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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. | ||||
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) | |||
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. |
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 | ( | const float | threshold = 0 |
) |
Calculate the center of mass with a threshold (Default 0, so only positive values are considered).
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 |
vector<Pixel> find_pixels_with_value | ( | float | val | ) |
Find pixels in the image with exactly the specified values.
val | The value to look for |
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.
float get_amplitude_thres | ( | float | thres | ) |
return the FFT amplitude which is greater than thres %
ImageFormatException | If the image is not a complex image. |
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 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.
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 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] |
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 605 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 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.
Definition at line 259 of file emdata_metadata.h.
int get_xoff | ( | ) | const [inline] |
int get_xsize | ( | ) | const [inline] |
Get the image x-dimensional size.
Definition at line 578 of file emdata_metadata.h.
References nx.
Referenced by EMAN::KMeansAnalyzer::analyze(), EMAN::MarchingCubes::draw_cube(), main(), and median().
00579 { 00580 return nx; 00581 }
int get_yoff | ( | ) | const [inline] |
int get_ysize | ( | ) | const [inline] |
Get the image y-dimensional size.
Definition at line 587 of file emdata_metadata.h.
References ny.
Referenced by EMAN::KMeansAnalyzer::analyze(), EMAN::MarchingCubes::draw_cube(), and median().
00588 { 00589 return ny; 00590 }
int get_zoff | ( | ) | const [inline] |
int get_zsize | ( | ) | const [inline] |
Get the image z-dimensional size.
Definition at line 596 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 540 of file emdata_metadata.h.
Referenced by 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.
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 676 of file emdata_metadata.h.
Referenced by 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?
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?
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?
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?
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?
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?
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?
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?
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 }
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 EMAN::KMeansAnalyzer::analyze(), set_fftodd(), set_fftpad(), set_FH(), set_flipped(), set_shuffled(), and EMAN::KMeansAnalyzer::update_centers().
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 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.
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 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 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.
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 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.
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.
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] |
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 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.
nxc | is the number of complex elements along x. |
Definition at line 924 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 380 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 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.
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.
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.
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.
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 281 of file emdata_metadata.h.
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.
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] |
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. |