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.

Static Public Member Functions

static ProcessorNEW ()

Static Public Attributes

static const string NAME = "xform"

Private Member Functions

float * transform (const EMData *const image, const Transform &t) const
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 1466 of file processor.h.


Member Function Documentation

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

Definition at line 8463 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().

08463                                                                             {
08464         int ndim = image->get_ndim();
08465         if (ndim != 2 && ndim != 3) throw ImageDimensionException("Transforming an EMData only works if it's 2D or 3D");
08466 
08467         if (! params.has_key("transform") ) throw InvalidParameterException("You must specify a Transform in order to perform this operation");
08468 }

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 1497 of file processor.h.

01498                         {
01499                                 return "The image is transformed using Transform parameter.";
01500                         }

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 1469 of file processor.h.

References NAME.

01470                         {
01471                                 return NAME;
01472                         }

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 1490 of file processor.h.

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

01491                         {
01492                                 TypeDict d;
01493                                 d.put("transform", EMObject::TRANSFORM, "The Transform object that will be applied to the image" );
01494                                 return d;
01495                         }

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

Definition at line 1473 of file processor.h.

01474                         {
01475                                 return new TransformProcessor();
01476                         }

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 8502 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().

08502                                                              {
08503         ENTERFUNC;
08504 
08505         assert_valid_aspect(image);
08506 
08507         Transform* t = params["transform"];
08508 
08509         EMData* p  = 0;
08510 #ifdef EMAN2_USING_CUDA
08511         if(EMData::usecuda == 1 && image->isrodataongpu()){     
08512                 //cout << "using CUDA xform" << endl;
08513                 p = new EMData(0,0,image->get_xsize(),image->get_ysize(),image->get_zsize(),image->get_attr_dict()); 
08514                 float * m = new float[12];
08515                 Transform inv = t->inverse();
08516                 inv.copy_matrix_into_array(m);
08517                 image->bindcudaarrayA(true);
08518                 p->runcuda(emdata_transform_cuda(m,image->get_xsize(),image->get_ysize(),image->get_zsize()));
08519                 image->unbindcudaarryA();
08520                 delete [] m;
08521                 p->update();
08522         }
08523 #endif
08524 
08525         if ( p == 0 ) {
08526                 float* des_data = transform(image,*t);
08527                 p = new EMData(des_data,image->get_xsize(),image->get_ysize(),image->get_zsize(),image->get_attr_dict());
08528         }
08529 
08530         //      all_translation += transform.get_trans();
08531 
08532         float scale = t->get_scale();
08533         if (scale != 1.0) {
08534                 p->scale_pixel(1.0f/scale);
08535 //              update_emdata_attributes(p,image->get_attr_dict(),scale);
08536         }
08537 
08538         if(t) {delete t; t=0;}
08539         EXITFUNC;
08540         return p;
08541 }

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 8543 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().

08543                                                       {
08544         ENTERFUNC;
08545 
08546         assert_valid_aspect(image);
08547 
08548         Transform* t = params["transform"];
08549 
08550         //      all_translation += transform.get_trans();
08551         bool use_cpu = true;
08552         
08553 #ifdef EMAN2_USING_CUDA
08554         if(EMData::usecuda == 1 && image->isrodataongpu()){
08555                 //cout << "CUDA xform inplace" << endl;
08556                 image->bindcudaarrayA(false);   
08557                 float * m = new float[12];
08558                 Transform inv = t->inverse();
08559                 inv.copy_matrix_into_array(m);  
08560                 image->runcuda(emdata_transform_cuda(m,image->get_xsize(),image->get_ysize(),image->get_zsize()));
08561                 image->unbindcudaarryA();
08562                 delete [] m;
08563                 use_cpu = false;
08564                 image->update();
08565         }
08566 #endif
08567         if ( use_cpu ) {
08568                 float* des_data = transform(image,*t);
08569                 image->set_data(des_data,image->get_xsize(),image->get_ysize(),image->get_zsize());
08570                 image->update();
08571         }
08572         float scale = t->get_scale();
08573         if (scale != 1.0f) {
08574                 image->scale_pixel(1.0f/scale);
08575 //              update_emdata_attributes(image,image->get_attr_dict(),scale);
08576         }
08577 
08578         if(t) {delete t; t=0;}
08579 
08580         EXITFUNC;
08581 }

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

Definition at line 8341 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().

08341                                                                                         {
08342 
08343         ENTERFUNC;
08344 
08345         Transform inv = t.inverse();
08346         int nx = image->get_xsize();
08347         int ny = image->get_ysize();
08348         int nz = image->get_zsize();
08349         int nxy = nx*ny;
08350 
08351         const float * const src_data = image->get_const_data();
08352         float *des_data = (float *) EMUtil::em_malloc(nx*ny*nz* sizeof(float));
08353 
08354         if (nz == 1) {
08355                 Vec2f offset(nx/2,ny/2);
08356                 for (int j = 0; j < ny; j++) {
08357                         for (int i = 0; i < nx; i++) {
08358                                 Vec2f coord(i-nx/2,j-ny/2);
08359                                 Vec2f soln = inv*coord;
08360                                 soln += offset;
08361 
08362                                 float x2 = soln[0];
08363                                 float y2 = soln[1];
08364 
08365                                 if (x2 < 0 || x2 >= nx || y2 < 0 || y2 >= ny ) {
08366                                         des_data[i + j * nx] = 0; // It may be tempting to set this value to the
08367                                         // mean but in fact this is not a good thing to do. Talk to S.Ludtke about it.
08368                                 }
08369                                 else {
08370                                         int ii = Util::fast_floor(x2);
08371                                         int jj = Util::fast_floor(y2);
08372                                         int k0 = ii + jj * nx;
08373                                         int k1 = k0 + 1;
08374                                         int k2 = k0 + nx;
08375                                         int k3 = k0 + nx + 1;
08376 
08377                                         if (ii == nx - 1) {
08378                                                 k1--;
08379                                                 k3--;
08380                                         }
08381                                         if (jj == ny - 1) {
08382                                                 k2 -= nx;
08383                                                 k3 -= nx;
08384                                         }
08385 
08386                                         float t = x2 - ii;
08387                                         float u = y2 - jj;
08388 
08389                                         des_data[i + j * nx] = Util::bilinear_interpolate(src_data[k0],src_data[k1], src_data[k2], src_data[k3],t,u);
08390                                 }
08391                         }
08392                 }
08393         }
08394         else {
08395                 size_t l=0, ii, k0, k1, k2, k3, k4, k5, k6, k7;
08396                 Vec3f offset(nx/2,ny/2,nz/2);
08397                 float x2, y2, z2, tuvx, tuvy, tuvz;
08398                 int ix, iy, iz;
08399                 for (int k = 0; k < nz; ++k) {
08400                         for (int j = 0; j < ny; ++j) {
08401                                 for (int i = 0; i < nx; ++i,++l) {
08402                                         Vec3f coord(i-nx/2,j-ny/2,k-nz/2);
08403                                         Vec3f soln = inv*coord;
08404                                         soln += offset;
08405 
08406                                         x2 = soln[0];
08407                                         y2 = soln[1];
08408                                         z2 = soln[2];
08409 
08410                                         if (x2 < 0 || y2 < 0 || z2 < 0 || x2 >= nx  || y2 >= ny  || z2>= nz ) {
08411                                                 des_data[l] = 0;
08412                                         }
08413                                         else {
08414                                                 ix = Util::fast_floor(x2);
08415                                                 iy = Util::fast_floor(y2);
08416                                                 iz = Util::fast_floor(z2);
08417                                                 tuvx = x2-ix;
08418                                                 tuvy = y2-iy;
08419                                                 tuvz = z2-iz;
08420                                                 ii = ix + iy * nx + iz * nxy;
08421 
08422                                                 k0 = ii;
08423                                                 k1 = k0 + 1;
08424                                                 k2 = k0 + nx;
08425                                                 k3 = k0 + nx+1;
08426                                                 k4 = k0 + nxy;
08427                                                 k5 = k1 + nxy;
08428                                                 k6 = k2 + nxy;
08429                                                 k7 = k3 + nxy;
08430 
08431                                                 if (ix == nx - 1) {
08432                                                         k1--;
08433                                                         k3--;
08434                                                         k5--;
08435                                                         k7--;
08436                                                 }
08437                                                 if (iy == ny - 1) {
08438                                                         k2 -= nx;
08439                                                         k3 -= nx;
08440                                                         k6 -= nx;
08441                                                         k7 -= nx;
08442                                                 }
08443                                                 if (iz == nz - 1) {
08444                                                         k4 -= nxy;
08445                                                         k5 -= nxy;
08446                                                         k6 -= nxy;
08447                                                         k7 -= nxy;
08448                                                 }
08449 
08450                                                 des_data[l] = Util::trilinear_interpolate(src_data[k0],
08451                                                                 src_data[k1], src_data[k2], src_data[k3], src_data[k4],
08452                                                                 src_data[k5], src_data[k6],     src_data[k7], tuvx, tuvy, tuvz);
08453                                         }
08454                                 }
08455                         }
08456                 }
08457         }
08458 
08459         EXITFUNC;
08460         return des_data;
08461 }


Member Data Documentation

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

Definition at line 1502 of file processor.h.

Referenced by get_name().


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