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 = "normalize.local"

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 5230 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 5245 of file processor.h.

05246                 {
05247                         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 feature size over which to equalize.";
05248                 }

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 5235 of file processor.h.

References NAME.

05236                 {
05237                         return NAME;
05238                 }

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 5250 of file processor.h.

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

05251                 {
05252                         TypeDict d;
05253                         d.put("threshold", EMObject::FLOAT, "an isosurface threshold at which all desired features are visible");
05254                         d.put("radius", EMObject::FLOAT, "a normalization size similar to an lp= value");
05255                         d.put("apix", EMObject::FLOAT, "Angstrom per pixel ratio");
05256                         return d;
05257                 }

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

Definition at line 5240 of file processor.h.

05241                 {
05242                         return new LocalNormProcessor();
05243                 }

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 5800 of file processor.cpp.

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

05801 {
05802         if (!image) {
05803                 LOGWARN("NULL Image");
05804                 return;
05805         }
05806         float apix = params["apix"];
05807         float threshold = params["threshold"];
05808         float radius = params["radius"];
05809 
05810         if (apix > 0) {
05811                 int ny = image->get_ysize();
05812                 radius = ny * apix / radius;
05813                 //printf("Norm filter radius=%1.1f\n", radius);
05814         }
05815 
05816         EMData *blur = image->copy();
05817         EMData *maskblur = image->copy();
05818 
05819         maskblur->process_inplace("threshold.binary", Dict("value", threshold));
05820         maskblur->process_inplace("filter.lowpass.gauss", Dict("cutoff_pixels", radius));
05821 //      maskblur->process_inplace("filter.highpass.tanh", Dict("highpass", -10.0f));
05822         maskblur->process_inplace("threshold.belowtozero", Dict("minval", 0.001f));
05823 //      maskblur->process_inplace("threshold.belowtozero", Dict("minval", 0.001f));
05824 
05825 
05826         blur->process_inplace("threshold.belowtozero", Dict("minval", threshold));
05827         blur->process_inplace("filter.lowpass.gauss", Dict("cutoff_pixels", radius));
05828 //      blur->process_inplace("filter.highpass.tanh", Dict("cutoff_abs", -10.0f));
05829 
05830         maskblur->div(*blur);
05831         image->mult(*maskblur);
05832 //      maskblur->write_image("norm.mrc", 0, EMUtil::IMAGE_MRC);
05833 
05834         if( maskblur )
05835         {
05836                 delete maskblur;
05837                 maskblur = 0;
05838         }
05839 
05840         if( blur )
05841         {
05842                 delete blur;
05843                 blur = 0;
05844         }
05845 }


Member Data Documentation

const string LocalNormProcessor::NAME = "normalize.local" [static]

Definition at line 5259 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Mon May 2 13:30:52 2011 for EMAN2 by  doxygen 1.4.7