Merge pull request #28 from spectre-team/feature/wavelet-denoising-in…

…tegration

Wavelet denoising integration

appveyor.yml

@@ -13,7 +13,7 @@ environment:
 configuration:
   - Debug
   - Release
-version: 3.13.0.{build}
+version: 3.14.0.{build}
 
 init:
 - cmd: echo Project - %APPVEYOR_PROJECT_NAME%

src/Spectre.libWavelet.Tests/DaubechiesFiltersDenoiserTest.cpp

@@ -0,0 +1,79 @@
+/*
+* DaubechiesFiltersDenoiserTest.cpp
+* Tests wavelet denoising using Daubechies filters.
+*
+Copyright 2018 Michal Gallus
+
+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 <gtest/gtest.h>
+#include "FloatingPointVectorMatcher.h"
+#include "Spectre.libWavelet\DaubechiesFiltersDenoiser.h"
+#include "Spectre.libWavelet\WaveletDecomposerRef.h"
+#include "Spectre.libWavelet\WaveletReconstructorRef.h"
+
+namespace
+{
+    using namespace spectre::algorithm::wavelet;
+
+    TEST(DaubechiesFiltersDenoiserInitialization, initializes)
+    {
+        EXPECT_NO_THROW(DaubechiesFiltersDenoiser());
+    }
+
+    class DaubechiesFiltersDenoiserTest : public ::testing::Test
+    {
+    public:
+        DaubechiesFiltersDenoiserTest()
+        {
+            signal = {
+                0.0,
+                1.0,
+                0.2,
+                0.0,
+                3.0,
+                6.0,
+                0.3,
+                7.0,
+                0.1,
+                0.2,
+                0.1
+            };
+            correctResult = {
+                -0.1322,
+                -0.0672,
+                -0.0567,
+                -0.0068,
+                0.6509,
+                1.2891,
+                -1.0844,
+                1.7828,
+                -0.1743,
+                0.0527,
+                -0.1567
+            };
+        }
+    protected:
+        Signal signal;
+        Signal correctResult;
+        DaubechiesFiltersDenoiser denoiser;
+    };
+
+    TEST_F(DaubechiesFiltersDenoiserTest, denoises_signal)
+    {
+        Signal denoisedSignal = denoiser.Denoise(signal);
+        auto doubleNear = double_near(0.001);
+        EXPECT_THAT(correctResult, testing::Pointwise(doubleNear, denoisedSignal));
+    }
+}

src/Spectre.libWavelet.Tests/Spectre.libWavelet.Tests.vcxproj

@@ -138,6 +138,7 @@
   </ItemDefinitionGroup>
   <ItemGroup>
     <ClCompile Include="..\Common\Main.cpp" />
+    <ClCompile Include="DaubechiesFiltersDenoiserTest.cpp" />
     <ClCompile Include="MedianAbsoluteDeviationNoiseEstimatorTest.cpp" />
     <ClCompile Include="ConvolutionTest.cpp" />
     <ClCompile Include="SoftThresholderTest.cpp" />

src/Spectre.libWavelet.Tests/Spectre.libWavelet.Tests.vcxproj.filters

@@ -39,6 +39,9 @@
     <ClCompile Include="MedianAbsoluteDeviationNoiseEstimatorTest.cpp">
       <Filter>Source Files</Filter>
     </ClCompile>
+    <ClCompile Include="DaubechiesFiltersDenoiserTest.cpp">
+      <Filter>Source Files</Filter>
+    </ClCompile>
   </ItemGroup>
   <ItemGroup>
     <None Include="packages.config" />

src/Spectre.libWavelet/DaubechiesFiltersDenoiser.cpp

@@ -0,0 +1,72 @@
+/*
+ * DaubechiesFiltersDenoiser.cpp
+ * Denoises the signal using undecimated wavelet transform.
+ *
+   Copyright 2018 Michal Gallus
+   
+   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 "DaubechiesFiltersDenoiser.h"
+#include "SoftThresholder.h"
+
+namespace spectre::algorithm::wavelet
+{
+DaubechiesFiltersDenoiser::DaubechiesFiltersDenoiser()
+{
+}
+
+static inline void ExtractCoefficientsForNoiseEstimation(Signal& highFrequencyCoeffs,
+    WaveletCoefficients& coefficients)
+{
+    CoefficientList& noiseEstimationCoefficients = coefficients.data[0][0];
+    auto chunkStart = noiseEstimationCoefficients.begin();
+    auto chunkEnd = chunkStart + highFrequencyCoeffs.size();
+    highFrequencyCoeffs.assign(chunkStart, chunkEnd);
+}
+
+static inline WaveletCoefficients TresholdSignal(const NoiseEstimator& noiseEstimator,
+    WaveletCoefficients& coefficients, size_t signalLength)
+{
+    Signal highFreqCoefficients(signalLength);
+    ExtractCoefficientsForNoiseEstimation(highFreqCoefficients, coefficients);
+    DataType noiseTreshold = noiseEstimator.Estimate(highFreqCoefficients);
+    SoftThresholder tresholder(noiseTreshold);
+    return tresholder(std::move(coefficients));
+}
+
+static inline WaveletCoefficients Decompose(const WaveletDecomposerRef& decomposer,
+    Signal& signal)
+{
+    return decomposer.Decompose(std::move(signal));
+}
+
+static inline Signal Reconstruct(const WaveletReconstructorRef& reconstructor,
+    WaveletCoefficients& coefficients, size_t signalLength)
+{
+    return reconstructor.Reconstruct(std::move(coefficients), signalLength);
+}
+
+Signal DaubechiesFiltersDenoiser::Denoise(Signal& signal) const
+{
+    const size_t signalLength = signal.size();
+
+    if (signalLength < 2)
+        return signal;
+
+    WaveletCoefficients coefficients = Decompose(m_Decomposer, signal);
+    coefficients = TresholdSignal(m_NoiseEstimator, coefficients, signalLength);
+    Signal denoisedSignal = Reconstruct(m_Reconstructor, coefficients, signalLength);
+
+    return denoisedSignal;
+}
+}

src/Spectre.libWavelet/DaubechiesFiltersDenoiser.h

@@ -0,0 +1,42 @@
+/*
+ * DaubechiesFiltersDenoiser.h
+ * Denoises the signal using undecimated wavelet transform.
+ *
+   Copyright 2018 Michal Gallus
+
+   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.
+*/
+#pragma once
+#include <memory>
+#include "DataTypes.h"
+#include "Spectre.libWavelet/MedianAbsoluteDeviationNoiseEstimator.h"
+#include "Spectre.libWavelet/WaveletDecomposerRef.h"
+#include "Spectre.libWavelet/WaveletReconstructorRef.h"
+
+namespace spectre::algorithm::wavelet
+{
+using NoiseEstimator = MedianAbsoluteDeviationNoiseEstimator;
+
+class DaubechiesFiltersDenoiser
+{
+public:
+    explicit DaubechiesFiltersDenoiser();
+    Signal Denoise(Signal& signal) const;
+private:
+    static constexpr unsigned m_Base = 4;
+    static constexpr unsigned m_LevelsOfDecomposition = 10;
+    const NoiseEstimator m_NoiseEstimator;
+    const WaveletDecomposerRef m_Decomposer;
+    const WaveletReconstructorRef m_Reconstructor;
+};
+}

src/Spectre.libWavelet/Spectre.libWavelet.vcxproj

@@ -129,6 +129,7 @@
     <ClInclude Include="AlgorithmConstants.h" />
     <ClInclude Include="Convolution.h" />
     <ClInclude Include="DataTypes.h" />
+    <ClInclude Include="DaubechiesFiltersDenoiser.h" />
     <ClInclude Include="MedianAbsoluteDeviationNoiseEstimator.h" />
     <ClInclude Include="PrecomputedDaubechiesCoefficients.h" />
     <ClInclude Include="SoftThresholder.h" />
@@ -139,6 +140,7 @@
   </ItemGroup>
   <ItemGroup>
     <ClCompile Include="Convolution.cpp" />
+    <ClCompile Include="DaubechiesFiltersDenoiser.cpp" />
     <ClCompile Include="MedianAbsoluteDeviationNoiseEstimator.cpp" />
     <ClCompile Include="SoftThresholder.cpp" />
     <ClCompile Include="WaveletDecomposerRef.cpp" />

src/Spectre.libWavelet/Spectre.libWavelet.vcxproj.filters

@@ -45,6 +45,9 @@
     <ClInclude Include="MedianAbsoluteDeviationNoiseEstimator.h">
       <Filter>Header Files</Filter>
     </ClInclude>
+    <ClInclude Include="DaubechiesFiltersDenoiser.h">
+      <Filter>Header Files</Filter>
+    </ClInclude>
   </ItemGroup>
   <ItemGroup>
     <ClCompile Include="SoftThresholder.cpp">
@@ -65,6 +68,9 @@
     <ClCompile Include="MedianAbsoluteDeviationNoiseEstimator.cpp">
       <Filter>Source Files</Filter>
     </ClCompile>
+    <ClCompile Include="DaubechiesFiltersDenoiser.cpp">
+      <Filter>Source Files</Filter>
+    </ClCompile>
   </ItemGroup>
   <ItemGroup>
     <None Include="packages.config" />