Phantom_project_v31
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_v3 Xray_project_v3 Phantom_create_v3
Parameters
$: Voxel volume, PDB or description file $: Output stack or image $--sampling_rate <Ts1> $--method <methodreal_space> where <method> can be:
Generating a set of projections $: File containing projection parameters Check the manual for a description of the parameters $: It is used for computing the assymetric unit $``: Do not create projections
Generating a single projection --xdim <size-1>
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.paramGenerating a set of projections using shears method
xmipp_phantom_project -i volume.vol -o images.stk --method shears --params uniformProjection_xmd.paramGenerating a top view from Z
xmipp_phantom_project -i volume.vol -o image.xmp --angles 0 0 0Generating a side view from Y
xmipp_phantom_project -i volume.vol -o image.xmp --angles 90 90 0Generating a side view from X
xmipp_phantom_project -i volume.vol -o image.xmp --angles 0 90 0In the following links you can find some examples of projection parameter files
http://sourceforge.net/p/testxmipp/code/ci/master/tree/input/phantomProject.param?format=raw
http://sourceforge.net/p/testxmipp/code/ci/master/tree/input/uniformProjection_xmd.param?format=raw
http://sourceforge.net/p/testxmipp/code/ci/master/tree/input/clusterProjection_xmd.param?format=raw
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 cylinder_with_axis.descr --oroot MRCproj --params[[MRCCrystalProj]]_xmd.paramIn the following links you can find some examples of projection parameter files
http://sourceforge.net/p/testxmipp/code/ci/master/tree/input/Crystal/MRCCrystalProj_xmd.param?format=raw
http://sourceforge.net/p/testxmipp/code/ci/master/tree/input/Crystal/cylinder_with_axis.descr?format=raw
http://sourceforge.net/p/testxmipp/code/ci/master/tree/input/Crystal/MRC_crystal_projection_xmd.param?format=raw
Figures (a) and (b) show the achievable resolution for different methods of projection.
(a) The achievable resolution for different methods for a volume of size 64*64
(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.