ProjectTomography

project_tomography

Purpose

This program allows you to generate projections from a 3D Xmipp volume as if it were a single axis tomographic series. The program is nearly identical to Project and here we only explain the differences. The volume description part is the same as in Project, the angular description is different since in this program you specify the tilt axis and the tilting angles instead of the more general projection geometry of Project. Finally, there are fewer options for noise.

Usage


$ project_tomography -i ...

Parameters

``
``
`` Show a document file with the projection angles at the same time that the volume is projected. Even when this option is not chosen, this program always save a file called[projection_seed]_movements.txt with a docfile with the perfect angles, the noisy angles and the shifts applied to the center
`` Show a document file with the projection angles but the projections are not generated

The structure of projection description file:

# Volume and projection files

# Volume description file, PDB file (with extension PDB), or volume file

``

# Projection seed, first projection number (by default, 1) and extension

[first projection number1] [extension=""] =

# Y and X projection dimensions

``

# Angle Definitions


# tilt axis, direction defined by rot and tilt angles
# Axes in the XY plane must have always tilt=90

``


# tilt axis offset (i.e., a point through which the tilt axis passes)

``


# tilt description (all angles in degrees

``

# Noise description


# In the following lines deviation is the true power of noise added
# to that variable, while average is like a bias directly added to
# the variable. Noise for angles are taken as degrees. The added
# noise is gaussian

# Noise (and bias) applied to angles

[rot bias0] =

# Noise (and bias) applied to pixels

[pixel bias0] =


# Noise (and bias) applied to particle center coordenates
# IMPORTANT: This option ONLY works when using a phantom described as a set of geometrical objects 
# That is, It does NOT work when the volume is defined using voxels

[center bias0] =

Examples and notes

Here you are an example of a tilt series from -60 to 60 degrees every 3 degrees. The tilt axis passes through the center of the volume and coincides with the X axis


# Volume and projection files ------------------------------------------------
# volume description file or volume file
../Src/phantom128.vol
# projection seed and extension (this last is optional)
g1ta 1 xmp
# Y and X projection dimensions
128 128
#
# Angle Set Source -----------------------------------------------------------
# tilt axis, direction defined by rot and tilt angles
0 90
# tilt axis offset
0 0 0
# Tilting description
-60 60 3
# Noise description ----------------------------------------------------------
#     noise (and bias) applied to angles
0
#     Noise (and bias) applied to pixels 
0
#     Noise (and bias) applied to particle center coordenates 
0

--Main.CoSS - 19 Aug 2008

ProjectTomography