From b0a4f4a57ba46d0b18d84acf21bd4cbdecf3ad94 Mon Sep 17 00:00:00 2001
From: Jordi Inglada <jordi.inglada@cesbio.cnes.fr>
Date: Tue, 27 Feb 2018 17:35:35 +0100
Subject: [PATCH] ENH: add options for the different strategies
---
.../app/otbSampleAugmentation.cxx | 75 +++++++++++++++++--
.../include/otbSampleAugmentation.h | 6 +-
.../AppClassification/test/CMakeLists.txt | 29 ++++++-
3 files changed, 101 insertions(+), 9 deletions(-)
diff --git a/Modules/Applications/AppClassification/app/otbSampleAugmentation.cxx b/Modules/Applications/AppClassification/app/otbSampleAugmentation.cxx
index 36fc02f8bf..a12e3912b1 100644
--- a/Modules/Applications/AppClassification/app/otbSampleAugmentation.cxx
+++ b/Modules/Applications/AppClassification/app/otbSampleAugmentation.cxx
@@ -99,6 +99,42 @@ private:
SetParameterDescription("exclude",
"List of field names in the input vector data that will not be generated in the output file.");
+ AddParameter(ParameterType_Choice, "strategy", "Augmentation strategy");
+
+ AddChoice("strategy.replicate","Replicate input samples");
+ SetParameterDescription("strategy.replicate","The new samples are generated "
+ "by replicating input samples which are randomly "
+ "selected with replacement.");
+
+ AddChoice("strategy.jitter","Jitter input samples");
+ SetParameterDescription("strategy.jitter","The new samples are generated "
+ "by adding gaussian noise to input samples which are "
+ "randomly selected with replacement.");
+ AddParameter(ParameterType_Float, "strategy.jitter.stdfactor",
+ "Factor for dividing the standard deviation of each feature");
+ SetParameterDescription("strategy.jitter.stdfactor",
+ "The noise added to the input samples will have the "
+ "standard deviation of the input features divided "
+ "by the value of this parameter. ");
+ SetDefaultParameterFloat("strategy.jitter.stdfactor",10000);
+
+ AddChoice("strategy.smote","Smote input samples");
+ SetParameterDescription("strategy.smote","The new samples are generated "
+ "by using the SMOTE algorithm (http://dx.doi.org/10.1613/jair.953) "
+ "on input samples which are "
+ "randomly selected with replacement.");
+ AddParameter(ParameterType_Int, "strategy.smote.neighbors",
+ "Number of nearest neighbors.");
+ SetParameterDescription("strategy.smote.neighbors",
+ "Number of nearest neighbors to be used in the "
+ "SMOTE algorithm");
+ SetDefaultParameterFloat("strategy.smote.neighbors", 5);
+
+ AddParameter(ParameterType_Int, "seed",
+ "Random seed.");
+ SetParameterDescription("seed",
+ "Seed for the random number generator.");
+ MandatoryOff("seed");
// Doc example parameter settings
SetDocExampleParameterValue("in", "samples.sqlite");
@@ -107,6 +143,8 @@ private:
SetDocExampleParameterValue("samples", "100");
SetDocExampleParameterValue("out","augmented_samples.sqlite");
SetDocExampleParameterValue( "exclude", "OGC_FID name class originfid" );
+ SetDocExampleParameterValue("strategy", "smote");
+ SetDocExampleParameterValue("strategy.smote.neighbors", "5");
SetOfficialDocLink();
}
@@ -186,12 +224,39 @@ private:
fieldName,
this->GetParameterInt("label"),
excludedFeatures);
+ int seed = std::time(nullptr);
+ if(IsParameterEnabled("seed")) seed = this->GetParameterInt("seed");
SampleVectorType newSamples;
- // sampleAugmentation::replicateSamples(inSamples, this->GetParameterInt("samples"),
- // newSamples);
- sampleAugmentation::smote(inSamples, this->GetParameterInt("samples"),
- newSamples,
- 4);
+ switch (this->GetParameterInt("strategy"))
+ {
+ // replicate
+ case 0:
+ {
+ otbAppLogINFO("Augmentation strategy : replicate");
+ sampleAugmentation::replicateSamples(inSamples, this->GetParameterInt("samples"),
+ newSamples);
+ }
+ break;
+ // jitter
+ case 1:
+ {
+ otbAppLogINFO("Augmentation strategy : jitter");
+ sampleAugmentation::jitterSamples(inSamples, this->GetParameterInt("samples"),
+ newSamples,
+ this->GetParameterFloat("strategy.jitter.stdfactor"),
+ seed);
+ }
+ break;
+ case 2:
+ {
+ otbAppLogINFO("Augmentation strategy : smote");
+ sampleAugmentation::smote(inSamples, this->GetParameterInt("samples"),
+ newSamples,
+ this->GetParameterInt("strategy.smote.neighbors"),
+ seed);
+ }
+ break;
+ }
writeSamples(vectors, output, newSamples, this->GetParameterInt("layer"),
fieldName,
this->GetParameterInt("label"),
diff --git a/Modules/Applications/AppClassification/include/otbSampleAugmentation.h b/Modules/Applications/AppClassification/include/otbSampleAugmentation.h
index 27b9f07847..43fd6657a0 100644
--- a/Modules/Applications/AppClassification/include/otbSampleAugmentation.h
+++ b/Modules/Applications/AppClassification/include/otbSampleAugmentation.h
@@ -58,7 +58,9 @@ SampleType estimateStds(SampleVectorType samples)
}
}
for(auto std : stds)
+ {
std = std::sqrt(std/nbSamples);
+ }
return stds;
}
@@ -86,7 +88,7 @@ void replicateSamples(const SampleVectorType& inSamples,
void jitterSamples(const SampleVectorType& inSamples,
const size_t nbSamples,
SampleVectorType& newSamples,
- float stdFactor=1.0,
+ float stdFactor=10000,
const int seed = std::time(nullptr))
{
newSamples.resize(nbSamples);
@@ -100,7 +102,7 @@ void jitterSamples(const SampleVectorType& inSamples,
auto stds = estimateStds(inSamples);
std::vector<std::normal_distribution<double>> gaussDis;
for(size_t i=0; i<nbComponents; ++i)
- gaussDis.emplace_back(std::normal_distribution<double>{0.0, stds[i]*stdFactor});
+ gaussDis.emplace_back(std::normal_distribution<double>{0.0, stds[i]/stdFactor});
for(size_t i=0; i<nbSamples; ++i)
{
newSamples[i] = inSamples[std::rand()%nbSamples];
diff --git a/Modules/Applications/AppClassification/test/CMakeLists.txt b/Modules/Applications/AppClassification/test/CMakeLists.txt
index c0ec37fea3..c134b6b355 100644
--- a/Modules/Applications/AppClassification/test/CMakeLists.txt
+++ b/Modules/Applications/AppClassification/test/CMakeLists.txt
@@ -974,12 +974,37 @@ otb_test_application(
)
#------------ SampleAgmentation TESTS ----------------
-otb_test_application(NAME apTvClSampleAugmentation
+otb_test_application(NAME apTvClSampleAugmentationReplicate
APP SampleAugmentation
OPTIONS -in ${INPUTDATA}/Classification/apTvClSampleExtractionOut.sqlite
-field class
-label 3
-samples 100
- -out ${TEMP}/apTvClSampleAugmentation.sqlite
+ -out ${TEMP}/apTvClSampleAugmentationReplicate.sqlite
-exclude originfid
+ -strategy replicate
+ )
+
+otb_test_application(NAME apTvClSampleAugmentationJitter
+ APP SampleAugmentation
+ OPTIONS -in ${INPUTDATA}/Classification/apTvClSampleExtractionOut.sqlite
+ -field class
+ -label 3
+ -samples 100
+ -out ${TEMP}/apTvClSampleAugmentationJitter.sqlite
+ -exclude originfid
+ -strategy jitter
+ -strategy.jitter.stdfactor 10000
+ )
+
+otb_test_application(NAME apTvClSampleAugmentationSmote
+ APP SampleAugmentation
+ OPTIONS -in ${INPUTDATA}/Classification/apTvClSampleExtractionOut.sqlite
+ -field class
+ -label 3
+ -samples 100
+ -out ${TEMP}/apTvClSampleAugmentationSmote.sqlite
+ -exclude originfid
+ -strategy smote
+ -strategy.smote.neighbors 5
)
--
GitLab