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:

Inheritance graph
[legend]
Collaboration diagram for EMAN::TransformProcessor:

Collaboration graph
[legend]
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 1316 of file processor.h.


Member Function Documentation

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

Definition at line 8352 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().

08352                                                                             {
08353         int ndim = image->get_ndim();
08354         if (ndim != 2 && ndim != 3) throw ImageDimensionException("Transforming an EMData only works if it's 2D or 3D");
08355 
08356         if (! params.has_key("transform") ) throw InvalidParameterException("You must specify a Transform in order to perform this operation");
08357 }

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 1347 of file processor.h.

01348                         {
01349                                 return "The image is transformed using Transform parameter.";
01350                         }

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 1319 of file processor.h.

References NAME.

01320                         {
01321                                 return NAME;
01322                         }

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 1340 of file processor.h.

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

01341                         {
01342                                 TypeDict d;
01343                                 d.put("transform", EMObject::TRANSFORM, "The Transform object that will be applied to the image" );
01344                                 return d;
01345                         }

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

Definition at line 1323 of file processor.h.

01324                         {
01325                                 return new TransformProcessor();
01326                         }

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 8391 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, and transform().

08391                                                              {
08392         ENTERFUNC;
08393 
08394         assert_valid_aspect(image);
08395 
08396         Transform* t = params["transform"];
08397 
08398         EMData* p  = 0;
08399 #ifdef EMAN2_USING_CUDA
08400         if(image->isrodataongpu()){     
08401                 //cout << "using CUDA xform" << endl;
08402                 p = new EMData(0,0,image->get_xsize(),image->get_ysize(),image->get_zsize()); 
08403                 float * m = new float[12];
08404                 Transform inv = t->inverse();
08405                 inv.copy_matrix_into_array(m);
08406                 image->bindcudaarrayA(true);
08407                 p->runcuda(emdata_transform_cuda(m,image->get_xsize(),image->get_ysize(),image->get_zsize()));
08408                 image->unbindcudaarryA();
08409                 delete [] m;
08410         }
08411 #endif
08412 
08413         if ( p == 0 ) {
08414                 float* des_data = transform(image,*t);
08415                 p = new EMData(des_data,image->get_xsize(),image->get_ysize(),image->get_zsize(),image->get_attr_dict());
08416         }
08417 
08418         //      all_translation += transform.get_trans();
08419 
08420         float scale = t->get_scale();
08421         if (scale != 1.0) {
08422                 p->scale_pixel(1.0f/scale);
08423 //              update_emdata_attributes(p,image->get_attr_dict(),scale);
08424         }
08425 
08426         if(t) {delete t; t=0;}
08427         EXITFUNC;
08428         return p;
08429 }

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 8431 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().

08431                                                       {
08432         ENTERFUNC;
08433 
08434         assert_valid_aspect(image);
08435 
08436         Transform* t = params["transform"];
08437 
08438         //      all_translation += transform.get_trans();
08439         bool use_cpu = true;
08440         
08441 #ifdef EMAN2_USING_CUDA
08442         if(image->isrodataongpu()){
08443                 image->bindcudaarrayA(false);   
08444                 float * m = new float[12];
08445                 Transform inv = t->inverse();
08446                 inv.copy_matrix_into_array(m);  
08447                 image->runcuda(emdata_transform_cuda(m,image->get_xsize(),image->get_ysize(),image->get_zsize()));
08448                 image->unbindcudaarryA();
08449                 delete [] m;
08450                 use_cpu = false;
08451         }
08452 #endif
08453         if ( use_cpu ) {
08454                 float* des_data = transform(image,*t);
08455                 image->set_data(des_data,image->get_xsize(),image->get_ysize(),image->get_zsize());
08456                 image->update();
08457         }
08458         float scale = t->get_scale();
08459         if (scale != 1.0f) {
08460                 image->scale_pixel(1.0f/scale);
08461 //              update_emdata_attributes(image,image->get_attr_dict(),scale);
08462         }
08463 
08464         if(t) {delete t; t=0;}
08465 
08466         EXITFUNC;
08467 }

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

Definition at line 8230 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().

08230                                                                                         {
08231 
08232         ENTERFUNC;
08233 
08234         Transform inv = t.inverse();
08235         int nx = image->get_xsize();
08236         int ny = image->get_ysize();
08237         int nz = image->get_zsize();
08238         int nxy = nx*ny;
08239 
08240         const float * const src_data = image->get_const_data();
08241         float *des_data = (float *) EMUtil::em_malloc(nx*ny*nz* sizeof(float));
08242 
08243         if (nz == 1) {
08244                 Vec2f offset(nx/2,ny/2);
08245                 for (int j = 0; j < ny; j++) {
08246                         for (int i = 0; i < nx; i++) {
08247                                 Vec2f coord(i-nx/2,j-ny/2);
08248                                 Vec2f soln = inv*coord;
08249                                 soln += offset;
08250 
08251                                 float x2 = soln[0];
08252                                 float y2 = soln[1];
08253 
08254                                 if (x2 < 0 || x2 >= nx || y2 < 0 || y2 >= ny ) {
08255                                         des_data[i + j * nx] = 0; // It may be tempting to set this value to the
08256                                         // mean but in fact this is not a good thing to do. Talk to S.Ludtke about it.
08257                                 }
08258                                 else {
08259                                         int ii = Util::fast_floor(x2);
08260                                         int jj = Util::fast_floor(y2);
08261                                         int k0 = ii + jj * nx;
08262                                         int k1 = k0 + 1;
08263                                         int k2 = k0 + nx;
08264                                         int k3 = k0 + nx + 1;
08265 
08266                                         if (ii == nx - 1) {
08267                                                 k1--;
08268                                                 k3--;
08269                                         }
08270                                         if (jj == ny - 1) {
08271                                                 k2 -= nx;
08272                                                 k3 -= nx;
08273                                         }
08274 
08275                                         float t = x2 - ii;
08276                                         float u = y2 - jj;
08277 
08278                                         des_data[i + j * nx] = Util::bilinear_interpolate(src_data[k0],src_data[k1], src_data[k2], src_data[k3],t,u);
08279                                 }
08280                         }
08281                 }
08282         }
08283         else {
08284                 size_t l=0, ii, k0, k1, k2, k3, k4, k5, k6, k7;
08285                 Vec3f offset(nx/2,ny/2,nz/2);
08286                 float x2, y2, z2, tuvx, tuvy, tuvz;
08287                 int ix, iy, iz;
08288                 for (int k = 0; k < nz; ++k) {
08289                         for (int j = 0; j < ny; ++j) {
08290                                 for (int i = 0; i < nx; ++i,++l) {
08291                                         Vec3f coord(i-nx/2,j-ny/2,k-nz/2);
08292                                         Vec3f soln = inv*coord;
08293                                         soln += offset;
08294 
08295                                         x2 = soln[0];
08296                                         y2 = soln[1];
08297                                         z2 = soln[2];
08298 
08299                                         if (x2 < 0 || y2 < 0 || z2 < 0 || x2 >= nx  || y2 >= ny  || z2>= nz ) {
08300                                                 des_data[l] = 0;
08301                                         }
08302                                         else {
08303                                                 ix = Util::fast_floor(x2);
08304                                                 iy = Util::fast_floor(y2);
08305                                                 iz = Util::fast_floor(z2);
08306                                                 tuvx = x2-ix;
08307                                                 tuvy = y2-iy;
08308                                                 tuvz = z2-iz;
08309                                                 ii = ix + iy * nx + iz * nxy;
08310 
08311                                                 k0 = ii;
08312                                                 k1 = k0 + 1;
08313                                                 k2 = k0 + nx;
08314                                                 k3 = k0 + nx+1;
08315                                                 k4 = k0 + nxy;
08316                                                 k5 = k1 + nxy;
08317                                                 k6 = k2 + nxy;
08318                                                 k7 = k3 + nxy;
08319 
08320                                                 if (ix == nx - 1) {
08321                                                         k1--;
08322                                                         k3--;
08323                                                         k5--;
08324                                                         k7--;
08325                                                 }
08326                                                 if (iy == ny - 1) {
08327                                                         k2 -= nx;
08328                                                         k3 -= nx;
08329                                                         k6 -= nx;
08330                                                         k7 -= nx;
08331                                                 }
08332                                                 if (iz == nz - 1) {
08333                                                         k4 -= nxy;
08334                                                         k5 -= nxy;
08335                                                         k6 -= nxy;
08336                                                         k7 -= nxy;
08337                                                 }
08338 
08339                                                 des_data[l] = Util::trilinear_interpolate(src_data[k0],
08340                                                                 src_data[k1], src_data[k2], src_data[k3], src_data[k4],
08341                                                                 src_data[k5], src_data[k6],     src_data[k7], tuvx, tuvy, tuvz);
08342                                         }
08343                                 }
08344                         }
08345                 }
08346         }
08347 
08348         EXITFUNC;
08349         return des_data;
08350 }


Member Data Documentation

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

Definition at line 1352 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Mon Mar 7 18:02:19 2011 for EMAN2 by  doxygen 1.4.7