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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 * | 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 | set_data (float *data) | |||
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. | ||||
void | clearupdate () | |||
turn off updates. | ||||
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. | ||||
vector< float > | calc_max_location_wrap_intp (const int maxshiftx=-1, const int maxshifty=-1, const int maxshiftz=-1) | |||
Calculates the wrapped coordinates of the maximum value, and uses quadration intp to subpixel prec 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). | ||||
size_t | calc_min_index () const | |||
Calculates the index of minimum-value pixel when assuming all pixels are in a 1D array. | ||||
size_t | 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 Transform &t3d) | |||
Define the 3D orientation of this particle Orientation information is extracted from a Transform object and stored internally in EMAN (az,alt,phi) format. | ||||
void | set_size (int nx, int ny=1, int nz=1, bool noalloc=false) | |||
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. |
size_t 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.
vector<float> calc_max_location_wrap_intp | ( | const int | maxshiftx = -1 , |
|
const int | maxshifty = -1 , |
|||
const int | maxshiftz = -1 | |||
) |
Calculates the wrapped coordinates of the maximum value, and uses quadration intp to subpixel prec 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.
size_t 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 clearupdate | ( | ) | [inline] |
turn off updates.
Useful to avoid wasteful recacling stats
Definition at line 150 of file emdata_metadata.h.
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(), EMAN::Util::constrained_helix(), EMAN::Util::constrained_helix_test(), is_fftpadded(), is_FH(), is_flipped(), is_shuffled(), EMAN::Util::multiref_polar_ali_2d_local(), EMAN::Util::multiref_polar_ali_2d_local_psi(), EMAN::Util::multiref_polar_ali_helical_90_local(), EMAN::Util::multiref_polar_ali_helical_local(), 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* get_const_data | ( | ) | const [inline] |
Get the image pixel density data in a 1D float array - const version of get_data.
Definition at line 89 of file emdata_metadata.h.
References get_data().
00089 { 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 83 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().
00083 { return rdata; }
vector<float> get_data_as_vector | ( | ) | const [inline] |
Get the pixel data as a vector.
Definition at line 651 of file emdata_metadata.h.
References copy(), data, get_data(), get_size(), and v.
00651 { 00652 int size = get_size(); 00653 vector<float> v(size); 00654 float* data = get_data(); 00655 std::copy(data,data+size,v.begin()); 00656 return v; 00657 }
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 662 of file emdata_metadata.h.
References ny.
00663 { 00664 if (nz <= 1) { 00665 if (ny <= 1) { 00666 return 1; 00667 } 00668 else { 00669 return 2; 00670 } 00671 } 00672 00673 return 3; 00674 }
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 643 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 320 of file emdata_metadata.h.
00321 { 00322 Dict rotation_dict; 00323 rotation_dict["type"] = "eman"; 00324 rotation_dict["alt"] = attr_dict["euler_alt"]; 00325 rotation_dict["az"] = attr_dict["euler_az"]; 00326 rotation_dict["phi"] = attr_dict["euler_phi"]; 00327 00328 Transform trans; 00329 trans.to_identity(); 00330 trans.set_rotation(rotation_dict); 00331 00332 return trans; 00333 }
Vec3f get_translation | ( | ) | const [inline] |
Get 'this' image's translation vector from the original location.
Definition at line 289 of file emdata_metadata.h.
int get_xoff | ( | ) | const [inline] |
int get_xsize | ( | ) | const [inline] |
Get the image x-dimensional size.
Definition at line 616 of file emdata_metadata.h.
References nx.
Referenced by EMAN::KMeansAnalyzer::analyze(), main(), and median().
00617 { 00618 return nx; 00619 }
int get_yoff | ( | ) | const [inline] |
int get_ysize | ( | ) | const [inline] |
Get the image y-dimensional size.
Definition at line 625 of file emdata_metadata.h.
References ny.
Referenced by EMAN::KMeansAnalyzer::analyze(), and median().
00626 { 00627 return ny; 00628 }
int get_zoff | ( | ) | const [inline] |
int get_zsize | ( | ) | const [inline] |
Get the image z-dimensional size.
Definition at line 634 of file emdata_metadata.h.
Referenced by EMAN::KMeansAnalyzer::analyze(), 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 570 of file emdata_metadata.h.
Referenced by is_fftpadded(), is_FH(), and is_shuffled().
00570 { 00571 return attr_dict.has_key(key); 00572 }
bool has_ctff | ( | ) | const [inline] |
check whether the image physical file has the CTF info or not.
Definition at line 159 of file emdata_metadata.h.
00160 { 00161 if (this->has_attr("ctf")) { 00162 return true; 00163 } 00164 else { 00165 return false; 00166 } 00167 }
bool is_complex | ( | ) | const [inline] |
Is this a complex image?
Definition at line 714 of file emdata_metadata.h.
Referenced by is_real(), EMAN::TestUtil::make_image_file_by_mode(), and EMAN::TestUtil::verify_image_file_by_mode().
00715 { 00716 if(attr_dict.has_key("is_complex")) { 00717 if (int(attr_dict["is_complex"])) { 00718 return true; 00719 } 00720 else { 00721 return false; 00722 } 00723 } 00724 else { 00725 return false; 00726 } 00727 }
bool is_complex_x | ( | ) | const [inline] |
Is this image a 1D FFT image in X direction?
Definition at line 793 of file emdata_metadata.h.
00794 { 00795 if(attr_dict.has_key("is_complex_x")) { 00796 if (int(attr_dict["is_complex_x"])) { 00797 return true; 00798 } 00799 else { 00800 return false; 00801 } 00802 } 00803 else { 00804 return false; 00805 } 00806 }
bool is_fftodd | ( | ) | const [inline] |
Does this image correspond to a (real-space) odd nx?
Definition at line 930 of file emdata_metadata.h.
Referenced by EMAN::FourierReconstructor::setup(), EMAN::FourierReconstructorSimple2D::setup(), and EMAN::FourierReconstructor::setup_seed().
00931 { 00932 if(flags & EMDATA_FFTODD) { 00933 return true; 00934 } 00935 else if( attr_dict.has_key("is_fftodd") && (int)attr_dict["is_fftodd"] == 1 ) { 00936 return true; 00937 } 00938 else { 00939 return false; 00940 } 00941 }
bool is_fftpadded | ( | ) | const [inline] |
Is this image already extended along x for ffts?
Definition at line 897 of file emdata_metadata.h.
References get_attr(), and has_attr().
00898 { 00899 if (flags & EMDATA_PAD) { 00900 return true; 00901 } 00902 00903 if(has_attr("is_fftpad")) { 00904 return get_attr("is_fftpad"); 00905 } 00906 00907 return false; 00908 00909 }
bool is_FH | ( | ) | const [inline] |
Is this a FH image?
Definition at line 697 of file emdata_metadata.h.
References get_attr(), and has_attr().
00698 { // PRB 00699 if (flags & EMDATA_FH) { 00700 return true; 00701 } 00702 00703 if(has_attr("is_fh")) { 00704 return get_attr("is_fh"); 00705 } 00706 00707 return false; 00708 }
bool is_flipped | ( | ) | const [inline] |
Is this image flipped?
Definition at line 827 of file emdata_metadata.h.
References get_attr().
00828 { 00829 if (flags & EMDATA_FLIP) { //keep here for back compatibility 00830 return true; 00831 } 00832 00833 if(attr_dict.has_key("is_flipped")) { 00834 if(get_attr("is_flipped")) { 00835 return true; 00836 } 00837 } 00838 00839 return false; 00840 00841 }
bool is_real | ( | ) | const [inline] |
Is this a real image?
Definition at line 733 of file emdata_metadata.h.
References is_complex().
00734 { 00735 return !is_complex(); 00736 }
bool is_ri | ( | ) | const [inline] |
Is this image a real/imaginary format complex image?
Definition at line 863 of file emdata_metadata.h.
00864 { 00865 if(attr_dict.has_key("is_complex_ri")) { 00866 if (int(attr_dict["is_complex_ri"])) { 00867 return true; 00868 } 00869 else { 00870 return false; 00871 } 00872 } 00873 else { 00874 return false; 00875 } 00876 }
bool is_shuffled | ( | ) | const [inline] |
Has this image been shuffled?
Definition at line 680 of file emdata_metadata.h.
References get_attr(), and has_attr().
00681 { // PRB 00682 if (flags & EMDATA_SHUFFLE) { 00683 return true; 00684 } 00685 00686 if(has_attr("is_shuffled")) { 00687 return get_attr("is_shuffled"); 00688 } 00689 00690 return false; 00691 }
void read_data | ( | string | fsp, | |
size_t | loc, | |||
const Region * | area = 0 , |
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const int | file_nx = 0 , |
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const int | file_ny = 0 , |
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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 778 of file emdata_metadata.h.
Referenced by EMAN::Util::TwoDTestFunc().
00779 { 00780 if (is_complex) { 00781 attr_dict["is_complex"] = int(1); 00782 } 00783 else { 00784 attr_dict["is_complex"] = int(0); 00785 } 00786 }
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 393 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 813 of file emdata_metadata.h.
00814 { 00815 if (is_complex_x) { 00816 attr_dict["is_complex_x"] = int(1); 00817 } 00818 else { 00819 attr_dict["is_complex_x"] = int(0); 00820 } 00821 }
void set_ctf | ( | Ctf * | ctf | ) |
Set the CTF parameter of this image.
ctf | The CTF parameter object. |
void set_data | ( | float * | data | ) | [inline] |
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 98 of file emdata_metadata.h.
References nx, ny, rdata, and update().
00098 { 00099 if (rdata) { EMUtil::em_free(rdata); rdata = 0; } 00100 #ifdef EMAN2_USING_CUDA 00101 //cout << "set data" << endl; 00102 // free_cuda_memory(); 00103 #endif 00104 rdata = data; 00105 nx = x; ny = y; nz = z; 00106 nxy = nx*ny; 00107 nxyz = (size_t)nx*ny*nz; 00108 update(); 00109 }
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 948 of file emdata_metadata.h.
References set_attr().
00949 { 00950 if (is_fftodd) { 00951 set_attr("is_fftodd", int(1)); 00952 } 00953 else { 00954 set_attr("is_fftodd", int(0)); 00955 } 00956 }
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 916 of file emdata_metadata.h.
References set_attr().
00917 { 00918 if (is_fftpadded) { 00919 set_attr("is_fftpad", int(1)); 00920 } 00921 else { 00922 set_attr("is_fftpad", int(0)); 00923 } 00924 }
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 761 of file emdata_metadata.h.
References set_attr().
00762 { // PRB 00763 if (is_FH) { 00764 // flags |= EMDATA_FH; 00765 set_attr("is_fh", (int)1); 00766 } 00767 else { 00768 // flags &= ~EMDATA_FH; 00769 set_attr("is_fh", (int)0); 00770 } 00771 }
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 848 of file emdata_metadata.h.
References set_attr().
00849 { 00850 if (is_flipped) { 00851 set_attr("is_flipped", (int)1); 00852 } 00853 else { 00854 set_attr("is_flipped", (int)0); 00855 } 00856 }
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 962 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 410 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 883 of file emdata_metadata.h.
Referenced by EMAN::Util::TwoDTestFunc().
00884 { 00885 if (is_ri) { 00886 attr_dict["is_complex_ri"] = int(1); 00887 } 00888 else { 00889 attr_dict["is_complex_ri"] = int(0); 00890 } 00891 }
void set_rotation | ( | const Transform & | t3d | ) | [inline] |
Define the 3D orientation of this particle Orientation information is extracted from a Transform object and stored internally in EMAN (az,alt,phi) format.
t3d | a Transform object containing the particle orientation |
Definition at line 356 of file emdata_metadata.h.
00357 { 00358 Dict d = t3d.get_rotation("eman"); 00359 attr_dict["orientation_convention"] = "EMAN"; 00360 attr_dict["euler_alt"] = (float) d["alt"]; 00361 attr_dict["euler_az"] = (float) d["az"]; 00362 attr_dict["euler_phi"] = (float) d["phi"];; 00363 }
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 342 of file emdata_metadata.h.
00343 { 00344 attr_dict["orientation_convention"] = "EMAN"; 00345 attr_dict["euler_alt"]=alt; 00346 attr_dict["euler_az"]=az; 00347 attr_dict["euler_phi"]=phi; 00348 }
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 743 of file emdata_metadata.h.
References set_attr().
00744 { // PRB 00745 if (is_shuffled) { 00746 // printf("entered correct part of set_shuffled \n"); 00747 // flags |= EMDATA_SHUFFLE; 00748 set_attr("is_shuffled", (int)1); 00749 } 00750 else { 00751 // flags &= ~EMDATA_SHUFFLE; 00752 set_attr("is_shuffled", (int)0); 00753 } 00754 }
void set_size | ( | int | nx, | |
int | ny = 1 , |
|||
int | nz = 1 , |
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bool | noalloc = false | |||
) |
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 311 of file emdata_metadata.h.
00312 { 00313 all_translation = Vec3f(dx, dy, dz); 00314 }
void set_translation | ( | const Vec3f & | t | ) | [inline] |
Set 'this' images' translation vector from the original location.
t | The new translation vector. |
Definition at line 299 of file emdata_metadata.h.
00300 { 00301 all_translation = t; 00302 }
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 143 of file emdata_metadata.h.
Referenced by EMAN::RotateInFSProcessor::process_inplace(), set_data(), and EMAN::Util::TwoDTestFunc().
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. |