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Functions | |
EMData * | real2FH (float OverSamplekB) |
returns the fourier harmonic transform (FH) image of the current image (in real space). | |
EMData * | FH2F (int Size, float OverSamplekB, int IntensityFlag=0) |
returns the fourier version of the image from the FH version. | |
EMData * | FH2Real (int Size, float OverSamplekB, int IntensityFlag=0) |
returns the real version of the image from the FH version. | |
EMData * | rotavg () |
Create a (1-D) rotationally averaged image. | |
EMData * | rotavg_i () |
Create a 2-D or 3-D rotationally averaged image. | |
EMData * | mult_radial (EMData *radial) |
Multiply radially a 2-D or 3-D image by a 1-D image. | |
vector< float > | cog () |
Calculates the Center of Gravity and the Radius of Gyration of the image. | |
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). | |
EMData * | average_circ_sub () const |
Subtract average outside of a circle. | |
void | onelinenn (int j, int n, int n2, EMData *wptr, EMData *bi, const Transform &tf) |
Helper function for method nn. | |
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. | |
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. | |
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. | |
void | symplane0 (EMData *norm) |
Calculate Wiener summation from the inserted 2D slice put the summation into 3D grids using nearest neighbour approximation a. | |
void | symplane1 (EMData *norm, EMData *norm2) |
Symmetrize plane 0 Modifies the current object. | |
void | symplane2 (EMData *norm, EMData *norm2, EMData *norm3) |
Symmetrize plane 0 Modifies the current object. | |
void | onelinenn_ctf (int j, int n, int n2, EMData *w, EMData *bi, const Transform &tf, int mult) |
Helper function for method nn4_ctf. | |
void | nn_ctf (EMData *w, EMData *myfft, const Transform &tf, int mult) |
Nearest Neighbor interpolation. | |
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. | |
void | nn_ctf_applied (EMData *w, EMData *myfft, const Transform &tf, int mult) |
Nearest Neighbor interpolation. | |
void | symplane0_ctf (EMData *w) |
Symmetrize plane 0 Modifies the current object. | |
EMData * | symvol (string symmetry) |
Symmetrize volume in real space. | |
EMData * | rot_scale_trans2D (float ang, float delx=0.0f, float dely=0.0f, float scale=1.0f) |
Rotate-Shift-Scale-Circulantly image. | |
EMData * | rot_scale_trans2D_background (float ang, float delx=0.0f, float dely=0.0f, float scale=1.0f) |
Rotate-Shift-Scale image. | |
EMData * | rot_scale_trans (const Transform &RA) |
Rotate-Shift-Scale-Circulantly image. | |
EMData * | rot_scale_trans_background (const Transform &RA) |
Rotate-Shift-Scale image. | |
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 | |
EMData * | rot_scale_conv (float ang, float delx, float dely, Util::KaiserBessel &kb, float scale=1.0) |
Rotate-Shift-Scale-Circulantly image using convolution. | |
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) |
float | get_pixel_conv (float delx, float dely, float delz, Util::KaiserBessel &kb) |
Get pixel value image using convolution. | |
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. | |
void | fft_shuffle () |
fft_shuffle -- Shuffle a Fourier image to put the origin at (0,ny/2) | |
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 | |
EMData * | extract_plane (const Transform &tf, Util::KaiserBessel &kb) |
extractplane -- Gridding convolution in 3D along a plane | |
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. | |
vector< float > | max_search () |
Search specified number peaks in 1D, 2D, or 3D real images. | |
vector< float > | peak_search (int ml, float invert) |
vector< float > | phase_cog () |
Calculate the Phase approximation to center of gravity This operations works for 1-2-3-d images. | |
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:. | |
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. | |
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. | |
void | depad () |
De-pad, and and remove Fourier extension convenience function. | |
void | depad_corner () |
De-pad, and and remove Fourier extension convenience function. | |
EMData * | norm_pad (bool do_norm, int npad=1, int valtype=0) |
Normalize, pad, and Fourier extend convenience function. | |
void | center_origin () |
void | center_origin_yz () |
void | center_origin_fft () |
Multiply a Fourier image by (-1)**(ix+iy+iz) to center it. | |
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. | |
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) |
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Subtract average outside of a circle.
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Calculate CCF in Fourier space as a function of spatial frequency between a pair of 2-3D images (corners not included). The input image 'with' must have the same size to 'this' image. Input images can be either real or Fourier in arbitrary combination.
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Multiply a Fourier image by (-1)**(ix+iy+iz) to center it.
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euclidean distance between two line
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Calculates the Center of Gravity and the Radius of Gyration of the image.
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Delete disconnected regions in a binary image. Works only for a volume.
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De-pad, and and remove Fourier extension convenience function.
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De-pad, and and remove Fourier extension convenience function.
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divkbsinh -- Divide image by a Kaiser-Bessel sinh window.
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extractplane -- Gridding convolution in 3D along a plane Note: Expected to be used in combination with fourier gridding projections.
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extractpoint -- Gridding convolution Note: Expected to be used in combination with fouriergridrot2d.
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fft_shuffle -- Shuffle a Fourier image to put the origin at (0,ny/2) Our usual FFT convention puts the origin at (0,0), but then grid points corresponding to iy > ny/2 correspond to (unnormalized) frequencies iy-ny. This routine rearranges the columns of the Fourier image so that iy varies from -ny/2 to ny/2 (or ny/2 - 1 for ny even). This method acts as a toggle, so to unshuffle a Fourier image just call this method a second time. |
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returns the fourier version of the image from the FH version. The current image is not changed. The result is in real/imaginary format. The FH switch is set off.
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returns the real version of the image from the FH version. The current image is not changed. The result is in real format.
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Truncate Fourier transform of an image, it will reduce its size. (It is a form of decimation).
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Get pixel value image using convolution. If the image is a volume, then all slices are rotated/translated/scaled.
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Value of 2-D analytic masking (or 2-D convolution) at off-grid point. The only requirement for the window function object is that it overload operator()(const float) and return a float.
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Apply helical symmetry. Works only for a volume.
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Search specified number peaks in 1D, 2D, or 3D real images. and output the peaks in descendent order: The numbers coming out are: image dimension, then 1D: pixel value, x coord, relative peak value, x coord( NX/2 center), ... 2D: pixel value, x coord, y coord, realative peak value, x coord(NX/2 center) y coord(NY/2 center) ... 3D pixel value, x coord, y coord, z coord, realative peak value, x coord(NX/2 center) y coord(NY/2 center) z coord(NZ/2 center) The function is supposed to return 0 dimension and first pixel value (0,0,0) when the image is constant. ...
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Multiply radially a 2-D or 3-D image by a 1-D image.
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Nearest Neighbor interpolation. Modifies the current object.
Referenced by EMAN::PawelProjector::backproject3d(), bnodes_(), crlist_(), delnb_(), delnod_(), EMAN::nnSSNR_ctfReconstructor::finish(), EMAN::nnSSNR_Reconstructor::finish(), EMAN::ImageSort::ImageSort(), nearnd_(), EMAN::Util::Normalize_ring(), EMAN::PawelProjector::prepcubes(), EMAN::PawelProjector::project3d(), slasq3_(), slasq4_(), svd(), trans_(), trmesh_(), and trprnt_(). |
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Nearest Neighbor interpolation. Modifies the current object.
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Nearest Neighbor interpolation. Modifies the current object. here it is assumed the projection data was already multiplied by the ctf...
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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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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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Normalize, pad, and Fourier extend convenience function.
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Helper function for method nn.
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Helper function for method nn4_ctf.
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Helper function for method nn4_ctf. here it is assumed the projection data was already multiplied by the ctf...
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Peak (with a radius of hf_p) search for particle picking:.
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Calculate the Phase approximation to center of gravity This operations works for 1-2-3-d images.
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returns the fourier harmonic transform (FH) image of the current image (in real space). The current image is not changed. The result is in real/imaginary format. The FH switch is set on.
Referenced by EMAN::Util::TwoDTestFunc(). |
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Definition at line 327 of file emdata_sparx.h. References x. 00327 { 00328 while ( x < 0.0f ) x += nx; 00329 while ( x >= (float)(nx) ) x -= nx; 00330 return x; 00331 }
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Definition at line 336 of file emdata_sparx.h. References x. 00336 { 00337 while ( x >= (float)(nx) ) x -= nx; 00338 while ( x <= -(float)(nx) ) x += nx; 00339 return x; 00340 }
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Rotate-Shift-Scale-Circulantly image using convolution. If the image is a volume, then all slices are rotated/translated/scaled.
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Rotate-Shift-Scale-Circulantly image. If the image is a volume, then all slices are rotated/translated/scaled.
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Rotate-Shift-Scale-Circulantly image. If the image is a volume, then all slices are rotated/translated/scaled.
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Rotate-Shift-Scale image. In contrast to rot_scale_trans2D, wrap aroud is not done circulantly so as to prevent artifacts from occurring. If the image is a volume, then all slices are rotated/translated/scaled.
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Rotate-Shift-Scale image. In contrast to rot_scale_trans, wrap around is not done circulantly so as to prevent artifacts occurring during rotation. If the image is a volume, then all slices are rotated/translated/scaled.
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Create a (1-D) rotationally averaged image.
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Create a 2-D or 3-D rotationally averaged image.
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Calculate Wiener summation from the inserted 2D slice put the summation into 3D grids using nearest neighbour approximation a. Map the 2D coordinates of the interted slice into 3D grid using 3D transformation b. calculate 2D CTF_K^2 and CTF_K*F_K, and put them on the voxel of 3D volume c. count the number of images entering each boxel wptr3 |
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Symmetrize plane 0 Modifies the current object.
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Symmetrize plane 0 Modifies the current object.
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Symmetrize plane 0 Modifies the current object.
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Symmetrize volume in real space.
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