#include <processor.h>
Inheritance diagram for EMAN::BeamstopProcessor:
Public Member Functions | |
void | process_inplace (EMData *image) |
To process an image in-place. | |
string | get_name () const |
Get the processor's name. | |
string | get_desc () const |
Get the descrition of this specific processor. | |
TypeDict | get_param_types () const |
Get processor parameter information in a dictionary. | |
Static Public Member Functions | |
Processor * | NEW () |
Static Public Attributes | |
const string | NAME = "mask.beamstop" |
If value1<0 also does radial subtract.
value1 | sig multiplier | |
value2 | x of center | |
value3 | y of center |
Definition at line 3756 of file processor.h.
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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 3771 of file processor.h. 03772 { 03773 return "Try to eliminate beamstop in electron diffraction patterns. value1=sig multiplier; value2,value3 are x,y of center, if value1<0 also does radial subtract."; 03774 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 3761 of file processor.h. 03762 {
03763 return NAME;
03764 }
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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 3776 of file processor.h. References EMAN::TypeDict::put(). 03777 { 03778 TypeDict d; 03779 d.put("value1", EMObject::FLOAT, "sig multiplier"); 03780 d.put("value2", EMObject::FLOAT, "x of center"); 03781 d.put("value3", EMObject::FLOAT, "y of center"); 03782 return d; 03783 }
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Definition at line 3766 of file processor.h. 03767 { 03768 return new BeamstopProcessor(); 03769 }
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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.
Implements EMAN::Processor. Definition at line 3047 of file processor.cpp. References data, EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ImageDimensionException, LOGERR, LOGWARN, nx, ny, EMAN::Util::round(), sqrt(), and EMAN::EMData::update(). 03048 { 03049 if (!image) { 03050 LOGWARN("NULL Image"); 03051 return; 03052 } 03053 if (image->get_zsize() > 1) { 03054 LOGERR("BeamstopProcessor doesn't support 3D model"); 03055 throw ImageDimensionException("3D model not supported"); 03056 } 03057 03058 float value1 = params["value1"]; 03059 float value2 = params["value2"]; 03060 float value3 = params["value3"]; 03061 03062 float thr = fabs(value1); 03063 float *data = image->get_data(); 03064 int cenx = (int) value2; 03065 int ceny = (int) value3; 03066 03067 int nx = image->get_xsize(); 03068 int ny = image->get_ysize(); 03069 03070 if (cenx <= 0) { 03071 cenx = nx / 2; 03072 } 03073 03074 if (ceny <= 0) { 03075 ceny = ny / 2; 03076 } 03077 03078 int mxr = (int) floor(sqrt(2.0f) * nx / 2); 03079 03080 float *mean_values = new float[mxr]; 03081 float *sigma_values = new float[mxr]; 03082 double sum = 0; 03083 int count = 0; 03084 double square_sum = 0; 03085 03086 for (int i = 0; i < mxr; i++) { 03087 sum = 0; 03088 count = 0; 03089 square_sum = 0; 03090 int nitems = 6 * i + 2; 03091 03092 for (int j = 0; j < nitems; j++) { 03093 float ang = j * 2 * M_PI / nitems; 03094 int x0 = (int) floor(cos(ang) * i + cenx); 03095 int y0 = (int) floor(sin(ang) * i + ceny); 03096 03097 if (x0 < 0 || y0 < 0 || x0 >= nx || y0 >= ny) { 03098 continue; 03099 } 03100 03101 float f = data[x0 + y0 * nx]; 03102 sum += f; 03103 square_sum += f * f; 03104 count++; 03105 } 03106 03107 mean_values[i] = (float)sum / count; 03108 sigma_values[i] = (float) sqrt(square_sum / count - mean_values[i] * mean_values[i]); 03109 } 03110 03111 03112 for (int k = 0; k < 5; k++) { 03113 for (int i = 0; i < mxr; i++) { 03114 sum = 0; 03115 count = 0; 03116 square_sum = 0; 03117 int nitems = 6 * i + 2; 03118 double thr1 = mean_values[i] - sigma_values[i] * thr; 03119 double thr2 = mean_values[i] + sigma_values[i]; 03120 03121 for (int j = 0; j < nitems; j++) { 03122 float ang = j * 2 * M_PI / nitems; 03123 int x0 = (int) floor(cos(ang) * i + cenx); 03124 int y0 = (int) floor(sin(ang) * i + ceny); 03125 03126 if (x0 < 0 || y0 < 0 || x0 >= nx || y0 >= ny || 03127 data[x0 + y0 * nx] < thr1 || data[x0 + y0 * nx] > thr2) { 03128 continue; 03129 } 03130 03131 sum += data[x0 + y0 * nx]; 03132 square_sum += data[x0 + y0 * nx] * data[x0 + y0 * nx]; 03133 count++; 03134 } 03135 03136 mean_values[i] = (float) sum / count; 03137 sigma_values[i] = (float) sqrt(square_sum / count - mean_values[i] * mean_values[i]); 03138 } 03139 } 03140 03141 for (int i = 0; i < nx; i++) { 03142 for (int j = 0; j < ny; j++) { 03143 03144 #ifdef _WIN32 03145 int r = Util::round(_hypot((float) i - cenx, (float) j - ceny)); 03146 #else 03147 int r = Util::round(hypot((float) i - cenx, (float) j - ceny)); 03148 #endif //_WIN32 03149 03150 if (value1 < 0) { 03151 if (data[i + j * nx] < (mean_values[r] - sigma_values[r] * thr)) { 03152 data[i + j * nx] = 0; 03153 } 03154 else { 03155 data[i + j * nx] -= mean_values[r]; 03156 } 03157 continue; 03158 } 03159 if (data[i + j * nx] > (mean_values[r] - sigma_values[r] * thr)) { 03160 continue; 03161 } 03162 data[i + j * nx] = mean_values[r]; 03163 } 03164 } 03165 03166 if( mean_values ) 03167 { 03168 delete[]mean_values; 03169 mean_values = 0; 03170 } 03171 03172 if( sigma_values ) 03173 { 03174 delete[]sigma_values; 03175 sigma_values = 0; 03176 } 03177 03178 image->update(); 03179 }
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Definition at line 135 of file processor.cpp. |