xmipp_image_base.cpp File Reference

#include "xmipp_image_base.h"
#include "xmipp_image.h"
#include "xmipp_error.h"
#include <stdlib.h>
#include "metadata_static.h"
#include "metadata_base.h"
#include "xmipp_funcs.h"
#include <tiffio.h>
#include <hdf5.h>

Include dependency graph for xmipp_image_base.cpp:

Go to the source code of this file.

Macros
#define	READ_AND_RETURN()

Functions
bool	isDynamicMRC (const char *envvar, const String &ext)
bool	isMRCStack (const FileName &ext_name)
bool	isMRCImageOrVolume (const FileName &ext_name)
std::ostream &	operator<< (std::ostream &o, const ImageBase &I)

Macro Definition Documentation

READ_AND_RETURN

#define READ_AND_RETURN

(

)

Value:

ImageFHandler* hFile = openFile(name); \
                                  int err = _read(name, hFile, params.datamode, params.select_img); \
                                  applyGeo(*row, params.only_apply_shifts, params.wrap); \
                                  closeFile(hFile); \
                                  return err

General read functionMacros for don't type

Definition at line 240 of file xmipp_image_base.cpp.

Function Documentation

isDynamicMRC()

bool isDynamicMRC	(	const char *	envvar,
		const String &	ext
	)

Definition at line 762 of file xmipp_image_base.cpp.

{
    FileName mrcExtensions;
    if (getenv(envvar))
        mrcExtensions=getenv(envvar);
    String plainExt = ext;
    size_t found = ext.find_first_of("%");
    if (found!=String::npos)
        plainExt = ext.substr(0, found);
    else
        return false;
    return mrcExtensions.contains(plainExt);
}

isMRCImageOrVolume()

bool isMRCImageOrVolume

(

const FileName &

ext_name

)

Definition at line 784 of file xmipp_image_base.cpp.

{
    return ext_name.contains("mrc") || ext_name.contains("map") ||
           ext_name.contains("rec") || isDynamicMRC("XMIPP_MRC_EXTENSIONS",ext_name);
}

isMRCStack()

bool isMRCStack

(

const FileName &

ext_name

)

Definition at line 776 of file xmipp_image_base.cpp.

{
    return ext_name.contains("mrcs") || ext_name.contains("st") ||
           ext_name.contains("preali") || ext_name.contains("ali") ||
           ext_name.contains("fixed") ||
           isDynamicMRC("XMIPP_MRC_STACK_EXTENSIONS",ext_name);
}

operator<<()

std::ostream& operator<<	(	std::ostream &	o,
		const ImageBase &	I
	)

Show image properties

Definition at line 1121 of file xmipp_image_base.cpp.

{
    o << std::endl;
    DataType * fileDT = NULL;
    if (!I.filename.empty())
    {
        o << "--- File information ---" << std::endl;
        o << "Filename       : " << I.filename << std::endl;
        o << "Endianess      : ";
        if (I.swap^IsLittleEndian())
            o << "Little"  << std::endl;
        else
            o << "Big" << std::endl;

        o << "Reversed       : ";
        if (I.swap)
            o << "True"  << std::endl;
        else
            o << "False" << std::endl;
        fileDT = new DataType;
        *fileDT = I.datatype();
        o << "Data type      : " << datatype2StrLong(*fileDT) << std::endl;
        o << "Data offset    : " << I.offset << std::endl;
    }

    o << "--- Image information ---" << std::endl;

    DataType myDT = I.myT();
    if ((fileDT == NULL || myDT != *fileDT) && I.dataMode >= DATA )
        o << "Memory datatype: " << datatype2StrLong(I.myT()) << std::endl;
    o << "Image type     : ";
    if (I.isComplex())
        o << "Fourier-space image" << std::endl;
    else
        o << "Real-space image" << std::endl;

    delete fileDT;

    size_t xdim, ydim, zdim, ndim;
    I.getDimensions(xdim, ydim, zdim, ndim);
    o << "Dimensions     : " << ndim << " x " << zdim << " x " << ydim << " x " << xdim;
    o << "  ((N)Objects x (Z)Slices x (Y)Rows x (X)Columns)" << std::endl;

    double sampling;
    I.MDMainHeader.getValueOrDefault(MDL_SAMPLINGRATE_X, sampling, 0);
    if (sampling > 0)
    {
        o << "Sampling rate  : " << std::endl;
        o << "                 X-rate (Angstrom/pixel) = " << sampling << std::endl;
        I.MDMainHeader.getValue(MDL_SAMPLINGRATE_Y, sampling);
        o << "                 Y-rate (Angstrom/pixel) = " << sampling << std::endl;
        I.MDMainHeader.getValue(MDL_SAMPLINGRATE_Z, sampling);
        o << "                 Z-rate (Angstrom/pixel) = " << sampling << std::endl;
    }

    std::stringstream oGeo;

    if (I.individualContainsLabel(MDL_ANGLE_ROT))
    {
        oGeo << "Euler angles   : " << std::endl;
        oGeo << "                 Phi   (rotation around Z axis)                  = " << I.rot() << std::endl;
        oGeo << "                 Theta (tilt, second rotation around new Y axis) = " << I.tilt() << std::endl;
        oGeo << "                 Psi   (third rotation around new Z axis)        = " << I.psi() << std::endl;
    }
    if (I.individualContainsLabel(MDL_SHIFT_X))
    {
        oGeo << "Origin Offsets : " << std::endl;
        oGeo << "                 Xoff  (origin offset in X-direction) = " << I.Xoff() << std::endl;
        oGeo << "                 Yoff  (origin offset in Y-direction) = " << I.Yoff() << std::endl;
        oGeo << "                 Zoff  (origin offset in Z-direction) = " << I.Zoff() << std::endl;
    }
    if (I.individualContainsLabel(MDL_SCALE))
        oGeo << "Scale          : " <<I.scale() << std::endl;
    if (I.individualContainsLabel(MDL_WEIGHT))
        oGeo << "Weight         : " << I.weight() << std::endl;
    if (I.individualContainsLabel(MDL_FLIP))
        oGeo << "Flip           : " << I.flip() << std::endl;

    if (!oGeo.str().empty())
        o << "--- Geometry ---" << std::endl << oGeo.str();

    return o;
}