// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ErodeDilateBadData::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getFeatureIdsArrayPath().getDataContainerName());
size_t totalPoints = m_FeatureIdsPtr.lock()->getNumberOfTuples();
Int32ArrayType::Pointer neighborsPtr = Int32ArrayType::CreateArray(totalPoints, "_INTERNAL_USE_ONLY_Neighbors");
m_Neighbors = neighborsPtr->getPointer(0);
neighborsPtr->initializeWithValue(-1);
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]),
};
int32_t good = 1;
int64_t count = 0;
int64_t kstride = 0, jstride = 0;
int32_t featurename = 0, feature = 0;
int32_t current = 0;
int32_t most = 0;
int64_t neighpoint = 0;
size_t numfeatures = 0;
for (size_t i = 0; i < totalPoints; i++)
{
featurename = m_FeatureIds[i];
if (featurename > numfeatures) { numfeatures = featurename; }
}
DimType neighpoints[6] = { 0, 0, 0, 0, 0, 0 };
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];
QVector<int32_t> n(numfeatures + 1, 0);
for (int32_t iteration = 0; iteration < m_NumIterations; iteration++)
{
for (DimType k = 0; k < dims[2]; k++)
{
kstride = dims[0] * dims[1] * k;
for (DimType j = 0; j < dims[1]; j++)
{
jstride = dims[0] * j;
for (DimType i = 0; i < dims[0]; i++)
{
count = kstride + jstride + i;
featurename = m_FeatureIds[count];
if (featurename == 0)
{
current = 0;
most = 0;
for (int32_t l = 0; l < 6; l++)
{
good = 1;
neighpoint = count + neighpoints[l];
if (l == 0 && (k == 0 || m_ZDirOn == false)) { good = 0; }
else if (l == 5 && (k == (dims[2] - 1) || m_ZDirOn == false)) { good = 0; }
else if (l == 1 && (j == 0 || m_YDirOn == false)) { good = 0; }
else if (l == 4 && (j == (dims[1] - 1) || m_YDirOn == false)) { good = 0; }
else if (l == 2 && (i == 0 || m_XDirOn == false)) { good = 0; }
else if (l == 3 && (i == (dims[0] - 1) || m_XDirOn == false)) { good = 0; }
if (good == 1)
{
feature = m_FeatureIds[neighpoint];
if (m_Direction == 0 && feature > 0)
{
m_Neighbors[neighpoint] = count;
}
if (feature > 0 && m_Direction == 1)
{
n[feature]++;
current = n[feature];
if (current > most)
{
most = current;
m_Neighbors[count] = neighpoint;
}
}
}
}
if (m_Direction == 1)
{
for (int32_t l = 0; l < 6; l++)
{
good = 1;
neighpoint = count + neighpoints[l];
if (l == 0 && k == 0) { good = 0; }
if (l == 5 && k == (dims[2] - 1)) { good = 0; }
if (l == 1 && j == 0) { good = 0; }
if (l == 4 && j == (dims[1] - 1)) { good = 0; }
if (l == 2 && i == 0) { good = 0; }
if (l == 3 && i == (dims[0] - 1)) { good = 0; }
if (good == 1)
{
feature = m_FeatureIds[neighpoint];
n[feature] = 0;
}
}
}
}
}
}
}
QString attrMatName = m_FeatureIdsArrayPath.getAttributeMatrixName();
QList<QString> voxelArrayNames = m->getAttributeMatrix(attrMatName)->getAttributeArrayNames();
for (size_t j = 0; j < totalPoints; j++)
{
featurename = m_FeatureIds[j];
int32_t neighbor = m_Neighbors[j];
if (neighbor >= 0)
{
if ( (featurename == 0 && m_FeatureIds[neighbor] > 0 && m_Direction == 1)
|| (featurename > 0 && m_FeatureIds[neighbor] == 0 && m_Direction == 0))
{
for(QList<QString>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
IDataArray::Pointer p = m->getAttributeMatrix(attrMatName)->getAttributeArray(*iter);
p->copyTuple(neighbor, j);
}
}
}
}
}
// If there is an error set this to something negative and also set a message
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RemoveFlaggedFeatures::assign_badpoints()
{
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(m_FeatureIdsArrayPath.getDataContainerName());
size_t totalPoints = m_FeatureIdsPtr.lock()->getNumberOfTuples();
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]),
};
Int32ArrayType::Pointer neighborsPtr = Int32ArrayType::CreateArray(totalPoints, "_INTERNAL_USE_ONLY_Neighbors");
m_Neighbors = neighborsPtr->getPointer(0);
neighborsPtr->initializeWithValue(-1);
int32_t good = 1;
int32_t current = 0;
int32_t most = 0;
int64_t neighpoint = 0;
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];
size_t counter = 1;
int64_t count = 0;
int64_t kstride = 0, jstride = 0;
int32_t featurename, feature;
int32_t neighbor;
QVector<int32_t> n(m_FlaggedFeaturesPtr.lock()->getNumberOfTuples(), 0);
while (counter != 0)
{
counter = 0;
for (DimType k = 0; k < dims[2]; k++)
{
kstride = dims[0] * dims[1] * k;
for (DimType j = 0; j < dims[1]; j++)
{
jstride = dims[0] * j;
for (DimType i = 0; i < dims[0]; i++)
{
count = kstride + jstride + i;
featurename = m_FeatureIds[count];
if (featurename < 0)
{
counter++;
current = 0;
most = 0;
for (int32_t l = 0; l < 6; l++)
{
good = 1;
neighpoint = count + neighpoints[l];
if (l == 0 && k == 0) { good = 0; }
if (l == 5 && k == (dims[2] - 1)) { good = 0; }
if (l == 1 && j == 0) { good = 0; }
if (l == 4 && j == (dims[1] - 1)) { good = 0; }
if (l == 2 && i == 0) { good = 0; }
if (l == 3 && i == (dims[0] - 1)) { good = 0; }
if (good == 1)
{
feature = m_FeatureIds[neighpoint];
if (feature >= 0)
{
n[feature]++;
current = n[feature];
if (current > most)
{
most = current;
m_Neighbors[count] = neighpoint;
}
}
}
}
for (int32_t l = 0; l < 6; l++)
{
good = 1;
neighpoint = count + neighpoints[l];
if (l == 0 && k == 0) { good = 0; }
if (l == 5 && k == (dims[2] - 1)) { good = 0; }
if (l == 1 && j == 0) { good = 0; }
if (l == 4 && j == (dims[1] - 1)) { good = 0; }
if (l == 2 && i == 0) { good = 0; }
if (l == 3 && i == (dims[0] - 1)) { good = 0; }
if (good == 1)
{
feature = m_FeatureIds[neighpoint];
if (feature >= 0) { n[feature] = 0; }
}
}
}
}
}
}
QString attrMatName = m_FeatureIdsArrayPath.getAttributeMatrixName();
QList<QString> voxelArrayNames = m->getAttributeMatrix(attrMatName)->getAttributeArrayNames();
for (size_t j = 0; j < totalPoints; j++)
{
featurename = m_FeatureIds[j];
neighbor = m_Neighbors[j];
if (neighbor >= 0)
{
if (featurename < 0 && m_FeatureIds[neighbor] >= 0)
{
for (QList<QString>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
IDataArray::Pointer p = m->getAttributeMatrix(attrMatName)->getAttributeArray(*iter);
p->copyTuple(neighbor, j);
}
}
}
}
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ErodeDilateCoordinationNumber::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getFeatureIdsArrayPath().getDataContainerName());
size_t totalPoints = m_FeatureIdsPtr.lock()->getNumberOfTuples();
Int32ArrayType::Pointer neighborsPtr = Int32ArrayType::CreateArray(totalPoints, "Neighbors");
m_Neighbors = neighborsPtr->getPointer(0);
neighborsPtr->initializeWithValue(-1);
size_t udims[3] = {0, 0, 0};
m->getGeometryAs<ImageGeom>()->getDimensions(udims);
int64_t dims[3] =
{
static_cast<int64_t>(udims[0]),
static_cast<int64_t>(udims[1]),
static_cast<int64_t>(udims[2]),
};
int32_t good = 1;
int64_t point = 0;
int64_t kstride = 0, jstride = 0;
int32_t featurename = 0, feature = 0;
int32_t coordination = 0;
int32_t current = 0;
int32_t most = 0;
int64_t neighpoint = 0;
size_t numfeatures = 0;
for(size_t i = 0; i < totalPoints; i++)
{
featurename = m_FeatureIds[i];
if (featurename > numfeatures) { numfeatures = featurename; }
}
int64_t neighpoints[6] = { 0, 0, 0, 0, 0, 0 };
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];
QString attrMatName = m_FeatureIdsArrayPath.getAttributeMatrixName();
QList<QString> voxelArrayNames = m->getAttributeMatrix(attrMatName)->getAttributeArrayNames();
QVector<int32_t> n(numfeatures + 1, 0);
QVector<int32_t> coordinationNumber(totalPoints, 0);
bool keepgoing = true;
int32_t counter = 1;
while (counter > 0 && keepgoing == true)
{
counter = 0;
if (m_Loop == false) { keepgoing = false; }
for (int64_t k = 0; k < dims[2]; k++)
{
kstride = dims[0] * dims[1] * k;
for (int64_t j = 0; j < dims[1]; j++)
{
jstride = dims[0] * j;
for (int64_t i = 0; i < dims[0]; i++)
{
point = kstride + jstride + i;
featurename = m_FeatureIds[point];
coordination = 0;
current = 0;
most = 0;
for (int32_t l = 0; l < 6; l++)
{
good = 1;
neighpoint = point + neighpoints[l];
if (l == 0 && k == 0) { good = 0; }
if (l == 5 && k == (dims[2] - 1)) { good = 0; }
if (l == 1 && j == 0) { good = 0; }
if (l == 4 && j == (dims[1] - 1)) { good = 0; }
if (l == 2 && i == 0) { good = 0; }
if (l == 3 && i == (dims[0] - 1)) { good = 0; }
if (good == 1)
{
feature = m_FeatureIds[neighpoint];
if ((featurename > 0 && feature == 0) || (featurename == 0 && feature > 0))
{
coordination = coordination + 1;
n[feature]++;
current = n[feature];
if (current > most)
{
most = current;
m_Neighbors[point] = neighpoint;
}
}
}
}
coordinationNumber[point] = coordination;
int32_t neighbor = m_Neighbors[point];
if (coordinationNumber[point] >= m_CoordinationNumber && coordinationNumber[point] > 0)
{
for (QList<QString>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
IDataArray::Pointer p = m->getAttributeMatrix(attrMatName)->getAttributeArray(*iter);
p->copyTuple(neighbor, point);
}
}
for (int32_t l = 0; l < 6; l++)
{
good = 1;
neighpoint = point + neighpoints[l];
if (l == 0 && k == 0) { good = 0; }
if (l == 5 && k == (dims[2] - 1)) { good = 0; }
if (l == 1 && j == 0) { good = 0; }
if (l == 4 && j == (dims[1] - 1)) { good = 0; }
if (l == 2 && i == 0) { good = 0; }
if (l == 3 && i == (dims[0] - 1)) { good = 0; }
if (good == 1)
{
feature = m_FeatureIds[neighpoint];
if (feature > 0) { n[feature] = 0; }
}
}
}
}
}
for (int64_t k = 0; k < dims[2]; k++)
{
kstride = static_cast<int64_t>(dims[0] * dims[1] * k);
for (int64_t j = 0; j < dims[1]; j++)
{
jstride = static_cast<int64_t>(dims[0] * j);
for (int64_t i = 0; i < dims[0]; i++)
{
point = kstride + jstride + i;
if (coordinationNumber[point] >= m_CoordinationNumber)
{
counter++;
}
}
}
}
}
// If there is an error set this to something negative and also set a message
notifyStatusMessage(getHumanLabel(), "Complete");
}