#include <analyzer_sparx.h>
Inheritance diagram for EMAN::PCAsmall:
Public Member Functions | |
PCAsmall () | |
virtual int | insert_image (EMData *image) |
insert a image to the list of input images | |
virtual vector< EMData * > | analyze () |
main function for Analyzer, analyze input images and create output images | |
string | get_name () const |
Get the Analyzer's name. | |
string | get_desc () const |
Get the Analyzer's description. | |
void | set_params (const Dict &new_params) |
Set the Analyzer parameters using a key/value dictionary. | |
TypeDict | get_param_types () const |
Get Analyzer parameter information in a dictionary. | |
Static Public Member Functions | |
Analyzer * | NEW () |
Static Public Attributes | |
const string | NAME = "pca" |
Protected Attributes | |
EMData * | mask |
int | nvec |
Private Attributes | |
float * | covmat |
int | ncov |
int | nimages |
float * | eigval |
Definition at line 45 of file analyzer_sparx.h.
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Definition at line 48 of file analyzer_sparx.h.
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main function for Analyzer, analyze input images and create output images
Implements EMAN::Analyzer. Definition at line 275 of file analyzer.cpp. References coveig(), covmat, eigval, eigvec, EMDeletePtr(), EMAN::EMData::get_data(), mask, ncov, rdata, reconstitute_image_mask(), EMAN::EMData::set_attr(), EMAN::EMData::set_size(), and status. 00276 { 00277 float *eigvec; 00278 int status = 0; 00279 // printf("start analyzing..., ncov = %d\n", ncov); 00280 eigval = (float*)calloc(ncov,sizeof(float)); 00281 eigvec = (float*)calloc(ncov*ncov,sizeof(float)); 00282 status = Util::coveig(ncov, covmat, eigval, eigvec); 00283 // for (int i=1; i<=nvec; i++) printf("eigval = %11.4e\n", 00284 // eigval[ncov-i]); 00285 00286 // pack eigenvectors into the return imagelist 00287 EMData *eigenimage = new EMData(); 00288 eigenimage->set_size(ncov,1,1); 00289 float *rdata = eigenimage->get_data(); 00290 for (int j = 1; j<= nvec; j++) { 00291 for (int i = 0; i < ncov; i++) rdata[i] = eigvec(i,ncov-j); 00292 00293 EMData* recons_eigvec = Util::reconstitute_image_mask(eigenimage,mask); 00294 recons_eigvec->set_attr( "eigval", eigval[j-1] ); 00295 images.push_back(recons_eigvec); 00296 } 00297 00298 free(eigvec); 00299 EMDeletePtr(eigenimage); 00300 00301 return images; 00302 }
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Get the Analyzer's description.
Implements EMAN::Analyzer. Definition at line 64 of file analyzer_sparx.h. 00065 { 00066 return "Principal component analysis"; 00067 }
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Get the Analyzer's name. Each Analyzer is identified by a unique name.
Implements EMAN::Analyzer. Definition at line 59 of file analyzer_sparx.h. 00060 {
00061 return NAME;
00062 }
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Get Analyzer parameter information in a dictionary. Each parameter has one record in the dictionary. Each record contains its name, data-type, and description.
Implements EMAN::Analyzer. Definition at line 83 of file analyzer_sparx.h. References EMAN::TypeDict::put(). 00084 { 00085 TypeDict d; 00086 d.put("mask", EMObject::EMDATA, "mask image"); 00087 d.put("nvec", EMObject::INT, "number of desired principal components"); 00088 return d; 00089 }
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insert a image to the list of input images
Implements EMAN::Analyzer. Definition at line 248 of file analyzer.cpp. References compress_image_mask(), covmat, EMDeletePtr(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), imgdata, mask, nimages, NullPointerException, and nx. 00249 { 00250 if(mask==0) 00251 throw NullPointerException("Null mask image pointer, set_params() first"); 00252 00253 EMData *maskedimage = Util::compress_image_mask(image,mask); 00254 00255 int nx = maskedimage->get_xsize(); 00256 float *imgdata = maskedimage->get_data(); 00257 if (nx != ncov) { 00258 fprintf(stderr,"insert_image: something is wrong...\n"); 00259 exit(1); 00260 } 00261 00262 // there is a faster version of the following rank-1 update 00263 nimages++; 00264 for (int j = 1; j <= nx; j++) 00265 for (int i = 1; i<=nx; i++) { 00266 covmat(i,j) += imgdata(i)*imgdata(j); 00267 } 00268 00269 EMDeletePtr(maskedimage); 00270 return 0; 00271 }
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Definition at line 69 of file analyzer_sparx.h. 00070 { 00071 return new PCAsmall(); 00072 }
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Set the Analyzer parameters using a key/value dictionary.
Reimplemented from EMAN::Analyzer. Definition at line 305 of file analyzer.cpp. References compress_image_mask(), covmat, EMDeletePtr(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), mask, ncov, nimages, nvec, nx, ny, and EMAN::EMData::set_size(). 00306 { 00307 params = new_params; 00308 mask = params["mask"]; 00309 nvec = params["nvec"]; 00310 00311 // count the number of pixels under the mask 00312 // (this is really ugly!!!) 00313 EMData *dummy = new EMData(); 00314 00315 int nx = mask->get_xsize(); 00316 int ny = mask->get_ysize(); 00317 int nz = mask->get_zsize(); 00318 00319 dummy->set_size(nx,ny,nz); 00320 00321 EMData *dummy1d = Util::compress_image_mask(dummy,mask); 00322 ncov = dummy1d->get_xsize(); 00323 EMDeletePtr(dummy); 00324 EMDeletePtr(dummy1d); 00325 00326 // allocate and set up the covriance matrix 00327 nimages = 0; 00328 covmat = (float*)calloc(ncov*ncov,sizeof(float)); 00329 }
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Definition at line 98 of file analyzer_sparx.h. Referenced by analyze(), insert_image(), and set_params(). |
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Definition at line 101 of file analyzer_sparx.h. Referenced by analyze(). |
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Definition at line 94 of file analyzer_sparx.h. Referenced by analyze(), insert_image(), and set_params(). |
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Definition at line 51 of file analyzer.cpp. |
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Definition at line 99 of file analyzer_sparx.h. Referenced by analyze(), and set_params(). |
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Definition at line 100 of file analyzer_sparx.h. Referenced by insert_image(), and set_params(). |
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Definition at line 95 of file analyzer_sparx.h. Referenced by set_params(). |