Xmipp  v3.23.11-Nereus
Public Member Functions | Public Attributes | List of all members
Projection Class Reference
Libraries » Reconstruction library » Fourier projectionLibraries » Reconstruction library » Fourier projectionLibraries » | Basic data library » | Projections (2D Image + Euler angles)

#include <fourier_projection.h>

Inheritance diagram for Projection:
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Collaboration diagram for Projection:
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Public Member Functions

void reset (int Ydim, int Xdim)
 
void setAngles (double _rot, double _tilt, double _psi)
 
void read (const FileName &fn, const bool only_apply_shifts=false, DataMode datamode=DATA, MDRow *row=nullptr)
 
void assign (const Projection &P)
 
- Public Member Functions inherited from Image< double >
 Image ()
 
 Image (int Xdim, int Ydim, int Zdim, int Ndim, const FileName &_filename)
 
 Image (int Xdim, int Ydim, int Zdim=1, int Ndim=1, bool _mmapOn=false)
 
 Image (const Image< double > &im)
 
 Image (const MultidimArray< double > &im)
 
virtual ~Image ()
 
void clear ()
 
void clearData ()
 
bool isComplexT () const
 
void getInverseAxisOrder (const std::array< int, 4 > &order, std::array< int, 4 > &result)
 
void transposeAxisSizes (const std::array< size_t, 4 > &sizes, const std::array< int, 4 > &order, std::array< size_t, 4 > &result)
 
void transposeInPlace (MultidimArray< double > &multidimArray, const std::array< int, 4 > &order)
 
void castPage2T (char *page, double *ptrDest, DataType datatype, size_t pageSize)
 
void castPage2T (char *page, std::complex< double > *ptrDest, DataType datatype, size_t pageSize)
 
void castPage2T (char *page, std::complex< double > *ptrDest, DataType datatype, size_t pageSize)
 
void castPage2Datatype (double *srcPtr, char *page, DataType datatype, size_t pageSize) const
 
void castPage2Datatype (std::complex< double > *srcPtr, char *page, DataType datatype, size_t pageSize) const
 
void castPage2Datatype (std::complex< double > *srcPtr, char *page, DataType datatype, size_t pageSize) const
 
void castConvertPage2Datatype (double *srcPtr, char *page, DataType datatype, size_t pageSize, double min0, double max0, CastWriteMode castMode=CW_CONVERT) const
 
void castConvertPage2Datatype (std::complex< double > *srcPtr, char *page, DataType datatype, size_t pageSize, double min0, double max0, CastWriteMode castMode) const
 
void castConvertPage2Datatype (std::complex< double > *srcPtr, char *page, DataType datatype, size_t pageSize, double min0, double max0, CastWriteMode castMode) const
 
void setPage2T (size_t offset, char *page, DataType datatype, size_t pageSize)
 
void getPageFromT (size_t offset, char *page, DataType datatype, size_t pageSize)
 
void getCastConvertPageFromT (size_t offset, char *page, DataType datatype, size_t pageSize, double min0, double max0, CastWriteMode castMode=CW_CONVERT) const
 
bool checkMmapT (DataType datatype) override
 
void mirrorY (void)
 
void mirrorX (void)
 
void selfApplyGeometry (int SplineDegree, bool wrap=xmipp_transformation::WRAP, bool only_apply_shifts=false)
 
int readPreview (const FileName &name, size_t Xdim, size_t Ydim=0, int select_slice=CENTRAL_SLICE, size_t select_img=FIRST_IMAGE)
 
void getPreview (ImageBase *imgBOut, size_t Xdim, size_t Ydim=0, int select_slice=CENTRAL_SLICE, size_t select_img=FIRST_IMAGE)
 
void movePointerTo (int select_slice=ALL_SLICES, size_t select_img=ALL_IMAGES)
 
void writePageAsDatatype (FILE *fimg, DataType datatype, size_t datasize_n)
 
Image< double > & operator= (const Image< double > &op1)
 
MultidimArray< double > & operator() ()
 
const MultidimArray< double > & operator() () const
 
double & operator() (int i, int j) const
 
double & operator() (int k, int i, int j) const
 
bool operator== (const Image< double > &i1) const
 
size_t getSize () const
 
void getTransformationMatrix (Matrix2D< double > &A, bool only_apply_shifts=false, const size_t n=0)
 
void sumWithFile (const FileName &fn)
 
- Public Member Functions inherited from ImageBase
void init ()
 
void copy (const ImageBase &other)
 
void clearHeader ()
 
bool isComplex () const
 
virtual ~ImageBase ()
 
bool isImage (const FileName &name)
 
bool isMapped ()
 
bool isRealImage (const FileName &name)
 
bool isComplexImage (const FileName &name)
 
void rename (const FileName &name)
 
void mapFile2Write (size_t Xdim, size_t Ydim, size_t Zdim, const FileName &_filename, bool createTempFile=false, size_t select_img=APPEND_IMAGE, bool isStack=false, int mode=WRITE_OVERWRITE)
 
int read (const FileName &name, DataMode datamode=DATA, size_t select_img=ALL_IMAGES, bool mapData=false, int mode=WRITE_READONLY)
 
int readBatch (const FileName &name, size_t start_img, size_t batch_size, DataMode datamode=DATA, bool mapData=false, int mode=WRITE_READONLY)
 
int readRange (const FileName &name, size_t start_img, size_t end_img, DataMode datamode=DATA, bool mapData=false, int mode=WRITE_READONLY)
 
int readApplyGeo (const FileName &name, const MDRow &row, const ApplyGeoParams &params=DefaultApplyGeoParams)
 
int readApplyGeo (const FileName &name, const MetaData &md, size_t objId, const ApplyGeoParams &params=DefaultApplyGeoParams)
 
int readApplyGeo (const MetaData &md, size_t objId, const ApplyGeoParams &params=DefaultApplyGeoParams)
 
void applyGeo (const MetaData &md, size_t objId, const ApplyGeoParams &params=DefaultApplyGeoParams)
 
void setGeo (const MDRow &row, size_t n=0)
 
int readMapped (const FileName &name, size_t select_img=ALL_IMAGES, int mode=WRITE_READONLY)
 
int readOrReadMapped (const FileName &name, size_t select_img=ALL_IMAGES, int mode=WRITE_READONLY)
 
int readOrReadPreview (const FileName &name, size_t Xdim, size_t Ydim, int select_slice=CENTRAL_SLICE, size_t select_img=FIRST_IMAGE, bool mapData=false)
 
void write (const FileName &name="", size_t select_img=ALL_IMAGES, bool isStack=false, int mode=WRITE_OVERWRITE, CastWriteMode castMode=CW_CAST, int _swapWrite=0)
 
void swapPage (char *page, size_t pageNrElements, DataType datatype, int swap=1)
 
void swapOnWrite ()
 
const FileName & name () const
 
void getDimensions (size_t &Xdim, size_t &Ydim, size_t &Zdim, size_t &Ndim) const
 
void getDimensions (ArrayDim &aDim)
 
ArrayDim getDimensions ()
 
void getInfo (ImageInfo &imgInfo) const
 
void getInfo (const FileName &name, ImageInfo &imgInfo)
 
void getOffsetAndSwap (size_t &_offset, int &_swap) const
 
int getSwap () const
 
MDRow & getGeometry (const size_t n=0)
 
void initGeometry (const size_t n=0)
 
bool individualContainsLabel (MDLabel label) const
 
bool mainContainsLabel (MDLabel label) const
 
double rot (const size_t n=0) const
 
double tilt (const size_t n=0) const
 
double psi (const size_t n=0) const
 
double Xoff (const size_t n=0) const
 
double Yoff (const size_t n=0) const
 
double Zoff (const size_t n=0) const
 
double weight (const size_t n=0) const
 
double scale (const size_t n=0) const
 
bool flip (const size_t n=0) const
 
DataType datatype () const
 
double samplingRateX () const
 
void setADimFile (ArrayDim aDim)
 
void setName (const FileName &_filename)
 
void setDataMode (DataMode mode)
 
void setEulerAngles (double rot, double tilt, double psi, const size_t n=0)
 
void getEulerAngles (double &rot, double &tilt, double &psi, const size_t n=0) const
 
void setRot (double rot, const size_t n=0)
 
void setTilt (double tilt, const size_t n=0)
 
void setPsi (double psi, const size_t n=0)
 
void setShifts (double xoff, double yoff, double zoff=0., const size_t n=0)
 
void getShifts (double &xoff, double &yoff, double &zoff, const size_t n=0) const
 
void setXoff (double xoff, const size_t n=0)
 
void setYoff (double yoff, const size_t n=0)
 
void setZoff (double zoff, const size_t n=0)
 
void setScale (double scale, const size_t n=0)
 
void getScale (double &scale, const size_t n=0)
 
void setFlip (bool flip, const size_t n=0)
 
void setWeight (double weight, const size_t n=0)
 

Public Attributes

Matrix1D< double > direction
 
Matrix2D< double > euler
 
Matrix2D< double > eulert
 
- Public Attributes inherited from Image< double >
MultidimArray< double > data
 
- Public Attributes inherited from ImageBase
MultidimArrayBase * mdaBase
 
std::vector< std::unique_ptr< MDRow > > MD
 
MDRowVec MDMainHeader
 

Additional Inherited Members

- Protected Member Functions inherited from Image< double >
void applyGeo (const MDRow &row, bool only_apply_shifts=false, bool wrap=xmipp_transformation::WRAP) override
 
void setDimensions (int Xdim, int Ydim, int Zdim, size_t Ndim)
 
- Protected Member Functions inherited from ImageBase
int readDM3 (size_t img_select, bool isStack=false)
 
int writeDM3 (size_t img_select, bool isStack=false, int mode=WRITE_OVERWRITE)
 
int readDM4 (size_t img_select, bool isStack=false)
 
int writeDM4 (size_t img_select, bool isStack=false, int mode=WRITE_OVERWRITE)
 
int readIMAGIC (size_t img_select)
 
int writeIMAGIC (size_t img_select=ALL_IMAGES, int mode=WRITE_OVERWRITE, const String &bitDepth="", CastWriteMode castMode=CW_CAST)
 
int readMRC (size_t select_img, bool isStack=false)
 
int readMRC (size_t start_img, size_t batch_size, bool isStack=false)
 
int writeMRC (size_t select_img, bool isStack=false, int mode=WRITE_OVERWRITE, const String &bitDepth="", CastWriteMode castMode=CW_CAST)
 
int readINF (size_t img_select, bool isStack=false)
 
int writeINF (size_t img_select, bool isStack=false, int mode=WRITE_OVERWRITE, String bitDepth="", CastWriteMode castMode=CW_CAST)
 
DataType datatypeRAW (String strDT)
 
int readRAW (size_t select_img, bool isStack=false)
 
int readSPIDER (size_t select_img)
 
int readSPIDER (size_t start_img, size_t batch_size)
 
int writeSPIDER (size_t select_img=ALL_IMAGES, bool isStack=false, int mode=WRITE_OVERWRITE)
 
int readSPE (size_t select_img, bool isStack=false)
 
int writeSPE (size_t select_img, bool isStack=false, int mode=WRITE_OVERWRITE)
 
int readTIA (int img_select, bool isStack=false)
 
int writeTIA (int img_select, bool isStack=false, int mode=WRITE_OVERWRITE)
 
int readJPEG (size_t select_img)
 
int writeJPEG (size_t select_img, bool isStack=false, int mode=WRITE_OVERWRITE, String bitDepth="", CastWriteMode castMode=CW_CONVERT)
 
void castTiffTile2T (size_t offset, char *tif_buf, unsigned int x, unsigned int y, unsigned int imageWidth, unsigned int imageLength, unsigned int tileWidth, unsigned int tileLength, unsigned short samplesPerPixel, DataType datatype)
 
void castTiffLine2T (size_t offset, char *tif_buf, unsigned int y, unsigned int imageWidth, unsigned int imageLength, unsigned short samplesPerPixel, DataType datatype)
 
DataType datatypeTIFF (TIFFDirHead dHead)
 
int readTIFF (size_t select_img, bool isStack=false)
 
int writeTIFF (size_t select_img, bool isStack=false, int mode=WRITE_OVERWRITE, String bitDepth="", CastWriteMode castMode=CW_CAST)
 
int readEM (size_t select_img, bool isStack=false)
 
int writeEM (size_t select_img=ALL_IMAGES, bool isStack=false, int mode=WRITE_OVERWRITE)
 
int readPIF (size_t select_img)
 
int writePIF (size_t select_img=ALL_IMAGES, bool isStack=false, int mode=WRITE_OVERWRITE)
 
DataType datatypeH5 (hid_t dataset)
 
hid_t H5Datatype (DataType datatype)
 
int readHDF5 (size_t select_img)
 
int writeHDF5 (size_t select_img, bool isStack=false, int mode=WRITE_OVERWRITE, String bitDepth="", CastWriteMode castMode=CW_CAST)
 
int readEER (size_t select_img)
 
ImageFHandler * openFile (const FileName &name, int mode=WRITE_READONLY) const
 
More...
 
void closeFile (ImageFHandler *hFile=NULL) const
 
int _read (const FileName &name, ImageFHandler *hFile, DataMode datamode=DATA, size_t select_img=ALL_IMAGES, bool mapData=false)
 
int _readBatch (const FileName &name, ImageFHandler *hFile, size_t start_img, size_t batch_size, DataMode datamode=DATA, bool mapData=false)
 
void _write (const FileName &name, ImageFHandler *hFile, size_t select_img=ALL_IMAGES, bool isStack=false, int mode=WRITE_OVERWRITE, CastWriteMode castMode=CW_CAST)
 
void setDatatype (DataType datatype)
 
- Protected Attributes inherited from ImageBase
FileName filename
 
FileName tempFilename
 
FileName dataFName
 
FILE * fimg
 
FILE * fhed
 
TIFF * tif
 
hid_t fhdf5
 
ImageFHandler * hFile
 
ArrayDim aDimFile
 
DataMode dataMode
 
size_t offset
 
int swap
 
int swapWrite
 
std::array< int, 4 > axisOrder
 
TransformType transform
 
size_t replaceNsize
 
bool _exists
 
bool mmapOnRead
 
bool mmapOnWrite
 
int mFd
 
size_t mappedSize
 
size_t mappedOffset
 
size_t virtualOffset
 
- Static Protected Attributes inherited from ImageBase
static constexpr std::array< int, 4 > defaultAxisOrder = {0,1,2,3}
 

Detailed Description

Projection class.

A projection is a 2D, double Image plus some information (about the direction of projection) which makes it suitable for 3D reconstruction. A projection is supposed to have the point (0,0) at the center of the image and not in the corners as usual matrices have.

The normal use of a projection is:

Projection P; // Create variable
P.reset(65, 65); // Init with zeros and set right origin
P.set_angles(30, 45, -50); // Set Euler angles

From now on, the projection can be treated as any other Image.

Definition at line 56 of file fourier_projection.h.

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