// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AlignSectionsMutualInformation::find_shifts(std::vector<int64_t>& xshifts, std::vector<int64_t>& yshifts)
{
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
int64_t totalPoints = m->getAttributeMatrix(getCellAttributeMatrixName())->getNumTuples();
Int32ArrayType::Pointer p = Int32ArrayType::CreateArray((totalPoints * 1), "_INTERNAL_USE_ONLY_MIFeatureIds");
m_FeatureIds = p->getPointer(0);
std::ofstream outFile;
if (getWriteAlignmentShifts() == true)
{
outFile.open(getAlignmentShiftFileName().toLatin1().data());
}
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]),
};
float disorientation = 0.0f;
float mindisorientation = std::numeric_limits<float>::max();
float** mutualinfo12 = NULL;
float* mutualinfo1 = NULL;
float* mutualinfo2 = NULL;
int32_t featurecount1 = 0, featurecount2 = 0;
int64_t newxshift = 0;
int64_t newyshift = 0;
int64_t oldxshift = 0;
int64_t oldyshift = 0;
float count = 0.0f;
DimType slice = 0;
int32_t refgnum = 0, curgnum = 0;
DimType refposition = 0;
DimType curposition = 0;
form_features_sections();
std::vector<std::vector<float> > misorients;
misorients.resize(dims[0]);
for (DimType a = 0; a < dims[0]; a++)
{
misorients[a].assign(dims[1], 0.0f);
}
for (DimType iter = 1; iter < dims[2]; iter++)
{
QString ss = QObject::tr("Aligning Sections || Determining Shifts || %1% Complete").arg(((float)iter / dims[2]) * 100);
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), ss);
mindisorientation = std::numeric_limits<float>::max();
slice = (dims[2] - 1) - iter;
featurecount1 = featurecounts[slice];
featurecount2 = featurecounts[slice + 1];
mutualinfo12 = new float *[featurecount1];
mutualinfo1 = new float[featurecount1];
mutualinfo2 = new float[featurecount2];
for (int32_t a = 0; a < featurecount1; a++)
{
mutualinfo1[a] = 0.0f;
mutualinfo12[a] = new float[featurecount2];
for (int32_t b = 0; b < featurecount2; b++)
{
mutualinfo12[a][b] = 0.0f;
mutualinfo2[b] = 0.0f;
}
}
oldxshift = -1;
oldyshift = -1;
newxshift = 0;
newyshift = 0;
for (DimType a = 0; a < dims[0]; a++)
{
for (DimType b = 0; b < dims[1]; b++)
{
misorients[a][b] = 0;
}
}
while (newxshift != oldxshift || newyshift != oldyshift)
{
oldxshift = newxshift;
oldyshift = newyshift;
for (int32_t j = -3; j < 4; j++)
{
for (int32_t k = -3; k < 4; k++)
{
disorientation = 0;
count = 0;
if (misorients[k + oldxshift + dims[0] / 2][j + oldyshift + dims[1] / 2] == 0 && abs(k + oldxshift) < (dims[0] / 2)
&& (j + oldyshift) < (dims[1] / 2))
{
for (DimType l = 0; l < dims[1]; l = l + 4)
{
for (DimType n = 0; n < dims[0]; n = n + 4)
{
if ((l + j + oldyshift) >= 0 && (l + j + oldyshift) < dims[1] && (n + k + oldxshift) >= 0 && (n + k + oldxshift) < dims[0])
{
refposition = ((slice + 1) * dims[0] * dims[1]) + (l * dims[0]) + n;
curposition = (slice * dims[0] * dims[1]) + ((l + j + oldyshift) * dims[0]) + (n + k + oldxshift);
refgnum = m_FeatureIds[refposition];
curgnum = m_FeatureIds[curposition];
if (curgnum >= 0 && refgnum >= 0)
{
mutualinfo12[curgnum][refgnum]++;
mutualinfo1[curgnum]++;
mutualinfo2[refgnum]++;
count++;
}
}
else
{
mutualinfo12[0][0]++;
mutualinfo1[0]++;
mutualinfo2[0]++;
}
}
}
float ha = 0.0f;
float hb = 0.0f;
float hab = 0.0f;
for (int32_t b = 0; b < featurecount1; b++)
{
mutualinfo1[b] = mutualinfo1[b] / count;
if (mutualinfo1[b] != 0) { ha = ha + mutualinfo1[b] * logf(mutualinfo1[b]); }
}
for (int32_t c = 0; c < featurecount2; c++)
{
mutualinfo2[c] = mutualinfo2[c] / float(count);
if (mutualinfo2[c] != 0) { hb = hb + mutualinfo2[c] * logf(mutualinfo2[c]); }
}
for (int32_t b = 0; b < featurecount1; b++)
{
for (int32_t c = 0; c < featurecount2; c++)
{
mutualinfo12[b][c] = mutualinfo12[b][c] / count;
if (mutualinfo12[b][c] != 0) { hab = hab + mutualinfo12[b][c] * logf(mutualinfo12[b][c]); }
float value = 0.0f;
if (mutualinfo1[b] > 0 && mutualinfo2[c] > 0) { value = (mutualinfo12[b][c] / (mutualinfo1[b] * mutualinfo2[c])); }
if (value != 0) { disorientation = disorientation + (mutualinfo12[b][c] * logf(value)); }
}
}
for (int32_t b = 0; b < featurecount1; b++)
{
for (int32_t c = 0; c < featurecount2; c++)
{
mutualinfo12[b][c] = 0.0f;
mutualinfo1[b] = 0.0f;
mutualinfo2[c] = 0.0f;
}
}
disorientation = 1.0f / disorientation;
misorients[k + oldxshift + dims[0] / 2][j + oldyshift + dims[1] / 2] = disorientation;
if (disorientation < mindisorientation)
{
newxshift = k + oldxshift;
newyshift = j + oldyshift;
mindisorientation = disorientation;
}
}
}
}
}
xshifts[iter] = xshifts[iter - 1] + newxshift;
yshifts[iter] = yshifts[iter - 1] + newyshift;
if (getWriteAlignmentShifts() == true)
{
outFile << slice << " " << slice + 1 << " " << newxshift << " " << newyshift << " " << xshifts[iter] << " " << yshifts[iter] << "\n";
}
delete[] mutualinfo1;
delete[] mutualinfo2;
for (int32_t i = 0; i < featurecount1; i++)
{
delete mutualinfo12[i];
}
delete[] mutualinfo12;
mutualinfo1 = NULL;
mutualinfo2 = NULL;
mutualinfo12 = NULL;
}
m->getAttributeMatrix(getCellAttributeMatrixName())->removeAttributeArray(DREAM3D::CellData::FeatureIds);
if (getWriteAlignmentShifts() == true)
{
outFile.close();
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AdaptiveAlignmentMutualInformation::find_shifts(std::vector<int64_t>& xshifts, std::vector<int64_t>& yshifts, std::vector<float>& xneedshifts, std::vector<float>& yneedshifts)
{
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
int64_t totalPoints = m->getAttributeMatrix(getCellAttributeMatrixName())->getNumTuples();
m_MIFeaturesPtr = Int32ArrayType::CreateArray((totalPoints * 1), "_INTERNAL_USE_ONLY_MIFeatureIds");
m_MIFeaturesPtr->initializeWithZeros();
int32_t* miFeatureIds = m_MIFeaturesPtr->getPointer(0);
size_t udims[3] = { 0, 0, 0 };
m->getGeometryAs<ImageGeom>()->getDimensions(udims);
uint64_t dims[3] =
{
static_cast<uint64_t>(udims[0]),
static_cast<uint64_t>(udims[1]),
static_cast<uint64_t>(udims[2]),
};
uint64_t maxstoredshifts = 1;
if (xneedshifts.size() > 0) maxstoredshifts = 20;
float disorientation = 0.0f;
std::vector<std::vector<int64_t>> newxshift(dims[2]);
std::vector<std::vector<int64_t>> newyshift(dims[2]);
std::vector<std::vector<float>> mindisorientation(dims[2]);
for (uint64_t a = 1; a < dims[2]; a++)
{
newxshift[a].resize(maxstoredshifts, 0);
newyshift[a].resize(maxstoredshifts, 0);
mindisorientation[a].resize(maxstoredshifts, std::numeric_limits<float>::max());
}
float** mutualinfo12 = NULL;
float* mutualinfo1 = NULL;
float* mutualinfo2 = NULL;
int32_t featurecount1 = 0, featurecount2 = 0;
int64_t oldxshift = 0;
int64_t oldyshift = 0;
float count = 0.0f;
uint64_t slice = 0;
int32_t refgnum = 0, curgnum = 0;
uint64_t refposition = 0;
uint64_t curposition = 0;
form_features_sections();
// Allocate a 2D Array which will be reused from slice to slice
// second dimension is assigned in each cycle separately
std::vector<std::vector<bool> > misorients(dims[0]);
const uint64_t halfDim0 = static_cast<uint64_t>(dims[0] * 0.5f);
const uint64_t halfDim1 = static_cast<uint64_t>(dims[1] * 0.5f);
uint64_t progInt = 0;
for (uint64_t iter = 1; iter < dims[2]; iter++)
{
progInt = static_cast<uint64_t>(iter * 100 / static_cast<float>(dims[2]));
QString ss = QObject::tr("Aligning Anisotropic Sections || Determining Shifts || %1% Complete").arg(progInt);
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), ss);
slice = (dims[2] - 1) - iter;
featurecount1 = featurecounts[slice];
featurecount2 = featurecounts[slice + 1];
mutualinfo12 = new float *[featurecount1];
mutualinfo1 = new float[featurecount1];
mutualinfo2 = new float[featurecount2];
for (int32_t a = 0; a < featurecount1; a++)
{
mutualinfo1[a] = 0.0f;
mutualinfo12[a] = new float[featurecount2];
for (int32_t b = 0; b < featurecount2; b++)
{
mutualinfo12[a][b] = 0.0f;
mutualinfo2[b] = 0.0f;
}
}
oldxshift = -1;
oldyshift = -1;
for (uint64_t i = 0; i < dims[0]; i++)
{
misorients[i].assign(dims[1], false);
}
while (newxshift[iter][0] != oldxshift || newyshift[iter][0] != oldyshift)
{
oldxshift = newxshift[iter][0];
oldyshift = newyshift[iter][0];
for (int32_t j = -3; j < 4; j++)
{
for (int32_t k = -3; k < 4; k++)
{
disorientation = 0;
count = 0;
if (llabs(k + oldxshift) < halfDim0 && llabs(j + oldyshift) < halfDim1 && misorients[k + oldxshift + halfDim0][j + oldyshift + halfDim1] == false)
{
for (uint64_t l = 0; l < dims[1]; l = l + 4)
{
for (uint64_t n = 0; n < dims[0]; n = n + 4)
{
if ((l + j + oldyshift) >= 0 && (l + j + oldyshift) < dims[1] && (n + k + oldxshift) >= 0 && (n + k + oldxshift) < dims[0])
{
refposition = ((slice + 1) * dims[0] * dims[1]) + (l * dims[0]) + n;
curposition = (slice * dims[0] * dims[1]) + ((l + j + oldyshift) * dims[0]) + (n + k + oldxshift);
refgnum = miFeatureIds[refposition];
curgnum = miFeatureIds[curposition];
if (curgnum >= 0 && refgnum >= 0)
{
mutualinfo12[curgnum][refgnum]++;
mutualinfo1[curgnum]++;
mutualinfo2[refgnum]++;
count++;
}
}
else
{
mutualinfo12[0][0]++;
mutualinfo1[0]++;
mutualinfo2[0]++;
}
}
}
float ha = 0.0f;
float hb = 0.0f;
float hab = 0.0f;
for (int32_t b = 0; b < featurecount1; b++)
{
mutualinfo1[b] = mutualinfo1[b] / count;
if (mutualinfo1[b] != 0) { ha = ha + mutualinfo1[b] * logf(mutualinfo1[b]); }
}
for (int32_t c = 0; c < featurecount2; c++)
{
mutualinfo2[c] = mutualinfo2[c] / float(count);
if (mutualinfo2[c] != 0) { hb = hb + mutualinfo2[c] * logf(mutualinfo2[c]); }
}
for (int32_t b = 0; b < featurecount1; b++)
{
for (int32_t c = 0; c < featurecount2; c++)
{
mutualinfo12[b][c] = mutualinfo12[b][c] / count;
if (mutualinfo12[b][c] != 0) { hab = hab + mutualinfo12[b][c] * logf(mutualinfo12[b][c]); }
float value = 0.0f;
if (mutualinfo1[b] > 0 && mutualinfo2[c] > 0) { value = (mutualinfo12[b][c] / (mutualinfo1[b] * mutualinfo2[c])); }
if (value != 0) { disorientation = disorientation + (mutualinfo12[b][c] * logf(value)); }
}
}
for (int32_t b = 0; b < featurecount1; b++)
{
for (int32_t c = 0; c < featurecount2; c++)
{
mutualinfo12[b][c] = 0.0f;
mutualinfo1[b] = 0.0f;
mutualinfo2[c] = 0.0f;
}
}
disorientation = 1.0f / disorientation;
misorients[k + oldxshift + halfDim0][j + oldyshift + halfDim1] = true;
// compare the new shift with currently stored ones
int64_t s = maxstoredshifts;
while (s - 1 >= 0 && disorientation < mindisorientation[iter][s - 1])
{
s--;
}
// new shift is stored with index 's' in the arrays
if (s < maxstoredshifts)
{
// lag the shifts already stored
for (int64_t t = maxstoredshifts - 1; t > s; t--)
{
newxshift[iter][t] = newxshift[iter][t - 1];
newyshift[iter][t] = newyshift[iter][t - 1];
mindisorientation[iter][t] = mindisorientation[iter][t - 1];
}
// store the new shift
newxshift[iter][s] = k + oldxshift;
newyshift[iter][s] = j + oldyshift;
mindisorientation[iter][s] = disorientation;
}
}
}
}
}
xshifts[iter] = xshifts[iter - 1] + newxshift[iter][0];
yshifts[iter] = yshifts[iter - 1] + newyshift[iter][0];
delete[] mutualinfo1;
delete[] mutualinfo2;
for (int32_t i = 0; i < featurecount1; i++)
{
delete mutualinfo12[i];
}
delete[] mutualinfo12;
mutualinfo1 = NULL;
mutualinfo2 = NULL;
mutualinfo12 = NULL;
}
std::vector<uint64_t> curindex(dims[2], 0);
// find corrected shifts
if (xneedshifts.size() > 0)
{
QString ss = QObject::tr("Aligning Anisotropic Sections || Correcting shifts");
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), ss);
std::vector<float> changedisorientation(dims[2], 0);
std::vector<uint64_t> changeindex(dims[2], 0);
std::vector<float> changeerror(dims[2], 0);
std::vector<float> xshiftsest; // cumulative x-shifts estimated from SEM images
std::vector<float> yshiftsest; // cumulative y-shifts estimated from SEM images
float curerror = 0;
float tolerance = 1.0f / static_cast<float>(dims[2]);
// evaluate error between current shifts and desired shifts
if (xneedshifts.size() == 1) // error is computed as misagreement between slopes
{
curerror = compute_error1(dims[2], 0, xneedshifts[0], yneedshifts[0], newxshift, newyshift, curindex);
}
else if (xneedshifts.size() > 1) // error is computed as misagreement with shifts estimated from SEM images
{
xshiftsest.resize(dims[2], 0);
yshiftsest.resize(dims[2], 0);
for (uint64_t iter = 1; iter < dims[2]; iter++)
{
xshiftsest[iter] = xshiftsest[iter - 1] + xneedshifts[iter - 1];
yshiftsest[iter] = yshiftsest[iter - 1] + yneedshifts[iter - 1];
}
curerror = compute_error2(dims[2], 0, xshiftsest, yshiftsest, newxshift, newyshift, curindex);
}
// iterative selection of a candidate shift, recomputing of current candidates, evaluation of error
if (curerror > tolerance)
{
float minchangedisorientation = 0;
float minchangeerror = 0;
int64_t minchangeindex = 0;
int64_t minchangeiter = 0;
float olderror = 0;
float newerror = 0;
uint64_t progInt = 0;
do
{
QString ss = QObject::tr("Aligning Anisotropic Sections || Correcting Shifts || Iteration %1").arg(++progInt);;
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), ss);
if (getCancel() == true)
{
return;
}
olderror = curerror;
for (uint64_t iter = 1; iter < dims[2]; iter++)
{
float newminerror = std::numeric_limits<float>::max();
float newmindisorientation = std::numeric_limits<float>::max();
uint64_t newminindex = 0;
for (uint64_t index = curindex[iter] + 1; index < maxstoredshifts; index++)
{
// recompute error for the configuration with this candidate changed
if (xneedshifts.size() == 1)
{
newerror = compute_error1(iter, index, xneedshifts[0], yneedshifts[0], newxshift, newyshift, curindex);
}
else if (xneedshifts.size() > 1)
{
newerror = compute_error2(iter, index, xshiftsest, yshiftsest, newxshift, newyshift, curindex);
}
// compare the new error with the best current error
if (newerror < curerror &&
mindisorientation[iter][index] / mindisorientation[iter][0] < newmindisorientation)
{
newminerror = newerror;
newminindex = index;
newmindisorientation = mindisorientation[iter][index] / mindisorientation[iter][0];
}
}
// assign best error, corresponding index and disorientation value for this slice
changeerror[iter] = newminerror;
changeindex[iter] = newminindex;
changedisorientation[iter] = newmindisorientation;
}
// among all slices, find the best candidate (with minimum disorientation change)
minchangedisorientation = std::numeric_limits<float>::max() - 1;
minchangeerror = std::numeric_limits<float>::max();
minchangeindex = 0;
minchangeiter = 0;
for (uint64_t iter = 1; iter < dims[2]; iter++)
{
if (changeerror[iter] < curerror &&
(changedisorientation[iter] < minchangedisorientation ||
(changedisorientation[iter] == minchangedisorientation &&
llabs(newxshift[iter][changeindex[iter]]) + llabs(newyshift[iter][changeindex[iter]]) < llabs(newxshift[iter][minchangeindex]) + llabs(newyshift[iter][minchangeindex]))))
{
minchangeiter = iter;
minchangeindex = changeindex[iter];
minchangedisorientation = changedisorientation[iter];
minchangeerror = changeerror[iter];
}
}
if (minchangeerror < curerror && minchangeerror >= tolerance)
{
// assign the best candidate
changedisorientation[minchangeiter] = minchangedisorientation;
curindex[minchangeiter] = minchangeindex;
// reassign current error
curerror = minchangeerror;
}
} while (minchangedisorientation < std::numeric_limits<float>::max() - 1 && curerror < olderror && curerror > tolerance);
}
}
if (getWriteAlignmentShifts() == true)
{
std::ofstream outFile;
outFile.open(getAlignmentShiftFileName().toLatin1().data());
for (uint64_t iter = 1; iter < dims[2]; iter++)
{
slice = (dims[2] - 1) - iter;
xshifts[iter] = xshifts[iter - 1] + newxshift[iter][curindex[iter]];
yshifts[iter] = yshifts[iter - 1] + newyshift[iter][curindex[iter]];
outFile << slice << " " << slice + 1 << " " << newxshift[iter][curindex[iter]] << " " << newyshift[iter][curindex[iter]] << " " << xshifts[iter] << " " << yshifts[iter] << "\n";
}
outFile.close();
}
m->getAttributeMatrix(getCellAttributeMatrixName())->removeAttributeArray(DREAM3D::CellData::FeatureIds);
}