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Angular_project_library_v3
Create a gallery of projections from a volume
Parameters
$: Input Volume $: stack with output files $--sym <symmetryc1> $--sampling_rate <Ts5>
Extra parameters $: symmetry used to define neighbors, by default same as sym $`--psi_sampling <psi`360> $`--max_tilt_angle <tmax`91> $`--min_tilt_angle <tmin`-91> $`--experimental_images <docfile`> $`--angular_distance <ang`20> $ ( requires --experimental_images ): create doc file with closest sampling points $ ( requires --experimental_images ): remove points far away from experimental data $ ( requires --angular_distance ): create doc file with sampling point neighbors $: use projection shears to generate projections $`--perturb <sigma`0.0> $`--groups <selfile`> $: if set each experimental point will have a unique neighbor
Sample at 2 degrees and use c6 symmetry:
xmipp_angular_project_library -i in.vol -o out.stk --sym c6 --sampling_rate 2
| sampling_rate | recommended value for perturb |
|---|---|
| 20 | 0.09 |
| 10 | 0.043 |
| 5 | 0.02 |
| 2.5 | 0.01 |
| 1 | 0.0044 |
| 0.5 | 0.0022 |
More or less we map an hexagonal (2D) onto the surface of the angular sphere.
Since search for neighboring sampling points is very expensive, neighbors of all the valid sampling points are computed and stored in a file when--compute_neighbors is enabled. This values only depend on the sampling (if--perturb is not used). The format of this file is (projection_matching is able to read it):
[vnum]
[size1]
[vec1_neighbors]
[vec1_psi]
[size2]
[vec2_neighbors]
[vec2_psi]
...
[sizen]
[vecn_neighbors]
[vecn_psi]
for the neighbors and X1_angle Y1_angle Z1_angle X1_vector Y1_vector Z1_vector X2_angle Y2_angle Z2_angle X2_vector Y2_vector Z2_vector ... Xn_angle Yn_angle Zn_angle Xn_vector Yn_vector Zn_vector for the sampling points where vnum is the number of vectors, sizen is the number of elements (sampling points) and vecn is the number of neighbors of that particular sampling point. An example of this file is as follow: ## User's comments266 <-- number of vector (projection directions) 63 <-- number of neighbors for sampling point 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 <-- sampling point 0 has 1,2,....,n as neighbors (total number 63) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 <-- psi value 63 <-- number of neighbors for sampling point 1 0 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 1 <-- sampling point 1 has 0,2,....,n as neighbors (total number 63) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 <-- psi value ... ... 0.858477 -0.512792 0.00781575 <-- sampling point 0 as vector -30.851 89.5522 0 <-- sampling point 0 as euler angles 0.868546 -0.495547 0.00780013 <-- sampling point 1 as vector -29.7068 89.5531 0 <-- sampling point 1 as Euler angles ...
- /IcosahedronGrid.doc: How to create the grid