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| CTFDescription1D () |
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void | read (const FileName &fn, bool disable_if_not_K=true) |
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void | readFromMetadataRow (const MetaData &MD, size_t id, bool disable_if_not_K=true) |
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void | readFromMdRow (const MDRow &row, bool disable_if_not_K=true) |
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void | setRow (MDRow &row) const |
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void | write (const FileName &fn) |
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void | readParams (XmippProgram *program) |
| Read parameters from the command line. More...
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void | clear () |
| Clear. More...
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void | clearNoise () |
| Clear noise. More...
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void | clearPureCtf () |
| Clear pure CTF. More...
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void | changeSamplingRate (double newTm) |
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void | produceSideInfo () |
| Produce Side information. More...
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void | precomputeValues (double X) |
| Precompute values for a given frequency. More...
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void | precomputeValues (const MultidimArray< double > &cont_x_freq) |
| Precompute values for an image. More...
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void | precomputeValues (int i) |
| Precompute values for a given frequency. More...
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double | getValueAt (bool show=false) const |
| Compute CTF at (U,V). Continuous frequencies. More...
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double | getValueDampingAt (bool show=false) const |
| Compute CTF damping at (U,V). Continuous frequencies. More...
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double | getValuePureAt (bool show=false) const |
| Compute CTF pure at (U,V). Continuous frequencies. More...
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double | getValuePureNoKAt () const |
| Compute CTF pure at (U,V). Continuous frequencies. More...
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double | getValueNoiseAt (bool show=false) const |
| Compute noise at (X,Y). Continuous frequencies, notice it is squared. More...
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double | getValuePureWithoutDampingAt (bool show=false) const |
| Compute pure CTF without damping at (U,V). Continuous frequencies. More...
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void | getSineAndCosineParts (double &sine_part, double &cosine_part, double E, double u2, double deltaf, bool show) const |
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double | getValuePureNoPrecomputedAt (double X, bool show=false) const |
| Compute CTF pure at (U,V). Continuous frequencies. More...
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void | lookFor (int n, const Matrix1D< double > &u, Matrix1D< double > &freq, int iwhat=0) |
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void | applyCTF (MultidimArray< std::complex< double > > &FFTI, const MultidimArray< double > &I, double Ts, bool absPhase=false) |
| Apply CTF to an image. More...
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void | applyCTF (MultidimArray< double > &I, double Ts, bool absPhase=false) |
| Apply CTF to an image. More...
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void | correctPhase (MultidimArray< std::complex< double > > &FFTI, const MultidimArray< double > &I, double Ts) |
| Correct phase flip of an image. More...
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void | correctPhase (MultidimArray< double > &I, double Ts) |
| Correct phase flip of an image. More...
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template<class T1 , class T2 > |
void | generateCTF (const MultidimArray< T1 > &sample_image, MultidimArray< T2 > &CTF, double Ts=-1) |
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void | getProfile (double fmax, int nsamples, MultidimArray< double > &profiles) |
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void | getAverageProfile (double fmax, int nsamples, MultidimArray< double > &profiles) |
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template<class T > |
double | initCTF (int Ydim, int Xdim, MultidimArray< T > &CTF, double Ts=-1) const |
| Function to initialize CTF to avoid duplicated code. More...
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template<class T > |
void | generateCTF (int Ydim, int Xdim, MultidimArray< T > &CTF, double Ts=-1) |
| Generate CTF image. More...
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template<class T > |
void | generateCTFWithoutDamping (int Ydim, int Xdim, MultidimArray< T > &CTF, double Ts=-1) |
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bool | hasPhysicalMeaning () |
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void | forcePhysicalMeaning () |
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double | lambda |
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double | K1 |
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double | K2 |
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double | K3 |
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double | K4 |
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double | K5 |
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double | K6 |
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double | K7 |
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double | Ksin |
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double | Kcos |
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double | D |
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PrecomputedForCTF | precomputed |
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std::vector< PrecomputedForCTF > | precomputedImage |
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int | precomputedImageXdim |
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double | K |
| Global gain. By default, 1. More...
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double | Tm |
| Sampling rate (A/pixel) More...
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double | kV |
| Accelerating Voltage (in KiloVolts) More...
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double | Defocus |
| Defocus (in Angstroms). Negative values are underfocused. More...
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double | Cs |
| Spherical aberration (in milimeters). Typical value 5.6. More...
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double | Ca |
| Chromatic aberration (in milimeters). Typical value 2. More...
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double | espr |
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double | ispr |
| Objective lens stability (deltaI/I) (ppm). Typical value 1. More...
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double | alpha |
| Convergence cone semiangle (in mrad). Typical value 0.5. More...
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double | DeltaF |
| Longitudinal mechanical displacement (ansgtrom). Typical value 100. More...
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double | DeltaR |
| Transversal mechanical displacement (ansgtrom). Typical value 3. More...
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double | Q0 |
| Factor for the importance of the Amplitude contrast. More...
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double | x0 |
| In the case of local CTF determination x0,xF,y0,yF determines the region where the CTF is determined. More...
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double | xF |
| In the case of local CTF determination x0,xF,y0,yF determines the region where the CTF is determined. More...
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double | y0 |
| In the case of local CTF determination x0,xF,y0,yF determines the region where the CTF is determined. More...
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double | yF |
| In the case of local CTF determination x0,xF,y0,yF determines the region where the CTF is determined. More...
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bool | isLocalCTF |
| Local CTF determination. More...
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bool | enable_CTFnoise |
| Enable CTFnoise part. More...
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bool | enable_CTF |
| Enable CTF part. More...
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double | base_line |
| Global base_line. More...
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double | gaussian_K |
| Gain for the gaussian term. More...
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double | sigma1 |
| Gaussian width. More...
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double | Gc1 |
| Gaussian center. More...
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double | sqrt_K |
| Gain for the square root term. More...
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double | sq |
| Sqrt width. More...
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double | gaussian_K2 |
| Gain for the second Gaussian term. More...
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double | sigma2 |
| Second Gaussian width. More...
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double | Gc2 |
| Second Gaussian center. More...
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double | bgR1 |
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double | bgR2 |
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double | bgR3 |
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double | envR0 |
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double | envR1 |
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double | envR2 |
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double | freq_max |
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double | phase_shift |
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double | VPP_radius |
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CTF class. Here goes how to compute the radial average of a parametric CTF:
#include <Reconstruction/CTF.hh>
CTF.
read(
"ctf_crio.param");
double sampling_rate=3.5;
double fmax=1.0/(2.0*sampling_rate);
for (
double f=0;
f<
fmax;
f+=fmax/100.0) {
double CTF_at_f=0;
double N=0;
for(
double ang=0; ang<2*
PI; ang+=0.01) {
N++;
}
std::cout <<
f <<
" " << CTF_at_f/N << std::endl;
}
return 0;
}
Here is another sample program for generating the CTF
#include <data/args.h>
#include <reconstruction/fourier_filter.h>
#include <data/xmipp_program.h>
int main(
int argc,
char **argv)
{
int Xdim;
try
{
}
{
std::cerr << XE << std::endl
<< "Usage: produce_imgs \n"
<< " -i <CTF descr file>\n"
<< " -o <filename root>\n"
<< " -xdim <xdim>\n"
;
return 1;
}
std::cerr << "fn_ctf = " << fn_ctf <<std::endl
<< "fn_root = " << fn_root <<std::endl
<< "Xdim = " << Xdim <<std::endl;
try
{
{
img(i,j)=ctfVal(i,j).real();
}
{
img(i,j)*=ctfVal(i,j).real();
}
img.
write(
"ctf.noisyless");
}
{
std::cout << XE << std::endl;
}
return 0;
}
Definition at line 210 of file ctf.h.