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

Fast real-space 3D projection. More...

#include <projector.h>

Inheritance diagram for EMAN::StandardProjector:

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Collaboration diagram for EMAN::StandardProjector:

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List of all members.

Public Member Functions

TypeDict get_param_types () const
 Get processor parameter information in a dictionary.
EMDataproject3d (EMData *image) const
EMDatabackproject3d (EMData *image) const
 Back-project a 2D image into a 3D image.
string get_name () const
 Get the projector's name.
string get_desc () const

Static Public Member Functions

ProjectorNEW ()

Static Public Attributes

const string NAME = "standard"

Detailed Description

Fast real-space 3D projection.

Parameters:
Transform object used for projection

Definition at line 304 of file projector.h.


Member Function Documentation

EMData * StandardProjector::backproject3d EMData image  )  const [virtual]
 

Back-project a 2D image into a 3D image.

Returns:
A 3D image from the backprojection.

Implements EMAN::Projector.

Definition at line 2080 of file projector.cpp.

02081 {
02082    // no implementation yet
02083    EMData *ret = new EMData();
02084    return ret;
02085 }

string EMAN::StandardProjector::get_desc  )  const [inline, virtual]
 

Implements EMAN::Projector.

Definition at line 323 of file projector.h.

00324                 {
00325                         return "Simple real-space projection. Most accurate.";
00326                 }

string EMAN::StandardProjector::get_name  )  const [inline, virtual]
 

Get the projector's name.

Each projector is indentified by unique name.

Returns:
The projector's name.

Implements EMAN::Projector.

Definition at line 318 of file projector.h.

00319                 {
00320                         return NAME;
00321                 }

TypeDict EMAN::StandardProjector::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::Projector.

Definition at line 307 of file projector.h.

References EMAN::TypeDict::put().

00308                 {
00309                         TypeDict d;
00310                         d.put("transform", EMObject::TRANSFORM, "Transform object used for projection");
00311                         return d;
00312                 }

Projector* EMAN::StandardProjector::NEW  )  [inline, static]
 

Definition at line 328 of file projector.h.

00329                 {
00330                         return new StandardProjector();
00331                 }

EMData * StandardProjector::project3d EMData image  )  const [virtual]
 

A "fix" for the segmentation fault when calling initmodel.py with standard projector. We'll look into this and make a real fix. -- Grant Tang

Implements EMAN::Projector.

Definition at line 872 of file projector.cpp.

References EMAN::Util::bilinear_interpolate(), EMAN::Transform::copy_matrix_into_array(), EMAN::Util::fast_floor(), EMAN::EMData::get_attr(), EMAN::EMData::get_data(), EMAN::EMData::get_ndim(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ImageDimensionException, EMAN::Transform::inverse(), EMAN::Util::linear_interpolate(), NullPointerException, nx, ny, proj, EMAN::EMData::set_attr(), EMAN::EMData::set_size(), standard_project(), t, EMAN::EMData::to_zero(), EMAN::Util::trilinear_interpolate(), EMAN::EMData::update(), v, EMAN::Vec2f, EMAN::Vec3f, EMAN::Vec3i, x, and y.

00873 {
00874         Transform* t3d = params["transform"];
00875         if ( t3d == NULL ) throw NullPointerException("The transform object containing the angles(required for projection), was not specified");
00876 //      Dict p = t3d->get_rotation();
00877         if ( image->get_ndim() == 3 )
00878         {
00879 
00880 #ifdef EMAN2_USING_CUDA
00881                 if(EMData::usecuda == 1) {
00882                         if(!image->isrodataongpu()) image->copy_to_cudaro();
00883                         //cout << "CUDA PROJ" << endl;
00884                         Transform* t3d = params["transform"];
00885                         if ( t3d == NULL ) throw NullPointerException("The transform object containing the angles(required for projection), was not specified");
00886                         float * m = new float[12];
00887                         t3d->copy_matrix_into_array(m);
00888                         image->bindcudaarrayA(true);
00889                         EMData* e = new EMData(0,0,image->get_xsize(),image->get_ysize(),1);
00890                         //EMData *e = new EMData();
00891                         //e->set_size(image->get_xsize(), image->get_ysize(), 1);
00892                         e->rw_alloc();
00893                         standard_project(m,e->cudarwdata, e->get_xsize(), e->get_ysize());
00894                         image->unbindcudaarryA();
00895                         delete [] m;
00896                 
00897                         e->update();
00898                         e->set_attr("xform.projection",t3d);
00899                         //e_>copy_from_device();
00900                         if(t3d) {delete t3d; t3d=0;}
00901                         return e;
00902                 }
00903 #endif
00904                 int nx = image->get_xsize();
00905                 int ny = image->get_ysize();
00906                 int nz = image->get_zsize();
00907 
00908 //              Transform3D r(Transform3D::EMAN, az, alt, phi);
00909                 Transform r = t3d->inverse(); // The inverse is taken here because we are rotating the coordinate system, not the image
00910                 int xy = nx * ny;
00911 
00912                 EMData *proj = new EMData();
00913                 proj->set_size(nx, ny, 1);
00914 
00915                 Vec3i offset(nx/2,ny/2,nz/2);
00916 
00917                 float *sdata = image->get_data();
00918                 float *ddata = proj->get_data();
00919                 for (int k = -nz / 2; k < nz - nz / 2; k++) {
00920                         int l = 0;
00921                         for (int j = -ny / 2; j < ny - ny / 2; j++) {
00922                                 ddata[l]=0;
00923                                 for (int i = -nx / 2; i < nx - nx / 2; i++,l++) {
00924 
00925                                         Vec3f coord(i,j,k);
00926                                         Vec3f soln = r*coord;
00927                                         soln += offset;
00928 
00932 //                                      printf(" ");
00933 
00934                                         float x2 = soln[0];
00935                                         float y2 = soln[1];
00936                                         float z2 = soln[2];
00937 
00938                                         float x = (float)Util::fast_floor(x2);
00939                                         float y = (float)Util::fast_floor(y2);
00940                                         float z = (float)Util::fast_floor(z2);
00941 
00942                                         float t = x2 - x;
00943                                         float u = y2 - y;
00944                                         float v = z2 - z;
00945 
00946                                         size_t ii = (size_t) ((size_t)x + (size_t)y * nx + (size_t)z * xy);
00947 // 
00948                                         if (x2 < 0 || y2 < 0 || z2 < 0 ) continue;
00949                                         if      (x2 > (nx-1) || y2  > (ny-1) || z2 > (nz-1) ) continue;
00950 
00951                                         if (x2 < (nx - 1) && y2 < (ny - 1) && z2 < (nz - 1)) {
00952                                                 ddata[l] +=
00953                                                                 Util::trilinear_interpolate(sdata[ii], sdata[ii + 1], sdata[ii + nx],
00954                                                                 sdata[ii + nx + 1], sdata[ii + xy],     sdata[ii + xy + 1], sdata[ii + xy + nx],
00955                                                                 sdata[ii + xy + nx + 1], t, u, v);
00956                                         }
00957                                         else if ( x2 == (nx - 1) && y2 == (ny - 1) && z2 == (nz - 1) ) {
00958                                                 ddata[l] += sdata[ii];
00959                                         }
00960                                         else if ( x2 == (nx - 1) && y2 == (ny - 1) ) {
00961                                                 ddata[l] +=     Util::linear_interpolate(sdata[ii], sdata[ii + xy],v);
00962                                         }
00963                                         else if ( x2 == (nx - 1) && z2 == (nz - 1) ) {
00964                                                 ddata[l] += Util::linear_interpolate(sdata[ii], sdata[ii + nx],u);
00965                                         }
00966                                         else if ( y2 == (ny - 1) && z2 == (nz - 1) ) {
00967                                                 ddata[l] += Util::linear_interpolate(sdata[ii], sdata[ii + 1],t);
00968                                         }
00969                                         else if ( x2 == (nx - 1) ) {
00970                                                 ddata[l] += Util::bilinear_interpolate(sdata[ii], sdata[ii + nx], sdata[ii + xy], sdata[ii + xy + nx],u,v);
00971                                         }
00972                                         else if ( y2 == (ny - 1) ) {
00973                                                 ddata[l] += Util::bilinear_interpolate(sdata[ii], sdata[ii + 1], sdata[ii + xy], sdata[ii + xy + 1],t,v);
00974                                         }
00975                                         else if ( z2 == (nz - 1) ) {
00976                                                 ddata[l] += Util::bilinear_interpolate(sdata[ii], sdata[ii + 1], sdata[ii + nx], sdata[ii + nx + 1],t,u);
00977                                         }
00978                                 }
00979                         }
00980                 }
00981                 proj->update();
00982                 proj->set_attr("xform.projection",t3d);
00983                 proj->set_attr("apix_x",(float)image->get_attr("apix_x"));
00984                 proj->set_attr("apix_y",(float)image->get_attr("apix_y"));
00985                 proj->set_attr("apix_z",(float)image->get_attr("apix_z"));
00986                 
00987                 if(t3d) {delete t3d; t3d=0;}
00988                 return proj;
00989         }
00990         else if ( image->get_ndim() == 2 ) {
00991 
00992                 Transform r = t3d->inverse(); // The inverse is taken here because we are rotating the coordinate system, not the image
00993 
00994                 int nx = image->get_xsize();
00995                 int ny = image->get_ysize();
00996 
00997                 EMData *proj = new EMData();
00998                 proj->set_size(nx, 1, 1);
00999                 proj->to_zero();
01000 
01001                 float *sdata = image->get_data();
01002                 float *ddata = proj->get_data();
01003 
01004                 Vec2f offset(nx/2,ny/2);
01005                 for (int j = -ny / 2; j < ny - ny / 2; j++) { // j represents a column of pixels in the direction of the angle
01006                         int l = 0;
01007                         for (int i = -nx / 2; i < nx - nx / 2; i++,l++) {
01008 
01009                                 Vec2f coord(i,j);
01010                                 Vec2f soln = r*coord;
01011                                 soln += offset;
01012 
01013                                 float x2 = soln[0];
01014                                 float y2 = soln[1];
01015 
01016                                 float x = (float)Util::fast_floor(x2);
01017                                 float y = (float)Util::fast_floor(y2);
01018 
01019                                 int ii = (int) (x + y * nx);
01020                                 float u = x2 - x;
01021                                 float v = y2 - y;
01022 
01023                                 if (x2 < 0 || y2 < 0 ) continue;
01024                                 if      (x2 > (nx-1) || y2  > (ny-1) ) continue;
01025 
01026                                 if (  x2 < (nx - 1) && y2 < (ny - 1) ) {
01027                                         ddata[l] += Util::bilinear_interpolate(sdata[ii], sdata[ii + 1], sdata[ii + nx],sdata[ii + nx + 1], u, v);
01028                                 }
01029                                 else if (x2 == (nx-1) && y2 == (ny-1) ) {
01030                                         ddata[l] += sdata[ii];
01031                                 }
01032                                 else if (x2 == (nx-1) ) {
01033                                         ddata[l] += Util::linear_interpolate(sdata[ii],sdata[ii + nx], v);
01034                                 }
01035                                 else if (y2 == (ny-1) ) {
01036                                         ddata[l] += Util::linear_interpolate(sdata[ii],sdata[ii + 1], u);
01037                                 }
01038                         }
01039                 }
01040                 proj->set_attr("xform.projection",t3d);
01041                 proj->update();
01042                 if(t3d) {delete t3d; t3d=0;}
01043                 return proj;
01044         }
01045         else throw ImageDimensionException("Standard projection works only for 2D and 3D images");
01046 }


Member Data Documentation

const string StandardProjector::NAME = "standard" [static]
 

Definition at line 57 of file projector.cpp.


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