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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

ProcessorNEW ()

Static Public Attributes

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 5089 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 5104 of file processor.h.

05105                 {
05106                         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.";
05107                 }

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 5094 of file processor.h.

05095                 {
05096                         return NAME;
05097                 }

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 5109 of file processor.h.

References EMAN::TypeDict::put().

05110                 {
05111                         TypeDict d;
05112                         d.put("threshold", EMObject::FLOAT, "an isosurface threshold at which all desired features are visible");
05113                         d.put("radius", EMObject::FLOAT, "a normalization size similar to an lp= value");
05114                         d.put("apix", EMObject::FLOAT, "Angstrom per pixel ratio");
05115                         return d;
05116                 }

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

Definition at line 5099 of file processor.h.

05100                 {
05101                         return new LocalNormProcessor();
05102                 }

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 5734 of file processor.cpp.

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

05735 {
05736         if (!image) {
05737                 LOGWARN("NULL Image");
05738                 return;
05739         }
05740         float apix = params["apix"];
05741         float threshold = params["threshold"];
05742         float radius = params["radius"];
05743 
05744         if (apix > 0) {
05745                 int ny = image->get_ysize();
05746                 radius = ny * apix / radius;
05747                 //printf("Norm filter radius=%1.1f\n", radius);
05748         }
05749 
05750         EMData *blur = image->copy();
05751         EMData *maskblur = image->copy();
05752 
05753         maskblur->process_inplace("threshold.binary", Dict("value", threshold));
05754         maskblur->process_inplace("filter.lowpass.gauss", Dict("cutoff_pixels", radius));
05755 //      maskblur->process_inplace("filter.highpass.tanh", Dict("highpass", -10.0f));
05756         maskblur->process_inplace("threshold.belowtozero", Dict("minval", 0.001f));
05757 //      maskblur->process_inplace("threshold.belowtozero", Dict("minval", 0.001f));
05758 
05759 
05760         blur->process_inplace("threshold.belowtozero", Dict("minval", threshold));
05761         blur->process_inplace("filter.lowpass.gauss", Dict("cutoff_pixels", radius));
05762 //      blur->process_inplace("filter.highpass.tanh", Dict("cutoff_abs", -10.0f));
05763 
05764         maskblur->div(*blur);
05765         image->mult(*maskblur);
05766 //      maskblur->write_image("norm.mrc", 0, EMUtil::IMAGE_MRC);
05767 
05768         if( maskblur )
05769         {
05770                 delete maskblur;
05771                 maskblur = 0;
05772         }
05773 
05774         if( blur )
05775         {
05776                 delete blur;
05777                 blur = 0;
05778         }
05779 }


Member Data Documentation

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

Definition at line 171 of file processor.cpp.


The documentation for this class was generated from the following files:
Generated on Thu Dec 9 13:48:14 2010 for EMAN2 by  doxygen 1.3.9.1