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Functions |
EMData * | real2FH (float OverSamplekB) |
| returns the fourier harmonic transform (FH) image of the current image (in real space).
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EMData * | copy_empty_head () const |
| copy header but not set size for the image
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EMData * | FH2F (int Size, float OverSamplekB, int IntensityFlag=0) |
| returns the fourier version of the image from the FH version.
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EMData * | FH2Real (int Size, float OverSamplekB, int IntensityFlag=0) |
| returns the real version of the image from the FH version.
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EMData * | rotavg () |
| Create a (1-D) rotationally averaged image.
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EMData * | rotavg_i () |
| Create a 2-D or 3-D rotationally averaged image.
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EMData * | mult_radial (EMData *radial) |
| Multiply radially a 2-D or 3-D image by a 1-D image.
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vector< float > | cog () |
| Calculates the Center of Gravity and the Radius of Gyration of the image.
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vector< float > | calc_fourier_shell_correlation (EMData *with, float w=1.0f) |
| Calculate CCF in Fourier space as a function of spatial frequency between a pair of 2-3D images (corners not included).
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EMData * | average_circ_sub () const |
| Subtract average outside of a circle.
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void | onelinenn (int j, int n, int n2, EMData *wptr, EMData *bi, const Transform &tf) |
| Helper function for method nn.
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void | onelinenn_mult (int j, int n, int n2, EMData *wptr, EMData *bi, const Transform &tf, int mult) |
void | nn (EMData *wptr, EMData *myfft, const Transform &tf, int mult=1) |
| Nearest Neighbor interpolation.
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void | insert_rect_slice (EMData *w, EMData *myfft, const Transform &trans, int sizeofprojection, float xratio, float yratio, float zratio, int npad, int mult) |
void | nn_SSNR (EMData *wptr, EMData *wptr2, EMData *myfft, const Transform &tf, int mult=1) |
| Nearest Neighbor interpolation, meanwhile return necessary data such as Kn, sum_k(F_k^n) ans sum_k(|F_k^n|^2) Modifies the current object.
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void | nn_SSNR_ctf (EMData *wptr, EMData *wptr2, EMData *wptr3, EMData *myfft, const Transform &tf, int mult=1) |
| Nearest Neighbor interpolation, meanwhile return necessary data such as Kn, sum_k(F_k^n) ans sum_k(|F_k^n|^2) Modifies the current object.
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void | symplane0 (EMData *norm) |
| Calculate Wiener summation from the inserted 2D slice put the summation into 3D grids using nearest neighbour approximation a.
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void | symplane1 (EMData *norm, EMData *norm2) |
| Symmetrize plane 0 Modifies the current object.
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void | symplane2 (EMData *norm, EMData *norm2, EMData *norm3) |
| Symmetrize plane 0 Modifies the current object.
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void | onelinenn_ctf (int j, int n, int n2, EMData *w, EMData *bi, const Transform &tf, int mult) |
| Helper function for method nn4_ctf.
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void | nn_ctf (EMData *w, EMData *myfft, const Transform &tf, int mult) |
| Nearest Neighbor interpolation.
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void | insert_rect_slice_ctf (EMData *w, EMData *myfft, const Transform &trans, int sizeofprojection, float xratio, float yratio, float zratio, int npad, int mult) |
| helper function to insert rectangualr slice for ctf rect case
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void | insert_rect_slice_ctf_applied (EMData *w, EMData *myfft, const Transform &trans, int sizeofprojection, float xratio, float yratio, float zratio, int npad, int mult) |
void | onelinenn_ctf_applied (int j, int n, int n2, EMData *w, EMData *bi, const Transform &tf, int mult) |
| Helper function for method nn4_ctf.
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void | nn_ctf_applied (EMData *w, EMData *myfft, const Transform &tf, int mult) |
| Nearest Neighbor interpolation.
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void | symplane0_ctf (EMData *w) |
| Symmetrize plane 0 Modifies the current object.
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void | symplane0_rect (EMData *w) |
EMData * | symvol (string symmetry) |
| Symmetrize volume in real space.
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EMData * | rot_scale_trans2D (float ang, float delx=0.0f, float dely=0.0f, float scale=1.0f) |
| Rotate-Shift-Scale-Circulantly image.
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EMData * | rot_scale_trans2D_background (float ang, float delx=0.0f, float dely=0.0f, float scale=1.0f) |
| Rotate-Shift-Scale image.
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EMData * | rot_scale_trans (const Transform &RA) |
| Rotate-Shift-Scale-Circulantly image.
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EMData * | rot_scale_trans_background (const Transform &RA) |
| Rotate-Shift-Scale image.
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float | restrict1 (float x, int nx) |
float | restrict2 (float x, int nx) |
float | cm_euc (EMData *sinoj, int n1, int n2) |
| euclidean distance between two line
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EMData * | rot_scale_conv (float ang, float delx, float dely, Util::KaiserBessel &kb, float scale=1.0) |
| Rotate-Shift-Scale-Circulantly image using convolution.
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EMData * | downsample (Util::sincBlackman &kb, float scale=1.0) |
EMData * | rot_scale_conv7 (float ang, float delx, float dely, Util::KaiserBessel &kb, float scale_input) |
EMData * | rot_scale_conv_new (float ang, float delx, float dely, Util::KaiserBessel &kb, float scale=1.0) |
EMData * | rot_scale_conv_new_background (float ang, float delx, float dely, Util::KaiserBessel &kb, float scale=1.0) |
EMData * | rot_scale_conv_new_3D (float phi, float theta, float psi, float delx, float dely, float delz, Util::KaiserBessel &kb, float scale=1.0, bool wrap=false) |
EMData * | rot_scale_conv_new_background_3D (float phi, float theta, float psi, float delx, float dely, float delz, Util::KaiserBessel &kb, float scale=1.0, bool wrap=false) |
float | get_pixel_conv (float delx, float dely, float delz, Util::KaiserBessel &kb) |
| Get pixel value image using convolution.
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float | get_pixel_filtered (float delx, float dely, float delz, Util::sincBlackman &kb) |
float | get_pixel_conv7 (float delx, float dely, float delz, Util::KaiserBessel &kb) |
float | getconvpt2d_kbi0 (float x, float y, Util::KaiserBessel::kbi0_win win, int size=7) |
| Value of 2-D analytic masking (or 2-D convolution) at off-grid point.
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void | fft_shuffle () |
| fft_shuffle -- Shuffle a Fourier image to put the origin at (0,ny/2)
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void | pad_corner (float *pad_image) |
void | shuffle_pad_corner (float *pad_image) |
std::complex< float > | extractpoint (float xin, float yin, Util::KaiserBessel &kb) |
| extractpoint -- Gridding convolution
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EMData * | extract_plane (const Transform &tf, Util::KaiserBessel &kb) |
| extractplane -- Gridding convolution in 3D along a plane
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EMData * | extract_plane_rect (const Transform &tf, Util::KaiserBessel &kbx, Util::KaiserBessel &kby, Util::KaiserBessel &kbz) |
EMData * | extract_plane_rect_fast (const Transform &tf, Util::KaiserBessel &kbx, Util::KaiserBessel &kby, Util::KaiserBessel &kbz) |
EMData * | fouriergridrot2d (float ang, float scale, Util::KaiserBessel &kb) |
EMData * | fouriergridrot_shift2d (float ang, float sx, float sy, Util::KaiserBessel &kb) |
void | divkbsinh (const Util::KaiserBessel &kb) |
| divkbsinh -- Divide image by a Kaiser-Bessel sinh window.
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void | divkbsinh_rect (const Util::KaiserBessel &kbx, const Util::KaiserBessel &kby, const Util::KaiserBessel &kbz) |
vector< float > | peak_search (int ml, float invert) |
| Search specified number peaks in 1D, 2D, or 3D real images.
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vector< float > | phase_cog () |
| Calculate the Phase approximation to center of gravity This operations works for 1-2-3-d images.
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float | find_3d_threshold (float mass, float pixel_size) |
vector< float > | peak_ccf (float hf_p) |
| Peak (with a radius of hf_p) search for particle picking:.
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EMData * | get_pow (float n_pow) |
EMData * | conjg () |
bool | peakcmp (const Pixel &p1, const Pixel &p2) |
EMData * | extractline (Util::KaiserBessel &kb, float nuxnew, float nuynew) |
EMData * | delete_disconnected_regions (int ix=0, int iy=0, int iz=0) |
| Delete disconnected regions in a binary image.
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EMData * | helicise (float pixel_size, float dp, float dphi, float section_use=1.0f, float radius=-1.0f, float minrad=-1.0f) |
| Apply helical symmetry.
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EMData * | helicise_grid (float pixel_size, float dp, float dphi, Util::KaiserBessel &kb, float section_use=1.0f, float radius=-1.0f, float minrad=-1.0f) |
void | depad () |
| De-pad, and and remove Fourier extension convenience function.
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void | depad_corner () |
| De-pad, and and remove Fourier extension convenience function.
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EMData * | norm_pad (bool do_norm, int npad=1, int valtype=0) |
| Normalize, pad, and Fourier extend convenience function.
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void | center_origin () |
void | center_origin_yz () |
void | center_origin_fft () |
| Multiply a Fourier image by (-1)**(ix+iy+iz) to center it.
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EMData * | FourInterpol (int nxni, int nyni=0, int nzni=0, bool RetReal=true) |
EMData * | FourTruncate (int nxni, int nyni=0, int nzni=0, bool RetReal=true) |
| Truncate Fourier transform of an image, it will reduce its size.
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EMData * | Four_ds (int nxni, int nyni=0, int nzni=0, bool RetReal=true) |
EMData * | Four_shuf_ds_cen_us (int nxni, int nyni=0, int nzni=0, bool RetReal=true) |
EMData * | filter_by_image (EMData *image, bool RetReal=true) |
EMData * | replace_amplitudes (EMData *image, bool RetReal=true) |