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EMAN::AutoMask2DProcessor Class Reference

Attempts to automatically mask out the particle, excluding other particles in the box, etc. More...

#include <processor.h>

Inheritance diagram for EMAN::AutoMask2DProcessor:

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Collaboration diagram for EMAN::AutoMask2DProcessor:
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List of all members.

Public Member Functions

virtual void process_inplace (EMData *image)
 To process an image in-place.
virtual string get_name () const
 Get the processor's name.
virtual TypeDict get_param_types () const
 Get processor parameter information in a dictionary.
virtual string get_desc () const
 Get the descrition of this specific processor.

Static Public Member Functions

ProcessorNEW ()

Static Public Attributes

const string NAME = "mask.auto2d"

Detailed Description

Attempts to automatically mask out the particle, excluding other particles in the box, etc.

Parameters:
threshold runs from ~ -2 to 2, negative numbers for dark protein and positive numbers for light protein (stain).
filter is expressed as a fraction of the fourier radius.

Definition at line 4856 of file processor.h.


Member Function Documentation

virtual string EMAN::AutoMask2DProcessor::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 4885 of file processor.h.

04886                 {
04887                         return "2D version of mask.auto3d";
04888                 }

virtual string EMAN::AutoMask2DProcessor::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 4861 of file processor.h.

04862                 {
04863                         return NAME;
04864                 }

virtual TypeDict EMAN::AutoMask2DProcessor::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 4871 of file processor.h.

References EMAN::TypeDict::put().

04872                 {
04873                         TypeDict d;
04874                         d.put("radius", EMObject::INT,"Pixel radius of a ball which is used to seed the flood filling operation. ");
04875                         d.put("nmaxseed",EMObject::INT,"Use the n highest valued pixels in the map as a seed. Alternative to radius. Useful for viruses.");
04876                         d.put("threshold", EMObject::FLOAT, "An isosurface threshold that suitably encases the mass.");
04877                         d.put("sigma", EMObject::FLOAT, "Alternative to threshold based on mean + x*sigma");
04878                         d.put("nshells", EMObject::INT, "The number of dilation operations");
04879                         d.put("nshellsgauss", EMObject::INT, "number of Gaussian pixels to expand, following the dilation operations");
04880                         d.put("return_mask", EMObject::BOOL, "If true the result of the operation will produce the mask, not the masked volume.");
04881                         d.put("verbose", EMObject::INT, "How verbose to be (stdout)");
04882                         return d;
04883                 }

Processor* EMAN::AutoMask2DProcessor::NEW  )  [inline, static]
 

Definition at line 4866 of file processor.h.

04867                 {
04868                         return new AutoMask2DProcessor();
04869                 }

void AutoMask2DProcessor::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 5206 of file processor.cpp.

References abs, EMAN::EMData::calc_n_highest_locations(), EMAN::EMData::get_attr(), EMAN::EMData::get_data(), EMAN::EMData::get_ndim(), EMAN::EMData::get_size(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::Dict::has_key(), ImageDimensionException, LOGWARN, EMAN::EMData::mult(), nx, ny, EMAN::EMData::process_inplace(), EMAN::Dict::set_default(), EMAN::EMData::set_size(), EMAN::EMData::set_value_at(), and EMAN::EMData::update().

05207 {
05208         if (!image) {
05209                 LOGWARN("NULL Image");
05210                 return;
05211         }
05212 
05213         if (image->get_ndim() != 2) {
05214                 throw ImageDimensionException("This processor only supports 2D images.");
05215         }
05216 
05217         /*
05218          The mask writing functionality was removed to comply with an EMAN2 policy which dictates that file io is not allowed from within a processor
05219          To get around this just use the return_mask parameter.
05220         string mask_output = params.set_default("write_mask", "");
05221         if ( mask_output != "") {
05222                 if (Util::is_file_exist(mask_output) ) throw InvalidParameterException("The mask output file name already exists. Please remove it if you don't need it.");
05223                 if (!EMUtil::is_valid_filename(mask_output)) throw InvalidParameterException("The mask output file name type is invalid or unrecognized");
05224         }
05225         */
05226 
05227         int radius=0;
05228         if (params.has_key("radius")) {
05229                 radius = params["radius"];
05230         }
05231         int nmaxseed=0;
05232         if (params.has_key("nmaxseed")) {
05233                 nmaxseed = params["nmaxseed"];
05234         }
05235 
05236         float threshold=0.0;
05237         if (params.has_key("sigma")) threshold=(float)(image->get_attr("mean"))+(float)(image->get_attr("sigma"))*(float)params["sigma"];
05238         else threshold=params["threshold"];
05239 
05240 
05241         int nshells = params["nshells"];
05242         int nshellsgauss = params["nshellsgauss"];
05243         int verbose=params.set_default("verbose",0);
05244 
05245         int nx = image->get_xsize();
05246         int ny = image->get_ysize();
05247 
05248         EMData *amask = new EMData();
05249         amask->set_size(nx, ny);
05250 
05251         float *dat = image->get_data();
05252         float *dat2 = amask->get_data();
05253         int i,j,k;
05254         size_t l = 0;
05255 
05256         if (verbose) printf("%f\t%f\t%f\n",(float)image->get_attr("mean"),(float)image->get_attr("sigma"),threshold);
05257 
05258         // Seeds with the highest valued pixels
05259         if (nmaxseed>0) {
05260                 vector<Pixel> maxs=image->calc_n_highest_locations(nmaxseed);
05261 
05262                 for (vector<Pixel>::iterator i=maxs.begin(); i<maxs.end(); i++) {
05263                         amask->set_value_at((*i).x,(*i).y,0,1.0);
05264                         if (verbose) printf("Seed at %d,%d,%d (%1.3f)\n",(*i).x,(*i).y,(*i).z,(*i).value);
05265                 }
05266         }
05267 
05268         // Seeds with a circle
05269         if (radius>0) {
05270                 // start with an initial circle
05271                 l=0;
05272                 for (j = -ny / 2; j < ny / 2; ++j) {
05273                         for (i = -nx / 2; i < nx / 2; ++i,++l) {
05274                                 if ( abs(j) > radius || abs(i) > radius) continue;
05275 //                              if ( (j * j + i * i) > (radius*radius) || dat[l] < threshold) continue;         // torn on the whole threshold issue here. Removing it prevents images from being totally masked out
05276                                 if ( (j * j + i * i) > (radius*radius) ) continue;
05277                                 dat2[l] = 1.0f;
05278                         }
05279                 }
05280         }
05281 
05282         // iteratively 'flood fills' the map... recursion would be better
05283         int done=0;
05284         int iter=0;
05285         while (!done) {
05286                 iter++;
05287                 done=1;
05288                 if (verbose && iter%10==0) printf("%d iterations\n",iter);
05289                 for (j=1; j<ny-1; ++j) {
05290                         for (i=1; i<nx-1; ++i) {
05291                                 l=i+j*nx;
05292                                 if (dat2[l]) continue;
05293                                 if (dat[l]>threshold && (dat2[l-1]||dat2[l+1]||dat2[l+nx]||dat2[l-nx])) {
05294                                         dat2[l]=1.0;
05295                                         done=0;
05296                                 }
05297                         }
05298                 }
05299         }
05300 
05301         amask->update();
05302 
05303         if (verbose) printf("extending mask\n");
05304         amask->process_inplace("mask.addshells.gauss", Dict("val1", nshells, "val2", nshellsgauss));
05305 
05306         bool return_mask = params.set_default("return_mask",false);
05307         if (return_mask) {
05308                 // Yes there is probably a much more efficient way of getting the mask itself, but I am only providing a stop gap at the moment.
05309                 memcpy(dat,dat2,image->get_size()*sizeof(float));
05310         } else {
05311                 image->mult(*amask);
05312         }
05313 
05314         // EMAN2 policy is not to allow file io from with a processor
05315         //if (mask_output != "") {
05316         //      amask->write_image(mask_output);
05317         //}
05318 
05319 
05320         delete amask;
05321 }


Member Data Documentation

const string AutoMask2DProcessor::NAME = "mask.auto2d" [static]
 

Definition at line 165 of file processor.cpp.


The documentation for this class was generated from the following files:
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