EMAN::EmIO Class Reference

EmIO defines I/O operations on EM image format. More...

#include <emio.h>

Inheritance diagram for EMAN::EmIO:

Collaboration diagram for EMAN::EmIO:

List of all members.

Public Member Functions

EmIO (const string &filename, IOMode rw_mode=READ_ONLY)

~EmIO ()

Static Public Member Functions

static bool is_valid (const void *first_block, off_t file_size=0)

static size_t get_mode_size (char data_type)

static int get_machine_type ()

static int to_em_datatype (char t)

Public Attributes

DEFINE_IMAGEIO_FUNC

Private Types

enum DataType {
  EM_EM_CHAR = 1, EM_EM_SHORT = 2, EM_EM_INT = 4, EM_EM_FLOAT = 5,
  EM_EM_COMPLEX = 8, EM_EM_DOUBLE = 9, EM_EM_UNKNOWN
}

enum MachineType {
  EM_OS8 = 0, EM_VAX = 1, EM_CONVEX = 2, EM_SGI = 3,
  EM_MAC = 5, EM_PC = 6, EM_UNKNOWN_MACHINE
}

Private Attributes

string filename

IOMode rw_mode

FILE * em_file

EMHeader emh

size_t mode_size

DataType mode

bool is_big_endian

bool initialized

bool is_new_file

Classes

struct EMHeader

Detailed Description

EmIO defines I/O operations on EM image format.

EM image = header + data with (data = nx * ny * nz).

An EM image file stores 1 single 2D or 3D image.

Definition at line 48 of file emio.h.

Member Enumeration Documentation

enum EMAN::EmIO::DataType [private]

Enumerator:

EM_EM_CHAR
EM_EM_SHORT
EM_EM_INT
EM_EM_FLOAT
EM_EM_COMPLEX
EM_EM_DOUBLE
EM_EM_UNKNOWN

Definition at line 77 of file emio.h.

00078                 {
00079                         EM_EM_CHAR = 1,
00080                         EM_EM_SHORT = 2,
00081                         EM_EM_INT = 4,
00082                         EM_EM_FLOAT = 5,
00083                         EM_EM_COMPLEX = 8,
00084                         EM_EM_DOUBLE = 9,
00085                         EM_EM_UNKNOWN
00086                 };

enum EMAN::EmIO::MachineType [private]

Enumerator:

EM_OS8
EM_VAX
EM_CONVEX
EM_SGI
EM_MAC
EM_PC
EM_UNKNOWN_MACHINE

Definition at line 88 of file emio.h.

00089                 {
00090                         EM_OS8 = 0,
00091                         EM_VAX = 1,
00092                         EM_CONVEX = 2,
00093                         EM_SGI = 3,
00094                         EM_MAC = 5,
00095                         EM_PC = 6,
00096                         EM_UNKNOWN_MACHINE
00097                 };

Constructor & Destructor Documentation

EmIO::EmIO	(	const string &	filename,
		IOMode	rw_mode = `READ_ONLY`
	)			`[explicit]`

Definition at line 43 of file emio.cpp.

References EM_EM_UNKNOWN, emh, is_big_endian, EMAN::ByteOrder::is_host_big_endian(), is_new_file, mode, and mode_size.

00044 :       filename(file), rw_mode(rw), em_file(0), initialized(false)
00045 {
00046         mode_size = 0;
00047         mode = EM_EM_UNKNOWN;
00048         is_big_endian = ByteOrder::is_host_big_endian();
00049         is_new_file = false;
00050         memset(&emh, 0, sizeof(EMHeader));
00051 }

EmIO::~EmIO ( )

Definition at line 53 of file emio.cpp.

References em_file.

00054 {
00055         if (em_file) {
00056                 fclose(em_file);
00057                 em_file = 0;
00058         }
00059 }

Member Function Documentation

bool EmIO::is_valid	(	const void *	first_block,
		off_t	file_size = `0`
	)			`[static]`

Definition at line 100 of file emio.cpp.

References data, EM_EM_CHAR, EM_EM_DOUBLE, EM_OS8, EM_PC, ENTERFUNC, get_mode_size(), EMAN::ByteOrder::is_data_big_endian(), EMAN::ByteOrder::is_host_big_endian(), nx, ny, and EMAN::ByteOrder::swap_bytes().

Referenced by EMAN::EMUtil::fast_get_image_type(), and EMAN::EMUtil::get_image_type().

00101 {
00102         ENTERFUNC;
00103 
00104         if (!first_block) {
00105                 return false;
00106         }
00107 
00108         const char *data = static_cast < const char *>(first_block);
00109         char machine = data[0];
00110         char is_new_ver = data[1];
00111         char data_type = data[3];
00112 
00113         const int *data1 = static_cast < const int *>(first_block);
00114         int nx = data1[1];
00115         int ny = data1[2];
00116         int nz = data1[3];
00117 
00118         bool data_big_endian = ByteOrder::is_data_big_endian(&nz);
00119         if (data_big_endian != ByteOrder::is_host_big_endian()) {
00120                 ByteOrder::swap_bytes(&nx);
00121                 ByteOrder::swap_bytes(&ny);
00122                 ByteOrder::swap_bytes(&nz);
00123         }
00124 
00125         const int max_dim = 1 << 20;
00126 
00127         if (((int) machine >= EM_OS8 && machine <= EM_PC) &&
00128                 (is_new_ver == 0 || is_new_ver == 1) &&
00129                 (data_type >= EM_EM_CHAR && data_type <= EM_EM_DOUBLE) &&
00130                 (nx > 1 && nx < max_dim) && (ny > 0 && ny < max_dim) && (nz > 0 && nz < max_dim)) {
00131                 if (file_size > 0) {
00132                         off_t file_size1 = (off_t)nx * (off_t)ny * (off_t)nz * (off_t)get_mode_size(data_type) + (off_t)sizeof(EMHeader);
00133                         if (file_size == file_size1) {
00134                                 return true;
00135                         }
00136                 }
00137                 else {
00138                         return true;
00139                 }
00140         }
00141 
00142         return false;
00143 }

size_t EmIO::get_mode_size ( char data_type ) [static]

Definition at line 344 of file emio.cpp.

References EM_EM_CHAR, EM_EM_COMPLEX, EM_EM_DOUBLE, EM_EM_FLOAT, EM_EM_INT, EM_EM_SHORT, and mode.

Referenced by is_valid().

00345 {
00346         int mode = (int) data_type;
00347         switch (mode) {
00348         case EM_EM_CHAR:
00349                 return sizeof(char);
00350         case EM_EM_SHORT:
00351                 return sizeof(short);
00352         case EM_EM_INT:
00353         case EM_EM_FLOAT:
00354         case EM_EM_COMPLEX:
00355                 return sizeof(int);
00356         case EM_EM_DOUBLE:
00357                 return sizeof(double);
00358         }
00359         return 0;
00360 }

int EmIO::get_machine_type ( ) [static]

Definition at line 319 of file emio.cpp.

References EM_MAC, EM_PC, EM_SGI, and EM_UNKNOWN_MACHINE.

00320 {
00321         int m = EM_UNKNOWN_MACHINE;
00322 #ifdef __sgi
00323         m = EM_SGI;
00324 #elif defined __linux__
00325         m = EM_PC;
00326 #elif defined __CYGWIN__
00327         m = EM_PC;
00328 #elif defined WIN32
00329         m = EM_PC;
00330 #elif defined MACOS
00331         m = EM_MAC;
00332 #elif defined macintosh
00333         m = EM_MAC;
00334 #elif defined __darwin__
00335         m = EM_MAC;
00336 #elif defined __APPLE__
00337         m = EM_MAC;
00338 #else
00339         m = EM_UNKNOWN_MACHINE;
00340 #endif
00341         return m;
00342 }

int EmIO::to_em_datatype ( char t ) [static]

Definition at line 297 of file emio.cpp.

References EMAN::EMUtil::EM_CHAR, EMAN::EMUtil::EM_DOUBLE, EM_EM_CHAR, EM_EM_COMPLEX, EM_EM_DOUBLE, EM_EM_FLOAT, EM_EM_INT, EM_EM_SHORT, EMAN::EMUtil::EM_FLOAT, EMAN::EMUtil::EM_FLOAT_COMPLEX, EMAN::EMUtil::EM_INT, EMAN::EMUtil::EM_SHORT, and EMAN::EMUtil::EM_UNKNOWN.

00298 {
00299         DataType type = static_cast < DataType > (t);
00300         switch (type) {
00301         case EM_EM_CHAR:
00302                 return EMUtil::EM_CHAR;
00303         case EM_EM_SHORT:
00304                 return EMUtil::EM_SHORT;
00305         case EM_EM_INT:
00306                 return EMUtil::EM_INT;
00307         case EM_EM_FLOAT:
00308                 return EMUtil::EM_FLOAT;
00309         case EM_EM_DOUBLE:
00310                 return EMUtil::EM_DOUBLE;
00311         case EM_EM_COMPLEX:
00312                 return EMUtil::EM_FLOAT_COMPLEX;
00313         default:
00314                 break;
00315         }
00316         return EMUtil::EM_UNKNOWN;
00317 }

Member Data Documentation

EMAN::EmIO::DEFINE_IMAGEIO_FUNC

Definition at line 54 of file emio.h.

string EMAN::EmIO::filename [private]

Definition at line 100 of file emio.h.

IOMode EMAN::EmIO::rw_mode [private]

Definition at line 101 of file emio.h.

FILE* EMAN::EmIO::em_file [private]

Definition at line 102 of file emio.h.

Referenced by ~EmIO().

EMHeader EMAN::EmIO::emh [private]

Definition at line 103 of file emio.h.

Referenced by EmIO().

size_t EMAN::EmIO::mode_size [private]

Definition at line 105 of file emio.h.

Referenced by EmIO().

DataType EMAN::EmIO::mode [private]

Definition at line 106 of file emio.h.

Referenced by EmIO(), and get_mode_size().

bool EMAN::EmIO::is_big_endian [private]

Definition at line 107 of file emio.h.

Referenced by EmIO().

bool EMAN::EmIO::initialized [private]

Definition at line 108 of file emio.h.

bool EMAN::EmIO::is_new_file [private]

Definition at line 109 of file emio.h.

Referenced by EmIO().

The documentation for this class was generated from the following files:


Public Member Functions
	EmIO (const string &filename, IOMode rw_mode=READ_ONLY)
	~EmIO ()
Static Public Member Functions
static bool	is_valid (const void *first_block, off_t file_size=0)
static size_t	get_mode_size (char data_type)
static int	get_machine_type ()
static int	to_em_datatype (char t)
Public Attributes
	DEFINE_IMAGEIO_FUNC
Private Types
enum	DataType { EM_EM_CHAR = 1, EM_EM_SHORT = 2, EM_EM_INT = 4, EM_EM_FLOAT = 5, EM_EM_COMPLEX = 8, EM_EM_DOUBLE = 9, EM_EM_UNKNOWN }
enum	MachineType { EM_OS8 = 0, EM_VAX = 1, EM_CONVEX = 2, EM_SGI = 3, EM_MAC = 5, EM_PC = 6, EM_UNKNOWN_MACHINE }
Private Attributes
string	filename
IOMode	rw_mode
FILE *	em_file
EMHeader	emh
size_t	mode_size
DataType	mode
bool	is_big_endian
bool	initialized
bool	is_new_file
Classes
struct	EMHeader