NumericalComparison<double> CompareWells(const string &queryFile, const string &goldFile,
float epsilon, double maxAbsVal) {
NumericalComparison<double> compare(epsilon);
string queryDir, queryWells, goldDir, goldWells;
FillInDirName(queryFile, queryDir, queryWells);
FillInDirName(goldFile, goldDir, goldWells);
RawWells queryW(queryDir.c_str(), queryWells.c_str());
RawWells goldW(goldDir.c_str(), goldWells.c_str());
struct WellData goldData;
goldData.flowValues = NULL;
struct WellData queryData;
queryData.flowValues = NULL;
cout << "Opening query." << endl;
queryW.OpenForRead();
cout << "Opening gold." << endl;
goldW.OpenForRead();
unsigned int numFlows = goldW.NumFlows();
while( !queryW.ReadNextRegionData(&queryData) ) {
assert(!goldW.ReadNextRegionData(&goldData));
for (unsigned int i = 0; i < numFlows; i++) {
if (isfinite(queryData.flowValues[i]) && isfinite(goldData.flowValues[i]) &&
(fabs(queryData.flowValues[i]) < maxAbsVal && fabs(goldData.flowValues[i]) < maxAbsVal)) {
compare.AddPair(queryData.flowValues[i], goldData.flowValues[i]);
}
}
}
const SampleStats<double> ssX = compare.GetXStats();
const SampleStats<double> ssY = compare.GetYStats();
cout << "query values: " << ssX.GetMean() << " +/- " << ssX.GetSD() << endl;
cout << "gold values: " << ssY.GetMean() << " +/- " << ssY.GetSD() << endl;
return compare;
}
void Traces::Init(Image *img, Mask *mask, int startFrame, int endFrame,
int dcOffsetStart, int dcOffsetEnd) {
mRefOut = NULL;
mFlow = -1;
mT0Step = 32;
mUseMeshNeighbors = 1;
mRow = (img->GetImage())->rows;
mCol = (img->GetImage())->cols;
startFrame = std::max(startFrame, 0);
if( endFrame > 0 )
endFrame = std::min(endFrame, (int)img->GetUnCompFrames());
else
endFrame = (int)img->GetUnCompFrames();
mFrames = endFrame - startFrame;
mTimes.resize(mFrames);
// copy(&raw->timestamps[0], &raw->timestamps[0] + mFrames, mTimes.begin());
// need to take into account variable frame compression here... ??
if (mIndexes.size() != mRow*mCol) {
mIndexes.resize(mRow*mCol);
}
fill(mIndexes.begin(), mIndexes.end(), -1);
vector<float> tBuff(mFrames, 0);
SampleStats<float> traceStats;
std::vector<float> sdTrace(mRow *mCol, 0);
// Figure out how much memory to allocate for data pool
int count = 0;
for (size_t rowIx = 0; rowIx < mRow; rowIx++) {
for (size_t colIx = 0; colIx < mCol; colIx++) {
size_t traceIdx = RowColToIndex(rowIx, colIx);
if (mask == NULL || !((*mask)[traceIdx] & MaskExclude)) {
count++;
}
}
}
// Allocate memory
if (mRawTraces != NULL) {
delete [] mRawTraces ;
}
mRawTraces = new int8_t[count * mFrames];
SampleQuantiles<float> chipTraceSdQuant(10000);
count = 0;
for (size_t rowIx = 0; rowIx < mRow; rowIx++) {
for (size_t colIx = 0; colIx < mCol; colIx++) {
size_t traceIdx = RowColToIndex(rowIx, colIx);
if (mask == NULL || !((*mask)[traceIdx] & MaskExclude)) {
mIndexes[traceIdx] = count++ * mFrames;
double mean = 0;
if (dcOffsetEnd > 0 && dcOffsetStart > 0) {
assert(dcOffsetEnd > dcOffsetStart);
for (int frameIx = dcOffsetStart; frameIx < dcOffsetEnd; frameIx++) {
mean += img->GetInterpolatedValue(frameIx,colIx,rowIx);
}
mean = mean / (dcOffsetEnd - dcOffsetStart);
}
float val = img->GetInterpolatedValue(startFrame,colIx,rowIx) - mean;
traceStats.Clear();
for (int frameIx = 0; frameIx < endFrame; frameIx++) {
val = (img->GetInterpolatedValue(frameIx,colIx,rowIx) - mean);
tBuff[frameIx] = val;
traceStats.AddValue(tBuff[frameIx]);
}
sdTrace[traceIdx] = traceStats.GetSD();
chipTraceSdQuant.AddValue(sdTrace[traceIdx]);
SetTraces(traceIdx, tBuff, mRawTraces);
}
}
}
mFlags.resize(mRow*mCol, 0);
double traceSDThresh = chipTraceSdQuant.GetMedian() - 5 * (chipTraceSdQuant.GetQuantile(.5) - chipTraceSdQuant.GetQuantile(.25));
traceSDThresh = max(0.0, traceSDThresh);
int badCount = 0;
for (size_t wellIx = 0; wellIx < sdTrace.size(); wellIx++) {
if (mask != NULL && ((*mask)[wellIx] & MaskExclude)) {
continue;
}
if (sdTrace[wellIx] <= traceSDThresh) {
mFlags[wellIx] = BAD_VAR;
badCount++;
}
}
cout << "Found: " << badCount << " wells <= sd: " << traceSDThresh << endl;
mT0.resize(0);
if(mask != NULL) {
if (mMask != NULL)
delete mMask;
mMask = new Mask(mask);
size_t size = mFlags.size();
for (size_t i = 0; i < size; i++) {
if ((*mMask)[i] & MaskExclude) {
mFlags[i] = NOT_AVAIL;
}
}
}
else {
mMask = NULL;
}
mSampleMap.resize(mRow * mCol);
mCurrentData = mRawTraces;
fill(mSampleMap.begin(), mSampleMap.end(), -1);
}
NumericalComparison<double> CompareWells(
const string &queryFile,
const string &goldFile,
float epsilon,
double maxAbsVal,
DumpMismatches &dump) {
NumericalComparison<double> compare(epsilon);
string queryDir, queryWells, goldDir, goldWells;
FillInDirName(queryFile, queryDir, queryWells);
FillInDirName(goldFile, goldDir, goldWells);
RawWells queryW(queryDir.c_str(), queryWells.c_str());
RawWells goldW(goldDir.c_str(), goldWells.c_str());
struct WellData goldData;
goldData.flowValues = NULL;
struct WellData queryData;
queryData.flowValues = NULL;
cout << "Opening query." << endl;
queryW.OpenForRead();
cout << "Opening gold." << endl;
goldW.OpenForRead();
// check if any 1.wells is saved as unsigned short
bool ushortg = goldW.GetSaveAsUShort();
bool ushortq = queryW.GetSaveAsUShort();
bool difType = false;
string fileName;
if(ushortg && (!ushortq))
{
difType = true;
cout << "RawWellsEquivalent WARNING: " << goldFile << " is saved as unsigned short and \n" << queryFile << " is saved as float. \nYou may want to re-run it with a bigger epsilon." << endl;
fileName = goldFile;
}
if(ushortq && (!ushortg))
{
difType = true;
cout << "RawWellsEquivalent WARNING: " << queryFile << " is saved as unsigned short and \n" << goldFile << " is saved as float. \nYou may want to re-run it with a bigger epsilon." << endl;
fileName = queryFile;
}
unsigned int numFlows = goldW.NumFlows();
while( !queryW.ReadNextRegionData(&queryData) ) {
assert(!goldW.ReadNextRegionData(&goldData));
for (unsigned int i = 0; i < numFlows; i++) {
if(difType)
{
float flowValues2 = -1.0;
if(ushortg)
{
flowValues2 = goldData.flowValues[i];
}
else if(ushortq)
{
flowValues2 = queryData.flowValues[i];
}
if(isfinite(flowValues2) && fabs(flowValues2) < maxAbsVal)
{
if(ushortg && isfinite(queryData.flowValues[i]) && fabs(queryData.flowValues[i]) < maxAbsVal)
{
compare.AddPair(queryData.flowValues[i], flowValues2);
}
else if(ushortq && isfinite(goldData.flowValues[i]) && fabs(goldData.flowValues[i]) < maxAbsVal)
{
compare.AddPair(flowValues2, goldData.flowValues[i]);
}
}
}
else
{
if (isfinite(queryData.flowValues[i]) && isfinite(goldData.flowValues[i]) &&
(fabs(queryData.flowValues[i]) < maxAbsVal && fabs(goldData.flowValues[i]) < maxAbsVal))
{
compare.AddPair(queryData.flowValues[i], goldData.flowValues[i]);
if (abs(goldData.flowValues[i] - queryData.flowValues[i]) > epsilon) {
if (dump.needDump())
dump.dumpMismatchWellData(goldData, queryData, i);
}
}
}
}
}
const SampleStats<double> ssX = compare.GetXStats();
const SampleStats<double> ssY = compare.GetYStats();
cout << "query values: " << ssX.GetMean() << " +/- " << ssX.GetSD() << endl;
cout << "gold values: " << ssY.GetMean() << " +/- " << ssY.GetSD() << endl;
return compare;
}
