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Added IBSI2 definitions in parameter file #1489

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Mar 23, 2022
Merged

Added IBSI2 definitions in parameter file #1489

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03107d1
Update FeatureExtraction.h
sarthakpati Mar 22, 2022
df241a7
actually using the ibsi2 function
sarthakpati Mar 22, 2022
61d8264
updated parameter file
sarthakpati Mar 22, 2022
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3 changes: 3 additions & 0 deletions src/applications/FeatureExtraction/data/1_params_default.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,9 @@ LBP,Neighborhood,Int,0:27,27,The total number of neighbors to consider for compu
LBP,Type,Int,0:3,2,0: original LBP | 1: uniform LBP | 2: rotation invariant LBP | 3: uniform + rotation invariant LBP
Collage,Radius,Int,(1:9),1,Radius around the center voxel/pixel (if defined as float it is assumed to be in world coordinates and if as Integer it is assumed to be in image coordinates); currently disabled for lattice computation
Collage,Bins,Int,,20,The number of bins (FBN) or size of each bin (FBS) to calculate for the Histogram
IBSI2,Bins,Int,,20,The number of bins (FBN) or size of each bin (FBS) to calculate for the Histogram; currently unused for IBSI2
IBSI2,Radius,Int,(1:9),1,Radius around the center voxel which can be in mm as well (needs to be defined as float in same space as input image/mask); currently unused for IBSI2
IBSI2,Offset,String,[Individual:Average:Combined],Combined,Either individual offset values or averaged computation for individual offsets might not work); currently unused for IBSI2
Lattice,FullImage,Int,0:1,0,Whether computations across the entire image need to happen in addition to lattice
Lattice,Window,mm,0:ImageSize,6.3,Window of single lattice node (number based on experiments by CBIG) - should be same as Step for non-overlapping tiles
Lattice,Step,mm,0:ImageSize,6.3,Step size to increase for consecutive lattice node (number based on experiments by CBIG) - should be same as Step for non-overlapping tiles
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2 changes: 1 addition & 1 deletion src/applications/FeatureExtraction/src/FeatureExtraction.h
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Expand Up @@ -140,7 +140,7 @@ enum FeatureFamily

static const char FeatureFamilyString[FeatureMax + 1][20] =
{ "Generic", "Intensity", "Histogram", "Volumetric", "Morphologic", "GLCM", "GLRLM", "GLSZM", "NGTDM", "NGLDM", "LBP",
"Collage", "Lattice", "FractalDimension", "GaborWavelets", "Laws", "EdgeEnhancement", "PowerSpectrum", "FeatureMax" };
"Collage", "IBSI2", "Lattice", "FractalDimension", "GaborWavelets", "Laws", "EdgeEnhancement", "PowerSpectrum", "FeatureMax" };

/**
\brief FeatureExtraction Class -The main class structure enclosing all the feature calculations functions.
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10 changes: 5 additions & 5 deletions src/applications/FeatureExtraction/src/FeatureExtraction.hxx
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Expand Up @@ -2972,32 +2972,32 @@ void FeatureExtraction< TImage >::Update()
if (TImage::ImageDimension == 3)
{
std::string currentFeatureFamily = FeatureFamilyString[f];
CalculateCOLLAGE(currentInputImage_patch, currentMask_patch, std::get<4>(temp->second));
CalculateIBSI2(currentInputImage_patch, currentMask_patch, std::get<4>(temp->second));
WriteFeatures(m_modality[i], allROIs[j].label, currentFeatureFamily, std::get<4>(temp->second),
"Axis=3D;Dimension=3D;Bins=" + m_Bins_string + ";Directions=" + std::to_string(m_Direction) +
";Radius=" + m_Radius_string, m_currentLatticeCenter, writeFeatureMapsAndLattice, allROIs[j].weight);

if (!writeFeatureMapsAndLattice && m_SliceComputation)
{
CalculateCOLLAGE(currentInputImage_patch, currentMask_patch_axisImages[0], std::get<4>(temp->second));
CalculateIBSI2(currentInputImage_patch, currentMask_patch_axisImages[0], std::get<4>(temp->second));
WriteFeatures(m_modality[i], allROIs[j].label, currentFeatureFamily + "_X", std::get<4>(temp->second),
"Axis=X;Dimension=2D;Bins=" + m_Bins_string + ";Directions=" + std::to_string(m_Direction) +
";Radius=" + m_Radius_string, m_currentLatticeCenter, writeFeatureMapsAndLattice, allROIs[j].weight);

CalculateCOLLAGE(currentInputImage_patch, currentMask_patch_axisImages[1], std::get<4>(temp->second));
CalculateIBSI2(currentInputImage_patch, currentMask_patch_axisImages[1], std::get<4>(temp->second));
WriteFeatures(m_modality[i], allROIs[j].label, currentFeatureFamily + "_Y", std::get<4>(temp->second),
"Axis=Y;Dimension=2D;Bins=" + m_Bins_string + ";Directions=" + std::to_string(m_Direction) +
";Radius=" + m_Radius_string, m_currentLatticeCenter, writeFeatureMapsAndLattice, allROIs[j].weight);

CalculateCOLLAGE(currentInputImage_patch, currentMask_patch_axisImages[2], std::get<4>(temp->second));
CalculateIBSI2(currentInputImage_patch, currentMask_patch_axisImages[2], std::get<4>(temp->second));
WriteFeatures(m_modality[i], allROIs[j].label, currentFeatureFamily + "_Z", std::get<4>(temp->second),
"Axis=2;Dimension=2D;Bins=" + m_Bins_string + ";Directions=" + std::to_string(m_Direction) +
";Radius=" + m_Radius_string, m_currentLatticeCenter, writeFeatureMapsAndLattice, allROIs[j].weight);
}
}
else
{
CalculateCOLLAGE(currentInputImage_patch, currentMask_patch, std::get<4>(temp->second));
CalculateIBSI2(currentInputImage_patch, currentMask_patch, std::get<4>(temp->second));
WriteFeatures(m_modality[i], allROIs[j].label, currentFeatureFamily, std::get<4>(temp->second),
"Axis=" + m_Axis + ";Dimension=" + std::to_string(m_Dimension) + ";Bins=" + m_Bins_string + ";Directions=" + std::to_string(m_Direction) +
";Radius=" + m_Radius_string, m_currentLatticeCenter, writeFeatureMapsAndLattice);
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