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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 5264 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 5279 of file processor.h.

05280                 {
05281                         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.";
05282                 }

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 5269 of file processor.h.

References NAME.

05270                 {
05271                         return NAME;
05272                 }

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 5284 of file processor.h.

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

05285                 {
05286                         TypeDict d;
05287                         d.put("threshold", EMObject::FLOAT, "an isosurface threshold at which all desired features are visible");
05288                         d.put("radius", EMObject::FLOAT, "a normalization size similar to an lp= value");
05289                         d.put("apix", EMObject::FLOAT, "Angstrom per pixel ratio");
05290                         return d;
05291                 }

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

Definition at line 5274 of file processor.h.

05275                 {
05276                         return new LocalNormProcessor();
05277                 }

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 5765 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().

05766 {
05767         if (!image) {
05768                 LOGWARN("NULL Image");
05769                 return;
05770         }
05771         float apix = params["apix"];
05772         float threshold = params["threshold"];
05773         float radius = params["radius"];
05774 
05775         if (apix > 0) {
05776                 int ny = image->get_ysize();
05777                 radius = ny * apix / radius;
05778                 //printf("Norm filter radius=%1.1f\n", radius);
05779         }
05780 
05781         EMData *blur = image->copy();
05782         EMData *maskblur = image->copy();
05783 
05784         maskblur->process_inplace("threshold.binary", Dict("value", threshold));
05785         maskblur->process_inplace("eman1.filter.lowpass.gaussian", Dict("lowpass", radius));
05786         maskblur->process_inplace("eman1.filter.highpass.tanh", Dict("highpass", -10.0f));
05787         maskblur->process_inplace("threshold.belowtozero", Dict("minval", 0.001f));
05788         maskblur->process_inplace("threshold.belowtozero", Dict("minval", 0.001f));
05789 
05790 
05791         blur->process_inplace("threshold.belowtozero", Dict("minval", threshold));
05792         blur->process_inplace("eman1.filter.lowpass.gaussian", Dict("lowpass", radius));
05793         blur->process_inplace("eman1.filter.highpass.tanh", Dict("highpass", -10.0f));
05794 
05795         maskblur->div(*blur);
05796         image->mult(*maskblur);
05797         maskblur->write_image("norm.mrc", 0, EMUtil::IMAGE_MRC);
05798 
05799         if( maskblur )
05800         {
05801                 delete maskblur;
05802                 maskblur = 0;
05803         }
05804 
05805         if( blur )
05806         {
05807                 delete blur;
05808                 blur = 0;
05809         }
05810 }


Member Data Documentation

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

Definition at line 5293 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Tue May 25 17:37:39 2010 for EMAN2 by  doxygen 1.4.4