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00036 #ifndef eman__emutil__h__
00037 #define eman__emutil__h__ 1
00038
00039 #include "emobject.h"
00040 #include "emassert.h"
00041 #include <string.h>
00042
00043 using std::string;
00044 using std::vector;
00045
00046
00047
00048
00049
00050 template <class T>
00051 inline void EMDeletePtr(T & x)
00052 {
00053 #ifdef _WIN32
00054 if(x != NULL) {
00055 delete x;
00056 x = NULL;
00057 }
00058 #else
00059 {Assert(x != NULL);}
00060 delete x;
00061 x = NULL;
00062 #endif
00063 }
00064
00065 template <class T>
00066 inline void EMDeleteArray(T & x)
00067 {
00068 #ifdef _WIN32
00069 if(x != NULL) {
00070 delete x;
00071 x = NULL;
00072 }
00073 #else
00074 {Assert(x != NULL);}
00075 delete [] x;
00076 x = NULL;
00077 #endif
00078 }
00079
00080 namespace EMAN
00081 {
00082 class Region;
00083 class ImageIO;
00084
00085 class EMUtil
00086 {
00087 public:
00092 enum EMDataType
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 };
00107
00110 enum ImageType
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 IMAGE_OMAP,
00138 IMAGE_SITUS,
00139 IMAGE_SER
00140 };
00141
00142 static EMData *vertical_acf(const EMData * image, int maxdy);
00143
00144 static EMData *make_image_median(const vector < EMData * >&image_list);
00145
00150 static ImageType get_image_ext_type(const string & file_ext);
00151
00156 static ImageType get_image_type(const string & filename);
00157
00164 static bool is_valid_filename(const string & filename);
00165
00170 static int get_image_count(const string & filename);
00171
00179 static ImageIO *get_imageio(const string & filename, int rw_mode,
00180 ImageType image_type = IMAGE_UNKNOWN);
00181
00186 static const char *get_imagetype_name(EMUtil::ImageType type);
00187
00192 static const char *get_datatype_string(EMDataType type);
00193
00203 static void get_region_dims(const Region * area, int nx, int *area_x, int ny,
00204 int *area_y, int nz = 1, int *area_z = 0);
00205
00214 static void get_region_origins(const Region * area, int *p_x0, int *p_y0,
00215 int *p_z0 = 0, int nz = 1, int image_index = 0);
00216
00236 static void process_region_io(void *cdata, FILE * file, int rw_mode,
00237 int image_index, size_t mode_size, int nx,
00238 int ny, int nz = 1, const Region * area = 0,
00239 bool need_flip = false, ImageType imgtype=IMAGE_UNKNOWN,
00240 int pre_row = 0, int post_row = 0);
00241
00242
00248 static void process_ascii_region_io(float *data, FILE * file, int rw_mode,
00249 int image_index, size_t mode_size,
00250 int nx, int ny, int nz,
00251 const Region * area, bool has_index_line,
00252 int nitems_per_line, const char *outformat);
00253
00254
00258 static void dump_dict(const Dict & dict);
00259
00265 static bool is_same_size(const EMData * image1, const EMData * image2);
00266
00272 static bool is_same_ctf(const EMData * image1, const EMData * image2);
00273
00274
00275 static bool is_complex_type(EMDataType datatype);
00276
00277 static void jump_lines(FILE * file, int nlines);
00278
00279 static vector<string> get_euler_names(const string & euler_type);
00280
00288 static vector<EMObject> get_all_attributes(const string & file_name, const string & attr_name);
00289
00303 static void getRenderMinMax(float * data, const int nx, const int ny, float& rendermin, float& rendermax, const int nz = 1);
00304
00305 #ifdef EM_HDF5
00306
00313 static EMObject read_hdf_attribute(const string & filename, const string & key, int image_index=0);
00314
00323 static int write_hdf_attribute(const string & filename, const string & key, EMObject value, int image_index=0);
00324
00332 static int delete_hdf_attribute(const string & filename, const string & key, int image_index=0);
00333 #endif //EM_HDF5
00334
00335 static bool cuda_available() {
00336
00337
00338
00339 return false;
00340
00341 }
00342
00343 inline static void* em_malloc(const size_t size) {
00344 return malloc(size);
00345 }
00346
00347 inline static void* em_calloc(const size_t nmemb,const size_t size) {
00348 return calloc(nmemb,size);
00349 }
00350
00351 inline static void* em_realloc(void* data,const size_t new_size) {
00352 return realloc(data, new_size);
00353 }
00354 inline static void em_memset(void* data, const int value, const size_t size) {
00355 memset(data, value, size);
00356 }
00357 inline static void em_free(void*data) {
00358 free(data);
00359 }
00360
00361 inline static void em_memcpy(void* dst,const void* const src,const size_t size) {
00362 memcpy(dst,src,size);
00363 }
00364 private:
00365 static ImageType fast_get_image_type(const string & filename,
00366 const void *first_block,
00367 off_t file_size);
00368
00369 static void jump_lines_by_items(FILE * file, int nitems, int nitems_per_line);
00370
00371
00372
00373 static void process_numbers_io(FILE * file, int rw_mode,
00374 int nitems_per_line,
00375 size_t mode_size, int start, int end,
00376 float *data, int *p_i,
00377 const char *outformat);
00378
00379 static void exclude_numbers_io(FILE * file, int rw_mode,
00380 int nitems_per_line,
00381 size_t mode_size, int start, int end,
00382 float * data, int *p_i,
00383 const char *outformat);
00384
00385 static void process_lines_io(FILE * file, int rw_mode,
00386 int nitems_per_line, size_t mode_size,
00387 int nitems, float *data, int *p_i,
00388 const char *outformat);
00389
00390
00391 };
00392
00393 struct ImageScore {
00394 int index;
00395 float score;
00396 ImageScore(int i=0, float s=0) : index(i), score(s) {}
00397 };
00398
00399 class ImageSort {
00400 public:
00401 ImageSort(int n);
00402 ~ImageSort();
00403
00404 void sort();
00405
00406 void set(int i, float score);
00407 int get_index(int i) const;
00408 float get_score(int i) const;
00409
00410 int size() const;
00411 private:
00412 ImageScore* image_scores;
00413 int n;
00414
00415 };
00416 }
00417
00418 #endif //eman__emutil__h__