#include <processor.h>
Inheritance diagram for EMAN::MedianShrinkProcessor:
Public Member Functions | |
virtual EMData * | process (const EMData *const image) |
The medianshrink processor has its own process function to minise memory usage - if this function was not over written the base Processor class would create copy of the input image and hand it to the process_inplace function. | |
virtual void | process_inplace (EMData *image) |
Median shrink the image. | |
string | get_desc () const |
Get the descrition of this specific processor. | |
virtual string | get_name () const |
Get the processor's name. | |
virtual TypeDict | get_param_types () const |
Get processor parameter information in a dictionary. | |
Static Public Member Functions | |
static Processor * | NEW () |
Static Public Attributes | |
static const string | NAME = "math.medianshrink" |
Private Member Functions | |
void | accrue_median (EMData *to, const EMData *const from, const int shrink_factor) |
Accrue the local median in the image 'from' to the image 'to' using the given shrinkfactor An internal function that encapsulates a routine common to both process and process inplace. |
n | The shrink factor |
Definition at line 3519 of file processor.h.
void MedianShrinkProcessor::accrue_median | ( | EMData * | to, | |
const EMData *const | from, | |||
const int | shrink_factor | |||
) | [private] |
Accrue the local median in the image 'from' to the image 'to' using the given shrinkfactor An internal function that encapsulates a routine common to both process and process inplace.
to | the smaller image that will store the calculated median values | |
from | the larger image that will be used to calculate the median values | |
shrink_factor | the shrink amount |
Definition at line 2011 of file processor.cpp.
References EMAN::EMData::get_const_data(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), rdata, and EMAN::EMData::scale_pixel().
Referenced by process(), and process_inplace().
02012 { 02013 02014 int nx_old = from->get_xsize(); 02015 int ny_old = from->get_ysize(); 02016 02017 int threed_shrink_factor = shrink_factor * shrink_factor; 02018 int z_shrink_factor = 1; 02019 if (from->get_zsize() > 1) { 02020 threed_shrink_factor *= shrink_factor; 02021 z_shrink_factor = shrink_factor; 02022 } 02023 02024 float *mbuf = new float[threed_shrink_factor]; 02025 02026 02027 int nxy_old = nx_old * ny_old; 02028 02029 int nx = to->get_xsize(); 02030 int ny = to->get_ysize(); 02031 int nz = to->get_zsize(); 02032 int nxy_new = nx * ny; 02033 02034 float * rdata = to->get_data(); 02035 const float *const data_copy = from->get_const_data(); 02036 02037 for (int l = 0; l < nz; l++) { 02038 int l_min = l * shrink_factor; 02039 int l_max = l * shrink_factor + z_shrink_factor; 02040 size_t cur_l = (size_t)l * nxy_new; 02041 02042 for (int j = 0; j < ny; j++) { 02043 int j_min = j * shrink_factor; 02044 int j_max = (j + 1) * shrink_factor; 02045 size_t cur_j = j * nx + cur_l; 02046 02047 for (int i = 0; i < nx; i++) { 02048 int i_min = i * shrink_factor; 02049 int i_max = (i + 1) * shrink_factor; 02050 02051 size_t k = 0; 02052 for (int l2 = l_min; l2 < l_max; l2++) { 02053 size_t cur_l2 = l2 * nxy_old; 02054 02055 for (int j2 = j_min; j2 < j_max; j2++) { 02056 size_t cur_j2 = j2 * nx_old + cur_l2; 02057 02058 for (int i2 = i_min; i2 < i_max; i2++) { 02059 mbuf[k] = data_copy[i2 + cur_j2]; 02060 ++k; 02061 } 02062 } 02063 } 02064 02065 for (k = 0; k < size_t(threed_shrink_factor / 2 + 1); k++) { 02066 for (int i2 = k + 1; i2 < threed_shrink_factor; i2++) { 02067 if (mbuf[i2] < mbuf[k]) { 02068 float f = mbuf[i2]; 02069 mbuf[i2] = mbuf[k]; 02070 mbuf[k] = f; 02071 } 02072 } 02073 } 02074 02075 rdata[i + cur_j] = mbuf[threed_shrink_factor / 2]; 02076 } 02077 } 02078 } 02079 02080 if( mbuf ) 02081 { 02082 delete[]mbuf; 02083 mbuf = 0; 02084 } 02085 02086 to->scale_pixel((float)shrink_factor); 02087 }
string EMAN::MedianShrinkProcessor::get_desc | ( | ) | const [inline, virtual] |
Get the descrition of this specific processor.
This function must be overwritten by a subclass.
Implements EMAN::Processor.
Definition at line 3542 of file processor.h.
03543 { 03544 return "Shrink an image by a given amount , using the median value found in the pixel neighborhood."; 03545 }
virtual string EMAN::MedianShrinkProcessor::get_name | ( | ) | const [inline, virtual] |
Get the processor's name.
Each processor is identified by a unique name.
Implements EMAN::Processor.
Definition at line 3547 of file processor.h.
References NAME.
03548 { 03549 return NAME; 03550 }
virtual TypeDict EMAN::MedianShrinkProcessor::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.
Reimplemented from EMAN::Processor.
Definition at line 3556 of file processor.h.
References EMAN::EMObject::INT, and EMAN::TypeDict::put().
03557 { 03558 TypeDict d; 03559 d.put("n", EMObject::INT, "The shrink factor"); 03560 return d; 03561 }
static Processor* EMAN::MedianShrinkProcessor::NEW | ( | ) | [inline, static] |
Definition at line 3551 of file processor.h.
03552 { 03553 return new MedianShrinkProcessor(); 03554 }
The medianshrink processor has its own process function to minise memory usage - if this function was not over written the base Processor class would create copy of the input image and hand it to the process_inplace function.
This latter approach mallocs and copies more memory than necessary
image | the image that will be used to generate a 'median shrunken' image |
ImageFormatException | if the image is complex | |
InvalidValueException | if the shrink amount is not a non zero, positive integer | |
InvalidValueException | if any of the image dimensions are not divisible by the the shrink amount |
Reimplemented from EMAN::Processor.
Definition at line 1978 of file processor.cpp.
References accrue_median(), EMAN::EMData::copy_head(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ImageFormatException, InvalidValueException, EMAN::EMData::is_complex(), EMAN::Processor::params, EMAN::Dict::set_default(), EMAN::EMData::set_size(), and EMAN::EMData::update().
01979 { 01980 if (image->is_complex()) throw ImageFormatException("Error, the median shrink processor does not work on complex images"); 01981 01982 int shrink_factor = params.set_default("n",0); 01983 if (shrink_factor <= 1) { 01984 throw InvalidValueException(shrink_factor, 01985 "median shrink: shrink factor must > 1"); 01986 } 01987 int nx = image->get_xsize(); 01988 int ny = image->get_ysize(); 01989 int nz = image->get_zsize(); 01990 01991 01992 // if ((nx % shrink_factor != 0) || (ny % shrink_factor != 0) || (nz > 1 && (nz % shrink_factor != 0))) { 01993 // throw InvalidValueException(shrink_factor, "Image size not divisible by shrink factor"); 01994 // } 01995 01996 01997 int shrunken_nx = nx / shrink_factor; 01998 int shrunken_ny = ny / shrink_factor; 01999 int shrunken_nz = 1; 02000 if (nz > 1) shrunken_nz = nz / shrink_factor; 02001 02002 // EMData* ret = new EMData(shrunken_nx, shrunken_ny, shrunken_nz); 02003 EMData *ret = image->copy_head(); 02004 ret->set_size(shrunken_nx, shrunken_ny, shrunken_nz); 02005 02006 accrue_median(ret,image,shrink_factor); 02007 ret->update(); 02008 return ret; 02009 }
void MedianShrinkProcessor::process_inplace | ( | EMData * | image | ) | [virtual] |
Median shrink the image.
image | the image the image that will be 'median shrunken' inplace |
ImageFormatException | if the image is complex | |
InvalidValueException | if the shrink amount is not a non zero, positive integer | |
InvalidValueException | if any of the image dimensions are not divisible by the the shrink amount |
Implements EMAN::Processor.
Definition at line 1942 of file processor.cpp.
References accrue_median(), EMAN::EMData::copy(), copy(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ImageFormatException, InvalidValueException, EMAN::EMData::is_complex(), EMAN::Processor::params, EMAN::Dict::set_default(), EMAN::EMData::set_size(), and EMAN::EMData::update().
01943 { 01944 if (image->is_complex()) throw ImageFormatException("Error, the median shrink processor does not work on complex images"); 01945 01946 int shrink_factor = params.set_default("n",0); 01947 if (shrink_factor <= 1) { 01948 throw InvalidValueException(shrink_factor, 01949 "median shrink: shrink factor must > 1"); 01950 } 01951 01952 int nx = image->get_xsize(); 01953 int ny = image->get_ysize(); 01954 int nz = image->get_zsize(); 01955 01956 // if ((nx % shrink_factor != 0) || (ny % shrink_factor != 0) || (nz > 1 && (nz % shrink_factor != 0))) { 01957 // throw InvalidValueException(shrink_factor, "Image size not divisible by shrink factor"); 01958 // } 01959 01960 01961 int shrunken_nx = nx / shrink_factor; 01962 int shrunken_ny = ny / shrink_factor; 01963 int shrunken_nz = 1; 01964 if (nz > 1) shrunken_nz = nz / shrink_factor; 01965 01966 EMData* copy = image->copy(); 01967 image->set_size(shrunken_nx, shrunken_ny, shrunken_nz); 01968 accrue_median(image,copy,shrink_factor); 01969 image->update(); 01970 if( copy ) 01971 { 01972 delete copy; 01973 copy = 0; 01974 } 01975 }
const string MedianShrinkProcessor::NAME = "math.medianshrink" [static] |