#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) |
|
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 };
|
|
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 };
|
|
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 }
|
|
Dump a Dict object.
Definition at line 947 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(). 00948 { 00949 vector < string > keys = dict.keys(); 00950 vector < EMObject > values = dict.values(); 00951 00952 for (unsigned int i = 0; i < keys.size(); i++) { 00953 EMObject obj = values[i]; 00954 if( !obj.is_null() ) { 00955 string val = obj.to_str(); 00956 00957 if (keys[i] == "datatype") { 00958 val = get_datatype_string((EMDataType) (int) obj); 00959 } 00960 00961 fprintf(stdout, "%25s\t%s\n", keys[i].c_str(), val.c_str()); 00962 } 00963 } 00964 }
|
|
Definition at line 344 of file emutil.h. 00344 {
00345 return calloc(nmemb,size);
00346 }
|
|
Definition at line 354 of file emutil.h. References data. Referenced by EMAN::EMData::free_memory(). 00354 { 00355 free(data); 00356 }
|
|
Definition at line 340 of file emutil.h. Referenced by EMAN::TransformProcessor::transform(). 00340 {
00341 return malloc(size);
00342 }
|
|
Definition at line 358 of file emutil.h. 00358 { 00359 memcpy(dst,src,size); 00360 }
|
|
Definition at line 351 of file emutil.h. References data. Referenced by EMAN::EMData::to_value(). 00351 { 00352 memset(data, value, size); 00353 }
|
|
Definition at line 348 of file emutil.h. References data. 00348 {
00349 return realloc(data, new_size);
00350 }
|
|
Definition at line 1369 of file emutil.cpp. References Assert, data, and portable_fseek(). Referenced by process_ascii_region_io(). 01372 { 01373 Assert(file); 01374 Assert(mode_size > 0); 01375 Assert(start >= 0); 01376 Assert(end <= nitems_per_line); 01377 Assert(data); 01378 Assert(p_i); 01379 Assert(outformat); 01380 01381 char line[MAXPATHLEN]; 01382 01383 if (rw_mode == ImageIO::READ_ONLY) { 01384 01385 if (!fgets(line, sizeof(line), file)) { 01386 Assert("read xplor file failed"); 01387 } 01388 01389 int nitems_in_line = (int) (strlen(line) / mode_size); 01390 Assert(end <= nitems_in_line); 01391 01392 vector<float> d(nitems_in_line); 01393 char *pline = line; 01394 01395 for (int i = 0; i < nitems_in_line; i++) { 01396 sscanf(pline, "%f", &d[i]); 01397 pline = pline + (int)mode_size; 01398 } 01399 01400 01401 for (int i = 0; i < start; i++) { 01402 data[*p_i] = d[i]; 01403 (*p_i)++; 01404 } 01405 01406 for (int i = end+1; i < nitems_in_line; i++) { 01407 data[*p_i] = d[i]; 01408 (*p_i)++; 01409 } 01410 } 01411 else { 01412 for (int i = 0; i < start; i++) { 01413 fprintf(file, outformat, data[*p_i]); 01414 (*p_i)++; 01415 } 01416 01417 portable_fseek(file, (end-start+1) * mode_size, SEEK_CUR); 01418 01419 for (int i = end+1; i < nitems_per_line; i++) { 01420 fprintf(file, outformat, data[*p_i]); 01421 (*p_i)++; 01422 } 01423 portable_fseek(file, 1, SEEK_CUR); 01424 } 01425 }
|
|
Definition at line 197 of file emutil.cpp. References Assert, EMAN::Util::get_filename_ext(), get_image_ext_type(), IMAGE_AMIRA, IMAGE_DF3, IMAGE_DM3, IMAGE_EM, IMAGE_EMIM, 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::EmIO::is_valid(), EMAN::Gatan2IO::is_valid(), EMAN::XplorIO::is_valid(), EMAN::AmiraIO::is_valid(), EMAN::SalIO::is_valid(), EMAN::IcosIO::is_valid(), EMAN::EmimIO::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(), EMAN::ImagicIO::is_valid(), and EMAN::MrcIO::is_valid(). Referenced by get_image_type(). 00200 { 00201 ENTERFUNC; 00202 Assert(filename != ""); 00203 Assert(first_block != 0); 00204 Assert(file_size > 0); 00205 00206 #ifdef ENABLE_V4L2 00207 if (filename.compare(0,5,"/dev/")==0) return IMAGE_V4L; 00208 #endif 00209 00210 string ext = Util::get_filename_ext(filename); 00211 if (ext == "") { 00212 return IMAGE_UNKNOWN; 00213 } 00214 ImageType image_type = get_image_ext_type(ext); 00215 00216 switch (image_type) { 00217 case IMAGE_MRC: 00218 if (MrcIO::is_valid(first_block, file_size)) { 00219 return IMAGE_MRC; 00220 } 00221 break; 00222 case IMAGE_IMAGIC: 00223 if (ImagicIO::is_valid(first_block)) { 00224 return IMAGE_IMAGIC; 00225 } 00226 break; 00227 case IMAGE_DM3: 00228 if (DM3IO::is_valid(first_block)) { 00229 return IMAGE_DM3; 00230 } 00231 break; 00232 #ifdef EM_HDF5 00233 case IMAGE_HDF: 00234 if (HdfIO2::is_valid(first_block)) { 00235 return IMAGE_HDF; 00236 } 00237 break; 00238 #endif 00239 case IMAGE_LST: 00240 if (LstIO::is_valid(first_block)) { 00241 return IMAGE_LST; 00242 } 00243 break; 00244 case IMAGE_LSTFAST: 00245 if (LstFastIO::is_valid(first_block)) { 00246 return IMAGE_LSTFAST; 00247 } 00248 break; 00249 #ifdef EM_TIFF 00250 case IMAGE_TIFF: 00251 if (TiffIO::is_valid(first_block)) { 00252 return IMAGE_TIFF; 00253 } 00254 break; 00255 #endif 00256 case IMAGE_SPIDER: 00257 if (SpiderIO::is_valid(first_block)) { 00258 return IMAGE_SPIDER; 00259 } 00260 break; 00261 case IMAGE_SINGLE_SPIDER: 00262 if (SingleSpiderIO::is_valid(first_block)) { 00263 return IMAGE_SINGLE_SPIDER; 00264 } 00265 break; 00266 case IMAGE_PIF: 00267 if (PifIO::is_valid(first_block)) { 00268 return IMAGE_PIF; 00269 } 00270 break; 00271 #ifdef EM_PNG 00272 case IMAGE_PNG: 00273 if (PngIO::is_valid(first_block)) { 00274 return IMAGE_PNG; 00275 } 00276 break; 00277 #endif 00278 case IMAGE_VTK: 00279 if (VtkIO::is_valid(first_block)) { 00280 return IMAGE_VTK; 00281 } 00282 break; 00283 case IMAGE_PGM: 00284 if (PgmIO::is_valid(first_block)) { 00285 return IMAGE_PGM; 00286 } 00287 break; 00288 case IMAGE_EMIM: 00289 if (EmimIO::is_valid(first_block)) { 00290 return IMAGE_EMIM; 00291 } 00292 break; 00293 case IMAGE_ICOS: 00294 if (IcosIO::is_valid(first_block)) { 00295 return IMAGE_ICOS; 00296 } 00297 break; 00298 case IMAGE_SAL: 00299 if (SalIO::is_valid(first_block)) { 00300 return IMAGE_SAL; 00301 } 00302 break; 00303 case IMAGE_AMIRA: 00304 if (AmiraIO::is_valid(first_block)) { 00305 return IMAGE_AMIRA; 00306 } 00307 break; 00308 case IMAGE_XPLOR: 00309 if (XplorIO::is_valid(first_block)) { 00310 return IMAGE_XPLOR; 00311 } 00312 break; 00313 case IMAGE_GATAN2: 00314 if (Gatan2IO::is_valid(first_block)) { 00315 return IMAGE_GATAN2; 00316 } 00317 break; 00318 case IMAGE_EM: 00319 if (EmIO::is_valid(first_block, file_size)) { 00320 return IMAGE_EM; 00321 } 00322 break; 00323 case IMAGE_DF3: 00324 if (EmIO::is_valid(first_block, file_size)) { 00325 return IMAGE_DF3; 00326 } 00327 break; 00328 default: 00329 return IMAGE_UNKNOWN; 00330 } 00331 EXITFUNC; 00332 return IMAGE_UNKNOWN; 00333 }
|
|
Get an attribute from a stack of image, returned as a vector.
Definition at line 1489 of file emutil.cpp. References Assert, read_images(), and v. 01490 { 01491 vector<EMObject> v; 01492 01493 Assert(file_name != ""); 01494 Assert(attr_name != ""); 01495 01496 vector<EMData *> vpImg = EMData::read_images(file_name, vector<int>(), true); 01497 vector<EMData *>::iterator iter; 01498 for(iter = vpImg.begin(); iter!=vpImg.end(); ++iter) { 01499 v.push_back((*iter)->get_attr_default(attr_name)); 01500 } 01501 01502 return v; 01503 }
|
|
Give each data type a meaningful name.
Definition at line 686 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(). 00687 { 00688 switch (type) { 00689 case EM_CHAR: 00690 return "CHAR"; 00691 case EM_UCHAR: 00692 return "UNSIGNED CHAR"; 00693 case EM_SHORT: 00694 return "SHORT"; 00695 case EM_USHORT: 00696 return "UNSIGNED SHORT"; 00697 case EM_INT: 00698 return "INT"; 00699 case EM_UINT: 00700 return "UNSIGNED INT"; 00701 case EM_FLOAT: 00702 return "FLOAT"; 00703 case EM_DOUBLE: 00704 return "DOUBLE"; 00705 case EM_SHORT_COMPLEX: 00706 return "SHORT_COMPLEX"; 00707 case EM_USHORT_COMPLEX: 00708 return "USHORT_COMPLEX"; 00709 case EM_FLOAT_COMPLEX: 00710 return "FLOAT_COMPLEX"; 00711 case EM_UNKNOWN: 00712 return "UNKNOWN"; 00713 } 00714 return "UNKNOWN"; 00715 }
|
|
Definition at line 1445 of file emutil.cpp. 01446 { 01447 vector<string> v; 01448 string b = "euler_"; 01449 01450 if (euler_type == "EMAN") { 01451 v.push_back(b + "alt"); 01452 v.push_back(b + "az"); 01453 v.push_back(b + "phi"); 01454 } 01455 else if (euler_type == "MRC") { 01456 v.push_back(b + "theta"); 01457 v.push_back(b + "phi"); 01458 v.push_back(b + "omega"); 01459 } 01460 else if (euler_type == "IMAGIC") { 01461 v.push_back(b + "alpha"); 01462 v.push_back(b + "beta"); 01463 v.push_back(b + "gamma"); 01464 } 01465 else if (euler_type == "SPIDER") { 01466 v.push_back(b + "phi"); 01467 v.push_back(b + "theta"); 01468 v.push_back(b + "gamma"); 01469 } 01470 else if (euler_type == "SPIN" || 01471 euler_type == "SGIROT") { 01472 v.push_back(b + "q"); 01473 v.push_back(b + "n1"); 01474 v.push_back(b + "n2"); 01475 v.push_back(b + "n3"); 01476 } 01477 01478 else if (euler_type == "QUATERNION") { 01479 v.push_back(b + "e0"); 01480 v.push_back(b + "e1"); 01481 v.push_back(b + "e2"); 01482 v.push_back(b + "e3"); 01483 } 01484 01485 return v; 01486 }
|
|
Get the number of images in an image file.
Definition at line 456 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(). 00457 { 00458 ENTERFUNC; 00459 Assert(filename != ""); 00460 00461 int nimg = 0; 00462 ImageIO *imageio = get_imageio(filename, ImageIO::READ_ONLY); 00463 00464 if (imageio) { 00465 nimg = imageio->get_nimg(); 00466 } 00467 #ifndef IMAGEIO_CACHE 00468 if( imageio ) 00469 { 00470 delete imageio; 00471 imageio = 0; 00472 } 00473 #endif 00474 EXITFUNC; 00475 return nimg; 00476 }
|
|
Get an image's format type from its filename extension.
Definition at line 58 of file emutil.cpp. References ImageType. Referenced by fast_get_image_type(), and is_valid_filename(). 00059 { 00060 ENTERFUNC; 00061 static bool initialized = false; 00062 static map < string, ImageType > imagetypes; 00063 00064 if (!initialized) { 00065 imagetypes["rec"] = IMAGE_MRC; 00066 imagetypes["mrc"] = IMAGE_MRC; 00067 imagetypes["MRC"] = IMAGE_MRC; 00068 imagetypes["ali"] = IMAGE_MRC; 00069 00070 imagetypes["tnf"] = IMAGE_MRC; 00071 imagetypes["TNF"] = IMAGE_MRC; 00072 00073 imagetypes["ccp4"] = IMAGE_MRC; 00074 imagetypes["map"] = IMAGE_MRC; 00075 00076 imagetypes["dm3"] = IMAGE_DM3; 00077 imagetypes["DM3"] = IMAGE_DM3; 00078 00079 imagetypes["spi"] = IMAGE_SPIDER; 00080 imagetypes["SPI"] = IMAGE_SPIDER; 00081 00082 imagetypes["spider"] = IMAGE_SPIDER; 00083 imagetypes["SPIDER"] = IMAGE_SPIDER; 00084 00085 imagetypes["spidersingle"] = IMAGE_SINGLE_SPIDER; 00086 imagetypes["SPIDERSINGLE"] = IMAGE_SINGLE_SPIDER; 00087 00088 imagetypes["singlespider"] = IMAGE_SINGLE_SPIDER; 00089 imagetypes["SINGLESPIDER"] = IMAGE_SINGLE_SPIDER; 00090 00091 imagetypes["img"] = IMAGE_IMAGIC; 00092 imagetypes["IMG"] = IMAGE_IMAGIC; 00093 00094 imagetypes["hed"] = IMAGE_IMAGIC; 00095 imagetypes["HED"] = IMAGE_IMAGIC; 00096 00097 imagetypes["imagic"] = IMAGE_IMAGIC; 00098 imagetypes["IMAGIC"] = IMAGE_IMAGIC; 00099 00100 imagetypes["pgm"] = IMAGE_PGM; 00101 imagetypes["PGM"] = IMAGE_PGM; 00102 00103 imagetypes["lst"] = IMAGE_LST; 00104 imagetypes["LST"] = IMAGE_LST; 00105 00106 imagetypes["lsx"] = IMAGE_LSTFAST; // but .lst or another extension would also be ok 00107 imagetypes["LSX"] = IMAGE_LSTFAST; 00108 00109 imagetypes["pif"] = IMAGE_PIF; 00110 imagetypes["PIF"] = IMAGE_PIF; 00111 00112 imagetypes["png"] = IMAGE_PNG; 00113 imagetypes["PNG"] = IMAGE_PNG; 00114 00115 imagetypes["h5"] = IMAGE_HDF; 00116 imagetypes["H5"] = IMAGE_HDF; 00117 00118 imagetypes["hd5"] = IMAGE_HDF; 00119 imagetypes["HD5"] = IMAGE_HDF; 00120 00121 imagetypes["hdf"] = IMAGE_HDF; 00122 imagetypes["HDF"] = IMAGE_HDF; 00123 00124 imagetypes["tif"] = IMAGE_TIFF; 00125 imagetypes["TIF"] = IMAGE_TIFF; 00126 00127 imagetypes["tiff"] = IMAGE_TIFF; 00128 imagetypes["TIFF"] = IMAGE_TIFF; 00129 00130 imagetypes["fts"] = IMAGE_FITS; 00131 imagetypes["FTS"] = IMAGE_FITS; 00132 00133 imagetypes["vtk"] = IMAGE_VTK; 00134 imagetypes["VTK"] = IMAGE_VTK; 00135 00136 imagetypes["hdr"] = IMAGE_SAL; 00137 imagetypes["HDR"] = IMAGE_SAL; 00138 00139 imagetypes["sal"] = IMAGE_SAL; 00140 imagetypes["SAL"] = IMAGE_SAL; 00141 00142 imagetypes["map"] = IMAGE_ICOS; 00143 imagetypes["MAP"] = IMAGE_ICOS; 00144 00145 imagetypes["icos"] = IMAGE_ICOS; 00146 imagetypes["ICOS"] = IMAGE_ICOS; 00147 00148 imagetypes["am"] = IMAGE_AMIRA; 00149 imagetypes["AM"] = IMAGE_AMIRA; 00150 00151 imagetypes["amira"] = IMAGE_AMIRA; 00152 imagetypes["AMIRA"] = IMAGE_AMIRA; 00153 00154 imagetypes["emim"] = IMAGE_EMIM; 00155 imagetypes["EMIM"] = IMAGE_EMIM; 00156 00157 imagetypes["xplor"] = IMAGE_XPLOR; 00158 imagetypes["XPLOR"] = IMAGE_XPLOR; 00159 00160 imagetypes["em"] = IMAGE_EM; 00161 imagetypes["EM"] = IMAGE_EM; 00162 00163 imagetypes["dm2"] = IMAGE_GATAN2; 00164 imagetypes["DM2"] = IMAGE_GATAN2; 00165 00166 imagetypes["v4l"] = IMAGE_V4L; 00167 imagetypes["V4L"] = IMAGE_V4L; 00168 00169 imagetypes["jpg"] = IMAGE_JPEG; 00170 imagetypes["JPG"] = IMAGE_JPEG; 00171 imagetypes["jpeg"] = IMAGE_JPEG; 00172 imagetypes["JPEG"] = IMAGE_JPEG; 00173 00174 imagetypes["df3"] = IMAGE_DF3; 00175 imagetypes["DF3"] = IMAGE_DF3; 00176 00177 initialized = true; 00178 } 00179 00180 ImageType result = IMAGE_UNKNOWN; 00181 00182 if (imagetypes.find(file_ext) != imagetypes.end()) { 00183 result = imagetypes[file_ext]; 00184 } 00185 00186 EXITFUNC; 00187 return result; 00188 }
|
|
Get an image's format type by processing the first 1K of the image.
Definition at line 336 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::MrcIO::is_valid(), 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::EmimIO::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(), LOGERR, portable_fseek(), and portable_ftell(). Referenced by get_imageio(), getRenderMinMax(), and main(). 00337 { 00338 ENTERFUNC; 00339 Assert(in_filename != ""); 00340 00341 #ifdef ENABLE_V4L2 00342 if (in_filename.compare(0,5,"/dev/")==0) return IMAGE_V4L; 00343 #endif 00344 00345 string filename = in_filename; 00346 00347 string old_ext = Util::get_filename_ext(filename); 00348 if (old_ext == ImagicIO::IMG_EXT) { 00349 filename = Util::change_filename_ext(filename, ImagicIO::HED_EXT); 00350 } 00351 00352 FILE *in = fopen(filename.c_str(), "rb"); 00353 if (!in) { 00354 throw FileAccessException(filename); 00355 } 00356 00357 char first_block[1024]; 00358 size_t n = fread(first_block, sizeof(char), sizeof(first_block), in); 00359 portable_fseek(in, 0, SEEK_END); 00360 off_t file_size = portable_ftell(in); 00361 00362 if (n == 0) { 00363 LOGERR("file '%s' is an empty file", filename.c_str()); 00364 fclose(in); 00365 return IMAGE_UNKNOWN; 00366 } 00367 fclose(in); 00368 00369 ImageType image_type = fast_get_image_type(filename, first_block, file_size); 00370 if (image_type != IMAGE_UNKNOWN) { 00371 return image_type; 00372 } 00373 00374 if (DM3IO::is_valid(first_block)) { 00375 image_type = IMAGE_DM3; 00376 } 00377 #ifdef EM_HDF5 00378 else if (HdfIO2::is_valid(first_block)) { 00379 image_type = IMAGE_HDF; 00380 } 00381 #endif 00382 else if (LstIO::is_valid(first_block)) { 00383 image_type = IMAGE_LST; 00384 } 00385 else if (LstFastIO::is_valid(first_block)) { 00386 image_type = IMAGE_LSTFAST; 00387 } 00388 #ifdef EM_TIFF 00389 else if (TiffIO::is_valid(first_block)) { 00390 image_type = IMAGE_TIFF; 00391 } 00392 #endif 00393 else if (SpiderIO::is_valid(first_block)) { 00394 image_type = IMAGE_SPIDER; 00395 } 00396 else if (SingleSpiderIO::is_valid(first_block)) { 00397 image_type = IMAGE_SINGLE_SPIDER; 00398 } 00399 else if (PifIO::is_valid(first_block)) { 00400 image_type = IMAGE_PIF; 00401 } 00402 #ifdef EM_PNG 00403 else if (PngIO::is_valid(first_block)) { 00404 image_type = IMAGE_PNG; 00405 } 00406 #endif 00407 else if (VtkIO::is_valid(first_block)) { 00408 image_type = IMAGE_VTK; 00409 } 00410 else if (PgmIO::is_valid(first_block)) { 00411 image_type = IMAGE_PGM; 00412 } 00413 else if (EmimIO::is_valid(first_block)) { 00414 image_type = IMAGE_EMIM; 00415 } 00416 else if (IcosIO::is_valid(first_block)) { 00417 image_type = IMAGE_ICOS; 00418 } 00419 else if (SalIO::is_valid(first_block)) { 00420 image_type = IMAGE_SAL; 00421 } 00422 else if (AmiraIO::is_valid(first_block)) { 00423 image_type = IMAGE_AMIRA; 00424 } 00425 else if (XplorIO::is_valid(first_block)) { 00426 image_type = IMAGE_XPLOR; 00427 } 00428 else if (Gatan2IO::is_valid(first_block)) { 00429 image_type = IMAGE_GATAN2; 00430 } 00431 else if (FitsIO::is_valid(first_block)) { 00432 image_type = IMAGE_FITS; 00433 } 00434 else if (EmIO::is_valid(first_block, file_size)) { 00435 image_type = IMAGE_EM; 00436 } 00437 else if (ImagicIO::is_valid(first_block)) { 00438 image_type = IMAGE_IMAGIC; 00439 } 00440 else if (Df3IO::is_valid(first_block)) { 00441 image_type = IMAGE_DF3; 00442 } 00443 else if (MrcIO::is_valid(first_block, file_size)) { 00444 image_type = IMAGE_MRC; 00445 } 00446 else { 00447 //LOGERR("I don't know this image's type: '%s'", filename.c_str()); 00448 throw ImageFormatException("invalid image type"); 00449 } 00450 00451 EXITFUNC; 00452 return image_type; 00453 }
|
|
Get an ImageIO object. It may be a newly created object. Or an object stored in the cache.
Definition at line 479 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_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_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(). 00481 { 00482 ENTERFUNC; 00483 Assert(filename != ""); 00484 Assert(rw == ImageIO::READ_ONLY || 00485 rw == ImageIO::READ_WRITE || 00486 rw == ImageIO::WRITE_ONLY); 00487 00488 ImageIO *imageio = 0; 00489 #ifdef IMAGEIO_CACHE 00490 imageio = GlobalCache::instance()->get_imageio(filename, rw); 00491 if (imageio) { 00492 return imageio; 00493 } 00494 #endif 00495 00496 ImageIO::IOMode rw_mode = static_cast < ImageIO::IOMode > (rw); 00497 00498 if (image_type == IMAGE_UNKNOWN) { 00499 if(rw == ImageIO::WRITE_ONLY || rw == ImageIO::READ_WRITE) { 00500 throw ImageFormatException("writing to this image format not supported."); 00501 } 00502 00503 image_type = get_image_type(filename); 00504 } 00505 00506 switch (image_type) { 00507 #ifdef ENABLE_V4L2 00508 case IMAGE_V4L: 00509 imageio = new V4L2IO(filename, rw_mode); 00510 break; 00511 #endif 00512 case IMAGE_MRC: 00513 imageio = new MrcIO(filename, rw_mode); 00514 break; 00515 case IMAGE_IMAGIC: 00516 imageio = new ImagicIO(filename, rw_mode); 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_EMIM: 00562 imageio = new EmimIO(filename, rw_mode); 00563 break; 00564 case IMAGE_ICOS: 00565 imageio = new IcosIO(filename, rw_mode); 00566 break; 00567 #ifdef EM_PNG 00568 case IMAGE_PNG: 00569 imageio = new PngIO(filename, rw_mode); 00570 break; 00571 #endif 00572 case IMAGE_SAL: 00573 imageio = new SalIO(filename, rw_mode); 00574 break; 00575 case IMAGE_AMIRA: 00576 imageio = new AmiraIO(filename, rw_mode); 00577 break; 00578 case IMAGE_GATAN2: 00579 imageio = new Gatan2IO(filename, rw_mode); 00580 break; 00581 case IMAGE_EM: 00582 imageio = new EmIO(filename, rw_mode); 00583 break; 00584 case IMAGE_XPLOR: 00585 imageio = new XplorIO(filename, rw_mode); 00586 break; 00587 case IMAGE_FITS: 00588 imageio = new FitsIO(filename, rw_mode); 00589 break; 00590 case IMAGE_DF3: 00591 imageio = new Df3IO(filename, rw_mode); 00592 break; 00593 default: 00594 break; 00595 } 00596 #ifdef IMAGEIO_CACHE 00597 GlobalCache::instance()->add_imageio(filename, rw, imageio); 00598 #endif 00599 EXITFUNC; 00600 return imageio; 00601 }
|
|
Give each image type a meaningful name.
Definition at line 605 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(). 00606 { 00607 switch (t) { 00608 case IMAGE_V4L: 00609 return "V4L2"; 00610 break; 00611 case IMAGE_MRC: 00612 return "MRC"; 00613 break; 00614 case IMAGE_SPIDER: 00615 return "SPIDER"; 00616 break; 00617 case IMAGE_SINGLE_SPIDER: 00618 return "Single-SPIDER"; 00619 break; 00620 case IMAGE_IMAGIC: 00621 return "IMAGIC"; 00622 break; 00623 case IMAGE_PGM: 00624 return "PGM"; 00625 break; 00626 case IMAGE_LST: 00627 return "LST"; 00628 break; 00629 case IMAGE_LSTFAST: 00630 return "Fast LST"; 00631 break; 00632 case IMAGE_PIF: 00633 return "PIF"; 00634 break; 00635 case IMAGE_PNG: 00636 return "PNG"; 00637 break; 00638 case IMAGE_HDF: 00639 return "HDF5"; 00640 break; 00641 case IMAGE_DM3: 00642 return "GatanDM3"; 00643 break; 00644 case IMAGE_TIFF: 00645 return "TIFF"; 00646 break; 00647 case IMAGE_VTK: 00648 return "VTK"; 00649 break; 00650 case IMAGE_SAL: 00651 return "HDR"; 00652 break; 00653 case IMAGE_ICOS: 00654 return "ICOS_MAP"; 00655 break; 00656 case IMAGE_EMIM: 00657 return "EMIM"; 00658 break; 00659 case IMAGE_GATAN2: 00660 return "GatanDM2"; 00661 break; 00662 case IMAGE_JPEG: 00663 return "JPEG"; 00664 break; 00665 case IMAGE_AMIRA: 00666 return "AmiraMesh"; 00667 break; 00668 case IMAGE_XPLOR: 00669 return "XPLOR"; 00670 break; 00671 case IMAGE_EM: 00672 return "EM"; 00673 break; 00674 case IMAGE_FITS: 00675 return "FITS"; 00676 break; 00677 case IMAGE_DF3: 00678 return "DF3"; 00679 break; 00680 case IMAGE_UNKNOWN: 00681 return "unknown"; 00682 } 00683 return "unknown"; 00684 }
|
|
Get a region's dimensions.
Definition at line 717 of file emutil.cpp. References Assert, EMAN::Region::get_ndim(), EMAN::Region::get_size(), and EMAN::Vec3i. Referenced by process_ascii_region_io(), and process_region_io(). 00719 { 00720 Assert(area_x); 00721 Assert(area_y); 00722 00723 if (!area) { 00724 *area_x = nx; 00725 *area_y = ny; 00726 if (area_z) { 00727 *area_z = nz; 00728 } 00729 } 00730 else { 00731 Vec3i size = area->get_size(); 00732 *area_x = size[0]; 00733 *area_y = size[1]; 00734 00735 if (area_z) { 00736 if (area->get_ndim() > 2 && nz > 1) { 00737 *area_z = size[2]; 00738 } 00739 else { 00740 *area_z = 1; 00741 } 00742 } 00743 00744 } 00745 }
|
|
Get a region's original locations.
Definition at line 747 of file emutil.cpp. References Assert, EMAN::Region::get_ndim(), and EMAN::Region::origin. 00749 { 00750 Assert(p_x0); 00751 Assert(p_y0); 00752 00753 if (area) { 00754 *p_x0 = static_cast < int >(area->origin[0]); 00755 *p_y0 = static_cast < int >(area->origin[1]); 00756 00757 if (p_z0 && nz > 1 && area->get_ndim() > 2) { 00758 *p_z0 = static_cast < int >(area->origin[2]); 00759 } 00760 } 00761 else { 00762 *p_x0 = 0; 00763 *p_y0 = 0; 00764 if (p_z0) { 00765 *p_z0 = nz > 1 ? 0 : image_index; 00766 } 00767 } 00768 }
|
|
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 1505 of file emutil.cpp. References data, get_image_type(), ImageFormatException, ImageType, EMAN::EMObject::init(), key, max, min, nx, ny, and sqrt(). 01506 { 01507 #ifdef _WIN32 01508 if (rendermax<=rendermin || _isnan(rendermin) || _isnan(rendermax)) { 01509 #else 01510 if (rendermax<=rendermin || std::isnan(rendermin) || std::isnan(rendermax)) { 01511 #endif 01512 float m=0.0f,s=0.0f; 01513 01514 size_t size = nx*ny*nz; 01515 float min=data[0],max=data[0]; 01516 01517 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; } 01518 m/=(float)(size); 01519 s=sqrt(s/(float)(size)-m*m); 01520 #ifdef _WIN32 01521 if (s<=0 || _isnan(s)) s=1.0; // this means all data values are the same 01522 #else 01523 if (s<=0 || std::isnan(s)) s=1.0; // this means all data values are the same 01524 #endif //_WIN32 01525 rendermin=m-s*5.0f; 01526 rendermax=m+s*5.0f; 01527 if (rendermin<=min) rendermin=min; 01528 if (rendermax>=max) rendermax=max; 01529 } 01530 }
|
|
Definition at line 977 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(). 00978 { 00979 if (datatype == EM_SHORT_COMPLEX || 00980 datatype == EM_USHORT_COMPLEX || 00981 datatype == EM_FLOAT_COMPLEX) { 00982 return true; 00983 } 00984 return false; 00985 }
|
|
Check whether two EMData images have the same CTF parameters.
Definition at line 1089 of file emutil.cpp. References EMAN::Ctf::equal(), EMAN::EMData::get_ctf(), EMAN::EMData::has_ctff(), and NullPointerException. Referenced by main(). 01090 { 01091 if (!image1) { 01092 throw NullPointerException("image1 is NULL"); 01093 } 01094 if (!image2) { 01095 throw NullPointerException("image2 is NULL"); 01096 } 01097 01098 Ctf *ctf1 = image1->get_ctf(); 01099 Ctf *ctf2 = image2->get_ctf(); 01100 01101 if ((!ctf1 && !ctf2) && (image1->has_ctff() == false && image2->has_ctff() == false)) { 01102 return true; 01103 } 01104 01105 if (ctf1 && ctf2) { 01106 bool result = ctf1->equal(ctf2); 01107 delete ctf1; 01108 ctf1 = 0; 01109 delete ctf2; 01110 ctf2 = 0; 01111 01112 return result; 01113 } 01114 return false; 01115 }
|
|
Check whether two EMData images are of the same size.
Definition at line 967 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::TranslationalAligner::align(), EMAN::NormalizeMaskProcessor::calc_mean(), EMAN::NormalizeMaskProcessor::calc_sigma(), EMAN::IndexMaskFileProcessor::process_inplace(), and EMAN::Cmp::validate_input_args(). 00968 { 00969 if (em1->get_xsize() == em2->get_xsize() && 00970 em1->get_ysize() == em2->get_ysize() && 00971 em1->get_zsize() == em2->get_zsize()) { 00972 return true; 00973 } 00974 return false; 00975 }
|
|
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 192 of file emutil.cpp. References get_image_ext_type(), and ImageType. 00192 { 00193 ImageType type = get_image_ext_type(Util::get_filename_ext(filename)); 00194 return (type != IMAGE_UNKNOWN); 00195 }
|
|
Definition at line 1308 of file emutil.cpp. References Assert. Referenced by jump_lines_by_items(), and process_ascii_region_io(). 01309 { 01310 Assert(file); 01311 01312 if (nlines > 0) { 01313 char line[MAXPATHLEN]; 01314 for (int l = 0; l < nlines; l++) { 01315 if (!fgets(line, sizeof(line), file)) { 01316 Assert("read xplor file failed"); 01317 } 01318 } 01319 } 01320 }
|
|
Definition at line 1289 of file emutil.cpp. References Assert, and jump_lines(). Referenced by process_ascii_region_io(). 01290 { 01291 Assert(file); 01292 Assert(nitems_per_line > 0); 01293 01294 if (nitems <= 0) { 01295 return; 01296 } 01297 01298 int nlines = nitems / nitems_per_line; 01299 if ((nitems % nitems_per_line) != 0) { 01300 nlines++; 01301 } 01302 if (nlines > 0) { 01303 jump_lines(file, nlines); 01304 } 01305 }
|
|
Definition at line 1024 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. 01025 { 01026 if (image_list.size() == 0) { 01027 return 0; 01028 } 01029 01030 EMData *image0 = image_list[0]; 01031 int image0_nx = image0->get_xsize(); 01032 int image0_ny = image0->get_ysize(); 01033 int image0_nz = image0->get_zsize(); 01034 size_t size = image0_nx * image0_ny * image0_nz; 01035 01036 EMData *result = new EMData(); 01037 01038 result->set_size(image0_nx, image0_ny, image0_nz); 01039 01040 float *dest = result->get_data(); 01041 int nitems = static_cast < int >(image_list.size()); 01042 float *srt = new float[nitems]; 01043 float **src = new float *[nitems]; 01044 01045 for (int i = 0; i < nitems; i++) { 01046 src[i] = image_list[i]->get_data(); 01047 } 01048 01049 for (size_t i = 0; i < size; i++) { 01050 for (int j = 0; j < nitems; j++) { 01051 srt[j] = src[j][i]; 01052 } 01053 01054 for (int j = 0; j < nitems; j++) { 01055 for (int k = j + 1; k < nitems; k++) { 01056 if (srt[j] < srt[k]) { 01057 float v = srt[j]; 01058 srt[j] = srt[k]; 01059 srt[k] = v; 01060 } 01061 } 01062 } 01063 01064 int l = nitems / 2; 01065 if (nitems < 3) { 01066 dest[i] = srt[l]; 01067 } 01068 else { 01069 dest[i] = (srt[l] + srt[l + 1] + srt[l - 1]) / 3.0f; 01070 } 01071 } 01072 01073 if( srt ) 01074 { 01075 delete[]srt; 01076 srt = 0; 01077 } 01078 if( src ) 01079 { 01080 delete[]src; 01081 src = 0; 01082 } 01083 01084 result->update(); 01085 01086 return result; 01087 }
|
|
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 1180 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(). 01184 { 01185 Assert(data != 0); 01186 Assert(file != 0); 01187 Assert(rw_mode == ImageIO::READ_ONLY || 01188 rw_mode == ImageIO::READ_WRITE || 01189 rw_mode == ImageIO::WRITE_ONLY); 01190 01191 int xlen = 0, ylen = 0, zlen = 0; 01192 get_region_dims(area, nx, &xlen, ny, &ylen, nz, &zlen); 01193 01194 int x0 = 0; 01195 int y0 = 0; 01196 int z0 = 0; 01197 01198 if (area) { 01199 x0 = (int)area->origin[0]; 01200 y0 = (int)area->origin[1]; 01201 z0 = (int)area->origin[2]; 01202 } 01203 01204 int nlines_per_sec = (nx *ny) / nitems_per_line; 01205 int nitems_last_line = (nx * ny) % nitems_per_line; 01206 if (nitems_last_line != 0) { 01207 nlines_per_sec++; 01208 } 01209 01210 if (has_index_line) { 01211 nlines_per_sec++; 01212 } 01213 01214 if (z0 > 0) { 01215 jump_lines(file, z0 * nlines_per_sec); 01216 } 01217 01218 01219 int nlines_pre_sec = (y0 * nx + x0) / nitems_per_line; 01220 int gap_nitems = nx - xlen; 01221 int ti = 0; 01222 int rlines = 0; 01223 01224 for (int k = 0; k < zlen; k++) { 01225 EMUtil::jump_lines(file, nlines_pre_sec+1); 01226 01227 int head_nitems = (y0 * nx + x0) % nitems_per_line; 01228 int tail_nitems = 0; 01229 bool is_head_read = false; 01230 01231 for (int j = 0; j < ylen; j++) { 01232 01233 if (head_nitems > 0 && !is_head_read) { 01234 EMUtil::process_numbers_io(file, rw_mode, nitems_per_line, mode_size, 01235 nitems_per_line-head_nitems, 01236 nitems_per_line-1, data, &ti, outformat); 01237 rlines++; 01238 } 01239 01240 EMUtil::process_lines_io(file, rw_mode, nitems_per_line, 01241 mode_size, (xlen - head_nitems), 01242 data, &ti, outformat); 01243 01244 rlines += ((xlen - head_nitems)/nitems_per_line); 01245 01246 tail_nitems = (xlen - head_nitems) % nitems_per_line; 01247 01248 if ((gap_nitems + tail_nitems) > 0) { 01249 head_nitems = nitems_per_line - 01250 (gap_nitems + tail_nitems) % nitems_per_line; 01251 } 01252 else { 01253 head_nitems = 0; 01254 } 01255 01256 is_head_read = false; 01257 01258 if (tail_nitems > 0) { 01259 if ((gap_nitems < (nitems_per_line-tail_nitems)) && 01260 (j != (ylen-1))) { 01261 EMUtil::exclude_numbers_io(file, rw_mode, nitems_per_line, 01262 mode_size, tail_nitems, 01263 tail_nitems+gap_nitems-1, data, &ti, outformat); 01264 is_head_read = true; 01265 rlines++; 01266 } 01267 else { 01268 EMUtil::process_numbers_io(file, rw_mode, nitems_per_line, mode_size, 01269 0, tail_nitems-1, data, &ti, outformat); 01270 rlines++; 01271 } 01272 } 01273 01274 if (gap_nitems > (nitems_per_line-tail_nitems)) { 01275 int gap_nlines = (gap_nitems - (nitems_per_line-tail_nitems)) / 01276 nitems_per_line; 01277 if (gap_nlines > 0 && j != (ylen-1)) { 01278 EMUtil::jump_lines(file, gap_nlines); 01279 } 01280 } 01281 } 01282 01283 int ytail_nitems = (ny-ylen-y0) * nx + (nx-xlen-x0) - (nitems_per_line-tail_nitems); 01284 EMUtil::jump_lines_by_items(file, ytail_nitems, nitems_per_line); 01285 } 01286 }
|
|
Definition at line 1427 of file emutil.cpp. References Assert, data, and process_numbers_io(). Referenced by process_ascii_region_io(). 01431 { 01432 Assert(file); 01433 Assert(data); 01434 Assert(p_i); 01435 01436 if (nitems > 0) { 01437 int nlines = nitems / nitems_per_line; 01438 for (int i = 0; i < nlines; i++) { 01439 EMUtil::process_numbers_io(file, rw_mode, nitems_per_line, mode_size, 0, 01440 nitems_per_line-1, data, p_i, outformat); 01441 } 01442 } 01443 }
|
|
Definition at line 1322 of file emutil.cpp. References Assert, data, and portable_fseek(). Referenced by process_ascii_region_io(), and process_lines_io(). 01325 { 01326 Assert(file); 01327 Assert(start >= 0); 01328 Assert(start <= end); 01329 Assert(end <= nitems_per_line); 01330 Assert(data); 01331 Assert(p_i); 01332 Assert(outformat); 01333 01334 char line[MAXPATHLEN]; 01335 01336 if (rw_mode == ImageIO::READ_ONLY) { 01337 if (!fgets(line, sizeof(line), file)) { 01338 Assert("read xplor file failed"); 01339 } 01340 01341 int nitems_in_line = (int) (strlen(line) / mode_size); 01342 Assert(end <= nitems_in_line); 01343 vector<float> d(nitems_in_line); 01344 char * pline = line; 01345 01346 for (int i = 0; i < nitems_in_line; i++) { 01347 sscanf(pline, "%f", &d[i]); 01348 pline += (int)mode_size; 01349 } 01350 01351 01352 for (int i = start; i <= end; i++) { 01353 data[*p_i] = d[i]; 01354 (*p_i)++; 01355 } 01356 } 01357 else { 01358 portable_fseek(file, mode_size * start, SEEK_CUR); 01359 for (int i = start; i <= end; i++) { 01360 fprintf(file, outformat, data[*p_i]); 01361 (*p_i)++; 01362 } 01363 01364 portable_fseek(file, mode_size * (nitems_per_line - end-1)+1, SEEK_CUR); 01365 } 01366 }
|
|
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 771 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. 00776 { 00777 Assert(vdata != 0); 00778 Assert(file != 0); 00779 Assert(rw_mode == ImageIO::READ_ONLY || 00780 rw_mode == ImageIO::READ_WRITE || 00781 rw_mode == ImageIO::WRITE_ONLY); 00782 00783 if (mode_size == 0) throw UnexpectedBehaviorException("The mode size was 0?"); 00784 00785 unsigned char * cdata = (unsigned char *)vdata; 00786 00787 int dx0 = 0; // data x0 00788 int dy0 = 0; // data y0 00789 int dz0 = 0; // data z0 00790 00791 int fx0 = 0; // file x0 00792 int fy0 = 0; // file y0 00793 int fz0 = nz > 1 ? 0 : image_index; // file z0 00794 00795 00796 int xlen = 0; 00797 int ylen = 0; 00798 int zlen = 0; 00799 get_region_dims(area, nx, &xlen, ny, &ylen, nz, &zlen); 00800 00801 if (area) { // Accommodate for all boundary overlaps of the region 00802 00803 Vec3i origin = area->get_origin(); 00804 00805 00806 fx0 = origin[0]; dx0 = origin[0]; 00807 fy0 = origin[1]; dy0 = origin[1]; 00808 if (nz > 1 && area->get_ndim() > 2) { 00809 fz0 = origin[2]; dz0 = origin[2]; 00810 } 00811 00812 if (need_flip) { 00813 Vec3i size = area->get_size(); 00814 fy0 = ny-(origin[1]+size[1]); 00815 } 00816 00817 if (fx0 < 0) { 00818 dx0 *= -1; 00819 xlen = xlen + fx0; // because there are less reads 00820 fx0 = 0; 00821 }else { 00822 dx0 = 0; 00823 //fx0 *= -1; 00824 } 00825 if (fy0 < 0) { 00826 dy0 *= -1; 00827 ylen = ylen + fy0; // because there are less reads 00828 fy0 = 0; 00829 }else { 00830 if (need_flip){ 00831 dy0*=-1; 00832 } 00833 else dy0 = 0; 00834 //fy0 *= -1; 00835 } 00836 if (fz0 < 0) { 00837 dz0 *= -1; 00838 zlen = zlen + fz0; // because there are less reads 00839 fz0 = 0; 00840 }else { 00841 dz0 = 0; 00842 //fz0 *= -1; 00843 } 00844 00845 if ((fx0 + xlen)> nx) xlen = nx-fx0; 00846 if ((fy0 + ylen)> ny) ylen = ny-fy0; 00847 if ((fz0 + zlen)> nz) zlen = nz-fz0; 00848 if ( xlen <= 0 || ylen <= 0 || zlen <= 0 ) return; // This is fine the region was entirely outside the image 00849 } 00850 00851 if ( xlen <= 0 ) { 00852 cout << "Xlen was too small " << xlen << endl; 00853 return; 00854 } 00855 00856 Vec3i size; 00857 if (area != 0) size = area->get_size(); 00858 else size = Vec3d(nx,ny,nz); 00859 00860 //size_t area_sec_size = xlen * ylen * mode_size; 00861 size_t memory_sec_size = size[0] * size[1] * mode_size; 00862 size_t img_row_size = nx * mode_size + pre_row + post_row; 00863 size_t area_row_size = xlen * mode_size; 00864 size_t memory_row_size = size[0] * mode_size; 00865 00866 if ( area_row_size <= 0 ) { 00867 cout << "Xlen was too small " << xlen << " mode_size " << mode_size << endl; 00868 return; 00869 } 00870 00871 size_t x_pre_gap = fx0 * mode_size; 00872 size_t x_post_gap = (nx - fx0 - xlen) * mode_size; 00873 00874 size_t y_pre_gap = fy0 * img_row_size; 00875 size_t y_post_gap = (ny - fy0 - ylen) * img_row_size; 00876 00877 portable_fseek(file, img_row_size * ny * fz0, SEEK_CUR); 00878 00879 float nxlendata[1]; 00880 int floatsize = (int) sizeof(float); 00881 nxlendata[0] = (float)(nx * floatsize); 00882 00883 for (int k = dz0; k < (dz0+zlen); k++) { 00884 if (y_pre_gap > 0) { 00885 portable_fseek(file, y_pre_gap, SEEK_CUR); 00886 } 00887 //long k2 = k * area_sec_size; 00888 long k2 = k*memory_sec_size; 00889 00890 for (int j = dy0; j < (dy0+ylen); j++) { 00891 if (pre_row > 0) { 00892 if (imgtype == IMAGE_ICOS && rw_mode != ImageIO::READ_ONLY && !area) { 00893 fwrite(nxlendata, floatsize, 1, file); 00894 } 00895 else { 00896 portable_fseek(file, pre_row, SEEK_CUR); 00897 } 00898 } 00899 00900 if (x_pre_gap > 0) { 00901 portable_fseek(file, x_pre_gap, SEEK_CUR); 00902 } 00903 00904 int jj = j; 00905 if (need_flip) { 00906 jj = (dy0+ylen) - 1 - j; 00907 if (dy0 > 0 ) { // region considerations add complications in the flipping scenario (imagic format) 00908 jj += dy0; 00909 } 00910 } 00911 00912 if (rw_mode == ImageIO::READ_ONLY) { 00913 if (fread(&cdata[k2 + jj * memory_row_size+dx0*mode_size], 00914 area_row_size, 1, file) != 1) { 00915 cout << jj << " " << k2 << " " << memory_row_size << " " << dx0 << " " << mode_size << " " << area_row_size << " " << cdata << "done" << endl; 00916 throw ImageReadException("", "incomplete data read"); 00917 } 00918 } 00919 else { 00920 if (fwrite(&cdata[k2 + jj * memory_row_size+dx0*mode_size], 00921 area_row_size, 1, file) != 1) { 00922 throw ImageWriteException("", "incomplete data write"); 00923 } 00924 } 00925 00926 if (x_post_gap > 0) { 00927 portable_fseek(file, x_post_gap, SEEK_CUR); 00928 } 00929 00930 if (post_row > 0) { 00931 if (imgtype == IMAGE_ICOS && rw_mode != ImageIO::READ_ONLY && !area) { 00932 fwrite(nxlendata, floatsize, 1, file); 00933 } 00934 else { 00935 portable_fseek(file, post_row, SEEK_CUR); 00936 } 00937 } 00938 } 00939 00940 if (y_post_gap > 0) { 00941 portable_fseek(file, y_post_gap, SEEK_CUR); 00942 } 00943 } 00944 }
|
|
Definition at line 988 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. 00989 { 00990 if (!image) { 00991 throw NullPointerException("NULL Image"); 00992 } 00993 00994 EMData *ret = new EMData(); 00995 int nx = image->get_xsize(); 00996 int ny = image->get_ysize(); 00997 00998 if (maxdy <= 1) { 00999 maxdy = ny / 8; 01000 } 01001 01002 ret->set_size(nx, maxdy, 1); 01003 01004 float *data = image->get_data(); 01005 float *ret_data = ret->get_data(); 01006 01007 for (int x = 0; x < nx; x++) { 01008 for (int y = 0; y < maxdy; y++) { 01009 float dot = 0; 01010 for (int yy = maxdy; yy < ny - maxdy; yy++) { 01011 dot += data[x + (yy + y) * nx] * data[x + (yy - y) * nx]; 01012 } 01013 ret_data[x + y * nx] = dot; 01014 } 01015 } 01016 01017 ret->update(); 01018 01019 return ret; 01020 }
|