#include <processor.h>
Inheritance diagram for EMAN::NormalizeMaskProcessor:
Public Member Functions | |
string | get_name () const |
Get the processor's name. | |
string | get_desc () const |
Get the descrition of this specific processor. | |
TypeDict | get_param_types () const |
Get processor parameter information in a dictionary. | |
Static Public Member Functions | |
static Processor * | NEW () |
Static Public Attributes | |
static const string | NAME = "normalize.mask" |
Protected Member Functions | |
float | calc_sigma (EMData *image) const |
float | calc_mean (EMData *image) const |
mask | the 1/0 mask defining a region to use for the zero-normalization | |
no_sigma | if this flag is zero, only average under the mask will be substracted. set this flag to 1, standard deviation not modified |
Definition at line 4131 of file processor.h.
float NormalizeMaskProcessor::calc_mean | ( | EMData * | image | ) | const [protected, virtual] |
Implements EMAN::NormalizeProcessor.
Definition at line 3472 of file processor.cpp.
References EMAN::EMData::get_data(), EMAN::EMData::get_edge_mean(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ImageDimensionException, EMAN::EMUtil::is_same_size(), LOGERR, LOGWARN, and EMAN::Processor::params.
03473 { 03474 if (!image) { 03475 LOGWARN("NULL Image"); 03476 return 0; 03477 } 03478 EMData *mask = params["mask"]; 03479 03480 if (!EMUtil::is_same_size(mask, image)) { 03481 LOGERR("normalize.maskProcessor: mask and image must be the same size"); 03482 throw ImageDimensionException("mask and image must be the same size"); 03483 } 03484 03485 float *data = image->get_data(); 03486 float *mask_data = mask->get_data(); 03487 size_t size = image->get_xsize() * image->get_ysize() * image->get_zsize(); 03488 double sum = 0; 03489 size_t n_norm = 0; 03490 03491 for (size_t i = 0; i < size; i++) { 03492 if (mask_data[i] > 0.5f) { 03493 sum += data[i]; 03494 n_norm++; 03495 } 03496 } 03497 03498 float mean = 0; 03499 if (n_norm == 0) { 03500 mean = image->get_edge_mean(); 03501 } 03502 else { 03503 mean = (float) sum / n_norm; 03504 } 03505 03506 return mean; 03507 }
float NormalizeMaskProcessor::calc_sigma | ( | EMData * | image | ) | const [protected, virtual] |
Reimplemented from EMAN::NormalizeProcessor.
Definition at line 3436 of file processor.cpp.
References EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ImageDimensionException, EMAN::EMUtil::is_same_size(), LOGERR, LOGWARN, EMAN::Processor::params, and sqrt().
03437 { 03438 if (!image) { 03439 LOGWARN("NULL Image"); 03440 return 0; 03441 } 03442 EMData *mask = params["mask"]; 03443 int no_sigma = params["no_sigma"]; 03444 03445 if(no_sigma == 0) { 03446 return 1; 03447 } 03448 else { 03449 if (!EMUtil::is_same_size(mask, image)) { 03450 LOGERR("normalize.maskProcessor: mask and image must be the same size"); 03451 throw ImageDimensionException("mask and image must be the same size"); 03452 } 03453 03454 float *data = image->get_data(); 03455 float *mask_data = mask->get_data(); 03456 size_t size = image->get_xsize() * image->get_ysize() * image->get_zsize(); 03457 double sum = 0; 03458 double sq2 = 0; 03459 size_t n_norm = 0; 03460 03461 for (size_t i = 0; i < size; i++) { 03462 if (mask_data[i] > 0.5f) { 03463 sum += data[i]; 03464 sq2 += data[i]*double (data[i]); 03465 n_norm++; 03466 } 03467 } 03468 return sqrt(static_cast<float>((sq2 - sum * sum /n_norm)/(n_norm -1))) ; 03469 } 03470 }
string EMAN::NormalizeMaskProcessor::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 4139 of file processor.h.
04140 { 04141 return "Uses a 1/0 mask defining a region to use for the zero-normalization.if no_sigma is 1, standard deviation not modified."; 04142 }
string EMAN::NormalizeMaskProcessor::get_name | ( | ) | const [inline, virtual] |
Get the processor's name.
Each processor is identified by a unique name.
Implements EMAN::Processor.
Definition at line 4134 of file processor.h.
References NAME.
04135 { 04136 return NAME; 04137 }
TypeDict EMAN::NormalizeMaskProcessor::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 4149 of file processor.h.
References EMAN::EMObject::EMDATA, EMAN::EMObject::INT, and EMAN::TypeDict::put().
04150 { 04151 TypeDict d; 04152 d.put("mask", EMObject::EMDATA, "the 1/0 mask defining a region to use for the zero-normalization"); 04153 d.put("no_sigma", EMObject::INT, "if this flag is zero, only average under the mask will be substracted. set this flag to 1, standard deviation not modified"); 04154 return d; 04155 }
static Processor* EMAN::NormalizeMaskProcessor::NEW | ( | ) | [inline, static] |
Definition at line 4144 of file processor.h.
04145 { 04146 return new NormalizeMaskProcessor(); 04147 }
const string NormalizeMaskProcessor::NAME = "normalize.mask" [static] |