EMAN::TransformProcessor Class Reference
[a function or class that is CUDA enabled]

Transform the image using a Transform object. More...

#include <processor.h>

Inheritance diagram for EMAN::TransformProcessor:

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Collaboration diagram for EMAN::TransformProcessor:

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List of all members.

Public Member Functions

virtual string get_name () const
 Get the processor's name.
virtual void process_inplace (EMData *image)
 
Exceptions:
ImageDimensionException if the image is not 2D or 3D
InvalidParameterException if the Transform parameter is not specified

virtual EMDataprocess (const EMData *const image)
 
Exceptions:
ImageDimensionException if the image is not 2D or 3D
InvalidParameterException if the Transform parameter is not specified

virtual TypeDict get_param_types () const
 Get processor parameter information in a dictionary.
virtual string get_desc () const
 Get the descrition of this specific processor.
float * transform (const EMData *const image, const Transform &t) const

Static Public Member Functions

static ProcessorNEW ()

Static Public Attributes

static const string NAME = "xform"

Private Member Functions

void assert_valid_aspect (const EMData *const image) const

Detailed Description

Transform the image using a Transform object.

Author:
David Woolford
Date:
September 2008
Parameters:
transform The Transform object that will be applied to the image

Definition at line 1511 of file processor.h.


Member Function Documentation

void TransformProcessor::assert_valid_aspect ( const EMData *const   image  )  const [private]

Definition at line 8535 of file processor.cpp.

References EMAN::EMData::get_ndim(), EMAN::Dict::has_key(), ImageDimensionException, InvalidParameterException, and EMAN::Processor::params.

Referenced by process(), and process_inplace().

08535                                                                             {
08536         int ndim = image->get_ndim();
08537         if (ndim != 2 && ndim != 3) throw ImageDimensionException("Transforming an EMData only works if it's 2D or 3D");
08538 
08539         if (! params.has_key("transform") ) throw InvalidParameterException("You must specify a Transform in order to perform this operation");
08540 }

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

Get the descrition of this specific processor.

This function must be overwritten by a subclass.

Returns:
The description of this processor.

Implements EMAN::Processor.

Definition at line 1542 of file processor.h.

01543                         {
01544                                 return "The image is transformed using Transform parameter.";
01545                         }

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

Get the processor's name.

Each processor is identified by a unique name.

Returns:
The processor's name.

Implements EMAN::Processor.

Definition at line 1514 of file processor.h.

References NAME.

01515                         {
01516                                 return NAME;
01517                         }

virtual TypeDict EMAN::TransformProcessor::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.

Returns:
A dictionary containing the parameter info.

Reimplemented from EMAN::Processor.

Definition at line 1535 of file processor.h.

References EMAN::TypeDict::put(), and EMAN::EMObject::TRANSFORM.

01536                         {
01537                                 TypeDict d;
01538                                 d.put("transform", EMObject::TRANSFORM, "The Transform object that will be applied to the image" );
01539                                 return d;
01540                         }

static Processor* EMAN::TransformProcessor::NEW (  )  [inline, static]

Definition at line 1518 of file processor.h.

01519                         {
01520                                 return new TransformProcessor();
01521                         }

EMData * TransformProcessor::process ( const EMData *const   image  )  [virtual]

Exceptions:
ImageDimensionException if the image is not 2D or 3D
InvalidParameterException if the Transform parameter is not specified

Reimplemented from EMAN::Processor.

Definition at line 8574 of file processor.cpp.

References assert_valid_aspect(), EMAN::Transform::copy_matrix_into_array(), emdata_transform_cuda(), ENTERFUNC, EXITFUNC, EMAN::EMData::get_attr_dict(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Processor::params, EMAN::EMData::scale_pixel(), t, transform(), and EMAN::EMData::update().

08574                                                              {
08575         ENTERFUNC;
08576 
08577         assert_valid_aspect(image);
08578 
08579         Transform* t = params["transform"];
08580 
08581         EMData* p  = 0;
08582 #ifdef EMAN2_USING_CUDA
08583         if(EMData::usecuda == 1 && image->isrodataongpu()){     
08584                 //cout << "using CUDA xform" << endl;
08585                 p = new EMData(0,0,image->get_xsize(),image->get_ysize(),image->get_zsize(),image->get_attr_dict()); 
08586                 float * m = new float[12];
08587                 Transform inv = t->inverse();
08588                 inv.copy_matrix_into_array(m);
08589                 image->bindcudaarrayA(true);
08590                 p->runcuda(emdata_transform_cuda(m,image->get_xsize(),image->get_ysize(),image->get_zsize()));
08591                 image->unbindcudaarryA();
08592                 delete [] m;
08593                 p->update();
08594         }
08595 #endif
08596 
08597         if ( p == 0 ) {
08598                 float* des_data = transform(image,*t);
08599                 p = new EMData(des_data,image->get_xsize(),image->get_ysize(),image->get_zsize(),image->get_attr_dict());
08600         }
08601 
08602         //      all_translation += transform.get_trans();
08603 
08604         float scale = t->get_scale();
08605         if (scale != 1.0) {
08606                 p->scale_pixel(1.0f/scale);
08607 //              update_emdata_attributes(p,image->get_attr_dict(),scale);
08608         }
08609 
08610         if(t) {delete t; t=0;}
08611         EXITFUNC;
08612         return p;
08613 }

void TransformProcessor::process_inplace ( EMData image  )  [virtual]

Exceptions:
ImageDimensionException if the image is not 2D or 3D
InvalidParameterException if the Transform parameter is not specified

Implements EMAN::Processor.

Definition at line 8615 of file processor.cpp.

References assert_valid_aspect(), EMAN::Transform::copy_matrix_into_array(), emdata_transform_cuda(), ENTERFUNC, EXITFUNC, EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Processor::params, EMAN::EMData::scale_pixel(), EMAN::EMData::set_data(), t, transform(), and EMAN::EMData::update().

08615                                                       {
08616         ENTERFUNC;
08617 
08618         assert_valid_aspect(image);
08619 
08620         Transform* t = params["transform"];
08621 
08622         //      all_translation += transform.get_trans();
08623         bool use_cpu = true;
08624         
08625 #ifdef EMAN2_USING_CUDA
08626         if(EMData::usecuda == 1 && image->isrodataongpu()){
08627                 //cout << "CUDA xform inplace" << endl;
08628                 image->bindcudaarrayA(false);   
08629                 float * m = new float[12];
08630                 Transform inv = t->inverse();
08631                 inv.copy_matrix_into_array(m);  
08632                 image->runcuda(emdata_transform_cuda(m,image->get_xsize(),image->get_ysize(),image->get_zsize()));
08633                 image->unbindcudaarryA();
08634                 delete [] m;
08635                 use_cpu = false;
08636                 image->update();
08637         }
08638 #endif
08639         if ( use_cpu ) {
08640                 float* des_data = transform(image,*t);
08641                 image->set_data(des_data,image->get_xsize(),image->get_ysize(),image->get_zsize());
08642                 image->update();
08643         }
08644         float scale = t->get_scale();
08645         if (scale != 1.0f) {
08646                 image->scale_pixel(1.0f/scale);
08647 //              update_emdata_attributes(image,image->get_attr_dict(),scale);
08648         }
08649 
08650         if(t) {delete t; t=0;}
08651 
08652         EXITFUNC;
08653 }

float * TransformProcessor::transform ( const EMData *const   image,
const Transform t 
) const

Definition at line 8413 of file processor.cpp.

References EMAN::Util::bilinear_interpolate(), EMAN::EMUtil::em_malloc(), ENTERFUNC, EXITFUNC, EMAN::Util::fast_floor(), EMAN::EMData::get_const_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), t, and EMAN::Util::trilinear_interpolate().

Referenced by process(), and process_inplace().

08413                                                                                         {
08414 
08415         ENTERFUNC;
08416 
08417         Transform inv = t.inverse();
08418         int nx = image->get_xsize();
08419         int ny = image->get_ysize();
08420         int nz = image->get_zsize();
08421         int nxy = nx*ny;
08422 
08423         const float * const src_data = image->get_const_data();
08424         float *des_data = (float *) EMUtil::em_malloc(nx*ny*nz* sizeof(float));
08425 
08426         if (nz == 1) {
08427                 Vec2f offset(nx/2,ny/2);
08428                 for (int j = 0; j < ny; j++) {
08429                         for (int i = 0; i < nx; i++) {
08430                                 Vec2f coord(i-nx/2,j-ny/2);
08431                                 Vec2f soln = inv*coord;
08432                                 soln += offset;
08433 
08434                                 float x2 = soln[0];
08435                                 float y2 = soln[1];
08436 
08437                                 if (x2 < 0 || x2 >= nx || y2 < 0 || y2 >= ny ) {
08438                                         des_data[i + j * nx] = 0; // It may be tempting to set this value to the
08439                                         // mean but in fact this is not a good thing to do. Talk to S.Ludtke about it.
08440                                 }
08441                                 else {
08442                                         int ii = Util::fast_floor(x2);
08443                                         int jj = Util::fast_floor(y2);
08444                                         int k0 = ii + jj * nx;
08445                                         int k1 = k0 + 1;
08446                                         int k2 = k0 + nx;
08447                                         int k3 = k0 + nx + 1;
08448 
08449                                         if (ii == nx - 1) {
08450                                                 k1--;
08451                                                 k3--;
08452                                         }
08453                                         if (jj == ny - 1) {
08454                                                 k2 -= nx;
08455                                                 k3 -= nx;
08456                                         }
08457 
08458                                         float t = x2 - ii;
08459                                         float u = y2 - jj;
08460 
08461                                         des_data[i + j * nx] = Util::bilinear_interpolate(src_data[k0],src_data[k1], src_data[k2], src_data[k3],t,u);
08462                                 }
08463                         }
08464                 }
08465         }
08466         else {
08467                 size_t l=0, ii, k0, k1, k2, k3, k4, k5, k6, k7;
08468                 Vec3f offset(nx/2,ny/2,nz/2);
08469                 float x2, y2, z2, tuvx, tuvy, tuvz;
08470                 int ix, iy, iz;
08471                 for (int k = 0; k < nz; ++k) {
08472                         for (int j = 0; j < ny; ++j) {
08473                                 for (int i = 0; i < nx; ++i,++l) {
08474                                         Vec3f coord(i-nx/2,j-ny/2,k-nz/2);
08475                                         Vec3f soln = inv*coord;
08476                                         soln += offset;
08477 
08478                                         x2 = soln[0];
08479                                         y2 = soln[1];
08480                                         z2 = soln[2];
08481 
08482                                         if (x2 < 0 || y2 < 0 || z2 < 0 || x2 >= nx  || y2 >= ny  || z2>= nz ) {
08483                                                 des_data[l] = 0;
08484                                         }
08485                                         else {
08486                                                 ix = Util::fast_floor(x2);
08487                                                 iy = Util::fast_floor(y2);
08488                                                 iz = Util::fast_floor(z2);
08489                                                 tuvx = x2-ix;
08490                                                 tuvy = y2-iy;
08491                                                 tuvz = z2-iz;
08492                                                 ii = ix + iy * nx + iz * nxy;
08493 
08494                                                 k0 = ii;
08495                                                 k1 = k0 + 1;
08496                                                 k2 = k0 + nx;
08497                                                 k3 = k0 + nx+1;
08498                                                 k4 = k0 + nxy;
08499                                                 k5 = k1 + nxy;
08500                                                 k6 = k2 + nxy;
08501                                                 k7 = k3 + nxy;
08502 
08503                                                 if (ix == nx - 1) {
08504                                                         k1--;
08505                                                         k3--;
08506                                                         k5--;
08507                                                         k7--;
08508                                                 }
08509                                                 if (iy == ny - 1) {
08510                                                         k2 -= nx;
08511                                                         k3 -= nx;
08512                                                         k6 -= nx;
08513                                                         k7 -= nx;
08514                                                 }
08515                                                 if (iz == nz - 1) {
08516                                                         k4 -= nxy;
08517                                                         k5 -= nxy;
08518                                                         k6 -= nxy;
08519                                                         k7 -= nxy;
08520                                                 }
08521 
08522                                                 des_data[l] = Util::trilinear_interpolate(src_data[k0],
08523                                                                 src_data[k1], src_data[k2], src_data[k3], src_data[k4],
08524                                                                 src_data[k5], src_data[k6],     src_data[k7], tuvx, tuvy, tuvz);
08525                                         }
08526                                 }
08527                         }
08528                 }
08529         }
08530 
08531         EXITFUNC;
08532         return des_data;
08533 }


Member Data Documentation

const string TransformProcessor::NAME = "xform" [static]

Definition at line 1547 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Thu May 3 10:09:48 2012 for EMAN2 by  doxygen 1.4.7