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COMP: Incorporate ali ghayoor's changes
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Kent Williams committed Apr 24, 2012
1 parent d71f2a8 commit f92ffcf
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Showing 3 changed files with 34 additions and 42 deletions.
8 changes: 0 additions & 8 deletions BRAINSConstellationDetector/landmarkStatistics/LmkStatistics.cxx
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Expand Up @@ -77,14 +77,6 @@ int main( int argc, char * argv[] )
for (unsigned int i=0; i<(2*k); i++)
{
temp = ReadSlicer3toITKLmk( argv[i+2] );
/*
std::cout << "\n\nTemp values of landmarks" << std::endl;
for( LandmarksMapType::const_iterator it = temp.begin(); it != temp.end(); ++it )
{
std::cout << it->first << " : (" << it->second[0] << ", " << it->second[1] << ", " << it->second[2] << ")" << std::endl;
}
std::cout << "==============================================================" << std::endl;
*/
LandmarksMapVector.push_back(temp);
}

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64 changes: 32 additions & 32 deletions BRAINSConstellationDetector/src/BRAINSConstellationModeler.cxx
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Expand Up @@ -73,13 +73,13 @@ void sample_variance(const std::vector<DType> & x, DType *mean, DType *var)

//
//
// ==============================================================================================
// ===========================================================================
int main(int argc, char *argv[])
{
std::cout.precision(20);
//
//
// /////////////////////////////////////////////////////////////////////////////////////////////
// ///////////////////////////////////////////////////////////////////
PARSE_ARGS;

const BRAINSUtils::StackPushITKDefaultNumberOfThreads TempDefaultNumberOfThreadsHolder(numberOfThreads);
Expand Down Expand Up @@ -286,50 +286,50 @@ int main(int argc, char *argv[])

// Instead of RC method, now we compute all the ac-pc aligned transforms by estimating the plane passing through RP, AC and PC points
RigidTransformType::Pointer ACPC_AlignedTransform = computeTmspFromPoints(origRP, origAC, origPC, origin);

// We cannot easily compute the Inverse transform by the following to lines, we need to use versor for percise transformation
// RigidTransformType::Pointer ACPC_AlignedTransform_INV = RigidTransformType::New();
// ACPC_AlignedTransform_INV->GetInverse(ACPC_AlignedTransform);

// AC-PC aligned TRANSFORM
VersorTransformType::Pointer finalTransform = VersorTransformType::New();
finalTransform->SetFixedParameters( ACPC_AlignedTransform->GetFixedParameters() );
finalTransform->SetFixedParameters( ACPC_AlignedTransform->GetFixedParameters() );
itk::Versor<double> versorRotation; //was commented before
const itk::Matrix<double,3,3> & NewCleanedOrthogonalized = itk::Orthogonalize3DRotationMatrix( ACPC_AlignedTransform->GetRotationMatrix() );
versorRotation.Set( NewCleanedOrthogonalized );
finalTransform->SetRotation( versorRotation );
finalTransform->SetTranslation( ACPC_AlignedTransform->GetTranslation() );
finalTransform->SetRotation( versorRotation );
finalTransform->SetTranslation( ACPC_AlignedTransform->GetTranslation() );
// inverse transform
VersorTransformType::Pointer ACPC_AlignedTransform_INV = VersorTransformType::New();
SImageType::PointType centerPoint = finalTransform->GetCenter(); //was commented before
centerPoint = finalTransform->GetCenter();
ACPC_AlignedTransform_INV->SetCenter( centerPoint );
ACPC_AlignedTransform_INV->SetIdentity();
finalTransform->GetInverse( ACPC_AlignedTransform_INV );
VersorTransformType::Pointer ACPC_AlignedTransform_INV = VersorTransformType::New();
SImageType::PointType centerPoint = finalTransform->GetCenter();
centerPoint = finalTransform->GetCenter();
ACPC_AlignedTransform_INV->SetCenter( centerPoint );
ACPC_AlignedTransform_INV->SetIdentity();
finalTransform->GetInverse( ACPC_AlignedTransform_INV );
//////////////////////////////////////////////////////////////////
//Transform points based on the new transform

//Transform points based on the new transform
cm_InMSPAlignedSpace[currentDataset] = ACPC_AlignedTransform_INV->TransformPoint(centerOfHeadMass);
rp_InMSPAlignedSpace[currentDataset] = ACPC_AlignedTransform_INV->TransformPoint(origRP);
ac_InMSPAlignedSpace[currentDataset] = ACPC_AlignedTransform_INV->TransformPoint(origAC);
pc_InMSPAlignedSpace[currentDataset] = ACPC_AlignedTransform_INV->TransformPoint(origPC);
vn4_InMSPAlignedSpace[currentDataset] = ACPC_AlignedTransform_INV->TransformPoint(origVN4);
cec_InMSPAlignedSpace[currentDataset] = ACPC_AlignedTransform_INV->TransformPoint(origCEC);


if( globalImagedebugLevel > 3 )
{
const SImageType::PointType finalRP = ACPC_AlignedTransform_INV->TransformPoint(origRP);
const SImageType::PointType finalAC = ACPC_AlignedTransform_INV->TransformPoint(origAC);
const SImageType::PointType finalPC = ACPC_AlignedTransform_INV->TransformPoint(origPC);
const SImageType::PointType finalVN4 = ACPC_AlignedTransform_INV->TransformPoint(origVN4);
// TransformResample( inputImage, referenceImage, defaultValue, interpolationMode, transform )

// TransformResample( inputImage, referenceImage, defaultValue, interpolationMode, transform )
SImageType::Pointer volumeACPC_Aligned =
TransformResample<SImageType, SImageType>( image, image, BackgroundFillValue,
GetInterpolatorFromString<SImageType>("Linear"),
ACPC_AlignedTransform.GetPointer() );

itkUtil::WriteImage<SImageType>( volumeACPC_Aligned, resultsDir + "/ACPC_Aligned_"
+ itksys::SystemTools::GetFilenameName( mDef[currentDataset].GetImageFilename() ) );
MakeLabelImage( volumeACPC_Aligned, finalRP, finalAC, finalPC, finalVN4, resultsDir + "/Mask_Resampled_"
Expand All @@ -343,20 +343,20 @@ int main(int argc, char *argv[])
std::cout << "Training template for " << it->first << std::endl;
const SImageType::PointType origPoint = it->second;
const SImageType::PointType transformedPoint = ACPC_AlignedTransform_INV->TransformPoint(origPoint);
/* PRINT FOR TEST */////////////////////////////////////////////
std::cout << "original point: " << it->second << std::endl;//[0] << "," << it->second[1] << "," << it->second[2] << ")" << std::endl;
std::cout << "transformed point: " << transformedPoint << std::endl;//[0] << "," << transformedPoint[1] << "," << transformedPoint[2] << ")" << std::endl;
/////////////////////////////////////////////////////////////////

/* PRINT FOR TEST /////////////////////////////////////////////
std::cout << "original point: " << it->second << std::endl;
std::cout << "transformed point: " << transformedPoint << std::endl;
/////////////////////////////////////////////////////////////*/


for( unsigned int currentAngle = 0; currentAngle < myModel.GetNumRotationSteps(); currentAngle++ )
{
// ////// create a rotation about the center with respect to the
// current test rotation angle
const float degree_current_angle = myModel.GetInitialRotationAngle() + myModel.GetInitialRotationStep() * currentAngle;
const float current_angle = degree_current_angle * vnl_math::pi / 180;

RigidTransformType::Pointer Point_Rotate = RigidTransformType::New();
Point_Rotate->SetCenter(transformedPoint);
Point_Rotate->SetRotation(current_angle, 0, 0);
Expand Down Expand Up @@ -391,15 +391,15 @@ int main(int argc, char *argv[])
MSPOptFile.close();
}
}
/* PRINT FOR TEST *////////////////////////////////////////////

/* PRINT FOR TEST ////////////////////////////////////////////
std::cout << "\nPROCESSING AC transformed values in MSP aligned space by 'Reflective Correlation' method:" << std::endl;
for( unsigned int currentDataset = 0; currentDataset < mDef.GetNumDataSets(); currentDataset++ )
{
std::cout << "====================================================================================" << std::endl;
std::cout << currentDataset+1 << "#: " << ac_InMSPAlignedSpace[currentDataset] << std::endl;
}
////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////*/

// -------------------------------
std::cout << "\nCompute vector means:" << std::endl;
Expand Down Expand Up @@ -503,14 +503,14 @@ int main(int argc, char *argv[])
decomposeRPAC(rp_InMSPAlignedSpace[currentDataset],
pc_InMSPAlignedSpace[currentDataset],
ac_InMSPAlignedSpace[currentDataset],
&curr_RPPC_to_RPAC_angle,
&curr_RPPC_to_RPAC_angle,
&curr_RPAC_over_RPPC);
RPPC_to_RPAC_angle[currentDataset] = curr_RPPC_to_RPAC_angle;
RPAC_over_RPPC[currentDataset] = curr_RPAC_over_RPPC;

// JOB2: CMtoRPMean
// // NOTE: This needs to be the average distance from the center of gravity.
SImageType::PointType::VectorType RPDistanceFromCenterOfMass =
SImageType::PointType::VectorType RPDistanceFromCenterOfMass =
rp_InMSPAlignedSpace[currentDataset] - cm_InMSPAlignedSpace[currentDataset];
CMtoRPMean += RPDistanceFromCenterOfMass;
}
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4 changes: 2 additions & 2 deletions Utilities/BRAINSMakeMD5SigFileAndMoveData.py
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Expand Up @@ -10,7 +10,7 @@
# of the Iowa PINC lab have access
# to generate data in this way.
#
#
#
import hashlib
import os
import argparse
Expand Down Expand Up @@ -55,7 +55,7 @@ def md5_for_file(f, block_size=2**20):
if not os.path.exists(destPath):
os.mkdir(destPath)
dest = destPath +'/'+value
print("mv {0} {1}".format(source,dest))
print("mv -f {0} {1}".format(source,dest))
md5FileName=fileName+'.md5'
f = open(md5FileName,'w')
f.write(value)
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