// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AlignSectionsMutualInformation::form_features_sections()
{
DREAM3D_RANDOMNG_NEW()
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
size_t udims[3] = { 0, 0, 0 };
m->getGeometryAs<ImageGeom>()->getDimensions(udims);
#if (CMP_SIZEOF_SIZE_T == 4)
typedef int32_t DimType;
#else
typedef int64_t DimType;
#endif
DimType dims[3] =
{
static_cast<DimType>(udims[0]),
static_cast<DimType>(udims[1]),
static_cast<DimType>(udims[2]),
};
DimType point = 0;
DimType seed = 0;
bool noseeds = false;
int32_t featurecount = 1;
DimType neighbor = 0;
QuatF q1 = QuaternionMathF::New();
QuatF q2 = QuaternionMathF::New();
QuatF* quats = reinterpret_cast<QuatF*>(m_Quats);
float w = 0.0f;
float n1 = 0.0f;
float n2 = 0.0f;
float n3 = 0.0f;
DimType randx = 0;
DimType randy = 0;
bool good = false;
DimType x = 0, y = 0, z = 0;
DimType col = 0, row = 0;
size_t size = 0;
size_t initialVoxelsListSize = 1000;
m_FeatureCounts->resize(dims[2]);
featurecounts = m_FeatureCounts->getPointer(0);
std::vector<DimType> voxelslist(initialVoxelsListSize, -1);
DimType neighpoints[4] = { 0, 0, 0, 0 };
neighpoints[0] = -dims[0];
neighpoints[1] = -1;
neighpoints[2] = 1;
neighpoints[3] = dims[0];
uint32_t phase1 = 0, phase2 = 0;
for (DimType slice = 0; slice < dims[2]; slice++)
{
QString ss = QObject::tr("Aligning Sections || Identifying Features on Sections || %1% Complete").arg(((float)slice / dims[2]) * 100);
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), ss);
featurecount = 1;
noseeds = false;
while (noseeds == false)
{
seed = -1;
randx = DimType(float(rg.genrand_res53()) * float(dims[0]));
randy = DimType(float(rg.genrand_res53()) * float(dims[1]));
for (DimType j = 0; j < dims[1]; ++j)
{
for (DimType i = 0; i < dims[0]; ++i)
{
x = randx + i;
y = randy + j;
z = slice;
if (x > dims[0] - 1) { x = x - dims[0]; }
if (y > dims[1] - 1) { y = y - dims[1]; }
point = (z * dims[0] * dims[1]) + (y * dims[0]) + x;
if ((m_UseGoodVoxels == false || m_GoodVoxels[point] == true) && m_FeatureIds[point] == 0 && m_CellPhases[point] > 0)
{
seed = point;
}
if (seed > -1) { break; }
}
if( seed > -1) { break; }
}
if (seed == -1) { noseeds = true; }
if (seed >= 0)
{
size = 0;
m_FeatureIds[seed] = featurecount;
voxelslist[size] = seed;
size++;
for (size_t j = 0; j < size; ++j)
{
DimType currentpoint = voxelslist[j];
col = currentpoint % dims[0];
row = (currentpoint / dims[0]) % dims[1];
QuaternionMathF::Copy(quats[currentpoint], q1);
phase1 = m_CrystalStructures[m_CellPhases[currentpoint]];
for (int32_t i = 0; i < 4; i++)
{
good = true;
neighbor = currentpoint + neighpoints[i];
if ((i == 0) && row == 0) { good = false; }
if ((i == 3) && row == (dims[1] - 1)) { good = false; }
if ((i == 1) && col == 0) { good = false; }
if ((i == 2) && col == (dims[0] - 1)) { good = false; }
if (good == true && m_FeatureIds[neighbor] <= 0 && m_CellPhases[neighbor] > 0)
{
w = std::numeric_limits<float>::max();
QuaternionMathF::Copy(quats[neighbor], q2);
phase2 = m_CrystalStructures[m_CellPhases[neighbor]];
if (phase1 == phase2)
{
w = m_OrientationOps[phase1]->getMisoQuat(q1, q2, n1, n2, n3);
}
if (w < m_MisorientationTolerance)
{
m_FeatureIds[neighbor] = featurecount;
voxelslist[size] = neighbor;
size++;
if (std::vector<DimType>::size_type(size) >= voxelslist.size())
{
size = voxelslist.size();
voxelslist.resize(size + initialVoxelsListSize);
for (std::vector<DimType>::size_type v = size; v < voxelslist.size(); ++v) { voxelslist[v] = -1; }
}
}
}
}
}
voxelslist.erase(std::remove(voxelslist.begin(), voxelslist.end(), -1), voxelslist.end());
featurecount++;
voxelslist.assign(initialVoxelsListSize, -1);
}
}
featurecounts[slice] = featurecount;
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SegmentGrains::execute()
{
setErrorCondition(0);
VoxelDataContainer* m = getVoxelDataContainer();
std::stringstream ss;
if(NULL == m)
{
setErrorCondition(-1);
ss << " DataContainer was NULL";
addErrorMessage(getHumanLabel(), ss.str(), -1);
return;
}
size_t udims[3] =
{ 0, 0, 0 };
m->getDimensions(udims);
#if (CMP_SIZEOF_SIZE_T == 4)
typedef int32_t DimType;
#else
typedef int64_t DimType;
#endif
DimType dims[3] =
{ static_cast<DimType>(udims[0]), static_cast<DimType>(udims[1]), static_cast<DimType>(udims[2]), };
size_t gnum = 1;
int seed = 0;
int neighbor;
bool good = 0;
DimType col, row, plane;
size_t size = 0;
size_t initialVoxelsListSize = 1000;
std::vector<int> voxelslist(initialVoxelsListSize, -1);
DimType neighpoints[6];
neighpoints[0] = -(dims[0] * dims[1]);
neighpoints[1] = -dims[0];
neighpoints[2] = -1;
neighpoints[3] = 1;
neighpoints[4] = dims[0];
neighpoints[5] = (dims[0] * dims[1]);
// Burn volume with tight orientation tolerance to simulate simultaneous growth/aglomeration
while (seed >= 0)
{
seed = getSeed(gnum);
if(seed >= 0)
{
size = 0;
voxelslist[size] = seed;
size++;
for (size_t j = 0; j < size; ++j)
{
// Get the current Voxel
size_t currentpoint = voxelslist[j];
// Figure out the Row, Col & Plane the voxel is located in
col = currentpoint % dims[0];
row = (currentpoint / dims[0]) % dims[1];
plane = currentpoint / (dims[0] * dims[1]);
// Now loop over its 6 neighbors
for (int i = 0; i < 6; i++)
{
good = true;
neighbor = currentpoint + neighpoints[i];
// Make sure we have a valid neighbor taking into account the edges of the volume
if(i == 0 && plane == 0) good = false;
if(i == 5 && plane == (dims[2] - 1)) good = false;
if(i == 1 && row == 0) good = false;
if(i == 4 && row == (dims[1] - 1)) good = false;
if(i == 2 && col == 0) good = false;
if(i == 3 && col == (dims[0] - 1)) good = false;
if(good == true)
{
// We got a good voxel to check so check to see if it can be grouped with this point
if(determineGrouping(currentpoint, neighbor, gnum) == true)
{
// The voxel can be grouped with this voxel so add it to the list of voxels for this grain
voxelslist[size] = neighbor;
// Increment the size of the list which affects the "j" loop
size++;
// Sanity check the size of the voxelslist vector. If it is not large enough, double the size of the vector
if(size >= voxelslist.size())
{
voxelslist.resize(size + size, -1); // The resize is a hit but the doubling mitigates the penalty somewhat
}
}
}
}
}
voxelslist.clear();
voxelslist.resize(initialVoxelsListSize, -1);
gnum++;
ss.str("");
ss << "Total Grains: " << gnum;
if(gnum%100 == 0) notifyStatusMessage(ss.str());
if (getCancel() == true)
{
setErrorCondition(-1);
break;
}
}
}
// If there is an error set this to something negative and also set a message
notifyStatusMessage("Completed");
}