Header file for image processing from micrograph structures. More...

#include "mg_processing.h"
#include "rwimg.h"

Functions
Bstring	image_type (Bstring type)
	Converts an image type string to a standard form. More...

Bproject *	project_create_from_image (Bimage *p, Bstring type)
	Creates a project structure using image file names. More...

Bproject *	project_create_from_images (Bstring *file_list, Bstring type)
	Creates a project structure using image file names. More...

double	micrograph_intensity (Bmicrograph mg, Bimage p, int flag)
	Gets the average of a micrograph and sets the dose. More...

double	micrograph_intensity (Bmicrograph *mg, int flag=0)
	Gets the average of a micrograph and sets the dose. More...

int	project_mg_avg_intensities (Bproject *project)
	Retrieves the average micrograph intensities. More...

int	project_catenate_micrographs (Bproject *project)
	Concatenates all micrograph image files into one file. More...

Bimage *	particle_read_img (Bparticle *part, int readflag)
	Reads a particle image file. More...

int	particle_write_img (Bparticle part, Bimage p, int compression)
	Writes a particle image file. More...

int	project_check_particles (Bproject *project)
	Checks particle numbers and box sizes. More...

Vector3< long >	micrograph_get_size (Bmicrograph *mg)
	Gets the size of a micrograph. More...

Vector3< double >	micrograph_get_nominal_origin (Bmicrograph *mg)
	Gets the nominal origin for a micrograph. More...

int	project_set_nominal_mg_origins (Bproject *project)
	Sets micrograph origins to the centers of the micrographs. More...

int	project_reset_origins (Bproject *project)
	Resets particle origins to nominal values. More...

int	project_set_part_img_origins (Bproject *project)
	Writes particle origins into particle image files. More...

long	project_delesect_edge_particles (Bproject *project)
	Deselects particles that are too close to the image edges. More...

int	project_get_part_box_size (Bproject *project)
	Gets the box size from particle image files. More...

Vector3< long >	particle_get_box_size (Bparticle *part)
	Gets the box size from particle image file. More...

int	project_write_particle_classes (Bproject *project)
	Writes particles to different stacks based on class. More...

int	project_trim_class_averages (Bproject *project, Bstring &list)
	Deletes selected class averages from the project.. More...

int	project_flip_particle_coordinates (Bproject *project, int flip)
	Reverses one or more particle coordinates. More...

int	project_set_views_from_images (Bproject *project)
	Gets views from particle images. More...

int	project_set_views_in_images (Bproject *project)
	Sets views in particle images from the project parameter structure. More...

int	project_bin_micrographs (Bproject *project, int bin, Bstring mgpath, Bstring partpath)
	Bins all micrographs a project. More...

int	project_change_pixel_size (Bproject *project, Vector3< double > new_pixel_size, Bstring mgpath, Bstring partpath)
	Changes all the micrograph fields linked to the pixel size. More...

Detailed Description

Header file for image processing from micrograph structures.

Author: Bernard Heymann

Date: Created: 20000426; Modified: 20210722

Function Documentation

◆ image_type()

Bstring image_type ( Bstring type )

Converts an image type string to a standard form.

Parameters

type	a string with a type definition.

Returns

Bstring standard type definition.

The input string is converted to the following strings:
mg      micrograph
frame   micrograph frames
rec     reconstruction
part    particle
fil     filament
ps      power spectrum
ft      Fourier transform

◆ micrograph_get_nominal_origin()

Vector3< double > micrograph_get_nominal_origin ( Bmicrograph * mg )

Gets the nominal origin for a micrograph.

Parameters

*mg	micrograph parameter structure.

Returns

Vector3<double> nominal origin.

The nominal origin is defined as the center of the micrograph.

◆ micrograph_get_size()

Vector3< long > micrograph_get_size ( Bmicrograph * mg )

Gets the size of a micrograph.

Parameters

*mg	micrograph parameter structure.

Returns

Vector3<long> size.

The micrograph image header is read.

◆ micrograph_intensity() [1/2]

double micrograph_intensity	(	Bmicrograph *	mg,
		Bimage *	p,
		int	flag
	)

Gets the average of a micrograph and sets the dose.

Parameters

*mg	micrograph parameter structure.
*p	image.
flag	1=force calculation of statistics of not available; 2=check Poisson

Returns

double intensity.

The micrograph image header is read.

◆ micrograph_intensity() [2/2]

double micrograph_intensity	(	Bmicrograph *	mg,
		int	flag
	)

Gets the average of a micrograph and sets the dose.

Parameters

*mg	micrograph parameter structure.
flag	flag to force calculation of statistics of not available.

Returns

double intensity.

The micrograph image header is read.

◆ particle_get_box_size()

Vector3< long > particle_get_box_size ( Bparticle * part )

Gets the box size from particle image file.

Parameters

*part particle.

Returns

Vector3<long> box size (0 if image does not exist).

Reads the particle file header and returns the box size.

◆ particle_read_img()

Bimage * particle_read_img	(	Bparticle *	part,
		int	readflag
	)

Reads a particle image file.

Parameters

*part	particle.
readflag	flag to indicate reading the data.

Returns

Bimage* image (NULL means failure).

The file name is taken from the particle record by preference,
otherwise from the micrograph record.

◆ particle_write_img()

int particle_write_img	(	Bparticle *	part,
		Bimage *	p,
		int	compression
	)

Writes a particle image file.

Parameters

*part	particle.
*p	image to be written.
compression	flag to indicate compression.

Returns

int images written.

The file name is taken from the particle record by preference,
otherwise from the micrograph record.

◆ project_bin_micrographs()

int project_bin_micrographs	(	Bproject *	project,
		int	bin,
		Bstring	mgpath,
		Bstring	partpath
	)

Bins all micrographs a project.

Parameters

*project	project parameter structure.
bin	binning value.
mgpath	binned micrograph path (must be allocated).
partpath	binned particle path (must be allocated).

Returns

int 0.

All micrographs in a project are binned by the indicated value.
New micrograph file names are generated with a "_b<n>" insert,
where the n indicates the bin value.
The path to the binned micrograph can be specified.

◆ project_catenate_micrographs()

int project_catenate_micrographs ( Bproject * project )

Concatenates all micrograph image files into one file.

Parameters

*project project structure.

Returns

int 0.

The new file name is the common part of the original
micrograph file names.

◆ project_change_pixel_size()

int project_change_pixel_size	(	Bproject *	project,
		Vector3< double >	new_pixel_size,
		Bstring	mgpath,
		Bstring	partpath
	)

Changes all the micrograph fields linked to the pixel size.

Parameters

*project	project parameter structure.
new_pixel_size	new pixel size.
mgpath	binned micrograph path (must be allocated).
partpath	binned particle path (must be allocated).

Returns

int 0.

The fields linked to pixel size are:
    pixel_size
    shift
    box, bad and marker radii
    particle origins and locations
    bad area and marker locations

◆ project_check_particles()

int project_check_particles ( Bproject * project )

Checks particle numbers and box sizes.

Parameters

*project project.

Returns

int error code (<0 means failure).

Reads each particle file header, checks the number of particles
and sets the box size for the micrograph.

◆ project_create_from_image()

Bproject * project_create_from_image	(	Bimage *	p,
		Bstring	type
	)

Creates a project structure using image file names.

Parameters

*p	image.
type	type of images: mg, frame, rec, part, fil.

Returns

Bproject* new project parameter structure.

The function sets up the project hierarchy from one image base on the type.
If the type is not specified, it is guessed based on the following rules:
    #sub-images = 1
        z=1 => micrograph
        z>1 => reconstruction
    #sub-images > 1
        z=1 => frames
        z>1
            x=y => particles
            x≠y => filaments

◆ project_create_from_images()

Bproject * project_create_from_images	(	Bstring *	file_list,
		Bstring	type
	)

Creates a project structure using image file names.

Parameters

*file_list	list of file names.
type	type of images: mg, frame, rec, part, fil.

Returns

Bproject* new project parameter structure.

The function sets up the project hierarchy from a list of file names.
Each file may represent a micrograph or a picked particle file.
If the image is equal or larger than 1024x1024, it is assumed to be
a micrograph, its name will be assigned as a micrograph
file name, and no particle tags will be added.
If the image is smaller than 1024x1024 or the make_part flag is set,
it is taken to be picked particles and the file name will
be assigned as a particle file name.

◆ project_delesect_edge_particles()

long project_delesect_edge_particles ( Bproject * project )

Deselects particles that are too close to the image edges.

Parameters

*project project.

Returns: long number of particles selected.

◆ project_flip_particle_coordinates()

int project_flip_particle_coordinates	(	Bproject *	project,
		int	flip
	)

Reverses one or more particle coordinates.

Parameters

*project	project parameter structure.
flip	axes to flip.

Returns

int 0.

The specification of axes to flip is embedded in the flip number:
    first bit  - x
    second bit - y
    third bit  - z

◆ project_get_part_box_size()

int project_get_part_box_size ( Bproject * project )

Gets the box size from particle image files.

Parameters

*project project.

Returns

int error code (<0 means failure).

Reads each particle file header and sets the box size for the micrograph.

◆ project_mg_avg_intensities()

int project_mg_avg_intensities ( Bproject * project )

Retrieves the average micrograph intensities.

Parameters

*project project parameter structure.

Returns

int 0.

For each micrograph the FOM is set to the micrograph average.

◆ project_reset_origins()

int project_reset_origins ( Bproject * project )

Resets particle origins to nominal values.

Parameters

*project project parameter structure.

Returns

int 0.

For each micrograph a particle image header is read and the origin
is set to to the middle of the image.

◆ project_set_nominal_mg_origins()

int project_set_nominal_mg_origins ( Bproject * project )

Sets micrograph origins to the centers of the micrographs.

Parameters

*project project parameter structure.

Returns

int 0.

For each micrograph the micrograph origin is set to the center.

◆ project_set_part_img_origins()

int project_set_part_img_origins ( Bproject * project )

Writes particle origins into particle image files.

Author: D. Belnap

Parameters

*project project.

Returns

int error code (<0 means failure).

Sets the origins (offsets from the first voxel) in an image header to
values set within a project.  Rewrites image to file.

◆ project_set_views_from_images()

int project_set_views_from_images ( Bproject * project )

Gets views from particle images.

Parameters

*project project parameter structure.

Returns: int 0.

◆ project_set_views_in_images()

int project_set_views_in_images ( Bproject * project )

Sets views in particle images from the project parameter structure.

Parameters

*project project parameter structure.

Returns: int 0.

◆ project_trim_class_averages()

int project_trim_class_averages	(	Bproject *	project,
		Bstring &	list
	)

Deletes selected class averages from the project..

Parameters

*project	project parameter structure.
&list	selection list.

Returns

int 0.

The new class average file name has an insert of "_del".

◆ project_write_particle_classes()

int project_write_particle_classes ( Bproject * project )

Writes particles to different stacks based on class.

Parameters

*project project.

Returns

int error code (<0 means failure).

Writes new particle image files, numbered by the selection number.

Functions

Detailed Description

Function Documentation

◆ image_type()

◆ micrograph_get_nominal_origin()

◆ micrograph_get_size()

◆ micrograph_intensity() [1/2]

◆ micrograph_intensity() [2/2]

◆ particle_get_box_size()

◆ particle_read_img()

◆ particle_write_img()

◆ project_bin_micrographs()

◆ project_catenate_micrographs()

◆ project_change_pixel_size()

◆ project_check_particles()

◆ project_create_from_image()

◆ project_create_from_images()

◆ project_delesect_edge_particles()

◆ project_flip_particle_coordinates()

◆ project_get_part_box_size()

◆ project_mg_avg_intensities()

◆ project_reset_origins()

◆ project_set_nominal_mg_origins()

◆ project_set_part_img_origins()

◆ project_set_views_from_images()

◆ project_set_views_in_images()

◆ project_trim_class_averages()

◆ project_write_particle_classes()