emdata_io.h File Reference

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Functions
void	_read_image (ImageIO *imageio, int img_index=0, bool header_only=false, const Region *region=0, bool is_3d=false)
	This file is a part of "emdata.h", to use functions in this file, you should "#include "emdata.h", NEVER directly include this file. More...
void	_write_image (ImageIO *imageio, int img_index=0, EMUtil::ImageType imgtype=EMUtil::IMAGE_UNKNOWN, bool header_only=false, const Region *region=0, EMUtil::EMDataType filestoragetype=EMUtil::EM_FLOAT, bool use_host_endian=true)
void	read_image (const string &filename, int img_index=0, bool header_only=false, const Region *region=0, bool is_3d=false, EMUtil::ImageType imgtype=EMUtil::IMAGE_UNKNOWN)
	read an image file and stores its information to this EMData object. More...
void	read_binedimage (const string &filename, int img_index=0, int binfactor=0, bool fast=false, bool is_3d=false)
	read in a binned image, bin while reading. More...
void	write_image (const string &filename, int img_index=0, EMUtil::ImageType imgtype=EMUtil::IMAGE_UNKNOWN, bool header_only=false, const Region *region=0, EMUtil::EMDataType filestoragetype=EMUtil::EM_FLOAT, bool use_host_endian=true)
	write the header and data out to an image. More...
void	append_image (const string &filename, EMUtil::ImageType imgtype=EMUtil::IMAGE_UNKNOWN, bool header_only=false)
	append to an image file; If the file doesn't exist, create one. More...
void	write_lst (const string &filename, const string &reffile="", int refn=-1, const string &comment="")
	Append data to a LST image file. More...
static vector< std::shared_ptr< EMData > >	read_images (const string &filename, vector< int > img_indices=vector< int >(), EMUtil::ImageType imgtype=EMUtil::IMAGE_UNKNOWN, bool header_only=false)
	Read a set of images from file specified by 'filename'. More...
static bool	write_images (const string &filename, vector< std::shared_ptr< EMData > > imgs, EMUtil::ImageType imgtype=EMUtil::IMAGE_UNKNOWN, bool header_only=false, const Region *region=nullptr, EMUtil::EMDataType filestoragetype=EMUtil::EM_FLOAT, bool use_host_endian=true)
	Write a set of images to file specified by 'filename'. More...
ostream &	operator<< (ostream &out, const EMData &obj)

Function Documentation

_read_image()

void _read_image ( ImageIO *  imageio, int  img_index = 0, bool  header_only = false, const Region *  region = 0, bool  is_3d = false  )

private

This file is a part of "emdata.h", to use functions in this file, you should "#include "emdata.h", NEVER directly include this file.

_write_image()

void _write_image ( ImageIO *  imageio, int  img_index = 0, EMUtil::ImageType  imgtype = EMUtil::IMAGE_UNKNOWN, bool  header_only = false, const Region *  region = 0, EMUtil::EMDataType  filestoragetype = EMUtil::EM_FLOAT, bool  use_host_endian = true  )

private

append_image()

void append_image	(	const string &	filename,
		EMUtil::ImageType	imgtype = EMUtil::IMAGE_UNKNOWN,
		bool	header_only = false
	)

append to an image file; If the file doesn't exist, create one.

Parameters

filename	The image file name.
imgtype	Write to the given image format type. if not specified, use the 'filename' extension to decide.
header_only	To write only the header or both header and data.

operator<<()

friend ostream & operator<<	(	ostream &	out,
		const EMData &	obj
	)

read_binedimage()

void EMData::read_binedimage	(	const string &	filename,
		int	img_index = 0,
		int	binfactor = 0,
		bool	fast = false,
		bool	is_3d = false
	)

read in a binned image, bin while reading.

For use in huge files(tomograms)

Parameters

filename	The image file name.
img_index	The nth image you want to read.
binfactor	The amout you want to bin by. Must be an integer
fast	Only bin xy slice every binfactor intervals, otherwise meanshrink z
is_3d	Whether to treat the image as a single 3D or a set of 2Ds. This is a hint for certain image formats which has no difference between 3D image and set of 2Ds.

Exceptions

ImageFormatException
ImageReadException

Definition at line 124 of file emdata_io.cpp.

{
        ENTERFUNC;
 
        ImageIO *imageio = EMUtil::get_imageio(filename, ImageIO::READ_ONLY);
 
        if (!imageio) {
                throw ImageFormatException("cannot create an image io");
        }
        else {
                int err = imageio->read_header(attr_dict, img_index, 0, is_3d);
                if (err) {
                        throw ImageReadException(filename, "imageio read header failed");
                }
                else {
                        attr_dict["source_path"] = filename;
                        attr_dict["source_n"] = img_index;
                        if (imageio->is_complex_mode()) {
                                set_complex(true);
                                set_fftpad(true);
                        }
                        if (attr_dict.has_key("is_fftodd") && (int)attr_dict["is_fftodd"] == 1) {
                                set_fftodd(true);
                        }
                        if ((int) attr_dict["is_complex_ri"] == 1) {
                                set_ri(true);
                        }
                        save_byteorder_to_dict(imageio);
 
                        int ori_nx = nx = attr_dict["nx"];
                        int ori_ny = ny = attr_dict["ny"];
                        int ori_nz = nz = attr_dict["nz"];
                        if (!fast) ori_nz-=ori_nz%binfactor;    // makes sure Z is a multiple of binfactor, hack to fix the poor logic in the original routine
                        attr_dict.erase("nx");
                        attr_dict.erase("ny");
                        attr_dict.erase("nz");
 
                        // At this point nx, ny and nz are all reduced by binfactor
                        set_size(nx/binfactor, ny/binfactor, nz/binfactor);
 
                        //here is where we read in the binned data
                        EMData* tempdata = new EMData();
                        size_t sizeofslice = nx*ny*sizeof(float);
 
                        //zbin factor use 1 to speed binning(but don't benfit by averaging in Z)
                        int zbin = binfactor;
                        if(fast) zbin = 1;
                        //verbose
                        float percent = 0.1f;
                        for(int k = 0; k < ori_nz; k+=binfactor){
                                if(k > ori_nz*percent){
                                        printf("%1.0f %% Done\n",100.0*float(k)/float(ori_nz));
                                        percent+=0.1f;
                                }
                                // read in a slice region
//                              printf("%d %d %d %d\n",k,ori_nx,ori_ny,zbin);
                                const Region* binregion = new Region(0,0,k,ori_nx,ori_ny,zbin);
                                tempdata->read_image(filename, 0, false, binregion);
                                // shrink the slice
                                if (binfactor > 1) tempdata->process_inplace("math.meanshrink",Dict("n",binfactor));
                                size_t offset = nx*ny*k/binfactor;
                                //add slice to total
                                EMUtil::em_memcpy(get_data()+offset,tempdata->get_data(),sizeofslice);
                                delete binregion;
                        }
 
                        delete tempdata;
                        update();
                }
        }
 
    EMUtil::close_imageio(filename, imageio);
        imageio = 0;
        EXITFUNC;
}

References EMAN::EMData::attr_dict, EMAN::EMUtil::close_imageio(), EMAN::EMUtil::em_memcpy(), EMAN::EMData::EMData(), ENTERFUNC, EMAN::Dict::erase(), EXITFUNC, get_data(), EMAN::EMUtil::get_imageio(), EMAN::Dict::has_key(), ImageFormatException, ImageReadException, EMAN::ImageIO::is_complex_mode(), EMAN::EMData::nx, EMAN::EMData::ny, EMAN::EMData::nz, EMAN::ImageIO::read_header(), EMAN::ImageIO::READ_ONLY, EMAN::EMData::save_byteorder_to_dict(), set_complex(), set_fftodd(), set_fftpad(), set_ri(), set_size(), and update().

read_image()

void read_image	(	const string &	filename,
		int	img_index = 0,
		bool	header_only = false,
		const Region *	region = 0,
		bool	is_3d = false,
		EMUtil::ImageType	imgtype = EMUtil::IMAGE_UNKNOWN
	)

read an image file and stores its information to this EMData object.

If a region is given, then only read a region of the image file. The region will be this EMData object. The given region must be inside the given image file. Otherwise, an error will be created.

Parameters

filename	The image file name.
img_index	The nth image you want to read.
header_only	To read only the header or both header and data.
region	To read only a region of the image.
is_3d	Whether to treat the image as a single 3D or a set of 2Ds. This is a hint for certain image formats which has no difference between 3D image and set of 2Ds.

Exceptions

ImageFormatException
ImageReadException

read_images()

static vector< std::shared_ptr< EMData > > read_images ( const string &  filename, vector< int >  img_indices = vector< int >(), EMUtil::ImageType  imgtype = EMUtil::IMAGE_UNKNOWN, bool  header_only = false  )

static

Read a set of images from file specified by 'filename'.

Which images are read is set by 'img_indices'.

Parameters

filename	The image file name.
img_indices	Which images are read. If it is empty, all images are read. If it is not empty, only those in this array are read.
header_only	If true, only read image header. If false, read both data and header.

Returns

The set of images read from filename.

Referenced by EMAN::EMUtil::get_all_attributes().

write_image()

void write_image	(	const string &	filename,
		int	img_index = 0,
		EMUtil::ImageType	imgtype = EMUtil::IMAGE_UNKNOWN,
		bool	header_only = false,
		const Region *	region = 0,
		EMUtil::EMDataType	filestoragetype = EMUtil::EM_FLOAT,
		bool	use_host_endian = true
	)

write the header and data out to an image.

If the img_index = -1, append the image to the given image file.

If the given image file already exists, this image format only stores 1 image, and no region is given, then truncate the image file to zero length before writing data out. For header writing only, no truncation happens.

If a region is given, then write a region only.

Parameters

filename	The image file name.
img_index	The nth image to write as.
imgtype	Write to the given image format type. if not specified, use the 'filename' extension to decide.
header_only	To write only the header or both header and data.
region	Define the region to write to.
filestoragetype	The image data type used in the output file.
use_host_endian	To write in the host computer byte order.

Exceptions

ImageFormatException
ImageWriteException

Referenced by bispecRotTransInvDirect(), bispecRotTransInvN(), EMAN::RotateInFSProcessor::process_inplace(), and write_lst().

write_images()

static bool write_images ( const string &  filename, vector< std::shared_ptr< EMData > >  imgs, EMUtil::ImageType  imgtype = EMUtil::IMAGE_UNKNOWN, bool  header_only = false, const Region *  region = nullptr, EMUtil::EMDataType  filestoragetype = EMUtil::EM_FLOAT, bool  use_host_endian = true  )

static

Write a set of images to file specified by 'filename'.

Which images are written is set by 'imgs'.

Parameters

filename	The image file name.
imgs	Which images are written.
imgtype	Write to the given image format type. if not specified, use the 'filename' extension to decide.
header_only	To write only the header or both header and data.
region	Define the region to write to.
filestoragetype	The image data type used in the output file.
use_host_endian	To write in the host computer byte order.

Returns

True if set of images are written successfully to filename.

write_lst()

void EMData::write_lst	(	const string &	filename,
		const string &	reffile = "",
		int	refn = -1,
		const string &	comment = ""
	)

Append data to a LST image file.

Parameters

filename	The LST image file name.
reffile	Reference file name.
refn	The reference file number.
comment	The comment to the added reference file.

See also

lstio.h

Definition at line 361 of file emdata_io.cpp.

{
        ENTERFUNC;
        attr_dict["LST.reffile"] = reffile;
        attr_dict["LST.refn"] = refn;
        attr_dict["LST.comment"] = comment;
        write_image(filename, -1, EMUtil::IMAGE_LST, false);
        EXITFUNC;
}

References EMAN::EMData::attr_dict, ENTERFUNC, EXITFUNC, EMAN::EMUtil::IMAGE_LST, and write_image().