#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) |
| virtual EMData * | process (const EMData *const image) |
| 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 | |
| Processor * | NEW () |
Static Public Attributes | |
| 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.
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Definition at line 8349 of file processor.cpp. References EMAN::EMData::get_ndim(), EMAN::Dict::has_key(), ImageDimensionException, and InvalidParameterException. 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 }
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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. 01444 {
01445 return "The image is transformed using Transform parameter.";
01446 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 1415 of file processor.h. 01416 {
01417 return NAME;
01418 }
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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(). 01437 {
01438 TypeDict d;
01439 d.put("transform", EMObject::TRANSFORM, "The Transform object that will be applied to the image" );
01440 return d;
01441 }
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Definition at line 1419 of file processor.h. 01420 {
01421 return new TransformProcessor();
01422 }
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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(), EMAN::EMData::get_attr_dict(), EMAN::Transform::get_scale(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Transform::inverse(), 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 }
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Implements EMAN::Processor. Definition at line 8428 of file processor.cpp. References assert_valid_aspect(), EMAN::Transform::copy_matrix_into_array(), emdata_transform_cuda(), EMAN::Transform::get_scale(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Transform::inverse(), 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 }
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Definition at line 8227 of file processor.cpp. References EMAN::Util::bilinear_interpolate(), EMAN::EMUtil::em_malloc(), EMAN::Util::fast_floor(), EMAN::EMData::get_const_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Transform::inverse(), nx, ny, t, EMAN::Util::trilinear_interpolate(), EMAN::Vec2f, and EMAN::Vec3f. 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 }
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Definition at line 86 of file processor.cpp. |
1.3.9.1