Xmipp

xmipp_phantom_project (v3.0)

Usage

This program is able to generate a set of projections from a volume. The projection is done using the information directly or from a file.

See also
tomo_project xray_project phantom_create

Parameters

--method <method=real_space>
Projection method
where <method> can be:
  • real_space Makes projections by ray tracing in real space
  • shears Use real-shears algorithm This algorithm is slower but more accurate. For a full description see
  • fourier <pad=2> <maxfreq=0.25> <interp=bspline> Takes a central slice in Fourier space
    pad: controls the padding factor.
    maxfreq: is the maximum frequency for the pixels and by default pixels with frequency more than 0.25 are not considered.
    interp: is the method for interpolation and the values can be:
    nearest: Nearest Neighborhood
    linear: Linear BSpline
    bspline: Cubic BSpline

:

Generating a set of projections

--only_create_angles
Do not create projections
:

Generating a single projection

--xdim <size=-1>
Size of the projection For geometric descriptions and voxel volumes this parameter is not necessary
:

Examples and notes

Generating a set of projections using fourier method

xmipp_phantom_project -i volume.vol -o images.stk --method fourier 3 0.25 bspline --params uniformProjection_xmd.param

Generating a set of projections using shears method

xmipp_phantom_project -i volume.vol -o images.stk --method shears --params uniformProjection_xmd.param

Generating a top view from Z

xmipp_phantom_project -i volume.vol -o image.xmp --angles 0 0 0

Generating a side view from Y

xmipp_phantom_project -i volume.vol -o image.xmp --angles 90 90 0

Generating a side view from X

xmipp_phantom_project -i volume.vol -o image.xmp --angles 0 90 0

In the following links you can find some examples of projection parameter files

http://sourceforge.net/p/testxmipp/code/ci/3.1/tree/input/phantomProject.param

http://sourceforge.net/p/testxmipp/code/ci/3.1/tree/input/uniformProjection_xmd.param

http://sourceforge.net/p/testxmipp/code/ci/3.1/tree/input/clusterProjection_xmd.param

Creating a 2D crystal In order to create a 2D crystal, you can pass --params as a projection file with a second block for crystal projection.:

xmipp_phantom_project -i input/Crystal/cylinder_with_axis.descr --params input/Crystal/MRC_projection_xmd.param  -o out.stk

In the following links you can find some examples of projection parameter files

http://sourceforge.net/p/testxmipp/code/ci/3.1/tree/input/Crystal/cylinder_with_axis.descr

http://sourceforge.net/p/testxmipp/code/ci/3.1/tree/input/Crystal/angles.doc

http://sourceforge.net/p/testxmipp/code/ci/3.1/tree/input/Crystal/MRC_projection_xmd.param

Figures (a) and (b) show the achievable resolution for different methods of projection.

Test_Resolution_Small.jpg

(a) The achievable resolution for different methods for a volume of size 64*64

 Test_Resolution_Big.jpg

(b) The achievable resolution for different methods for a volume of size 400*400

As it can be seen in these two figures, Fourier method with cubic B-Spline interpolation for both padding two and padding one provides the best resolution. However, there is a preference on padding one because of less memory and time complexity.

User's comments

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