VtkIO reads/writes VTK image file. More...

#include <vtkio.h>

Inheritance diagram for EMAN::VtkIO:

Collaboration diagram for EMAN::VtkIO:

Public Member Functions
	VtkIO (const string &fname, IOMode rw_mode=READ_ONLY)

	~VtkIO ()

Public Member Functions inherited from EMAN::ImageIO
	ImageIO (const string &fname, IOMode rw)

virtual	~ImageIO ()

virtual int	read_header (Dict &dict, int image_index=0, const Region *area=0, bool is_3d=false)=0
	Read the header from an image. More...

virtual int	write_header (const Dict &dict, int image_index=0, const Region *area=0, EMUtil::EMDataType filestoragetype=EMUtil::EM_FLOAT, bool use_host_endian=true)=0
	Write a header to an image. More...

virtual int	read_data (float data, int image_index=0, const Region area=0, bool is_3d=false)=0
	Read the data from an image. More...

virtual int	read_data_8bit (unsigned char data, int image_index=0, const Region area=0, bool is_3d=false, float minval=0.0f, float maxval=0.0f)
	Read the data from an image as an 8 bit array, regardless of format. More...

virtual int	write_data (float data, int image_index=0, const Region area=0, EMUtil::EMDataType filestoragetype=EMUtil::EM_FLOAT, bool use_host_endian=true)=0
	Write data to an image. More...

virtual int	read_ctf (Ctf &ctf, int image_index=0)
	Read CTF data from this image. More...

virtual void	write_ctf (const Ctf &ctf, int image_index=0)
	Write CTF data to this image. More...

virtual void	flush ()=0
	Flush the IO buffer. More...

virtual int	get_nimg ()
	Return the number of images in this image file. More...

virtual bool	is_complex_mode ()=0
	Is this an complex image or not. More...

virtual bool	is_image_big_endian ()=0
	Is this image in big endian or not. More...

virtual bool	is_single_image_format () const
	Is this image format only storing 1 image or not. More...

template<class T >
void	become_host_endian (T *data, size_t n=1)
	Convert data of this image into host endian format. More...

string	get_filename () const

Static Public Member Functions
static bool	is_valid (const void *first_block)

Public Attributes
	DEFINE_IMAGEIO_FUNC

Private Types
enum	VtkType { VTK_UNKNOWN , VTK_ASCII , VTK_BINARY }

enum	DataType { DATATYPE_UNKNOWN , BIT , UNSIGNED_CHAR , CHAR , UNSIGNED_SHORT , SHORT , UNSIGNED_INT , INT , UNSIGNED_LONG , LONG , FLOAT , DOUBLE }

enum	DatasetType { DATASET_UNKNOWN , STRUCTURED_POINTS , STRUCTURED_GRID , RECTILINEAR_GRID , UNSTRUCTURED_GRID , POLYDATA }

Private Member Functions
int	to_em_datatype (int vtk_datatype)

int	get_mode_size (DataType d)

void	read_dataset (DatasetType dstype)

DataType	get_datatype_from_name (const string &datatype_name)

DatasetType	get_datasettype_from_name (const string &dataset_name)

Private Attributes
bool	is_big_endian

bool	is_new_file

DataType	datatype

VtkType	filetype

int	nx

int	ny

int	nz

float	originx

float	originy

float	originz

float	spacingx

float	spacingy

float	spacingz

off_t	file_offset

Static Private Attributes
static const char *	MAGIC = "# vtk DataFile Version"

Additional Inherited Members
Public Types inherited from EMAN::ImageIO
enum	IOMode { READ_ONLY = 1 , READ_WRITE = 2 , WRITE_ONLY = 3 }

Protected Member Functions inherited from EMAN::ImageIO
virtual void	init ()=0
	Do some initialization before doing the read/write. More...

void	check_read_access (int image_index)
	Validate 'image_index' in file reading. More...

void	check_read_access (int image_index, const float *data)
	Validate 'image_index' and 'data' in file reading. More...

void	check_write_access (IOMode rw_mode, int image_index, int max_nimg=0)
	Validate rw_mode and image_index in file writing. More...

void	check_write_access (IOMode rw_mode, int image_index, int max_nimg, const float *data)
	Validate rw_mode, image_index, and data pointer in file writing. More...

void	check_region (const Region *area, const FloatSize &max_size, bool is_new_file=false, bool inbounds_only=true)
	Validate image I/O region. More...

void	check_region (const Region *area, const IntSize &max_size, bool is_new_file=false, bool inbounds_only=true)
	Validate image I/O region. More...

FILE *	sfopen (const string &filename, IOMode mode, bool *is_new=0, bool overwrite=false)
	Run fopen safely. More...

Protected Attributes inherited from EMAN::ImageIO
string	filename

IOMode	rw_mode

FILE *	file = nullptr

bool	initialized = false

Detailed Description

VtkIO reads/writes VTK image file.

VTK is a file format used by the Visual Toolkit. (http://public.kitware.com/VTK/)

There are 2 VTK formats: ASCII or Binary.

ASCII format It has 5 parts:

1) file version and indentifier. It is one line with "# vtk DataFile Version x.x".
2) description header. one line. it is 256 char maximum.
3) file format. one word. either "ASCII" or "BINARY".
4) dataset structure. it describes the geometry and topology of the dataset. It must be one line containing the keyword "DATASET" followed by a keyword describing the type of dataset. This part is optional.
5) dataset attributes. It begins with POINT_DATA or CELL_DATA.

Binary format It has the same 5 parts like ASCII format,followed by data in binary format. The data are stored in big endian by default..

A VTK file contains 1 2D or 3D image.

Definition at line 72 of file vtkio.h.

Member Enumeration Documentation

◆ DatasetType

enum EMAN::VtkIO::DatasetType

private

Enumerator
DATASET_UNKNOWN
STRUCTURED_POINTS
STRUCTURED_GRID
RECTILINEAR_GRID
UNSTRUCTURED_GRID
POLYDATA

Definition at line 107 of file vtkio.h.

                {
                        DATASET_UNKNOWN,
                        STRUCTURED_POINTS,
                        STRUCTURED_GRID,
                        RECTILINEAR_GRID,
                        UNSTRUCTURED_GRID,
                        POLYDATA
                };

◆ DataType

enum EMAN::VtkIO::DataType

private

Enumerator
DATATYPE_UNKNOWN
BIT
UNSIGNED_CHAR
CHAR
UNSIGNED_SHORT
SHORT
UNSIGNED_INT
INT
UNSIGNED_LONG
LONG
FLOAT
DOUBLE

Definition at line 91 of file vtkio.h.

                {
                        DATATYPE_UNKNOWN,
                        BIT,
                        UNSIGNED_CHAR,
                        CHAR,                   
                        UNSIGNED_SHORT,
                        SHORT,
                        UNSIGNED_INT,
                        INT,
                        UNSIGNED_LONG,
                        LONG,
                        FLOAT,
                        DOUBLE
                };

◆ VtkType

enum EMAN::VtkIO::VtkType

private

Enumerator
VTK_UNKNOWN
VTK_ASCII
VTK_BINARY

Definition at line 84 of file vtkio.h.

                {
                        VTK_UNKNOWN,
                        VTK_ASCII,
                        VTK_BINARY                      
                };

Constructor & Destructor Documentation

◆ VtkIO()

VtkIO::VtkIO	(	const string &	fname,
		IOMode	rw_mode = `READ_ONLY`
	)

explicit

Definition at line 43 of file vtkio.cpp.

:       ImageIO(fname, rw)
{
        is_big_endian = ByteOrder::is_host_big_endian();
        is_new_file = false;
 
        datatype = DATATYPE_UNKNOWN;
        filetype = VTK_UNKNOWN;
        nx = 0;
        ny = 0;
        nz = 0;
        originx = 0;
        originy = 0;
        originz = 0;
        spacingx = 0;
        spacingy = 0;
        spacingz = 0;
        file_offset = 0;
}

References datatype, DATATYPE_UNKNOWN, file_offset, filetype, is_big_endian, EMAN::ByteOrder::is_host_big_endian(), is_new_file, nx, ny, nz, originx, originy, originz, spacingx, spacingy, spacingz, and VTK_UNKNOWN.

◆ ~VtkIO()

VtkIO::~VtkIO ( )

Definition at line 63 of file vtkio.cpp.

{
        if (file) {
                fclose(file);
                file = 0;
        }
}

References EMAN::ImageIO::file.

Member Function Documentation

◆ get_datasettype_from_name()

VtkIO::DatasetType VtkIO::get_datasettype_from_name ( const string & dataset_name )

private

Definition at line 427 of file vtkio.cpp.

{
 
        static bool initialized = false;
        static map < string, DatasetType > types;
 
        if (!initialized) {
                types["STRUCTURED_POINTS"] = STRUCTURED_POINTS;
                types["STRUCTURED_GRID"] = STRUCTURED_GRID;
                types["RECTILINEAR_GRID"] = RECTILINEAR_GRID;
                types["UNSTRUCTURED_GRID"] = UNSTRUCTURED_GRID;
                types["POLYDATA"] = POLYDATA;
        }
 
        DatasetType result = DATASET_UNKNOWN;
        if (types.find(dataset_name) != types.end()) {
                result = types[dataset_name];
        }
        return result;
}

References DATASET_UNKNOWN, EMAN::ImageIO::initialized, POLYDATA, RECTILINEAR_GRID, STRUCTURED_GRID, STRUCTURED_POINTS, and UNSTRUCTURED_GRID.

◆ get_datatype_from_name()

VtkIO::DataType VtkIO::get_datatype_from_name ( const string & datatype_name )

private

Definition at line 394 of file vtkio.cpp.

{
        static bool initialized = false;
        static map < string, VtkIO::DataType > datatypes;
 
        if (!initialized) {
                datatypes["bit"] = BIT;
 
                datatypes["unsigned_char"] = UNSIGNED_CHAR;
                datatypes["char"] = CHAR;
 
                datatypes["unsigned_short"] = UNSIGNED_SHORT;
                datatypes["short"] = SHORT;
 
                datatypes["unsigned_int"] = UNSIGNED_INT;
                datatypes["int"] = INT;
 
                datatypes["unsigned_long"] = UNSIGNED_LONG;
                datatypes["long"] = LONG;
 
                datatypes["float"] = FLOAT;
                datatypes["double"] = DOUBLE;
                initialized = true;
        }
 
        DataType result = DATATYPE_UNKNOWN;
 
        if (datatypes.find(datatype_name) != datatypes.end()) {
                result = datatypes[datatype_name];
        }
        return result;
}

References BIT, CHAR, DATATYPE_UNKNOWN, DOUBLE, FLOAT, EMAN::ImageIO::initialized, INT, LONG, SHORT, UNSIGNED_CHAR, UNSIGNED_INT, UNSIGNED_LONG, and UNSIGNED_SHORT.

◆ get_mode_size()

int VtkIO::get_mode_size ( DataType d )

private

Definition at line 368 of file vtkio.cpp.

{
        switch (d) {
        case UNSIGNED_CHAR:
        case CHAR:
                return sizeof(char);
        case UNSIGNED_SHORT:
        case SHORT:
                return sizeof(short);
        case UNSIGNED_INT:
        case INT:
                return sizeof(int);
        case UNSIGNED_LONG:
        case LONG:
                return sizeof(long);
        case FLOAT:
                return sizeof(float);
        case DOUBLE:
                return sizeof(double);
        default:
                LOGERR("don't support this data type '%d'", d);
                break;
        }
        return 0;
}

References CHAR, DOUBLE, FLOAT, INT, LOGERR, LONG, SHORT, UNSIGNED_CHAR, UNSIGNED_INT, UNSIGNED_LONG, and UNSIGNED_SHORT.

◆ is_valid()

bool VtkIO::is_valid ( const void * first_block )

static

Definition at line 160 of file vtkio.cpp.

{
        ENTERFUNC;
        bool result = false;
        if (first_block) {
                result = Util::check_file_by_magic(first_block, MAGIC);
        }
        EXITFUNC;
        return result;
}

References EMAN::Util::check_file_by_magic(), ENTERFUNC, EXITFUNC, and MAGIC.

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

◆ read_dataset()

void VtkIO::read_dataset ( DatasetType dstype )

private

Definition at line 448 of file vtkio.cpp.

{
        char buf[1024];
        int bufsz = sizeof(buf);
 
        if (dstype == STRUCTURED_POINTS) {
                int nlines = 3;
                int i = 0;
                while (i < nlines && fgets(buf, bufsz, file)) {
                        if (samestr(buf, "DIMENSIONS")) {
                                sscanf(buf, "DIMENSIONS %d %d %d", &nx, &ny, &nz);
                        }
                        else if (samestr(buf, "ORIGIN")) {
                                sscanf(buf, "ORIGIN %f %f %f", &originx, &originy, &originz);
                        }
                        else if (samestr(buf, "SPACING") || samestr(buf, "ASPECT_RATIO")) {
                                if (samestr(buf, "SPACING")) {
                                        sscanf(buf, "SPACING %f %f %f", &spacingx, &spacingy, &spacingz);
                                }
                                else {
                                        sscanf(buf, "ASPECT_RATIO %f %f %f", &spacingx, &spacingy, &spacingz);
                                }
 
                                if (spacingx != spacingy || spacingx != spacingz || spacingy != spacingz) {
                                        throw ImageReadException(filename,
                                                                                         "not support non-uniform spacing VTK so far\n");
                                }
                        }
                        i++;
                }
 
                if (i != nlines) {
                        throw ImageReadException(filename, "read VTK file failed");
                }
        }
        else {
                throw ImageReadException(filename, "only STRUCTURED_POINTS is supported so far");
        }
}

References EMAN::ImageIO::file, EMAN::ImageIO::filename, ImageReadException, nx, ny, nz, originx, originy, originz, samestr(), spacingx, spacingy, spacingz, and STRUCTURED_POINTS.

◆ to_em_datatype()

int VtkIO::to_em_datatype ( int vtk_datatype )

private

Definition at line 353 of file vtkio.cpp.

{
        DataType d = static_cast < DataType > (vtk_datatype);
        switch (d) {
        case UNSIGNED_SHORT:
                return EMUtil::EM_USHORT;
        case FLOAT:
                return EMUtil::EM_FLOAT;
        default:
                break;
        }
        return EMUtil::EM_UNKNOWN;
}

References EMAN::EMUtil::EM_FLOAT, EMAN::EMUtil::EM_UNKNOWN, EMAN::EMUtil::EM_USHORT, FLOAT, and UNSIGNED_SHORT.

Member Data Documentation

◆ datatype

DataType EMAN::VtkIO::datatype

private

Definition at line 127 of file vtkio.h.

Referenced by VtkIO().

◆ DEFINE_IMAGEIO_FUNC

EMAN::VtkIO::DEFINE_IMAGEIO_FUNC

Definition at line 78 of file vtkio.h.

◆ file_offset

off_t EMAN::VtkIO::file_offset

private

Definition at line 138 of file vtkio.h.

Referenced by VtkIO().

◆ filetype

VtkType EMAN::VtkIO::filetype

private

Definition at line 128 of file vtkio.h.

Referenced by VtkIO().

◆ is_big_endian

bool EMAN::VtkIO::is_big_endian

private

Definition at line 124 of file vtkio.h.

Referenced by VtkIO().

◆ is_new_file

bool EMAN::VtkIO::is_new_file

private

Definition at line 125 of file vtkio.h.

Referenced by VtkIO().

◆ MAGIC

const char * VtkIO::MAGIC = "# vtk DataFile Version"

staticprivate

Definition at line 82 of file vtkio.h.

Referenced by is_valid().

◆ nx

int EMAN::VtkIO::nx

private

Definition at line 129 of file vtkio.h.

Referenced by read_dataset(), and VtkIO().

◆ ny

int EMAN::VtkIO::ny

private

Definition at line 130 of file vtkio.h.

Referenced by read_dataset(), and VtkIO().

◆ nz

int EMAN::VtkIO::nz

private

Definition at line 131 of file vtkio.h.

Referenced by read_dataset(), and VtkIO().

◆ originx

float EMAN::VtkIO::originx

private

Definition at line 132 of file vtkio.h.

Referenced by read_dataset(), and VtkIO().

◆ originy

float EMAN::VtkIO::originy

private

Definition at line 133 of file vtkio.h.

Referenced by read_dataset(), and VtkIO().

◆ originz

float EMAN::VtkIO::originz

private

Definition at line 134 of file vtkio.h.

Referenced by read_dataset(), and VtkIO().

◆ spacingx

float EMAN::VtkIO::spacingx

private

Definition at line 135 of file vtkio.h.

Referenced by read_dataset(), and VtkIO().

◆ spacingy

float EMAN::VtkIO::spacingy

private

Definition at line 136 of file vtkio.h.

Referenced by read_dataset(), and VtkIO().

◆ spacingz

float EMAN::VtkIO::spacingz

private

Definition at line 137 of file vtkio.h.

Referenced by read_dataset(), and VtkIO().

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

Public Member Functions

Static Public Member Functions

Public Attributes

Private Types

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ DatasetType

◆ DataType

◆ VtkType

Constructor & Destructor Documentation

◆ VtkIO()

◆ ~VtkIO()

Member Function Documentation

◆ get_datasettype_from_name()

◆ get_datatype_from_name()

◆ get_mode_size()

◆ is_valid()

◆ read_dataset()

◆ to_em_datatype()

Member Data Documentation

◆ datatype

◆ DEFINE_IMAGEIO_FUNC

◆ file_offset

◆ filetype

◆ is_big_endian

◆ is_new_file

◆ MAGIC

◆ nx

◆ ny

◆ nz

◆ originx

◆ originy

◆ originz

◆ spacingx

◆ spacingy

◆ spacingz