Content-type: text/html Manpage of seedSpikes


Section: User Commands (1)
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seedSpikes - Create a seed model for particles ("spikes") on the surface of a sphere or cylinder.  


seedSpikes inputModel outputModel
seedSpikes inputModel outputModel type
seedSpikes inputModel outputModel type delta
seedSpikes inputModel outputModel type delta dR
seedSpikes inputModel outputModel type delta dR maxPos
seedSpikes inputModel outputModel type delta dR maxPos dza  


Given an input model defining a number of spheres or cylinders (see below for conventions), generate a new model with candidate spikes distributed over these surfaces. The candidate spikes will be placed dR voxels outside the surfaces with an approximate spacing of delta. Delta can be specified either in degrees (if positive) or voxels (if negative). The output model will be suitable for use with spikeInit to create an initial motive list followed by semi-automatic particle picking using PEET's flgNoReferenceRefinement option for matching with a user-supplied template.
inputModel = string
The path to the input model. In the spherical case, the input model must consist of single-point objects with coordinates defining the centers and point sizes equal to the radii of the spheres. In the cylindrical case, each object must contain only a single 2-point contour defining the radius, axis, and extent of the cylinder. For helices, in addition to the definition of the cylinder in contour 1, each object must also contain a second contour containing 1 or more start points for the helical strands.
outputModel = string
The path to the output model. Spikes corresponding to each sphere or cylinder will be put into an odd-numbered object, followed by an even-numbered object containing the (input) description of the shape. This format is suitable for use with spikeInit.
type = < 'sphere' | 'cylinder' | 'helix' > (Default = 'sphere').
Specify spherical, cylindrical, or helical processing.
delta = float (Default = 10 degrees)
Approximate spacing between seeded spike locations. For spheres and simple cylinders, delta may be specfied either in degrees (if positive) or voxels (if negative). For helices, delta must contain a pair of signed numbers representing the angular spacing between neighboring helix points in degrees and the axial distance between them in voxels.
dR = float (Default = 0 voxels)
How far outside (if positive) or inside (if negative) the surface the seeds should be placed.
maxPos = array of 1 or 3 floats ([xmax, ymax, zmax]; Default = [])
If specified, seeds will only be placed within 0..xmax, 0..ymax, and 0..zmax. This can be used to prevent seeding points close to the edges or completely outside of the corresponding volume. If only 1 number is specified, it will be applied to all 3 dimensions.
dza = float (optional)
Axial seed in voxels spacing for cylinders only. If omitted, axial spacing will be the same as the circumferential spacing.


John Heumann  


averageAll(1), alignSubset(1), modifyMotiveList(1), PEET(1), spikeInit(1)




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Time: 18:16:05 GMT, January 11, 2021