void initFiles(void) {
initSysop();
createDirOrDie("NiKom:DatoCfg");
createDirOrDie("NiKom:Moten");
createZeroFilledFile("NiKom:DatoCfg/Sysinfo.dat", sizeof(struct SysInfo));
createEmptyFile("NiKom:DatoCfg/Möten.dat");
createEmptyFile("NiKom:DatoCfg/ConferenceTexts.dat");
createEmptyFile("NiKom:DatoCfg/Areor.dat");
createEmptyFile("NiKom:DatoCfg/Grupper.dat");
createZeroFilledFile("NiKom:DatoCfg/Senaste.dat", sizeof(struct Inloggning) * MAXSENASTE);
}
void SandBoxDir::fill(const QStringList& filePaths)
{
Q_FOREACH(const QString& filePath, filePaths) {
QFileInfo info(*this, filePath);
mkpath(info.absolutePath());
createEmptyFile(info.absoluteFilePath());
}
void *shmServerConstructor(void *arg) {
//Create the key file for shm and sem keyfiles
deleteFile(SHMKEYPATH);
deleteFile(SEMKEYPATH);
createEmptyFile(SHMKEYPATH);
createEmptyFile(SEMKEYPATH);
//initiator first
shmServerInitiator();
//Create Clients' Check status
shmServer.gsThreadID = pthread_create(&shmServer.gsThread, NULL,
shmServerClientCheck, NULL);
trace_printf("Thread shmServerClientCheck successfully");
pthread_join(shmServer.gsThread, NULL);
trace_printf("Join threads Done");
shmServerDestructor();
return (void *) NULL;
}
/* createEmptyFile */
PyObject *
xmipp_createEmptyFile(PyObject *obj, PyObject *args, PyObject *kwargs)
{
int Xdim,Ydim,Zdim;
size_t Ndim;
Zdim=1;
Ndim=1;
PyObject * input;
if (PyArg_ParseTuple(args, "Oii|ii", &input, &Xdim, &Ydim, &Zdim,
&Ndim))
{
createEmptyFile(PyString_AsString(input),Xdim,Ydim,Zdim,Ndim,true,WRITE_REPLACE);
Py_RETURN_NONE;
}
return NULL;
}
int QDesktopViewWidget::qt_metacall(QMetaObject::Call _c, int _id, void **_a)
{
_id = QListWidget::qt_metacall(_c, _id, _a);
if (_id < 0)
return _id;
if (_c == QMetaObject::InvokeMetaMethod) {
switch (_id) {
case 0: iconClicked((*reinterpret_cast< QListWidgetItem*(*)>(_a[1]))); break;
case 1: layoutDirection(); break;
case 2: populatedDesktop(); break;
case 3: resizeIcons(); break;
case 4: createFolder(); break;
case 5: createLauncher(); break;
case 6: createEmptyFile(); break;
case 7: showDesktopIcons(); break;
case 8: execDesktopSettings(); break;
default: ;
}
_id -= 9;
}
return _id;
}
void ProgXrayImport::run()
{
// Delete output stack if it exists
fnOut = fnRoot + ".mrc";
fnOut.deleteFile();
/* Turn off error handling */
H5Eset_auto(H5E_DEFAULT, NULL, NULL);
if (dSource == MISTRAL)
H5File.openFile(fnInput, H5F_ACC_RDONLY);
// Reading bad pixels mask
if ( !fnBPMask.empty() )
{
std::cerr << "Reading bad pixels mask from "+fnBPMask << "." << std::endl;
bpMask.read(fnBPMask);
if ( (cropSizeX + cropSizeY ) > 0 )
bpMask().selfWindow(cropSizeY,cropSizeX,
(int)(YSIZE(bpMask())-cropSizeY-1),(int)(XSIZE(bpMask())-cropSizeX-1));
STARTINGX(bpMask()) = STARTINGY(bpMask()) = 0;
}
// Setting the image projections list
switch (dSource)
{
case MISTRAL:
{
inMD.read(fnInput);
H5File.getDataset("NXtomo/data/rotation_angle", anglesArray, false);
H5File.getDataset("NXtomo/instrument/sample/ExpTimes", expTimeArray, false);
H5File.getDataset("NXtomo/instrument/sample/current", cBeamArray);
/* In case there is no angles information we set them to to an increasing sequence
* just to be able to continue importing data */
if ( anglesArray.size() != inMD.size() )
{
reportWarning("Input file does not contains angle information. Default sequence used.");
anglesArray.resizeNoCopy(inMD.size());
anglesArray.enumerate();
}
// 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 tomogram exposition time information.");
expTimeArray.initConstant(anglesArray.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 tomogram current beam information.");
cBeamArray.initConstant(anglesArray.size(), 1.);
}
// Since Alba does not provide slit width, we set to ones
slitWidthArray.initConstant(anglesArray.size(), 1.);
}
break;
case BESSY:
{
size_t objId;
for (size_t i = tIni; i <= tEnd; ++i)
{
objId = inMD.addObject();
inMD.setValue(MDL_IMAGE, fnInput + formatString("/img%d.spe", i), objId);
}
break;
}
case GENERIC:
{
// Get Darkfield
std::cerr << "Getting darkfield from "+fnInput << " ..." << std::endl;
getDarkfield(fnInput, IavgDark);
if (XSIZE(IavgDark())!=0)
IavgDark.write(fnRoot+"_darkfield.xmp");
std::vector<FileName> listDir;
fnInput.getFiles(listDir);
size_t objId;
for (size_t i = 0; i < listDir.size(); ++i)
{
if (!listDir[i].hasImageExtension())
continue;
objId = inMD.addObject();
inMD.setValue(MDL_IMAGE, fnInput+"/"+listDir[i], objId);
}
}
break;
}
inMD.findObjects(objIds);
size_t nIm = inMD.size();
// Create empty output stack file
getImageInfo(inMD, imgInfo);
/* Get the flatfield:: We get the FF after the image list because we need the image size to adapt the FF
* in case they were already cropped.
*/
if (!fnFlat.empty())
{
std::cout << "Getting flatfield from "+fnFlat << " ..." << std::endl;
getFlatfield(fnFlat,IavgFlat);
if ( XSIZE(IavgFlat()) != 0 )
{
FileName ffName = fnRoot+"_flatfield_avg.xmp";
IavgFlat.write(ffName);
fMD.setValue(MDL_IMAGE, ffName, fMD.addObject());
}
}
createEmptyFile(fnOut, imgInfo.adim.xdim-cropSizeXi-cropSizeXe, imgInfo.adim.ydim-cropSizeYi-cropSizeYe, 1, nIm);
// Process images
td = new ThreadTaskDistributor(nIm, XMIPP_MAX(1, nIm/30));
tm = new ThreadManager(thrNum, this);
std::cerr << "Getting data from " << fnInput << " ...\n";
init_progress_bar(nIm);
tm->run(runThread);
progress_bar(nIm);
// Write Metadata and angles
MetaData MDSorted;
MDSorted.sort(outMD,MDL_ANGLE_TILT);
MDSorted.write("tomo@"+fnRoot + ".xmd");
if ( fMD.size() > 0 )
fMD.write("flatfield@"+fnRoot + ".xmd", MD_APPEND);
// We also reference initial and final images at 0 degrees for Mistral tomograms
if ( dSource == MISTRAL )
{
fMD.clear();
FileName degree0Fn = "NXtomo/instrument/sample/0_degrees_initial_image";
if ( H5File.checkDataset(degree0Fn.c_str()))
fMD.setValue(MDL_IMAGE, degree0Fn + "@" + fnInput, fMD.addObject());
degree0Fn = "NXtomo/instrument/sample/0_degrees_final_image";
if ( H5File.checkDataset(degree0Fn.c_str()))
fMD.setValue(MDL_IMAGE, degree0Fn + "@" + fnInput, fMD.addObject());
if ( fMD.size() > 0 )
fMD.write("degree0@"+fnRoot + ".xmd", MD_APPEND);
}
// Write tlt file for IMOD
std::ofstream fhTlt;
fhTlt.open((fnRoot+".tlt").c_str());
if (!fhTlt)
REPORT_ERROR(ERR_IO_NOWRITE,fnRoot+".tlt");
FOR_ALL_OBJECTS_IN_METADATA(MDSorted)
{
double tilt;
MDSorted.getValue(MDL_ANGLE_TILT,tilt,__iter.objId);
fhTlt << tilt << std::endl;
}
fhTlt.close();
delete td;
delete tm;
}
void ProgVolumePCA::run()
{
show();
produce_side_info();
const MultidimArray<int> &imask=mask.imask;
size_t Nvoxels=imask.sum();
MultidimArray<float> v;
v.initZeros(Nvoxels);
// Add all volumes to the analyzer
FileName fnVol;
FOR_ALL_OBJECTS_IN_METADATA(mdVols)
{
mdVols.getValue(MDL_IMAGE,fnVol,__iter.objId);
V.read(fnVol);
// Construct vector
const MultidimArray<double> &mV=V();
size_t idx=0;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mV)
{
if (DIRECT_MULTIDIM_ELEM(imask,n))
DIRECT_MULTIDIM_ELEM(v,idx++)=DIRECT_MULTIDIM_ELEM(mV,n);
}
analyzer.addVector(v);
}
// Construct PCA basis
analyzer.subtractAvg();
analyzer.learnPCABasis(NPCA,100);
// Project onto the PCA basis
Matrix2D<double> proj;
analyzer.projectOnPCABasis(proj);
std::vector<double> dimredProj;
dimredProj.resize(NPCA);
int i=0;
FOR_ALL_OBJECTS_IN_METADATA(mdVols)
{
memcpy(&dimredProj[0],&MAT_ELEM(proj,i,0),NPCA*sizeof(double));
mdVols.setValue(MDL_DIMRED,dimredProj,__iter.objId);
i++;
}
if (fnVolsOut!="")
mdVols.write(fnVolsOut);
else
mdVols.write(fnVols);
// Save the basis
const MultidimArray<double> &mV=V();
for (int i=NPCA-1; i>=0; --i)
{
V().initZeros();
size_t idx=0;
const MultidimArray<double> &mPCA=analyzer.PCAbasis[i];
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mV)
{
if (DIRECT_MULTIDIM_ELEM(imask,n))
DIRECT_MULTIDIM_ELEM(mV,n)=DIRECT_MULTIDIM_ELEM(mPCA,idx++);
}
if (fnBasis!="")
V.write(fnBasis,i+1,true,WRITE_OVERWRITE);
}
// Generate the PCA volumes
if (listOfPercentiles.size()>0 && fnOutStack!="" && fnAvgVol!="")
{
Image<double> Vavg;
if (fnAvgVol!="")
Vavg.read(fnAvgVol);
else
Vavg().initZeros(V());
Matrix1D<double> p;
proj.toVector(p);
Matrix1D<double> psorted=p.sort();
Image<double> Vpca;
Vpca()=Vavg();
createEmptyFile(fnOutStack,(int)XSIZE(Vavg()),(int)YSIZE(Vavg()),(int)ZSIZE(Vavg()),listOfPercentiles.size());
std::cout << "listOfPercentiles.size()=" << listOfPercentiles.size() << std::endl;
for (size_t i=0; i<listOfPercentiles.size(); i++)
{
int idx=(int)round(textToFloat(listOfPercentiles[i].c_str())/100.0*VEC_XSIZE(p));
std::cout << "Percentile " << listOfPercentiles[i] << " -> idx=" << idx << " p(idx)=" << psorted(idx) << std::endl;
Vpca()+=psorted(idx)*V();
Vpca.write(fnOutStack,i+1,true,WRITE_REPLACE);
}
}
}