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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 () | |||
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. | ||||
MCArray3D * | get_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< Vec3i > | mask_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. |
float calc_center_density | ( | ) |
Calculates the density value at the peak of the image histogram, sort of like the mode of the density.
FloatPoint calc_center_of_mass | ( | ) |
Calculate the center of mass using an algorithm written by S Ludtke.
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.
threshold | The specified pixel value. Returned pixels should have higher values than it. |
int calc_max_index | ( | ) | const |
Calculates the index of maximum-value pixel when assuming all pixels are in a 1D array.
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.
int calc_min_index | ( | ) | const |
Calculates the index of minimum-value pixel when assuming all pixels are in a 1D array.
IntPoint calc_min_location | ( | ) | const |
Calculates 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.
n | The number of highest value pixels should be returned. |
float calc_sigma_diff | ( | ) |
Calculates sigma above and below the mean and returns the difference between them.
void del_attr | ( | const string & | attr_name | ) |
Delete the attribute from dictionary.
attr_name | the attribute name to be removed |
void del_attr_dict | ( | const vector< string > & | del_keys | ) |
Delete the attributes from the dictionary.
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.
x0 | X-axis translation amount. | |
y0 | Y-axis translation amount. |
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.
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.
x0 | X-axis translation amount. | |
y0 | Y-axis translation amount. |
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.
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.
x0 | X-axis translation amount. | |
y0 | Y-axis translation amount. | |
z0 | Z-axis translation amount. |
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.
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.
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.
x0 | X-axis translation amount. | |
y0 | Y-axis translation amount. | |
z0 | Z-axis translation amount. |
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.
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.
attr_name | The header attribute name. |
NotExistingObjectException | when attribute not exist |
Referenced by ali3d_d(), is_fftpadded(), is_FH(), is_flipped(), is_shuffled(), EMAN::Util::multiref_polar_ali_2d_local(), EMAN::Util::multiref_polar_ali_2d_local_psi(), EMAN::KMeansAnalyzer::reseed(), 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.
attr_name | The header attribute name. | |
em_obj | the default attribute to return when this attr_name not exist in attr_dict |
Dict get_attr_dict | ( | ) | const |
Get the image attribute dictionary containing all the image attribute names and attribute values.
int get_changecount | ( | ) | const [inline] |
float get_circle_mean | ( | ) |
Calculates the circular edge mean by applying a circular mask on 'this' image.
const float* const get_const_data | ( | ) | const [inline] |
Get the image pixel density data in a 1D float array - const version of get_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.
float* get_data | ( | ) | const [inline] |
Get the image pixel density data in a 1D float array.
Definition at line 72 of file emdata_metadata.h.
References rdata.
Referenced by CleanStack(), CleanStack_Cart(), cmplx(), EMAN::Util::ener_tot(), get_const_data(), get_data_as_vector(), get_value_at(), EMAN::PCA::Lanczos(), EMAN::EMUtil::make_image_median(), operator()(), ReadStackandDist_Cart(), set_value_at(), set_value_at_fast(), and unified().
00072 { return rdata; }
vector<float> get_data_as_vector | ( | ) | const [inline] |
Get the pixel data as a vector.
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.
EMData* get_fft_amplitude | ( | ) |
return the amplitudes of the FFT including the left half
ImageFormatException | If the image is not a complex image. |
EMData* get_fft_amplitude2D | ( | ) |
return the amplitudes of the 2D FFT including the left half PRB
ImageFormatException | If the image is not a complex image. |
EMData* get_fft_phase | ( | ) |
return the phases of the FFT including the left half
ImageFormatException | If the image is not a complex image. |
int get_flags | ( | ) | const [inline] |
int get_ndim | ( | ) | const [inline] |
Get 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] |
int get_pathnum | ( | ) | const [inline] |
size_t get_size | ( | ) | const [inline] |
Get the number of allocated floats in the image (nx*ny*nz).
Definition at line 600 of file emdata_metadata.h.
Referenced by get_data_as_vector().
int get_supp_pickle | ( | ) | const |
Transform get_transform | ( | ) | const [inline] |
Get 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.
Definition at line 254 of file emdata_metadata.h.
int get_xoff | ( | ) | const [inline] |
int get_xsize | ( | ) | const [inline] |
Get the image x-dimensional size.
Definition at line 573 of file emdata_metadata.h.
References nx.
Referenced by EMAN::KMeansAnalyzer::analyze(), EMAN::MarchingCubes::draw_cube(), main(), and median().
00574 { 00575 return nx; 00576 }
int get_yoff | ( | ) | const [inline] |
int get_ysize | ( | ) | const [inline] |
Get the image y-dimensional size.
Definition at line 582 of file emdata_metadata.h.
References ny.
Referenced by EMAN::KMeansAnalyzer::analyze(), EMAN::MarchingCubes::draw_cube(), and median().
00583 { 00584 return ny; 00585 }
int get_zoff | ( | ) | const [inline] |
int get_zsize | ( | ) | const [inline] |
Get the image z-dimensional size.
Definition at line 591 of file emdata_metadata.h.
Referenced by EMAN::KMeansAnalyzer::analyze(), EMAN::MarchingCubes::draw_cube(), and median().
bool has_attr | ( | const string & | key | ) | const [inline] |
Ask if the header has a particular attribute.
key | the header attribute name |
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.
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?
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?
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?
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?
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?
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?
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?
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?
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?
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 }
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.
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. |
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).
void set_attr | ( | const string & | key, | |
EMObject | val | |||
) |
Set a header attribute's value.
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.
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.
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.
key | The header attribute name. | |
val | The attribute value. |
void set_changecount | ( | int | c | ) | [inline] |
void set_complex | ( | bool | is_complex | ) | [inline] |
Mark this image as a complex image.
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.
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().
void set_complex_x | ( | bool | is_complex_x | ) | [inline] |
Marks this image a 1D FFT image in X direction.
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.
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!
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.
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.
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.
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] |
void set_flipped | ( | bool | is_flipped | ) | [inline] |
Mark this image as flipped.
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.
nxc | is the number of complex elements along x. |
Definition at line 919 of file emdata_metadata.h.
void set_path | ( | const string & | new_path | ) | [inline] |
void set_pathnum | ( | int | n | ) | [inline] |
Set the number of paths.
n | The number of paths. |
Definition at line 375 of file emdata_metadata.h.
void set_ri | ( | bool | is_ri | ) | [inline] |
Mark this image as a real/imaginary format complex image.
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.
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.
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.
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.
nx | x size of this image. | |
ny | y size of this image. | |
nz | z size of this image. $ |
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.
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.
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] |
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.
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. |