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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
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 (const float threshold=0)
 Calculate the center of mass with a threshold (Default 0, so only positive values are considered).
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.
vector< Pixel > find_pixels_with_value (float val)
 Find pixels in the image with exactly the specified values.
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)
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)
float get_amplitude_thres (float thres)
 return the FFT amplitude which is greater than thres
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 const float  threshold = 0  ) 
 

Calculate the center of mass with a threshold (Default 0, so only positive values are considered).

Author:
Steve Ludtke
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

vector<Pixel> find_pixels_with_value float  val  ) 
 

Find pixels in the image with exactly the specified values.

Parameters:
val The value to look for
Returns:
An array of pixels with the specified values

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.

float get_amplitude_thres float  thres  ) 
 

return the FFT amplitude which is greater than thres

Exceptions:
ImageFormatException If the image is not a complex image.
Returns:
The FFT amplitude which is greater than thres .

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::update_centers().

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 943 of file emdata_metadata.h.

00944 {
00945         return changecount;
00946 }

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.

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 613 of file emdata_metadata.h.

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

00613                                                 {
00614         int size = get_size();
00615         vector<float> v(size);
00616         float* data = get_data();
00617         std::copy(data,data+size,v.begin());
00618         return v;
00619 }

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 933 of file emdata_metadata.h.

00934 {
00935         return flags;
00936 }

int get_ndim  )  const [inline]
 

Get image dimension.

Returns:
image dimension.

Definition at line 624 of file emdata_metadata.h.

References ny.

00625 {
00626         if (nz <= 1) {
00627                 if (ny <= 1) {
00628                         return 1;
00629                 }
00630                 else {
00631                         return 2;
00632                 }
00633         }
00634 
00635         return 3;
00636 }

string get_path  )  const [inline]
 

Definition at line 982 of file emdata_metadata.h.

00983 {
00984         return path;
00985 }

int get_pathnum  )  const [inline]
 

Definition at line 987 of file emdata_metadata.h.

00988 {
00989         return pathnum;
00990 }

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 605 of file emdata_metadata.h.

References nx, and ny.

Referenced by get_data_as_vector().

00606 {
00607         return (size_t)nx*(size_t)ny*(size_t)nz;
00608 }

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 290 of file emdata_metadata.h.

00291 {
00292         Dict rotation_dict;
00293         rotation_dict["type"] = "eman";
00294         rotation_dict["alt"] = attr_dict["euler_alt"];
00295         rotation_dict["az"] = attr_dict["euler_az"];
00296         rotation_dict["phi"] = attr_dict["euler_phi"];
00297 
00298         Transform trans;
00299         trans.to_identity();
00300         trans.set_rotation(rotation_dict);
00301 
00302         return trans;
00303 }

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 259 of file emdata_metadata.h.

00260 {
00261         return all_translation;
00262 }

int get_xoff  )  const [inline]
 

Definition at line 953 of file emdata_metadata.h.

00954 {
00955         return xoff;
00956 }

int get_xsize  )  const [inline]
 

Get the image x-dimensional size.

Returns:
Image x-dimensional size.

Definition at line 578 of file emdata_metadata.h.

Referenced by EMAN::KMeansAnalyzer::analyze(), and main().

00579 {
00580         return nx;
00581 }

int get_yoff  )  const [inline]
 

Definition at line 958 of file emdata_metadata.h.

00959 {
00960         return yoff;
00961 }

int get_ysize  )  const [inline]
 

Get the image y-dimensional size.

Returns:
Image y-dimensional size.

Definition at line 587 of file emdata_metadata.h.

Referenced by EMAN::KMeansAnalyzer::analyze().

00588 {
00589         return ny;
00590 }

int get_zoff  )  const [inline]
 

Definition at line 963 of file emdata_metadata.h.

00964 {
00965         return zoff;
00966 }

int get_zsize  )  const [inline]
 

Get the image z-dimensional size.

Returns:
Image z-dimensional size.

Definition at line 596 of file emdata_metadata.h.

Referenced by EMAN::KMeansAnalyzer::analyze().

00597 {
00598         return nz;
00599 }

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 540 of file emdata_metadata.h.

References key.

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

00540                                               {
00541         return attr_dict.has_key(key);
00542 }

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.

References has_attr().

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 676 of file emdata_metadata.h.

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

00677 {
00678         if(attr_dict.has_key("is_complex")) {
00679                 if (int(attr_dict["is_complex"])) {
00680                         return true;
00681                 }
00682                 else {
00683                         return false;
00684                 }
00685         }
00686         else {
00687                 return false;
00688         }
00689 }

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 755 of file emdata_metadata.h.

00756 {
00757         if(attr_dict.has_key("is_complex_x")) {
00758                 if (int(attr_dict["is_complex_x"])) {
00759                         return true;
00760                 }
00761                 else {
00762                         return false;
00763                 }
00764         }
00765         else {
00766                 return false;
00767         }
00768 }

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 892 of file emdata_metadata.h.

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

00893 {
00894         if(flags & EMDATA_FFTODD) {
00895                 return true;
00896         }
00897         else if( attr_dict.has_key("is_fftodd") && (int)attr_dict["is_fftodd"] == 1 ) {
00898                 return true;
00899         }
00900         else {
00901                 return false;
00902         }
00903 }

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 859 of file emdata_metadata.h.

References get_attr(), and has_attr().

00860 {
00861         if (flags & EMDATA_PAD) {
00862                 return true;
00863         }
00864 
00865         if(has_attr("is_fftpad")) {
00866                 return get_attr("is_fftpad");
00867         }
00868 
00869         return false;
00870 
00871 }

bool is_FH  )  const [inline]
 

Is this a FH image?

Returns:
Whether this is a FH image or not.

Definition at line 659 of file emdata_metadata.h.

References get_attr(), and has_attr().

00660 {  //     PRB
00661         if (flags & EMDATA_FH) {
00662                 return true;
00663         }
00664 
00665         if(has_attr("is_fh")) {
00666                 return get_attr("is_fh");
00667         }
00668 
00669         return false;
00670 }

bool is_flipped  )  const [inline]
 

Is this image flipped?

Returns:
Whether this image is flipped or not.

Definition at line 789 of file emdata_metadata.h.

References get_attr().

00790 {
00791         if (flags & EMDATA_FLIP) { //keep here for back compatibility
00792                 return true;
00793         }
00794 
00795         if(attr_dict.has_key("is_flipped")) {
00796                 if(get_attr("is_flipped")) {
00797                         return true;
00798                 }
00799         }
00800 
00801         return false;
00802 
00803 }

bool is_real  )  const [inline]
 

Is this a real image?

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

Definition at line 695 of file emdata_metadata.h.

References is_complex().

00696 {
00697         return !is_complex();
00698 }

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 825 of file emdata_metadata.h.

00826 {
00827         if(attr_dict.has_key("is_complex_ri")) {
00828                 if (int(attr_dict["is_complex_ri"])) {
00829                         return true;
00830                 }
00831                 else {
00832                         return false;
00833                 }
00834         }
00835         else {
00836                 return false;
00837         }
00838 }

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 642 of file emdata_metadata.h.

References get_attr(), and has_attr().

00643 {  //     PRB
00644         if (flags & EMDATA_SHUFFLE) {
00645                 return true;
00646         }
00647 
00648         if(has_attr("is_shuffled")) {
00649                 return get_attr("is_shuffled");
00650         }
00651 
00652         return false;
00653 }

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 948 of file emdata_metadata.h.

00949 {
00950         changecount = c;
00951 }

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 740 of file emdata_metadata.h.

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

00741 {
00742         if (is_complex) {
00743                 attr_dict["is_complex"] = int(1);
00744         }
00745         else {
00746                 attr_dict["is_complex"] = int(0);
00747         }
00748 }

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 363 of file emdata_metadata.h.

References nx, ny, and set_size().

00363                                                   {
00364         set_size(nx*2, ny, nz);
00365 }

void set_complex_x bool  is_complex_x  )  [inline]
 

Definition at line 775 of file emdata_metadata.h.

00776 {
00777         if (is_complex_x) {
00778                 attr_dict["is_complex_x"] = int(1);
00779         }
00780         else {
00781                 attr_dict["is_complex_x"] = int(0);
00782         }
00783 }

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 910 of file emdata_metadata.h.

References set_attr().

00911 {
00912         if (is_fftodd) {
00913                 set_attr("is_fftodd", int(1));
00914         }
00915         else {
00916                 set_attr("is_fftodd", int(0));
00917         }
00918 }

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 878 of file emdata_metadata.h.

References set_attr().

00879 {
00880         if (is_fftpadded) {
00881                 set_attr("is_fftpad", int(1));
00882         }
00883         else {
00884                 set_attr("is_fftpad", int(0));
00885         }
00886 }

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 723 of file emdata_metadata.h.

References set_attr().

00724 { // PRB
00725         if (is_FH) {
00726 //              flags |=  EMDATA_FH;
00727                 set_attr("is_fh", (int)1);
00728         }
00729         else {
00730 //              flags &= ~EMDATA_FH;
00731                 set_attr("is_fh", (int)0);
00732         }
00733 }

void set_flags int  f  )  [inline]
 

Definition at line 938 of file emdata_metadata.h.

00939 {
00940         flags = f;
00941 }

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 810 of file emdata_metadata.h.

References set_attr().

00811 {
00812         if (is_flipped) {
00813                 set_attr("is_flipped", (int)1);
00814         }
00815         else {
00816                 set_attr("is_flipped", (int)0);
00817         }
00818 }

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 924 of file emdata_metadata.h.

00925 {
00926         attr_dict["nxc"] = nxc;
00927 }

void set_path const string &  new_path  )  [inline]
 

Set the path.

Parameters:
new_path The new path.

Definition at line 371 of file emdata_metadata.h.

00372 {
00373         path = new_path;
00374 }

void set_pathnum int  n  )  [inline]
 

Set the number of paths.

Parameters:
n The number of paths.

Definition at line 380 of file emdata_metadata.h.

00381 {
00382         pathnum = n;
00383 }

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 845 of file emdata_metadata.h.

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

00846 {
00847         if (is_ri) {
00848                 attr_dict["is_complex_ri"] = int(1);
00849         }
00850         else {
00851                 attr_dict["is_complex_ri"] = int(0);
00852         }
00853 }

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 326 of file emdata_metadata.h.

00327 {
00328         Dict d = t3d.get_rotation(Transform3D::EMAN);
00329         attr_dict["orientation_convention"] = "EMAN";
00330         attr_dict["euler_alt"] = (float) d["alt"];
00331         attr_dict["euler_az"] = (float) d["az"];
00332         attr_dict["euler_phi"] = (float) d["phi"];;
00333 }

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 312 of file emdata_metadata.h.

00313 {
00314     attr_dict["orientation_convention"] = "EMAN";
00315         attr_dict["euler_alt"]=alt;
00316         attr_dict["euler_az"]=az;
00317         attr_dict["euler_phi"]=phi;
00318 }

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 705 of file emdata_metadata.h.

References set_attr().

00706 { // PRB
00707         if (is_shuffled) {
00708 //              printf("entered correct part of set_shuffled \n");
00709 //              flags |=  EMDATA_SHUFFLE;
00710                 set_attr("is_shuffled", (int)1);
00711         }
00712         else {
00713 //              flags &= ~EMDATA_SHUFFLE;
00714                 set_attr("is_shuffled", (int)0);
00715         }
00716 }

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 281 of file emdata_metadata.h.

References EMAN::Vec3f.

00282 {
00283         all_translation = Vec3f(dx, dy, dz);
00284 }

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 269 of file emdata_metadata.h.

00270 {
00271         all_translation = t;
00272 }

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

Definition at line 968 of file emdata_metadata.h.

00969 {
00970         xoff = x;
00971         yoff = y;
00972         zoff = z;
00973 }

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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