void SC_Statistics::CalcMode(const SC_DoubleArray& data)
{
if (nOK == 0)
return;
// min == max
if (realResults[soVar] < stdEps)
{
realResults[soMode] = realResults[soMean];
return;
}
// Scott, 1979 algorithm for bin width
// W = (3.49)(std.dev.)[(#samples)^(-1/3)]
double width = 3.49 * realResults[soStdDev] * (pow(realResults[soN], -0.3333));
if (width < stdEps)
{
realResults[soMode] = realResults[soMean];
return;
}
double maxNBins = (realResults[soMax] - realResults[soMin]) / width;
if (maxNBins > 10000.0)
return;
int nbins = int(ceil(maxNBins));
// note just linear bins
width = (realResults[soMax] - realResults[soMin]) / double(nbins);
SC_IntArray binCount(nbins, 0);
for (int i = 0; i < data.Size(); i++)
{
double dVal = data[i];
if (RealIsNull(dVal) || (dVal < realResults[soMin])) // can happen if stats calc was log
continue;
int binIndex = int(floor((dVal - realResults[soMin]) / width));
// pathological case == maxVal
if (binIndex == nbins)
binIndex--;
binCount[binIndex]++;
}
int maxBin = 0;
int maxCount = binCount[0];
for (int i = 1; i < nbins; i++)
if (binCount[i] > maxCount)
{
maxBin = i;
maxCount = binCount[i];
}
realResults[soMode] = realResults[soMin] + (double(maxBin) + 0.5) * width;
}
/**
* This gets called every time the scatter plot is re-drawn. This returns the
* counts for each DN (x), DN (y), or if the bin is alarmed this returns the
* max count.
*
* @param x The X-Dn value
* @param y The Y-Dn value
* @return The bin's colorizable-value
*/
double ScatterPlotData::value(double x, double y) const {
double value = 0;
QPair<int, int> indices = binXYIndices(x, y);
int index = binIndex(indices.first, indices.second);
if (index != -1 && (*m_alarmedBins)[index])
value = m_maxCount;
else
value = binCount(indices.first, indices.second);
return value;
}
void CMT::estimate(const std::vector<std::pair<cv::KeyPoint, int> >& keypointsIN, cv::Point2f& center, float& scaleEstimate, float& medRot, std::vector<std::pair<cv::KeyPoint, int> >& keypoints)
{
center = cv::Point2f(NAN,NAN);
scaleEstimate = NAN;
medRot = NAN;
//At least 2 keypoints are needed for scale
if(keypointsIN.size() > 1)
{
//sort
std::vector<PairInt> list;
for(int i = 0; i < keypointsIN.size(); i++)
list.push_back(std::make_pair(keypointsIN[i].second, i));
std::sort(&list[0], &list[0]+list.size(), comparatorPair<int>);
for(int i = 0; i < list.size(); i++)
keypoints.push_back(keypointsIN[list[i].second]);
std::vector<int> ind1;
std::vector<int> ind2;
for(int i = 0; i < list.size(); i++)
for(int j = 0; j < list.size(); j++)
{
if(i != j && keypoints[i].second != keypoints[j].second)
{
ind1.push_back(i);
ind2.push_back(j);
}
}
if(ind1.size() > 0)
{
std::vector<int> class_ind1;
std::vector<int> class_ind2;
std::vector<cv::KeyPoint> pts_ind1;
std::vector<cv::KeyPoint> pts_ind2;
for(int i = 0; i < ind1.size(); i++)
{
class_ind1.push_back(keypoints[ind1[i]].second-1);
class_ind2.push_back(keypoints[ind2[i]].second-1);
pts_ind1.push_back(keypoints[ind1[i]].first);
pts_ind2.push_back(keypoints[ind2[i]].first);
}
std::vector<float> scaleChange;
std::vector<float> angleDiffs;
for(int i = 0; i < pts_ind1.size(); i++)
{
cv::Point2f p = pts_ind2[i].pt - pts_ind1[i].pt;
//This distance might be 0 for some combinations,
//as it can happen that there is more than one keypoint at a single location
float dist = sqrt(p.dot(p));
float origDist = squareForm[class_ind1[i]][class_ind2[i]];
scaleChange.push_back(dist/origDist);
//Compute angle
float angle = atan2(p.y, p.x);
float origAngle = angles[class_ind1[i]][class_ind2[i]];
float angleDiff = angle - origAngle;
//Fix long way angles
if(fabs(angleDiff) > CV_PI)
angleDiff -= sign(angleDiff) * 2 * CV_PI;
angleDiffs.push_back(angleDiff);
}
scaleEstimate = median(scaleChange);
if(!estimateScale)
scaleEstimate = 1;
medRot = median(angleDiffs);
if(!estimateRotation)
medRot = 0;
votes = std::vector<cv::Point2f>();
for(int i = 0; i < keypoints.size(); i++)
votes.push_back(keypoints[i].first.pt - scaleEstimate * rotate(springs[keypoints[i].second-1], medRot));
//Compute linkage between pairwise distances
std::vector<Cluster> linkageData = linkage(votes);
//Perform hierarchical distance-based clustering
std::vector<int> T = fcluster(linkageData, thrOutlier);
//Count votes for each cluster
std::vector<int> cnt = binCount(T);
//Get largest class
int Cmax = argmax(cnt);
//Remember outliers
outliers = std::vector<std::pair<cv::KeyPoint, int> >();
std::vector<std::pair<cv::KeyPoint, int> > newKeypoints;
std::vector<cv::Point2f> newVotes;
for(int i = 0; i < keypoints.size(); i++)
{
if(T[i] != Cmax)
outliers.push_back(keypoints[i]);
else
{
newKeypoints.push_back(keypoints[i]);
newVotes.push_back(votes[i]);
}
}
keypoints = newKeypoints;
center = cv::Point2f(0,0);
for(int i = 0; i < newVotes.size(); i++)
center += newVotes[i];
center *= (1.0/newVotes.size());
}
}
}
void PeaksWorkspace::saveNexus(::NeXus::File * file) const
{
//Number of Peaks
const size_t np(peaks.size());
// Column vectors for peaks table
std::vector<int> detectorID(np);
std::vector<double> H(np);
std::vector<double> K(np);
std::vector<double> L(np);
std::vector<double> intensity(np);
std::vector<double> sigmaIntensity(np);
std::vector<double> binCount(np);
std::vector<double> initialEnergy(np);
std::vector<double> finalEnergy(np);
std::vector<double> waveLength(np);
std::vector<double> scattering(np);
std::vector<double> dSpacing(np);
std::vector<double> TOF(np);
std::vector<int> runNumber(np);
std::vector<double> goniometerMatrix(9 * np);
// Populate column vectors from Peak Workspace
for (size_t i = 0; i < np; i++)
{
Peak p = peaks[i];
detectorID[i] = p.getDetectorID();
H[i] = p.getH();
K[i] = p.getK();
L[i] = p.getL();
intensity[i] = p.getIntensity();
sigmaIntensity[i] = p.getSigmaIntensity();
binCount[i] = p.getBinCount();
initialEnergy[i] = p.getInitialEnergy();
finalEnergy[i] = p.getFinalEnergy();
waveLength[i] = p.getWavelength();
scattering[i] = p.getScattering();
dSpacing[i] = p.getDSpacing();
TOF[i] = p.getTOF();
runNumber[i] = p.getRunNumber();
{
Matrix<double> gm = p.getGoniometerMatrix();
goniometerMatrix[9 * i] = gm[0][0];
goniometerMatrix[9 * i + 1] = gm[1][0];
goniometerMatrix[9 * i + 2] = gm[2][0];
goniometerMatrix[9 * i + 3] = gm[0][1];
goniometerMatrix[9 * i + 4] = gm[1][1];
goniometerMatrix[9 * i + 5] = gm[2][1];
goniometerMatrix[9 * i + 6] = gm[0][2];
goniometerMatrix[9 * i + 7] = gm[1][2];
goniometerMatrix[9 * i + 8] = gm[1][2];
}
// etc.
}
// Start Peaks Workspace in Nexus File
std::string specifyInteger = "An integer";
std::string specifyDouble = "A double";
file->makeGroup("peaks_workspace", "NXentry", true); // For when peaksWorkspace can be loaded
// Detectors column
file->writeData("column_1", detectorID);
file->openData("column_1");
file->putAttr("name", "Dectector ID");
file->putAttr("interpret_as", specifyInteger);
file->putAttr("units", "Not known");
file->closeData();
// H column
file->writeData("column_2", H);
file->openData("column_2");
file->putAttr("name", "H");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// K column
file->writeData("column_3", K);
file->openData("column_3");
file->putAttr("name", "K");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// L column
file->writeData("column_4", L);
file->openData("column_4");
file->putAttr("name", "L");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Intensity column
file->writeData("column_5", intensity);
file->openData("column_5");
file->putAttr("name", "Intensity");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Sigma Intensity column
file->writeData("column_6", sigmaIntensity);
file->openData("column_6");
file->putAttr("name", "Sigma Intensity");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Bin Count column
file->writeData("column_7", binCount);
file->openData("column_7");
file->putAttr("name", "Bin Count");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Initial Energy column
file->writeData("column_8", initialEnergy);
file->openData("column_8");
file->putAttr("name", "Initial Energy");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Final Energy column
file->writeData("column_9", finalEnergy);
file->openData("column_9");
file->putAttr("name", "Final Energy");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Wave Length Column
file->writeData("column_10", waveLength);
file->openData("column_10");
file->putAttr("name", "Wave Length");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Scattering Column
file->writeData("column_11", scattering);
file->openData("column_11");
file->putAttr("name", "Scattering");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// D Spacing Column
file->writeData("column_12", dSpacing);
file->openData("column_12");
file->putAttr("name", "D Spacing");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// TOF Column
file->writeData("column_13", TOF);
file->openData("column_13");
file->putAttr("name", "TOF");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
//Run Number column
file->writeData("column_14", runNumber);
file->openData("column_14");
file->putAttr("name", "Run Number");
file->putAttr("interpret_as", specifyInteger);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Goniometer Matrix Column
std::vector<int> array_dims;
array_dims.push_back(static_cast<int>(peaks.size()));
array_dims.push_back(9);
file->writeData("column_15", goniometerMatrix, array_dims);
file->openData("column_15");
file->putAttr("name", "Goniometer Matrix");
file->putAttr("interpret_as", "A matrix of 3x3 doubles");
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// QLab & QSample are calculated and do not need to be saved
file->closeGroup(); // end of peaks workpace
}
/**
* Get the count (number of values) which fall into the bin at index.
*
* @param binIndex The bin we're getting the data from
* @return The total number of cube DNs which fall into the given bin
*/
int ScatterPlotData::binCount(int binIndex) const {
QPair<int, int> indices = binXYIndices(binIndex);
return binCount(indices.first, indices.second);
}
