#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 | |
Processor * | NEW () |
Static Public Attributes | |
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 3474 of file processor.h.
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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.
Definition at line 1939 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(), nx, ny, rdata, and EMAN::EMData::scale_pixel(). Referenced by process(), and process_inplace(). 01940 { 01941 01942 int nx_old = from->get_xsize(); 01943 int ny_old = from->get_ysize(); 01944 01945 int threed_shrink_factor = shrink_factor * shrink_factor; 01946 int z_shrink_factor = 1; 01947 if (from->get_zsize() > 1) { 01948 threed_shrink_factor *= shrink_factor; 01949 z_shrink_factor = shrink_factor; 01950 } 01951 01952 float *mbuf = new float[threed_shrink_factor]; 01953 01954 01955 int nxy_old = nx_old * ny_old; 01956 01957 int nx = to->get_xsize(); 01958 int ny = to->get_ysize(); 01959 int nz = to->get_zsize(); 01960 int nxy_new = nx * ny; 01961 01962 float * rdata = to->get_data(); 01963 const float *const data_copy = from->get_const_data(); 01964 01965 for (int l = 0; l < nz; l++) { 01966 int l_min = l * shrink_factor; 01967 int l_max = l * shrink_factor + z_shrink_factor; 01968 size_t cur_l = (size_t)l * nxy_new; 01969 01970 for (int j = 0; j < ny; j++) { 01971 int j_min = j * shrink_factor; 01972 int j_max = (j + 1) * shrink_factor; 01973 size_t cur_j = j * nx + cur_l; 01974 01975 for (int i = 0; i < nx; i++) { 01976 int i_min = i * shrink_factor; 01977 int i_max = (i + 1) * shrink_factor; 01978 01979 size_t k = 0; 01980 for (int l2 = l_min; l2 < l_max; l2++) { 01981 size_t cur_l2 = l2 * nxy_old; 01982 01983 for (int j2 = j_min; j2 < j_max; j2++) { 01984 size_t cur_j2 = j2 * nx_old + cur_l2; 01985 01986 for (int i2 = i_min; i2 < i_max; i2++) { 01987 mbuf[k] = data_copy[i2 + cur_j2]; 01988 ++k; 01989 } 01990 } 01991 } 01992 01993 for (k = 0; k < size_t(threed_shrink_factor / 2 + 1); k++) { 01994 for (int i2 = k + 1; i2 < threed_shrink_factor; i2++) { 01995 if (mbuf[i2] < mbuf[k]) { 01996 float f = mbuf[i2]; 01997 mbuf[i2] = mbuf[k]; 01998 mbuf[k] = f; 01999 } 02000 } 02001 } 02002 02003 rdata[i + cur_j] = mbuf[threed_shrink_factor / 2]; 02004 } 02005 } 02006 } 02007 02008 if( mbuf ) 02009 { 02010 delete[]mbuf; 02011 mbuf = 0; 02012 } 02013 02014 to->scale_pixel((float)shrink_factor); 02015 }
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Get the descrition of this specific processor. This function must be overwritten by a subclass.
Implements EMAN::Processor. Definition at line 3497 of file processor.h. 03498 { 03499 return "Shrink an image by a given amount , using the median value found in the pixel neighborhood."; 03500 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 3502 of file processor.h. 03503 {
03504 return NAME;
03505 }
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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 3511 of file processor.h. References EMAN::TypeDict::put(). 03512 { 03513 TypeDict d; 03514 d.put("n", EMObject::INT, "The shrink factor"); 03515 return d; 03516 }
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Definition at line 3506 of file processor.h. 03507 { 03508 return new MedianShrinkProcessor(); 03509 }
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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
Reimplemented from EMAN::Processor. Definition at line 1906 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(), nx, ny, EMAN::Dict::set_default(), EMAN::EMData::set_size(), and EMAN::EMData::update(). 01907 { 01908 if (image->is_complex()) throw ImageFormatException("Error, the median shrink processor does not work on complex images"); 01909 01910 int shrink_factor = params.set_default("n",0); 01911 if (shrink_factor <= 1) { 01912 throw InvalidValueException(shrink_factor, 01913 "median shrink: shrink factor must > 1"); 01914 } 01915 int nx = image->get_xsize(); 01916 int ny = image->get_ysize(); 01917 int nz = image->get_zsize(); 01918 01919 01920 // if ((nx % shrink_factor != 0) || (ny % shrink_factor != 0) || (nz > 1 && (nz % shrink_factor != 0))) { 01921 // throw InvalidValueException(shrink_factor, "Image size not divisible by shrink factor"); 01922 // } 01923 01924 01925 int shrunken_nx = nx / shrink_factor; 01926 int shrunken_ny = ny / shrink_factor; 01927 int shrunken_nz = 1; 01928 if (nz > 1) shrunken_nz = nz / shrink_factor; 01929 01930 // EMData* ret = new EMData(shrunken_nx, shrunken_ny, shrunken_nz); 01931 EMData *ret = image->copy_head(); 01932 ret->set_size(shrunken_nx, shrunken_ny, shrunken_nz); 01933 01934 accrue_median(ret,image,shrink_factor); 01935 ret->update(); 01936 return ret; 01937 }
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Median shrink the image.
Implements EMAN::Processor. Definition at line 1870 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(), nx, ny, EMAN::Dict::set_default(), EMAN::EMData::set_size(), and EMAN::EMData::update(). 01871 { 01872 if (image->is_complex()) throw ImageFormatException("Error, the median shrink processor does not work on complex images"); 01873 01874 int shrink_factor = params.set_default("n",0); 01875 if (shrink_factor <= 1) { 01876 throw InvalidValueException(shrink_factor, 01877 "median shrink: shrink factor must > 1"); 01878 } 01879 01880 int nx = image->get_xsize(); 01881 int ny = image->get_ysize(); 01882 int nz = image->get_zsize(); 01883 01884 // if ((nx % shrink_factor != 0) || (ny % shrink_factor != 0) || (nz > 1 && (nz % shrink_factor != 0))) { 01885 // throw InvalidValueException(shrink_factor, "Image size not divisible by shrink factor"); 01886 // } 01887 01888 01889 int shrunken_nx = nx / shrink_factor; 01890 int shrunken_ny = ny / shrink_factor; 01891 int shrunken_nz = 1; 01892 if (nz > 1) shrunken_nz = nz / shrink_factor; 01893 01894 EMData* copy = image->copy(); 01895 image->set_size(shrunken_nx, shrunken_ny, shrunken_nz); 01896 accrue_median(image,copy,shrink_factor); 01897 image->update(); 01898 if( copy ) 01899 { 01900 delete copy; 01901 copy = 0; 01902 } 01903 }
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Definition at line 127 of file processor.cpp. |