void BackGround::GetBackground_One_pass( string srcfilename,string outputdir,unsigned int width,unsigned int height, cv::Size win_stride)
{
Init(width,height);
LoadPictures(srcfilename);
SetOutputDir(outputdir);
string filepath;
ifstream fin(m_srcfilename.c_str(),ios_base::in);
if(!fin.is_open())
{
#ifdef DEBUG_OUTPUT
cout<<"Open File Error"<<endl;
#endif
exit(1);
}
cv::Mat tmpimg;
while(getline(fin,filepath))
{
m_input.release();
tmpimg=cv::imread(filepath,0);
cv::copyMakeBorder(tmpimg,m_input,40,40,40,40,cv::BORDER_REPLICATE);
SetPrefix(GetFileName(filepath.c_str()));
OutputBackground_OnePass(win_stride);
}
fin.close();
}
void BackGround::InitOutputPerBackground(string srcfilename,string outputdir,unsigned int width,unsigned int height,double scale,double scalefactor,double step)
{
Init(width,height);
LoadPictures(srcfilename);
SetOutputDir(outputdir);
m_fin.open(m_srcfilename.c_str(),ios_base::in);
if(!m_fin.is_open())
{
#ifdef DEBUG_OUTPUT
cout<<"Open File Error"<<endl;
#endif
exit(1);
}
m_currentroi.width=m_bgroi.width;
m_currentroi.height=m_bgroi.height;
m_scale=scale;
m_scalefactor=scalefactor;
m_step=step;
}
void BackGround::GetBackground(string srcfilename,string outputdir,unsigned int width,unsigned int height,double scale,double scalefactor,double step)
{
Init(width,height);
LoadPictures(srcfilename);
SetOutputDir(outputdir);
string filepath;
ifstream fin(m_srcfilename.c_str(),ios_base::in);
if(!fin.is_open())
{
#ifdef DEBUG_OUTPUT
cout<<"Open File Error"<<endl;
#endif
exit(1);
}
while(getline(fin,filepath))
{
m_input.release();
m_input=cv::imread(filepath,0);
SetPrefix(GetFileName(filepath.c_str()));
OutputBackground(scale,scalefactor,step);
}
fin.close();
}
// Radomized trials for registering a point cloud and mesh
// sample noise is dependent on surface normal orientation
// (assumes mesh itself has no measurement noise)
void Run_ParameterizedTest_Mesh_SurfaceNoise(TestParameters params)
{
std::stringstream ss;
std::string loadSourceMeshPath = params.inputDir + "/" + params.sourceMeshFile;
std::string loadTargetMeshPath = params.inputDir + "/" + params.targetMeshFile;
std::string saveSourceMeshPath = params.outputCommonDir + "/SaveMeshSource";
std::string saveTargetMeshPath = params.outputCommonDir + "/SaveMeshTarget";
std::string saveNoisyTargetMeshPath = params.outputCommonDir + "/SaveMeshTargetNoisy";
std::string saveTargetCov = params.outputCommonDir + "/SaveTargetCov.txt";
// test parameters
params.GenerateSamplesFunc = GenerateSamplePointSet_PointCloud_SurfaceNoise;
CustomTestParams_PointCloud_SurfaceNoise &customParams
= dynamic_cast<CustomTestParams_PointCloud_SurfaceNoise&> (*params.pCustomTestParams);
// load target mesh
cisstMesh mesh_target;
CreateMesh(mesh_target, loadTargetMeshPath, &saveTargetMeshPath);
// load source mesh
// NOTE: the sample point set is randomly generated from this mesh
cisstMesh mesh_source;
CreateMesh(mesh_source, loadSourceMeshPath, &saveSourceMeshPath);
// generate noisy target mesh
// NOTE: the sample point set is registered to this mesh
cisstMesh noisyTargetMesh;
if (params.noiseMeshSD != 0.0)
{
std::cout << "ERROR: noisy mesh currently disabled" << std::endl;
return;
//std::string normRVFile = params.inputDir + "/GaussianValues.txt";
//std::ifstream randnStream_MeshNoise(normRVFile.c_str());
//GenerateNoisyMesh(mesh_target, noisyTargetMesh, randnStream_MeshNoise, params.noiseMeshSD, &saveNoisyTargetMeshPath);
}
else
{
noisyTargetMesh = mesh_target;
}
// build mesh covariance tree from noisy mesh
cisstCovTree_Mesh *pTree;
int nThresh = 5; // Cov Tree Params
double diagThresh = 5.0; // ''
std::cout << "Building covariance tree .... " << std::endl;
pTree = new cisstCovTree_Mesh(noisyTargetMesh, nThresh, diagThresh);
std::cout << "Tree built: NNodes=" << pTree->NumNodes() << " NData=" << pTree->NumData()
<< " TreeDepth=" << pTree->TreeDepth() << std::endl;
assert(pTree->NumNodes());
// Apply target noise model
if (customParams.bTargetCov_ApplySurfaceModel)
{
// define mesh noise model (surface-model)
noisyTargetMesh.ComputeTriangleNoiseModels(
customParams.surfaceModel_InPlaneSD,
customParams.surfaceModel_PerpPlaneSD);
// save target covariance model
noisyTargetMesh.SaveTriangleCovariances(saveTargetCov);
}
// ICP Options
cisstICP::Options opt_ICP;
opt_ICP.auxOutputDir = params.outputBaseDir + "/AuxiliaryFiles/";
opt_ICP.maxIter = 100;
opt_ICP.termHoldIter = 2;
opt_ICP.minE = -std::numeric_limits<double>::max();
opt_ICP.tolE = 0.0;
opt_ICP.dPosThresh = 0.1;
opt_ICP.dAngThresh = 0.1*(cmnPI / 180);
opt_ICP.dPosTerm = 0.001;
opt_ICP.dAngTerm = 0.001*(cmnPI / 180);
params.opt_ICP = opt_ICP;
#define nNoises 9
#define nOffsets 2
#define nTests (nNoises*nOffsets)
//#define nOutliers 6
//#define nTests (nNoises*nOffsets*nOutliers)
//double percentOutliers[nOutliers] = { 0.05, 0.1, 0.2, 0.3, 0.4, 0.5 };
double noiseInPlaneSDArr[nNoises] = { 0.5, 1.0, 2.0, 0.5, 1.0, 0.5, 1.0, 2.0, 2.0 };
double noisePerpPlaneSDArr[nNoises] = { 0.5, 1.0, 2.0, 1.0, 2.0, 2.0, 0.5, 1.0, 0.5 };
//double noiseInPlaneSDArr[nNoises] = { 0.5, 1.0 };
//double noisePerpPlaneSDArr[nNoises] = { 0.5, 1.0 };
double minOffsetAngArr[nOffsets] = { 30, 15 }; //{ 10, 30 }; //{0, 10, 30, 60};
double maxOffsetAngArr[nOffsets] = { 60, 30 }; //{ 30, 60 }; //{10, 30, 60, 90};
double minOffsetPosArr[nOffsets] = { 30, 15 }; //{ 10, 30 }; //{0, 10, 30, 60};
double maxOffsetPosArr[nOffsets] = { 60, 30 }; //{ 30, 60 }; //{10, 30, 60, 100};
std::vector<unsigned int> randSeed_SamplesArr(nTests, 0); // sample generater
std::vector<unsigned int> randSeed_XfmsArr(nTests, 0); // initial offset xfm generater
for (unsigned int i = 0; i < nTests; i++)
{
randSeed_SamplesArr[i] = i + 23;
randSeed_XfmsArr[i] = i + 127;
}
std::string outputCommonDir = params.outputCommonDir;
params.nSamples = customParams.nGoodSamples;
//--- Parameterized Trials ---//
for (unsigned int offset = 0; offset < nOffsets; offset++)
{
for (unsigned int noise = 0; noise < nNoises; noise++)
{
unsigned int testNum = offset*nNoises + noise;
ss.str("");
ss << "Noise_Prll" << noiseInPlaneSDArr[noise] << "Perp" << noisePerpPlaneSDArr[noise]
<< "_Offset_R" << minOffsetAngArr[offset] << "-" << maxOffsetAngArr[offset]
<< "T" << minOffsetPosArr[offset] << "-" << maxOffsetPosArr[offset];
//<< "_Outliers" << percentOutliers[outlier];
std::string outputSubFolder = ss.str();
params.minOffsetAng = minOffsetAngArr[offset];
params.maxOffsetAng = maxOffsetAngArr[offset];
params.minOffsetPos = minOffsetPosArr[offset];
params.maxOffsetPos = maxOffsetPosArr[offset];
params.randSeed_Samples = randSeed_SamplesArr[testNum];
params.randSeed_Xfms = randSeed_XfmsArr[testNum];
customParams.sampleNoise_InPlaneSD = noiseInPlaneSDArr[noise];
customParams.sampleNoise_PerpPlaneSD = noisePerpPlaneSDArr[noise];
// hold number of good samples constant and increase sample size to
// achieve the desired percentage of outliers
//double p = percentOutliers[outlier];
//unsigned int nOutlierSamps = (unsigned int)(p/(1-p) * customParams.nGoodSamples);
//params.nSamples = customParams.nGoodSamples + nOutlierSamps;
// TODO: remove change to output common files to separate directories below
// Run StdICP
{
params.AlgorithmDescription = "StdICP";
//params.AlgorithmDescription = "StdICP_Verbose";
params.algType = TestParameters::StdICP;
SetOutputDir(params, outputCommonDir, outputSubFolder);
vctDynamicVector<vct3> dummySamples; // these will be set later by the sample generator routine
params.pAlg = new cisstAlgorithmICP_StdICP_Mesh(pTree, dummySamples);
Run_ParameterizedTest(mesh_source, pTree, params);
delete params.pAlg; params.pAlg = NULL;
}
// Run IMLP
{
params.AlgorithmDescription = "IMLP";
//params.AlgorithmDescription = "IMLP_Verbose";
params.algType = TestParameters::IMLP;
SetOutputDir(params, outputCommonDir, outputSubFolder);
vctDynamicVector<vct3> dummySamples; // these will be set later by the sample generator routine
vctDynamicVector<vct3x3> dummySampleCov; // ''
cisstAlgorithmICP_IMLP_Mesh *pAlg =
new cisstAlgorithmICP_IMLP_Mesh(
pTree, dummySamples, dummySampleCov, dummySampleCov, customParams.outlier_ChiSquareThreshold);
params.pAlg = pAlg;
Run_ParameterizedTest(mesh_source, pTree, params);
delete params.pAlg; params.pAlg = NULL;
}
// Run IMLP_MD (Mahalanobis Distance Match Criteria)
{
params.AlgorithmDescription = "IMLP-MD";
//params.AlgorithmDescription = "IMLP-MD_Verbose";
params.algType = TestParameters::IMLP;
SetOutputDir(params, outputCommonDir, outputSubFolder);
vctDynamicVector<vct3> dummySamples; // these will be set later by the sample generator routine
vctDynamicVector<vct3x3> dummySampleCov; // ''
cisstAlgorithmICP_IMLP_MahalDist_Mesh *pAlg =
new cisstAlgorithmICP_IMLP_MahalDist_Mesh(
pTree, dummySamples, dummySampleCov, dummySampleCov, customParams.outlier_ChiSquareThreshold);
params.pAlg = pAlg;
Run_ParameterizedTest(mesh_source, pTree, params);
delete params.pAlg; params.pAlg = NULL;
}
// Run IMLP_CP (Closest Point Match Criteria)
{
params.AlgorithmDescription = "IMLP-CP";
//params.AlgorithmDescription = "IMLP-CP_Verbose";
params.algType = TestParameters::IMLP;
SetOutputDir(params, outputCommonDir, outputSubFolder);
vctDynamicVector<vct3> dummySamples; // these will be set later by the sample generator routine
vctDynamicVector<vct3x3> dummySampleCov; // ''
cisstAlgorithmICP_IMLP_ClosestPoint_Mesh *pAlg =
new cisstAlgorithmICP_IMLP_ClosestPoint_Mesh(
pTree, dummySamples, dummySampleCov, dummySampleCov, customParams.outlier_ChiSquareThreshold);
params.pAlg = pAlg;
Run_ParameterizedTest(mesh_source, pTree, params);
delete params.pAlg; params.pAlg = NULL;
}
}
}
}
// Radomized trials for registering 2 point clouds
// sample noise is dependent on surface normal orientation
// (assumes mesh itself has no measurement noise)
void Run_ParameterizedTest_PointCloud_SurfaceNoise(TestParameters params)
{
std::stringstream ss;
//std::string workingDir = "../ICP_TestData";
//std::string baseOutputFolder = "RandomTestData_PointCloud_SurfaceNoise"; // "RandomTests_Plane2Plane_Term0.001G_5.0,0.5_ChiSqu0.95_A0_Sigma2/";
//std::string sourceMeshFile = "RIGHTHEMIPELVIS_centered.mesh";
//std::string targetMeshFile = sourceMeshFile;
//// Create folders for output files
//std::string baseOutputDir = workingDir + "/" + baseOutputFolder;
//std::string commonOutputDir = baseOutputDir + "/CommonFiles";
//CreateDir(baseOutputDir);
//CreateDir(commonOutputDir);
std::string loadSourceMeshPath = params.inputDir + "/" + params.sourceMeshFile;
std::string loadTargetMeshPath = params.inputDir + "/" + params.targetMeshFile;
std::string saveSourceMeshPath = params.outputCommonDir + "/SaveMeshSource";
std::string saveTargetMeshPath = params.outputCommonDir + "/SaveMeshTarget";
std::string saveNoisyTargetMeshPath = params.outputCommonDir + "/SaveMeshTargetNoisy";
//// test parameters
//TestParameters params;
//params.TestDescription = "Run_ParameterizedTest_PointCloud_SurfaceNoise";
//params.inputDir = workingDir;
//params.sourceMeshFile = sourceMeshFile;
//params.targetMeshFile = targetMeshFile;
//params.numTrials = 2; // 300;
//params.nSamples = 100;
//params.nValidationSamples = 100;
//params.noiseMeshSD = 0.0;
//params.randSeed_MeshNoise = 0;
params.GenerateSamplesFunc = GenerateSamplePointSet_PointCloud_SurfaceNoise;
CustomTestParams_PointCloud_SurfaceNoise &customParams
= dynamic_cast<CustomTestParams_PointCloud_SurfaceNoise&> (*params.pCustomTestParams);
//// custom test parameters
//// NOTE: target point cloud noise model
//// perpendicular noise must be specified
//// in-plane noise is set to avg distance from triangle center to each vertex
//CustomTestParams_PointCloud_SurfaceNoise customParams;
//params.pCustomTestParams = &customParams;
//customParams.percentOutliers = 0.0;
//customParams.bSampleCov_ApplyNoiseModel = true;
//customParams.bSampleCov_ApplySurfaceModel = true;
//customParams.bTargetCov_ApplySurfaceModel = true;
//customParams.bTargetCov_DynamicSurfaceModel = false;
//customParams.surfaceModel_InPlaneSD = 5.0;
//customParams.surfaceModel_PerpPlaneSD = 0.5;
//customParams.minPosOffsetOutlier = 10.0;
//customParams.maxPosOffsetOutlier = 20.0;
// load target mesh
cisstMesh mesh_target;
CreateMesh(mesh_target, loadTargetMeshPath, &saveTargetMeshPath);
// load source mesh
// NOTE: the sample point set is randomly generated from this mesh
cisstMesh mesh_source;
CreateMesh(mesh_source, loadSourceMeshPath, &saveSourceMeshPath);
// generate noisy target mesh
// NOTE: the sample point set is registered to this mesh
cisstMesh noisyTargetMesh;
if (params.noiseMeshSD > 0.0)
{
std::cout << "ERROR: noisy mesh currently disabled" << std::endl;
return;
//std::string normRVFile = params.inputDir + "/GaussianValues.txt";
//std::ifstream randnStream_MeshNoise(normRVFile.c_str());
//GenerateNoisyMesh(mesh_target, noisyTargetMesh, randnStream_MeshNoise, params.noiseMeshSD, &saveNoisyTargetMeshPath);
}
else
{
noisyTargetMesh = mesh_target;
}
// build point cloud covariance tree from noisy mesh
// and define point cloud noise model (but don't add more noise)
cisstCovTree_PointCloud *pTree;
int nThresh = 5; // Cov Tree Params
double diagThresh = 5.0; // ''
std::cout << "Building covariance tree .... " << std::endl;
double targetModel_InPlaneSD = params.noiseMeshSD;
double targetModel_PerpPlaneSD = params.noiseMeshSD;
if (customParams.bTargetCov_ApplySurfaceModel)
{
targetModel_InPlaneSD += customParams.surfaceModel_InPlaneSD;
targetModel_PerpPlaneSD += customParams.surfaceModel_PerpPlaneSD;
}
if (customParams.bTargetCov_DynamicSurfaceModel && customParams.bTargetCov_ApplySurfaceModel)
{
// set target surface noise model dynamically from mesh
pTree = new cisstCovTree_PointCloud(noisyTargetMesh, nThresh, diagThresh, targetModel_PerpPlaneSD);
std::cout << "Tree built: NNodes=" << pTree->NumNodes() << " NData=" << pTree->NumData()
<< " TreeDepth=" << pTree->TreeDepth() << std::endl;
std::cout << " Point Cloud Noise Model:" << std::endl
<< " perp-plane variance = " << pow(customParams.surfaceModel_PerpPlaneSD, 2) << std::endl
<< " in-plane variance = " << pTree->avgVarInPlane << " (avg)" << std::endl;
assert(pTree->NumNodes());
}
else
{
// set static target surface noise model
pTree = new cisstCovTree_PointCloud(noisyTargetMesh, nThresh, diagThresh, targetModel_PerpPlaneSD, targetModel_InPlaneSD);
std::cout << "Tree built: NNodes=" << pTree->NumNodes() << " NData=" << pTree->NumData()
<< " TreeDepth=" << pTree->TreeDepth() << std::endl;
std::cout << " Point Cloud Noise Model:" << std::endl
<< " perp-plane variance = " << pow(customParams.surfaceModel_PerpPlaneSD, 2) << std::endl
<< " in-plane variance = " << pow(customParams.surfaceModel_InPlaneSD, 2) << std::endl;
assert(pTree->NumNodes());
}
// save target point cloud and covariance model
std::string saveTargetPointCloud = params.outputCommonDir + "/SaveTargetPointCloud.pts";
std::string saveTargetCov = params.outputCommonDir + "/SaveTargetCov.txt";
pTree->SavePointCloud(saveTargetPointCloud);
pTree->SavePointCloudCov(saveTargetCov);
// ICP Options
cisstICP::Options opt_ICP;
opt_ICP.auxOutputDir = params.outputBaseDir + "/AuxiliaryFiles/";
opt_ICP.maxIter = 100;
opt_ICP.termHoldIter = 2;
opt_ICP.minE = -std::numeric_limits<double>::max();
opt_ICP.tolE = 0.0;
opt_ICP.dPosThresh = 0.1;
opt_ICP.dAngThresh = 0.1*(cmnPI / 180);
opt_ICP.dPosTerm = 0.001;
opt_ICP.dAngTerm = 0.001*(cmnPI / 180);
params.opt_ICP = opt_ICP;
//// CPD Options
//CPD::Options opt_CPD;
//opt_CPD.maxIter = opt_ICP.maxIter;
//opt_CPD.termHoldIter = opt_ICP.termHoldIter;
//opt_CPD.minE = opt_ICP.minE;
//opt_CPD.tolE = opt_ICP.tolE;
//opt_CPD.dPosThresh = opt_ICP.dPosThresh;
//opt_CPD.dAngThresh = opt_ICP.dAngThresh;
//opt_CPD.dPosTerm = opt_ICP.dPosTerm;
//opt_CPD.dAngTerm = opt_ICP.dAngTerm;
//opt_CPD.w = customParams.w;
//params.opt_CPD = opt_CPD;
#define nNoises 9
#define nOffsets 2
#define nTests (nNoises*nOffsets)
//#define nOutliers 6
//#define nTests (nNoises*nOffsets*nOutliers)
//double percentOutliers[nOutliers] = { 0.05, 0.1, 0.2, 0.3, 0.4, 0.5 };
double noiseInPlaneSDArr[nNoises] = { 0.5, 1.0, 2.0, 0.5, 1.0, 0.5, 1.0, 2.0, 2.0 };
double noisePerpPlaneSDArr[nNoises] = { 0.5, 1.0, 2.0, 1.0, 2.0, 2.0, 0.5, 1.0, 0.5 };
//double noiseInPlaneSDArr[nNoises] = { 0.5, 1.0 };
//double noisePerpPlaneSDArr[nNoises] = { 0.5, 1.0 };
double minOffsetAngArr[nOffsets] = { 30, 15 }; //{ 10, 30 }; //{0, 10, 30, 60};
double maxOffsetAngArr[nOffsets] = { 60, 30 }; //{ 30, 60 }; //{10, 30, 60, 90};
double minOffsetPosArr[nOffsets] = { 30, 15 }; //{ 10, 30 }; //{0, 10, 30, 60};
double maxOffsetPosArr[nOffsets] = { 60, 30 }; //{ 30, 60 }; //{10, 30, 60, 100};
std::vector<unsigned int> randSeed_SamplesArr(nTests, 0); // sample generater
std::vector<unsigned int> randSeed_XfmsArr(nTests, 0); // initial offset xfm generater
for (unsigned int i = 0; i < nTests; i++)
{
randSeed_SamplesArr[i] = i + 23;
randSeed_XfmsArr[i] = i + 127;
}
std::string outputCommonDir = params.outputCommonDir;
params.nSamples = customParams.nGoodSamples;
//--- Parameterized Trials ---//
for (unsigned int offset = 0; offset < nOffsets; offset++)
{
for (unsigned int noise = 0; noise < nNoises; noise++)
{
unsigned int testNum = offset*nNoises + noise;
ss.str("");
ss << "Noise_Prll" << noiseInPlaneSDArr[noise] << "Perp" << noisePerpPlaneSDArr[noise]
<< "_Offset_R" << minOffsetAngArr[offset] << "-" << maxOffsetAngArr[offset]
<< "T" << minOffsetPosArr[offset] << "-" << maxOffsetPosArr[offset];
//<< "_Outliers" << percentOutliers[outlier];
std::string outputSubFolder = ss.str();
params.minOffsetAng = minOffsetAngArr[offset];
params.maxOffsetAng = maxOffsetAngArr[offset];
params.minOffsetPos = minOffsetPosArr[offset];
params.maxOffsetPos = maxOffsetPosArr[offset];
params.randSeed_Samples = randSeed_SamplesArr[testNum];
params.randSeed_Xfms = randSeed_XfmsArr[testNum];
customParams.sampleNoise_InPlaneSD = noiseInPlaneSDArr[noise];
customParams.sampleNoise_PerpPlaneSD = noisePerpPlaneSDArr[noise];
// hold number of good samples constant and increase sample size to
// achieve the desired percentage of outliers
//double p = percentOutliers[outlier];
//unsigned int nOutlierSamps = (unsigned int)(p/(1-p) * customParams.nGoodSamples);
//params.nSamples = customParams.nGoodSamples + nOutlierSamps;
// TODO: remove change to output common files to separate directories below
// Run StdICP
{
params.AlgorithmDescription = "StdICP";
//params.AlgorithmDescription = "StdICP_Verbose";
params.algType = TestParameters::StdICP;
SetOutputDir(params, outputCommonDir, outputSubFolder);
vctDynamicVector<vct3> dummySamples; // these will be set later by the sample generator routine
params.pAlg = new cisstAlgorithmICP_StdICP_PointCloud(pTree, dummySamples);
Run_ParameterizedTest(mesh_source, pTree, params);
delete params.pAlg; params.pAlg = NULL;
}
// Run IMLP
{
params.AlgorithmDescription = "IMLP";
//params.AlgorithmDescription = "IMLP_Verbose";
params.algType = TestParameters::IMLP;
SetOutputDir(params, outputCommonDir, outputSubFolder);
vctDynamicVector<vct3> dummySamples; // these will be set later by the sample generator routine
vctDynamicVector<vct3x3> dummySampleCov; // ''
cisstAlgorithmICP_IMLP_PointCloud *pAlg =
new cisstAlgorithmICP_IMLP_PointCloud(
pTree, dummySamples, dummySampleCov, dummySampleCov, customParams.outlier_ChiSquareThreshold);
params.pAlg = pAlg;
Run_ParameterizedTest(mesh_source, pTree, params);
delete params.pAlg; params.pAlg = NULL;
}
// Run IMLP_MD (Mahalanobis Distance Match Criteria)
{
params.AlgorithmDescription = "IMLP-MD";
//params.AlgorithmDescription = "IMLP-MD_Verbose";
params.algType = TestParameters::IMLP;
SetOutputDir(params, outputCommonDir, outputSubFolder);
vctDynamicVector<vct3> dummySamples; // these will be set later by the sample generator routine
vctDynamicVector<vct3x3> dummySampleCov; // ''
cisstAlgorithmICP_IMLP_MahalDist_PointCloud *pAlg =
new cisstAlgorithmICP_IMLP_MahalDist_PointCloud(
pTree, dummySamples, dummySampleCov, dummySampleCov, customParams.outlier_ChiSquareThreshold);
params.pAlg = pAlg;
Run_ParameterizedTest(mesh_source, pTree, params);
delete params.pAlg; params.pAlg = NULL;
}
// Run IMLP_CP (Closest Point Match Criteria)
{
params.AlgorithmDescription = "IMLP-CP";
//params.AlgorithmDescription = "IMLP-CP_Verbose";
params.algType = TestParameters::IMLP;
SetOutputDir(params, outputCommonDir, outputSubFolder);
vctDynamicVector<vct3> dummySamples; // these will be set later by the sample generator routine
vctDynamicVector<vct3x3> dummySampleCov; // ''
cisstAlgorithmICP_IMLP_ClosestPoint_PointCloud *pAlg =
new cisstAlgorithmICP_IMLP_ClosestPoint_PointCloud(
pTree, dummySamples, dummySampleCov, dummySampleCov, customParams.outlier_ChiSquareThreshold);
params.pAlg = pAlg;
Run_ParameterizedTest(mesh_source, pTree, params);
delete params.pAlg; params.pAlg = NULL;
}
}
}
}
/* ********************************************************************* */
int Setup (Input *input, Cmd_Line *cmd_line, char *ini_file)
/*!
* Open and parse the initialization file.
* Assign values to the input structure.
*
* \param [out] input pointer to an Input structure
* \param [in] cmd_line pointer to a Cmd_Line structure (useful, e.g.,
* to resize the domain using the \c -xres option)
* \param [in] ini_file the name of the initialization file (default
* is "pluto.ini") specified with the \c -i option.
*
*********************************************************************** */
{
int idim, ip, ipos, itype, nlines;
char *bound_opt[NOPT], str_var[512], *str;
char *glabel[] = {"X1-grid", "X2-grid","X3-grid"};
char *bbeg_label[] = {"X1-beg", "X2-beg","X3-beg"};
char *bend_label[] = {"X1-end", "X2-end","X3-end"};
double dbl_var, rx;
Output *output;
FILE *fp;
for (itype = 0; itype < NOPT; itype++) {
bound_opt[itype] = "0000";
}
/* ---------------------------------------------------
available options are given as two set of names;
This facilitates when updating the code and
people are too lazy to read the manual !
--------------------------------------------------- */
bound_opt[OUTFLOW] = "outflow";
bound_opt[REFLECTIVE] = "reflective";
bound_opt[AXISYMMETRIC] = "axisymmetric";
bound_opt[EQTSYMMETRIC] = "eqtsymmetric";
bound_opt[PERIODIC] = "periodic";
bound_opt[SHEARING] = "shearingbox";
bound_opt[USERDEF] = "userdef";
input->log_freq = 1; /* -- default -- */
nlines = ParamFileRead(ini_file);
/* ------------------------------------------------------------
[Grid] Section
------------------------------------------------------------ */
for (idim = 0; idim < 3; idim++){
input->npatch[idim] = atoi(ParamFileGet(glabel[idim], 1));
input->npoint[idim] = 0;
ipos = 1;
for (ip = 1; ip <= input->npatch[idim]; ip++) {
input->patch_left_node[idim][ip] = atof(ParamFileGet(glabel[idim], ++ipos));
input->patch_npoint[idim][ip] = atoi(ParamFileGet(glabel[idim], ++ipos));
input->npoint[idim] += input->patch_npoint[idim][ip];
input->grid_is_uniform[idim] = 0;
strcpy (str_var, ParamFileGet(glabel[idim], ++ipos));
/*
printf ("%f %d %s\n",input->patch_left_node[idim][ip],input->patch_npoint[idim][ip],str_var);
*/
if (strcmp(str_var,"u") == 0 || strcmp(str_var,"uniform") == 0) {
input->patch_type[idim][ip] = UNIFORM_GRID;
if (input->npatch[idim] == 1) input->grid_is_uniform[idim] = 1;
}else if (strcmp(str_var,"s") == 0 || strcmp(str_var,"strecthed") == 0) {
input->patch_type[idim][ip] = STRETCHED_GRID;
}else if (strcmp(str_var,"l+") == 0){
input->patch_type[idim][ip] = LOGARITHMIC_INC_GRID;
}else if (strcmp(str_var,"l-") == 0){
input->patch_type[idim][ip] = LOGARITHMIC_DEC_GRID;
}else{
printf ("\nSetup: You must specify either 'u', 's', 'l+' or 'l-' as grid-type in %s\n",
ini_file);
QUIT_PLUTO(1);
}
}
input->patch_left_node[idim][ip] = atof(ParamFileGet(glabel[idim], ++ipos));
if ( (ipos+1) != (input->npatch[idim]*3 + 3)) {
printf ("! Setup: domain #%d setup is not properly defined \n", idim);
QUIT_PLUTO(1);
}
if (idim >= DIMENSIONS && input->npoint[idim] != 1) {
printf ("! Setup: %d point(s) on dim. %d is NOT valid, resetting to 1\n",
input->npoint[idim],idim+1);
input->npoint[idim] = 1;
input->npatch[idim] = 1;
input->patch_npoint[idim][1] = 1;
}
}
/* ------------------------------------------------------------
Change the resolution if cmd_line->xres has been given
------------------------------------------------------------ */
if (cmd_line->xres > 1) {
rx = (double)cmd_line->xres/(double)input->patch_npoint[IDIR][1];
for (idim = 0; idim < DIMENSIONS; idim++){
if (input->npatch[idim] > 1){
printf ("! Setup: -xres option works on uniform, single patch grid\n");
QUIT_PLUTO(1);
}
dbl_var = (double)input->patch_npoint[idim][1];
input->patch_npoint[idim][1] = MAX( (int)(dbl_var*rx), 1);
dbl_var = (double)input->npoint[idim];
input->npoint[idim] = MAX( (int)(dbl_var*rx), 1);
}
}
/* ------------------------------------------------------------
[Time] Section
------------------------------------------------------------ */
input->cfl = atof(ParamFileGet("CFL", 1));
if (ParamExist ("CFL_par")) input->cfl_par = atof(ParamFileGet("CFL_par", 1));
else input->cfl_par = 0.8/(double)DIMENSIONS;
if (ParamExist ("rmax_par")) input->rmax_par = atof(ParamFileGet("rmax_par", 1));
else input->rmax_par = 100.0;
input->cfl_max_var = atof(ParamFileGet("CFL_max_var", 1));
input->tstop = atof(ParamFileGet("tstop", 1));
input->first_dt = atof(ParamFileGet("first_dt", 1));
/* ------------------------------------------------------------
[Solver] Section
------------------------------------------------------------ */
sprintf (input->solv_type,"%s",ParamFileGet("Solver",1));
/* ------------------------------------------------------------
[Boundary] Section
------------------------------------------------------------ */
for (idim = 0; idim < 3; idim++){
str = ParamFileGet(bbeg_label[idim], 1);
COMPARE (str, bound_opt[itype], itype);
if (itype == NOPT) {
printf ("! Setup: don't know how to put left boundary '%s' \n", str);
QUIT_PLUTO(1);
}
input->lft_bound_side[idim] = itype;
}
for (idim = 0; idim < 3; idim++){
str = ParamFileGet(bend_label[idim], 1);
COMPARE (str, bound_opt[itype], itype);
if (itype == NOPT) {
printf ("! Setup: don't know how to put left boundary '%s' \n", str);
QUIT_PLUTO(1);
}
input->rgt_bound_side[idim] = itype;
}
/* ------------------------------------------------------------
[Output] Section
------------------------------------------------------------ */
input->user_var = atoi(ParamFileGet("uservar", 1));
for (ip = 0; ip < input->user_var; ip++){
if ( (str = ParamFileGet("uservar", 2 + ip)) != NULL){
sprintf (input->user_var_name[ip], "%s", str);
}else{
printf ("! Setup: missing name after user var name '%s'\n",
input->user_var_name[ip-1]);
QUIT_PLUTO(1);
}
}
/* ---- set output directory ---- */
sprintf (input->output_dir, "%s","./"); /* default value is current directory */
if (ParamExist("output_dir")){
str = ParamFileGet("output_dir",1);
sprintf (input->output_dir, "%s",str);
}
SetOutputDir(input->output_dir);
/* -- check if we have write access and if the directory exists -- */
sprintf (str_var,"%s/tmp09123.txt",input->output_dir); /* -- test file -- */
fp = fopen(str_var,"w"); /* -- open test file for writing -- */
if (fp == NULL){
printf ("! Setup: cannot access directory '%s'.\n", input->output_dir);
printf ("! Please check that the directory exists\n");
printf ("! and you have write permission.\n");
QUIT_PLUTO(1);
}else{
fclose(fp);
remove(str_var); /* -- remove file -- */
}
/* ---- dbl output ---- */
ipos = 0;
output = input->output + (ipos++);
output->type = DBL_OUTPUT;
output->cgs = 0; /* cannot write .dbl using cgs units */
GetOutputFrequency(output, "dbl");
sprintf (output->mode,"%s",ParamFileGet("dbl",3));
#ifdef USE_ASYNC_IO
if ( strcmp(output->mode,"single_file")
&& strcmp(output->mode,"single_file_async")
&& strcmp(output->mode,"multiple_files")){
printf ("! Setup: expecting 'single_file', 'single_file_async' ");
printf ("or 'multiple_files' in dbl output\n");
QUIT_PLUTO(1);
}
#else
if ( strcmp(output->mode,"single_file")
&& strcmp(output->mode,"multiple_files")){
printf (
"! Setup: expecting 'single_file' or 'multiple_files' in dbl output\n");
QUIT_PLUTO(1);
}
#endif
/* ---- flt output ---- */
if (ParamExist("flt")){
output = input->output + (ipos++);
output->type = FLT_OUTPUT;
GetOutputFrequency(output, "flt");
sprintf (output->mode,"%s",ParamFileGet("flt",3));
#ifdef USE_ASYNC_IO
if ( strcmp(output->mode,"single_file")
&& strcmp(output->mode,"single_file_async")
&& strcmp(output->mode,"multiple_files")){
printf ("! Setup: expecting 'single_file', 'single_file_async' ");
printf ("or 'multiple_files' in flt output\n");
QUIT_PLUTO(1);
}
#else
if ( strcmp(output->mode,"single_file")
&& strcmp(output->mode,"multiple_files")){
printf (
"! Setup: expecting 'single_file' or 'multiple_files' in flt output\n");
QUIT_PLUTO(1);
}
#endif
if (ParamFileHasBoth ("flt","cgs")) output->cgs = 1;
else output->cgs = 0;
}
/* -- hdf5 output -- */
if (ParamExist("dbl.h5")){
output = input->output + (ipos++);
output->type = DBL_H5_OUTPUT;
output->cgs = 0; /* cannot write .h5 using cgs units */
GetOutputFrequency(output, "dbl.h5");
}
if (ParamExist("flt.h5")){
output = input->output + (ipos++);
output->type = FLT_H5_OUTPUT;
output->cgs = 0; /* cannot write .h5 using cgs units */
GetOutputFrequency(output, "flt.h5");
}
/* -- vtk output -- */
if (ParamExist ("vtk")){
output = input->output + (ipos++);
output->type = VTK_OUTPUT;
GetOutputFrequency(output, "vtk");
if (ParamFileGet("vtk",3) == NULL){
printf ("! Setup: extra field missing in vtk output\n");
QUIT_PLUTO(1);
}
sprintf (output->mode,"%s",ParamFileGet("vtk",3));
if ( strcmp(output->mode,"single_file")
&& strcmp(output->mode,"multiple_files")){
printf ("! Setup: expecting 'single_file' or 'multiple_files' in\n");
printf (" vtk output\n");
QUIT_PLUTO(1);
}
if (ParamFileHasBoth ("vtk","cgs")) output->cgs = 1;
else output->cgs = 0;
}
/* -- tab output -- */
if (ParamExist ("tab")){
output = input->output + (ipos++);
output->type = TAB_OUTPUT;
GetOutputFrequency(output, "tab");
if (ParamFileHasBoth ("tab","cgs")) output->cgs = 1;
else output->cgs = 0;
}
/* -- ppm output -- */
if (ParamExist ("ppm")){
output = input->output + (ipos++);
output->type = PPM_OUTPUT;
output->cgs = 0; /* Cannot write ppm in cgs units */
GetOutputFrequency(output, "ppm");
}
/* -- png output -- */
if (ParamExist ("png")){
output = input->output + (ipos++);
output->type = PNG_OUTPUT;
output->cgs = 0; /* Cannot write png in cgs units */
GetOutputFrequency(output, "png");
}
/* -- log frequency -- */
input->log_freq = atoi(ParamFileGet("log", 1));
input->log_freq = MAX(input->log_freq, 1);
/* -- set default for remaining output type -- */
while (ipos < MAX_OUTPUT_TYPES){
output = input->output + ipos;
output->type = -1;
output->cgs = 0;
output->dt = -1.0;
output->dn = -1;
output->dclock = -1.0;
ipos++;
}
/* -- analysis -- */
if (ParamExist ("analysis")){
input->anl_dt = atof(ParamFileGet("analysis", 1));
input->anl_dn = atoi(ParamFileGet("analysis", 2));
}else{
input->anl_dt = -1.0; /* -- defaults -- */
input->anl_dn = -1;
}
/* ------------------------------------------------------------
[Parameters] Section
------------------------------------------------------------ */
fp = fopen(ini_file,"r");
/* -- find position at "[Parameters" -- */
for (ipos = 0; ipos <= nlines; ipos++){
fgets(str_var, 512, fp);
if (strlen(str_var) > 0) {
str = strtok (str_var,"]");
if (strcmp(str,"[Parameters") == 0) break;
}
}
fgets(str_var, 512, fp);
for (ip = 0; ip < USER_DEF_PARAMETERS; ip++){
fscanf (fp,"%s \n", str_var);
dbl_var = atof(ParamFileGet(str_var,1));
input->aux[ip] = dbl_var;
fgets(str_var, sizeof(str_var), fp); /* use fgets to advance to next line */
}
fclose(fp);
return(0);
}