#include <processor.h>
Inheritance diagram for EMAN::Processor:
Public Types | |
TOP_HAT_LOW_PASS | |
TOP_HAT_HIGH_PASS | |
TOP_HAT_BAND_PASS | |
TOP_HOMOMORPHIC | |
GAUSS_LOW_PASS | |
GAUSS_HIGH_PASS | |
GAUSS_BAND_PASS | |
GAUSS_INVERSE | |
GAUSS_HOMOMORPHIC | |
BUTTERWORTH_LOW_PASS | |
BUTTERWORTH_HIGH_PASS | |
BUTTERWORTH_HOMOMORPHIC | |
KAISER_I0 | |
KAISER_SINH | |
KAISER_I0_INVERSE | |
KAISER_SINH_INVERSE | |
SHIFT | |
TANH_LOW_PASS | |
TANH_HIGH_PASS | |
TANH_HOMOMORPHIC | |
TANH_BAND_PASS | |
RADIAL_TABLE | |
CTF_ | |
enum | fourier_filter_types { TOP_HAT_LOW_PASS, TOP_HAT_HIGH_PASS, TOP_HAT_BAND_PASS, TOP_HOMOMORPHIC, GAUSS_LOW_PASS, GAUSS_HIGH_PASS, GAUSS_BAND_PASS, GAUSS_INVERSE, GAUSS_HOMOMORPHIC, BUTTERWORTH_LOW_PASS, BUTTERWORTH_HIGH_PASS, BUTTERWORTH_HOMOMORPHIC, KAISER_I0, KAISER_SINH, KAISER_I0_INVERSE, KAISER_SINH_INVERSE, SHIFT, TANH_LOW_PASS, TANH_HIGH_PASS, TANH_HOMOMORPHIC, TANH_BAND_PASS, RADIAL_TABLE, CTF_ } |
Fourier filter Processor type enum. More... | |
Public Member Functions | |
virtual | ~Processor () |
virtual void | process_inplace (EMData *image)=0 |
To process an image in-place. | |
virtual EMData * | process (const EMData *const image) |
To proccess an image out-of-place. | |
virtual void | process_list_inplace (vector< EMData * > &images) |
To process multiple images using the same algorithm. | |
virtual string | get_name () const =0 |
Get the processor's name. | |
virtual Dict | get_params () const |
Get the processor parameters in a key/value dictionary. | |
virtual void | set_params (const Dict &new_params) |
Set the processor parameters using a key/value dictionary. | |
virtual TypeDict | get_param_types () const |
Get processor parameter information in a dictionary. | |
virtual string | get_desc () const =0 |
Get the descrition of this specific processor. | |
Static Public Member Functions | |
static string | get_group_desc () |
Get the description of this group of processors. | |
static void | EMFourierFilterInPlace (EMData *fimage, Dict params) |
Compute a Fourier-filter processed image in place. | |
static EMData * | EMFourierFilter (EMData *fimage, Dict params) |
Compute a Fourier-processor processed image without altering the original image. | |
Protected Attributes | |
Dict | params |
Static Private Member Functions | |
static EMData * | EMFourierFilterFunc (EMData *fimage, Dict params, bool doInPlace=true) |
Compute a Fourier-filter processed image. |
vector<string> all_processors = Factory<Processor>::get_list();
EMData *img = ...; img->process_inplace("PROCESSORNAME", Dict("sigma", 12));
string get_name() const { return "processorname"; } static Processor *NEW() { return XYZProcessor(); }
static string get_group_desc();
string get_desc() const;
Dict get_params() const; void set_params(const Dict & new_params); TypeDict get_param_types() const;
Definition at line 93 of file processor.h.
Fourier filter Processor type enum.
New Fourier filter processors are computed in a single function, EMFourierFilterFunc, that uses a large switch statement to apply the correct filter processor. This enum specifies the filter processor to be applied.
Definition at line 186 of file processor.h.
00186 { 00187 TOP_HAT_LOW_PASS, 00188 TOP_HAT_HIGH_PASS, 00189 TOP_HAT_BAND_PASS, 00190 TOP_HOMOMORPHIC, 00191 GAUSS_LOW_PASS, 00192 GAUSS_HIGH_PASS, 00193 GAUSS_BAND_PASS, 00194 GAUSS_INVERSE, 00195 GAUSS_HOMOMORPHIC, 00196 BUTTERWORTH_LOW_PASS, 00197 BUTTERWORTH_HIGH_PASS, 00198 BUTTERWORTH_HOMOMORPHIC, 00199 KAISER_I0, 00200 KAISER_SINH, 00201 KAISER_I0_INVERSE, 00202 KAISER_SINH_INVERSE, 00203 SHIFT, 00204 TANH_LOW_PASS, 00205 TANH_HIGH_PASS, 00206 TANH_HOMOMORPHIC, 00207 TANH_BAND_PASS, 00208 RADIAL_TABLE, 00209 CTF_, 00210 };
virtual EMAN::Processor::~Processor | ( | ) | [inline, virtual] |
Compute a Fourier-processor processed image without altering the original image.
fimage | Input image object to be processeded, either a real-space image or a Fourier-space image. Image may be 1-, 2-, or 3-dimensional. | |
[in] | params | Processor parameters. Different processors require different parameters, so we this routine accepts a dictionary of parameters and looks up the appropriate params for the chosen processor processor at run time. All processors use the "dopad" parameter to determine whether the Fourier workspace array should be zero- padded to twice the original length (dopad == 1) or not zero-padded at all (dopad == 0). |
Definition at line 268 of file processor.h.
References EMFourierFilterFunc(), and params.
00268 { 00269 bool doInPlace = false; 00270 return EMFourierFilterFunc(fimage, params, doInPlace); 00271 }
EMData * Processor::EMFourierFilterFunc | ( | EMData * | fimage, | |
Dict | params, | |||
bool | doInPlace = true | |||
) | [static, private] |
Compute a Fourier-filter processed image.
This function is called by either of the convience functions EMFourierFilter or EMFourierFilterInPlace.
fimage | Input image object to be processed, either a real-space image or a Fourier-space image. Image may be 1-, 2-, or 3-dimensional. Image fimage will not be changed unless inplace == true. | |
[in] | params | Processor parameters. Different processor processors require different parameters, so we this routine accepts a dictionary of parameters and looks up the appropriate params for the chosen processor processor at run time. All processors use the "dopad" parameter to determine whether the Fourier workspace array should be zero- padded to twice the original length (dopad == 1) or not zero-padded at all (dopad == 0). |
[in] | doInPlace | Inplace flag. If this flag is true then fimage will contain the processeded image when this function returns. |
Definition at line 58 of file fourierfilter.cpp.
References BUTTERWORTH_HIGH_PASS, BUTTERWORTH_HOMOMORPHIC, BUTTERWORTH_LOW_PASS, EMAN::EMData::cmplx(), EMAN::EMData::copy(), CTF_, EMAN::EMData::depad(), EMAN::EMData::do_fft_inplace(), EMAN::EMData::do_ift_inplace(), EXITFUNC, GAUSS_BAND_PASS, GAUSS_HIGH_PASS, GAUSS_HOMOMORPHIC, GAUSS_INVERSE, GAUSS_LOW_PASS, EMAN::EMData::get_data(), EMAN::EMData::get_ndim(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Util::KaiserBessel::i0win(), iimag(), EMAN::EMData::is_complex(), EMAN::EMData::is_fftodd(), KAISER_I0, KAISER_I0_INVERSE, KAISER_SINH, KAISER_SINH_INVERSE, log10(), LOGERR, max, EMAN::EMData::norm_pad(), nx, ny, params, pihalf, RADIAL_TABLE, EMAN::EMData::set_array_offsets(), SHIFT, sign, EMAN::Util::KaiserBessel::sinhwin(), EMAN::Dict::size(), sqrt(), TANH_BAND_PASS, TANH_HIGH_PASS, TANH_HOMOMORPHIC, TANH_LOW_PASS, tf(), TOP_HAT_BAND_PASS, TOP_HAT_HIGH_PASS, TOP_HAT_LOW_PASS, TOP_HOMOMORPHIC, twopi, EMAN::EMData::update(), and v.
Referenced by EMFourierFilter(), and EMFourierFilterInPlace().
00059 { 00060 int nx, ny, nz, nyp2, nzp2, ix, iy, iz, jx, jy, jz; 00061 float dx, dy, dz, omega=0, omegaL=0, omegaH=0; 00062 float center=0, gamma=0, argx, argy, argz; 00063 float aa, eps, ord=0, cnst=0, aL, aH, cnstL=0, cnstH=0; 00064 bool complex_input; 00065 vector<float> table; 00066 int undoctf=0; 00067 float voltage=100.0f, ak=0.0f, cs=2.0f, ps=1.0f, b_factor=0.0f, wgh=0.1f, sign=-1.0f; 00068 if (!fimage) return NULL; 00069 const int ndim = fimage->get_ndim(); 00070 // Set amount of Fourier padding 00071 // dopad should be a bool, but EMObject Dict's can't store bools. 00072 int dopad = params["dopad"]; 00073 int npad; 00074 if (0 == dopad) { 00075 // no padding 00076 npad = 1; 00077 } else if (1 == dopad) { 00078 // 2x padding (hard-wired) 00079 npad = 2; 00080 } else if (2 == dopad) { 00081 npad = 4; 00082 } else { 00083 // invalid entry 00084 LOGERR("The dopad parameter must be 0 (false) or 1 (true)"); 00085 return NULL; // FIXME: replace w/ exception throw 00086 } 00087 00088 // If the input image is already a Fourier image, then we want to 00089 // have this routine return a Fourier image 00090 complex_input = fimage->is_complex(); 00091 if ( complex_input && 1 == dopad ) { 00092 // Cannot pad Fourier input image 00093 LOGERR("Cannot pad Fourier input image"); 00094 return NULL; // FIXME: replace w/ exception throw 00095 } 00096 00097 Util::KaiserBessel* kbptr = 0; 00098 00099 00100 nx = fimage->get_xsize(); 00101 ny = fimage->get_ysize(); 00102 nz = fimage->get_zsize(); 00103 // We manifestly assume no zero-padding here, just the 00104 // necessary extension along x for the fft 00105 if (complex_input) nx = (nx - 2 + fimage->is_fftodd()); 00106 00107 const int nxp = npad*nx; 00108 const int nyp = (ny > 1) ? npad*ny : 1; 00109 const int nzp = (nz > 1) ? npad*nz : 1; 00110 00111 int lsd2 = (nxp + 2 - nxp%2) / 2; // Extended x-dimension of the complex image 00112 int lsd3 = lsd2 - 1; 00113 00114 // Perform padding (if necessary) and fft, if the image is not already an fft image 00115 EMData* fp = NULL; // workspace image 00116 if (complex_input) { 00117 if (doInPlace) { 00118 // it's okay to change the original image 00119 fp = fimage; 00120 } else { 00121 // fimage must remain pristine 00122 fp = fimage->copy(); 00123 } 00124 } else { 00125 if (doInPlace) { 00126 if (npad>1) { 00127 LOGERR("Cannot pad with inplace filter"); 00128 return NULL; // FIXME, exception 00129 } 00130 fp=fimage; 00131 fp->do_fft_inplace(); 00132 } else { 00133 fp = fimage->norm_pad( false, npad, 1); 00134 fp->do_fft_inplace(); 00135 } 00136 } 00137 fp->set_array_offsets(1,1,1); 00138 00139 // And the filter type is: 00140 int filter_type = params["filter_type"]; 00141 00142 nyp2 = nyp/2; nzp2 = nzp/2; 00143 dx = 1.0f/float(nxp); 00144 #ifdef _WIN32 00145 dy = 1.0f/_cpp_max(float(nyp),1.0f); 00146 dz = 1.0f/_cpp_max(float(nzp),1.0f); 00147 #else 00148 dy = 1.0f/std::max(float(nyp),1.0f); 00149 dz = 1.0f/std::max(float(nzp),1.0f); 00150 #endif //_WIN32 00151 float dx2 = dx*dx, dy2 = dy*dy, dz2 = dz*dz; 00152 00153 vector<float>::size_type tsize; 00154 float sz[3]; 00155 float szmax; 00156 vector<float>::size_type maxsize; 00157 float xshift=0.0, yshift=0.0, zshift=0.0; 00158 00159 // For the given type of filter set up any necessary parameters for the 00160 // filter calculation. FIXME: Need parameter bounds checking! 00161 switch (filter_type) { 00162 case TOP_HAT_LOW_PASS: 00163 case TOP_HAT_HIGH_PASS: 00164 omega = params["cutoff_abs"]; 00165 omega = 1.0f/omega/omega; 00166 break; 00167 case TOP_HAT_BAND_PASS: 00168 omegaL = params["low_cutoff_frequency"]; 00169 omegaH = params["high_cutoff_frequency"]; 00170 omegaL = 1.0f/omegaL/omegaL; 00171 omegaH = 1.0f/omegaH/omegaH; 00172 break; 00173 case TOP_HOMOMORPHIC: 00174 omegaL = params["low_cutoff_frequency"]; 00175 omegaH = params["high_cutoff_frequency"]; 00176 gamma = params["value_at_zero_frequency"]; 00177 omegaL = 1.0f/omegaL/omegaL; 00178 omegaH = 1.0f/omegaH/omegaH; 00179 break; 00180 case GAUSS_LOW_PASS: 00181 case GAUSS_HIGH_PASS: 00182 case GAUSS_INVERSE: 00183 omega = params["cutoff_abs"]; 00184 omega = 0.5f/omega/omega; 00185 break; 00186 case GAUSS_BAND_PASS: 00187 omega = params["cutoff_abs"]; 00188 center = params["center"]; 00189 omega = 0.5f/omega/omega; 00190 break; 00191 case GAUSS_HOMOMORPHIC: 00192 omega = params["cutoff_abs"]; 00193 gamma = params["value_at_zero_frequency"]; 00194 omega = 0.5f/omega/omega; 00195 gamma = 1.0f-gamma; 00196 break; 00197 case BUTTERWORTH_LOW_PASS: 00198 case BUTTERWORTH_HIGH_PASS: 00199 omegaL = params["low_cutoff_frequency"]; 00200 omegaH = params["high_cutoff_frequency"]; 00201 eps = 0.882f; 00202 aa = 10.624f; 00203 ord = 2.0f*log10(eps/sqrt(aa*aa-1.0f))/log10(omegaL/omegaH); 00204 omegaL = omegaL/pow(eps,2.0f/ord); 00205 break; 00206 case BUTTERWORTH_HOMOMORPHIC: 00207 omegaL = params["low_cutoff_frequency"]; 00208 omegaH = params["high_cutoff_frequency"]; 00209 gamma = params["value_at_zero_frequency"]; 00210 eps = 0.882f; 00211 aa = 10.624f; 00212 ord = 2.0f*log10(eps/sqrt(pow(aa,2)-1.0f))/log10(omegaL/omegaH); 00213 omegaL = omegaL/pow(eps,2.0f/ord); 00214 gamma = 1.0f-gamma; 00215 break; 00216 case SHIFT: 00217 xshift = params["x_shift"]; 00218 yshift = params["y_shift"]; 00219 zshift = params["z_shift"]; 00220 //origin_type = params["origin_type"]; 00221 break; 00222 case TANH_LOW_PASS: 00223 case TANH_HIGH_PASS: 00224 omega = params["cutoff_abs"]; 00225 aa = params["fall_off"]; 00226 cnst = float(pihalf/aa/omega); 00227 break; 00228 case TANH_HOMOMORPHIC: 00229 omega = params["cutoff_abs"]; 00230 aa = params["fall_off"]; 00231 gamma = params["value_at_zero_frequency"]; 00232 cnst = float(pihalf/aa/omega); 00233 gamma=1.0f-gamma; 00234 break; 00235 case TANH_BAND_PASS: 00236 omegaL = params["low_cutoff_frequency"]; 00237 aL = params["Low_fall_off"]; 00238 omegaH = params["high_cutoff_frequency"]; 00239 aH = params["high_fall_off"]; 00240 cnstL = float(pihalf/aL/(omegaH-omegaL)); 00241 cnstH = float(pihalf/aH/(omegaH-omegaL)); 00242 break; 00243 case CTF_: 00244 dz = params["defocus"]; 00245 cs = params["Cs"]; 00246 voltage = params["voltage"]; 00247 ps = params["Pixel_size"]; 00248 b_factor = params["B_factor"]; 00249 wgh = params["amp_contrast"]; 00250 sign = params["sign"]; 00251 undoctf = params["undo"]; 00252 ix = params["binary"]; 00253 if(ix == 1) {undoctf = 2; b_factor=0.0;} //ignore B-factor for the binary CTF 00254 break; 00255 case KAISER_I0: 00256 case KAISER_SINH: 00257 case KAISER_I0_INVERSE: 00258 case KAISER_SINH_INVERSE: 00259 { 00260 float alpha = params["alpha"]; 00261 int K = params["K"]; 00262 float r = params["r"]; 00263 float v = params["v"]; 00264 int N = params["N"]; 00265 kbptr = new Util::KaiserBessel(alpha, K, r, v, N); 00266 break; 00267 }//without this bracket, compiler on water will complain about crosses initialization 00268 case RADIAL_TABLE: 00269 table = params["table"]; 00270 tsize = table.size(); 00271 sz[0] = static_cast<float>(lsd2); 00272 sz[1] = static_cast<float>(nyp2); 00273 sz[2] = static_cast<float>(nzp2); 00274 szmax = *max_element(&sz[0],&sz[3]); 00275 // for 2d, sqrt(2) = 1.414, relax a little bit to 1.6 00276 // for 3d, sqrt(3) = 1.732, relax a little bit to 1.9 00277 if (nzp > 1) {maxsize = vector<float>::size_type(1.9*szmax);} else {maxsize = vector<float>::size_type(1.6*szmax);} 00278 for (vector<float>::size_type i = tsize+1; i < maxsize; i++) table.push_back(0.f); 00279 break; 00280 default: 00281 LOGERR("Unknown Fourier Filter type"); 00282 return NULL; // FIXME: replace w/ exception throw 00283 } 00284 // Perform actual calculation 00285 // Gaussian bandpass is the only one with center for frequencies 00286 if(filter_type == GAUSS_BAND_PASS) { 00287 for ( iz = 1; iz <= nzp; iz++) { 00288 jz=iz-1; if(jz>nzp2) jz=jz-nzp; 00289 argz = (float(jz)-center)*(float(jz)-center)*dz2; 00290 for ( iy = 1; iy <= nyp; iy++) { 00291 jy=iy-1; if(jy>nyp2) jy=jy-nyp; 00292 argy = argz + (float(jy)-center)*(float(jy)-center)*dy2; 00293 for ( ix = 1; ix <= lsd2; ix++) { 00294 jx=ix-1; argx = argy + (float(jx)-center)*(float(jx)-center)/float((nxp-1)*(nxp-1)); 00295 // RHS of filter calculation for Gaussian bandpass 00296 fp->cmplx(ix,iy,iz) *= exp(-0.125f*argx*omega); 00297 } 00298 } 00299 } 00300 } else { 00301 switch (filter_type) { 00302 case TOP_HAT_LOW_PASS: 00303 for ( iz = 1; iz <= nzp; iz++) { 00304 jz=iz-1; if (jz>nzp2) jz=jz-nzp; argz = float(jz*jz)*dz2; 00305 for ( iy = 1; iy <= nyp; iy++) { 00306 jy=iy-1; if (jy>nyp2) jy=jy-nyp; argy = argz + float(jy*jy)*dy2; 00307 for ( ix = 1; ix <= lsd2; ix++) { 00308 jx=ix-1; argx = argy + float(jx*jx)*dx2; 00309 if (argx*omega>1.0f) fp->cmplx(ix,iy,iz) = 0; 00310 } 00311 } 00312 } 00313 break; 00314 case TOP_HAT_HIGH_PASS: 00315 for ( iz = 1; iz <= nzp; iz++) { 00316 jz=iz-1; if (jz>nzp2) jz=jz-nzp; argz = float(jz*jz)*dz2; 00317 for ( iy = 1; iy <= nyp; iy++) { 00318 jy=iy-1; if (jy>nyp2) jy=jy-nyp; argy = argz + float(jy*jy)*dy2; 00319 for ( ix = 1; ix <= lsd2; ix++) { 00320 jx=ix-1; argx = argy + float(jx*jx)*dx2; 00321 if (argx*omega<=1.0f) fp->cmplx(ix,iy,iz) = 0; 00322 } 00323 } 00324 } break; 00325 case TOP_HAT_BAND_PASS: 00326 for ( iz = 1; iz <= nzp; iz++) { 00327 jz=iz-1; if (jz>nzp2) jz=jz-nzp; argz = float(jz*jz)*dz2; 00328 for ( iy = 1; iy <= nyp; iy++) { 00329 jy=iy-1; if (jy>nyp2) jy=jy-nyp; argy = argz + float(jy*jy)*dy2; 00330 for ( ix = 1; ix <= lsd2; ix++) { 00331 jx=ix-1; argx = argy + float(jx*jx)*dx2; 00332 if (argx*omegaL<1.0f || argx*omegaH>=1.0f) fp->cmplx(ix,iy,iz) = 0; 00333 } 00334 } 00335 } 00336 break; 00337 case TOP_HOMOMORPHIC: 00338 for ( iz = 1; iz <= nzp; iz++) { 00339 jz=iz-1; if (jz>nzp2) jz=jz-nzp; argz = float(jz*jz)*dz2; 00340 for ( iy = 1; iy <= nyp; iy++) { 00341 jy=iy-1; if (jy>nyp2) jy=jy-nyp; argy = argz + float(jy*jy)*dy2; 00342 for ( ix = 1; ix <= lsd2; ix++) { 00343 jx=ix-1; argx = argy + float(jx*jx)*dx2; 00344 if (argx*omegaH>1.0f) fp->cmplx(ix,iy,iz) = 0.0f; 00345 else if (argx*omegaL<=1.0f) fp->cmplx(ix,iy,iz) *= gamma; 00346 } 00347 } 00348 } 00349 break; 00350 case GAUSS_LOW_PASS : 00351 for ( iz = 1; iz <= nzp; iz++) { 00352 jz=iz-1; if (jz>nzp2) jz=jz-nzp; argz = float(jz*jz)*dz2; 00353 for ( iy = 1; iy <= nyp; iy++) { 00354 jy=iy-1; if (jy>nyp2) jy=jy-nyp; argy = argz + float(jy*jy)*dy2; 00355 for ( ix = 1; ix <= lsd2; ix++) { 00356 jx=ix-1; argx = argy + float(jx*jx)*dx2; 00357 fp->cmplx(ix,iy,iz) *= exp(-argx*omega); 00358 } 00359 } 00360 } 00361 break; 00362 case GAUSS_HIGH_PASS: 00363 for ( iz = 1; iz <= nzp; iz++) { 00364 jz=iz-1; if (jz>nzp2) jz=jz-nzp; argz = float(jz*jz)*dz2; 00365 for ( iy = 1; iy <= nyp; iy++) { 00366 jy=iy-1; if (jy>nyp2) jy=jy-nyp; argy = argz + float(jy*jy)*dy2; 00367 for ( ix = 1; ix <= lsd2; ix++) { 00368 jx=ix-1; argx = argy + float(jx*jx)*dx2; 00369 fp->cmplx(ix,iy,iz) *= 1.0f-exp(-argx*omega); 00370 } 00371 } 00372 } 00373 break; 00374 case GAUSS_HOMOMORPHIC: 00375 for ( iz = 1; iz <= nzp; iz++) { 00376 jz=iz-1; if (jz>nzp2) jz=jz-nzp; argz = float(jz*jz)*dz2; 00377 for ( iy = 1; iy <= nyp; iy++) { 00378 jy=iy-1; if (jy>nyp2) jy=jy-nyp; argy = argz + float(jy*jy)*dy2; 00379 for ( ix = 1; ix <= lsd2; ix++) { 00380 jx=ix-1; argx = argy + float(jx*jx)*dx2; 00381 fp->cmplx(ix,iy,iz) *= 1.0f-gamma*exp(-argx*omega); 00382 } 00383 } 00384 } 00385 break; 00386 case GAUSS_INVERSE : 00387 for ( iz = 1; iz <= nzp; iz++) { 00388 jz=iz-1; if (jz>nzp2) jz=jz-nzp; argz = float(jz*jz)*dz2; 00389 for ( iy = 1; iy <= nyp; iy++) { 00390 jy=iy-1; if (jy>nyp2) jy=jy-nyp; argy = argz + float(jy*jy)*dy2; 00391 for ( ix = 1; ix <= lsd2; ix++) { 00392 jx=ix-1; argx = argy + float(jx*jx)*dx2; 00393 fp->cmplx(ix,iy,iz) *= exp(argx*omega); 00394 } 00395 } 00396 } 00397 break; 00398 case KAISER_I0: // K-B filter 00399 for ( iz = 1; iz <= nzp; iz++) { 00400 jz=iz-1; if (jz>nzp2) jz=jz-nzp; 00401 float nuz = jz*dz; 00402 for ( iy = 1; iy <= nyp; iy++) { 00403 jy=iy-1; if (jy>nyp2) jy=jy-nyp; 00404 float nuy = jy*dy; 00405 for ( ix = 1; ix <= lsd2; ix++) { 00406 jx=ix-1; 00407 float nux = jx*dx; 00408 //if (!kbptr) 00409 // throw 00410 // NullPointerException("kbptr null!"); 00411 switch (ndim) { 00412 case 3: 00413 fp->cmplx(ix,iy,iz) *= kbptr->i0win(nux)*kbptr->i0win(nuy)*kbptr->i0win(nuz); 00414 break; 00415 case 2: 00416 fp->cmplx(ix,iy,iz) *= kbptr->i0win(nux)*kbptr->i0win(nuy); 00417 break; 00418 case 1: 00419 fp->cmplx(ix,iy,iz)*= kbptr->i0win(nux); 00420 break; 00421 } 00422 } 00423 } 00424 } 00425 break; 00426 case KAISER_SINH: // Sinh filter 00427 for ( iz = 1; iz <= nzp; iz++) { 00428 jz=iz-1; if (jz>nzp2) jz=jz-nzp; 00429 for ( iy = 1; iy <= nyp; iy++) { 00430 jy=iy-1; if(jy>nyp2) jy=jy-nyp; 00431 for ( ix = 1; ix <= lsd2; ix++) { 00432 jx=ix-1; 00433 //if (!kbptr) 00434 // throw 00435 // NullPointerException("kbptr null!"); 00436 switch (ndim) { 00437 case 3: 00438 fp->cmplx(ix,iy,iz)*= kbptr->sinhwin((float)jx)*kbptr->sinhwin((float)jy)*kbptr->sinhwin((float)jz); 00439 break; 00440 case 2: 00441 fp->cmplx(ix,iy,iz)*= kbptr->sinhwin((float)jx)*kbptr->sinhwin((float)jy); 00442 break; 00443 case 1: 00444 fp->cmplx(ix,iy,iz)*= kbptr->sinhwin((float)jx); 00445 //float argu = kbptr->sinhwin((float) jx); 00446 //cout << jx<<" "<< nux<<" "<<argu<<endl; 00447 break; 00448 } 00449 } 00450 } 00451 } 00452 break; 00453 case KAISER_I0_INVERSE: // 1./(K-B filter) 00454 for ( iz = 1; iz <= nzp; iz++) { 00455 jz=iz-1; if (jz>nzp2) jz=jz-nzp; 00456 float nuz = jz*dz; 00457 for ( iy = 1; iy <= nyp; iy++) { 00458 jy=iy-1; if(jy>nyp2) jy=jy-nyp; 00459 float nuy = jy*dy; 00460 for ( ix = 1; ix <= lsd2; ix++) { 00461 jx=ix-1; 00462 float nux = jx*dx; 00463 //if (!kbptr) 00464 // throw 00465 // NullPointerException("kbptr null!"); 00466 switch (ndim) { 00467 case 3: 00468 fp->cmplx(ix,iy,iz) /= (kbptr->i0win(nux)*kbptr->i0win(nuy)*kbptr->i0win(nuz)); 00469 break; 00470 case 2: 00471 fp->cmplx(ix,iy,iz) /= (kbptr->i0win(nux)*kbptr->i0win(nuy)); 00472 break; 00473 case 1: 00474 fp->cmplx(ix,iy,iz) /= kbptr->i0win(nux); 00475 break; 00476 } 00477 } 00478 } 00479 } 00480 break; 00481 case KAISER_SINH_INVERSE: // 1./sinh 00482 for ( iz = 1; iz <= nzp; iz++) { 00483 jz=iz-1; if (jz>nzp2) jz=jz-nzp; 00484 for ( iy = 1; iy <= nyp; iy++) { 00485 jy=iy-1; if (jy>nyp2) jy=jy-nyp; 00486 for ( ix = 1; ix <= lsd2; ix++) { 00487 jx=ix-1; 00488 //if (!kbptr) 00489 // throw 00490 // NullPointerException("kbptr null!"); 00491 switch (ndim) { 00492 case 3: 00493 fp->cmplx(ix,iy,iz) /= (kbptr->sinhwin((float)jx)*kbptr->sinhwin((float)jy)*kbptr->sinhwin((float)jz)); 00494 break; 00495 case 2: 00496 fp->cmplx(ix,iy,iz) /= (kbptr->sinhwin((float)jx)*kbptr->sinhwin((float)jy)); 00497 break; 00498 case 1: 00499 fp->cmplx(ix,iy,iz) /= kbptr->sinhwin((float)jx); 00500 //float argu = kbptr->sinhwin((float) jx); 00501 //cout << jx<<" "<< nux<<" "<<argu<<endl; 00502 break; 00503 } 00504 } 00505 } 00506 } 00507 break; 00508 case BUTTERWORTH_LOW_PASS: 00509 for ( iz = 1; iz <= nzp; iz++) { 00510 jz=iz-1; if (jz>nzp2) jz=jz-nzp; argz = float(jz*jz)*dz2; 00511 for ( iy = 1; iy <= nyp; iy++) { 00512 jy=iy-1; if (jy>nyp2) jy=jy-nyp; argy = argz + float(jy*jy)*dy2; 00513 for ( ix = 1; ix <= lsd2; ix++) { 00514 jx=ix-1; argx = argy + float(jx*jx)*dx2; 00515 fp->cmplx(ix,iy,iz) *= sqrt(1.0f/(1.0f+pow(sqrt(argx)/omegaL,ord))); 00516 } 00517 } 00518 } 00519 break; 00520 case BUTTERWORTH_HIGH_PASS: 00521 for ( iz = 1; iz <= nzp; iz++) { 00522 jz=iz-1; if (jz>nzp2) jz=jz-nzp; argz = float(jz*jz)*dz2; 00523 for ( iy = 1; iy <= nyp; iy++) { 00524 jy=iy-1; if (jy>nyp2) jy=jy-nyp; argy = argz + float(jy*jy)*dy2; 00525 for ( ix = 1; ix <= lsd2; ix++) { 00526 jx=ix-1; argx = argy + float(jx*jx)*dx2; 00527 fp->cmplx(ix,iy,iz) *= 1.0f-sqrt(1.0f/(1.0f+pow(sqrt(argx)/omegaL,ord))); 00528 } 00529 } 00530 } 00531 break; 00532 case BUTTERWORTH_HOMOMORPHIC: 00533 for ( iz = 1; iz <= nzp; iz++) { 00534 jz=iz-1; if (jz>nzp2) jz=jz-nzp; argz = float(jz*jz)*dz2; 00535 for ( iy = 1; iy <= nyp; iy++) { 00536 jy=iy-1; if (jy>nyp2) jy=jy-nyp; argy = argz + float(jy*jy)*dy2; 00537 for ( ix = 1; ix <= lsd2; ix++) { 00538 jx=ix-1; argx = argy + float(jx*jx)*dx2; 00539 fp->cmplx(ix,iy,iz) *= 1.0f-gamma*sqrt(1.0f/(1.0f+pow(sqrt(argx)/omegaL,ord))); 00540 } 00541 } 00542 } 00543 break; 00544 case SHIFT: 00545 //if (origin_type) { 00546 for ( iz = 1; iz <= nzp; iz++) { 00547 jz=iz-1; if (jz>nzp2) jz=jz-nzp; 00548 for ( iy = 1; iy <= nyp; iy++) { 00549 jy=iy-1; if (jy>nyp2) jy=jy-nyp; 00550 for ( ix = 1; ix <= lsd2; ix++) { 00551 jx=ix-1; 00552 fp->cmplx(ix,iy,iz) *= exp(-float(twopi)*iimag*(xshift*jx/nx + yshift*jy/ny+ zshift*jz/nz)); 00553 } 00554 } 00555 } 00556 /*} else { 00557 for ( iz = 1; iz <= nzp; iz++) { 00558 jz=iz-1; if (jz>nzp2) jz=jz-nzp; 00559 if (iz>nzp2) { kz=iz-nzp2; } else { kz=iz+nzp2; } 00560 for ( iy = 1; iy <= nyp; iy++) { 00561 jy=iy-1; if (jy>nyp2) jy=jy-nyp; 00562 if (iy>nyp2) { ky=iy-nyp2; } else { ky=iy+nyp2; } 00563 for ( ix = 1; ix <= lsd2; ix++) { 00564 jx=ix-1; 00565 fp->cmplx(ix,ky,kz) *= exp(-float(twopi)*iimag*(xshift*jx/nx + yshift*jy/ny+ zshift*jz/nz)); 00566 } 00567 } 00568 } 00569 }*/ 00570 break; 00571 case TANH_LOW_PASS: 00572 for ( iz = 1; iz <= nzp; iz++) { 00573 jz=iz-1; if (jz>nzp2) jz=jz-nzp; argz = float(jz*jz)*dz2; 00574 for ( iy = 1; iy <= nyp; iy++) { 00575 jy=iy-1; if (jy>nyp2) jy=jy-nyp; argy = argz + float(jy*jy)*dy2; 00576 for ( ix = 1; ix <= lsd2; ix++) { 00577 jx=ix-1; argx = sqrt(argy + float(jx*jx)*dx2); 00578 fp->cmplx(ix,iy,iz) *= 0.5f*(tanh(cnst*(argx+omega))-tanh(cnst*(argx-omega))); 00579 } 00580 } 00581 } 00582 break; 00583 case TANH_HIGH_PASS: 00584 for ( iz = 1; iz <= nzp; iz++) { 00585 jz=iz-1; if (jz>nzp2) jz=jz-nzp; argz = float(jz*jz)*dz2; 00586 for ( iy = 1; iy <= nyp; iy++) { 00587 jy=iy-1; if (jy>nyp2) jy=jy-nyp; argy = argz + float(jy*jy)*dy2; 00588 for ( ix = 1; ix <= lsd2; ix++) { 00589 jx=ix-1; sqrt(argx = argy + float(jx*jx)*dx2); 00590 fp->cmplx(ix,iy,iz) *= 1.0f-0.5f*(tanh(cnst*(argx+omega))-tanh(cnst*(argx-omega))); 00591 } 00592 } 00593 } 00594 break; 00595 case TANH_HOMOMORPHIC: 00596 for ( iz = 1; iz <= nzp; iz++) { 00597 jz=iz-1; if (jz>nzp2) jz=jz-nzp; argz = float(jz*jz)*dz2; 00598 for ( iy = 1; iy <= nyp; iy++) { 00599 jy=iy-1; if (jy>nyp2) jy=jy-nyp; argy = argz + float(jy*jy)*dy2; 00600 for ( ix = 1; ix <= lsd2; ix++) { 00601 jx=ix-1; argx = sqrt(argy + float(jx*jx)*dx2); 00602 fp->cmplx(ix,iy,iz) *= 1.0f-gamma*0.5f*(tanh(cnst*(argx+omega))-tanh(cnst*(argx-omega))); 00603 } 00604 } 00605 } 00606 break; 00607 case TANH_BAND_PASS: 00608 for ( iz = 1; iz <= nzp; iz++) { 00609 jz=iz-1; if (jz>nzp2) jz=jz-nzp; argz = float(jz*jz)*dz2; 00610 for ( iy = 1; iy <= nyp; iy++) { 00611 jy=iy-1; if (jy>nyp2) jy=jy-nyp; argy = argz + float(jy*jy)*dy2; 00612 for ( ix = 1; ix <= lsd2; ix++) { 00613 jx=ix-1; argx = sqrt(argy + float(jx*jx)*dx2); 00614 fp->cmplx(ix,iy,iz) *= 0.5f*(tanh(cnstH*(argx+omegaH))-tanh(cnstH*(argx-omegaH))-tanh(cnstL*(argx+omegaL))+tanh(cnstL*(argx-omegaL))); 00615 } 00616 } 00617 } 00618 break; 00619 case RADIAL_TABLE: 00620 for ( iz = 1; iz <= nzp; iz++) { 00621 jz=iz-1; if (jz>nzp2) jz=jz-nzp; argz = float(jz*jz)*dz2; 00622 for ( iy = 1; iy <= nyp; iy++) { 00623 jy=iy-1; if (jy>nyp2) jy=jy-nyp; argy = argz + float(jy*jy)*dy2; 00624 for ( ix = 1; ix <= lsd2; ix++) { 00625 jx=ix-1; argx = argy + float(jx*jx)*dx2; 00626 float rf = sqrt( argx )*nxp; 00627 int ir = int(rf); 00628 float df = rf - float(ir); 00629 float f = table[ir] + df * (table[ir+1] - table[ir]); // (1-df)*table[ir]+df*table[ir+1]; 00630 fp->cmplx(ix,iy,iz) *= f; 00631 } 00632 } 00633 } 00634 break; 00635 case CTF_: 00636 for ( iz = 1; iz <= nzp; iz++) { 00637 jz=iz-1; if (jz>nzp2) jz=jz-nzp; 00638 for ( iy = 1; iy <= nyp; iy++) { 00639 jy=iy-1; if (jy>nyp2) jy=jy-nyp; 00640 for ( ix = 1; ix <= lsd2; ix++) { 00641 jx=ix-1; 00642 if(ny>1 && nz<=1 ) ak=sqrt(static_cast<float>(jx)/lsd3*static_cast<float>(jx)/lsd3 + 00643 static_cast<float>(jy)/nyp2*static_cast<float>(jy)/nyp2)/ps/2.0f; 00644 else if(ny<=1) ak=sqrt(static_cast<float>(jx)/lsd3*static_cast<float>(jx)/lsd3)/ps/2.0f; 00645 else if(nz>1) ak=sqrt(static_cast<float>(jx)/lsd3*static_cast<float>(jx)/lsd3 + 00646 static_cast<float>(jy)/nyp2*static_cast<float>(jy)/nyp2 + 00647 static_cast<float>(jz)/nzp2*static_cast<float>(jz)/nzp2)/ps/2.0f; 00648 float tf=Util::tf(dz, ak, voltage, cs, wgh, b_factor, sign); 00649 switch (undoctf) { 00650 case 0: 00651 fp->cmplx(ix,iy,iz) *= tf; 00652 break; 00653 case 1: 00654 if( tf>0 && tf < 1e-5 ) tf = 1e-5f; 00655 if( tf<0 && tf > -1e-5 ) tf = -1e-5f; 00656 fp->cmplx(ix,iy,iz) /= tf; 00657 break; 00658 case 2: 00659 if(tf < 0.0f) fp->cmplx(ix,iy,iz) *= -1.0f; 00660 break; 00661 } 00662 } 00663 } 00664 } 00665 break; 00666 } 00667 } 00668 delete kbptr; kbptr = 0; 00669 if (!complex_input) { 00670 fp->do_ift_inplace(); 00671 fp->depad(); 00672 } 00673 00674 // Return a complex (Fourier) filtered image 00675 // Note: fp and fimage are the _same_ object if doInPlace 00676 // is true, so in that case fimage has been filtered. 00677 // We always return an image (pointer), but if the function 00678 // was called with doInPlace == true then the calling function 00679 // will probably ignore the return value. 00680 00681 // ELSE Return a real-space filtered image 00682 // 00683 // On 12/15/2006 Wei Zhang comment: 00684 // If input is reald and doInPlace == true, we might need delete fp after copy its 00685 // data back to fimage, since fp is allocated inside this function and is ignored 00686 // by caller if doInPlace == true. As a reminder, the caller is EMFourierFuncInPlace 00687 // 00688 fp->set_array_offsets(0,0,0); 00689 fp->update(); 00690 if (doInPlace && !complex_input) { 00691 // copy workspace data into the original image 00692 float* orig = fimage->get_data(); 00693 float* work = fp->get_data(); 00694 for (int i = 0; i < nx*ny*nz; i++) orig[i] = work[i]; 00695 fimage->update(); 00696 } 00697 return fp; 00698 EXITFUNC; 00699 }
static void EMAN::Processor::EMFourierFilterInPlace | ( | EMData * | fimage, | |
Dict | params | |||
) | [inline, static] |
Compute a Fourier-filter processed image in place.
fimage | Input image object to be processed, either a real-space image or a Fourier-space image. Image may be 1-, 2-, or 3-dimensional. The original input image is not touched by this routine. | |
[in] | params | Processor parameters. Different processors require different parameters, so we this routine accepts a dictionary of parameters and looks up the appropriate params for the chosen processor at run time. All processors use the "dopad" parameter to determine whether the Fourier workspace array should be zero- padded to twice the original length (dopad == 1) or not zero-padded at all (dopad == 0). |
Definition at line 237 of file processor.h.
References EMFourierFilterFunc(), and params.
Referenced by EMAN::CTF_Processor::process_inplace(), EMAN::NewBandpassTanhProcessor::process_inplace(), EMAN::NewHomomorphicTanhProcessor::process_inplace(), EMAN::NewHighpassTanhProcessor::process_inplace(), EMAN::NewLowpassTanhProcessor::process_inplace(), EMAN::NewHomomorphicButterworthProcessor::process_inplace(), EMAN::NewHighpassButterworthProcessor::process_inplace(), EMAN::NewLowpassButterworthProcessor::process_inplace(), EMAN::NewRadialTableProcessor::process_inplace(), EMAN::InverseKaiserSinhProcessor::process_inplace(), EMAN::InverseKaiserI0Processor::process_inplace(), EMAN::SHIFTProcessor::process_inplace(), EMAN::NewInverseGaussProcessor::process_inplace(), EMAN::NewHomomorphicGaussProcessor::process_inplace(), EMAN::NewBandpassGaussProcessor::process_inplace(), EMAN::NewHighpassGaussProcessor::process_inplace(), EMAN::NewLowpassGaussProcessor::process_inplace(), EMAN::NewHomomorphicTopHatProcessor::process_inplace(), EMAN::NewBandpassTopHatProcessor::process_inplace(), EMAN::NewHighpassTopHatProcessor::process_inplace(), and EMAN::NewLowpassTopHatProcessor::process_inplace().
00237 { 00238 bool doInPlace = true; 00239 EMFourierFilterFunc(fimage, params, doInPlace); 00240 }
virtual string EMAN::Processor::get_desc | ( | ) | const [pure virtual] |
Get the descrition of this specific processor.
This function must be overwritten by a subclass.
Implemented in EMAN::XYZProcessor, EMAN::SNREvalProcessor, EMAN::AmpweightFourierProcessor, EMAN::ConvolutionProcessor, EMAN::XGradientProcessor, EMAN::YGradientProcessor, EMAN::ZGradientProcessor, EMAN::Wiener2DAutoAreaProcessor, EMAN::DistanceSegmentProcessor, EMAN::KmeansSegmentProcessor, EMAN::Wiener2DFourierProcessor, EMAN::LinearRampFourierProcessor, EMAN::LowpassSharpCutoffProcessor, EMAN::HighpassSharpCutoffProcessor, EMAN::LowpassGaussProcessor, EMAN::LowpassAutoBProcessor, EMAN::HighpassAutoPeakProcessor, EMAN::HighpassGaussProcessor, EMAN::LowpassTanhProcessor, EMAN::HighpassTanhProcessor, EMAN::HighpassButterworthProcessor, EMAN::LinearRampProcessor, EMAN::AbsoluateValueProcessor, EMAN::BooleanProcessor, EMAN::InvertCarefullyProcessor, EMAN::ValuePowProcessor, EMAN::ValueSquaredProcessor, EMAN::ValueSqrtProcessor, EMAN::ToZeroProcessor, EMAN::Rotate180Processor, EMAN::TransformProcessor, EMAN::IntTranslateProcessor, EMAN::ScaleTransformProcessor, EMAN::ClampingProcessor, EMAN::NSigmaClampingProcessor, EMAN::ToMinvalProcessor, EMAN::CutToZeroProcessor, EMAN::BinarizeProcessor, EMAN::BinarizeFourierProcessor, EMAN::CollapseProcessor, EMAN::LinearXformProcessor, EMAN::ExpProcessor, EMAN::FiniteProcessor, EMAN::RangeThresholdProcessor, EMAN::SigmaProcessor, EMAN::LogProcessor, EMAN::CircularMaskProcessor, EMAN::MaskSharpProcessor, EMAN::MaskEdgeMeanProcessor, EMAN::MaskNoiseProcessor, EMAN::MaskGaussProcessor, EMAN::MaskGaussNonuniformProcessor, EMAN::MaskGaussInvProcessor, EMAN::LinearPyramidProcessor, EMAN::MakeRadiusSquaredProcessor, EMAN::MakeRadiusProcessor, EMAN::ComplexNormPixel, EMAN::AreaProcessor, EMAN::LaplacianProcessor, EMAN::ZeroConstantProcessor, EMAN::BoxMedianProcessor, EMAN::BoxSigmaProcessor, EMAN::BoxMaxProcessor, EMAN::MinusPeakProcessor, EMAN::PeakOnlyProcessor, EMAN::DiffBlockProcessor, EMAN::CutoffBlockProcessor, EMAN::MaxShrinkProcessor, EMAN::MinShrinkProcessor, EMAN::MeanShrinkProcessor, EMAN::MedianShrinkProcessor, EMAN::FFTResampleProcessor, EMAN::GradientRemoverProcessor, EMAN::GradientPlaneRemoverProcessor, EMAN::FlattenBackgroundProcessor, EMAN::RampProcessor, EMAN::VerticalStripeProcessor, EMAN::RealToFFTProcessor, EMAN::SigmaZeroEdgeProcessor, EMAN::BeamstopProcessor, EMAN::MeanZeroEdgeProcessor, EMAN::AverageXProcessor, EMAN::DecayEdgeProcessor, EMAN::ZeroEdgeRowProcessor, EMAN::ZeroEdgePlaneProcessor, EMAN::BilateralProcessor, EMAN::NormalizeUnitProcessor, EMAN::NormalizeUnitSumProcessor, EMAN::NormalizeStdProcessor, EMAN::NormalizeMaskProcessor, EMAN::NormalizeRampNormVar, EMAN::NormalizeByMassProcessor, EMAN::NormalizeEdgeMeanProcessor, EMAN::NormalizeCircleMeanProcessor, EMAN::NormalizeLREdgeMeanProcessor, EMAN::NormalizeMaxMinProcessor, EMAN::NormalizeRowProcessor, EMAN::NormalizeToLeastSquareProcessor, EMAN::RotationalAverageProcessor, EMAN::RotationalSubstractProcessor, EMAN::TransposeProcessor, EMAN::FlipProcessor, EMAN::AddNoiseProcessor, EMAN::AddSigmaNoiseProcessor, EMAN::AddRandomNoiseProcessor, EMAN::FourierToCornerProcessor, EMAN::FourierToCenterProcessor, EMAN::PhaseToCenterProcessor, EMAN::PhaseToCornerProcessor, EMAN::AutoMask2DProcessor, EMAN::AutoMaskAsymUnit, EMAN::AutoMask3DProcessor, EMAN::AutoMask3D2Processor, EMAN::AddMaskShellProcessor, EMAN::PhaseToMassCenterProcessor, EMAN::ToMassCenterProcessor, EMAN::ACFCenterProcessor, EMAN::SNRProcessor, EMAN::FileFourierProcessor, EMAN::SymSearchProcessor, EMAN::LocalNormProcessor, EMAN::IndexMaskFileProcessor, EMAN::CoordinateMaskFileProcessor, EMAN::PaintProcessor, EMAN::DirectionalSumProcessor, EMAN::WatershedProcessor, EMAN::BinaryOperateProcessor< Type >, EMAN::MatchSFProcessor, EMAN::SetSFProcessor, EMAN::SmartMaskProcessor, EMAN::IterBinMaskProcessor, EMAN::TestImagePureGaussian, EMAN::TestImageFourierNoiseGaussian, EMAN::TestImageFourierNoiseProfile, EMAN::CTFSNRWeightProcessor, EMAN::TestImageLineWave, EMAN::TestTomoImage, EMAN::TestImageGradient, EMAN::TestImageAxes, EMAN::TestImageGaussian, EMAN::TestImageScurve, EMAN::TestImageSphericalWave, EMAN::TestImageSinewave, EMAN::TestImageSinewaveCircular, EMAN::TestImageSquarecube, EMAN::TestImageEllipse, EMAN::TestImageHollowEllipse, EMAN::TestImageCirclesphere, EMAN::TestImageNoiseUniformRand, EMAN::TestImageNoiseGauss, EMAN::TestImageCylinder, EMAN::CCDNormProcessor, EMAN::WaveletProcessor, EMAN::TomoTiltEdgeMaskProcessor, EMAN::TomoTiltAngleWeightProcessor, EMAN::FFTProcessor, EMAN::RadialProcessor, EMAN::HistogramBin, EMAN::ModelEMCylinderProcessor, EMAN::ApplyPolynomialProfileToHelix, EMAN::BinarySkeletonizerProcessor, EMAN::MirrorProcessor, EMAN::NewLowpassTopHatProcessor, EMAN::NewHighpassTopHatProcessor, EMAN::NewBandpassTopHatProcessor, EMAN::NewHomomorphicTopHatProcessor, EMAN::NewLowpassGaussProcessor, EMAN::NewHighpassGaussProcessor, EMAN::NewBandpassGaussProcessor, EMAN::NewHomomorphicGaussProcessor, EMAN::NewInverseGaussProcessor, EMAN::SHIFTProcessor, EMAN::InverseKaiserI0Processor, EMAN::InverseKaiserSinhProcessor, EMAN::NewRadialTableProcessor, EMAN::NewLowpassButterworthProcessor, EMAN::NewHighpassButterworthProcessor, EMAN::NewHomomorphicButterworthProcessor, EMAN::NewLowpassTanhProcessor, EMAN::NewHighpassTanhProcessor, EMAN::NewHomomorphicTanhProcessor, EMAN::NewBandpassTanhProcessor, and EMAN::CTF_Processor.
static string EMAN::Processor::get_group_desc | ( | ) | [inline, static] |
Get the description of this group of processors.
This function is defined in a parent class. It gives a introduction to a group of processors.
Reimplemented in EMAN::ImageProcessor, EMAN::FourierProcessor, EMAN::FourierAnlProcessor, EMAN::LowpassFourierProcessor, EMAN::HighpassFourierProcessor, EMAN::RealPixelProcessor, EMAN::CoordinateProcessor, EMAN::ComplexPixelProcessor, EMAN::BoxStatProcessor, EMAN::NormalizeProcessor, EMAN::TestImageProcessor, and EMAN::NewFourierProcessor.
Definition at line 163 of file processor.h.
00164 { 00165 return "EMAN processors are in-place image processors. You may apply a processor to process a single image or process multiple images. Processor class is the base class for all processor. <br> \ 00166 The basic design of EMAN Processors: <br>\ 00167 1) Each Processor class defines an image-processinging algorithm. <br>\ 00168 2) All the Processor classes in EMAN are managed by a Factory pattern. So each Processor class must define: <br> a) a unique name to idenfity itself in the factory. <br>b) a static method to register itself in the factory.<br>\ 00169 3) Each Processor class defines its own parameter set.<br>\ 00170 4) Each Processor class defines functions to return its documentation including parameter information, and processor description. These functions enable EMAN to generate processor manuals dynamically."; 00171 }
virtual string EMAN::Processor::get_name | ( | ) | const [pure virtual] |
Get the processor's name.
Each processor is identified by a unique name.
Implemented in EMAN::XYZProcessor, EMAN::SNREvalProcessor, EMAN::AmpweightFourierProcessor, EMAN::ConvolutionProcessor, EMAN::XGradientProcessor, EMAN::YGradientProcessor, EMAN::ZGradientProcessor, EMAN::Wiener2DAutoAreaProcessor, EMAN::DistanceSegmentProcessor, EMAN::KmeansSegmentProcessor, EMAN::Wiener2DFourierProcessor, EMAN::LinearRampFourierProcessor, EMAN::LowpassSharpCutoffProcessor, EMAN::HighpassSharpCutoffProcessor, EMAN::LowpassGaussProcessor, EMAN::LowpassAutoBProcessor, EMAN::HighpassAutoPeakProcessor, EMAN::HighpassGaussProcessor, EMAN::LowpassTanhProcessor, EMAN::HighpassTanhProcessor, EMAN::HighpassButterworthProcessor, EMAN::LinearRampProcessor, EMAN::AbsoluateValueProcessor, EMAN::BooleanProcessor, EMAN::InvertCarefullyProcessor, EMAN::ValuePowProcessor, EMAN::ValueSquaredProcessor, EMAN::ValueSqrtProcessor, EMAN::ToZeroProcessor, EMAN::Rotate180Processor, EMAN::TransformProcessor, EMAN::IntTranslateProcessor, EMAN::ScaleTransformProcessor, EMAN::ClampingProcessor, EMAN::NSigmaClampingProcessor, EMAN::ToMinvalProcessor, EMAN::CutToZeroProcessor, EMAN::BinarizeProcessor, EMAN::BinarizeFourierProcessor, EMAN::CollapseProcessor, EMAN::LinearXformProcessor, EMAN::ExpProcessor, EMAN::FiniteProcessor, EMAN::RangeThresholdProcessor, EMAN::SigmaProcessor, EMAN::LogProcessor, EMAN::MaskSharpProcessor, EMAN::MaskEdgeMeanProcessor, EMAN::MaskNoiseProcessor, EMAN::MaskGaussProcessor, EMAN::MaskGaussNonuniformProcessor, EMAN::MaskGaussInvProcessor, EMAN::LinearPyramidProcessor, EMAN::MakeRadiusSquaredProcessor, EMAN::MakeRadiusProcessor, EMAN::ComplexNormPixel, EMAN::LaplacianProcessor, EMAN::ZeroConstantProcessor, EMAN::BoxMedianProcessor, EMAN::BoxSigmaProcessor, EMAN::BoxMaxProcessor, EMAN::MinusPeakProcessor, EMAN::PeakOnlyProcessor, EMAN::DiffBlockProcessor, EMAN::CutoffBlockProcessor, EMAN::MaxShrinkProcessor, EMAN::MinShrinkProcessor, EMAN::MeanShrinkProcessor, EMAN::MedianShrinkProcessor, EMAN::FFTResampleProcessor, EMAN::GradientRemoverProcessor, EMAN::GradientPlaneRemoverProcessor, EMAN::FlattenBackgroundProcessor, EMAN::RampProcessor, EMAN::VerticalStripeProcessor, EMAN::RealToFFTProcessor, EMAN::SigmaZeroEdgeProcessor, EMAN::BeamstopProcessor, EMAN::MeanZeroEdgeProcessor, EMAN::AverageXProcessor, EMAN::DecayEdgeProcessor, EMAN::ZeroEdgeRowProcessor, EMAN::ZeroEdgePlaneProcessor, EMAN::BilateralProcessor, EMAN::NormalizeUnitProcessor, EMAN::NormalizeUnitSumProcessor, EMAN::NormalizeStdProcessor, EMAN::NormalizeMaskProcessor, EMAN::NormalizeRampNormVar, EMAN::NormalizeByMassProcessor, EMAN::NormalizeEdgeMeanProcessor, EMAN::NormalizeCircleMeanProcessor, EMAN::NormalizeLREdgeMeanProcessor, EMAN::NormalizeMaxMinProcessor, EMAN::NormalizeRowProcessor, EMAN::NormalizeToLeastSquareProcessor, EMAN::RotationalAverageProcessor, EMAN::RotationalSubstractProcessor, EMAN::TransposeProcessor, EMAN::FlipProcessor, EMAN::AddNoiseProcessor, EMAN::AddSigmaNoiseProcessor, EMAN::AddRandomNoiseProcessor, EMAN::FourierToCornerProcessor, EMAN::FourierToCenterProcessor, EMAN::PhaseToCenterProcessor, EMAN::PhaseToCornerProcessor, EMAN::AutoMask2DProcessor, EMAN::AutoMaskAsymUnit, EMAN::AutoMask3DProcessor, EMAN::AutoMask3D2Processor, EMAN::AddMaskShellProcessor, EMAN::PhaseToMassCenterProcessor, EMAN::ToMassCenterProcessor, EMAN::ACFCenterProcessor, EMAN::SNRProcessor, EMAN::FileFourierProcessor, EMAN::SymSearchProcessor, EMAN::LocalNormProcessor, EMAN::IndexMaskFileProcessor, EMAN::CoordinateMaskFileProcessor, EMAN::PaintProcessor, EMAN::DirectionalSumProcessor, EMAN::WatershedProcessor, EMAN::BinaryOperateProcessor< Type >, EMAN::MatchSFProcessor, EMAN::SetSFProcessor, EMAN::SmartMaskProcessor, EMAN::IterBinMaskProcessor, EMAN::TestImagePureGaussian, EMAN::TestImageFourierNoiseGaussian, EMAN::TestImageFourierNoiseProfile, EMAN::CTFSNRWeightProcessor, EMAN::TestImageLineWave, EMAN::TestTomoImage, EMAN::TestImageGradient, EMAN::TestImageAxes, EMAN::TestImageGaussian, EMAN::TestImageScurve, EMAN::TestImageSphericalWave, EMAN::TestImageSinewave, EMAN::TestImageSinewaveCircular, EMAN::TestImageSquarecube, EMAN::TestImageEllipse, EMAN::TestImageHollowEllipse, EMAN::TestImageCirclesphere, EMAN::TestImageNoiseUniformRand, EMAN::TestImageNoiseGauss, EMAN::TestImageCylinder, EMAN::CCDNormProcessor, EMAN::WaveletProcessor, EMAN::TomoTiltEdgeMaskProcessor, EMAN::TomoTiltAngleWeightProcessor, EMAN::FFTProcessor, EMAN::RadialProcessor, EMAN::HistogramBin, EMAN::ModelEMCylinderProcessor, EMAN::ApplyPolynomialProfileToHelix, EMAN::BinarySkeletonizerProcessor, EMAN::MirrorProcessor, EMAN::NewLowpassTopHatProcessor, EMAN::NewHighpassTopHatProcessor, EMAN::NewBandpassTopHatProcessor, EMAN::NewHomomorphicTopHatProcessor, EMAN::NewLowpassGaussProcessor, EMAN::NewHighpassGaussProcessor, EMAN::NewBandpassGaussProcessor, EMAN::NewHomomorphicGaussProcessor, EMAN::NewInverseGaussProcessor, EMAN::SHIFTProcessor, EMAN::InverseKaiserI0Processor, EMAN::InverseKaiserSinhProcessor, EMAN::NewRadialTableProcessor, EMAN::NewLowpassButterworthProcessor, EMAN::NewHighpassButterworthProcessor, EMAN::NewHomomorphicButterworthProcessor, EMAN::NewLowpassTanhProcessor, EMAN::NewHighpassTanhProcessor, EMAN::NewHomomorphicTanhProcessor, EMAN::NewBandpassTanhProcessor, and EMAN::CTF_Processor.
virtual TypeDict EMAN::Processor::get_param_types | ( | ) | const [inline, virtual] |
Get processor parameter information in a dictionary.
Each parameter has one record in the dictionary. Each record contains its name, data-type, and description.
Reimplemented in EMAN::XYZProcessor, EMAN::FourierProcessor, EMAN::FourierAnlProcessor, EMAN::SNREvalProcessor, EMAN::AmpweightFourierProcessor, EMAN::ConvolutionProcessor, EMAN::XGradientProcessor, EMAN::YGradientProcessor, EMAN::ZGradientProcessor, EMAN::Wiener2DAutoAreaProcessor, EMAN::DistanceSegmentProcessor, EMAN::KmeansSegmentProcessor, EMAN::Wiener2DFourierProcessor, EMAN::LowpassFourierProcessor, EMAN::HighpassFourierProcessor, EMAN::LowpassAutoBProcessor, EMAN::LinearRampProcessor, EMAN::InvertCarefullyProcessor, EMAN::ValuePowProcessor, EMAN::ToZeroProcessor, EMAN::TransformProcessor, EMAN::IntTranslateProcessor, EMAN::ScaleTransformProcessor, EMAN::ClampingProcessor, EMAN::NSigmaClampingProcessor, EMAN::ToMinvalProcessor, EMAN::CutToZeroProcessor, EMAN::BinarizeProcessor, EMAN::BinarizeFourierProcessor, EMAN::CollapseProcessor, EMAN::LinearXformProcessor, EMAN::ExpProcessor, EMAN::FiniteProcessor, EMAN::RangeThresholdProcessor, EMAN::SigmaProcessor, EMAN::CircularMaskProcessor, EMAN::MaskSharpProcessor, EMAN::MaskEdgeMeanProcessor, EMAN::MaskGaussProcessor, EMAN::MaskGaussNonuniformProcessor, EMAN::MaskGaussInvProcessor, EMAN::AreaProcessor, EMAN::BoxStatProcessor, EMAN::PeakOnlyProcessor, EMAN::DiffBlockProcessor, EMAN::CutoffBlockProcessor, EMAN::MaxShrinkProcessor, EMAN::MinShrinkProcessor, EMAN::MeanShrinkProcessor, EMAN::MedianShrinkProcessor, EMAN::FFTResampleProcessor, EMAN::GradientPlaneRemoverProcessor, EMAN::FlattenBackgroundProcessor, EMAN::BeamstopProcessor, EMAN::DecayEdgeProcessor, EMAN::ZeroEdgeRowProcessor, EMAN::ZeroEdgePlaneProcessor, EMAN::BilateralProcessor, EMAN::NormalizeMaskProcessor, EMAN::NormalizeByMassProcessor, EMAN::NormalizeToLeastSquareProcessor, EMAN::TransposeProcessor, EMAN::FlipProcessor, EMAN::AddNoiseProcessor, EMAN::AddRandomNoiseProcessor, EMAN::AutoMask2DProcessor, EMAN::AutoMaskAsymUnit, EMAN::AutoMask3DProcessor, EMAN::AutoMask3D2Processor, EMAN::AddMaskShellProcessor, EMAN::PhaseToMassCenterProcessor, EMAN::ToMassCenterProcessor, EMAN::ACFCenterProcessor, EMAN::SNRProcessor, EMAN::FileFourierProcessor, EMAN::SymSearchProcessor, EMAN::LocalNormProcessor, EMAN::IndexMaskFileProcessor, EMAN::CoordinateMaskFileProcessor, EMAN::PaintProcessor, EMAN::DirectionalSumProcessor, EMAN::WatershedProcessor, EMAN::BinaryOperateProcessor< Type >, EMAN::MatchSFProcessor, EMAN::SetSFProcessor, EMAN::SmartMaskProcessor, EMAN::IterBinMaskProcessor, EMAN::TestImagePureGaussian, EMAN::TestImageFourierNoiseGaussian, EMAN::TestImageFourierNoiseProfile, EMAN::CTFSNRWeightProcessor, EMAN::TestImageLineWave, EMAN::TestImageGradient, EMAN::TestImageAxes, EMAN::TestImageGaussian, EMAN::TestImageScurve, EMAN::TestImageSphericalWave, EMAN::TestImageSinewave, EMAN::TestImageSinewaveCircular, EMAN::TestImageSquarecube, EMAN::TestImageEllipse, EMAN::TestImageHollowEllipse, EMAN::TestImageCirclesphere, EMAN::TestImageNoiseUniformRand, EMAN::TestImageNoiseGauss, EMAN::TestImageCylinder, EMAN::CCDNormProcessor, EMAN::WaveletProcessor, EMAN::TomoTiltEdgeMaskProcessor, EMAN::TomoTiltAngleWeightProcessor, EMAN::FFTProcessor, EMAN::RadialProcessor, EMAN::HistogramBin, EMAN::ModelEMCylinderProcessor, EMAN::ApplyPolynomialProfileToHelix, EMAN::BinarySkeletonizerProcessor, EMAN::MirrorProcessor, EMAN::NewFourierProcessor, EMAN::NewBandpassTopHatProcessor, EMAN::NewHomomorphicTopHatProcessor, EMAN::NewBandpassGaussProcessor, EMAN::NewHomomorphicGaussProcessor, EMAN::SHIFTProcessor, EMAN::InverseKaiserI0Processor, EMAN::InverseKaiserSinhProcessor, EMAN::NewRadialTableProcessor, EMAN::NewLowpassButterworthProcessor, EMAN::NewHighpassButterworthProcessor, EMAN::NewHomomorphicButterworthProcessor, EMAN::NewLowpassTanhProcessor, EMAN::NewHighpassTanhProcessor, EMAN::NewHomomorphicTanhProcessor, EMAN::NewBandpassTanhProcessor, and EMAN::CTF_Processor.
Definition at line 152 of file processor.h.
00153 { 00154 return TypeDict(); 00155 }
virtual Dict EMAN::Processor::get_params | ( | ) | const [inline, virtual] |
Get the processor parameters in a key/value dictionary.
Definition at line 133 of file processor.h.
References params.
00134 { 00135 return params; 00136 }
To proccess an image out-of-place.
For those processors which can only be processed out-of-place, override this function to give the right behavior.
image | The image will be copied, actual process happen on copy of image. |
Reimplemented in EMAN::Wiener2DAutoAreaProcessor, EMAN::DistanceSegmentProcessor, EMAN::KmeansSegmentProcessor, EMAN::Wiener2DFourierProcessor, EMAN::TransformProcessor, EMAN::IntTranslateProcessor, EMAN::ScaleTransformProcessor, EMAN::MaxShrinkProcessor, EMAN::MinShrinkProcessor, EMAN::MeanShrinkProcessor, EMAN::MedianShrinkProcessor, EMAN::FFTResampleProcessor, EMAN::TransposeProcessor, and EMAN::DirectionalSumProcessor.
Definition at line 490 of file processor.cpp.
References EMAN::EMData::copy(), and process_inplace().
Referenced by EMAN::EMData::process().
00491 { 00492 EMData * result = image->copy(); 00493 process_inplace(result); 00494 return result; 00495 }
virtual void EMAN::Processor::process_inplace | ( | EMData * | image | ) | [pure virtual] |
To process an image in-place.
For those processors which can only be processed out-of-place, override this function to just print out some error message to remind user call the out-of-place version.
image | The image to be processed. |
Implemented in EMAN::XYZProcessor, EMAN::ImageProcessor, EMAN::FourierProcessor, EMAN::FourierAnlProcessor, EMAN::SNREvalProcessor, EMAN::AmpweightFourierProcessor, EMAN::ConvolutionProcessor, EMAN::XGradientProcessor, EMAN::YGradientProcessor, EMAN::ZGradientProcessor, EMAN::Wiener2DAutoAreaProcessor, EMAN::DistanceSegmentProcessor, EMAN::KmeansSegmentProcessor, EMAN::Wiener2DFourierProcessor, EMAN::RealPixelProcessor, EMAN::Rotate180Processor, EMAN::TransformProcessor, EMAN::IntTranslateProcessor, EMAN::ScaleTransformProcessor, EMAN::ClampingProcessor, EMAN::NSigmaClampingProcessor, EMAN::ToMinvalProcessor, EMAN::BinarizeFourierProcessor, EMAN::CoordinateProcessor, EMAN::LinearPyramidProcessor, EMAN::ComplexPixelProcessor, EMAN::AreaProcessor, EMAN::BoxStatProcessor, EMAN::DiffBlockProcessor, EMAN::CutoffBlockProcessor, EMAN::MaxShrinkProcessor, EMAN::MinShrinkProcessor, EMAN::MeanShrinkProcessor, EMAN::MedianShrinkProcessor, EMAN::FFTResampleProcessor, EMAN::GradientRemoverProcessor, EMAN::GradientPlaneRemoverProcessor, EMAN::FlattenBackgroundProcessor, EMAN::RampProcessor, EMAN::VerticalStripeProcessor, EMAN::RealToFFTProcessor, EMAN::SigmaZeroEdgeProcessor, EMAN::BeamstopProcessor, EMAN::MeanZeroEdgeProcessor, EMAN::AverageXProcessor, EMAN::DecayEdgeProcessor, EMAN::ZeroEdgeRowProcessor, EMAN::ZeroEdgePlaneProcessor, EMAN::BilateralProcessor, EMAN::NormalizeProcessor, EMAN::NormalizeRampNormVar, EMAN::NormalizeByMassProcessor, EMAN::NormalizeRowProcessor, EMAN::NormalizeToLeastSquareProcessor, EMAN::RotationalAverageProcessor, EMAN::RotationalSubstractProcessor, EMAN::TransposeProcessor, EMAN::FlipProcessor, EMAN::AddNoiseProcessor, EMAN::AddRandomNoiseProcessor, EMAN::FourierToCornerProcessor, EMAN::FourierToCenterProcessor, EMAN::PhaseToCenterProcessor, EMAN::PhaseToCornerProcessor, EMAN::AutoMask2DProcessor, EMAN::AutoMaskAsymUnit, EMAN::AutoMask3DProcessor, EMAN::AutoMask3D2Processor, EMAN::AddMaskShellProcessor, EMAN::PhaseToMassCenterProcessor, EMAN::ToMassCenterProcessor, EMAN::ACFCenterProcessor, EMAN::SNRProcessor, EMAN::FileFourierProcessor, EMAN::SymSearchProcessor, EMAN::LocalNormProcessor, EMAN::IndexMaskFileProcessor, EMAN::CoordinateMaskFileProcessor, EMAN::PaintProcessor, EMAN::DirectionalSumProcessor, EMAN::WatershedProcessor, EMAN::BinaryOperateProcessor< Type >, EMAN::SmartMaskProcessor, EMAN::IterBinMaskProcessor, EMAN::TestImagePureGaussian, EMAN::TestImageFourierNoiseGaussian, EMAN::TestImageFourierNoiseProfile, EMAN::CTFSNRWeightProcessor, EMAN::TestImageLineWave, EMAN::TestTomoImage, EMAN::TestImageGradient, EMAN::TestImageAxes, EMAN::TestImageGaussian, EMAN::TestImageScurve, EMAN::TestImageSphericalWave, EMAN::TestImageSinewave, EMAN::TestImageSinewaveCircular, EMAN::TestImageSquarecube, EMAN::TestImageEllipse, EMAN::TestImageHollowEllipse, EMAN::TestImageCirclesphere, EMAN::TestImageNoiseUniformRand, EMAN::TestImageNoiseGauss, EMAN::TestImageCylinder, EMAN::CCDNormProcessor, EMAN::WaveletProcessor, EMAN::TomoTiltEdgeMaskProcessor, EMAN::TomoTiltAngleWeightProcessor, EMAN::FFTProcessor, EMAN::RadialProcessor, EMAN::HistogramBin, EMAN::ModelEMCylinderProcessor, EMAN::ApplyPolynomialProfileToHelix, EMAN::BinarySkeletonizerProcessor, EMAN::MirrorProcessor, EMAN::NewLowpassTopHatProcessor, EMAN::NewHighpassTopHatProcessor, EMAN::NewBandpassTopHatProcessor, EMAN::NewHomomorphicTopHatProcessor, EMAN::NewLowpassGaussProcessor, EMAN::NewHighpassGaussProcessor, EMAN::NewBandpassGaussProcessor, EMAN::NewHomomorphicGaussProcessor, EMAN::NewInverseGaussProcessor, EMAN::SHIFTProcessor, EMAN::InverseKaiserI0Processor, EMAN::InverseKaiserSinhProcessor, EMAN::NewRadialTableProcessor, EMAN::NewLowpassButterworthProcessor, EMAN::NewHighpassButterworthProcessor, EMAN::NewHomomorphicButterworthProcessor, EMAN::NewLowpassTanhProcessor, EMAN::NewHighpassTanhProcessor, EMAN::NewHomomorphicTanhProcessor, EMAN::NewBandpassTanhProcessor, and EMAN::CTF_Processor.
Referenced by process(), EMAN::EMData::process_inplace(), and process_list_inplace().
virtual void EMAN::Processor::process_list_inplace | ( | vector< EMData * > & | images | ) | [inline, virtual] |
To process multiple images using the same algorithm.
images | Multiple images to be processed. |
Definition at line 118 of file processor.h.
References process_inplace().
00119 { 00120 for (size_t i = 0; i < images.size(); i++) { 00121 process_inplace(images[i]); 00122 } 00123 }
virtual void EMAN::Processor::set_params | ( | const Dict & | new_params | ) | [inline, virtual] |
Set the processor parameters using a key/value dictionary.
new_params | A dictionary containing the new parameters. |
Reimplemented in EMAN::SNREvalProcessor, EMAN::AmpweightFourierProcessor, EMAN::Wiener2DAutoAreaProcessor, EMAN::Wiener2DFourierProcessor, EMAN::LowpassFourierProcessor, EMAN::HighpassFourierProcessor, EMAN::LinearRampProcessor, EMAN::RealPixelProcessor, EMAN::InvertCarefullyProcessor, EMAN::ValuePowProcessor, EMAN::CollapseProcessor, EMAN::LinearXformProcessor, EMAN::ExpProcessor, EMAN::FiniteProcessor, EMAN::RangeThresholdProcessor, EMAN::SigmaProcessor, EMAN::CircularMaskProcessor, EMAN::MaskSharpProcessor, EMAN::MaskEdgeMeanProcessor, EMAN::MaskGaussProcessor, EMAN::MaskGaussNonuniformProcessor, EMAN::AreaProcessor, EMAN::PeakOnlyProcessor, and EMAN::PaintProcessor.
Definition at line 141 of file processor.h.
References params.
00142 { 00143 params = new_params; 00144 }
Dict EMAN::Processor::params [mutable, protected] |
Definition at line 313 of file processor.h.
Referenced by EMAN::TransformProcessor::assert_valid_aspect(), EMAN::MaskGaussInvProcessor::calc_locals(), EMAN::NormalizeMaskProcessor::calc_mean(), EMAN::NormalizeMaskProcessor::calc_sigma(), EMAN::SetSFProcessor::create_radial_func(), EMAN::MatchSFProcessor::create_radial_func(), EMAN::LowpassAutoBProcessor::create_radial_func(), EMFourierFilter(), EMFourierFilterFunc(), EMFourierFilterInPlace(), get_params(), EMAN::NewFourierProcessor::preprocess(), EMAN::LowpassAutoBProcessor::preprocess(), EMAN::HighpassAutoPeakProcessor::preprocess(), EMAN::HighpassFourierProcessor::preprocess(), EMAN::LowpassFourierProcessor::preprocess(), EMAN::MinShrinkProcessor::process(), EMAN::MaxShrinkProcessor::process(), EMAN::BinarySkeletonizerProcessor::process(), EMAN::ScaleTransformProcessor::process(), EMAN::IntTranslateProcessor::process(), EMAN::TransformProcessor::process(), EMAN::DirectionalSumProcessor::process(), EMAN::MeanShrinkProcessor::process(), EMAN::FFTResampleProcessor::process(), EMAN::MedianShrinkProcessor::process(), EMAN::KmeansSegmentProcessor::process(), EMAN::DistanceSegmentProcessor::process(), EMAN::XYZProcessor::process_inplace(), EMAN::CTF_Processor::process_inplace(), EMAN::NewBandpassTanhProcessor::process_inplace(), EMAN::NewHomomorphicTanhProcessor::process_inplace(), EMAN::NewHighpassTanhProcessor::process_inplace(), EMAN::NewLowpassTanhProcessor::process_inplace(), EMAN::NewHomomorphicButterworthProcessor::process_inplace(), EMAN::NewHighpassButterworthProcessor::process_inplace(), EMAN::NewLowpassButterworthProcessor::process_inplace(), EMAN::NewRadialTableProcessor::process_inplace(), EMAN::InverseKaiserSinhProcessor::process_inplace(), EMAN::InverseKaiserI0Processor::process_inplace(), EMAN::SHIFTProcessor::process_inplace(), EMAN::NewInverseGaussProcessor::process_inplace(), EMAN::NewHomomorphicGaussProcessor::process_inplace(), EMAN::NewBandpassGaussProcessor::process_inplace(), EMAN::NewHighpassGaussProcessor::process_inplace(), EMAN::NewLowpassGaussProcessor::process_inplace(), EMAN::NewHomomorphicTopHatProcessor::process_inplace(), EMAN::NewBandpassTopHatProcessor::process_inplace(), EMAN::NewHighpassTopHatProcessor::process_inplace(), EMAN::NewLowpassTopHatProcessor::process_inplace(), EMAN::BinaryOperateProcessor< Type >::process_inplace(), EMAN::MinShrinkProcessor::process_inplace(), EMAN::MaxShrinkProcessor::process_inplace(), EMAN::ApplyPolynomialProfileToHelix::process_inplace(), EMAN::ModelEMCylinderProcessor::process_inplace(), EMAN::TomoTiltEdgeMaskProcessor::process_inplace(), EMAN::TomoTiltAngleWeightProcessor::process_inplace(), EMAN::ConvolutionProcessor::process_inplace(), EMAN::HistogramBin::process_inplace(), EMAN::NSigmaClampingProcessor::process_inplace(), EMAN::ClampingProcessor::process_inplace(), EMAN::ScaleTransformProcessor::process_inplace(), EMAN::IntTranslateProcessor::process_inplace(), EMAN::TransformProcessor::process_inplace(), EMAN::MirrorProcessor::process_inplace(), EMAN::RadialProcessor::process_inplace(), EMAN::FFTProcessor::process_inplace(), EMAN::WaveletProcessor::process_inplace(), EMAN::CCDNormProcessor::process_inplace(), EMAN::TestImageCylinder::process_inplace(), EMAN::TestImageNoiseGauss::process_inplace(), EMAN::TestImageNoiseUniformRand::process_inplace(), EMAN::TestImageEllipse::process_inplace(), EMAN::TestImageHollowEllipse::process_inplace(), EMAN::TestImageCirclesphere::process_inplace(), EMAN::TestImageSquarecube::process_inplace(), EMAN::TestImageSinewaveCircular::process_inplace(), EMAN::TestImageSinewave::process_inplace(), EMAN::TestImageSphericalWave::process_inplace(), EMAN::TestImagePureGaussian::process_inplace(), EMAN::TestImageAxes::process_inplace(), EMAN::TestImageGradient::process_inplace(), EMAN::TestImageGaussian::process_inplace(), EMAN::TestImageLineWave::process_inplace(), EMAN::TestImageFourierNoiseProfile::process_inplace(), EMAN::CTFSNRWeightProcessor::process_inplace(), EMAN::TestImageFourierNoiseGaussian::process_inplace(), EMAN::IterBinMaskProcessor::process_inplace(), EMAN::AutoMask3D2Processor::process_inplace(), EMAN::AutoMask3DProcessor::process_inplace(), EMAN::SmartMaskProcessor::process_inplace(), EMAN::CoordinateMaskFileProcessor::process_inplace(), EMAN::IndexMaskFileProcessor::process_inplace(), EMAN::SymSearchProcessor::process_inplace(), EMAN::LocalNormProcessor::process_inplace(), EMAN::FileFourierProcessor::process_inplace(), EMAN::SNRProcessor::process_inplace(), EMAN::PhaseToMassCenterProcessor::process_inplace(), EMAN::ToMassCenterProcessor::process_inplace(), EMAN::AddMaskShellProcessor::process_inplace(), EMAN::AddRandomNoiseProcessor::process_inplace(), EMAN::AutoMask2DProcessor::process_inplace(), EMAN::AutoMaskAsymUnit::process_inplace(), EMAN::AddNoiseProcessor::process_inplace(), EMAN::FlipProcessor::process_inplace(), EMAN::BilateralProcessor::process_inplace(), EMAN::BinarizeFourierProcessor::process_inplace(), EMAN::NormalizeToLeastSquareProcessor::process_inplace(), EMAN::NormalizeByMassProcessor::process_inplace(), EMAN::ZeroEdgePlaneProcessor::process_inplace(), EMAN::ZeroEdgeRowProcessor::process_inplace(), EMAN::DecayEdgeProcessor::process_inplace(), EMAN::BeamstopProcessor::process_inplace(), EMAN::GradientPlaneRemoverProcessor::process_inplace(), EMAN::FlattenBackgroundProcessor::process_inplace(), EMAN::MeanShrinkProcessor::process_inplace(), EMAN::FFTResampleProcessor::process_inplace(), EMAN::MedianShrinkProcessor::process_inplace(), EMAN::CutoffBlockProcessor::process_inplace(), EMAN::DiffBlockProcessor::process_inplace(), EMAN::BoxStatProcessor::process_inplace(), EMAN::ToMinvalProcessor::process_inplace(), EMAN::WatershedProcessor::process_inplace(), EMAN::PaintProcessor::set_params(), EMAN::PeakOnlyProcessor::set_params(), EMAN::AreaProcessor::set_params(), EMAN::MaskGaussNonuniformProcessor::set_params(), EMAN::MaskGaussProcessor::set_params(), EMAN::MaskEdgeMeanProcessor::set_params(), EMAN::MaskSharpProcessor::set_params(), EMAN::CircularMaskProcessor::set_params(), EMAN::SigmaProcessor::set_params(), EMAN::RangeThresholdProcessor::set_params(), EMAN::FiniteProcessor::set_params(), EMAN::ExpProcessor::set_params(), EMAN::LinearXformProcessor::set_params(), EMAN::CollapseProcessor::set_params(), EMAN::ValuePowProcessor::set_params(), EMAN::InvertCarefullyProcessor::set_params(), EMAN::RealPixelProcessor::set_params(), EMAN::LinearRampProcessor::set_params(), EMAN::HighpassFourierProcessor::set_params(), EMAN::LowpassFourierProcessor::set_params(), EMAN::Wiener2DFourierProcessor::set_params(), EMAN::Wiener2DAutoAreaProcessor::set_params(), EMAN::AmpweightFourierProcessor::set_params(), EMAN::SNREvalProcessor::set_params(), and set_params().