Reconstruct_art_v3

!xmipp_reconstruct_art (v3.0)

Usage

Generate 3D reconstructions from projections using the ART algorithm (even with SIRT). A history file with the information of the reconstruction process is created. You can also give symmetry elements to specify different points of view reusing the projections you have. The reconstruction is performed using some basis (blobs or voxels) in different grids (BCC (by default), FCC or CC).

Parameters

I/O Parameters $: Metadata file with input projections $: Output rootname. If not supplied, input name is taken without extension. The created files are as follows:outputname.vol 3D reconstruction in voxelsoutputname.basis 3D reconstruction in basis if the--save_basis option is enabled). The grid parameters are also stored in the same fileoutputname.hist History and information about the 3D reconstruction process $--ctf <ctf_file> $: apply unmatched forward/backward projectors $`--start <basisvolume_file`> $`--max_tilt <alpha`10.e+6> $`--ref_trans_after <n`-1> $`--ref_trans_step <v`-1> $`--sparse <eps`-1> $`--diffusion <eps`-1> $`--surface <surf_mask_file`> $`--POCS_freq <f`1> $`--known_volume <value`-1> $: Force ther resulting volume to be positive $--goldmask <value1.e+6> $: Remove external zero-valued border pixels created by alignment of tomograms $: Do not apply shifts as stored in the 2D-image headers $: Perform variability analysis $: Refine input projection before backprojecting $``: Perform a companion noisy reconstruction. If given, the algorithm will perform two reconstructions. One with the input data, and another one with pure noise images applying exactly the same procedure as to the signal projections. This reconstruction is further used by the SSNR program in order to calculate the VSSNR or the SSNR itself. The created files are as follows:[fn_root]_noise.vol Reconstruction of the pure noise`[fn_root]_noise_proj.sel` Selection file with the pure noise images`[fn_root]_signal_proj.sel` Selection file with the signal images (a reordered version of the input (-i) selfile)`[fn_root]_noise_proj.stk` Pure noise images used for the reconstruction $`--ray_length <r`-1>

Symmetry parameters $--sym <sym_file> $--sym_each <n0> $--force_sym <n0> $: Do not generate symmetry subgroup $: Do not use symmetrized projections

Iteration parameters $``: Relaxation factor, by default 0.01 (recommended range 0.0 - 0.1). A list of lambda values is also accepted as "-l lambda0 lambda1 ..." $-n <noit1> $`--stop_at &lt;it_stop`0&gt; $`--equation_mode <mode`ARTK> where <mode> can be:

• • $--sort_last <N2> $ or: Instead of orthogonal sort, projections are presented randomly to the algorithm $ or: No sort must be applied $: Perform weighted least squares ART $: Relaxation factor for WLS residual, by default 0.5. A list of kappa values is also accepted as "-k kappa0 kappa1 ..."

Basis Parameters $--basis <basis_typeblobs> where <basis_type> can be:

• • $ or: blob parameters and grid relative size adjusted to use big blobs $ or: blobs optimal for direct visualization

Grid parameters $-g <gridsz1.41> if gridsz -1 => gridsz2^(1/2) -2> gridsz2^(1/3) $--grid_type <typeBCC> where <type> can be:

• • $-R <interest_sphere-1> $--ext <proj_ext0> $--output_size <Xsize0> <Ysize=0> <Zsize=0> $--sampling_rate <Ts1>

Parallel parameters $--thr <N1> $--parallel_mode <modeART> where <mode> can be:

• • $--block_size <n1> =: Number of projections to each block (SART andBiCAV)

Debugging options $``: Print the matrix of the system Ax=b. The format is:

   Equation system (Ax=b) ----------------------    

pixel=

--> <a1> <a2> ... </verbatim> I.e., for the pixel p (pixels are numbered lexicographically) with experimental value b, the equation axb is set. a is the corresponding row of matrix A. The coefficient a_i is equal to the contribution of the basis i to pixel p. x is the number of basis $--show_iv <n10> $: Show error for each projection $: Give some statistical information during the process, they might be useful to see how the process is going. The mean squared error for each projection is shown by default $: Save intermediate projections. This option allows deep debugging as it save all projections and volumes involved in the reconstruction process. After each step you are asked to press a key, so that you could inspect carefully the results. The names for these files are: PPPtheo, PPPread, PPPcorr, PPPdiff PPPbasis.basis, PPPvol.vol[[PPPvolPOCS1]],[[PPPvolPOCS2]],[[PPPvolPOCS3]] $`--save_intermediate <n`0> $: Save also the 3D reconstruction in basis each time that you have to save the reconstructed volume $: You are prompted to give the number of the following projection to be presented to the algorithm $: Skip all those projections generated by symmetry (symmetries different from -1)

Examples and notes

• Basis volume definition: The basis volume is defined internally such that it should cover the space cube corresponding to(-Xdim/2,-Xdim/2,-Xdim/2) to(X dim /2,Xdim/2,Xdim/2) where Xdim is the X dimension of the projections.
• Voxel volume definition: The final reconstructed volume is defined in such a way that it covers the whole basis volume. For these two definitions and the fact that the basis has got some radius (normally 2) the final reconstructions are a little wider than the original projections (usually2*radius+1)
• Crystal reconstructions: Crystal projections must be the deformed projections of the deformed volume. I mean, the lattice vectors of the volume to reconstruct need not to lie on a grid point inside the BCC, FCC or CC grid. If we ant to force that they lie on a grid point we have to deform the volume. When he have this deformed volume and we project it, the two 3D lattice vectors project to two different 2D lattice vectors, that in principle there is no relationship between them. We must force this two 2D lattice vectors to align witha(Xdim,0) and =b(0,Ydim)= by deforming the projection. This is the second deformation. This complex projections are either generated from phantoms using the program Project or from lists of Fourier spots coming out from MRC as APH files by applying the programSpots2RealSpace2D.
• Surface constraints: These constraints force the volume to be 0 at known places. This has got the beneficial consequence that mass tends to be compacted where it should be.
• Grids: This program defines three grids for working with data. The typical simple cubic grid, the face-centered grid (fcc) and the body-centered cubic grid (bcc). We define these grids as follows: | Simple Cubic Grid | /image002.gif is a positive real number called sampling distance. SeeGabor H., Geometry of Digital Spaces, Birkhauser, 1998, MassachussetsSpots2RealSpace2D. /image013.gif ³. For defining the bcc grid two simple cubic grids are used, it can be seen from the definition for the bcc above that the valid positions for even values ofz,x andy have to be also even, in the case of odd values ofz ,x andy have to be odd. Consequently, the relative size used in the BCC grid is equivalent to 2 /image013.gif above. For defining the fcc grid four simple cubic grids are used, it can be seen from the definition for the fcc above that the valid positions for even values ofz, the sum ofx andy has to be even; in the case of odd values ofz the sum ofx andy has to be odd. Consequently, the relative size used in the FCC grid is equivalent to 2 Basic reconstructing commands:

   reconstruct_art -i projections.sel -o artrec

Create the equivalent noisy reconstruction:

reconstruct_art -i projections.sel -o artrec --noisy_reconstruction

Reconstruct using SIRT parallelization algorithm for five iterations:

reconstruct_art -i projections.sel -o artrec -n 5 --parallel_mode SIRT

Save the basis information at each iteration:

reconstruct_art -i projections.sel -o artrec -n 3 --save_basis

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