#include <processor.h>
Inheritance diagram for EMAN::TransformProcessor:
Public Member Functions | |||||||
virtual string | get_name () const | ||||||
Get the processor's name. | |||||||
virtual void | process_inplace (EMData *image) | ||||||
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virtual EMData * | process (const EMData *const image) | ||||||
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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 Processor * | NEW () | ||||||
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 |
transform | The Transform object that will be applied to the image |
Definition at line 1412 of file processor.h.
void TransformProcessor::assert_valid_aspect | ( | const EMData *const | image | ) | const [private] |
Definition at line 8349 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().
08349 { 08350 int ndim = image->get_ndim(); 08351 if (ndim != 2 && ndim != 3) throw ImageDimensionException("Transforming an EMData only works if it's 2D or 3D"); 08352 08353 if (! params.has_key("transform") ) throw InvalidParameterException("You must specify a Transform in order to perform this operation"); 08354 }
virtual string EMAN::TransformProcessor::get_desc | ( | ) | const [inline, virtual] |
Get the descrition of this specific processor.
This function must be overwritten by a subclass.
Implements EMAN::Processor.
Definition at line 1443 of file processor.h.
virtual string EMAN::TransformProcessor::get_name | ( | ) | const [inline, virtual] |
Get the processor's name.
Each processor is identified by a unique name.
Implements EMAN::Processor.
Definition at line 1415 of file processor.h.
References NAME.
01416 { 01417 return NAME; 01418 }
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.
Reimplemented from EMAN::Processor.
Definition at line 1436 of file processor.h.
References EMAN::TypeDict::put(), and EMAN::EMObject::TRANSFORM.
01437 { 01438 TypeDict d; 01439 d.put("transform", EMObject::TRANSFORM, "The Transform object that will be applied to the image" ); 01440 return d; 01441 }
static Processor* EMAN::TransformProcessor::NEW | ( | ) | [inline, static] |
ImageDimensionException | if the image is not 2D or 3D | |
InvalidParameterException | if the Transform parameter is not specified |
Reimplemented from EMAN::Processor.
Definition at line 8388 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().
08388 { 08389 ENTERFUNC; 08390 08391 assert_valid_aspect(image); 08392 08393 Transform* t = params["transform"]; 08394 08395 EMData* p = 0; 08396 #ifdef EMAN2_USING_CUDA 08397 if(image->isrodataongpu()){ 08398 //cout << "using CUDA xform" << endl; 08399 p = new EMData(0,0,image->get_xsize(),image->get_ysize(),image->get_zsize(),image->get_attr_dict()); 08400 float * m = new float[12]; 08401 Transform inv = t->inverse(); 08402 inv.copy_matrix_into_array(m); 08403 image->bindcudaarrayA(true); 08404 p->runcuda(emdata_transform_cuda(m,image->get_xsize(),image->get_ysize(),image->get_zsize())); 08405 image->unbindcudaarryA(); 08406 delete [] m; 08407 } 08408 #endif 08409 08410 if ( p == 0 ) { 08411 float* des_data = transform(image,*t); 08412 p = new EMData(des_data,image->get_xsize(),image->get_ysize(),image->get_zsize(),image->get_attr_dict()); 08413 } 08414 08415 // all_translation += transform.get_trans(); 08416 08417 float scale = t->get_scale(); 08418 if (scale != 1.0) { 08419 p->scale_pixel(1.0f/scale); 08420 // update_emdata_attributes(p,image->get_attr_dict(),scale); 08421 } 08422 08423 if(t) {delete t; t=0;} 08424 EXITFUNC; 08425 return p; 08426 }
void TransformProcessor::process_inplace | ( | EMData * | image | ) | [virtual] |
ImageDimensionException | if the image is not 2D or 3D | |
InvalidParameterException | if the Transform parameter is not specified |
Implements EMAN::Processor.
Definition at line 8428 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().
08428 { 08429 ENTERFUNC; 08430 08431 assert_valid_aspect(image); 08432 08433 Transform* t = params["transform"]; 08434 08435 // all_translation += transform.get_trans(); 08436 bool use_cpu = true; 08437 08438 #ifdef EMAN2_USING_CUDA 08439 if(image->isrodataongpu()){ 08440 image->bindcudaarrayA(false); 08441 float * m = new float[12]; 08442 Transform inv = t->inverse(); 08443 inv.copy_matrix_into_array(m); 08444 image->runcuda(emdata_transform_cuda(m,image->get_xsize(),image->get_ysize(),image->get_zsize())); 08445 image->unbindcudaarryA(); 08446 delete [] m; 08447 use_cpu = false; 08448 } 08449 #endif 08450 if ( use_cpu ) { 08451 float* des_data = transform(image,*t); 08452 image->set_data(des_data,image->get_xsize(),image->get_ysize(),image->get_zsize()); 08453 image->update(); 08454 } 08455 float scale = t->get_scale(); 08456 if (scale != 1.0f) { 08457 image->scale_pixel(1.0f/scale); 08458 // update_emdata_attributes(image,image->get_attr_dict(),scale); 08459 } 08460 08461 if(t) {delete t; t=0;} 08462 08463 EXITFUNC; 08464 }
float * TransformProcessor::transform | ( | const EMData *const | image, | |
const Transform & | t | |||
) | const [private] |
Definition at line 8227 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().
08227 { 08228 08229 ENTERFUNC; 08230 08231 Transform inv = t.inverse(); 08232 int nx = image->get_xsize(); 08233 int ny = image->get_ysize(); 08234 int nz = image->get_zsize(); 08235 int nxy = nx*ny; 08236 08237 const float * const src_data = image->get_const_data(); 08238 float *des_data = (float *) EMUtil::em_malloc(nx*ny*nz* sizeof(float)); 08239 08240 if (nz == 1) { 08241 Vec2f offset(nx/2,ny/2); 08242 for (int j = 0; j < ny; j++) { 08243 for (int i = 0; i < nx; i++) { 08244 Vec2f coord(i-nx/2,j-ny/2); 08245 Vec2f soln = inv*coord; 08246 soln += offset; 08247 08248 float x2 = soln[0]; 08249 float y2 = soln[1]; 08250 08251 if (x2 < 0 || x2 >= nx || y2 < 0 || y2 >= ny ) { 08252 des_data[i + j * nx] = 0; // It may be tempting to set this value to the 08253 // mean but in fact this is not a good thing to do. Talk to S.Ludtke about it. 08254 } 08255 else { 08256 int ii = Util::fast_floor(x2); 08257 int jj = Util::fast_floor(y2); 08258 int k0 = ii + jj * nx; 08259 int k1 = k0 + 1; 08260 int k2 = k0 + nx; 08261 int k3 = k0 + nx + 1; 08262 08263 if (ii == nx - 1) { 08264 k1--; 08265 k3--; 08266 } 08267 if (jj == ny - 1) { 08268 k2 -= nx; 08269 k3 -= nx; 08270 } 08271 08272 float t = x2 - ii; 08273 float u = y2 - jj; 08274 08275 des_data[i + j * nx] = Util::bilinear_interpolate(src_data[k0],src_data[k1], src_data[k2], src_data[k3],t,u); 08276 } 08277 } 08278 } 08279 } 08280 else { 08281 size_t l=0, ii, k0, k1, k2, k3, k4, k5, k6, k7; 08282 Vec3f offset(nx/2,ny/2,nz/2); 08283 float x2, y2, z2, tuvx, tuvy, tuvz; 08284 int ix, iy, iz; 08285 for (int k = 0; k < nz; ++k) { 08286 for (int j = 0; j < ny; ++j) { 08287 for (int i = 0; i < nx; ++i,++l) { 08288 Vec3f coord(i-nx/2,j-ny/2,k-nz/2); 08289 Vec3f soln = inv*coord; 08290 soln += offset; 08291 08292 x2 = soln[0]; 08293 y2 = soln[1]; 08294 z2 = soln[2]; 08295 08296 if (x2 < 0 || y2 < 0 || z2 < 0 || x2 >= nx || y2 >= ny || z2>= nz ) { 08297 des_data[l] = 0; 08298 } 08299 else { 08300 ix = Util::fast_floor(x2); 08301 iy = Util::fast_floor(y2); 08302 iz = Util::fast_floor(z2); 08303 tuvx = x2-ix; 08304 tuvy = y2-iy; 08305 tuvz = z2-iz; 08306 ii = ix + iy * nx + iz * nxy; 08307 08308 k0 = ii; 08309 k1 = k0 + 1; 08310 k2 = k0 + nx; 08311 k3 = k0 + nx+1; 08312 k4 = k0 + nxy; 08313 k5 = k1 + nxy; 08314 k6 = k2 + nxy; 08315 k7 = k3 + nxy; 08316 08317 if (ix == nx - 1) { 08318 k1--; 08319 k3--; 08320 k5--; 08321 k7--; 08322 } 08323 if (iy == ny - 1) { 08324 k2 -= nx; 08325 k3 -= nx; 08326 k6 -= nx; 08327 k7 -= nx; 08328 } 08329 if (iz == nz - 1) { 08330 k4 -= nxy; 08331 k5 -= nxy; 08332 k6 -= nxy; 08333 k7 -= nxy; 08334 } 08335 08336 des_data[l] = Util::trilinear_interpolate(src_data[k0], 08337 src_data[k1], src_data[k2], src_data[k3], src_data[k4], 08338 src_data[k5], src_data[k6], src_data[k7], tuvx, tuvy, tuvz); 08339 } 08340 } 08341 } 08342 } 08343 } 08344 08345 EXITFUNC; 08346 return des_data; 08347 }
const string TransformProcessor::NAME = "xform" [static] |