EMAN::PCAsmall Class Reference

Principal component analysis. More...

#include <analyzer_sparx.h>

Inheritance diagram for EMAN::PCAsmall:

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List of all members.

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

static Analyzer * NEW ()

Protected Attributes

EMData * mask
int nvec

Private Attributes

float * covmat
int ncov
int nimages
float * eigval

Detailed Description

Principal component analysis.

Definition at line 45 of file analyzer_sparx.h.

Constructor & Destructor Documentation

EMAN::PCAsmall::PCAsmall (  )  [inline]

Definition at line 48 of file analyzer_sparx.h.

Referenced by NEW().

00048 : mask(0), nvec(0) {}

Member Function Documentation

int PCAsmall::insert_image ( EMData *  image  )  [virtual]

insert a image to the list of input images

Parameters:
image 
Returns:
int 0 for success, <0 for fail

Implements EMAN::Analyzer.

Definition at line 251 of file analyzer.cpp.

References compress_image_mask(), covmat, EMDeletePtr(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), imgdata, mask, ncov, nimages, NullPointerException, and nx.

00252 {
00253         if(mask==0)
00254                 throw NullPointerException("Null mask image pointer, set_params() first");
00255 
00256    EMData *maskedimage = Util::compress_image_mask(image,mask);
00257 
00258    int nx = maskedimage->get_xsize();
00259    float *imgdata = maskedimage->get_data();
00260    if (nx != ncov) {
00261       fprintf(stderr,"insert_image: something is wrong...\n");
00262       exit(1);
00263    }
00264 
00265    // there is a faster version of the following rank-1 update
00266    nimages++;
00267    for (int j = 1; j <= nx; j++)
00268        for (int i = 1; i<=nx; i++) {
00269            covmat(i,j) += imgdata(i)*imgdata(j);
00270    }
00271 
00272    EMDeletePtr(maskedimage);
00273    return 0;
00274 }

vector< EMData * > PCAsmall::analyze (  )  [virtual]

main function for Analyzer, analyze input images and create output images

Returns:
vector<EMData *> result os images analysis

Implements EMAN::Analyzer.

Definition at line 278 of file analyzer.cpp.

References coveig(), covmat, eigval, eigvec, EMDeletePtr(), EMAN::EMData::get_data(), EMAN::Analyzer::images, mask, ncov, nvec, rdata, reconstitute_image_mask(), EMAN::EMData::set_attr(), EMAN::EMData::set_size(), and status.

00279 {
00280         float *eigvec;
00281         int status = 0;
00282 //              printf("start analyzing..., ncov = %d\n", ncov);
00283         eigval = (float*)calloc(ncov,sizeof(float));
00284         eigvec = (float*)calloc(ncov*ncov,sizeof(float));
00285         status = Util::coveig(ncov, covmat, eigval, eigvec);
00286 //       for (int i=1; i<=nvec; i++) printf("eigval = %11.4e\n",
00287 //            eigval[ncov-i]);
00288 
00289         // pack eigenvectors into the return imagelist
00290         EMData *eigenimage = new EMData();
00291         eigenimage->set_size(ncov,1,1);
00292         float *rdata = eigenimage->get_data();
00293         for (int j = 1; j<= nvec; j++) {
00294             for (int i = 0; i < ncov; i++) rdata[i] = eigvec(i,ncov-j);
00295 
00296                 EMData* recons_eigvec = Util::reconstitute_image_mask(eigenimage,mask);
00297                 recons_eigvec->set_attr( "eigval", eigval[j-1] );
00298             images.push_back(recons_eigvec);
00299         }
00300 
00301         free(eigvec);
00302         EMDeletePtr(eigenimage);
00303 
00304         return images;
00305 }

string EMAN::PCAsmall::get_name (  )  const [inline, virtual]

Get the Analyzer's name.

Each Analyzer is identified by a unique name.

Returns:
The Analyzer's name.

Implements EMAN::Analyzer.

Definition at line 59 of file analyzer_sparx.h.

00060                 {
00061                         return "pca";
00062                 }

string EMAN::PCAsmall::get_desc (  )  const [inline, virtual]

Get the Analyzer's description.

Returns:
The Analyzer's description.

Implements EMAN::Analyzer.

Definition at line 64 of file analyzer_sparx.h.

00065                 {
00066                         return "Principal component analysis";
00067                 }

static Analyzer* EMAN::PCAsmall::NEW (  )  [inline, static]

Definition at line 69 of file analyzer_sparx.h.

References PCAsmall().

Referenced by EMAN::Factory< T >::Factory().

00070                 {
00071                         return new PCAsmall();
00072                 }

void PCAsmall::set_params ( const Dict &  new_params  )  [virtual]

Set the Analyzer parameters using a key/value dictionary.

Parameters:
new_params A dictionary containing the new parameters.

Reimplemented from EMAN::Analyzer.

Definition at line 308 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, EMAN::Analyzer::params, and EMAN::EMData::set_size().

00309 {
00310         params = new_params;
00311         mask = params["mask"];
00312         nvec = params["nvec"];
00313 
00314         // count the number of pixels under the mask
00315         // (this is really ugly!!!)
00316         EMData *dummy = new EMData();
00317 
00318         int nx = mask->get_xsize();
00319         int ny = mask->get_ysize();
00320         int nz = mask->get_zsize();
00321 
00322         dummy->set_size(nx,ny,nz);
00323 
00324         EMData *dummy1d = Util::compress_image_mask(dummy,mask);
00325         ncov = dummy1d->get_xsize();
00326         EMDeletePtr(dummy);
00327         EMDeletePtr(dummy1d);
00328 
00329         // allocate and set up the covriance matrix
00330         nimages = 0;
00331         covmat = (float*)calloc(ncov*ncov,sizeof(float));
00332 }

TypeDict EMAN::PCAsmall::get_param_types (  )  const [inline, virtual]

Get Analyzer parameter information in a dictionary.

Each parameter has one record in the dictionary. Each record contains its name, data-type, and description.

Returns:
A dictionary containing the parameter info.

Implements EMAN::Analyzer.

Definition at line 83 of file analyzer_sparx.h.

References EMAN::EMObject::EMDATA, EMAN::EMObject::INT, and 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                 }

Member Data Documentation

EMData* EMAN::PCAsmall::mask [protected]

Definition at line 92 of file analyzer_sparx.h.

Referenced by analyze(), insert_image(), and set_params().

int EMAN::PCAsmall::nvec [protected]

Definition at line 93 of file analyzer_sparx.h.

Referenced by analyze(), and set_params().

float* EMAN::PCAsmall::covmat [private]

Definition at line 96 of file analyzer_sparx.h.

Referenced by analyze(), insert_image(), and set_params().

int EMAN::PCAsmall::ncov [private]

Definition at line 97 of file analyzer_sparx.h.

Referenced by analyze(), insert_image(), and set_params().

int EMAN::PCAsmall::nimages [private]

Definition at line 98 of file analyzer_sparx.h.

Referenced by insert_image(), and set_params().

float* EMAN::PCAsmall::eigval [private]

Definition at line 99 of file analyzer_sparx.h.

Referenced by analyze().

The documentation for this class was generated from the following files:
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