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emdata_metadata.h File Reference

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Functions

EMData * get_fft_amplitude ()
 return the amplitudes of the FFT including the left half
EMData * get_fft_amplitude2D ()
 return the amplitudes of the 2D FFT including the left half PRB
Exceptions:
ImageFormatException If the image is not a complex image.

EMData * get_fft_phase ()
 return the phases of the FFT including the left half
float * get_data () const
 Get the image pixel density data in a 1D float array.
const float *const get_const_data () const
 Get the image pixel density data in a 1D float array - const version of get_data.
void set_data (float *data, const int x, const int y, const int z)
 Set the data explicitly data pointer must be allocated using malloc!
void write_data (string fsp, size_t loc, const Region *const area=0, const int file_nx=0, const int file_ny=0, const int file_nz=0)
 Dump the image pixel data in native byte order to a disk file.
void read_data (string fsp, size_t loc, const Region *area=0, const int file_nx=0, const int file_ny=0, const int file_nz=0)
 Read the image pixel data in native byte order from a disk file.
void update ()
 Mark EMData as changed, statistics, etc will be updated at need.
bool has_ctff () const
 check whether the image physical file has the CTF info or not.
float calc_center_density ()
 Calculates the density value at the peak of the image histogram, sort of like the mode of the density.
float calc_sigma_diff ()
 Calculates sigma above and below the mean and returns the difference between them.
IntPoint calc_min_location () const
 Calculates the coordinates of the minimum-value pixel.
IntPoint calc_max_location () const
 Calculates the coordinates of the maximum-value pixel.
IntPoint calc_max_location_wrap (const int maxshiftx=-1, const int maxshifty=-1, const int maxshiftz=-1)
 Calculates the wrapped coordinates of the maximum value This function is useful in the context of Fourier correlation you can call this function to find the correct translational shift when using calc_ccf etc.
FloatPoint calc_center_of_mass ()
 Calculate the center of mass using an algorithm written by S Ludtke.
int calc_min_index () const
 Calculates the index of minimum-value pixel when assuming all pixels are in a 1D array.
int calc_max_index () const
 Calculates the index of maximum-value pixel when assuming all pixels are in a 1D array.
vector< Pixel > calc_highest_locations (float threshold) const
 Calculate and return a sorted list of pixels whose values are above a specified threshold.
vector< Pixel > calc_n_highest_locations (int n)
 Calculate and return a sorted list of N highest pixels in the map.
float get_edge_mean () const
 Calculates the mean pixel values around the (1 pixel) edge of the image.
float get_circle_mean ()
 Calculates the circular edge mean by applying a circular mask on 'this' image.
Ctf * get_ctf () const
 Get ctf parameter of this image.
void set_ctf (Ctf *ctf)
 Set the CTF parameter of this image.
Vec3f get_translation () const
 Get 'this' image's translation vector from the original location.
void set_translation (const Vec3f &t)
 Set 'this' images' translation vector from the original location.
void set_translation (float dx, float dy, float dz)
 Set 'this' images' translation vector from the original location.
Transform get_transform () const
 Get the 3D orientation of 'this' image.
void set_rotation (float az, float alt, float phi)
 Define the 3D orientation of this particle, also used to indicate relative rotations for reconstructions.
void set_rotation (const Transform3D &t3d)
 Define the 3D orientation of this particle Orientation information is extracted from a Transform3D object and stored internally in EMAN (az,alt,phi) format.
void set_size (int nx, int ny=1, int nz=1)
 Resize this EMData's main board memory pointer.
void set_complex_size (int nx, int ny=1, int nz=1)
 Resize 'this' complex image.
void set_path (const string &new_path)
 Set the path.
void set_pathnum (int n)
 Set the number of paths.
MArray2D get_2dview () const
 Get image raw pixel data in a 2D multi-array format.
MArray3D get_3dview () const
 Get image raw pixel data in a 3D multi-array format.
MCArray2D get_2dcview () const
 Get complex image raw pixel data in a 2D multi-array format.
MCArray3D get_3dcview () const
 Get complex image raw pixel data in a 3D multi-array format.
MCArray3Dget_3dcviewptr () const
 Get pointer to a complex image raw pixel data in a 3D multi-array format.
MArray2D get_2dview (int x0, int y0) const
 Get image raw pixel data in a 2D multi-array format.
MArray3D get_3dview (int x0, int y0, int z0) const
 Get image raw pixel data in a 3D multi-array format.
MCArray2D get_2dcview (int x0, int y0) const
 Get complex image raw pixel data in a 2D multi-array format.
MCArray3D get_3dcview (int x0, int y0, int z0) const
 Get complex image raw pixel data in a 3D multi-array format.
EMObject get_attr (const string &attr_name) const
 The generic way to get any image header information given a header attribute name.
EMObject get_attr_default (const string &attr_name, const EMObject &em_obj=EMObject()) const
 The generic way to get any image header information given a header attribute name.
void set_attr (const string &key, EMObject val)
 Set a header attribute's value.
void set_attr_python (const string &key, EMObject val)
 Set a header attribute's value from Python.
bool has_attr (const string &key) const
 Ask if the header has a particular attribute.
Dict get_attr_dict () const
 Get the image attribute dictionary containing all the image attribute names and attribute values.
void set_attr_dict (const Dict &new_dict)
 Merge the new values with the existing dictionary.
void del_attr (const string &attr_name)
 Delete the attribute from dictionary.
void del_attr_dict (const vector< string > &del_keys)
 Delete the attributes from the dictionary.
int get_xsize () const
 Get the image x-dimensional size.
int get_ysize () const
 Get the image y-dimensional size.
int get_zsize () const
 Get the image z-dimensional size.
size_t get_size () const
 Get the number of allocated floats in the image (nx*ny*nz).
vector< float > get_data_as_vector () const
 Get the pixel data as a vector.
int get_ndim () const
 Get image dimension.
bool is_shuffled () const
 Has this image been shuffled?
bool is_FH () const
 Is this a FH image?
bool is_complex () const
 Is this a complex image?
bool is_real () const
 Is this a real image?
void set_shuffled (bool is_shuffled)
 Mark this image as a shuffled image.
void set_FH (bool is_FH)
 Mark this complex image as a FH image.
void set_complex (bool is_complex)
 Mark this image as a complex image.
bool is_complex_x () const
 Is this image a 1D FFT image in X direction?
void set_complex_x (bool is_complex_x)
 Marks this image a 1D FFT image in X direction.
bool is_flipped () const
 Is this image flipped?
void set_flipped (bool is_flipped)
 Mark this image as flipped.
bool is_ri () const
 Is this image a real/imaginary format complex image?
void set_ri (bool is_ri)
 Mark this image as a real/imaginary format complex image.
bool is_fftpadded () const
 Is this image already extended along x for ffts?
void set_fftpad (bool is_fftpadded)
 Mark this image as already extended along x for ffts.
bool is_fftodd () const
 Does this image correspond to a (real-space) odd nx?
void set_fftodd (bool is_fftodd)
 Mark this image as having (real-space) odd nx.
void set_nxc (int nxc)
 Set the number of complex elements along x.
int get_flags () const
void set_flags (int f)
int get_changecount () const
void set_changecount (int c)
int get_xoff () const
int get_yoff () const
int get_zoff () const
void set_xyzoff (int x, int y, int z)
void scale_pixel (float scale_factor) const
 Scale the angstrom per pixel of this image by a uniform amount Alters the EMData metadata I had to make this function public for access from the Processors (David Woolford).
string get_path () const
int get_pathnum () const
std::string get_data_pickle () const
void set_data_pickle (std::string vf)
int get_supp_pickle () const
void set_supp_pickle (int i)
vector< Vec3imask_contig_region (const float &val, const Vec3i &seed)
void set_attr_dict_explicit (const Dict &new_dict)
 Make the attributes of this EMData exactly equal to the argument dictionary Originally introduced because set_attr_dict does automatic resizing, which is undersirable in some circumstances.


Function Documentation

float calc_center_density  ) 
 

Calculates the density value at the peak of the image histogram, sort of like the mode of the density.

Returns:
The density value at the peak of the image histogram.

FloatPoint calc_center_of_mass  ) 
 

Calculate the center of mass using an algorithm written by S Ludtke.

Author:
David Woolford
Date:
Fri Jun 6th 2008

vector<Pixel> calc_highest_locations float  threshold  )  const
 

Calculate and return a sorted list of pixels whose values are above a specified threshold.

The pixels are sorted from high to low.

Parameters:
threshold The specified pixel value. Returned pixels should have higher values than it.
Returns:
A sorted list of pixels with their values, and locations. Their values are higher than threshold.

int calc_max_index  )  const
 

Calculates the index of maximum-value pixel when assuming all pixels are in a 1D array.

Returns:
Index of the maximum-value pixel.

IntPoint calc_max_location  )  const
 

Calculates the coordinates of the maximum-value pixel.

Returns:
The coordinates of the maximum-value pixel.

IntPoint calc_max_location_wrap const int  maxshiftx = -1,
const int  maxshifty = -1,
const int  maxshiftz = -1
 

Calculates the wrapped coordinates of the maximum value This function is useful in the context of Fourier correlation you can call this function to find the correct translational shift when using calc_ccf etc.

Returns:
the wrapped coordinates of the maximum
Author:
David Woolford
Date:
Fri Jun 6th 2008

int calc_min_index  )  const
 

Calculates the index of minimum-value pixel when assuming all pixels are in a 1D array.

Returns:
Index of the minimum-value pixel.

IntPoint calc_min_location  )  const
 

Calculates the coordinates of the minimum-value pixel.

Returns:
The coordinates of the minimum-value pixel.

vector<Pixel> calc_n_highest_locations int  n  ) 
 

Calculate and return a sorted list of N highest pixels in the map.

Parameters:
n The number of highest value pixels should be returned.
Returns:
A sorted list of N pixels with their values, and locations.

float calc_sigma_diff  ) 
 

Calculates sigma above and below the mean and returns the difference between them.

Returns:
The difference between sigma above and below the mean.

void del_attr const string &  attr_name  ) 
 

Delete the attribute from dictionary.

Parameters:
attr_name the attribute name to be removed

void del_attr_dict const vector< string > &  del_keys  ) 
 

Delete the attributes from the dictionary.

Parameters:
del_keys the attrutes' names to be removed

MCArray2D get_2dcview int  x0,
int  y0
const
 

Get complex image raw pixel data in a 2D multi-array format.

The data coordinates is translated by (x0,y0) such that array[y0][x0] points to the pixel at the origin location. the data coordiates translated by (x0,y0). The array shares the memory space with the image data.

It should be used on 2D image only.

Parameters:
x0 X-axis translation amount.
y0 Y-axis translation amount.
Returns:
2D multi-array format of the raw data.

MCArray2D get_2dcview  )  const
 

Get complex image raw pixel data in a 2D multi-array format.

The array shares the memory space with the image data.

It should be used on 2D image only.

Returns:
2D multi-array format of the raw data.

MArray2D get_2dview int  x0,
int  y0
const
 

Get image raw pixel data in a 2D multi-array format.

The data coordinates is translated by (x0,y0) such that array[y0][x0] points to the pixel at the origin location. the data coordiates translated by (x0,y0). The array shares the memory space with the image data.

It should be used on 2D image only.

Parameters:
x0 X-axis translation amount.
y0 Y-axis translation amount.
Returns:
2D multi-array format of the raw data.

MArray2D get_2dview  )  const
 

Get image raw pixel data in a 2D multi-array format.

The array shares the memory space with the image data. Notice: the subscription order is d[y][x] in Python, it's d[x][y] in C++

It should be used on 2D image only.

Returns:
2D multi-array format of the raw data.

MCArray3D get_3dcview int  x0,
int  y0,
int  z0
const
 

Get complex image raw pixel data in a 3D multi-array format.

The data coordinates is translated by (x0,y0,z0) such that array[z0][y0][x0] points to the pixel at the origin location. the data coordiates translated by (x0,y0,z0). The array shares the memory space with the image data.

It should be used on 3D image only.

Parameters:
x0 X-axis translation amount.
y0 Y-axis translation amount.
z0 Z-axis translation amount.
Returns:
3D multi-array format of the raw data.

MCArray3D get_3dcview  )  const
 

Get complex image raw pixel data in a 3D multi-array format.

The array shares the memory space with the image data.

It should be used on 3D image only.

Returns:
3D multi-array format of the raw data.

MCArray3D* get_3dcviewptr  )  const
 

Get pointer to a complex image raw pixel data in a 3D multi-array format.

The array shares the memory space with the image data.

It should be used on 3D image only.

Returns:
Pointer to a 3D multi-array format of the raw data.

MArray3D get_3dview int  x0,
int  y0,
int  z0
const
 

Get image raw pixel data in a 3D multi-array format.

The data coordinates is translated by (x0,y0,z0) such that array[z0][y0][x0] points to the pixel at the origin location. the data coordiates translated by (x0,y0,z0). The array shares the memory space with the image data.

It should be used on 3D image only.

Parameters:
x0 X-axis translation amount.
y0 Y-axis translation amount.
z0 Z-axis translation amount.
Returns:
3D multi-array format of the raw data.

MArray3D get_3dview  )  const
 

Get image raw pixel data in a 3D multi-array format.

The array shares the memory space with the image data. Notice: the subscription order is d[z][y][x] in Python, it's d[x][y][z] in C++ --grant Tang

It should be used on 3D image only.

Returns:
3D multi-array format of the raw data.

EMObject get_attr const string &  attr_name  )  const
 

The generic way to get any image header information given a header attribute name.

If the attribute does not exist, it will raise an exception.

Parameters:
attr_name The header attribute name.
Returns:
The attribute value.
Exceptions:
NotExistingObjectException when attribute not exist

Referenced by is_fftpadded(), is_FH(), is_flipped(), is_shuffled(), and EMAN::KMeansAnalyzer::reseed().

EMObject get_attr_default const string &  attr_name,
const EMObject &  em_obj = EMObject()
const
 

The generic way to get any image header information given a header attribute name.

If the attribute does not exist, it will return a default EMObject() object, which will be converted to None in Python. Or return any object user submit.

Parameters:
attr_name The header attribute name.
em_obj the default attribute to return when this attr_name not exist in attr_dict
Returns:
The attribute value, default to None.

Dict get_attr_dict  )  const
 

Get the image attribute dictionary containing all the image attribute names and attribute values.

Returns:
The image attribute dictionary containing all attribute names and values.

int get_changecount  )  const [inline]
 

Definition at line 938 of file emdata_metadata.h.

00939 {
00940         return changecount;
00941 }

float get_circle_mean  ) 
 

Calculates the circular edge mean by applying a circular mask on 'this' image.

Returns:
The circular edge mean.

const float* const get_const_data  )  const [inline]
 

Get the image pixel density data in a 1D float array - const version of get_data.

Returns:
The image pixel density data.

Definition at line 78 of file emdata_metadata.h.

References get_data().

00078 { return get_data(); }

Ctf* get_ctf  )  const
 

Get ctf parameter of this image.

Returns:
The ctf parameter.

float* get_data  )  const [inline]
 

Get the image pixel density data in a 1D float array.

Returns:
The image pixel density data.

Definition at line 72 of file emdata_metadata.h.

References rdata.

Referenced by cmplx(), get_const_data(), get_data_as_vector(), get_value_at(), operator()(), set_value_at(), and set_value_at_fast().

00072 { return rdata; }

vector<float> get_data_as_vector  )  const [inline]
 

Get the pixel data as a vector.

Returns:
a vector containing the pixel data.

Definition at line 608 of file emdata_metadata.h.

References copy(), data, get_data(), get_size(), and v.

00608                                                 {
00609         int size = get_size();
00610         vector<float> v(size);
00611         float* data = get_data();
00612         std::copy(data,data+size,v.begin());
00613         return v;
00614 }

std::string get_data_pickle  )  const
 

float get_edge_mean  )  const
 

Calculates the mean pixel values around the (1 pixel) edge of the image.

Returns:
The mean pixel values around the (1 pixel) edge.

EMData* get_fft_amplitude  ) 
 

return the amplitudes of the FFT including the left half

Exceptions:
ImageFormatException If the image is not a complex image.
Returns:
The current FFT image's amplitude image.

EMData* get_fft_amplitude2D  ) 
 

return the amplitudes of the 2D FFT including the left half PRB

Exceptions:
ImageFormatException If the image is not a complex image.

Returns:
The current FFT image's amplitude image.

EMData* get_fft_phase  ) 
 

return the phases of the FFT including the left half

Exceptions:
ImageFormatException If the image is not a complex image.
Returns:
The current FFT image's phase image.

int get_flags  )  const [inline]
 

Definition at line 928 of file emdata_metadata.h.

00929 {
00930         return flags;
00931 }

int get_ndim  )  const [inline]
 

Get image dimension.

Returns:
image dimension.

Definition at line 619 of file emdata_metadata.h.

References ny.

00620 {
00621         if (nz <= 1) {
00622                 if (ny <= 1) {
00623                         return 1;
00624                 }
00625                 else {
00626                         return 2;
00627                 }
00628         }
00629 
00630         return 3;
00631 }

string get_path  )  const [inline]
 

Definition at line 977 of file emdata_metadata.h.

00978 {
00979         return path;
00980 }

int get_pathnum  )  const [inline]
 

Definition at line 982 of file emdata_metadata.h.

00983 {
00984         return pathnum;
00985 }

size_t get_size  )  const [inline]
 

Get the number of allocated floats in the image (nx*ny*nz).

Returns:
nx*ny*nz

Definition at line 600 of file emdata_metadata.h.

References nx, and ny.

Referenced by get_data_as_vector(), and EMAN::AddNoiseProcessor::process_inplace().

00601 {
00602         return (size_t)nx*(size_t)ny*(size_t)nz;
00603 }

int get_supp_pickle  )  const
 

Transform get_transform  )  const [inline]
 

Get the 3D orientation of 'this' image.

Returns:
The 3D orientation of 'this' image.

Definition at line 285 of file emdata_metadata.h.

00286 {
00287         Dict rotation_dict;
00288         rotation_dict["type"] = "eman";
00289         rotation_dict["alt"] = attr_dict["euler_alt"];
00290         rotation_dict["az"] = attr_dict["euler_az"];
00291         rotation_dict["phi"] = attr_dict["euler_phi"];
00292 
00293         Transform trans;
00294         trans.to_identity();
00295         trans.set_rotation(rotation_dict);
00296 
00297         return trans;
00298 }

Vec3f get_translation  )  const [inline]
 

Get 'this' image's translation vector from the original location.

Returns:
'this' image's translation vector from the original location.

Definition at line 254 of file emdata_metadata.h.

00255 {
00256         return all_translation;
00257 }

int get_xoff  )  const [inline]
 

Definition at line 948 of file emdata_metadata.h.

00949 {
00950         return xoff;
00951 }

int get_xsize  )  const [inline]
 

Get the image x-dimensional size.

Returns:
Image x-dimensional size.

Definition at line 573 of file emdata_metadata.h.

References nx.

Referenced by EMAN::KMeansAnalyzer::analyze(), EMAN::MarchingCubes::draw_cube(), EMAN::FourierReconstructorSimple2D::insert_slice(), main(), EMAN::TestImageFourierNoiseProfile::process_inplace(), EMAN::CTFSNRWeightProcessor::process_inplace(), EMAN::TestImageFourierNoiseGaussian::process_inplace(), EMAN::FlattenBackgroundProcessor::process_inplace(), and EMAN::Util::svdcmp().

00574 {
00575         return nx;
00576 }

int get_yoff  )  const [inline]
 

Definition at line 953 of file emdata_metadata.h.

00954 {
00955         return yoff;
00956 }

int get_ysize  )  const [inline]
 

Get the image y-dimensional size.

Returns:
Image y-dimensional size.

Definition at line 582 of file emdata_metadata.h.

References ny.

Referenced by EMAN::KMeansAnalyzer::analyze(), EMAN::OptVarianceCmp::cmp(), EMAN::MarchingCubes::draw_cube(), EMAN::TestImageFourierNoiseProfile::process_inplace(), EMAN::CTFSNRWeightProcessor::process_inplace(), EMAN::TestImageFourierNoiseGaussian::process_inplace(), and EMAN::Util::svdcmp().

00583 {
00584         return ny;
00585 }

int get_zoff  )  const [inline]
 

Definition at line 958 of file emdata_metadata.h.

00959 {
00960         return zoff;
00961 }

int get_zsize  )  const [inline]
 

Get the image z-dimensional size.

Returns:
Image z-dimensional size.

Definition at line 591 of file emdata_metadata.h.

Referenced by EMAN::KMeansAnalyzer::analyze(), EMAN::MarchingCubes::draw_cube(), EMAN::TestImageFourierNoiseProfile::process_inplace(), EMAN::CTFSNRWeightProcessor::process_inplace(), EMAN::TestImageFourierNoiseGaussian::process_inplace(), and EMAN::Util::svdcmp().

00592 {
00593         return nz;
00594 }

bool has_attr const string &  key  )  const [inline]
 

Ask if the header has a particular attribute.

Parameters:
key the header attribute name
Returns:
whether or not the header has the name as a key/value entry

Definition at line 535 of file emdata_metadata.h.

Referenced by is_fftpadded(), is_FH(), and is_shuffled().

00535                                               {
00536         return attr_dict.has_key(key);
00537 }

bool has_ctff  )  const [inline]
 

check whether the image physical file has the CTF info or not.

Returns:
True if it has the CTF information. Otherwise, false.

Definition at line 138 of file emdata_metadata.h.

00139 {
00140         if (this->has_attr("ctf")) {
00141                 return true;
00142         }
00143         else {
00144                 return false;
00145         }
00146 }

bool is_complex  )  const [inline]
 

Is this a complex image?

Returns:
Whether this is a complex image or not.

Definition at line 671 of file emdata_metadata.h.

Referenced by is_real(), EMAN::TestUtil::make_image_file_by_mode(), and EMAN::TestUtil::verify_image_file_by_mode().

00672 {
00673         if(attr_dict.has_key("is_complex")) {
00674                 if (int(attr_dict["is_complex"])) {
00675                         return true;
00676                 }
00677                 else {
00678                         return false;
00679                 }
00680         }
00681         else {
00682                 return false;
00683         }
00684 }

bool is_complex_x  )  const [inline]
 

Is this image a 1D FFT image in X direction?

Returns:
Whether this image is a 1D FFT image in X direction.

Definition at line 750 of file emdata_metadata.h.

00751 {
00752         if(attr_dict.has_key("is_complex_x")) {
00753                 if (int(attr_dict["is_complex_x"])) {
00754                         return true;
00755                 }
00756                 else {
00757                         return false;
00758                 }
00759         }
00760         else {
00761                 return false;
00762         }
00763 }

bool is_fftodd  )  const [inline]
 

Does this image correspond to a (real-space) odd nx?

Returns:
Whether this image has a (real-space) odd nx.

Definition at line 887 of file emdata_metadata.h.

Referenced by EMAN::FourierReconstructor::setup(), EMAN::FourierReconstructorSimple2D::setup(), and EMAN::FourierReconstructor::setup_seed().

00888 {
00889         if(flags & EMDATA_FFTODD) {
00890                 return true;
00891         }
00892         else if( attr_dict.has_key("is_fftodd") && (int)attr_dict["is_fftodd"] == 1 ) {
00893                 return true;
00894         }
00895         else {
00896                 return false;
00897         }
00898 }

bool is_fftpadded  )  const [inline]
 

Is this image already extended along x for ffts?

Returns:
Whether this image is extended along x for ffts.

Definition at line 854 of file emdata_metadata.h.

References get_attr(), and has_attr().

00855 {
00856         if (flags & EMDATA_PAD) {
00857                 return true;
00858         }
00859 
00860         if(has_attr("is_fftpad")) {
00861                 return get_attr("is_fftpad");
00862         }
00863 
00864         return false;
00865 
00866 }

bool is_FH  )  const [inline]
 

Is this a FH image?

Returns:
Whether this is a FH image or not.

Definition at line 654 of file emdata_metadata.h.

References get_attr(), and has_attr().

00655 {  //     PRB
00656         if (flags & EMDATA_FH) {
00657                 return true;
00658         }
00659 
00660         if(has_attr("is_fh")) {
00661                 return get_attr("is_fh");
00662         }
00663 
00664         return false;
00665 }

bool is_flipped  )  const [inline]
 

Is this image flipped?

Returns:
Whether this image is flipped or not.

Definition at line 784 of file emdata_metadata.h.

References get_attr().

00785 {
00786         if (flags & EMDATA_FLIP) { //keep here for back compatibility
00787                 return true;
00788         }
00789 
00790         if(attr_dict.has_key("is_flipped")) {
00791                 if(get_attr("is_flipped")) {
00792                         return true;
00793                 }
00794         }
00795 
00796         return false;
00797 
00798 }

bool is_real  )  const [inline]
 

Is this a real image?

Returns:
Whether this is image is real (not complex) or not.

Definition at line 690 of file emdata_metadata.h.

References is_complex().

00691 {
00692         return !is_complex();
00693 }

bool is_ri  )  const [inline]
 

Is this image a real/imaginary format complex image?

Returns:
Whether this image is real/imaginary format complex image.

Definition at line 820 of file emdata_metadata.h.

00821 {
00822         if(attr_dict.has_key("is_complex_ri")) {
00823                 if (int(attr_dict["is_complex_ri"])) {
00824                         return true;
00825                 }
00826                 else {
00827                         return false;
00828                 }
00829         }
00830         else {
00831                 return false;
00832         }
00833 }

bool is_shuffled  )  const [inline]
 

Has this image been shuffled?

Returns:
Whether this image has been shuffled to put origin in the center.

Definition at line 637 of file emdata_metadata.h.

References get_attr(), and has_attr().

00638 {  //     PRB
00639         if (flags & EMDATA_SHUFFLE) {
00640                 return true;
00641         }
00642 
00643         if(has_attr("is_shuffled")) {
00644                 return get_attr("is_shuffled");
00645         }
00646 
00647         return false;
00648 }

vector<Vec3i> mask_contig_region const float &  val,
const Vec3i seed
 

void read_data string  fsp,
size_t  loc,
const Region *  area = 0,
const int  file_nx = 0,
const int  file_ny = 0,
const int  file_nz = 0
 

Read the image pixel data in native byte order from a disk file.

The image should already have the correct dimensions.

Parameters:
fsp The filename to read the image data from
loc Location to seek to in the file before writing (size_t)
area The image region you want to read, default 0 means read the whole image
file_nx Image x size.
file_ny Image y size.
file_nz Image z size.
Author:
Steve Ludtke
Date:
Mon Jun 23, 2008

void scale_pixel float  scale_factor  )  const
 

Scale the angstrom per pixel of this image by a uniform amount Alters the EMData metadata I had to make this function public for access from the Processors (David Woolford).

Author:
Unknown

void set_attr const string &  key,
EMObject  val
 

Set a header attribute's value.

Parameters:
key The header attribute name.
val The attribute value.

Referenced by set_fftodd(), set_fftpad(), set_FH(), set_flipped(), and set_shuffled().

void set_attr_dict const Dict &  new_dict  ) 
 

Merge the new values with the existing dictionary.

Parameters:
new_dict The new attribute dictionary.

void set_attr_dict_explicit const Dict &  new_dict  )  [private]
 

Make the attributes of this EMData exactly equal to the argument dictionary Originally introduced because set_attr_dict does automatic resizing, which is undersirable in some circumstances.

Parameters:
new_dict The attribute dictionary that will become this image's attribute dictionary.

void set_attr_python const string &  key,
EMObject  val
 

Set a header attribute's value from Python.

Parameters:
key The header attribute name.
val The attribute value.

void set_changecount int  c  )  [inline]
 

Definition at line 943 of file emdata_metadata.h.

00944 {
00945         changecount = c;
00946 }

void set_complex bool  is_complex  )  [inline]
 

Mark this image as a complex image.

Parameters:
is_complex If true, a complex image. If false, a real image.

Definition at line 735 of file emdata_metadata.h.

Referenced by EMAN::Util::TwoDTestFunc().

00736 {
00737         if (is_complex) {
00738                 attr_dict["is_complex"] = int(1);
00739         }
00740         else {
00741                 attr_dict["is_complex"] = int(0);
00742         }
00743 }

void set_complex_size int  nx,
int  ny = 1,
int  nz = 1
 

Resize 'this' complex image.

Parameters:
nx x size of this image.
ny y size of this image.
nz z size of this image.

Definition at line 358 of file emdata_metadata.h.

References ny, and set_size().

00358                                                   {
00359         set_size(nx*2, ny, nz);
00360 }

void set_complex_x bool  is_complex_x  )  [inline]
 

Marks this image a 1D FFT image in X direction.

Parameters:
is_complex_x If true, a 1D FFT image in X direction; If false, not such an image.

Definition at line 770 of file emdata_metadata.h.

00771 {
00772         if (is_complex_x) {
00773                 attr_dict["is_complex_x"] = int(1);
00774         }
00775         else {
00776                 attr_dict["is_complex_x"] = int(0);
00777         }
00778 }

void set_ctf Ctf *  ctf  ) 
 

Set the CTF parameter of this image.

Parameters:
ctf The CTF parameter object.

void set_data float *  data,
const int  x,
const int  y,
const int  z
[inline]
 

Set the data explicitly data pointer must be allocated using malloc!

Parameters:
data a pointer to the pixel data which is stored in memory. Takes possession
x the number of pixels in the x direction
y the number of pixels in the y direction
z the number of pixels in the z direction

Definition at line 87 of file emdata_metadata.h.

References nx, ny, rdata, and update().

00087                                                                          {
00088         if (rdata) { EMUtil::em_free(rdata); rdata = 0; }
00089 #ifdef EMAN2_USING_CUDA
00090         free_cuda_memory();
00091 #endif
00092         rdata = data;
00093         nx = x; ny = y; nz = z;
00094         nxy = nx*ny;
00095         nxyz = nx*ny*nz;
00096         update();
00097 }

void set_data_pickle std::string  vf  ) 
 

void set_fftodd bool  is_fftodd  )  [inline]
 

Mark this image as having (real-space) odd nx.

Parameters:
is_fftodd If true, mark as nx odd; If false, mark as nx not odd.

Definition at line 905 of file emdata_metadata.h.

References set_attr().

00906 {
00907         if (is_fftodd) {
00908                 set_attr("is_fftodd", int(1));
00909         }
00910         else {
00911                 set_attr("is_fftodd", int(0));
00912         }
00913 }

void set_fftpad bool  is_fftpadded  )  [inline]
 

Mark this image as already extended along x for ffts.

Parameters:
is_fftpadded If true, mark as padded along x; If false, mark as not padded along x.

Definition at line 873 of file emdata_metadata.h.

References set_attr().

00874 {
00875         if (is_fftpadded) {
00876                 set_attr("is_fftpad", int(1));
00877         }
00878         else {
00879                 set_attr("is_fftpad", int(0));
00880         }
00881 }

void set_FH bool  is_FH  )  [inline]
 

Mark this complex image as a FH image.

Parameters:
is_FH If true, a FH image. If false, not a FH image.

Definition at line 718 of file emdata_metadata.h.

References set_attr().

00719 { // PRB
00720         if (is_FH) {
00721 //              flags |=  EMDATA_FH;
00722                 set_attr("is_fh", (int)1);
00723         }
00724         else {
00725 //              flags &= ~EMDATA_FH;
00726                 set_attr("is_fh", (int)0);
00727         }
00728 }

void set_flags int  f  )  [inline]
 

Definition at line 933 of file emdata_metadata.h.

00934 {
00935         flags = f;
00936 }

void set_flipped bool  is_flipped  )  [inline]
 

Mark this image as flipped.

Parameters:
is_flipped If true, mark this image as flipped; If false, mark this image as not flipped.

Definition at line 805 of file emdata_metadata.h.

References set_attr().

00806 {
00807         if (is_flipped) {
00808                 set_attr("is_flipped", (int)1);
00809         }
00810         else {
00811                 set_attr("is_flipped", (int)0);
00812         }
00813 }

void set_nxc int  nxc  )  [inline]
 

Set the number of complex elements along x.

Parameters:
nxc is the number of complex elements along x.

Definition at line 919 of file emdata_metadata.h.

00920 {
00921         attr_dict["nxc"] = nxc;
00922 }

void set_path const string &  new_path  )  [inline]
 

Set the path.

Parameters:
new_path The new path.

Definition at line 366 of file emdata_metadata.h.

00367 {
00368         path = new_path;
00369 }

void set_pathnum int  n  )  [inline]
 

Set the number of paths.

Parameters:
n The number of paths.

Definition at line 375 of file emdata_metadata.h.

00376 {
00377         pathnum = n;
00378 }

void set_ri bool  is_ri  )  [inline]
 

Mark this image as a real/imaginary format complex image.

Parameters:
is_ri If true, mark as real/imaginary format; If false, mark as amp/phase format.

Definition at line 840 of file emdata_metadata.h.

Referenced by EMAN::Util::TwoDTestFunc().

00841 {
00842         if (is_ri) {
00843                 attr_dict["is_complex_ri"] = int(1);
00844         }
00845         else {
00846                 attr_dict["is_complex_ri"] = int(0);
00847         }
00848 }

void set_rotation const Transform3D &  t3d  )  [inline]
 

Define the 3D orientation of this particle Orientation information is extracted from a Transform3D object and stored internally in EMAN (az,alt,phi) format.

Parameters:
t3d a Transform3D object containing the particle orientation

Definition at line 321 of file emdata_metadata.h.

00322 {
00323         Dict d = t3d.get_rotation(Transform3D::EMAN);
00324         attr_dict["orientation_convention"] = "EMAN";
00325         attr_dict["euler_alt"] = (float) d["alt"];
00326         attr_dict["euler_az"] = (float) d["az"];
00327         attr_dict["euler_phi"] = (float) d["phi"];;
00328 }

void set_rotation float  az,
float  alt,
float  phi
[inline]
 

Define the 3D orientation of this particle, also used to indicate relative rotations for reconstructions.

Parameters:
az 'az' Euler angle in EMAN convention.
alt 'alt' Euler angle in EMAN convention.
phi 'phi' Euler angle in EMAN convention.

Definition at line 307 of file emdata_metadata.h.

00308 {
00309     attr_dict["orientation_convention"] = "EMAN";
00310         attr_dict["euler_alt"]=alt;
00311         attr_dict["euler_az"]=az;
00312         attr_dict["euler_phi"]=phi;
00313 }

void set_shuffled bool  is_shuffled  )  [inline]
 

Mark this image as a shuffled image.

Parameters:
is_shuffled If true, a shuffled image. If false, not a shuffled image.

Definition at line 700 of file emdata_metadata.h.

References set_attr().

00701 { // PRB
00702         if (is_shuffled) {
00703 //              printf("entered correct part of set_shuffled \n");
00704 //              flags |=  EMDATA_SHUFFLE;
00705                 set_attr("is_shuffled", (int)1);
00706         }
00707         else {
00708 //              flags &= ~EMDATA_SHUFFLE;
00709                 set_attr("is_shuffled", (int)0);
00710         }
00711 }

void set_size int  nx,
int  ny = 1,
int  nz = 1
 

Resize this EMData's main board memory pointer.

Parameters:
nx x size of this image.
ny y size of this image.
nz z size of this image. $
Exceptions:
BadAllocException if memory allocation returns a null pointer

Referenced by set_complex_size().

void set_supp_pickle int  i  ) 
 

void set_translation float  dx,
float  dy,
float  dz
[inline]
 

Set 'this' images' translation vector from the original location.

Parameters:
dx The translation distance in x direction.
dy The translation distance in y direction.
dz The translation distance in z direction.

Definition at line 276 of file emdata_metadata.h.

00277 {
00278         all_translation = Vec3f(dx, dy, dz);
00279 }

void set_translation const Vec3f t  )  [inline]
 

Set 'this' images' translation vector from the original location.

Parameters:
t The new translation vector.

Definition at line 264 of file emdata_metadata.h.

00265 {
00266         all_translation = t;
00267 }

void set_xyzoff int  x,
int  y,
int  z
[inline]
 

Definition at line 963 of file emdata_metadata.h.

00964 {
00965         xoff = x;
00966         yoff = y;
00967         zoff = z;
00968 }

void update  )  [inline]
 

Mark EMData as changed, statistics, etc will be updated at need.

Definition at line 128 of file emdata_metadata.h.

Referenced by set_data(), and EMAN::Util::TwoDTestFunc().

00129 {
00130         flags |= EMDATA_NEEDUPD | EMDATA_GPU_NEEDS_UPDATE | EMDATA_GPU_RO_NEEDS_UPDATE;
00131         changecount++;
00132 }

void write_data string  fsp,
size_t  loc,
const Region *const   area = 0,
const int  file_nx = 0,
const int  file_ny = 0,
const int  file_nz = 0
 

Dump the image pixel data in native byte order to a disk file.

Parameters:
fsp The filename to write the image data to
loc Location to seek to in the file before writing (size_t)
area The image region you want to read, default 0 means read the whole image
file_nx Image x size.
file_ny Image y size.
file_nz Image z size.
Author:
Steve Ludtke
Date:
Mon Jun 23, 2008


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