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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 5385 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 5400 of file processor.h.

05401                 {
05402                         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.";
05403                 }

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 5390 of file processor.h.

05391                 {
05392                         return NAME;
05393                 }

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 5405 of file processor.h.

References EMAN::TypeDict::put().

05406                 {
05407                         TypeDict d;
05408                         d.put("threshold", EMObject::FLOAT, "Only values above the threshold will be used to compute the normalization. Generally a good isosurface value.");
05409                         d.put("radius", EMObject::FLOAT, "Fourier filter radius expressed in pixels in Fourier space. cutoff_pixels in filter.lowpass.gauss");
05410                         d.put("apix", EMObject::FLOAT, "Angstroms per pixel");
05411                         return d;
05412                 }

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

Definition at line 5395 of file processor.h.

05396                 {
05397                         return new LocalNormProcessor();
05398                 }

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 6055 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().

06056 {
06057         if (!image) {
06058                 LOGWARN("NULL Image");
06059                 return;
06060         }
06061         float apix = params["apix"];
06062         float threshold = params["threshold"];
06063         float radius = params["radius"];
06064 
06065         if (apix > 0) {
06066                 int ny = image->get_ysize();
06067                 radius = ny * apix / radius;
06068                 //printf("Norm filter radius=%1.1f\n", radius);
06069         }
06070 
06071         EMData *blur = image->copy();
06072         EMData *maskblur = image->copy();
06073 
06074         maskblur->process_inplace("threshold.binary", Dict("value", threshold));
06075         maskblur->process_inplace("filter.lowpass.gauss", Dict("cutoff_pixels", radius));
06076 //      maskblur->process_inplace("filter.highpass.tanh", Dict("highpass", -10.0f));
06077         maskblur->process_inplace("threshold.belowtozero", Dict("minval", 0.001f));
06078 //      maskblur->process_inplace("threshold.belowtozero", Dict("minval", 0.001f));
06079 
06080 
06081         blur->process_inplace("threshold.belowtozero", Dict("minval", threshold));
06082         blur->process_inplace("filter.lowpass.gauss", Dict("cutoff_pixels", radius));
06083 //      blur->process_inplace("filter.highpass.tanh", Dict("cutoff_abs", -10.0f));
06084 
06085         maskblur->div(*blur);
06086         image->mult(*maskblur);
06087 //      maskblur->write_image("norm.mrc", 0, EMUtil::IMAGE_MRC);
06088 
06089         if( maskblur )
06090         {
06091                 delete maskblur;
06092                 maskblur = 0;
06093         }
06094 
06095         if( blur )
06096         {
06097                 delete blur;
06098                 blur = 0;
06099         }
06100 }


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 Tue Jun 11 13:42:40 2013 for EMAN2 by  doxygen 1.3.9.1