#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 1498 of file processor.h.
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Definition at line 8249 of file processor.cpp. References EMAN::EMData::get_ndim(), EMAN::Dict::has_key(), ImageDimensionException, and InvalidParameterException. Referenced by process(), and process_inplace(). 08249 { 08250 int ndim = image->get_ndim(); 08251 if (ndim != 2 && ndim != 3) throw ImageDimensionException("Transforming an EMData only works if it's 2D or 3D"); 08252 08253 if (! params.has_key("transform") ) throw InvalidParameterException("You must specify a Transform in order to perform this operation"); 08254 }
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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 1529 of file processor.h. 01530 { 01531 return "The image is transformed using Transform parameter."; 01532 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 1501 of file processor.h. 01502 {
01503 return NAME;
01504 }
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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 1522 of file processor.h. References EMAN::TypeDict::put(). 01523 { 01524 TypeDict d; 01525 d.put("transform", EMObject::TRANSFORM, "The Transform object that will be applied to the image" ); 01526 return d; 01527 }
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Definition at line 1505 of file processor.h. 01506 { 01507 return new TransformProcessor(); 01508 }
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Reimplemented from EMAN::Processor. Definition at line 8288 of file processor.cpp. References assert_valid_aspect(), EMAN::Transform::copy_matrix_into_array(), EMDataForCuda::data, 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(), EMDataForCuda::nx, EMDataForCuda::ny, EMDataForCuda::nz, EMAN::EMData::scale_pixel(), t, and transform(). 08288 { 08289 ENTERFUNC; 08290 08291 assert_valid_aspect(image); 08292 08293 Transform* t = params["transform"]; 08294 08295 EMData* p = 0; 08296 #ifdef EMAN2_USING_CUDA 08297 if (image->gpu_operation_preferred()) { 08298 // cout << "cuda transform" << endl; 08299 float * m = new float[12]; 08300 Transform inv = t->inverse(); 08301 inv.copy_matrix_into_array(m); 08302 image->bind_cuda_texture(); 08303 EMDataForCuda* tmp = emdata_transform_cuda(m,image->get_xsize(),image->get_ysize(),image->get_zsize()); 08304 image->unbind_cuda_texture(); 08305 delete [] m; 08306 if (tmp == 0) throw; 08307 08308 p = new EMData(); 08309 p->set_gpu_rw_data(tmp->data,tmp->nx,tmp->ny,tmp->nz); 08310 free(tmp); 08311 } 08312 #endif 08313 if ( p == 0 ) { 08314 float* des_data = transform(image,*t); 08315 p = new EMData(des_data,image->get_xsize(),image->get_ysize(),image->get_zsize(),image->get_attr_dict()); 08316 } 08317 08318 // all_translation += transform.get_trans(); 08319 08320 float scale = t->get_scale(); 08321 if (scale != 1.0) { 08322 p->scale_pixel(1.0f/scale); 08323 // update_emdata_attributes(p,image->get_attr_dict(),scale); 08324 } 08325 08326 if(t) {delete t; t=0;} 08327 EXITFUNC; 08328 return p; 08329 }
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Implements EMAN::Processor. Definition at line 8331 of file processor.cpp. References assert_valid_aspect(), EMAN::Transform::copy_matrix_into_array(), EMDataForCuda::data, emdata_transform_cuda(), EMAN::Transform::get_scale(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Transform::inverse(), EMDataForCuda::nx, EMDataForCuda::ny, EMDataForCuda::nz, EMAN::EMData::scale_pixel(), EMAN::EMData::set_data(), t, transform(), and EMAN::EMData::update(). 08331 { 08332 ENTERFUNC; 08333 08334 assert_valid_aspect(image); 08335 08336 Transform* t = params["transform"]; 08337 08338 // all_translation += transform.get_trans(); 08339 bool use_cpu = true; 08340 #ifdef EMAN2_USING_CUDA 08341 if (image->gpu_operation_preferred()) { 08342 use_cpu = false; 08343 float * m = new float[12]; 08344 Transform inv = t->inverse(); 08345 inv.copy_matrix_into_array(m); 08346 image->bind_cuda_texture(); 08347 EMDataForCuda* tmp = emdata_transform_cuda(m,image->get_xsize(),image->get_ysize(),image->get_zsize()); 08348 image->unbind_cuda_texture(); 08349 delete [] m; 08350 if (tmp == 0) throw; 08351 image->set_gpu_rw_data(tmp->data,tmp->nx,tmp->ny,tmp->nz); 08352 free(tmp); 08353 } 08354 #endif 08355 if ( use_cpu ) { 08356 float* des_data = transform(image,*t); 08357 image->set_data(des_data,image->get_xsize(),image->get_ysize(),image->get_zsize()); 08358 image->update(); 08359 } 08360 float scale = t->get_scale(); 08361 if (scale != 1.0) { 08362 image->scale_pixel(1.0f/scale); 08363 // update_emdata_attributes(image,image->get_attr_dict(),scale); 08364 } 08365 08366 if(t) {delete t; t=0;} 08367 08368 EXITFUNC; 08369 }
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Definition at line 8127 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(). 08127 { 08128 08129 ENTERFUNC; 08130 08131 Transform inv = t.inverse(); 08132 int nx = image->get_xsize(); 08133 int ny = image->get_ysize(); 08134 int nz = image->get_zsize(); 08135 int nxy = nx*ny; 08136 08137 const float * const src_data = image->get_const_data(); 08138 float *des_data = (float *) EMUtil::em_malloc(nx*ny*nz* sizeof(float)); 08139 08140 if (nz == 1) { 08141 Vec2f offset(nx/2,ny/2); 08142 for (int j = 0; j < ny; j++) { 08143 for (int i = 0; i < nx; i++) { 08144 Vec2f coord(i-nx/2,j-ny/2); 08145 Vec2f soln = inv*coord; 08146 soln += offset; 08147 08148 float x2 = soln[0]; 08149 float y2 = soln[1]; 08150 08151 if (x2 < 0 || x2 >= nx || y2 < 0 || y2 >= ny ) { 08152 des_data[i + j * nx] = 0; // It may be tempting to set this value to the 08153 // mean but in fact this is not a good thing to do. Talk to S.Ludtke about it. 08154 } 08155 else { 08156 int ii = Util::fast_floor(x2); 08157 int jj = Util::fast_floor(y2); 08158 int k0 = ii + jj * nx; 08159 int k1 = k0 + 1; 08160 int k2 = k0 + nx; 08161 int k3 = k0 + nx + 1; 08162 08163 if (ii == nx - 1) { 08164 k1--; 08165 k3--; 08166 } 08167 if (jj == ny - 1) { 08168 k2 -= nx; 08169 k3 -= nx; 08170 } 08171 08172 float t = x2 - ii; 08173 float u = y2 - jj; 08174 08175 des_data[i + j * nx] = Util::bilinear_interpolate(src_data[k0],src_data[k1], src_data[k2], src_data[k3],t,u); 08176 } 08177 } 08178 } 08179 } 08180 else { 08181 size_t l=0, ii, k0, k1, k2, k3, k4, k5, k6, k7; 08182 Vec3f offset(nx/2,ny/2,nz/2); 08183 float x2, y2, z2, tuvx, tuvy, tuvz; 08184 int ix, iy, iz; 08185 for (int k = 0; k < nz; ++k) { 08186 for (int j = 0; j < ny; ++j) { 08187 for (int i = 0; i < nx; ++i,++l) { 08188 Vec3f coord(i-nx/2,j-ny/2,k-nz/2); 08189 Vec3f soln = inv*coord; 08190 soln += offset; 08191 08192 x2 = soln[0]; 08193 y2 = soln[1]; 08194 z2 = soln[2]; 08195 08196 if (x2 < 0 || y2 < 0 || z2 < 0 || x2 >= nx || y2 >= ny || z2>= nz ) { 08197 des_data[l] = 0; 08198 } 08199 else { 08200 ix = Util::fast_floor(x2); 08201 iy = Util::fast_floor(y2); 08202 iz = Util::fast_floor(z2); 08203 tuvx = x2-ix; 08204 tuvy = y2-iy; 08205 tuvz = z2-iz; 08206 ii = ix + iy * nx + iz * nxy; 08207 08208 k0 = ii; 08209 k1 = k0 + 1; 08210 k2 = k0 + nx; 08211 k3 = k0 + nx+1; 08212 k4 = k0 + nxy; 08213 k5 = k1 + nxy; 08214 k6 = k2 + nxy; 08215 k7 = k3 + nxy; 08216 08217 if (ix == nx - 1) { 08218 k1--; 08219 k3--; 08220 k5--; 08221 k7--; 08222 } 08223 if (iy == ny - 1) { 08224 k2 -= nx; 08225 k3 -= nx; 08226 k6 -= nx; 08227 k7 -= nx; 08228 } 08229 if (iz == nz - 1) { 08230 k4 -= nxy; 08231 k5 -= nxy; 08232 k6 -= nxy; 08233 k7 -= nxy; 08234 } 08235 08236 des_data[l] = Util::trilinear_interpolate(src_data[k0], 08237 src_data[k1], src_data[k2], src_data[k3], src_data[k4], 08238 src_data[k5], src_data[k6], src_data[k7], tuvx, tuvy, tuvz); 08239 } 08240 } 08241 } 08242 } 08243 } 08244 08245 EXITFUNC; 08246 return des_data; 08247 }
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Definition at line 88 of file processor.cpp. |