.confmatout");
}
void DoUpdateParameters() override
diff --git a/Modules/Applications/AppClassification/app/otbTrainVectorRegression.cxx b/Modules/Applications/AppClassification/app/otbTrainVectorRegression.cxx
new file mode 100644
index 0000000000000000000000000000000000000000..c98e69ee0c94b0b1882a4bd0ffab112e6020e53d
--- /dev/null
+++ b/Modules/Applications/AppClassification/app/otbTrainVectorRegression.cxx
@@ -0,0 +1,122 @@
+/*
+ * Copyright (C) 2005-2019 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 "otbTrainVectorBase.h"
+
+namespace otb
+{
+namespace Wrapper
+{
+
+class TrainVectorRegression : public TrainVectorBase<float, float>
+{
+public:
+ typedef TrainVectorRegression Self;
+ typedef TrainVectorBase<float, float> Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ itkNewMacro(Self) itkTypeMacro(Self, Superclass)
+
+ typedef Superclass::SampleType SampleType;
+ typedef Superclass::ListSampleType ListSampleType;
+ typedef Superclass::TargetListSampleType TargetListSampleType;
+
+protected:
+ TrainVectorRegression()
+ {
+ this->m_RegressionFlag = true;
+ }
+
+ void DoInit() override
+ {
+ SetName("TrainVectorRegression");
+ SetDescription(
+ "Train a regression algorithm based on geometries with "
+ "list of features to consider and a predictor.");
+
+ SetDocLongDescription(
+ "This application trains a regression algorithm based on "
+ "a predictor geometries and a list of features to consider for "
+ "regression.\nThis application is based on LibSVM, OpenCV Machine "
+ "Learning (2.3.1 and later), and Shark ML The output of this application "
+ "is a text model file, whose format corresponds to the ML model type "
+ "chosen. There is no image or vector data output.");
+
+ SetDocLimitations("None");
+ SetDocAuthors("OTB Team");
+ SetDocSeeAlso("TrainVectorClassifier");
+
+ SetOfficialDocLink();
+
+ Superclass::DoInit();
+
+ AddParameter(ParameterType_Float, "io.mse", "Mean Square Error");
+ SetParameterDescription("io.mse", "Mean square error computed with the validation predictors");
+ SetParameterRole("io.mse", Role_Output);
+ this->MandatoryOff("io.mse");
+ }
+
+ void DoUpdateParameters() override
+ {
+ Superclass::DoUpdateParameters();
+ }
+
+ double ComputeMSE(const TargetListSampleType& list1, const TargetListSampleType& list2)
+ {
+ assert(list1.Size() == list2.Size());
+ double mse = 0.;
+ for (TargetListSampleType::InstanceIdentifier i = 0; i < list1.Size(); ++i)
+ {
+ auto elem1 = list1.GetMeasurementVector(i);
+ auto elem2 = list2.GetMeasurementVector(i);
+
+ mse += (elem1[0] - elem2[0]) * (elem1[0] - elem2[0]);
+ }
+ mse /= static_cast<double>(list1.Size());
+ return mse;
+ }
+
+
+ void DoExecute() override
+ {
+ m_FeaturesInfo.SetClassFieldNames(GetChoiceNames("cfield"), GetSelectedItems("cfield"));
+
+ if (m_FeaturesInfo.m_SelectedCFieldIdx.empty() && GetClassifierCategory() == Supervised)
+ {
+ otbAppLogFATAL(<< "No field has been selected for data labelling!");
+ }
+
+ Superclass::DoExecute();
+
+ otbAppLogINFO("Computing training performances");
+
+ auto mse = ComputeMSE(*m_ClassificationSamplesWithLabel.labeledListSample, *m_PredictedList);
+
+ otbAppLogINFO("Mean Square Error = " << mse);
+ this->SetParameterFloat("io.mse", mse);
+ }
+
+private:
+};
+}
+}
+
+OTB_APPLICATION_EXPORT(otb::Wrapper::TrainVectorRegression)
diff --git a/Modules/Applications/AppClassification/include/otbTrainVectorBase.h b/Modules/Applications/AppClassification/include/otbTrainVectorBase.h
index 37869068157660e37b5063fd69303be97023df2f..bc5c716aef98324bcd14882b451fc2636dbfe9cc 100644
--- a/Modules/Applications/AppClassification/include/otbTrainVectorBase.h
+++ b/Modules/Applications/AppClassification/include/otbTrainVectorBase.h
@@ -49,21 +49,22 @@ bool IsNotAlphaNum(char c)
return !std::isalnum( c );
}
-class TrainVectorBase : public LearningApplicationBase<float, int>
+template <class TInputValue, class TOutputValue>
+class TrainVectorBase : public LearningApplicationBase<TInputValue, TOutputValue>
{
public:
/** Standard class typedefs. */
typedef TrainVectorBase Self;
- typedef LearningApplicationBase<float, int> Superclass;
+ typedef LearningApplicationBase<TInputValue, TOutputValue> Superclass;
typedef itk::SmartPointer <Self> Pointer;
typedef itk::SmartPointer<const Self> ConstPointer;
/** Standard macro */
itkTypeMacro(Self, Superclass);
- typedef Superclass::SampleType SampleType;
- typedef Superclass::ListSampleType ListSampleType;
- typedef Superclass::TargetListSampleType TargetListSampleType;
+ typedef typename Superclass::SampleType SampleType;
+ typedef typename Superclass::ListSampleType ListSampleType;
+ typedef typename Superclass::TargetListSampleType TargetListSampleType;
typedef double ValueType;
typedef itk::VariableLengthVector <ValueType> MeasurementType;
@@ -86,8 +87,8 @@ protected:
class SamplesWithLabel
{
public:
- ListSampleType::Pointer listSample;
- TargetListSampleType::Pointer labeledListSample;
+ typename ListSampleType::Pointer listSample;
+ typename TargetListSampleType::Pointer labeledListSample;
SamplesWithLabel()
{
listSample = ListSampleType::New();
@@ -178,13 +179,18 @@ protected:
SamplesWithLabel m_TrainingSamplesWithLabel;
SamplesWithLabel m_ClassificationSamplesWithLabel;
- TargetListSampleType::Pointer m_PredictedList;
+ typename TargetListSampleType::Pointer m_PredictedList;
FeaturesInfo m_FeaturesInfo;
void DoInit() override;
void DoUpdateParameters() override;
void DoExecute() override;
+private:
+ /**
+ * Get the field of the input feature corresponding to the input field
+ */
+ inline TOutputValue GetFeatureField(const ogr::Feature& feature, int field);
};
}
diff --git a/Modules/Applications/AppClassification/include/otbTrainVectorBase.hxx b/Modules/Applications/AppClassification/include/otbTrainVectorBase.hxx
index fb5e582dae4dc6073b77a5a2f1f2659831e1b3e9..c1e4f88f1cf9f428a038da63d99161e26daa9f66 100644
--- a/Modules/Applications/AppClassification/include/otbTrainVectorBase.hxx
+++ b/Modules/Applications/AppClassification/include/otbTrainVectorBase.hxx
@@ -27,100 +27,98 @@ namespace otb
namespace Wrapper
{
-void TrainVectorBase::DoInit()
+template <class TInputValue, class TOutputValue>
+void
+TrainVectorBase<TInputValue, TOutputValue>
+::DoInit()
{
// Common Parameters for all Learning Application
- AddParameter( ParameterType_Group, "io", "Input and output data" );
- SetParameterDescription( "io",
+ this->AddParameter( ParameterType_Group, "io", "Input and output data" );
+ this->SetParameterDescription( "io",
"This group of parameters allows setting input and output data." );
- AddParameter( ParameterType_InputVectorDataList, "io.vd", "Input Vector Data" );
- SetParameterDescription( "io.vd",
+ this->AddParameter( ParameterType_InputVectorDataList, "io.vd", "Input Vector Data" );
+ this->SetParameterDescription( "io.vd",
"Input geometries used for training (note: all geometries from the layer will be used)" );
- AddParameter( ParameterType_InputFilename, "io.stats", "Input XML image statistics file" );
- MandatoryOff( "io.stats" );
- SetParameterDescription( "io.stats",
+ this->AddParameter( ParameterType_InputFilename, "io.stats", "Input XML image statistics file" );
+ this->MandatoryOff( "io.stats" );
+ this->SetParameterDescription( "io.stats",
"XML file containing mean and variance of each feature." );
- AddParameter( ParameterType_OutputFilename, "io.out", "Output model" );
- SetParameterDescription( "io.out",
+ this->AddParameter( ParameterType_OutputFilename, "io.out", "Output model" );
+ this->SetParameterDescription( "io.out",
"Output file containing the model estimated (.txt format)." );
- AddParameter( ParameterType_Int, "layer", "Layer Index" );
- SetParameterDescription( "layer",
+ this->AddParameter( ParameterType_Int, "layer", "Layer Index" );
+ this->SetParameterDescription( "layer",
"Index of the layer to use in the input vector file." );
- MandatoryOff( "layer" );
- SetDefaultParameterInt( "layer", 0 );
+ this->MandatoryOff( "layer" );
+ this->SetDefaultParameterInt( "layer", 0 );
- AddParameter(ParameterType_ListView, "feat", "Field names for training features");
- SetParameterDescription("feat",
+ this->AddParameter(ParameterType_ListView, "feat", "Field names for training features");
+ this->SetParameterDescription("feat",
"List of field names in the input vector data to be used as features for training.");
// Add validation data used to compute confusion matrix or contingency table
- AddParameter( ParameterType_Group, "valid", "Validation data" );
- SetParameterDescription( "valid",
+ this->AddParameter( ParameterType_Group, "valid", "Validation data" );
+ this->SetParameterDescription( "valid",
"This group of parameters defines validation data." );
- AddParameter( ParameterType_InputVectorDataList, "valid.vd",
+ this->AddParameter( ParameterType_InputVectorDataList, "valid.vd",
"Validation Vector Data" );
- SetParameterDescription( "valid.vd", "Geometries used for validation "
+ this->SetParameterDescription( "valid.vd", "Geometries used for validation "
"(must contain the same fields used for training, all geometries from the layer will be used)" );
- MandatoryOff( "valid.vd" );
+ this->MandatoryOff( "valid.vd" );
- AddParameter( ParameterType_Int, "valid.layer", "Layer Index" );
- SetParameterDescription( "valid.layer",
+ this->AddParameter( ParameterType_Int, "valid.layer", "Layer Index" );
+ this->SetParameterDescription( "valid.layer",
"Index of the layer to use in the validation vector file." );
- MandatoryOff( "valid.layer" );
- SetDefaultParameterInt( "valid.layer", 0 );
+ this->MandatoryOff( "valid.layer" );
+ this->SetDefaultParameterInt( "valid.layer", 0 );
// Add class field if we used validation
- AddParameter( ParameterType_ListView, "cfield",
+ this->AddParameter( ParameterType_ListView, "cfield",
"Field containing the class integer label for supervision" );
- SetParameterDescription( "cfield",
+ this->SetParameterDescription( "cfield",
"Field containing the class id for supervision. "
"The values in this field shall be cast into integers. "
"Only geometries with this field available will be taken into account." );
- SetListViewSingleSelectionMode( "cfield", true );
+ this->SetListViewSingleSelectionMode( "cfield", true );
- // Add a new parameter to compute confusion matrix / contingency table
- AddParameter( ParameterType_OutputFilename, "io.confmatout",
- "Output confusion matrix or contingency table" );
- SetParameterDescription( "io.confmatout",
- "Output file containing the confusion matrix or contingency table (.csv format)."
- "The contingency table is output when we unsupervised algorithms is used otherwise the confusion matrix is output." );
- MandatoryOff( "io.confmatout" );
-
- AddParameter(ParameterType_Bool, "v", "Verbose mode");
- SetParameterDescription("v", "Verbose mode, display the contingency table result.");
- SetParameterInt("v", 1);
+ this->AddParameter(ParameterType_Bool, "v", "Verbose mode");
+ this->SetParameterDescription("v", "Verbose mode, display the contingency table result.");
+ this->SetParameterInt("v", 1);
// Doc example parameter settings
- SetDocExampleParameterValue( "io.vd", "vectorData.shp" );
- SetDocExampleParameterValue( "io.stats", "meanVar.xml" );
- SetDocExampleParameterValue( "io.out", "svmModel.svm" );
- SetDocExampleParameterValue( "feat", "perimeter area width" );
- SetDocExampleParameterValue( "cfield", "predicted" );
+ this->SetDocExampleParameterValue( "io.vd", "vectorData.shp" );
+ this->SetDocExampleParameterValue( "io.stats", "meanVar.xml" );
+ this->SetDocExampleParameterValue( "io.out", "svmModel.svm" );
+ this->SetDocExampleParameterValue( "feat", "perimeter area width" );
+ this->SetDocExampleParameterValue( "cfield", "predicted" );
// Add parameters for the classifier choice
Superclass::DoInit();
- AddRANDParameter();
+ this->AddRANDParameter();
}
-void TrainVectorBase::DoUpdateParameters()
+template <class TInputValue, class TOutputValue>
+void
+TrainVectorBase<TInputValue, TOutputValue>
+::DoUpdateParameters()
{
// if vector data is present and updated then reload fields
- if( HasValue( "io.vd" ) )
+ if( this->HasValue( "io.vd" ) )
{
- std::vector<std::string> vectorFileList = GetParameterStringList( "io.vd" );
+ std::vector<std::string> vectorFileList = this->GetParameterStringList( "io.vd" );
ogr::DataSource::Pointer ogrDS = ogr::DataSource::New( vectorFileList[0], ogr::DataSource::Modes::Read );
ogr::Layer layer = ogrDS->GetLayer( static_cast<size_t>( this->GetParameterInt( "layer" ) ) );
ogr::Feature feature = layer.ogr().GetNextFeature();
- ClearChoices( "feat" );
- ClearChoices( "cfield" );
+ this->ClearChoices( "feat" );
+ this->ClearChoices( "cfield" );
for( int iField = 0; iField < feature.ogr().GetFieldCount(); iField++ )
{
@@ -134,20 +132,23 @@ void TrainVectorBase::DoUpdateParameters()
if( fieldType == OFTInteger || fieldType == OFTInteger64 || fieldType == OFTReal )
{
std::string tmpKey = "feat." + key.substr( 0, static_cast<unsigned long>( end - key.begin() ) );
- AddChoice( tmpKey, item );
+ this->AddChoice( tmpKey, item );
}
- if( fieldType == OFTString || fieldType == OFTInteger || fieldType == OFTInteger64 )
+ if( fieldType == OFTString || fieldType == OFTInteger || fieldType == OFTInteger64 || fieldType == OFTReal )
{
std::string tmpKey = "cfield." + key.substr( 0, static_cast<unsigned long>( end - key.begin() ) );
- AddChoice( tmpKey, item );
+ this->AddChoice( tmpKey, item );
}
}
}
}
-void TrainVectorBase::DoExecute()
+template <class TInputValue, class TOutputValue>
+void
+TrainVectorBase<TInputValue, TOutputValue>
+::DoExecute()
{
- m_FeaturesInfo.SetFieldNames( GetChoiceNames( "feat" ), GetSelectedItems( "feat" ));
+ m_FeaturesInfo.SetFieldNames( this->GetChoiceNames( "feat" ), this->GetSelectedItems( "feat" ));
// Check input parameters
if( m_FeaturesInfo.m_SelectedIdx.empty() )
@@ -158,29 +159,35 @@ void TrainVectorBase::DoExecute()
ShiftScaleParameters measurement = GetStatistics( m_FeaturesInfo.m_NbFeatures );
ExtractAllSamples( measurement );
- this->Train( m_TrainingSamplesWithLabel.listSample, m_TrainingSamplesWithLabel.labeledListSample, GetParameterString( "io.out" ) );
+ this->Train( m_TrainingSamplesWithLabel.listSample, m_TrainingSamplesWithLabel.labeledListSample, this->GetParameterString( "io.out" ) );
m_PredictedList =
- this->Classify( m_ClassificationSamplesWithLabel.listSample, GetParameterString( "io.out" ) );
+ this->Classify( m_ClassificationSamplesWithLabel.listSample, this->GetParameterString( "io.out" ) );
}
-
-void TrainVectorBase::ExtractAllSamples(const ShiftScaleParameters &measurement)
+template <class TInputValue, class TOutputValue>
+void
+TrainVectorBase<TInputValue, TOutputValue>
+::ExtractAllSamples(const ShiftScaleParameters &measurement)
{
m_TrainingSamplesWithLabel = ExtractTrainingSamplesWithLabel(measurement);
m_ClassificationSamplesWithLabel = ExtractClassificationSamplesWithLabel(measurement);
}
-TrainVectorBase::SamplesWithLabel
-TrainVectorBase::ExtractTrainingSamplesWithLabel(const ShiftScaleParameters &measurement)
+template <class TInputValue, class TOutputValue>
+typename TrainVectorBase<TInputValue, TOutputValue>::SamplesWithLabel
+TrainVectorBase<TInputValue, TOutputValue>
+::ExtractTrainingSamplesWithLabel(const ShiftScaleParameters &measurement)
{
return ExtractSamplesWithLabel( "io.vd", "layer", measurement);
}
-TrainVectorBase::SamplesWithLabel
-TrainVectorBase::ExtractClassificationSamplesWithLabel(const ShiftScaleParameters &measurement)
+template <class TInputValue, class TOutputValue>
+typename TrainVectorBase<TInputValue, TOutputValue>::SamplesWithLabel
+TrainVectorBase<TInputValue, TOutputValue>
+::ExtractClassificationSamplesWithLabel(const ShiftScaleParameters &measurement)
{
- if(GetClassifierCategory() == Supervised)
+ if(this->GetClassifierCategory() == Superclass::Supervised)
{
SamplesWithLabel tmpSamplesWithLabel;
SamplesWithLabel validationSamplesWithLabel = ExtractSamplesWithLabel( "valid.vd", "valid.layer", measurement );
@@ -206,15 +213,16 @@ TrainVectorBase::ExtractClassificationSamplesWithLabel(const ShiftScaleParameter
}
}
-
-TrainVectorBase::ShiftScaleParameters
-TrainVectorBase::GetStatistics(unsigned int nbFeatures)
+template <class TInputValue, class TOutputValue>
+typename TrainVectorBase<TInputValue, TOutputValue>::ShiftScaleParameters
+TrainVectorBase<TInputValue, TOutputValue>
+::GetStatistics(unsigned int nbFeatures)
{
ShiftScaleParameters measurement = ShiftScaleParameters();
- if( HasValue( "io.stats" ) && IsParameterEnabled( "io.stats" ) )
+ if( this->HasValue( "io.stats" ) && this->IsParameterEnabled( "io.stats" ) )
{
- StatisticsReader::Pointer statisticsReader = StatisticsReader::New();
- std::string XMLfile = GetParameterString( "io.stats" );
+ typename StatisticsReader::Pointer statisticsReader = StatisticsReader::New();
+ std::string XMLfile = this->GetParameterString( "io.stats" );
statisticsReader->SetFileName( XMLfile );
measurement.meanMeasurementVector = statisticsReader->GetStatisticVectorByName( "mean" );
measurement.stddevMeasurementVector = statisticsReader->GetStatisticVectorByName( "stddev" );
@@ -229,16 +237,34 @@ TrainVectorBase::GetStatistics(unsigned int nbFeatures)
return measurement;
}
+// Template specialization for the integer case (i.e.classification), to avoid a cast from double to integer
+template <>
+inline int
+TrainVectorBase<float, int>
+::GetFeatureField(const ogr::Feature & feature, int fieldIndex)
+{
+ return(feature[fieldIndex].GetValue<int>());
+}
+
+template <class TInputValue, class TOutputValue>
+inline TOutputValue
+TrainVectorBase<TInputValue, TOutputValue>
+::GetFeatureField(const ogr::Feature & feature, int fieldIndex)
+{
+ return(feature[fieldIndex].GetValue<double>());
+}
-TrainVectorBase::SamplesWithLabel
-TrainVectorBase::ExtractSamplesWithLabel(std::string parameterName, std::string parameterLayer,
+template <class TInputValue, class TOutputValue>
+typename TrainVectorBase<TInputValue, TOutputValue>::SamplesWithLabel
+TrainVectorBase<TInputValue, TOutputValue>
+::ExtractSamplesWithLabel(std::string parameterName, std::string parameterLayer,
const ShiftScaleParameters &measurement)
{
SamplesWithLabel samplesWithLabel;
- if( HasValue( parameterName ) && IsParameterEnabled( parameterName ) )
+ if( this->HasValue( parameterName ) && this->IsParameterEnabled( parameterName ) )
{
- ListSampleType::Pointer input = ListSampleType::New();
- TargetListSampleType::Pointer target = TargetListSampleType::New();
+ typename ListSampleType::Pointer input = ListSampleType::New();
+ typename TargetListSampleType::Pointer target = TargetListSampleType::New();
input->SetMeasurementVectorSize( m_FeaturesInfo.m_NbFeatures );
std::vector<std::string> fileList = this->GetParameterStringList( parameterName );
@@ -251,7 +277,7 @@ TrainVectorBase::ExtractSamplesWithLabel(std::string parameterName, std::string
bool goesOn = feature.addr() != 0;
if( !goesOn )
{
- otbAppLogWARNING( "The layer " << GetParameterInt( parameterLayer ) << " of " << fileList[k]
+ otbAppLogWARNING( "The layer " << this->GetParameterInt( parameterLayer ) << " of " << fileList[k]
<< " is empty, input is skipped." );
continue;
}
@@ -284,14 +310,14 @@ TrainVectorBase::ExtractSamplesWithLabel(std::string parameterName, std::string
MeasurementType mv;
mv.SetSize( m_FeaturesInfo.m_NbFeatures );
for( unsigned int idx = 0; idx < m_FeaturesInfo.m_NbFeatures; ++idx )
- mv[idx] = feature.ogr().GetFieldAsDouble( featureFieldIndex[idx] );
+ mv[idx] = feature[featureFieldIndex[idx]].GetValue<double>();
input->PushBack( mv );
if(cFieldIndex>=0 && ogr::Field(feature,cFieldIndex).HasBeenSet())
- target->PushBack( feature.ogr().GetFieldAsInteger( cFieldIndex ) );
+ target->PushBack(GetFeatureField(feature,cFieldIndex));
else
- target->PushBack( 0 );
+ target->PushBack( 0. );
feature = layer.ogr().GetNextFeature();
goesOn = feature.addr() != 0;
@@ -300,7 +326,7 @@ TrainVectorBase::ExtractSamplesWithLabel(std::string parameterName, std::string
- ShiftScaleFilterType::Pointer shiftScaleFilter = ShiftScaleFilterType::New();
+ typename ShiftScaleFilterType::Pointer shiftScaleFilter = ShiftScaleFilterType::New();
shiftScaleFilter->SetInput( input );
shiftScaleFilter->SetShifts( measurement.meanMeasurementVector );
shiftScaleFilter->SetScales( measurement.stddevMeasurementVector );
diff --git a/Modules/Applications/AppClassification/test/CMakeLists.txt b/Modules/Applications/AppClassification/test/CMakeLists.txt
index 2379deb501c3c6233fb1a1a6b34e8fe99a78c6e0..15286ce99c373666820979ebc1f73d7c848169f6 100644
--- a/Modules/Applications/AppClassification/test/CMakeLists.txt
+++ b/Modules/Applications/AppClassification/test/CMakeLists.txt
@@ -837,6 +837,22 @@ if(OTB_USE_OPENCV)
${TEMP}/apTvClTrainVectorClassifierModel.rf)
endif()
+#----------- TrainVectorRegression TESTS ----------------
+if(OTB_USE_OPENCV)
+ otb_test_application(NAME apTvClTrainVectorRegression
+ APP TrainVectorRegression
+ OPTIONS -io.vd ${INPUTDATA}/Classification/apTvClSampleExtractionOut.sqlite
+ -feat value_0 value_1 value_2 value_3
+ -cfield class
+ -classifier rf
+ -io.out ${TEMP}/apTvClTrainVectorRegressionModel.rf
+ -io.mse ${TEMP}/apTvClTrainVectorRegressionModel.txt
+ TESTENVOPTIONS ${TEMP}/apTvClTrainVectorRegressionModel.txt
+ VALID ${ascii_comparison}
+ ${OTBAPP_BASELINE_FILES}/apTvClTrainVectorRegressionModel.txt
+ ${TEMP}/apTvClTrainVectorRegressionModel.txt)
+endif()
+
#----------- TrainVectorClassifier unsupervised TESTS ----------------
if(OTB_USE_SHARK)
otb_test_application(NAME apTvClTrainVectorUnsupervised
diff --git a/Modules/Applications/AppImageUtils/app/otbRescale.cxx b/Modules/Applications/AppImageUtils/app/otbRescale.cxx
index 703215872f1ad4ba111438a819108497b338fba3..0a50d18e46ceffab913d0e97a0930c0d3a1ed6b4 100644
--- a/Modules/Applications/AppImageUtils/app/otbRescale.cxx
+++ b/Modules/Applications/AppImageUtils/app/otbRescale.cxx
@@ -59,7 +59,7 @@ private:
"Input minimum and maximum values is automatically computed for all image bands.");
SetDocLimitations("None");
SetDocAuthors("OTB-Team");
- SetDocSeeAlso(" ");
+ SetDocSeeAlso("DynamicConvert");
AddDocTag(Tags::Deprecated);
AddDocTag(Tags::Manip);
diff --git a/Modules/Applications/AppSegmentation/app/otbLSMSSmallRegionsMerging.cxx b/Modules/Applications/AppSegmentation/app/otbLSMSSmallRegionsMerging.cxx
index 29c8d8c6aed5d2d92c36a44344da5f4b3a970dd0..6f8f839953e039d408f676a8f7c70231db5ec3ba 100644
--- a/Modules/Applications/AppSegmentation/app/otbLSMSSmallRegionsMerging.cxx
+++ b/Modules/Applications/AppSegmentation/app/otbLSMSSmallRegionsMerging.cxx
@@ -96,12 +96,14 @@ private:
" application is not compatible with in-memory connection since it does"
" its own internal streaming.");
SetDocAuthors("David Youssefi");
- SetDocSeeAlso( "[1] Michel, J., Youssefi, D., & Grizonnet, M. (2015). Stable"
- " mean-shift algorithm and its application to the segmentation of"
- " arbitrarily large remote sensing images. IEEE Transactions on"
- " Geoscience and Remote Sensing, 53(2), 952-964.\n"
- "[2] LSMSegmentation\n"
- "[3] LSMSVectorization");
+ SetDocSeeAlso(
+ "Alternative: SmallRegionsMerging\n"
+ "[1] Michel, J., Youssefi, D., & Grizonnet, M. (2015). Stable"
+ " mean-shift algorithm and its application to the segmentation of"
+ " arbitrarily large remote sensing images. IEEE Transactions on"
+ " Geoscience and Remote Sensing, 53(2), 952-964.\n"
+ "[2] LSMSSegmentation\n"
+ "[3] LSMSVectorization");
AddDocTag(Tags::Segmentation);
AddDocTag(Tags::Deprecated);
AddDocTag("LSMS");
diff --git a/Modules/Wrappers/ApplicationEngine/include/otbWrapperApplication.h b/Modules/Wrappers/ApplicationEngine/include/otbWrapperApplication.h
index 3e087664964ec72fda368b33c054875825afd4c8..4da58cf694656ef7fa65856fc0af418f8da2ff3d 100644
--- a/Modules/Wrappers/ApplicationEngine/include/otbWrapperApplication.h
+++ b/Modules/Wrappers/ApplicationEngine/include/otbWrapperApplication.h
@@ -669,6 +669,9 @@ public:
void AddDocTag(const std::string&);
+ /** return wether the application has the "deprecated tag or not */
+ bool IsDeprecated();
+
DocExampleStructure::Pointer GetDocExample();
unsigned int GetNumberOfExamples();
std::string GetExampleComment(unsigned int id);
diff --git a/Modules/Wrappers/ApplicationEngine/src/otbWrapperApplication.cxx b/Modules/Wrappers/ApplicationEngine/src/otbWrapperApplication.cxx
index 3657c6a54a6d9fb0450623ab54b432ccbc597fc2..085ae8c098cdb74b0130e5659091c75960921b42 100644
--- a/Modules/Wrappers/ApplicationEngine/src/otbWrapperApplication.cxx
+++ b/Modules/Wrappers/ApplicationEngine/src/otbWrapperApplication.cxx
@@ -256,6 +256,11 @@ void Application::AddDocTag(const std::string & tag)
}
}
+bool Application::IsDeprecated()
+{
+ return std::find(m_DocTags.begin(), m_DocTags.end(), Tags::Deprecated) != m_DocTags.end();
+}
+
DocExampleStructure::Pointer Application::GetDocExample()
{
if (!IsInitialized())
diff --git a/Modules/Wrappers/CommandLine/include/otbWrapperCommandLineLauncher.h b/Modules/Wrappers/CommandLine/include/otbWrapperCommandLineLauncher.h
index 9e097a67cfafd11f96efc38867ea37e4b643d62b..e6a26418b2af0f7664a3eb338cd1fa45744c1da9 100644
--- a/Modules/Wrappers/CommandLine/include/otbWrapperCommandLineLauncher.h
+++ b/Modules/Wrappers/CommandLine/include/otbWrapperCommandLineLauncher.h
@@ -112,9 +112,6 @@ public:
/** Create and display the help of the application */
void DisplayHelp(bool longHelp=false);
- /** Create and display the long help of the application */
- void DisplayLongHelp();
-
/** Performs specific action for testing environment */
void LoadTestEnv();
diff --git a/Modules/Wrappers/CommandLine/src/otbWrapperCommandLineLauncher.cxx b/Modules/Wrappers/CommandLine/src/otbWrapperCommandLineLauncher.cxx
index 4cdb8ee984d82b12abc715c8beadfa4e22d9f3bb..2e31ce8356f15ab9db6a59cd87038f937165cbe9 100644
--- a/Modules/Wrappers/CommandLine/src/otbWrapperCommandLineLauncher.cxx
+++ b/Modules/Wrappers/CommandLine/src/otbWrapperCommandLineLauncher.cxx
@@ -282,7 +282,12 @@ bool CommandLineLauncher::BeforeExecute()
return false;
}
- return true;
+ if (m_Application->IsDeprecated())
+ {
+ m_Application->GetLogger()->Warning("This application is deprecated and will be removed in a future OTB release.\n");
+ }
+
+ return true;
}
bool CommandLineLauncher::LoadPath()
@@ -584,6 +589,12 @@ void CommandLineLauncher::DisplayHelp(bool longHelp)
std::cerr<<std::endl;
std::cerr << "This is the " << m_Application->GetName() << " application, version " << OTB_VERSION_STRING << std::endl << std::endl;
+ if (m_Application->IsDeprecated())
+ {
+ std::cerr << "WARNING: This application is deprecated, it will be removed in a future OTB release." << std::endl;
+ std::cerr << std::endl;
+ }
+
std::cerr << m_Application->GetDescription() << std::endl;
if(longHelp)
diff --git a/Modules/Wrappers/QtWidget/src/appmainwindow.ui b/Modules/Wrappers/QtWidget/src/appmainwindow.ui
index c376f1984f3cec0518739bf1dd22fe3b6fb4f4be..88eb9a25bdf45af1a55696859d6a5f87c1177356 100644
--- a/Modules/Wrappers/QtWidget/src/appmainwindow.ui
+++ b/Modules/Wrappers/QtWidget/src/appmainwindow.ui
@@ -117,6 +117,13 @@
</widget>
</widget>
</item>
+ <item alignment="Qt::AlignHCenter|Qt::AlignVCenter">
+ <widget class="QLabel" name="deprecation">
+ <property name="text">
+ <string>Deprecation status</string>
+ </property>
+ </widget>
+ </item>
<item>
<widget class="QLabel" name="message">
<property name="text">
diff --git a/Modules/Wrappers/QtWidget/src/otbWrapperQtWidgetMainWindow.cxx b/Modules/Wrappers/QtWidget/src/otbWrapperQtWidgetMainWindow.cxx
index 93c3f459e2e43b49d43e879a84e3f83ccfa30345..282c710ec25cc52408d97e2808a0726f5cb9c14d 100644
--- a/Modules/Wrappers/QtWidget/src/otbWrapperQtWidgetMainWindow.cxx
+++ b/Modules/Wrappers/QtWidget/src/otbWrapperQtWidgetMainWindow.cxx
@@ -70,6 +70,18 @@ QtMainWindow::QtMainWindow(Application::Pointer app, QtWidgetView* gui, QWidget*
// Setup the progress bar to observe the model
ui->progressBar->SetModel(gui->GetModel());
+ // Fill and display the deprecation status label if needed, or hide it.
+ if (app->IsDeprecated())
+ {
+ ui->deprecation->setVisible(true);
+ ui->deprecation->setText("<font color='#E65100'>This application is deprecated and will be removed in a future release.</font>");
+ }
+ else
+ {
+ ui->deprecation->setVisible(false);
+ ui->deprecation->setText("");
+ }
+
// Connect application progress text to the QLabel
connect(ui->progressBar, &QtWidgetSimpleProgressReport::SetText, ui->message, &QLabel::setText);
diff --git a/Modules/Wrappers/SWIG/src/otbApplication.i b/Modules/Wrappers/SWIG/src/otbApplication.i
index a3b9590f34b84880213124c43438a4728612bed0..d03ad7b1e9551e17289aaa586f797fa5f51917ea 100644
--- a/Modules/Wrappers/SWIG/src/otbApplication.i
+++ b/Modules/Wrappers/SWIG/src/otbApplication.i
@@ -225,6 +225,7 @@ public:
unsigned long itk::Object::AddObserver(const EventObject & event,
Command * command);
+ bool IsDeprecated();
#if SWIGPYTHON
%extend
@@ -901,6 +902,8 @@ public:
application = _otbApplication.Registry_CreateApplicationWithoutLogger(name)
if application is not None:
application.SetupLogger()
+ if application.IsDeprecated():
+ application.GetLogger().Warning("This application is deprecated and will be removed in a future OTB release")
return application
}
#else
diff --git a/Modules/Wrappers/SWIG/src/otbPythonLogOutput.i b/Modules/Wrappers/SWIG/src/otbPythonLogOutput.i
index 4bd7852b2ee7540e8cacb172ecbca7ba2d376ffa..748c8bfef4820b6bd9a04c6d19d8c57f61ca7a84 100644
--- a/Modules/Wrappers/SWIG/src/otbPythonLogOutput.i
+++ b/Modules/Wrappers/SWIG/src/otbPythonLogOutput.i
@@ -72,6 +72,15 @@ public:
virtual void AddLogOutput(itkLogOutput *output);
static Logger * Instance();
void ResetOutputs();
+
+ // Wrap message methods so we can print stuff from Python
+ void Debug(std::string const & message);
+ void Info(std::string const & message);
+ void Warning(std::string const & message);
+ void Critical(std::string const & message);
+ void Error(std::string const & message);
+ void Fatal(std::string const & message);
+
protected:
Logger();
virtual ~Logger();