ctf3dsetup(1) General Commands Manual ctf3dsetup(1)
NAME
ctf3dsetup
SYNOPSIS
ctf3dsetup options tilt_com_file
DESCRIPTION
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.
An uncorrected aligned stack must be available, as specified in the
command file used for CTF correction, 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 without affecting the validity of
the correction. If you wish to erase gold beads in the aligned stack,
you can also apply this in advance, which is not the standard process-
ing 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.
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.
If an X-axis tilt is included in either the reconstruction or correc-
tion command files, then the program evaluates whether it is similar
enough in the two operations. 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 differ-
ent X-axis tilt values, which occurs at the extremes of the reconstruc-
tion in Y. If this defocus is larger than a certain fraction of the
slab thickness, the program issues a warning.
OPTIONS
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 (-r) 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-
puted.
-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
stack
-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.
-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
-StandardInput
Read parameter entries from standard input
EXAMPLES
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
just:
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
like:
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
like:
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.
FILES
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.
AUTHOR
David Mastronarde
SEE ALSO
ctfphaseflip, tilt, ccderaser
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.11.0 ctf3dsetup(1)