ctf3dsetup(1)               General Commands Manual              ctf3dsetup(1)


       ctf3dsetup   options   tilt_com_file

       Ctf3dsetup creates command files for a tomographic reconstruction with
       CTF correction in 3-D.  These command files will generate a series of
       aligned stacks corrected for different Z depths in the tomogram, and
       subsets of the tomogram in Z at the corresponding Z depths.  These sub-
       sets are referred to as slabs.  The number of slabs can be entered
       directly, or a maximum slab thickness in nanometers can be entered
       instead.  When processing with the standard command files managed by
       Etomo or Batchruntomo, only the name of the Tilt command needs
       to be entered, but an alternative command file for CTF correction can
       also be entered.

       The program can be run either starting with an aligned stack, or by
       reconstructing directly from a corrected, unaligned stack.  The
       requirements are different in the two cases.

   Reconstructions from Aligned Images
       To use an aligned stack, an uncorrected aligned stack must be avail-
       able, as specified in the command file used for CTF correction, desired
       parameters must be set in that file, and the defocus file must exist.
       If you wish to apply 2-D filtering (i.e., dose weighting), you can
       apply this to the uncorrected stack in advance without affecting the
       validity of the correction.  Alternatively, you can use the -filter
       option to have this step done for you, but the parameters for this fil-
       tering must already be set in the command file for filtering.  If you
       wish to erase gold beads in the aligned stack, you can also apply this
       in advance, which is not the standard processing order, or you can use
       the -erase option to have this step done on each corrected stack.  In
       the latter case, the model for erasing the beads must already exist,
       and parameters must be set already in the command file for gold eras-

   Reconstructions from Raw Images
       To use just the raw stack, an aligned stack need not exist and is
       ignored. Desired parameters must be set in the command file for CTF
       correction, and the defocus file must exist.  If 2-D filtering is to be
       done, it will be done on the raw stack by the command files produced
       here, and parameters must be set already in the command file for fil-
       tering.  If gold beads are to be erased, that will happen after creat-
       ing the CTF-corrected raw stack for each defocus level, the parameters
       must be set in the gold erasing command file, and the model for erasing
       must exist already.  In this case you may want to make an aligned stack
       for assessing the erasing, but neither the binning of this aligned
       stack nor that of tomogram on which beads are founds needs to match the
       reduction, if any, of the raw stack.

       Reconstructions from raw images cannot take account of corrections for
       a distortion field or magnification gradients and will not be valid if
       either of these corrections were used when making the aligned stack.
       The program will examine the Newstack log and/or command files from
       making both the coarse and final aligned stacks and issue a warning if
       either of these contains distortion corrections.

   Computational Resources and Strategies
       CTF correction and reconstruction can be run on either CPUs or GPUs,
       depending on whether use of a GPU is specified in the command file for
       reconstruction.  A different choice in the command file for correction
       will be ignored.  The jobs will run either on multiple CPUs or multiple
       GPUs, not a mixture of the two, so the number of "processing units"
       referred to next means the number of GPUs when running on GPU.

       This program provides two different computational strategies; the
       choice between them depends on what CPU or GPU resources are available.
       It can produce one command file per slab, each one doing all operations
       for that slab (CTF correction of the full image, optional gold erasing,
       and reconstruction of the full slab.)  These command files are suitable
       for running the slabs in parallel with each other.  The other strategy
       is to do the slabs sequentially, but use parallel processing (if there
       are multiple processing units) in both the CTF correction and recon-
       struction steps.  See the options -parallel and -procs for more
       details.  Running the slabs in parallel is probably more efficient if
       there are multiple processing units but will require more temporary
       storage.  If you are running on the GPU and computing the slabs sequen-
       tially with parallel processing, enter the number of GPUs you expect to
       run it on with the -procs option.  If you have just one GPU, you can
       omit the -procs option unless you want to try loading it with more than
       one job, which may or may not be useful.

   Correcting for X-axis Tilt
       When reconstructing from an aligned stack, if an X-axis tilt is
       included in either the reconstruction or correction command files, then
       the program evaluates whether it is similar enough in the two opera-
       tions.  If an X-axis tilt is being applied at all during correction, it
       should closely match the value used for reconstruction, otherwise the
       program gives a warning.  If there is an X-axis tilt in reconstruction
       but not correction, the program will determine the maximum difference
       in defocus produced by the two different X-axis tilt values, which
       occurs at the extremes of the reconstruction in Y.  If this defocus is
       larger than a certain fraction of the slab thickness, the program
       issues a warning.

       When reconstructing from the raw stack, the X-axis tilt in the recon-
       struction command file is unconditionally used for the correction.
       There is no additional time involved in using the X-axis tilt in this
       case because the CTF correction has to be done in diagonal strips of
       full-sized FFTs anyway.

       Ctf3dsetup uses the PIP package for input (see the manual page for
       pip).  Options can be specified either as command line arguments
       (with the -) or one per line in a command file (without the -).
       Options can be abbreviated to unique letters; the currently valid
       abbreviations for short names are shown in parentheses.

       -reccom (-rec) OR -TiltCommandFile       File name
              Command file for reconstruction, which can be entered with or
              without its extension of ".com".  If this option is not entered,
              a non-option argument is used for this command file.  This entry
              is required one way or the other.

       -ctfcom (-c) OR -CorrectionComFile       File name
              Command file for CTF correction, which can be entered with or
              without its extension of ".com".  If this option is not entered,
              "ctfcorrection" will be substituted for "tilt" in the name of
              the command file for reconstruction.

       -slabs (-s) OR -NumberOfSlabs       Integer
              Number of reconstructions to make at different depths in Z with
              different corrections for CTF.  Either this option or -thickness
              must be entered, but not both.  This entry must be at least 3.

       -thickness (-th) OR -SlabThicknessInNm   Integer
              The maximum thickness of reconstructions at different depths, in
              nanometers.  This value, if entered, must be less than half of
              the tomogram thickness so that at least 3 three slabs are com-

       -invert (-i) OR -InvertSlabZOffsets      Integer
              1 to invert the sign of the offset in Z applied when doing the
              CTF correction for each slab.  This would be needed if the tomo-
              gram is upside-down from its orientation in the microscope, by
              rotation and/or inversion in Z.  Tests with the most common
              sources of this problem indicate that this occurs whenever tilt
              angles need inversion in Ctfplotter and Ctfphaseflip; thus
              the default is to use the value of the -invert option in the
              command file for CTF correction, with the option here available
              to override that value.  See the section on Inverting Tilt
              Angles in the Ctfplotter man page for more details.

       -parallel (-pa) OR -RunSlabsInParallel
              Make each slab with one processor or GPU by creating a chunk
              file containing both the Ctfphaseflip and Tilt commands.
              This arrangement is the most efficient if there are more slabs
              than GPUs or processors, but requires more storage, as there
              will be as many created aligned stacks as processors.  The
              default is to make each slab sequentially, with parallel pro-
              cessing (if any) used to create the aligned stack then recon-
              struct the slab.  In this case only one corrected aligned stack
              exists at any time.

       -procs (-pr) OR -NumberOfProcessors      Integer
              Use this option to specify the number of processors or GPUs that
              you expect to run the command files on.  It is appropriate only
              when computing slabs sequentially and cannot be entered with the
              -parallel option.  It is passed directly to Splittilt unless
              it is 1, in which case the processing is not divided into
              chunks.  The default is 8 unless the Tilt command file contains
              the option to use the GPU, in which case it is 1.

       -perproc (-pe) OR -ChunksPerProcessor    Integer
              Use this option to set the number of chunks per processor when
              correction and reconstruction are divided into chunks; it will
              be multiplied by the number of processors to give a value for
              the -TargetChunks option to Splittilt and used to determine
              the number of slices to be corrected per chunk in Splitcorrec-
              tion(1).  The default is 3.

       -erase (-e) OR -EraseFiducials
              Run a command file to erase gold after CTF correction of aligned

       -goldcom (-g) OR -GoldEraserComFile      File name
              Name of command file to use for erasing gold.  If this option is
              not entered, "golderaser" will be substituted for "tilt" in the
              name of the command file for reconstruction.

       -filter (-f) OR -FilterIn2D
              Filter images in 2-D.  If filtering is desired, this entry is
              needed when reconstructing from a raw stack, but when using an
              aligned stack, the filtering may be done either beforehand or
              with this option.

       -2dcom (-2) OR -2DFilterComFile     File name
              Name of command file to use for 2-D filtering.  If this option
              is not entered, "mtffilter" will be substituted for "tilt" in
              the name of the command file for reconstruction.

       -unaligned (-un) OR -UseUnalignedImages
              Use the raw, unaligned stack for CTF correction and reconstruc-
              tion.  This should be the only option that is needed to use the
              raw stack, other than the -reduce option if desired, when this
              program is run inside a directory with a full set of processing
              files from one data set.

       -reduce (-red) OR -FourierReduceByFactor      Integer
              Reduce the raw stack by the given factor by using Newstack to
              crop its Fourier transform and use this reduced stack for pro-
              cessing from unaligned images.

       -raw (-ra) OR -RawStackFile    File name
              Name of raw image stack.  This option is needed when using
              unaligned images only if this filename cannot be determined by
              analyzing command files in the directory.

       -pixel (-pi) OR -RawPixelSize       Floating point
              Pixel size of raw image stack in nanometers.  This entry is
              needed when using unaligned images only if the pixel size is 1.0
              in the image file header, and the pixel size is not found in a
              track.com file.

       -xform (-x) OR -AlignTransformFile       File name
              File with the linear transformations that were used to align the
              images.  This option is needed when using unaligned images only
              if this filename cannot be determined by analyzing command files
              in the directory.

       -axis (-a) OR -AxisAngle       Floating point
              Angle that the tilt axis is rotated from vertical (counterclock-
              wise positive), for correcting unaligned images in their origi-
              nal orientation.  This entry is needed only if it cannot be
              found in an alignment log file.

       -vertical (-v) OR -VerticalSlices
              Do vertical slices with interpolation between slices instead of
              old-style X-axis tilting, regardless of the time penalty.

       -oldstyle (-o) OR -OldStyleXtilting
              Do old-style X-axis tilting, with direct backprojection into
              each output voxel, instead of vertical slices with interpolation
              between slices.

       -tempdir (-te) OR -TemporaryDirectory    Text string
              Directory to use for temporary files.  The default is that the
              temporary files will be placed in the current directory.

       -leave (-l) OR -LeaveTempFiles
              Leave temporary CTF-corrected stacks and reconstructed slabs

       -boundary (-b) OR -BoundaryPixels   Integer
              Set the number of boundary pixels saved in separate files to the
              given value when slabs are computed sequentially and each CTF
              correction and reconstruction is parallelized.  The boundary
              pixels are rewritten to the output file (aligned stack or slab
              reconstruction) after all chunks are done.

       -help (-h) OR -usage
              Print help output

              Read parameter entries from standard input

       These examples illustrate how to run with various sets of processing
       units.  They assume that 25-nm slabs are wanted and that all command
       files have standard names.

       To run on one GPU, make command files with:

         ctf3dsetup -thick 25 tilt

       These command files will create the slabs sequentially with separate
       files for CTF correction and reconstruction.  They can be run with

          subm ctf3d*.com

       To run on several GPUs, you almost certainly have space for as many
       temporary stacks as GPUs, so you can make command files to run slabs in
       parallel with:

          ctf3dsetup -thick 25 -parallel tilt

       All of the operations for a slab are within one command file.  If the
       GPUs are on separate machines, you can use the parallel processing
       interface in Etomo or run them with Processchunks with a command

          processchunks machine1,machine2,machine3,machine4 ctf3d

       If the GPUs are on the local machine, run them with a command like:

          processchunks -G localhost:1:2:3:4 ctf3d

       so that jobs are directed to different GPUs by Processchunks;
       whereas for multiple GPUs per remote machine you can use a command

          processchunks -G machine1:1:2,machine2:1:2 ctf3d

       You can also run slabs in parallel on multiple CPUs if there is no risk
       of running out of space for temporary files, using the ctf3dsetup com-
       mand above.  You can run them in the Etomo parallel processing inter-
       face, or run them with processchunks using a command like

          processchunks 12 ctf3d

       for the local machine, or

          processchunks machine1:4,machine2:4,machine3:4 ctf3d

       for 4 cores per specified machine.

       If space for temporary files might be limited, generate the slabs
       sequentially, doing parallel processing within each slab, with a com-
       mand like:

          ctf3dsetup -proc 16 -thick 25 tilt

       and run this with the Etomo parallel processing interface or the kinds
       of commands just given for running on CPUs.

       The command files have the prefix "ctf3d-".  The final reconstruction
       is named with "_3dctf" added to the root of the output file name in the
       reconstruction command file.

       David Mastronarde

       ctfphaseflip, tilt, ccderaser

       Email bug reports to mast at colorado dot edu.

IMOD                                4.12.57                      ctf3dsetup(1)