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emdata_sparx.h File Reference

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Functions

EMData * real2FH (float OverSamplekB)
 returns the fourier harmonic transform (FH) image of the current image (in real space).
EMData * copy_empty_head () const
 copy header but not set size for the image
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 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.
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 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
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.
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.
void symplane0_rect (EMData *w)
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)
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.
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 * 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.
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.
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.
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.
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)


Function Documentation

EMData* average_circ_sub  )  const
 

Subtract average outside of a circle.

Returns:
image with sbtracted average outside of a circle.

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).

The input image 'with' must have the same size to 'this' image. Input images can be either real or Fourier in arbitrary combination.

Parameters:
[in] with The image used to caculate the fourier shell
[in] w Ring/shell width in Fourier space.
Exceptions:
ImageFormatException If the 2 images are not same size.
NullPointerException if the input image is null
Cannot calculate FSC for 1D images
Returns:
Vector of 3*k FSC results (frequencies, FSC values, error) k - length of FSC curve, depends on dimensions of the image and ring width 1 column - normalized frequency [0,0.5] 2 column - FSC, 3 column - error of the FSC = 1/sqrt(n), where n is the number of Fourier coefficients within given shell.

void center_origin  ) 
 

void center_origin_fft  ) 
 

Multiply a Fourier image by (-1)**(ix+iy+iz) to center it.

void center_origin_yz  ) 
 

float cm_euc EMData *  sinoj,
int  n1,
int  n2
 

euclidean distance between two line

Parameters:
sinoj 
n1 
n2 

vector<float> cog  ) 
 

Calculates the Center of Gravity and the Radius of Gyration of the image.

Returns:
the mass and the radius as vectors.

EMData* conjg  ) 
 

EMData* copy_empty_head  )  const
 

copy header but not set size for the image

EMData* delete_disconnected_regions int  ix = 0,
int  iy = 0,
int  iz = 0
 

Delete disconnected regions in a binary image.

Works only for a volume.

Parameters:
[in] ix: x coordinate (with respect to the center) from which the search of the compact region begins.
[in] iy: y coordinate (with respect to the center) from which the search of the compact region begins.
[in] iz: z coordinate (with respect to the center) from which the search of the compact region begins.
Returns:
New binary image

void depad  ) 
 

De-pad, and and remove Fourier extension convenience function.

Purpose: De-pad, and and remove Fourier extension from a real image.
Method: Remove padding and extension along x for fft,
and return the new image.
Returns:
depadded input image.

void depad_corner  ) 
 

De-pad, and and remove Fourier extension convenience function.

Purpose: De-pad, and and remove Fourier extension from a real image.
Method: Remove padding and extension along x for fft,
and return the new image.
Returns:
depadded input image.

void divkbsinh const Util::KaiserBessel &  kb  ) 
 

divkbsinh -- Divide image by a Kaiser-Bessel sinh window.

Parameters:
[in] kb Kaiser-Bessel window object
Note: Ideally this method really should be a "processor" instead, but at the moment a KaiserBessel object cannot be passed as part of a Dict, making the usual EMData::project() interface rather awkward here.

void divkbsinh_rect const Util::KaiserBessel &  kbx,
const Util::KaiserBessel &  kby,
const Util::KaiserBessel &  kbz
 

EMData* downsample Util::sincBlackman &  kb,
float  scale = 1.0
 

EMData* extract_plane const Transform &  tf,
Util::KaiserBessel &  kb
 

extractplane -- Gridding convolution in 3D along a plane

Note: Expected to be used in combination with fourier gridding projections.

Parameters:
[in] tf transform matrix defining the intended plane.
[in] kb Kaiser-Bessel window
Returns:
Complex gridding plane
See also:
P.A. Penczek, R. Renka, and H. Schomberg, J. Opt. Soc. Am. A _21_, 499-509 (2004)

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* extractline Util::KaiserBessel &  kb,
float  nuxnew,
float  nuynew
 

std::complex<float> extractpoint float  xin,
float  yin,
Util::KaiserBessel &  kb
 

extractpoint -- Gridding convolution

Note: Expected to be used in combination with fouriergridrot2d.

Parameters:
[in] xin x-position
[in] yin y-position
[in] kb Kaiser-Bessel window
Returns:
Complex gridding result
See also:
P.A. Penczek, R. Renka, and H. Schomberg, J. Opt. Soc. Am. A _21_, (2004)

void fft_shuffle  ) 
 

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.

EMData* FH2F int  Size,
float  OverSamplekB,
int  IntensityFlag = 0
 

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.

Parameters:
Size is the size of the image to be returned
OverSamplekB is a parameter controlling the fineness of the Fourier sampling
IntensityFlag =0 is the usual; =1 means that the input was an intensity
Returns:
the shuffled version of the FFT

EMData* FH2Real int  Size,
float  OverSamplekB,
int  IntensityFlag = 0
 

returns the real version of the image from the FH version.

The current image is not changed. The result is in real format.

Parameters:
Size is the size of the image to be returned
OverSamplekB is a parameter controlling the fineness of the Fourier sampling
IntensityFlag =0 is the usual; =1 means that the input was an intensity
Returns:
the real version of the data

EMData* filter_by_image EMData *  image,
bool  RetReal = true
 

float find_3d_threshold float  mass,
float  pixel_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* fouriergridrot2d float  ang,
float  scale,
Util::KaiserBessel &  kb
 

EMData* fouriergridrot_shift2d float  ang,
float  sx,
float  sy,
Util::KaiserBessel &  kb
 

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.

(It is a form of decimation).

Parameters:
[in] nxni new x size (has to be larger/equal than the original x size)
[in] nyni new y size (has to be larger/equal than the original y size)
[in] nzni new z size (has to be larger/equal than the original z size)
RetReal 
Returns:
New truncated up image.

float get_pixel_conv float  delx,
float  dely,
float  delz,
Util::KaiserBessel &  kb
 

Get pixel value image using convolution.

If the image is a volume, then all slices are rotated/translated/scaled.

Parameters:
[in] delx Amount to shift rotation origin along x
[in] dely Amount to shift rotation origin along y
[in] delz Amount to shift rotation origin along z
[in] kb convolution kernel
Exceptions:
ImageDimensionException can not rotate 1 D image
Returns:
New rotated/shifted/scaled image

float get_pixel_conv7 float  delx,
float  dely,
float  delz,
Util::KaiserBessel &  kb
 

float get_pixel_filtered float  delx,
float  dely,
float  delz,
Util::sincBlackman &  kb
 

EMData* get_pow float  n_pow  ) 
 

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.

The only requirement for the window function object is that it overload operator()(const float) and return a float.

Parameters:
[in] x x-value of the desired (potentially off-grid) point
[in] y y-value of the desired (potentially off-grid) point
[in] win Window (mask/kernel) function object.
[in] size Size of real-space kernel/mask.
Returns:
Value of masked/convolved image at (x,y)

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.

Works only for a volume.

Parameters:
[in] pixel_size: pixel size in Angstroms.
[in] dp: repeat in z direction in Angstroms.
[in] dphi: angular repeat in degrees.
[in] section_use: how much of z section to use for symmetrization (between zero and one).
[in] radius: radius of the structure (default nx/2-1).
Returns:
New image

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 insert_rect_slice EMData *  w,
EMData *  myfft,
const Transform &  trans,
int  sizeofprojection,
float  xratio,
float  yratio,
float  zratio,
int  npad,
int  mult
 

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

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
 

EMData* mult_radial EMData *  radial  ) 
 

Multiply radially a 2-D or 3-D image by a 1-D image.

Parameters:
radial the 1-D image multiply to
Exceptions:
ImageDimensionException If 'this' image is 1D.
Returns:
2-D or 3-D radially multiplied image

void nn EMData *  wptr,
EMData *  myfft,
const Transform &  tf,
int  mult = 1
 

Nearest Neighbor interpolation.

Modifies the current object.

Parameters:
wptr Normalization data.
myfft FFT data.
tf Transform reference
mult 

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_().

void nn_ctf EMData *  w,
EMData *  myfft,
const Transform &  tf,
int  mult
 

Nearest Neighbor interpolation.

Modifies the current object.

Parameters:
w Normalization data.
myfft FFT data.
tf Transform reference
mult 

void nn_ctf_applied EMData *  w,
EMData *  myfft,
const Transform &  tf,
int  mult
 

Nearest Neighbor interpolation.

Modifies the current object. here it is assumed the projection data was already multiplied by the ctf...

Parameters:
w Normalization data.
myfft FFT data.
tf Transform reference
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.

Parameters:
wptr Normalization data.
wptr2 
myfft FFT data.
tf Transform reference
mult 

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.

Parameters:
wptr Normalization data.
wptr2 
wptr3 
myfft 
tf Transform reference
mult 

EMData* norm_pad bool  do_norm,
int  npad = 1,
int  valtype = 0
 

Normalize, pad, and Fourier extend convenience function.

Purpose: Create a new [normalized] [zero-padded] Fourier image.
Method: Normalize (if requested), pad with zeros (if
requested), extend along x for fft, and return the new image.
Parameters:
[in] do_norm If true then perform normalization.
[in] npad Amount of zero-padding to use (defaults to 2 if do_pad is true).
valtype 
Returns:
[normalized,] [zero-padded,] [ft-extended] input image.

void onelinenn int  j,
int  n,
int  n2,
EMData *  wptr,
EMData *  bi,
const Transform &  tf
 

Helper function for method nn.

Parameters:
j y fourier index (frequency)
n number of real elements.
n2 Number of complex elements.
wptr Normalization matrix [0:n2][1:n][1:n]
bi Fourier transform matrix [0:n2][1:n]
tf Transform reference

void onelinenn_ctf int  j,
int  n,
int  n2,
EMData *  w,
EMData *  bi,
const Transform &  tf,
int  mult
 

Helper function for method nn4_ctf.

Parameters:
j y fourier index (frequency)
n number of real elements.
n2 Number of complex elements.
w Normalization matrix [0:n2][1:n][1:n]
bi Fourier transform matrix [0:n2][1:n]
tf Transform reference
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.

here it is assumed the projection data was already multiplied by the ctf...

Parameters:
j y fourier index (frequency)
n number of real elements.
n2 Number of complex elements.
w Normalization matrix [0:n2][1:n][1:n]
bi Fourier transform matrix [0:n2][1:n]
tf Transform reference
mult 

void onelinenn_mult int  j,
int  n,
int  n2,
EMData *  wptr,
EMData *  bi,
const Transform &  tf,
int  mult
 

void pad_corner float *  pad_image  ) 
 

vector<float> peak_ccf float  hf_p  ) 
 

Peak (with a radius of hf_p) search for particle picking:.

Parameters:
hf_p 

vector<float> peak_search int  ml,
float  invert
 

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. ...

Parameters:
[in] ml 
[in] invert 

bool peakcmp const Pixel &  p1,
const Pixel &  p2
[static, private]
 

vector<float> phase_cog  ) 
 

Calculate the Phase approximation to center of gravity This operations works for 1-2-3-d images.

Returns:
both the center of gravity and the phase approximated center of gravity values.

EMData* real2FH float  OverSamplekB  ) 
 

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.

Parameters:
OverSamplekB is a parameter controlling the fineness of the Fourier sampling
Returns:
the Fourier Harmonic image

Referenced by EMAN::Util::TwoDTestFunc().

EMData* replace_amplitudes EMData *  image,
bool  RetReal = true
 

float restrict1 float  x,
int  nx
[inline, static]
 

Definition at line 339 of file emdata_sparx.h.

References x.

00339                                                                {
00340                         while ( x < 0.0f )          x += nx;
00341                         while ( x >= (float)(nx) )  x -= nx;
00342                         return x;
00343                 }

float restrict2 float  x,
int  nx
[inline, static]
 

Definition at line 348 of file emdata_sparx.h.

References x.

00348                                                                {
00349                         while ( x >=  (float)(nx) )  x -= nx;
00350                         while ( x <= -(float)(nx) )  x += nx;
00351                         return x;
00352                 }

EMData* rot_scale_conv float  ang,
float  delx,
float  dely,
Util::KaiserBessel &  kb,
float  scale = 1.0
 

Rotate-Shift-Scale-Circulantly image using convolution.

If the image is a volume, then all slices are rotated/translated/scaled.

Parameters:
[in] ang Rotation angle in degrees.
[in] delx Amount to shift rotation origin along x
[in] dely Amount to shift rotation origin along y
[in] kb convolution kernel
[in] scale Scaling factor (default=1.0)
Exceptions:
ImageDimensionException can not rotate 1 D image
ImageDimensionException can not rotate 3 D image
Returns:
New rotated/shifted/scaled image

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_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 float  ang,
float  delx,
float  dely,
Util::KaiserBessel &  kb,
float  scale = 1.0
 

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
 

EMData* rot_scale_trans const Transform &  RA  ) 
 

Rotate-Shift-Scale-Circulantly image.

If the image is a volume, then all slices are rotated/translated/scaled.

Parameters:
[in] RA Transform object
Exceptions:
ImageDimensionException can not rotate 1 D image
Returns:
New rotated/shifted/scaled image

EMData* rot_scale_trans2D float  ang,
float  delx = 0.0f,
float  dely = 0.0f,
float  scale = 1.0f
 

Rotate-Shift-Scale-Circulantly image.

If the image is a volume, then all slices are rotated/translated/scaled.

Parameters:
[in] ang Rotation angle in degrees.
[in] delx Amount to shift rotation origin along x
[in] dely Amount to shift rotation origin along y
[in] scale Scaling factor (default=1.0)
Exceptions:
ImageDimensionException can not rotate 1 D image
ImageDimensionException can not rotate 3 D image
Returns:
New rotated/shifted/scaled image

EMData* rot_scale_trans2D_background float  ang,
float  delx = 0.0f,
float  dely = 0.0f,
float  scale = 1.0f
 

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.

Parameters:
[in] ang Rotation angle in degrees.
[in] delx Amount to shift rotation origin along x (default=0.0)
[in] dely Amount to shift rotation origin along y (default=0.0)
[in] scale Scaling factor (default=1.0)
Exceptions:
ImageDimensionException can not rotate 1 D image
ImageDimensionException can not rotate 3 D image
Returns:
New rotated/shifted/scaled image

EMData* rot_scale_trans_background const Transform &  RA  ) 
 

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.

Parameters:
[in] RA Transform object
Exceptions:
ImageDimensionException can not rotate 1 D image
Returns:
New rotated/shifted/scaled image

EMData* rotavg  ) 
 

Create a (1-D) rotationally averaged image.

Exceptions:
ImageDimensionException If 'this' image is 1D.
Returns:
1-D rotationally-averaged image

EMData* rotavg_i  ) 
 

Create a 2-D or 3-D rotationally averaged image.

Exceptions:
ImageDimensionException If 'this' image is 1D.
Returns:
2-D or 3-D rotationally-averaged image

void shuffle_pad_corner float *  pad_image  ) 
 

void symplane0 EMData *  norm  ) 
 

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

void symplane0_ctf EMData *  w  ) 
 

Symmetrize plane 0 Modifies the current object.

Parameters:
w Normalization data.

void symplane0_rect EMData *  w  ) 
 

void symplane1 EMData *  norm,
EMData *  norm2
 

Symmetrize plane 0 Modifies the current object.

Parameters:
norm Normalization data.
norm2 

void symplane2 EMData *  norm,
EMData *  norm2,
EMData *  norm3
 

Symmetrize plane 0 Modifies the current object.

Parameters:
norm Normalization data.
norm2 
norm3 

EMData* symvol string  symmetry  ) 
 

Symmetrize volume in real space.

Parameters:
[in] symmetry Point group of the target volume.
Returns:
New symmetrized volume object.


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