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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)
virtual EMDataprocess (const EMData *const image)
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

ProcessorNEW ()

Static Public Attributes

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 8550 of file processor.cpp.

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

Referenced by process(), and process_inplace().

08550                                                                             {
08551         int ndim = image->get_ndim();
08552         if (ndim != 2 && ndim != 3) throw ImageDimensionException("Transforming an EMData only works if it's 2D or 3D");
08553 
08554         if (! params.has_key("transform") ) throw InvalidParameterException("You must specify a Transform in order to perform this operation");
08555 }

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.

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().

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

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 8589 of file processor.cpp.

References assert_valid_aspect(), EMAN::Transform::copy_matrix_into_array(), emdata_transform_cuda(), EMAN::EMData::get_attr_dict(), EMAN::Transform::get_scale(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Transform::inverse(), EMAN::EMData::scale_pixel(), t, transform(), and EMAN::EMData::update().

08589                                                              {
08590         ENTERFUNC;
08591 
08592         assert_valid_aspect(image);
08593 
08594         Transform* t = params["transform"];
08595 
08596         EMData* p  = 0;
08597 #ifdef EMAN2_USING_CUDA
08598         if(EMData::usecuda == 1 && image->isrodataongpu()){     
08599                 //cout << "using CUDA xform" << endl;
08600                 p = new EMData(0,0,image->get_xsize(),image->get_ysize(),image->get_zsize(),image->get_attr_dict()); 
08601                 float * m = new float[12];
08602                 Transform inv = t->inverse();
08603                 inv.copy_matrix_into_array(m);
08604                 image->bindcudaarrayA(true);
08605                 p->runcuda(emdata_transform_cuda(m,image->get_xsize(),image->get_ysize(),image->get_zsize()));
08606                 image->unbindcudaarryA();
08607                 delete [] m;
08608                 p->update();
08609         }
08610 #endif
08611 
08612         if ( p == 0 ) {
08613                 float* des_data = transform(image,*t);
08614                 p = new EMData(des_data,image->get_xsize(),image->get_ysize(),image->get_zsize(),image->get_attr_dict());
08615         }
08616 
08617         //      all_translation += transform.get_trans();
08618 
08619         float scale = t->get_scale();
08620         if (scale != 1.0) {
08621                 p->scale_pixel(1.0f/scale);
08622 //              update_emdata_attributes(p,image->get_attr_dict(),scale);
08623         }
08624 
08625         if(t) {delete t; t=0;}
08626         EXITFUNC;
08627         return p;
08628 }

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 8630 of file processor.cpp.

References assert_valid_aspect(), EMAN::Transform::copy_matrix_into_array(), emdata_transform_cuda(), EMAN::Transform::get_scale(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Transform::inverse(), EMAN::EMData::scale_pixel(), EMAN::EMData::set_data(), t, transform(), and EMAN::EMData::update().

08630                                                       {
08631         ENTERFUNC;
08632 
08633         assert_valid_aspect(image);
08634 
08635         Transform* t = params["transform"];
08636 
08637         //      all_translation += transform.get_trans();
08638         bool use_cpu = true;
08639         
08640 #ifdef EMAN2_USING_CUDA
08641         if(EMData::usecuda == 1 && image->isrodataongpu()){
08642                 //cout << "CUDA xform inplace" << endl;
08643                 image->bindcudaarrayA(false);   
08644                 float * m = new float[12];
08645                 Transform inv = t->inverse();
08646                 inv.copy_matrix_into_array(m);  
08647                 image->runcuda(emdata_transform_cuda(m,image->get_xsize(),image->get_ysize(),image->get_zsize()));
08648                 image->unbindcudaarryA();
08649                 delete [] m;
08650                 use_cpu = false;
08651                 image->update();
08652         }
08653 #endif
08654         if ( use_cpu ) {
08655                 float* des_data = transform(image,*t);
08656                 image->set_data(des_data,image->get_xsize(),image->get_ysize(),image->get_zsize());
08657                 image->update();
08658         }
08659         float scale = t->get_scale();
08660         if (scale != 1.0f) {
08661                 image->scale_pixel(1.0f/scale);
08662 //              update_emdata_attributes(image,image->get_attr_dict(),scale);
08663         }
08664 
08665         if(t) {delete t; t=0;}
08666 
08667         EXITFUNC;
08668 }

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

Definition at line 8428 of file processor.cpp.

References EMAN::Util::bilinear_interpolate(), EMAN::EMUtil::em_malloc(), EMAN::Util::fast_floor(), EMAN::EMData::get_const_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Transform::inverse(), nx, ny, t, EMAN::Util::trilinear_interpolate(), EMAN::Vec2f, and EMAN::Vec3f.

Referenced by EMAN::ScaleAligner::align(), EMAN::ScaleAlignerABS::align_using_base(), process(), and process_inplace().

08428                                                                                         {
08429 
08430         ENTERFUNC;
08431 
08432         Transform inv = t.inverse();
08433         int nx = image->get_xsize();
08434         int ny = image->get_ysize();
08435         int nz = image->get_zsize();
08436         int nxy = nx*ny;
08437 
08438         const float * const src_data = image->get_const_data();
08439         float *des_data = (float *) EMUtil::em_malloc(nx*ny*nz* sizeof(float));
08440 
08441         if (nz == 1) {
08442                 Vec2f offset(nx/2,ny/2);
08443                 for (int j = 0; j < ny; j++) {
08444                         for (int i = 0; i < nx; i++) {
08445                                 Vec2f coord(i-nx/2,j-ny/2);
08446                                 Vec2f soln = inv*coord;
08447                                 soln += offset;
08448 
08449                                 float x2 = soln[0];
08450                                 float y2 = soln[1];
08451 
08452                                 if (x2 < 0 || x2 >= nx || y2 < 0 || y2 >= ny ) {
08453                                         des_data[i + j * nx] = 0; // It may be tempting to set this value to the
08454                                         // mean but in fact this is not a good thing to do. Talk to S.Ludtke about it.
08455                                 }
08456                                 else {
08457                                         int ii = Util::fast_floor(x2);
08458                                         int jj = Util::fast_floor(y2);
08459                                         int k0 = ii + jj * nx;
08460                                         int k1 = k0 + 1;
08461                                         int k2 = k0 + nx;
08462                                         int k3 = k0 + nx + 1;
08463 
08464                                         if (ii == nx - 1) {
08465                                                 k1--;
08466                                                 k3--;
08467                                         }
08468                                         if (jj == ny - 1) {
08469                                                 k2 -= nx;
08470                                                 k3 -= nx;
08471                                         }
08472 
08473                                         float t = x2 - ii;
08474                                         float u = y2 - jj;
08475 
08476                                         des_data[i + j * nx] = Util::bilinear_interpolate(src_data[k0],src_data[k1], src_data[k2], src_data[k3],t,u);
08477                                 }
08478                         }
08479                 }
08480         }
08481         else {
08482                 size_t l=0, ii, k0, k1, k2, k3, k4, k5, k6, k7;
08483                 Vec3f offset(nx/2,ny/2,nz/2);
08484                 float x2, y2, z2, tuvx, tuvy, tuvz;
08485                 int ix, iy, iz;
08486                 for (int k = 0; k < nz; ++k) {
08487                         for (int j = 0; j < ny; ++j) {
08488                                 for (int i = 0; i < nx; ++i,++l) {
08489                                         Vec3f coord(i-nx/2,j-ny/2,k-nz/2);
08490                                         Vec3f soln = inv*coord;
08491                                         soln += offset;
08492 
08493                                         x2 = soln[0];
08494                                         y2 = soln[1];
08495                                         z2 = soln[2];
08496 
08497                                         if (x2 < 0 || y2 < 0 || z2 < 0 || x2 >= nx  || y2 >= ny  || z2>= nz ) {
08498                                                 des_data[l] = 0;
08499                                         }
08500                                         else {
08501                                                 ix = Util::fast_floor(x2);
08502                                                 iy = Util::fast_floor(y2);
08503                                                 iz = Util::fast_floor(z2);
08504                                                 tuvx = x2-ix;
08505                                                 tuvy = y2-iy;
08506                                                 tuvz = z2-iz;
08507                                                 ii = ix + iy * nx + iz * nxy;
08508 
08509                                                 k0 = ii;
08510                                                 k1 = k0 + 1;
08511                                                 k2 = k0 + nx;
08512                                                 k3 = k0 + nx+1;
08513                                                 k4 = k0 + nxy;
08514                                                 k5 = k1 + nxy;
08515                                                 k6 = k2 + nxy;
08516                                                 k7 = k3 + nxy;
08517 
08518                                                 if (ix == nx - 1) {
08519                                                         k1--;
08520                                                         k3--;
08521                                                         k5--;
08522                                                         k7--;
08523                                                 }
08524                                                 if (iy == ny - 1) {
08525                                                         k2 -= nx;
08526                                                         k3 -= nx;
08527                                                         k6 -= nx;
08528                                                         k7 -= nx;
08529                                                 }
08530                                                 if (iz == nz - 1) {
08531                                                         k4 -= nxy;
08532                                                         k5 -= nxy;
08533                                                         k6 -= nxy;
08534                                                         k7 -= nxy;
08535                                                 }
08536 
08537                                                 des_data[l] = Util::trilinear_interpolate(src_data[k0],
08538                                                                 src_data[k1], src_data[k2], src_data[k3], src_data[k4],
08539                                                                 src_data[k5], src_data[k6],     src_data[k7], tuvx, tuvy, tuvz);
08540                                         }
08541                                 }
08542                         }
08543                 }
08544         }
08545 
08546         EXITFUNC;
08547         return des_data;
08548 }


Member Data Documentation

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

Definition at line 86 of file processor.cpp.


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