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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 5346 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 5361 of file processor.h.

05362                 {
05363                         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.";
05364                 }

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 5351 of file processor.h.

05352                 {
05353                         return NAME;
05354                 }

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 5366 of file processor.h.

References EMAN::TypeDict::put().

05367                 {
05368                         TypeDict d;
05369                         d.put("threshold", EMObject::FLOAT, "an isosurface threshold at which all desired features are visible");
05370                         d.put("radius", EMObject::FLOAT, "a normalization size similar to an lp= value");
05371                         d.put("apix", EMObject::FLOAT, "Angstrom per pixel ratio");
05372                         return d;
05373                 }

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

Definition at line 5356 of file processor.h.

05357                 {
05358                         return new LocalNormProcessor();
05359                 }

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 5990 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().

05991 {
05992         if (!image) {
05993                 LOGWARN("NULL Image");
05994                 return;
05995         }
05996         float apix = params["apix"];
05997         float threshold = params["threshold"];
05998         float radius = params["radius"];
05999 
06000         if (apix > 0) {
06001                 int ny = image->get_ysize();
06002                 radius = ny * apix / radius;
06003                 //printf("Norm filter radius=%1.1f\n", radius);
06004         }
06005 
06006         EMData *blur = image->copy();
06007         EMData *maskblur = image->copy();
06008 
06009         maskblur->process_inplace("threshold.binary", Dict("value", threshold));
06010         maskblur->process_inplace("filter.lowpass.gauss", Dict("cutoff_pixels", radius));
06011 //      maskblur->process_inplace("filter.highpass.tanh", Dict("highpass", -10.0f));
06012         maskblur->process_inplace("threshold.belowtozero", Dict("minval", 0.001f));
06013 //      maskblur->process_inplace("threshold.belowtozero", Dict("minval", 0.001f));
06014 
06015 
06016         blur->process_inplace("threshold.belowtozero", Dict("minval", threshold));
06017         blur->process_inplace("filter.lowpass.gauss", Dict("cutoff_pixels", radius));
06018 //      blur->process_inplace("filter.highpass.tanh", Dict("cutoff_abs", -10.0f));
06019 
06020         maskblur->div(*blur);
06021         image->mult(*maskblur);
06022 //      maskblur->write_image("norm.mrc", 0, EMUtil::IMAGE_MRC);
06023 
06024         if( maskblur )
06025         {
06026                 delete maskblur;
06027                 maskblur = 0;
06028         }
06029 
06030         if( blur )
06031         {
06032                 delete blur;
06033                 blur = 0;
06034         }
06035 }


Member Data Documentation

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

Definition at line 177 of file processor.cpp.


The documentation for this class was generated from the following files:
Generated on Fri Aug 10 16:38:03 2012 for EMAN2 by  doxygen 1.3.9.1