IMP::em::Volume< T > Class Template Reference

Detailed Description

Template class for managing 3D Electron Microscopy volumes in IMP.


Public Member Functions
void	adjust_header ()
void	compute_locations ()
IMP::algebra::Matrix3D< T > &	get_data ()
	Return the matrix of data of the volume.
ImageHeader &	get_header ()
	Return the header of the volume.
long	get_number_of_voxels () const
	Returns the number of voxels of the map.
bool	is_part_of_volume (T x, T y, T z) const
bool	is_xyz_ind_part_of_volume (int i, int j, int k) const
void	read (String filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings)
	Reads the volume from the file.
void	reset_data (float const val)
	Clears all the data in the volume and sets it to the given value.
	Volume (int Zdim, int Ydim, int Xdim)
	Constructor with size.
	Volume ()
	Empty constructor.
void	write (String filename, bool force_reversed=false)
	Writes the volume to a file.
Protected Attributes
IMP::algebra::Matrix3D< T >	data_
	Matrix3D with the data for each voxel of the volume.
ImageHeader	header_
	Header for the volume with all the pertinent information.
IMP::algebra::Matrix3D < IMP::algebra::VectorD< 3 > >	locations_
	Matrix with the locations (z,y,x) of the volume voxels.
bool	locations_calculated_
	True if the locations have being calculated.
String	name_
	Name of the volume. Frequently it will be the name of the file.
bool	normalized_
	True if the volume values have been normalized.
bool	rms_calculated_
	True if the rms of the values in the volume have been computed.

template<typename T >

void IMP::em::Volume< T >::adjust_header ( )

Adjusts the information of the imager header taking into account the dimensions of the data and setting the time, date, type, etc ...

template<typename T >

void IMP::em::Volume< T >::compute_locations ( )

Computes the x,y,z coordinates (location) associated with each voxel of the volume and stores it in the locations_ matrix.

template<typename T >

bool IMP::em::Volume< T >::is_part_of_volume	(	T	x,
		T	y,
		T	z
	)			const

Returns true if coordinates of a given point belong to those covered by the volume

Parameters:

template<typename T >

bool IMP::em::Volume< T >::is_xyz_ind_part_of_volume	(	int	i,
		int	j,
		int	k
	)			const

Returns true if the physical index for the element of the matrix that contains the data in the map is within the range.

Parameters:

template<typename T >

Reads the volume from the file.

Parameters:

`[in]`	filename	name of the file
`[in]`	skip_type_check	true if the check for type of image is skipped
`[in]`	force_reversed	true to force reverse reading
`[in]`	skip_extra_checkings	true to skip the extra stringent tests

template<typename T >

void IMP::em::Volume< T >::reset_data ( float const val )

Clears all the data in the volume and sets it to the given value.

Parameters:

[in] val value to set

The documentation for this class was generated from the following file: