#include <emutil.h>
Public Types | |
enum | EMDataType { EM_UNKNOWN, EM_CHAR, EM_UCHAR, EM_SHORT, EM_USHORT, EM_INT, EM_UINT, EM_FLOAT, EM_DOUBLE, EM_SHORT_COMPLEX, EM_USHORT_COMPLEX, EM_FLOAT_COMPLEX } |
Image pixel data type used in EMAN. More... | |
enum | ImageType { IMAGE_UNKNOWN, IMAGE_MRC, IMAGE_SPIDER, IMAGE_SINGLE_SPIDER, IMAGE_IMAGIC, IMAGE_HDF, IMAGE_DM3, IMAGE_TIFF, IMAGE_PGM, IMAGE_LST, IMAGE_PIF, IMAGE_VTK, IMAGE_PNG, IMAGE_SAL, IMAGE_ICOS, IMAGE_EMIM, IMAGE_GATAN2, IMAGE_AMIRA, IMAGE_XPLOR, IMAGE_EM, IMAGE_V4L, IMAGE_JPEG, IMAGE_FITS, IMAGE_LSTFAST, IMAGE_DF3 } |
Image format types. More... | |
Static Public Member Functions | |
EMData * | vertical_acf (const EMData *image, int maxdy) |
EMData * | make_image_median (const vector< EMData * > &image_list) |
ImageType | get_image_ext_type (const string &file_ext) |
Get an image's format type from its filename extension. | |
ImageType | get_image_type (const string &filename) |
Get an image's format type by processing the first 1K of the image. | |
bool | is_valid_filename (const string &filename) |
Ask whether or not the given filename is a valid EM image filename This is the same thing as checking whether or not the return value of EMUtil.get_image_ext_type is IMAGE_UNKNOWN. | |
int | get_image_count (const string &filename) |
Get the number of images in an image file. | |
ImageIO * | get_imageio (const string &filename, int rw_mode, ImageType image_type=IMAGE_UNKNOWN) |
Get an ImageIO object. | |
const char * | get_imagetype_name (EMUtil::ImageType type) |
Give each image type a meaningful name. | |
const char * | get_datatype_string (EMDataType type) |
Give each data type a meaningful name. | |
void | get_region_dims (const Region *area, int nx, int *area_x, int ny, int *area_y, int nz=1, int *area_z=0) |
Get a region's dimensions. | |
void | get_region_origins (const Region *area, int *p_x0, int *p_y0, int *p_z0=0, int nz=1, int image_index=0) |
Get a region's original locations. | |
void | process_region_io (void *cdata, FILE *file, int rw_mode, int image_index, size_t mode_size, int nx, int ny, int nz=1, const Region *area=0, bool need_flip=false, ImageType imgtype=IMAGE_UNKNOWN, int pre_row=0, int post_row=0) |
Process image region IO. | |
void | process_ascii_region_io (float *data, FILE *file, int rw_mode, int image_index, size_t mode_size, int nx, int ny, int nz, const Region *area, bool has_index_line, int nitems_per_line, const char *outformat) |
Works for regions that are outside the image data dimension area. | |
void | dump_dict (const Dict &dict) |
Dump a Dict object. | |
bool | is_same_size (const EMData *image1, const EMData *image2) |
Check whether two EMData images are of the same size. | |
bool | is_same_ctf (const EMData *image1, const EMData *image2) |
Check whether two EMData images have the same CTF parameters. | |
bool | is_complex_type (EMDataType datatype) |
void | jump_lines (FILE *file, int nlines) |
vector< string > | get_euler_names (const string &euler_type) |
vector< EMObject > | get_all_attributes (const string &file_name, const string &attr_name) |
Get an attribute from a stack of image, returned as a vector. | |
void | getRenderMinMax (float *data, const int nx, const int ny, float &rendermin, float &rendermax, const int nz=1) |
Calculate the min and max pixel value acceptedfor image nomalization, if we did not get them from image attribute dictionary, or they are not valid values rendermin = mean - 3*sigma rendermax = mean + 3*sigma. | |
bool | cuda_available () |
void * | em_malloc (const size_t size) |
void * | em_calloc (const size_t nmemb, const size_t size) |
void * | em_realloc (void *data, const size_t new_size) |
void | em_memset (void *data, const int value, const size_t size) |
void | em_free (void *data) |
void | em_memcpy (void *dst, const void *const src, const size_t size) |
Static Private Member Functions | |
ImageType | fast_get_image_type (const string &filename, const void *first_block, off_t file_size) |
void | jump_lines_by_items (FILE *file, int nitems, int nitems_per_line) |
void | process_numbers_io (FILE *file, int rw_mode, int nitems_per_line, size_t mode_size, int start, int end, float *data, int *p_i, const char *outformat) |
void | exclude_numbers_io (FILE *file, int rw_mode, int nitems_per_line, size_t mode_size, int start, int end, float *data, int *p_i, const char *outformat) |
void | process_lines_io (FILE *file, int rw_mode, int nitems_per_line, size_t mode_size, int nitems, float *data, int *p_i, const char *outformat) |
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Image pixel data type used in EMAN. EM_U means "EM unsigned". for example, EM_USHORT means EM unsigned short.
Definition at line 92 of file emutil.h. Referenced by dump_dict(). 00093 { 00094 EM_UNKNOWN, 00095 EM_CHAR, 00096 EM_UCHAR, 00097 EM_SHORT, 00098 EM_USHORT, 00099 EM_INT, 00100 EM_UINT, 00101 EM_FLOAT, 00102 EM_DOUBLE, 00103 EM_SHORT_COMPLEX, 00104 EM_USHORT_COMPLEX, 00105 EM_FLOAT_COMPLEX 00106 };
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Image format types.
Definition at line 110 of file emutil.h. Referenced by fast_get_image_type(), get_image_ext_type(), get_image_type(), getRenderMinMax(), and is_valid_filename(). 00111 { 00112 IMAGE_UNKNOWN, 00113 IMAGE_MRC, 00114 IMAGE_SPIDER, 00115 IMAGE_SINGLE_SPIDER, 00116 IMAGE_IMAGIC, 00117 IMAGE_HDF, 00118 IMAGE_DM3, 00119 IMAGE_TIFF, 00120 IMAGE_PGM, 00121 IMAGE_LST, 00122 IMAGE_PIF, 00123 IMAGE_VTK, 00124 IMAGE_PNG, 00125 IMAGE_SAL, 00126 IMAGE_ICOS, 00127 IMAGE_EMIM, 00128 IMAGE_GATAN2, 00129 IMAGE_AMIRA, 00130 IMAGE_XPLOR, 00131 IMAGE_EM, 00132 IMAGE_V4L, 00133 IMAGE_JPEG, 00134 IMAGE_FITS, 00135 IMAGE_LSTFAST, 00136 IMAGE_DF3 00137 };
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Definition at line 332 of file emutil.h. 00332 { 00333 //#ifdef EMAN2_USING_CUDA 00334 // return true; 00335 //#else 00336 return false; 00337 //#endif 00338 }
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Dump a Dict object.
Definition at line 944 of file emutil.cpp. References EMDataType, get_datatype_string(), EMAN::EMObject::is_null(), EMAN::Dict::keys(), EMAN::EMObject::to_str(), and EMAN::Dict::values(). Referenced by main(). 00945 { 00946 vector < string > keys = dict.keys(); 00947 vector < EMObject > values = dict.values(); 00948 00949 for (unsigned int i = 0; i < keys.size(); i++) { 00950 EMObject obj = values[i]; 00951 if( !obj.is_null() ) { 00952 string val = obj.to_str(); 00953 00954 if (keys[i] == "datatype") { 00955 val = get_datatype_string((EMDataType) (int) obj); 00956 } 00957 00958 fprintf(stdout, "%25s\t%s\n", keys[i].c_str(), val.c_str()); 00959 } 00960 } 00961 }
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Definition at line 344 of file emutil.h. 00344 {
00345 return calloc(nmemb,size);
00346 }
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Definition at line 354 of file emutil.h. References data. Referenced by EMAN::EMData::free_memory(), and EMAN::EMData::free_rdata(). 00354 { 00355 free(data); 00356 }
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Definition at line 340 of file emutil.h. Referenced by EMAN::TransformProcessor::transform(). 00340 {
00341 return malloc(size);
00342 }
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Definition at line 358 of file emutil.h. 00358 { 00359 memcpy(dst,src,size); 00360 }
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Definition at line 351 of file emutil.h. References data. 00351 { 00352 memset(data, value, size); 00353 }
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Definition at line 348 of file emutil.h. References data. 00348 {
00349 return realloc(data, new_size);
00350 }
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Definition at line 1366 of file emutil.cpp. References Assert, data, and portable_fseek(). Referenced by process_ascii_region_io(). 01369 { 01370 Assert(file); 01371 Assert(mode_size > 0); 01372 Assert(start >= 0); 01373 Assert(end <= nitems_per_line); 01374 Assert(data); 01375 Assert(p_i); 01376 Assert(outformat); 01377 01378 char line[MAXPATHLEN]; 01379 01380 if (rw_mode == ImageIO::READ_ONLY) { 01381 01382 if (!fgets(line, sizeof(line), file)) { 01383 Assert("read xplor file failed"); 01384 } 01385 01386 int nitems_in_line = (int) (strlen(line) / mode_size); 01387 Assert(end <= nitems_in_line); 01388 01389 vector<float> d(nitems_in_line); 01390 char *pline = line; 01391 01392 for (int i = 0; i < nitems_in_line; i++) { 01393 sscanf(pline, "%f", &d[i]); 01394 pline = pline + (int)mode_size; 01395 } 01396 01397 01398 for (int i = 0; i < start; i++) { 01399 data[*p_i] = d[i]; 01400 (*p_i)++; 01401 } 01402 01403 for (int i = end+1; i < nitems_in_line; i++) { 01404 data[*p_i] = d[i]; 01405 (*p_i)++; 01406 } 01407 } 01408 else { 01409 for (int i = 0; i < start; i++) { 01410 fprintf(file, outformat, data[*p_i]); 01411 (*p_i)++; 01412 } 01413 01414 portable_fseek(file, (end-start+1) * mode_size, SEEK_CUR); 01415 01416 for (int i = end+1; i < nitems_per_line; i++) { 01417 fprintf(file, outformat, data[*p_i]); 01418 (*p_i)++; 01419 } 01420 portable_fseek(file, 1, SEEK_CUR); 01421 } 01422 }
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Definition at line 201 of file emutil.cpp. References Assert, EMAN::Util::get_filename_ext(), get_image_ext_type(), IMAGE_AMIRA, IMAGE_DF3, IMAGE_DM3, IMAGE_EM, IMAGE_GATAN2, IMAGE_HDF, IMAGE_ICOS, IMAGE_IMAGIC, IMAGE_LST, IMAGE_LSTFAST, IMAGE_MRC, IMAGE_PGM, IMAGE_PIF, IMAGE_PNG, IMAGE_SAL, IMAGE_SINGLE_SPIDER, IMAGE_SPIDER, IMAGE_TIFF, IMAGE_VTK, IMAGE_XPLOR, ImageType, EMAN::ImagicIO::is_valid(), EMAN::EmIO::is_valid(), EMAN::Gatan2IO::is_valid(), EMAN::XplorIO::is_valid(), EMAN::AmiraIO::is_valid(), EMAN::SalIO::is_valid(), EMAN::IcosIO::is_valid(), EMAN::PgmIO::is_valid(), EMAN::VtkIO::is_valid(), EMAN::PifIO::is_valid(), EMAN::SingleSpiderIO::is_valid(), EMAN::SpiderIO::is_valid(), EMAN::LstFastIO::is_valid(), EMAN::LstIO::is_valid(), EMAN::DM3IO::is_valid(), and EMAN::MrcIO::is_valid(). Referenced by get_image_type(). 00204 { 00205 ENTERFUNC; 00206 Assert(filename != ""); 00207 Assert(first_block != 0); 00208 Assert(file_size > 0); 00209 00210 #ifdef ENABLE_V4L2 00211 if (filename.compare(0,5,"/dev/")==0) return IMAGE_V4L; 00212 #endif 00213 00214 string ext = Util::get_filename_ext(filename); 00215 if (ext == "") { 00216 return IMAGE_UNKNOWN; 00217 } 00218 ImageType image_type = get_image_ext_type(ext); 00219 00220 switch (image_type) { 00221 case IMAGE_MRC: 00222 if (MrcIO::is_valid(first_block, file_size)) { 00223 return IMAGE_MRC; 00224 } 00225 break; 00226 case IMAGE_DM3: 00227 if (DM3IO::is_valid(first_block)) { 00228 return IMAGE_DM3; 00229 } 00230 break; 00231 #ifdef EM_HDF5 00232 case IMAGE_HDF: 00233 if (HdfIO2::is_valid(first_block)) { 00234 return IMAGE_HDF; 00235 } 00236 break; 00237 #endif 00238 case IMAGE_LST: 00239 if (LstIO::is_valid(first_block)) { 00240 return IMAGE_LST; 00241 } 00242 break; 00243 case IMAGE_LSTFAST: 00244 if (LstFastIO::is_valid(first_block)) { 00245 return IMAGE_LSTFAST; 00246 } 00247 break; 00248 #ifdef EM_TIFF 00249 case IMAGE_TIFF: 00250 if (TiffIO::is_valid(first_block)) { 00251 return IMAGE_TIFF; 00252 } 00253 break; 00254 #endif 00255 case IMAGE_SPIDER: 00256 if (SpiderIO::is_valid(first_block)) { 00257 return IMAGE_SPIDER; 00258 } 00259 break; 00260 case IMAGE_SINGLE_SPIDER: 00261 if (SingleSpiderIO::is_valid(first_block)) { 00262 return IMAGE_SINGLE_SPIDER; 00263 } 00264 break; 00265 case IMAGE_PIF: 00266 if (PifIO::is_valid(first_block)) { 00267 return IMAGE_PIF; 00268 } 00269 break; 00270 #ifdef EM_PNG 00271 case IMAGE_PNG: 00272 if (PngIO::is_valid(first_block)) { 00273 return IMAGE_PNG; 00274 } 00275 break; 00276 #endif 00277 case IMAGE_VTK: 00278 if (VtkIO::is_valid(first_block)) { 00279 return IMAGE_VTK; 00280 } 00281 break; 00282 case IMAGE_PGM: 00283 if (PgmIO::is_valid(first_block)) { 00284 return IMAGE_PGM; 00285 } 00286 break; 00287 case IMAGE_ICOS: 00288 if (IcosIO::is_valid(first_block)) { 00289 return IMAGE_ICOS; 00290 } 00291 break; 00292 case IMAGE_SAL: 00293 if (SalIO::is_valid(first_block)) { 00294 return IMAGE_SAL; 00295 } 00296 break; 00297 case IMAGE_AMIRA: 00298 if (AmiraIO::is_valid(first_block)) { 00299 return IMAGE_AMIRA; 00300 } 00301 break; 00302 case IMAGE_XPLOR: 00303 if (XplorIO::is_valid(first_block)) { 00304 return IMAGE_XPLOR; 00305 } 00306 break; 00307 case IMAGE_GATAN2: 00308 if (Gatan2IO::is_valid(first_block)) { 00309 return IMAGE_GATAN2; 00310 } 00311 break; 00312 case IMAGE_EM: 00313 if (EmIO::is_valid(first_block, file_size)) { 00314 return IMAGE_EM; 00315 } 00316 break; 00317 case IMAGE_DF3: 00318 if (EmIO::is_valid(first_block, file_size)) { 00319 return IMAGE_DF3; 00320 } 00321 break; 00322 case IMAGE_IMAGIC: 00323 if (ImagicIO::is_valid(first_block)) { 00324 return IMAGE_IMAGIC; 00325 } 00326 break; 00327 default: 00328 return IMAGE_UNKNOWN; 00329 } 00330 EXITFUNC; 00331 return IMAGE_UNKNOWN; 00332 }
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Get an attribute from a stack of image, returned as a vector.
Definition at line 1486 of file emutil.cpp. References Assert, read_images(), and v. 01487 { 01488 vector<EMObject> v; 01489 01490 Assert(file_name != ""); 01491 Assert(attr_name != ""); 01492 01493 vector< shared_ptr<EMData> > vpImg = EMData::read_images(file_name, vector<int>(), true); 01494 vector< shared_ptr<EMData> >::const_iterator iter; 01495 for(iter = vpImg.begin(); iter!=vpImg.end(); ++iter) { 01496 v.push_back((*iter)->get_attr_default(attr_name)); 01497 } 01498 01499 return v; 01500 }
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Give each data type a meaningful name.
Definition at line 683 of file emutil.cpp. References EM_CHAR, EM_DOUBLE, EM_FLOAT, EM_FLOAT_COMPLEX, EM_INT, EM_SHORT, EM_SHORT_COMPLEX, EM_UCHAR, EM_UINT, EM_UNKNOWN, EM_USHORT, and EM_USHORT_COMPLEX. Referenced by dump_dict(). 00684 { 00685 switch (type) { 00686 case EM_CHAR: 00687 return "CHAR"; 00688 case EM_UCHAR: 00689 return "UNSIGNED CHAR"; 00690 case EM_SHORT: 00691 return "SHORT"; 00692 case EM_USHORT: 00693 return "UNSIGNED SHORT"; 00694 case EM_INT: 00695 return "INT"; 00696 case EM_UINT: 00697 return "UNSIGNED INT"; 00698 case EM_FLOAT: 00699 return "FLOAT"; 00700 case EM_DOUBLE: 00701 return "DOUBLE"; 00702 case EM_SHORT_COMPLEX: 00703 return "SHORT_COMPLEX"; 00704 case EM_USHORT_COMPLEX: 00705 return "USHORT_COMPLEX"; 00706 case EM_FLOAT_COMPLEX: 00707 return "FLOAT_COMPLEX"; 00708 case EM_UNKNOWN: 00709 return "UNKNOWN"; 00710 } 00711 return "UNKNOWN"; 00712 }
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Definition at line 1442 of file emutil.cpp. 01443 { 01444 vector<string> v; 01445 string b = "euler_"; 01446 01447 if (euler_type == "EMAN") { 01448 v.push_back(b + "alt"); 01449 v.push_back(b + "az"); 01450 v.push_back(b + "phi"); 01451 } 01452 else if (euler_type == "MRC") { 01453 v.push_back(b + "theta"); 01454 v.push_back(b + "phi"); 01455 v.push_back(b + "omega"); 01456 } 01457 else if (euler_type == "IMAGIC") { 01458 v.push_back(b + "alpha"); 01459 v.push_back(b + "beta"); 01460 v.push_back(b + "gamma"); 01461 } 01462 else if (euler_type == "SPIDER") { 01463 v.push_back(b + "phi"); 01464 v.push_back(b + "theta"); 01465 v.push_back(b + "gamma"); 01466 } 01467 else if (euler_type == "SPIN" || 01468 euler_type == "SGIROT") { 01469 v.push_back(b + "q"); 01470 v.push_back(b + "n1"); 01471 v.push_back(b + "n2"); 01472 v.push_back(b + "n3"); 01473 } 01474 01475 else if (euler_type == "QUATERNION") { 01476 v.push_back(b + "e0"); 01477 v.push_back(b + "e1"); 01478 v.push_back(b + "e2"); 01479 v.push_back(b + "e3"); 01480 } 01481 01482 return v; 01483 }
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Get the number of images in an image file.
Definition at line 452 of file emutil.cpp. References Assert, get_imageio(), and EMAN::ImageIO::get_nimg(). Referenced by EMAN::PCA::dopca_ooc(), EMAN::PCA::Lanczos_ooc(), main(), ReadStackandDist(), and ReadStackandDist_Cart(). 00453 { 00454 ENTERFUNC; 00455 Assert(filename != ""); 00456 00457 int nimg = 0; 00458 ImageIO *imageio = get_imageio(filename, ImageIO::READ_ONLY); 00459 00460 if (imageio) { 00461 nimg = imageio->get_nimg(); 00462 } 00463 #ifndef IMAGEIO_CACHE 00464 if( imageio ) 00465 { 00466 delete imageio; 00467 imageio = 0; 00468 } 00469 #endif 00470 EXITFUNC; 00471 return nimg; 00472 }
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Get an image's format type from its filename extension.
Definition at line 62 of file emutil.cpp. References ImageType. Referenced by fast_get_image_type(), and is_valid_filename(). 00063 { 00064 ENTERFUNC; 00065 static bool initialized = false; 00066 static map < string, ImageType > imagetypes; 00067 00068 if (!initialized) { 00069 imagetypes["rec"] = IMAGE_MRC; 00070 imagetypes["mrc"] = IMAGE_MRC; 00071 imagetypes["MRC"] = IMAGE_MRC; 00072 imagetypes["ali"] = IMAGE_MRC; 00073 00074 imagetypes["tnf"] = IMAGE_MRC; 00075 imagetypes["TNF"] = IMAGE_MRC; 00076 00077 imagetypes["ccp4"] = IMAGE_MRC; 00078 imagetypes["map"] = IMAGE_MRC; 00079 00080 imagetypes["dm3"] = IMAGE_DM3; 00081 imagetypes["DM3"] = IMAGE_DM3; 00082 00083 imagetypes["spi"] = IMAGE_SPIDER; 00084 imagetypes["SPI"] = IMAGE_SPIDER; 00085 00086 imagetypes["spider"] = IMAGE_SPIDER; 00087 imagetypes["SPIDER"] = IMAGE_SPIDER; 00088 00089 imagetypes["spidersingle"] = IMAGE_SINGLE_SPIDER; 00090 imagetypes["SPIDERSINGLE"] = IMAGE_SINGLE_SPIDER; 00091 00092 imagetypes["singlespider"] = IMAGE_SINGLE_SPIDER; 00093 imagetypes["SINGLESPIDER"] = IMAGE_SINGLE_SPIDER; 00094 00095 imagetypes["img"] = IMAGE_IMAGIC; 00096 imagetypes["IMG"] = IMAGE_IMAGIC; 00097 00098 imagetypes["hed"] = IMAGE_IMAGIC; 00099 imagetypes["HED"] = IMAGE_IMAGIC; 00100 00101 imagetypes["imagic"] = IMAGE_IMAGIC; 00102 imagetypes["IMAGIC"] = IMAGE_IMAGIC; 00103 00104 imagetypes["pgm"] = IMAGE_PGM; 00105 imagetypes["PGM"] = IMAGE_PGM; 00106 00107 imagetypes["lst"] = IMAGE_LST; 00108 imagetypes["LST"] = IMAGE_LST; 00109 00110 imagetypes["lsx"] = IMAGE_LSTFAST; // but .lst or another extension would also be ok 00111 imagetypes["LSX"] = IMAGE_LSTFAST; 00112 00113 imagetypes["pif"] = IMAGE_PIF; 00114 imagetypes["PIF"] = IMAGE_PIF; 00115 00116 imagetypes["png"] = IMAGE_PNG; 00117 imagetypes["PNG"] = IMAGE_PNG; 00118 00119 imagetypes["h5"] = IMAGE_HDF; 00120 imagetypes["H5"] = IMAGE_HDF; 00121 00122 imagetypes["hd5"] = IMAGE_HDF; 00123 imagetypes["HD5"] = IMAGE_HDF; 00124 00125 imagetypes["hdf"] = IMAGE_HDF; 00126 imagetypes["HDF"] = IMAGE_HDF; 00127 00128 imagetypes["tif"] = IMAGE_TIFF; 00129 imagetypes["TIF"] = IMAGE_TIFF; 00130 00131 imagetypes["tiff"] = IMAGE_TIFF; 00132 imagetypes["TIFF"] = IMAGE_TIFF; 00133 00134 imagetypes["fts"] = IMAGE_FITS; 00135 imagetypes["FTS"] = IMAGE_FITS; 00136 00137 imagetypes["vtk"] = IMAGE_VTK; 00138 imagetypes["VTK"] = IMAGE_VTK; 00139 00140 imagetypes["hdr"] = IMAGE_SAL; 00141 imagetypes["HDR"] = IMAGE_SAL; 00142 00143 imagetypes["sal"] = IMAGE_SAL; 00144 imagetypes["SAL"] = IMAGE_SAL; 00145 00146 imagetypes["map"] = IMAGE_ICOS; 00147 imagetypes["MAP"] = IMAGE_ICOS; 00148 00149 imagetypes["icos"] = IMAGE_ICOS; 00150 imagetypes["ICOS"] = IMAGE_ICOS; 00151 00152 imagetypes["am"] = IMAGE_AMIRA; 00153 imagetypes["AM"] = IMAGE_AMIRA; 00154 00155 imagetypes["amira"] = IMAGE_AMIRA; 00156 imagetypes["AMIRA"] = IMAGE_AMIRA; 00157 00158 imagetypes["emim"] = IMAGE_EMIM; 00159 imagetypes["EMIM"] = IMAGE_EMIM; 00160 00161 imagetypes["xplor"] = IMAGE_XPLOR; 00162 imagetypes["XPLOR"] = IMAGE_XPLOR; 00163 00164 imagetypes["em"] = IMAGE_EM; 00165 imagetypes["EM"] = IMAGE_EM; 00166 00167 imagetypes["dm2"] = IMAGE_GATAN2; 00168 imagetypes["DM2"] = IMAGE_GATAN2; 00169 00170 imagetypes["v4l"] = IMAGE_V4L; 00171 imagetypes["V4L"] = IMAGE_V4L; 00172 00173 imagetypes["jpg"] = IMAGE_JPEG; 00174 imagetypes["JPG"] = IMAGE_JPEG; 00175 imagetypes["jpeg"] = IMAGE_JPEG; 00176 imagetypes["JPEG"] = IMAGE_JPEG; 00177 00178 imagetypes["df3"] = IMAGE_DF3; 00179 imagetypes["DF3"] = IMAGE_DF3; 00180 00181 initialized = true; 00182 } 00183 00184 ImageType result = IMAGE_UNKNOWN; 00185 00186 if (imagetypes.find(file_ext) != imagetypes.end()) { 00187 result = imagetypes[file_ext]; 00188 } 00189 00190 EXITFUNC; 00191 return result; 00192 }
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Get an image's format type by processing the first 1K of the image.
Definition at line 335 of file emutil.cpp. References Assert, EMAN::Util::change_filename_ext(), fast_get_image_type(), FileAccessException, EMAN::Util::get_filename_ext(), ImageFormatException, ImageType, in, EMAN::Df3IO::is_valid(), EMAN::ImagicIO::is_valid(), EMAN::EmIO::is_valid(), EMAN::FitsIO::is_valid(), EMAN::Gatan2IO::is_valid(), EMAN::XplorIO::is_valid(), EMAN::AmiraIO::is_valid(), EMAN::SalIO::is_valid(), EMAN::IcosIO::is_valid(), EMAN::PgmIO::is_valid(), EMAN::VtkIO::is_valid(), EMAN::PifIO::is_valid(), EMAN::LstFastIO::is_valid(), EMAN::LstIO::is_valid(), EMAN::DM3IO::is_valid(), EMAN::MrcIO::is_valid(), EMAN::SingleSpiderIO::is_valid(), EMAN::SpiderIO::is_valid(), LOGERR, portable_fseek(), and portable_ftell(). Referenced by get_imageio(), getRenderMinMax(), and main(). 00336 { 00337 ENTERFUNC; 00338 Assert(in_filename != ""); 00339 00340 #ifdef ENABLE_V4L2 00341 if (in_filename.compare(0,5,"/dev/")==0) return IMAGE_V4L; 00342 #endif 00343 00344 string filename = in_filename; 00345 00346 string old_ext = Util::get_filename_ext(filename); 00347 if (old_ext == ImagicIO::IMG_EXT) { 00348 filename = Util::change_filename_ext(filename, ImagicIO::HED_EXT); 00349 } 00350 00351 FILE *in = fopen(filename.c_str(), "rb"); 00352 if (!in) { 00353 throw FileAccessException(filename); 00354 } 00355 00356 char first_block[1024]; 00357 size_t n = fread(first_block, sizeof(char), sizeof(first_block), in); 00358 portable_fseek(in, 0, SEEK_END); 00359 off_t file_size = portable_ftell(in); 00360 00361 if (n == 0) { 00362 LOGERR("file '%s' is an empty file", filename.c_str()); 00363 fclose(in); 00364 return IMAGE_UNKNOWN; 00365 } 00366 fclose(in); 00367 00368 ImageType image_type = fast_get_image_type(filename, first_block, file_size); 00369 if (image_type != IMAGE_UNKNOWN) { 00370 return image_type; 00371 } 00372 00373 if (SpiderIO::is_valid(first_block)) { 00374 image_type = IMAGE_SPIDER; 00375 } 00376 else if (SingleSpiderIO::is_valid(first_block)) { 00377 image_type = IMAGE_SINGLE_SPIDER; 00378 } 00379 else if (MrcIO::is_valid(first_block, file_size)) { 00380 image_type = IMAGE_MRC; 00381 } 00382 else if (DM3IO::is_valid(first_block)) { 00383 image_type = IMAGE_DM3; 00384 } 00385 #ifdef EM_HDF5 00386 else if (HdfIO2::is_valid(first_block)) { 00387 image_type = IMAGE_HDF; 00388 } 00389 #endif 00390 else if (LstIO::is_valid(first_block)) { 00391 image_type = IMAGE_LST; 00392 } 00393 else if (LstFastIO::is_valid(first_block)) { 00394 image_type = IMAGE_LSTFAST; 00395 } 00396 #ifdef EM_TIFF 00397 else if (TiffIO::is_valid(first_block)) { 00398 image_type = IMAGE_TIFF; 00399 } 00400 #endif 00401 else if (PifIO::is_valid(first_block)) { 00402 image_type = IMAGE_PIF; 00403 } 00404 #ifdef EM_PNG 00405 else if (PngIO::is_valid(first_block)) { 00406 image_type = IMAGE_PNG; 00407 } 00408 #endif 00409 else if (VtkIO::is_valid(first_block)) { 00410 image_type = IMAGE_VTK; 00411 } 00412 else if (PgmIO::is_valid(first_block)) { 00413 image_type = IMAGE_PGM; 00414 } 00415 else if (IcosIO::is_valid(first_block)) { 00416 image_type = IMAGE_ICOS; 00417 } 00418 else if (SalIO::is_valid(first_block)) { 00419 image_type = IMAGE_SAL; 00420 } 00421 else if (AmiraIO::is_valid(first_block)) { 00422 image_type = IMAGE_AMIRA; 00423 } 00424 else if (XplorIO::is_valid(first_block)) { 00425 image_type = IMAGE_XPLOR; 00426 } 00427 else if (Gatan2IO::is_valid(first_block)) { 00428 image_type = IMAGE_GATAN2; 00429 } 00430 else if (FitsIO::is_valid(first_block)) { 00431 image_type = IMAGE_FITS; 00432 } 00433 else if (EmIO::is_valid(first_block, file_size)) { 00434 image_type = IMAGE_EM; 00435 } 00436 else if (ImagicIO::is_valid(first_block)) { 00437 image_type = IMAGE_IMAGIC; 00438 } 00439 else if (Df3IO::is_valid(first_block)) { 00440 image_type = IMAGE_DF3; 00441 } 00442 else { 00443 //LOGERR("I don't know this image's type: '%s'", filename.c_str()); 00444 throw ImageFormatException("invalid image type"); 00445 } 00446 00447 EXITFUNC; 00448 return image_type; 00449 }
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Get an ImageIO object. It may be a newly created object. Or an object stored in the cache.
Definition at line 475 of file emutil.cpp. References EMAN::GlobalCache::add_imageio(), Assert, get_image_type(), EMAN::GlobalCache::get_imageio(), IMAGE_AMIRA, IMAGE_DF3, IMAGE_DM3, IMAGE_EM, IMAGE_FITS, IMAGE_GATAN2, IMAGE_HDF, IMAGE_ICOS, IMAGE_IMAGIC, IMAGE_JPEG, IMAGE_LST, IMAGE_LSTFAST, IMAGE_MRC, IMAGE_PGM, IMAGE_PIF, IMAGE_PNG, IMAGE_SAL, IMAGE_SINGLE_SPIDER, IMAGE_SPIDER, IMAGE_TIFF, IMAGE_V4L, IMAGE_VTK, IMAGE_XPLOR, ImageFormatException, and EMAN::GlobalCache::instance(). Referenced by EMAN::LstIO::calc_ref_image_index(), EMAN::LstFastIO::calc_ref_image_index(), get_image_count(), and EMAN::EMData::read_image(). 00477 { 00478 ENTERFUNC; 00479 Assert(filename != ""); 00480 Assert(rw == ImageIO::READ_ONLY || 00481 rw == ImageIO::READ_WRITE || 00482 rw == ImageIO::WRITE_ONLY); 00483 00484 ImageIO *imageio = 0; 00485 #ifdef IMAGEIO_CACHE 00486 imageio = GlobalCache::instance()->get_imageio(filename, rw); 00487 if (imageio) { 00488 return imageio; 00489 } 00490 #endif 00491 00492 ImageIO::IOMode rw_mode = static_cast < ImageIO::IOMode > (rw); 00493 00494 if (image_type == IMAGE_UNKNOWN) { 00495 if(rw == ImageIO::WRITE_ONLY || rw == ImageIO::READ_WRITE) { 00496 throw ImageFormatException("writing to this image format not supported."); 00497 } 00498 00499 image_type = get_image_type(filename); 00500 } 00501 00502 switch (image_type) { 00503 #ifdef ENABLE_V4L2 00504 case IMAGE_V4L: 00505 imageio = new V4L2IO(filename, rw_mode); 00506 break; 00507 #endif 00508 case IMAGE_MRC: 00509 imageio = new MrcIO(filename, rw_mode); 00510 break; 00511 case IMAGE_IMAGIC: 00512 imageio = new ImagicIO2(filename, rw_mode); 00513 if (rw_mode==ImageIO::READ_ONLY && ((ImagicIO2 *)imageio)->init_test()==-1 ) { 00514 delete imageio; 00515 imageio = new ImagicIO(filename, rw_mode); 00516 } 00517 break; 00518 case IMAGE_DM3: 00519 imageio = new DM3IO(filename, rw_mode); 00520 break; 00521 #ifdef EM_TIFF 00522 case IMAGE_TIFF: 00523 imageio = new TiffIO(filename, rw_mode); 00524 break; 00525 #endif 00526 #ifdef EM_HDF5 00527 case IMAGE_HDF: 00528 imageio = new HdfIO2(filename, rw_mode); 00529 if (((HdfIO2 *)imageio)->init_test()==-1) { 00530 delete imageio; 00531 imageio = new HdfIO(filename, rw_mode); 00532 } 00533 break; 00534 #endif 00535 case IMAGE_LST: 00536 imageio = new LstIO(filename, rw_mode); 00537 break; 00538 case IMAGE_LSTFAST: 00539 imageio = new LstFastIO(filename, rw_mode); 00540 break; 00541 case IMAGE_PIF: 00542 imageio = new PifIO(filename, rw_mode); 00543 break; 00544 case IMAGE_VTK: 00545 imageio = new VtkIO(filename, rw_mode); 00546 break; 00547 case IMAGE_SPIDER: 00548 imageio = new SpiderIO(filename, rw_mode); 00549 break; 00550 case IMAGE_SINGLE_SPIDER: 00551 imageio = new SingleSpiderIO(filename, rw_mode); 00552 break; 00553 case IMAGE_PGM: 00554 imageio = new PgmIO(filename, rw_mode); 00555 break; 00556 #ifdef EM_JPEG 00557 case IMAGE_JPEG: 00558 imageio = new JpegIO(filename,rw_mode); 00559 break; 00560 #endif 00561 case IMAGE_ICOS: 00562 imageio = new IcosIO(filename, rw_mode); 00563 break; 00564 #ifdef EM_PNG 00565 case IMAGE_PNG: 00566 imageio = new PngIO(filename, rw_mode); 00567 break; 00568 #endif 00569 case IMAGE_SAL: 00570 imageio = new SalIO(filename, rw_mode); 00571 break; 00572 case IMAGE_AMIRA: 00573 imageio = new AmiraIO(filename, rw_mode); 00574 break; 00575 case IMAGE_GATAN2: 00576 imageio = new Gatan2IO(filename, rw_mode); 00577 break; 00578 case IMAGE_EM: 00579 imageio = new EmIO(filename, rw_mode); 00580 break; 00581 case IMAGE_XPLOR: 00582 imageio = new XplorIO(filename, rw_mode); 00583 break; 00584 case IMAGE_FITS: 00585 imageio = new FitsIO(filename, rw_mode); 00586 break; 00587 case IMAGE_DF3: 00588 imageio = new Df3IO(filename, rw_mode); 00589 break; 00590 default: 00591 break; 00592 } 00593 #ifdef IMAGEIO_CACHE 00594 GlobalCache::instance()->add_imageio(filename, rw, imageio); 00595 #endif 00596 EXITFUNC; 00597 return imageio; 00598 }
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Give each image type a meaningful name.
Definition at line 602 of file emutil.cpp. References IMAGE_AMIRA, IMAGE_DF3, IMAGE_DM3, IMAGE_EM, IMAGE_EMIM, IMAGE_FITS, IMAGE_GATAN2, IMAGE_HDF, IMAGE_ICOS, IMAGE_IMAGIC, IMAGE_JPEG, IMAGE_LST, IMAGE_LSTFAST, IMAGE_MRC, IMAGE_PGM, IMAGE_PIF, IMAGE_PNG, IMAGE_SAL, IMAGE_SINGLE_SPIDER, IMAGE_SPIDER, IMAGE_TIFF, IMAGE_UNKNOWN, IMAGE_V4L, IMAGE_VTK, and IMAGE_XPLOR. Referenced by main(). 00603 { 00604 switch (t) { 00605 case IMAGE_V4L: 00606 return "V4L2"; 00607 break; 00608 case IMAGE_MRC: 00609 return "MRC"; 00610 break; 00611 case IMAGE_SPIDER: 00612 return "SPIDER"; 00613 break; 00614 case IMAGE_SINGLE_SPIDER: 00615 return "Single-SPIDER"; 00616 break; 00617 case IMAGE_IMAGIC: 00618 return "IMAGIC"; 00619 break; 00620 case IMAGE_PGM: 00621 return "PGM"; 00622 break; 00623 case IMAGE_LST: 00624 return "LST"; 00625 break; 00626 case IMAGE_LSTFAST: 00627 return "Fast LST"; 00628 break; 00629 case IMAGE_PIF: 00630 return "PIF"; 00631 break; 00632 case IMAGE_PNG: 00633 return "PNG"; 00634 break; 00635 case IMAGE_HDF: 00636 return "HDF5"; 00637 break; 00638 case IMAGE_DM3: 00639 return "GatanDM3"; 00640 break; 00641 case IMAGE_TIFF: 00642 return "TIFF"; 00643 break; 00644 case IMAGE_VTK: 00645 return "VTK"; 00646 break; 00647 case IMAGE_SAL: 00648 return "HDR"; 00649 break; 00650 case IMAGE_ICOS: 00651 return "ICOS_MAP"; 00652 break; 00653 case IMAGE_EMIM: 00654 return "EMIM"; 00655 break; 00656 case IMAGE_GATAN2: 00657 return "GatanDM2"; 00658 break; 00659 case IMAGE_JPEG: 00660 return "JPEG"; 00661 break; 00662 case IMAGE_AMIRA: 00663 return "AmiraMesh"; 00664 break; 00665 case IMAGE_XPLOR: 00666 return "XPLOR"; 00667 break; 00668 case IMAGE_EM: 00669 return "EM"; 00670 break; 00671 case IMAGE_FITS: 00672 return "FITS"; 00673 break; 00674 case IMAGE_DF3: 00675 return "DF3"; 00676 break; 00677 case IMAGE_UNKNOWN: 00678 return "unknown"; 00679 } 00680 return "unknown"; 00681 }
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Get a region's dimensions.
Definition at line 714 of file emutil.cpp. References Assert, EMAN::Region::get_ndim(), EMAN::Region::get_size(), and EMAN::Vec3i. Referenced by process_ascii_region_io(), process_region_io(), EMAN::MrcIO::read_fei_header(), and EMAN::MrcIO::read_mrc_header(). 00716 { 00717 Assert(area_x); 00718 Assert(area_y); 00719 00720 if (!area) { 00721 *area_x = nx; 00722 *area_y = ny; 00723 if (area_z) { 00724 *area_z = nz; 00725 } 00726 } 00727 else { 00728 Vec3i size = area->get_size(); 00729 *area_x = size[0]; 00730 *area_y = size[1]; 00731 00732 if (area_z) { 00733 if (area->get_ndim() > 2 && nz > 1) { 00734 *area_z = size[2]; 00735 } 00736 else { 00737 *area_z = 1; 00738 } 00739 } 00740 00741 } 00742 }
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Get a region's original locations.
Definition at line 744 of file emutil.cpp. References Assert, EMAN::Region::get_ndim(), and EMAN::Region::origin. 00746 { 00747 Assert(p_x0); 00748 Assert(p_y0); 00749 00750 if (area) { 00751 *p_x0 = static_cast < int >(area->origin[0]); 00752 *p_y0 = static_cast < int >(area->origin[1]); 00753 00754 if (p_z0 && nz > 1 && area->get_ndim() > 2) { 00755 *p_z0 = static_cast < int >(area->origin[2]); 00756 } 00757 } 00758 else { 00759 *p_x0 = 0; 00760 *p_y0 = 0; 00761 if (p_z0) { 00762 *p_z0 = nz > 1 ? 0 : image_index; 00763 } 00764 } 00765 }
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Calculate the min and max pixel value acceptedfor image nomalization, if we did not get them from image attribute dictionary, or they are not valid values rendermin = mean - 3*sigma rendermax = mean + 3*sigma.
Definition at line 1502 of file emutil.cpp. References data, get_image_type(), ImageFormatException, ImageType, EMAN::EMObject::init(), key, max, min, nx, ny, and sqrt(). 01503 { 01504 #ifdef _WIN32 01505 if (rendermax<=rendermin || _isnan(rendermin) || _isnan(rendermax)) { 01506 #else 01507 if (rendermax<=rendermin || std::isnan(rendermin) || std::isnan(rendermax)) { 01508 #endif 01509 float m=0.0f,s=0.0f; 01510 01511 size_t size = (size_t)nx*ny*nz; 01512 float min=data[0],max=data[0]; 01513 01514 for (size_t i=0; i<size; ++i) { m+=data[i]; s+=data[i]*data[i]; min=data[i]<min?data[i]:min; max=data[i]>max?data[i]:max; } 01515 m/=(float)(size); 01516 s=sqrt(s/(float)(size)-m*m); 01517 #ifdef _WIN32 01518 if (s<=0 || _isnan(s)) s=1.0; // this means all data values are the same 01519 #else 01520 if (s<=0 || std::isnan(s)) s=1.0; // this means all data values are the same 01521 #endif //_WIN32 01522 rendermin=m-s*5.0f; 01523 rendermax=m+s*5.0f; 01524 if (rendermin<=min) rendermin=min; 01525 if (rendermax>=max) rendermax=max; 01526 } 01527 }
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Definition at line 974 of file emutil.cpp. References EM_SHORT_COMPLEX, and EM_USHORT_COMPLEX. Referenced by EMAN::TestUtil::make_image_file_by_mode(), and EMAN::TestUtil::verify_image_file_by_mode(). 00975 { 00976 if (datatype == EM_SHORT_COMPLEX || 00977 datatype == EM_USHORT_COMPLEX || 00978 datatype == EM_FLOAT_COMPLEX) { 00979 return true; 00980 } 00981 return false; 00982 }
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Check whether two EMData images have the same CTF parameters.
Definition at line 1086 of file emutil.cpp. References EMAN::Ctf::equal(), EMAN::EMData::get_ctf(), EMAN::EMData::has_ctff(), and NullPointerException. Referenced by main(). 01087 { 01088 if (!image1) { 01089 throw NullPointerException("image1 is NULL"); 01090 } 01091 if (!image2) { 01092 throw NullPointerException("image2 is NULL"); 01093 } 01094 01095 Ctf *ctf1 = image1->get_ctf(); 01096 Ctf *ctf2 = image2->get_ctf(); 01097 01098 if ((!ctf1 && !ctf2) && (image1->has_ctff() == false && image2->has_ctff() == false)) { 01099 return true; 01100 } 01101 01102 if (ctf1 && ctf2) { 01103 bool result = ctf1->equal(ctf2); 01104 delete ctf1; 01105 ctf1 = 0; 01106 delete ctf2; 01107 ctf2 = 0; 01108 01109 return result; 01110 } 01111 return false; 01112 }
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Check whether two EMData images are of the same size.
Definition at line 964 of file emutil.cpp. References EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), and EMAN::EMData::get_zsize(). Referenced by EMAN::CtfAverager::add_image(), EMAN::CtfCAutoAverager::add_image(), EMAN::CtfCWautoAverager::add_image(), EMAN::IterationAverager::add_image(), EMAN::MinMaxAverager::add_image(), EMAN::ImageAverager::add_image(), EMAN::TomoAverager::add_image(), EMAN::TranslationalAligner::align(), EMAN::NormalizeMaskProcessor::calc_mean(), EMAN::NormalizeMaskProcessor::calc_sigma(), EMAN::IndexMaskFileProcessor::process_inplace(), and EMAN::Cmp::validate_input_args(). 00965 { 00966 if (em1->get_xsize() == em2->get_xsize() && 00967 em1->get_ysize() == em2->get_ysize() && 00968 em1->get_zsize() == em2->get_zsize()) { 00969 return true; 00970 } 00971 return false; 00972 }
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Ask whether or not the given filename is a valid EM image filename This is the same thing as checking whether or not the return value of EMUtil.get_image_ext_type is IMAGE_UNKNOWN.
Definition at line 196 of file emutil.cpp. References get_image_ext_type(), and ImageType. 00196 { 00197 ImageType type = get_image_ext_type(Util::get_filename_ext(filename)); 00198 return (type != IMAGE_UNKNOWN); 00199 }
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Definition at line 1305 of file emutil.cpp. References Assert. Referenced by jump_lines_by_items(), and process_ascii_region_io(). 01306 { 01307 Assert(file); 01308 01309 if (nlines > 0) { 01310 char line[MAXPATHLEN]; 01311 for (int l = 0; l < nlines; l++) { 01312 if (!fgets(line, sizeof(line), file)) { 01313 Assert("read xplor file failed"); 01314 } 01315 } 01316 } 01317 }
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Definition at line 1286 of file emutil.cpp. References Assert, and jump_lines(). Referenced by process_ascii_region_io(). 01287 { 01288 Assert(file); 01289 Assert(nitems_per_line > 0); 01290 01291 if (nitems <= 0) { 01292 return; 01293 } 01294 01295 int nlines = nitems / nitems_per_line; 01296 if ((nitems % nitems_per_line) != 0) { 01297 nlines++; 01298 } 01299 if (nlines > 0) { 01300 jump_lines(file, nlines); 01301 } 01302 }
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Definition at line 1021 of file emutil.cpp. References EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::EMData::set_size(), EMAN::EMData::update(), and v. 01022 { 01023 if (image_list.size() == 0) { 01024 return 0; 01025 } 01026 01027 EMData *image0 = image_list[0]; 01028 int image0_nx = image0->get_xsize(); 01029 int image0_ny = image0->get_ysize(); 01030 int image0_nz = image0->get_zsize(); 01031 size_t size = (size_t)image0_nx * image0_ny * image0_nz; 01032 01033 EMData *result = new EMData(); 01034 01035 result->set_size(image0_nx, image0_ny, image0_nz); 01036 01037 float *dest = result->get_data(); 01038 int nitems = static_cast < int >(image_list.size()); 01039 float *srt = new float[nitems]; 01040 float **src = new float *[nitems]; 01041 01042 for (int i = 0; i < nitems; i++) { 01043 src[i] = image_list[i]->get_data(); 01044 } 01045 01046 for (size_t i = 0; i < size; ++i) { 01047 for (int j = 0; j < nitems; j++) { 01048 srt[j] = src[j][i]; 01049 } 01050 01051 for (int j = 0; j < nitems; j++) { 01052 for (int k = j + 1; k < nitems; k++) { 01053 if (srt[j] < srt[k]) { 01054 float v = srt[j]; 01055 srt[j] = srt[k]; 01056 srt[k] = v; 01057 } 01058 } 01059 } 01060 01061 int l = nitems / 2; 01062 if (nitems < 3) { 01063 dest[i] = srt[l]; 01064 } 01065 else { 01066 dest[i] = (srt[l] + srt[l + 1] + srt[l - 1]) / 3.0f; 01067 } 01068 } 01069 01070 if( srt ) 01071 { 01072 delete[]srt; 01073 srt = 0; 01074 } 01075 if( src ) 01076 { 01077 delete[]src; 01078 src = 0; 01079 } 01080 01081 result->update(); 01082 01083 return result; 01084 }
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Works for regions that are outside the image data dimension area. The only function that calls this is in xplorio.cpp - that function throws if the region is invalid. Definition at line 1177 of file emutil.cpp. References Assert, data, exclude_numbers_io(), get_region_dims(), jump_lines(), jump_lines_by_items(), nx, ny, EMAN::Region::origin, process_lines_io(), and process_numbers_io(). 01181 { 01182 Assert(data != 0); 01183 Assert(file != 0); 01184 Assert(rw_mode == ImageIO::READ_ONLY || 01185 rw_mode == ImageIO::READ_WRITE || 01186 rw_mode == ImageIO::WRITE_ONLY); 01187 01188 int xlen = 0, ylen = 0, zlen = 0; 01189 get_region_dims(area, nx, &xlen, ny, &ylen, nz, &zlen); 01190 01191 int x0 = 0; 01192 int y0 = 0; 01193 int z0 = 0; 01194 01195 if (area) { 01196 x0 = (int)area->origin[0]; 01197 y0 = (int)area->origin[1]; 01198 z0 = (int)area->origin[2]; 01199 } 01200 01201 int nlines_per_sec = (nx *ny) / nitems_per_line; 01202 int nitems_last_line = (nx * ny) % nitems_per_line; 01203 if (nitems_last_line != 0) { 01204 nlines_per_sec++; 01205 } 01206 01207 if (has_index_line) { 01208 nlines_per_sec++; 01209 } 01210 01211 if (z0 > 0) { 01212 jump_lines(file, z0 * nlines_per_sec); 01213 } 01214 01215 01216 int nlines_pre_sec = (y0 * nx + x0) / nitems_per_line; 01217 int gap_nitems = nx - xlen; 01218 int ti = 0; 01219 int rlines = 0; 01220 01221 for (int k = 0; k < zlen; k++) { 01222 EMUtil::jump_lines(file, nlines_pre_sec+1); 01223 01224 int head_nitems = (y0 * nx + x0) % nitems_per_line; 01225 int tail_nitems = 0; 01226 bool is_head_read = false; 01227 01228 for (int j = 0; j < ylen; j++) { 01229 01230 if (head_nitems > 0 && !is_head_read) { 01231 EMUtil::process_numbers_io(file, rw_mode, nitems_per_line, mode_size, 01232 nitems_per_line-head_nitems, 01233 nitems_per_line-1, data, &ti, outformat); 01234 rlines++; 01235 } 01236 01237 EMUtil::process_lines_io(file, rw_mode, nitems_per_line, 01238 mode_size, (xlen - head_nitems), 01239 data, &ti, outformat); 01240 01241 rlines += ((xlen - head_nitems)/nitems_per_line); 01242 01243 tail_nitems = (xlen - head_nitems) % nitems_per_line; 01244 01245 if ((gap_nitems + tail_nitems) > 0) { 01246 head_nitems = nitems_per_line - 01247 (gap_nitems + tail_nitems) % nitems_per_line; 01248 } 01249 else { 01250 head_nitems = 0; 01251 } 01252 01253 is_head_read = false; 01254 01255 if (tail_nitems > 0) { 01256 if ((gap_nitems < (nitems_per_line-tail_nitems)) && 01257 (j != (ylen-1))) { 01258 EMUtil::exclude_numbers_io(file, rw_mode, nitems_per_line, 01259 mode_size, tail_nitems, 01260 tail_nitems+gap_nitems-1, data, &ti, outformat); 01261 is_head_read = true; 01262 rlines++; 01263 } 01264 else { 01265 EMUtil::process_numbers_io(file, rw_mode, nitems_per_line, mode_size, 01266 0, tail_nitems-1, data, &ti, outformat); 01267 rlines++; 01268 } 01269 } 01270 01271 if (gap_nitems > (nitems_per_line-tail_nitems)) { 01272 int gap_nlines = (gap_nitems - (nitems_per_line-tail_nitems)) / 01273 nitems_per_line; 01274 if (gap_nlines > 0 && j != (ylen-1)) { 01275 EMUtil::jump_lines(file, gap_nlines); 01276 } 01277 } 01278 } 01279 01280 int ytail_nitems = (ny-ylen-y0) * nx + (nx-xlen-x0) - (nitems_per_line-tail_nitems); 01281 EMUtil::jump_lines_by_items(file, ytail_nitems, nitems_per_line); 01282 } 01283 }
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Definition at line 1424 of file emutil.cpp. References Assert, data, and process_numbers_io(). Referenced by process_ascii_region_io(). 01428 { 01429 Assert(file); 01430 Assert(data); 01431 Assert(p_i); 01432 01433 if (nitems > 0) { 01434 int nlines = nitems / nitems_per_line; 01435 for (int i = 0; i < nlines; i++) { 01436 EMUtil::process_numbers_io(file, rw_mode, nitems_per_line, mode_size, 0, 01437 nitems_per_line-1, data, p_i, outformat); 01438 } 01439 } 01440 }
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Definition at line 1319 of file emutil.cpp. References Assert, data, and portable_fseek(). Referenced by process_ascii_region_io(), and process_lines_io(). 01322 { 01323 Assert(file); 01324 Assert(start >= 0); 01325 Assert(start <= end); 01326 Assert(end <= nitems_per_line); 01327 Assert(data); 01328 Assert(p_i); 01329 Assert(outformat); 01330 01331 char line[MAXPATHLEN]; 01332 01333 if (rw_mode == ImageIO::READ_ONLY) { 01334 if (!fgets(line, sizeof(line), file)) { 01335 Assert("read xplor file failed"); 01336 } 01337 01338 int nitems_in_line = (int) (strlen(line) / mode_size); 01339 Assert(end <= nitems_in_line); 01340 vector<float> d(nitems_in_line); 01341 char * pline = line; 01342 01343 for (int i = 0; i < nitems_in_line; i++) { 01344 sscanf(pline, "%f", &d[i]); 01345 pline += (int)mode_size; 01346 } 01347 01348 01349 for (int i = start; i <= end; i++) { 01350 data[*p_i] = d[i]; 01351 (*p_i)++; 01352 } 01353 } 01354 else { 01355 portable_fseek(file, mode_size * start, SEEK_CUR); 01356 for (int i = start; i <= end; i++) { 01357 fprintf(file, outformat, data[*p_i]); 01358 (*p_i)++; 01359 } 01360 01361 portable_fseek(file, mode_size * (nitems_per_line - end-1)+1, SEEK_CUR); 01362 } 01363 }
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Process image region IO. It eithers read a region from an image file. Or write a region to an image file. Works for regions that are outside the image data dimension area.(David Woolford, April 23 2009)
Definition at line 768 of file emutil.cpp. References Assert, EMAN::Region::get_ndim(), EMAN::Region::get_origin(), get_region_dims(), EMAN::Region::get_size(), IMAGE_ICOS, ImageReadException, ImageWriteException, nx, ny, portable_fseek(), UnexpectedBehaviorException, EMAN::Vec3d, and EMAN::Vec3i. 00773 { 00774 Assert(vdata != 0); 00775 Assert(file != 0); 00776 Assert(rw_mode == ImageIO::READ_ONLY || 00777 rw_mode == ImageIO::READ_WRITE || 00778 rw_mode == ImageIO::WRITE_ONLY); 00779 00780 if (mode_size == 0) throw UnexpectedBehaviorException("The mode size was 0?"); 00781 00782 unsigned char * cdata = (unsigned char *)vdata; 00783 00784 int dx0 = 0; // data x0 00785 int dy0 = 0; // data y0 00786 int dz0 = 0; // data z0 00787 00788 int fx0 = 0; // file x0 00789 int fy0 = 0; // file y0 00790 int fz0 = nz > 1 ? 0 : image_index; // file z0 00791 00792 00793 int xlen = 0; 00794 int ylen = 0; 00795 int zlen = 0; 00796 get_region_dims(area, nx, &xlen, ny, &ylen, nz, &zlen); 00797 00798 if (area) { // Accommodate for all boundary overlaps of the region 00799 00800 Vec3i origin = area->get_origin(); 00801 00802 00803 fx0 = origin[0]; dx0 = origin[0]; 00804 fy0 = origin[1]; dy0 = origin[1]; 00805 if (nz > 1 && area->get_ndim() > 2) { 00806 fz0 = origin[2]; dz0 = origin[2]; 00807 } 00808 00809 if (need_flip) { 00810 Vec3i size = area->get_size(); 00811 fy0 = ny-(origin[1]+size[1]); 00812 } 00813 00814 if (fx0 < 0) { 00815 dx0 *= -1; 00816 xlen = xlen + fx0; // because there are less reads 00817 fx0 = 0; 00818 }else { 00819 dx0 = 0; 00820 //fx0 *= -1; 00821 } 00822 if (fy0 < 0) { 00823 dy0 *= -1; 00824 ylen = ylen + fy0; // because there are less reads 00825 fy0 = 0; 00826 }else { 00827 if (need_flip){ 00828 dy0*=-1; 00829 } 00830 else dy0 = 0; 00831 //fy0 *= -1; 00832 } 00833 if (fz0 < 0) { 00834 dz0 *= -1; 00835 zlen = zlen + fz0; // because there are less reads 00836 fz0 = 0; 00837 }else { 00838 dz0 = 0; 00839 //fz0 *= -1; 00840 } 00841 00842 if ((fx0 + xlen)> nx) xlen = nx-fx0; 00843 if ((fy0 + ylen)> ny) ylen = ny-fy0; 00844 if ((fz0 + zlen)> nz) zlen = nz-fz0; 00845 if ( xlen <= 0 || ylen <= 0 || zlen <= 0 ) return; // This is fine the region was entirely outside the image 00846 } 00847 00848 if ( xlen <= 0 ) { 00849 cout << "Xlen was too small " << xlen << endl; 00850 return; 00851 } 00852 00853 Vec3i size; 00854 if (area != 0) size = area->get_size(); 00855 else size = Vec3d(nx,ny,nz); 00856 00857 //size_t area_sec_size = xlen * ylen * mode_size; 00858 size_t memory_sec_size = size[0] * size[1] * mode_size; 00859 size_t img_row_size = nx * mode_size + pre_row + post_row; 00860 size_t area_row_size = xlen * mode_size; 00861 size_t memory_row_size = size[0] * mode_size; 00862 00863 if ( area_row_size <= 0 ) { 00864 cout << "Xlen was too small " << xlen << " mode_size " << mode_size << endl; 00865 return; 00866 } 00867 00868 size_t x_pre_gap = fx0 * mode_size; 00869 size_t x_post_gap = (nx - fx0 - xlen) * mode_size; 00870 00871 size_t y_pre_gap = fy0 * img_row_size; 00872 size_t y_post_gap = (ny - fy0 - ylen) * img_row_size; 00873 00874 portable_fseek(file, img_row_size * ny * fz0, SEEK_CUR); 00875 00876 float nxlendata[1]; 00877 int floatsize = (int) sizeof(float); 00878 nxlendata[0] = (float)(nx * floatsize); 00879 00880 for (int k = dz0; k < (dz0+zlen); k++) { 00881 if (y_pre_gap > 0) { 00882 portable_fseek(file, y_pre_gap, SEEK_CUR); 00883 } 00884 //long k2 = k * area_sec_size; 00885 long k2 = k*memory_sec_size; 00886 00887 for (int j = dy0; j < (dy0+ylen); j++) { 00888 if (pre_row > 0) { 00889 if (imgtype == IMAGE_ICOS && rw_mode != ImageIO::READ_ONLY && !area) { 00890 fwrite(nxlendata, floatsize, 1, file); 00891 } 00892 else { 00893 portable_fseek(file, pre_row, SEEK_CUR); 00894 } 00895 } 00896 00897 if (x_pre_gap > 0) { 00898 portable_fseek(file, x_pre_gap, SEEK_CUR); 00899 } 00900 00901 int jj = j; 00902 if (need_flip) { 00903 jj = (dy0+ylen) - 1 - j; 00904 if (dy0 > 0 ) { // region considerations add complications in the flipping scenario (imagic format) 00905 jj += dy0; 00906 } 00907 } 00908 00909 if (rw_mode == ImageIO::READ_ONLY) { 00910 if (fread(&cdata[k2 + jj * memory_row_size+dx0*mode_size], 00911 area_row_size, 1, file) != 1) { 00912 cout << jj << " " << k2 << " " << memory_row_size << " " << dx0 << " " << mode_size << " " << area_row_size << " " << cdata << "done" << endl; 00913 throw ImageReadException("", "incomplete data read"); 00914 } 00915 } 00916 else { 00917 if (fwrite(&cdata[k2 + jj * memory_row_size+dx0*mode_size], 00918 area_row_size, 1, file) != 1) { 00919 throw ImageWriteException("", "incomplete data write"); 00920 } 00921 } 00922 00923 if (x_post_gap > 0) { 00924 portable_fseek(file, x_post_gap, SEEK_CUR); 00925 } 00926 00927 if (post_row > 0) { 00928 if (imgtype == IMAGE_ICOS && rw_mode != ImageIO::READ_ONLY && !area) { 00929 fwrite(nxlendata, floatsize, 1, file); 00930 } 00931 else { 00932 portable_fseek(file, post_row, SEEK_CUR); 00933 } 00934 } 00935 } 00936 00937 if (y_post_gap > 0) { 00938 portable_fseek(file, y_post_gap, SEEK_CUR); 00939 } 00940 } 00941 }
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Definition at line 985 of file emutil.cpp. References data, dot(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), NullPointerException, nx, ny, EMAN::EMData::set_size(), EMAN::EMData::update(), x, and y. 00986 { 00987 if (!image) { 00988 throw NullPointerException("NULL Image"); 00989 } 00990 00991 EMData *ret = new EMData(); 00992 int nx = image->get_xsize(); 00993 int ny = image->get_ysize(); 00994 00995 if (maxdy <= 1) { 00996 maxdy = ny / 8; 00997 } 00998 00999 ret->set_size(nx, maxdy, 1); 01000 01001 float *data = image->get_data(); 01002 float *ret_data = ret->get_data(); 01003 01004 for (int x = 0; x < nx; x++) { 01005 for (int y = 0; y < maxdy; y++) { 01006 float dot = 0; 01007 for (int yy = maxdy; yy < ny - maxdy; yy++) { 01008 dot += data[x + (yy + y) * nx] * data[x + (yy - y) * nx]; 01009 } 01010 ret_data[x + y * nx] = dot; 01011 } 01012 } 01013 01014 ret->update(); 01015 01016 return ret; 01017 }
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