EMAN2
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A processor designed specifically for tomographic tilt series data. More...
#include <processor.h>
Classes | |
class | GaussianFunctoid |
Public Member Functions | |
virtual void | process_inplace (EMData *image) |
To process an image in-place. More... | |
virtual string | get_name () const |
Get the processor's name. More... | |
virtual TypeDict | get_param_types () const |
Get processor parameter information in a dictionary. More... | |
virtual string | get_desc () const |
Get the descrition of this specific processor. More... | |
Public Member Functions inherited from EMAN::Processor | |
virtual | ~Processor () |
virtual EMData * | process (const EMData *const image) |
To proccess an image out-of-place. More... | |
virtual void | process_list_inplace (vector< EMData * > &images) |
To process multiple images using the same algorithm. More... | |
virtual Dict | get_params () const |
Get the processor parameters in a key/value dictionary. More... | |
virtual void | set_params (const Dict &new_params) |
Set the processor parameters using a key/value dictionary. More... | |
Static Public Member Functions | |
static Processor * | NEW () |
Static Public Member Functions inherited from EMAN::Processor | |
static string | get_group_desc () |
Get the description of this group of processors. More... | |
static void | EMFourierFilterInPlace (EMData *fimage, Dict params) |
Compute a Fourier-filter processed image in place. More... | |
static EMData * | EMFourierFilter (EMData *fimage, Dict params) |
Compute a Fourier-processor processed image without altering the original image. More... | |
Static Public Attributes | |
static const string | NAME = "tomo.tiltedgemask" |
Additional Inherited Members | |
Public Types inherited from EMAN::Processor | |
enum | fourier_filter_types { TOP_HAT_LOW_PASS , TOP_HAT_HIGH_PASS , TOP_HAT_BAND_PASS , TOP_HOMOMORPHIC , GAUSS_LOW_PASS , GAUSS_HIGH_PASS , GAUSS_BAND_PASS , GAUSS_INVERSE , GAUSS_HOMOMORPHIC , BUTTERWORTH_LOW_PASS , BUTTERWORTH_HIGH_PASS , BUTTERWORTH_HOMOMORPHIC , KAISER_I0 , KAISER_SINH , KAISER_I0_INVERSE , KAISER_SINH_INVERSE , SHIFT , TANH_LOW_PASS , TANH_HIGH_PASS , TANH_HOMOMORPHIC , TANH_BAND_PASS , RADIAL_TABLE , CTF_ } |
Fourier filter Processor type enum. More... | |
Protected Attributes inherited from EMAN::Processor | |
Dict | params |
A processor designed specifically for tomographic tilt series data.
This processors masks out 'mass' in tilted images that is not present in the zero-tilt (0 degrees) image. It does this based on the tilt angle. The tilt angle can be extracted from the image metadata (stored as the euler_alt attribute), or it may be specified explicitly (specifying the angle is the default behavior). The masked out regions at both sides of the image are set to 0 by default, but can also be set to the mean of the nearest non-masked data edge (in the y direction), or similarly the mean of both non-masked data edges on either side of the image. A gaussian fall-off is optional (but off by default).
biedgemean | Mutually exclusive of edgemean. Experimental. Causes the pixels in the masked out areas to take the average value of both the left and right edge pixel strips |
edgemean | Mutually exclusive of biedgemean. Masked pixels values assume the mean edge pixel value, independently, for both sides of the image |
angle | The angle that the image is, with respect to the zero tilt image |
angle_fim | Read fim as 'from image metadata' - this causes the altitude angle stored in by the image object (i.e. as extracted from the header, as currently stored in memory) to be used as the angle. This overrides the angle argument |
gauss_falloff | Causes the edge masking to have a smooth Gaussian fall-off - this parameter specifies how many pixels the fall-off will proceed over. Default is 0 |
gauss_sigma | The sigma of the Gaussian function used to smooth the edge fall-off (functional form is exp(-(pixel distance)^2/sigma^2) |
Definition at line 9005 of file processor.h.
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inlinevirtual |
Get the descrition of this specific processor.
This function must be overwritten by a subclass.
Implements EMAN::Processor.
Definition at line 9032 of file processor.h.
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inlinevirtual |
Get the processor's name.
Each processor is identified by a unique name.
Implements EMAN::Processor.
Definition at line 9010 of file processor.h.
References NAME.
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inlinevirtual |
Get processor parameter information in a dictionary.
Each parameter has one record in the dictionary. Each record contains its name, data-type, and description.
Reimplemented from EMAN::Processor.
Definition at line 9020 of file processor.h.
References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().
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inlinestatic |
Definition at line 9015 of file processor.h.
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virtual |
To process an image in-place.
For those processors which can only be processed out-of-place, override this function to just print out some error message to remind user call the out-of-place version.
image | The image to be processed. |
Implements EMAN::Processor.
Definition at line 12776 of file processor.cpp.
References EMAN::Transform::get_params(), InvalidParameterException, EMAN::Processor::params, and EMAN::Dict::set_default().
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static |
Definition at line 9037 of file processor.h.
Referenced by get_name().