#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 }
|
|
||||||||||||||||
|
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 }
|
|
||||||||||||||||||||||||||||||||
|
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 }
|
|
||||||||||||||||||||||||||||
|
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 }
|
|
||||||||||||||||||||||||||||
|
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 }
|
|
||||||||||||
|
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 }
|
|
|
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 }
|
|
||||||||||||||||
|
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 }
|
|
|
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 }
|
|
||||||||||||||||||||||||||||||||||||||||||||||||||||
|
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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|
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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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|
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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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|
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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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1.3.9.1