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ENH: do not recompute variables in ComputeAttenuation method
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@dzenanz
dzenanz committed Mar 29, 2022
1 parent e4a0665 commit f158edc
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Showing 2 changed files with 42 additions and 23 deletions.
16 changes: 14 additions & 2 deletions include/itkAttenuationImageFilter.h
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Original file line number Diff line number Diff line change
Expand Up @@ -200,7 +200,11 @@ class ITK_TEMPLATE_EXPORT AttenuationImageFilter : public ImageToImageFilter<TIn
AttenuationImageFilter();
~AttenuationImageFilter() override = default;

/** Verify inputs and allocate buffers before threaded execution */

void
VerifyPreconditions() const override;

/** Allocate buffers and other initializations before threaded execution. */
void
BeforeThreadedGenerateData() override;

Expand Down Expand Up @@ -237,12 +241,20 @@ class ITK_TEMPLATE_EXPORT AttenuationImageFilter : public ImageToImageFilter<TIn

unsigned int m_Direction = 0;

float m_ScanStepMM = 1.0f;

unsigned int m_FixedEstimationDepth = 0;

float m_SamplingFrequencyMHz = 0.0f;

float m_FrequencyBandStartMHz = 0.0f;
float m_FrequencyBandEndMHz = 0.0f;
float m_FrequencyDelta = 0.0f;

// Frequency band to consider for attenuation
unsigned int m_StartComponent = 0;
unsigned int m_EndComponent = 0;
unsigned int m_ConsideredComponents = 1;

bool m_ConsiderNegativeAttenuations = false;

Expand All @@ -253,7 +265,7 @@ class ITK_TEMPLATE_EXPORT AttenuationImageFilter : public ImageToImageFilter<TIn
ImageRegionSplitterDirection::Pointer m_RegionSplitter = ImageRegionSplitterDirection::New();

/** Cache mask image reference before threaded execution to reduce calls to GetMaskImage() */
const MaskImageType * m_ThreadedInputMaskImage;
mutable const MaskImageType * m_ThreadedInputMaskImage;

/** Output mask image may be eroded via m_PadUpperBounds and m_PadLowerBounds
* along scan line direction */
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49 changes: 28 additions & 21 deletions include/itkAttenuationImageFilter.hxx
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Original file line number Diff line number Diff line change
Expand Up @@ -88,9 +88,10 @@ AttenuationImageFilter<TInputImage, TOutputImage, TMaskImage>::GetImageRegionSpl

template <typename TInputImage, typename TOutputImage, typename TMaskImage>
void
AttenuationImageFilter<TInputImage, TOutputImage, TMaskImage>::BeforeThreadedGenerateData()
AttenuationImageFilter<TInputImage, TOutputImage, TMaskImage>::VerifyPreconditions() const
{
// Verify inputs
Superclass::VerifyPreconditions();

if (this->GetInputMaskImage() == nullptr)
{
itkExceptionMacro("Filter requires a mask image for inclusion estimates!");
Expand All @@ -109,7 +110,12 @@ AttenuationImageFilter<TInputImage, TOutputImage, TMaskImage>::BeforeThreadedGen
{
itkExceptionMacro("RF sampling frequency was not set!");
}
}

template <typename TInputImage, typename TOutputImage, typename TMaskImage>
void
AttenuationImageFilter<TInputImage, TOutputImage, TMaskImage>::BeforeThreadedGenerateData()
{
Superclass::BeforeThreadedGenerateData();

// Initialize metric image
Expand All @@ -122,6 +128,19 @@ AttenuationImageFilter<TInputImage, TOutputImage, TMaskImage>::BeforeThreadedGen
m_OutputMaskImage->SetRegions(inputMaskImage->GetLargestPossibleRegion());
m_OutputMaskImage->Allocate();
m_OutputMaskImage->FillBuffer(0.0f);

// Initialize iVars used in ComputeAttenuation()
float nyquistFrequency = m_SamplingFrequencyMHz / 2;
float numComponents = this->GetInput()->GetNumberOfComponentsPerPixel();
m_FrequencyDelta = nyquistFrequency / numComponents;
m_StartComponent = m_FrequencyBandStartMHz / m_FrequencyDelta;
m_EndComponent = m_FrequencyBandEndMHz / m_FrequencyDelta;
if (m_EndComponent == 0) // If m_FrequencyBandEndMHz is not set
{
m_EndComponent = numComponents - 1; // Use all components
}
m_ConsideredComponents = m_EndComponent - m_StartComponent + 1;
m_ScanStepMM = this->GetInput()->GetSpacing()[m_Direction];
}

template <typename TInputImage, typename TOutputImage, typename TMaskImage>
Expand Down Expand Up @@ -184,7 +203,7 @@ AttenuationImageFilter<TInputImage, TOutputImage, TMaskImage>::ThreadedGenerateD
target[m_Direction] = start[m_Direction] + m_FixedEstimationDepth;
}

float estimatedAttenuation = ComputeAttenuation(target, start);
float estimatedAttenuation = ComputeAttenuation(target, start);

// Update the corresponding pixel in the metric image
if (estimatedAttenuation > 0.0 || m_ConsiderNegativeAttenuations)
Expand Down Expand Up @@ -219,34 +238,22 @@ typename AttenuationImageFilter<TInputImage, TOutputImage, TMaskImage>::OutputPi
AttenuationImageFilter<TInputImage, TOutputImage, TMaskImage>::ComputeAttenuation(const InputIndexType & end,
const InputIndexType & start) const
{
const float nyquistFrequency = m_SamplingFrequencyMHz / 2;

// Number and width of RF spectra frequency bins over the range (0, nyquist_frequency]
const unsigned int numComponents = this->GetInput()->GetNumberOfComponentsPerPixel();
const float frequencyDelta = nyquistFrequency / numComponents;

// Frequency band to consider for attenuation
const unsigned int startComponent = m_FrequencyBandStartMHz / frequencyDelta;
const unsigned int endComponent = m_FrequencyBandEndMHz / frequencyDelta;
const unsigned int consideredComponents = endComponent - startComponent + 1;

// Get RF spectra frequency bins at start and end pixel positions
auto input = this->GetInput();
InputPixelType endSample = input->GetPixel(end);
InputPixelType startSample = input->GetPixel(start);

// Get distance between start and end pixel positions (assume mm units)
const float scanStepMM = input->GetSpacing()[m_Direction];
const unsigned int pixelDistance = end[m_Direction] - start[m_Direction];
float distanceMM = pixelDistance * scanStepMM;
float distanceMM = pixelDistance * m_ScanStepMM;

Eigen::Matrix<float, Eigen::Dynamic, 2> A(consideredComponents, 2);
Eigen::Matrix<float, Eigen::Dynamic, 1> b(consideredComponents);
for (unsigned i = 0; i < consideredComponents; i++)
Eigen::Matrix<float, Eigen::Dynamic, 2> A(m_ConsideredComponents, 2);
Eigen::Matrix<float, Eigen::Dynamic, 1> b(m_ConsideredComponents);
for (unsigned i = 0; i < m_ConsideredComponents; i++)
{
A(i, 0) = 1;
A(i, 1) = (1 + i + startComponent) * frequencyDelta; // x_i = frequency
b(i) = endSample[i + startComponent] / (startSample[i + startComponent] + itk::Math::eps); // y_i = ratio
A(i, 1) = (1 + i + m_StartComponent) * m_FrequencyDelta; // x_i = frequency
b(i) = endSample[i + m_StartComponent] / (startSample[i + m_StartComponent] + itk::Math::eps); // y_i = ratio
}

// from https://eigen.tuxfamily.org/dox/group__LeastSquares.html
Expand Down

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