Commit 2cce295e authored by Cédric Traizet's avatar Cédric Traizet

Merge branch 'develop' into remove_java_superbuild

parents 9bb9edb6 78d7f56c
Pipeline #1394 passed with stages
in 10 minutes and 31 seconds
......@@ -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
......
......@@ -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(" ", "_")
......
.. _{label}:
{heading}
{deprecation_string}
{description}
Description
......
......@@ -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
......
......@@ -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);
}
......
......@@ -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
......
/*
* 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)
......@@ -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);
};
}
......
......@@ -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
......
......@@ -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);
......
......@@ -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");
......
......@@ -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);
......
......@@ -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())
......
......@@ -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();
......
......@@ -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)
......
......@@ -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">
......
......@@ -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);
......
......@@ -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
......
......@@ -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();
......
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