EMAN::LocalNormProcessor Class Reference

This processor attempts to perform a 'local normalization' so low density and high density features will be on a more even playing field in an isosurface display. More...

#include <processor.h>

Inheritance diagram for EMAN::LocalNormProcessor:

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Collaboration diagram for EMAN::LocalNormProcessor:

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List of all members.

Public Member Functions

void process_inplace (EMData *image)
 To process an image in-place.
virtual string get_name () const
 Get the processor's name.
virtual string get_desc () const
 Get the descrition of this specific processor.
virtual TypeDict get_param_types () const
 Get processor parameter information in a dictionary.

Static Public Member Functions

static ProcessorNEW ()

Static Public Attributes

static const string NAME = "misc.localnorm"

Detailed Description

This processor attempts to perform a 'local normalization' so low density and high density features will be on a more even playing field in an isosurface display.

threshold is an isosurface threshold at which all desired features are visible, radius is a normalization size similar to an lp= value.

Parameters:
threshold an isosurface threshold at which all desired features are visible
radius a normalization size similar to an lp= value
apix Angstrom per pixel ratio

Definition at line 5304 of file processor.h.


Member Function Documentation

virtual string EMAN::LocalNormProcessor::get_desc (  )  const [inline, virtual]

Get the descrition of this specific processor.

This function must be overwritten by a subclass.

Returns:
The description of this processor.

Implements EMAN::Processor.

Definition at line 5319 of file processor.h.

05320                 {
05321                         return "This processor attempts to perform a 'local normalization' so low density and high density features will be on a more even playing field in an isosurface display. threshold is an isosurface threshold at which all desired features are visible, radius is a normalization size similar to an lp= value.";
05322                 }

virtual string EMAN::LocalNormProcessor::get_name (  )  const [inline, virtual]

Get the processor's name.

Each processor is identified by a unique name.

Returns:
The processor's name.

Implements EMAN::Processor.

Definition at line 5309 of file processor.h.

References NAME.

05310                 {
05311                         return NAME;
05312                 }

virtual TypeDict EMAN::LocalNormProcessor::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.

Returns:
A dictionary containing the parameter info.

Reimplemented from EMAN::Processor.

Definition at line 5324 of file processor.h.

References EMAN::EMObject::FLOAT, and EMAN::TypeDict::put().

05325                 {
05326                         TypeDict d;
05327                         d.put("threshold", EMObject::FLOAT, "an isosurface threshold at which all desired features are visible");
05328                         d.put("radius", EMObject::FLOAT, "a normalization size similar to an lp= value");
05329                         d.put("apix", EMObject::FLOAT, "Angstrom per pixel ratio");
05330                         return d;
05331                 }

static Processor* EMAN::LocalNormProcessor::NEW (  )  [inline, static]

Definition at line 5314 of file processor.h.

05315                 {
05316                         return new LocalNormProcessor();
05317                 }

void LocalNormProcessor::process_inplace ( EMData image  )  [virtual]

To process an image in-place.

For those processors which can only be processed out-of-place, override this function to just print out some error message to remind user call the out-of-place version.

Parameters:
image The image to be processed.

Implements EMAN::Processor.

Definition at line 5872 of file processor.cpp.

References EMAN::EMData::copy(), EMAN::EMData::div(), EMAN::EMData::get_ysize(), EMAN::EMUtil::IMAGE_MRC, LOGWARN, EMAN::EMData::mult(), EMAN::Processor::params, EMAN::EMData::process_inplace(), and EMAN::EMData::write_image().

05873 {
05874         if (!image) {
05875                 LOGWARN("NULL Image");
05876                 return;
05877         }
05878         float apix = params["apix"];
05879         float threshold = params["threshold"];
05880         float radius = params["radius"];
05881 
05882         if (apix > 0) {
05883                 int ny = image->get_ysize();
05884                 radius = ny * apix / radius;
05885                 //printf("Norm filter radius=%1.1f\n", radius);
05886         }
05887 
05888         EMData *blur = image->copy();
05889         EMData *maskblur = image->copy();
05890 
05891         maskblur->process_inplace("threshold.binary", Dict("value", threshold));
05892         maskblur->process_inplace("eman1.filter.lowpass.gaussian", Dict("lowpass", radius));
05893         maskblur->process_inplace("eman1.filter.highpass.tanh", Dict("highpass", -10.0f));
05894         maskblur->process_inplace("threshold.belowtozero", Dict("minval", 0.001f));
05895         maskblur->process_inplace("threshold.belowtozero", Dict("minval", 0.001f));
05896 
05897 
05898         blur->process_inplace("threshold.belowtozero", Dict("minval", threshold));
05899         blur->process_inplace("eman1.filter.lowpass.gaussian", Dict("lowpass", radius));
05900         blur->process_inplace("eman1.filter.highpass.tanh", Dict("highpass", -10.0f));
05901 
05902         maskblur->div(*blur);
05903         image->mult(*maskblur);
05904         maskblur->write_image("norm.mrc", 0, EMUtil::IMAGE_MRC);
05905 
05906         if( maskblur )
05907         {
05908                 delete maskblur;
05909                 maskblur = 0;
05910         }
05911 
05912         if( blur )
05913         {
05914                 delete blur;
05915                 blur = 0;
05916         }
05917 }


Member Data Documentation

const string LocalNormProcessor::NAME = "misc.localnorm" [static]

Definition at line 5333 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Mon Jul 19 12:43:57 2010 for EMAN2 by  doxygen 1.4.7