Main Page | Modules | Namespace List | Class Hierarchy | Alphabetical List | Class List | Directories | File List | Namespace Members | Class Members | File Members

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:

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

Collaboration graph
[legend]
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 340 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 2243 of file projector.cpp.

02244 {
02245    // no implementation yet
02246    EMData *ret = new EMData();
02247    return ret;
02248 }

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

Implements EMAN::Projector.

Definition at line 359 of file projector.h.

00360                 {
00361                         return "Simple real-space projection. Most accurate.";
00362                 }

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 354 of file projector.h.

00355                 {
00356                         return NAME;
00357                 }

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 343 of file projector.h.

References EMAN::TypeDict::put().

00344                 {
00345                         TypeDict d;
00346                         d.put("transform", EMObject::TRANSFORM, "Transform object used for projection");
00347                         return d;
00348                 }

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

Definition at line 364 of file projector.h.

00365                 {
00366                         return new StandardProjector();
00367                 }

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 879 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.

00880 {
00881         Transform* t3d = params["transform"];
00882         if ( t3d == NULL ) throw NullPointerException("The transform object containing the angles(required for projection), was not specified");
00883 //      Dict p = t3d->get_rotation();
00884         if ( image->get_ndim() == 3 )
00885         {
00886 
00887 #ifdef EMAN2_USING_CUDA
00888                 if(EMData::usecuda == 1) {
00889                         if(!image->isrodataongpu()) image->copy_to_cudaro();
00890                         //cout << "CUDA PROJ" << endl;
00891                         Transform* t3d = params["transform"];
00892                         if ( t3d == NULL ) throw NullPointerException("The transform object containing the angles(required for projection), was not specified");
00893                         float * m = new float[12];
00894                         t3d->copy_matrix_into_array(m);
00895                         image->bindcudaarrayA(true);
00896                         //EMData* e = new EMData(0,0,image->get_xsize(),image->get_ysize(),1);
00897                         EMData *e = new EMData();
00898                         e->set_size_cuda(image->get_xsize(), image->get_ysize(), 1);
00899                         e->rw_alloc();
00900                         standard_project(m,e->getcudarwdata(), e->get_xsize(), e->get_ysize());
00901                         image->unbindcudaarryA();
00902                         delete [] m;
00903                 
00904                         e->update();
00905                         e->set_attr("xform.projection",t3d);
00906                         e->set_attr("apix_x",(float)image->get_attr("apix_x"));
00907                         e->set_attr("apix_y",(float)image->get_attr("apix_y"));
00908                         e->set_attr("apix_z",(float)image->get_attr("apix_z"));
00909                         //e_>copy_from_device();
00910                         if(t3d) {delete t3d; t3d=0;}
00911                         return e;
00912                 }
00913 #endif
00914                 int nx = image->get_xsize();
00915                 int ny = image->get_ysize();
00916                 int nz = image->get_zsize();
00917 
00918 //              Transform3D r(Transform3D::EMAN, az, alt, phi);
00919                 Transform r = t3d->inverse(); // The inverse is taken here because we are rotating the coordinate system, not the image
00920                 int xy = nx * ny;
00921 
00922                 EMData *proj = new EMData();
00923                 proj->set_size(nx, ny, 1);
00924 
00925                 Vec3i offset(nx/2,ny/2,nz/2);
00926 
00927                 float *sdata = image->get_data();
00928                 float *ddata = proj->get_data();
00929                 for (int k = -nz / 2; k < nz - nz / 2; k++) {
00930                         int l = 0;
00931                         for (int j = -ny / 2; j < ny - ny / 2; j++) {
00932                                 ddata[l]=0;
00933                                 for (int i = -nx / 2; i < nx - nx / 2; i++,l++) {
00934 
00935                                         Vec3f coord(i,j,k);
00936                                         Vec3f soln = r*coord;
00937                                         soln += offset;
00938 
00942 //                                      printf(" ");
00943 
00944                                         float x2 = soln[0];
00945                                         float y2 = soln[1];
00946                                         float z2 = soln[2];
00947 
00948                                         float x = (float)Util::fast_floor(x2);
00949                                         float y = (float)Util::fast_floor(y2);
00950                                         float z = (float)Util::fast_floor(z2);
00951 
00952                                         float t = x2 - x;
00953                                         float u = y2 - y;
00954                                         float v = z2 - z;
00955 
00956                                         size_t ii = (size_t) ((size_t)x + (size_t)y * nx + (size_t)z * xy);
00957 // 
00958                                         if (x2 < 0 || y2 < 0 || z2 < 0 ) continue;
00959                                         if      (x2 > (nx-1) || y2  > (ny-1) || z2 > (nz-1) ) continue;
00960 
00961                                         if (x2 < (nx - 1) && y2 < (ny - 1) && z2 < (nz - 1)) {
00962                                                 ddata[l] +=
00963                                                                 Util::trilinear_interpolate(sdata[ii], sdata[ii + 1], sdata[ii + nx],
00964                                                                 sdata[ii + nx + 1], sdata[ii + xy],     sdata[ii + xy + 1], sdata[ii + xy + nx],
00965                                                                 sdata[ii + xy + nx + 1], t, u, v);
00966                                         }
00967                                         else if ( x2 == (nx - 1) && y2 == (ny - 1) && z2 == (nz - 1) ) {
00968                                                 ddata[l] += sdata[ii];
00969                                         }
00970                                         else if ( x2 == (nx - 1) && y2 == (ny - 1) ) {
00971                                                 ddata[l] +=     Util::linear_interpolate(sdata[ii], sdata[ii + xy],v);
00972                                         }
00973                                         else if ( x2 == (nx - 1) && z2 == (nz - 1) ) {
00974                                                 ddata[l] += Util::linear_interpolate(sdata[ii], sdata[ii + nx],u);
00975                                         }
00976                                         else if ( y2 == (ny - 1) && z2 == (nz - 1) ) {
00977                                                 ddata[l] += Util::linear_interpolate(sdata[ii], sdata[ii + 1],t);
00978                                         }
00979                                         else if ( x2 == (nx - 1) ) {
00980                                                 ddata[l] += Util::bilinear_interpolate(sdata[ii], sdata[ii + nx], sdata[ii + xy], sdata[ii + xy + nx],u,v);
00981                                         }
00982                                         else if ( y2 == (ny - 1) ) {
00983                                                 ddata[l] += Util::bilinear_interpolate(sdata[ii], sdata[ii + 1], sdata[ii + xy], sdata[ii + xy + 1],t,v);
00984                                         }
00985                                         else if ( z2 == (nz - 1) ) {
00986                                                 ddata[l] += Util::bilinear_interpolate(sdata[ii], sdata[ii + 1], sdata[ii + nx], sdata[ii + nx + 1],t,u);
00987                                         }
00988                                 }
00989                         }
00990                 }
00991                 proj->update();
00992                 proj->set_attr("xform.projection",t3d);
00993                 proj->set_attr("apix_x",(float)image->get_attr("apix_x"));
00994                 proj->set_attr("apix_y",(float)image->get_attr("apix_y"));
00995                 proj->set_attr("apix_z",(float)image->get_attr("apix_z"));
00996                 
00997                 if(t3d) {delete t3d; t3d=0;}
00998                 return proj;
00999         }
01000         else if ( image->get_ndim() == 2 ) {
01001 
01002                 Transform r = t3d->inverse(); // The inverse is taken here because we are rotating the coordinate system, not the image
01003 
01004                 int nx = image->get_xsize();
01005                 int ny = image->get_ysize();
01006 
01007                 EMData *proj = new EMData();
01008                 proj->set_size(nx, 1, 1);
01009                 proj->to_zero();
01010 
01011                 float *sdata = image->get_data();
01012                 float *ddata = proj->get_data();
01013 
01014                 Vec2f offset(nx/2,ny/2);
01015                 for (int j = -ny / 2; j < ny - ny / 2; j++) { // j represents a column of pixels in the direction of the angle
01016                         int l = 0;
01017                         for (int i = -nx / 2; i < nx - nx / 2; i++,l++) {
01018 
01019                                 Vec2f coord(i,j);
01020                                 Vec2f soln = r*coord;
01021                                 soln += offset;
01022 
01023                                 float x2 = soln[0];
01024                                 float y2 = soln[1];
01025 
01026                                 float x = (float)Util::fast_floor(x2);
01027                                 float y = (float)Util::fast_floor(y2);
01028 
01029                                 int ii = (int) (x + y * nx);
01030                                 float u = x2 - x;
01031                                 float v = y2 - y;
01032 
01033                                 if (x2 < 0 || y2 < 0 ) continue;
01034                                 if      (x2 > (nx-1) || y2  > (ny-1) ) continue;
01035 
01036                                 if (  x2 < (nx - 1) && y2 < (ny - 1) ) {
01037                                         ddata[l] += Util::bilinear_interpolate(sdata[ii], sdata[ii + 1], sdata[ii + nx],sdata[ii + nx + 1], u, v);
01038                                 }
01039                                 else if (x2 == (nx-1) && y2 == (ny-1) ) {
01040                                         ddata[l] += sdata[ii];
01041                                 }
01042                                 else if (x2 == (nx-1) ) {
01043                                         ddata[l] += Util::linear_interpolate(sdata[ii],sdata[ii + nx], v);
01044                                 }
01045                                 else if (y2 == (ny-1) ) {
01046                                         ddata[l] += Util::linear_interpolate(sdata[ii],sdata[ii + 1], u);
01047                                 }
01048                         }
01049                 }
01050                 proj->set_attr("xform.projection",t3d);
01051                 proj->update();
01052                 if(t3d) {delete t3d; t3d=0;}
01053                 return proj;
01054         }
01055         else throw ImageDimensionException("Standard projection works only for 2D and 3D images");
01056 }


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:
Generated on Tue Jun 11 13:49:21 2013 for EMAN2 by  doxygen 1.3.9.1