struct hapmapSnpsCombined *fixStrandAndMerge(struct hashEl *helCEU, struct hashEl *helCHB,
struct hashEl *helJPT, struct hashEl *helYRI)
/* force everything to positive strand */
{
boolean allMatch = TRUE;
helCEU = forcePositive(helCEU);
helCHB = forcePositive(helCHB);
helJPT = forcePositive(helJPT);
helYRI = forcePositive(helYRI);
/* need a sanity check for alleles */
allMatch = matchingAlleles(helCEU, helCHB, helJPT, helYRI);
if (!allMatch) return NULL;
return mergeOne(helCEU, helCHB, helJPT, helYRI);
}
void runThread(ThreadArgument &thArg)
{
int thread_id = thArg.thread_id;
ProgXrayImport * ptrProg= (ProgXrayImport *)thArg.workClass;
MetaData localMD;
Image<double> Iaux;
FileName fnImgIn, fnImgOut;
size_t first = 0, last = 0;
MultidimArray<char> mask;
while (ptrProg->td->getTasks(first, last))
{
for (size_t i=first; i<=last; i++)
{
ptrProg->inMD.getValue(MDL_IMAGE, fnImgIn, ptrProg->objIds[i]);
MDRow rowGeo;
ptrProg->readGeoInfo(fnImgIn, rowGeo);
// ptrProg->readAndCrop(fnImgIn, Iaux, ptrProg->cropSizeX, ptrProg->cropSizeY);
Iaux.read(fnImgIn);
Iaux().selfWindow(ptrProg->cropSizeYi,ptrProg->cropSizeXi,
(int)(YSIZE(Iaux())-ptrProg->cropSizeYe-1),(int)(XSIZE(Iaux())-ptrProg->cropSizeXe-1));
Iaux().resetOrigin();
if (XSIZE(ptrProg->IavgDark())!=0)
{
Iaux()-=ptrProg->IavgDark();
forcePositive(Iaux());
}
double currentBeam = 1;
double expTime = 1;
double slitWidth = 1;
if ( ptrProg->dSource == ptrProg->MISTRAL )
{
size_t idx = fnImgIn.getPrefixNumber();
currentBeam = dMi(ptrProg->cBeamArray, idx-1);
expTime = dMi(ptrProg->expTimeArray, idx-1);
slitWidth = dMi(ptrProg->slitWidthArray, idx-1);
}
else
ptrProg->readCorrectionInfo(fnImgIn, currentBeam, expTime, slitWidth);
Iaux() *= 1.0/(currentBeam*expTime*slitWidth);
if (XSIZE(ptrProg->IavgFlat())!=0)
Iaux()/=ptrProg->IavgFlat();
// Assign median filter to zero valued pixels to avoid -inf when applying log10
Iaux().equal(0,mask);
mask.resizeNoCopy(Iaux());
if (XSIZE(ptrProg->bpMask()) != 0)
mask += ptrProg->bpMask();
boundMedianFilter(Iaux(), mask);
if (ptrProg->logFix)
{
Iaux().selfLog();
if (ptrProg->selfAttFix)
Iaux() *= -1.;
}
fnImgOut.compose(i+1, ptrProg->fnOut);
size_t objId = localMD.addObject();
localMD.setValue(MDL_IMAGE,fnImgOut,objId);
localMD.setRow(rowGeo, objId); //
// localMD.setValue(MDL_ANGLE_TILT,Iaux.tilt(),objId);
Iaux.write(fnImgOut);
if (thread_id==0)
progress_bar(i);
}
}
//Lock for update the total counter
ptrProg->mutex.lock();
ptrProg->outMD.unionAll(localMD);
ptrProg->mutex.unlock();
}
void ProgXrayImport::getFlatfield(const FileName &fnFFinput,
Image<double> &Iavg)
{
// Process the flatfield images
MultidimArray<double> &mdaIavg = Iavg();
Matrix1D<double> expTimeArray, cBeamArray, slitWidthArray; // Local vectors
DataSource ldSource = dSource;
// Checking if fnFFinput is a single file to obtain the flatfield avg from
if (extFlat && isImage(fnFFinput))
{
fMD.read(fnFFinput);
ldSource = NONE;
}
else
{
switch (ldSource)
{
case MISTRAL:
if (!H5File.checkDataset(fnFFinput.getBlockName().c_str()))
break;
{
fMD.read(fnFFinput);
H5File.getDataset("NXtomo/instrument/bright_field/ExpTimes", expTimeArray, false);
H5File.getDataset("NXtomo/instrument/bright_field/current", cBeamArray, false);
// If expTime is empty or only one single value in nexus file then we fill with 1
if (expTimeArray.size() < 2)
{
reportWarning("Input file does not contains flatfields' exposition time information.");
expTimeArray.initConstant(fMD.size(), 1.);
}
// If current is empty or only one single value in nexus file then we fill with 1
if (cBeamArray.size() < 2)
{
reportWarning("Input file does not contains flatfields' current beam information.");
cBeamArray.initConstant(fMD.size(), 1.);
}
}
// Since Alba does not provide slit width, we set to ones
slitWidthArray.initConstant(fMD.size(), 1.);
break;
case BESSY:
{
size_t objId;
for (size_t i = fIni; i <= fEnd; ++i)
{
objId = fMD.addObject();
fMD.setValue(MDL_IMAGE, fnFFinput + formatString("/img%d.spe", i), objId);
}
break;
}
case GENERIC:
{
// Get Darkfield
std::cout << "Getting darkfield from "+fnFFinput << " ..." << std::endl;
getDarkfield(fnFFinput, IavgDark);
if (darkFix)
IavgDark.write(fnRoot+"_"+fnFFinput.removeDirectories()+"_darkfield.xmp");
std::vector<FileName> listDir;
fnFFinput.getFiles(listDir);
size_t objId;
for (size_t i = 0; i < listDir.size(); ++i)
{
if (!listDir[i].hasImageExtension())
continue;
objId = fMD.addObject();
fMD.setValue(MDL_IMAGE, fnFFinput+"/"+listDir[i], objId);
}
}
break;
}
}
if ( fMD.size() == 0 )
{
reportWarning("XrayImport::getFlatfield: No images to process");
return;
}
ImageInfo imFFInfo;
getImageInfo(fMD, imFFInfo);
if ( (imFFInfo.adim.xdim != imgInfo.adim.xdim) || (imFFInfo.adim.ydim != imgInfo.adim.ydim) )
{
reportWarning(formatString("XrayImport:: Flatfield images size %dx%d different from Tomogram images size %dx%d",
imFFInfo.adim.xdim,imFFInfo.adim.ydim,imgInfo.adim.xdim,imgInfo.adim.ydim));
std::cout << "Setting crop values to fit the smallest dimensions." <<std::endl;
// This shift in the crop sizes is exclusive of Mistral data
cropSizeXi = (imgInfo.adim.xdim - std::min(imgInfo.adim.xdim-cropSizeX*2, imFFInfo.adim.xdim))/2 + 1;
cropSizeYi = (imgInfo.adim.ydim - std::min(imgInfo.adim.ydim-cropSizeY*2, imFFInfo.adim.ydim))/2 + 1;
cropSizeXe = cropSizeXi - 2;
cropSizeYe = cropSizeYi - 2;
}
int cropX = (imFFInfo.adim.xdim - (imgInfo.adim.xdim-cropSizeXi-cropSizeXe))/2;// - 1;
int cropY = (imFFInfo.adim.ydim - (imgInfo.adim.ydim-cropSizeYi-cropSizeYe))/2;// - 1;
int N = 0;
Image<double> Iaux;
FileName fnImg;
FOR_ALL_OBJECTS_IN_METADATA(fMD)
{
fMD.getValue(MDL_IMAGE, fnImg, __iter.objId);
readAndCrop(fnImg, Iaux, cropX, cropY);
if ( darkFix )
{
Iaux() -= IavgDark();
forcePositive(Iaux());
}
double currentBeam = 1;
double expTime = 1;
double slitWidth = 1;
switch (ldSource)
{
case MISTRAL:
{
size_t idx = fnImg.getPrefixNumber();
currentBeam = dMi(cBeamArray, idx-1);
expTime = dMi(expTimeArray, idx-1);
slitWidth = dMi(slitWidthArray, idx-1);
}
break;
case BESSY:
case GENERIC:
readCorrectionInfo(fnImg, currentBeam, expTime, slitWidth);
break;
default:
break;
}
Iaux() *= 1.0/(currentBeam*expTime*slitWidth);
if ( N == 0 )
mdaIavg = Iaux();
else
mdaIavg += Iaux();
N++;
}
darkFix = false; // We reset just in case there is no dark field for tomo images
mdaIavg*=1.0/N;
/* Create a mask with zero valued pixels to apply boundaries median filter
* to avoid dividing by zero when normalizing */
MultidimArray<char> &mdaMask = MULTIDIM_ARRAY(bpMask);
if ( !fnBPMask.empty() && !mdaIavg.sameShape(mdaMask) )
REPORT_ERROR(ERR_MULTIDIM_SIZE, "XrayImport: Mask size does not match flat fields size.");
if (BPFactor > 0)
{
double avg, std;
mdaIavg.computeAvgStdev(avg, std);
mdaMask.resize(mdaIavg, false);
double th = avg - std*BPFactor;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mdaMask)
dAi(mdaMask, n) = dAi(mdaIavg, n) < th;
}
else if (fnBPMask.empty())
mdaIavg.equal(0,mdaMask);
MultidimArray<char> mask = mdaMask;
boundMedianFilter(mdaIavg,mask);
}