void actualPhaseFlip(MultidimArray<double> &I, CTFDescription ctf)
{
// Perform the Fourier transform
FourierTransformer transformer;
MultidimArray< std::complex<double> > M_inFourier;
transformer.FourierTransform(I,M_inFourier,false);
Matrix1D<double> freq(2); // Frequencies for Fourier plane
int yDim=YSIZE(I);
int xDim=XSIZE(I);
double iTm=1.0/ctf.Tm;
for (size_t i=0; i<YSIZE(M_inFourier); ++i)
{
FFT_IDX2DIGFREQ(i, yDim, YY(freq));
YY(freq) *= iTm;
for (size_t j=0; j<XSIZE(M_inFourier); ++j)
{
FFT_IDX2DIGFREQ(j, xDim, XX(freq));
XX(freq) *= iTm;
ctf.precomputeValues(XX(freq),YY(freq));
if (ctf.getValuePureWithoutDampingAt()<0)
DIRECT_A2D_ELEM(M_inFourier,i,j)*=-1;
}
}
// Perform inverse Fourier transform and finish
transformer.inverseFourierTransform();
}
void ProgCTFPhaseFlipping::run()
{
show();
// Read the micrograph in an array of doubles
Image<double> M_in;
M_in.read(fn_in);
// Read CTF
CTFDescription ctf;
ctf.clear();
ctf.read(fnt_ctf);
ctf.changeSamplingRate(ctf.Tm*downsampling);
ctf.produceSideInfo();
actualPhaseFlip(M_in(),ctf);
M_in.write(fn_out);
}
PyObject *
Image_applyCTF(PyObject *obj, PyObject *args, PyObject *kwargs)
{
PyObject *input = NULL;
double Ts=1.0;
try
{
PyArg_ParseTuple(args, "Od", &input,&Ts);
if (input != NULL)
{
PyObject *pyStr;
if ((pyStr = PyObject_Str(input)) != NULL)
{
FileName fnCTF=PyString_AsString(pyStr);
ImageObject *self = (ImageObject*) obj;
ImageGeneric *image = self->image;
image->convert2Datatype(DT_Double);
MultidimArray<double> * pImage=NULL;
MULTIDIM_ARRAY_GENERIC(*image).getMultidimArrayPointer(pImage);
self->image->data->getMultidimArrayPointer(pImage);
CTFDescription ctf;
ctf.enable_CTF=true;
ctf.enable_CTFnoise=false;
ctf.read(fnCTF);
ctf.produceSideInfo();
ctf.applyCTF(*pImage,Ts);
Py_RETURN_NONE;
}
}
}
catch (XmippError &xe)
{
PyErr_SetString(PyXmippError, xe.msg.c_str());
}
return NULL;
}