#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 4040 of file processor.h.
float NormalizeMaskProcessor::calc_mean | ( | EMData * | image | ) | const [protected, virtual] |
Implements EMAN::NormalizeProcessor.
Definition at line 3487 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, mean(), and EMAN::Processor::params.
03488 { 03489 if (!image) { 03490 LOGWARN("NULL Image"); 03491 return 0; 03492 } 03493 EMData *mask = params["mask"]; 03494 03495 if (!EMUtil::is_same_size(mask, image)) { 03496 LOGERR("normalize.maskProcessor: mask and image must be the same size"); 03497 throw ImageDimensionException("mask and image must be the same size"); 03498 } 03499 03500 float *data = image->get_data(); 03501 float *mask_data = mask->get_data(); 03502 size_t size = (size_t)image->get_xsize() * image->get_ysize() * image->get_zsize(); 03503 double sum = 0; 03504 size_t n_norm = 0; 03505 03506 for (size_t i = 0; i < size; ++i) { 03507 if (mask_data[i] > 0.5f) { 03508 sum += data[i]; 03509 n_norm++; 03510 } 03511 } 03512 03513 float mean = 0; 03514 if (n_norm == 0) { 03515 mean = image->get_edge_mean(); 03516 } 03517 else { 03518 mean = (float) sum / n_norm; 03519 } 03520 03521 return mean; 03522 }
float NormalizeMaskProcessor::calc_sigma | ( | EMData * | image | ) | const [protected, virtual] |
Reimplemented from EMAN::NormalizeProcessor.
Definition at line 3451 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().
03452 { 03453 if (!image) { 03454 LOGWARN("NULL Image"); 03455 return 0; 03456 } 03457 EMData *mask = params["mask"]; 03458 int no_sigma = params["no_sigma"]; 03459 03460 if(no_sigma == 0) { 03461 return 1; 03462 } 03463 else { 03464 if (!EMUtil::is_same_size(mask, image)) { 03465 LOGERR("normalize.maskProcessor: mask and image must be the same size"); 03466 throw ImageDimensionException("mask and image must be the same size"); 03467 } 03468 03469 float *data = image->get_data(); 03470 float *mask_data = mask->get_data(); 03471 size_t size = (size_t)image->get_xsize() * image->get_ysize() * image->get_zsize(); 03472 double sum = 0; 03473 double sq2 = 0; 03474 size_t n_norm = 0; 03475 03476 for (size_t i = 0; i < size; ++i) { 03477 if (mask_data[i] > 0.5f) { 03478 sum += data[i]; 03479 sq2 += data[i]*double (data[i]); 03480 n_norm++; 03481 } 03482 } 03483 return sqrt(static_cast<float>((sq2 - sum * sum /n_norm)/(n_norm -1))) ; 03484 } 03485 }
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 4048 of file processor.h.
04049 { 04050 return "Uses a 1/0 mask defining a region to use for the zero-normalization.if no_sigma is 1, standard deviation not modified."; 04051 }
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 4043 of file processor.h.
References NAME.
04044 { 04045 return NAME; 04046 }
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 4058 of file processor.h.
References EMAN::EMObject::EMDATA, EMAN::EMObject::INT, and EMAN::TypeDict::put().
04059 { 04060 TypeDict d; 04061 d.put("mask", EMObject::EMDATA, "the 1/0 mask defining a region to use for the zero-normalization"); 04062 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"); 04063 return d; 04064 }
static Processor* EMAN::NormalizeMaskProcessor::NEW | ( | ) | [inline, static] |
Definition at line 4053 of file processor.h.
04054 { 04055 return new NormalizeMaskProcessor(); 04056 }
const string NormalizeMaskProcessor::NAME = "normalize.mask" [static] |