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ENH: ComputeBiasedFeatures now accepts uint8/bool for the SurfaceFeat…
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…ures Array

Signed-off-by: Michael Jackson <[email protected]>
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@imikejackson
imikejackson committed May 25, 2024
1 parent 21360d9 commit dd255f4
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Showing 3 changed files with 83 additions and 74 deletions.
144 changes: 76 additions & 68 deletions src/Plugins/SimplnxCore/src/SimplnxCore/Filters/Algorithms/ComputeBiasedFeatures.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

#include "simplnx/DataStructure/DataArray.hpp"
#include "simplnx/DataStructure/Geometry/ImageGeom.hpp"
#include "simplnx/Utilities/DataArrayUtilities.hpp"

using namespace nx::core;

Expand Down Expand Up @@ -42,41 +43,43 @@ Result<> ComputeBiasedFeatures::operator()()
}

// -----------------------------------------------------------------------------
void ComputeBiasedFeatures::findBoundingBoxFeatures()
Result<> ComputeBiasedFeatures::findBoundingBoxFeatures()
{
const ImageGeom imageGeometry = m_DataStructure.getDataRefAs<ImageGeom>(m_InputValues->ImageGeometryPath);
const auto& centroids = m_DataStructure.getDataRefAs<Float32Array>(m_InputValues->CentroidsArrayPath);
const auto& surfaceFeatures = m_DataStructure.getDataRefAs<BoolArray>(m_InputValues->SurfaceFeaturesArrayPath);
Int32Array* phases = nullptr;
Int32Array* phasesPtr = nullptr;
if(m_InputValues->CalcByPhase)
{
phases = m_DataStructure.getDataAs<Int32Array>(m_InputValues->PhasesArrayPath);
phasesPtr = m_DataStructure.getDataAs<Int32Array>(m_InputValues->PhasesArrayPath);
}
auto& biasedFeatures = m_DataStructure.getDataRefAs<BoolArray>(m_InputValues->BiasedFeaturesArrayName);
biasedFeatures.fill(false);

std::unique_ptr<MaskCompare> surfaceFeatures = nullptr;
try
{
surfaceFeatures = InstantiateMaskCompare(m_DataStructure, m_InputValues->SurfaceFeaturesArrayPath);
} catch(const std::out_of_range& exception)
{
// This really should NOT be happening as the path was verified during preflight BUT we may be calling this from
// somewhere else that is NOT going through the normal nx::core::IFilter API of Preflight and Execute
std::string message = fmt::format("Surface Features Array DataPath does not exist or is not of the correct type (Bool | UInt8) {}", m_InputValues->SurfaceFeaturesArrayPath.toString());
return MakeErrorResult(-54900, message);
}

const usize size = centroids.getNumberOfTuples();
float boundBox[6] = {0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f};
float32 coords[6] = {0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f};
float32 x = 0.0f;
float32 y = 0.0f;
float32 z = 0.0f;
float32 dist[7] = {
0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,
};
float32 minDist = std::numeric_limits<float32>::max();
int32 sideToMove = 0;
int32 move = 0;
std::vector<float32> boundBox = {0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f};
std::vector<float32> coords = {0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f};

// loop first to determine number of phases if calcByPhase is being used
int32 numPhases = 1;
if(m_InputValues->CalcByPhase)
{
for(usize i = 1; i < size; i++)
{
if((*phases)[i] > numPhases)
if((*phasesPtr)[i] > numPhases)
{
numPhases = (*phases)[i];
numPhases = (*phasesPtr)[i];
}
}
}
Expand All @@ -87,10 +90,10 @@ void ComputeBiasedFeatures::findBoundingBoxFeatures()
m_MessageHandler(IFilter::Message::Type::Info, fmt::format("Working on Phase {} of {}", iter, numPhases));
}
// reset boundBox for each phase
const BoundingBox3D<float32> bb = imageGeometry.getBoundingBoxf();
const BoundingBox3D<float32> boundingBox = imageGeometry.getBoundingBoxf();

auto min = bb.getMinPoint();
auto max = bb.getMaxPoint();
const auto& min = boundingBox.getMinPoint();
const auto& max = boundingBox.getMaxPoint();
boundBox[0] = min.getX();
boundBox[1] = max.getX();
boundBox[2] = min.getY();
Expand All @@ -100,28 +103,26 @@ void ComputeBiasedFeatures::findBoundingBoxFeatures()

for(usize i = 1; i < size; i++)
{
if(surfaceFeatures[i] && (!m_InputValues->CalcByPhase || (*phases)[i] == iter))
if(surfaceFeatures->isTrue(i) && (!m_InputValues->CalcByPhase || (*phasesPtr)[i] == iter))
{
sideToMove = 0;
move = 1;
minDist = std::numeric_limits<float32>::max();
x = centroids[3 * i];
y = centroids[3 * i + 1];
z = centroids[3 * i + 2];
coords[0] = x;
coords[1] = x;
coords[2] = y;
coords[3] = y;
coords[4] = z;
coords[5] = z;
int32 sideToMove = 0;
int32 move = 1;
float32 minDist = std::numeric_limits<float32>::max();

coords[0] = centroids[3 * i];
coords[1] = centroids[3 * i];
coords[2] = centroids[3 * i + 1];
coords[3] = centroids[3 * i + 1];
coords[4] = centroids[3 * i + 2];
coords[5] = centroids[3 * i + 2];
for(int32 j = 1; j < 7; j++)
{
dist[j] = std::numeric_limits<float32>::max();
float32 dist = std::numeric_limits<float32>::max();
if(j % 2 == 1)
{
if(coords[j - 1] > boundBox[j - 1])
{
dist[j] = (coords[j - 1] - boundBox[j - 1]);
dist = (coords[j - 1] - boundBox[j - 1]);
}
if(coords[j - 1] <= boundBox[j - 1])
{
Expand All @@ -132,16 +133,16 @@ void ComputeBiasedFeatures::findBoundingBoxFeatures()
{
if(coords[j - 1] < boundBox[j - 1])
{
dist[j] = (boundBox[j - 1] - coords[j - 1]);
dist = (boundBox[j - 1] - coords[j - 1]);
}
if(coords[j - 1] >= boundBox[j - 1])
{
move = 0;
}
}
if(dist[j] < minDist)
if(dist < minDist)
{
minDist = dist[j];
minDist = dist;
sideToMove = j - 1;
}
}
Expand All @@ -153,7 +154,7 @@ void ComputeBiasedFeatures::findBoundingBoxFeatures()
}
for(usize j = 1; j < size; j++)
{
if(!m_InputValues->CalcByPhase || (*phases)[j] == iter)
if(!m_InputValues->CalcByPhase || (*phasesPtr)[j] == iter)
{
if(centroids[3 * j] <= boundBox[0])
{
Expand Down Expand Up @@ -184,35 +185,43 @@ void ComputeBiasedFeatures::findBoundingBoxFeatures()

if(getCancel())
{
return;
return {};
}
}

return {};
}

// -----------------------------------------------------------------------------
void ComputeBiasedFeatures::findBoundingBoxFeatures2D()
Result<> ComputeBiasedFeatures::findBoundingBoxFeatures2D()
{
const ImageGeom imageGeometry = m_DataStructure.getDataRefAs<ImageGeom>(m_InputValues->ImageGeometryPath);
const SizeVec3 imageDimensions = imageGeometry.getDimensions();
const FloatVec3 imageOrigin = imageGeometry.getOrigin();
const auto& centroids = m_DataStructure.getDataRefAs<Float32Array>(m_InputValues->CentroidsArrayPath);
const auto& surfaceFeatures = m_DataStructure.getDataRefAs<BoolArray>(m_InputValues->SurfaceFeaturesArrayPath);
auto& biasedFeatures = m_DataStructure.getDataRefAs<BoolArray>(m_InputValues->BiasedFeaturesArrayName);
biasedFeatures.fill(false);

std::unique_ptr<MaskCompare> maskCompare = nullptr;
try
{
maskCompare = InstantiateMaskCompare(m_DataStructure, m_InputValues->SurfaceFeaturesArrayPath);
} catch(const std::out_of_range& exception)
{
// This really should NOT be happening as the path was verified during preflight BUT we may be calling this from
// somewhere else that is NOT going through the normal nx::core::IFilter API of Preflight and Execute
std::string message = fmt::format("Surface Features Array DataPath does not exist or is not of the correct type (Bool | UInt8) {}", m_InputValues->SurfaceFeaturesArrayPath.toString());
return MakeErrorResult(-54900, message);
}

const usize size = centroids.getNumberOfTuples();

float32 coords[4] = {0.0f, 0.0f, 0.0f, 0.0f};
float32 x = 0.0f;
float32 y = 0.0f;
float32 dist[5] = {0.0f, 0.0f, 0.0f, 0.0f, 0.0f};
float32 minDist = std::numeric_limits<float32>::max();
int32 sideToMove = 0;
int32 move = 0;
std::vector<float32> coords = {0.0f, 0.0f, 0.0f, 0.0f};

float32 xOrigin = 0.0f;
float32 yOrigin = 0.0f;
int32 xPoints = 0, yPoints = 0;
int32 xPoints = 0;
int32 yPoints = 0;
FloatVec3 spacing;

usize centroidShift0 = 0;
Expand Down Expand Up @@ -249,29 +258,27 @@ void ComputeBiasedFeatures::findBoundingBoxFeatures2D()
centroidShift1 = 1;
}

float32 boundBox[6] = {xOrigin, xOrigin + xPoints * spacing[0], yOrigin, yOrigin + yPoints * spacing[1], 0.0f, 0.0f};
std::vector<float32> boundBox = {xOrigin, xOrigin + static_cast<float32>(xPoints) * spacing[0], yOrigin, yOrigin + static_cast<float32>(yPoints) * spacing[1], 0.0f, 0.0f};

for(usize i = 1; i < size; i++)
{
if(surfaceFeatures[i])
if(maskCompare->isTrue(i))
{
sideToMove = 0;
move = 1;
minDist = std::numeric_limits<float32>::max();
x = centroids[3 * i + centroidShift0];
y = centroids[3 * i + centroidShift1];
coords[0] = x;
coords[1] = x;
coords[2] = y;
coords[3] = y;
int32 sideToMove = 0;
int32 move = 1;
float32 minDist = std::numeric_limits<float32>::max();
coords[0] = centroids[3 * i + centroidShift0];
coords[1] = centroids[3 * i + centroidShift0];
coords[2] = centroids[3 * i + centroidShift1];
coords[3] = centroids[3 * i + centroidShift1];
for(int32 j = 1; j < 5; j++)
{
dist[j] = std::numeric_limits<float32>::max();
float32 dist = std::numeric_limits<float32>::max();
if(j % 2 == 1)
{
if(coords[j - 1] > boundBox[j - 1])
{
dist[j] = (coords[j - 1] - boundBox[j - 1]);
dist = (coords[j - 1] - boundBox[j - 1]);
}
if(coords[j - 1] <= boundBox[j - 1])
{
Expand All @@ -282,16 +289,16 @@ void ComputeBiasedFeatures::findBoundingBoxFeatures2D()
{
if(coords[j - 1] < boundBox[j - 1])
{
dist[j] = (boundBox[j - 1] - coords[j - 1]);
dist = (boundBox[j - 1] - coords[j - 1]);
}
if(coords[j - 1] >= boundBox[j - 1])
{
move = 0;
}
}
if(dist[j] < minDist)
if(dist < minDist)
{
minDist = dist[j];
minDist = dist;
sideToMove = j - 1;
}
}
Expand All @@ -303,7 +310,7 @@ void ComputeBiasedFeatures::findBoundingBoxFeatures2D()

if(getCancel())
{
return;
return {};
}
}
for(usize j = 1; j < size; j++)
Expand All @@ -327,7 +334,8 @@ void ComputeBiasedFeatures::findBoundingBoxFeatures2D()

if(getCancel())
{
return;
return {};
}
}
return {};
}
4 changes: 2 additions & 2 deletions src/Plugins/SimplnxCore/src/SimplnxCore/Filters/Algorithms/ComputeBiasedFeatures.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -40,8 +40,8 @@ class SIMPLNXCORE_EXPORT ComputeBiasedFeatures
const std::atomic_bool& getCancel();

protected:
void findBoundingBoxFeatures();
void findBoundingBoxFeatures2D();
Result<> findBoundingBoxFeatures();
Result<> findBoundingBoxFeatures2D();

private:
DataStructure& m_DataStructure;
Expand Down
9 changes: 5 additions & 4 deletions src/Plugins/SimplnxCore/src/SimplnxCore/Filters/ComputeBiasedFeaturesFilter.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ Parameters ComputeBiasedFeaturesFilter::parameters() const
params.insert(std::make_unique<ArraySelectionParameter>(k_CentroidsArrayPath_Key, "Centroids", "X, Y, Z coordinates of Feature center of mass", DataPath{},
ArraySelectionParameter::AllowedTypes{DataType::float32}, ArraySelectionParameter::AllowedComponentShapes{{3}}));
params.insert(std::make_unique<ArraySelectionParameter>(k_SurfaceFeaturesArrayPath_Key, "Surface Features", "Flag of 1 if Feature touches an outer surface or of 0 if it does not", DataPath{},
ArraySelectionParameter::AllowedTypes{DataType::boolean}, ArraySelectionParameter::AllowedComponentShapes{{1}}));
ArraySelectionParameter::AllowedTypes{DataType::boolean, DataType::uint8}, ArraySelectionParameter::AllowedComponentShapes{{1}}));
params.insert(std::make_unique<ArraySelectionParameter>(k_PhasesArrayPath_Key, "Phases", "Specifies to which Ensemble each Feature belongs. Only required if Apply Phase by Phase is checked",
DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::int32}, ArraySelectionParameter::AllowedComponentShapes{{1}}));
params.insertSeparator(Parameters::Separator{"Output Feature Data"});
Expand Down Expand Up @@ -102,10 +102,11 @@ IFilter::PreflightResult ComputeBiasedFeaturesFilter::preflightImpl(const DataSt
if(!tupleValidityCheck)
{
return {MakeErrorResult<OutputActions>(-7460, fmt::format("The following DataArrays all must have equal number of tuples but this was not satisfied.\n{}", tupleValidityCheck.error()))};
};
}

auto action = std::make_unique<CreateArrayAction>(DataType::boolean, dataStructure.getDataRefAs<BoolArray>(pSurfaceFeaturesArrayPathValue).getTupleShape(), std::vector<usize>{1},
pCentroidsArrayPathValue.replaceName(pBiasedFeaturesArrayNameValue));
const auto& surfaceFeaturesMaskArray = dataStructure.getDataRefAs<IDataArray>(pSurfaceFeaturesArrayPathValue);
auto action =
std::make_unique<CreateArrayAction>(DataType::boolean, surfaceFeaturesMaskArray.getTupleShape(), std::vector<usize>{1}, pCentroidsArrayPathValue.replaceName(pBiasedFeaturesArrayNameValue));
resultOutputActions.value().appendAction(std::move(action));

return {std::move(resultOutputActions), std::move(preflightUpdatedValues)};
Expand Down

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