Xmipp

xmipp_xray_project (v3.0)

Usage

Generate projections as in a X-ray microscope from a 3D Xmipp volume.

See also
xray_psf_create xray_import phantom_create

Parameters

-i, --input <volume_file>
Volume file to be projected.
--oroot <rootname> ( requires --params )
Output rootname
or -o, --output <image_file> ( requires --angles )
Output image

Generating a set of projections

--params <parameters_file> ( requires --oroot )
File containing projection parameters Check the manual for a description of the parameters

Generating a single projection

--angles <tilt> <axisRot=90> <axisTilt=90> ( requires -o )
Tilt angle for a single projection. (axisRot, axisTilt) is the direction of the rotation axis.

Global projection options

--show_angles
Print angles value for each projection.
--only_create_angles
Projections are not calculated, only the angles values.

Xray options

-s, --sampling_rate <Ts>
Sampling rate of the volume to be projected (nm). If empty, same value as X-Y plane sampling from PSF.
--psf <psf_param_file=>
XRay-Microscope parameters file. If not set, then default parameters are chosen.
--thr <threads=1>
Number of concurrent threads.

Examples and notes

Generating a set of projections using a projection parameter file and two threads:
xmipp_xray_project -i volume.vol --oroot images --params projParams.xmd -s 10 --psf psf_560.xmd --thr 2
Generating a single projection at 45 degrees around X axis:
xmipp_xray_project -i volume.vol -o image.spi --angles 45 0 90 -s 10 --psf psf_560.xmd
Generating a single projection at 45 degrees around Y axis with default PSF:
xmipp_xray_project -i volume.vol -o image.spi --angles 45 90 90 -s 10
In the following link you can find an example of projection parameter file:

http://sourceforge.net/p/testxmipp/code/ci/3.0/tree/input/tomoProjection.param

In the following link you can find an example of X-ray microscope parameters file:

http://sourceforge.net/p/testxmipp/code/ci/3.0/tree/input/xray_psf.xmd

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