batchruntomo(1)             General Commands Manual            batchruntomo(1)



NAME
       batchruntomo - Align tilt series and generate tomograms automatically

SYNOPSIS
       batchruntomo  [options]  directive_files...


DESCRIPTION
       Batchruntomo runs all the operations required to align a tilt series
       and build a tomogram, following a set of instructions called "direc-
       tives" provided in a text file.  These directives indicate either
       parameter settings or which pathway to follow at various points in the
       processing sequence.  The program will perform operations in a fixed
       order determined by these choices; the order of the directives does not
       affect this order.  The program can work on more than one data set and
       can also move the tilt series from their current location into a sepa-
       rate directory for each data set, which is created if necessary.  It
       accepts tilt series with the extension ".mrc" and changes the extension
       to ".st" so that other programs will work correctly.


   Directives
       Directives consist of key-value pairs separated by equals signs, where
       the key has 2 to 4 components separated by periods.  The first compo-
       nent is a prefix that indicates the type of directive or the stage at
       which it is applied.  The value may be blank if appropriate but the
       equals sign must be present.  There are currently three prefixes:
       "setupset", for directives involved when setting up a data set; "com-
       param", for directives used to set options in command files; and "run-
       time", for directives interpreted by Batchruntomo or etomo.  A descrip-
       tion of all directives is contained in the file
        "IMOD/com/directives.csv", which is in comma-separated values format.
       It is accessible in a more readable form from the IMOD help index via
       the link "Directives for batch processing and Etomo templates" (avail-
       able from "imodhelp" or when accessing the html package of IMOD docu-
       mentation with a browser).

       "setupset" directives have two forms.  The majority have the form
          setupset.copyarg.<copytomocoms short option name>=value
       These directives will be processed mostly generically by Etomo and sent
       to Copytomocoms as command line arguments.  The short option name
       must be given in full.

       Other "setupset" directives are interpreted exclusively by Batchruntomo
       or etomo and have the form
          setupset.<parameter or option>=value

       "comparam" directives are interpreted generically when a command file
       is created either by Copytomocoms or by Makecomfile.  They have
       the form
          comparam.<root name of file>.<program>.<Long option name>=value
       The root name of the command file may include an axis letter ("a" or
       "b").  For a single axis data set, directives without a letter and with
       an "a" are treated as equivalent and ones with "b" are ignored.  For a
       dual axis data set, a directive without a letter can apply to either
       axis, but will be overridden by a directive with a letter matching the
       specific axis, regardless of which one occurs later in the processing
       sequence.  The long option name must be given in full.  Options to
       Tilt must match the case shown in the Tilt man page, even though
       Tilt accepts case-insensitive options.

       Because "comparam" directives are treated generically, they are not
       restricted to the ones listed in the table of directives.  Any valid
       option can be used, although some would be meaningless in the context
       of automation and some would conflict with the management provided by
       Copytomocoms or be overridden by Makecomfile.

       "runtime" directives have the form
          runtime.<Processing step>.<axis>.<parameter or option>=value
       Here the processing step and parameter have names that have been made
       up just for the directive.  The convention is for the processing step
       to be capitalized and the parameter to start with lower case.  The axis
       must be either "a", "b", or "any".  For a single axis data set, direc-
       tives with "any" or "a" are treated as equivalent and ones with "b" are
       ignored.  For a dual axis data set, a directive with "any" can apply to
       either axis, but will be overridden by a directive with a letter match-
       ing the specific axis, regardless of which one occurs later in the pro-
       cessing sequence.

       Boolean directives must have a value of either 0 or 1: 1 to turn the
       option 1 or 0 to turn it off; no other values (including blank) are
       allowed.  If a boolean directive is not present then the option is off,
       unless it has been turned on by an entry in a template file (see
       below).  For any other kind of directive, the value can be blank, which
       causes the option in question to be removed from consideration.
       Specifically, for a "comparam" directive, a blank value will cause the
       option to be removed from the command file if present.  For other kinds
       of directives, a blank value removes the setting of the parameter by a
       previous directive in a template file.

       If a processing step is being skipped or bypassed by an alternative
       method of processing, then all the directives related to it have no
       effect on the processing that is done.  It is thus generally safe to
       leave unused directives in a file.  Such directives with prefix "com-
       param" will be used to set parameters in command files produced by
       Copytomocoms, but directives for parameters in other command files
       will have no effect because those files will not be produced.  Direc-
       tives with prefix "runtime" are simply ignored if they are not relevant
       to the chosen processing sequence.


   Template Files
       Template files can contain parameters that can be used meaningfully for
       multiple, similar data sets.  Directives exist to define a microscope
       template file, a system template file, and a user template file.  The
       idea is for the microscope file to have parameters specific to a micro-
       scope or microscope/camera combination, and to have the other template
       files contain other parameters that would not be dataset-specific.
       Each file consists of a subset of directives just like those described
       for defining options for the batch processing.  There is a heirarchy
       among these directives.  They are always processed in the order scope
       template, system template, user template, and batch directive file, and
       entries later in this sequence override ones that appeared earlier.
       Batchruntomo reads the template files and uses their contents along
       with those of the directive file to determine the values for parame-
       ters.  It also passes whatever template files exist, plus the batch
       file, to Etomo for it to use when setting arguments for calling Copyto-
       mocoms(1), and Etomo passes the files on to Copytomocoms to use for
       setting parameters.  Batchruntomo passes them to Makecomfile to use
       similarly when making optional command files.

       The program checks all directives after it reads them, including the
       ones from a template file, against the master list in "directives.csv".
       All "setupset" and "runtime" directives must match ones in this file.
       It is possible to enter "comparam" directives not listed in this file,
       provided that the command file name and program name match those of
       other directives in the master file.  The program will consult the
       autodoc file for the program to determine whether the option is valid.
       It will issue a warning if an autodoc cannot be found; otherwise, it
       will be able to determine validity definitively.

   Processing Steps Available
       This section describes some of the capabilities and current limitations
       of various steps.

       X-ray removal is optional; if selected, automatic X-ray removal will be
       done, and "clip stats" will be run on the fixed stack.  There is also a
       directive to run Archiveorig to make a compressed difference between
       corrected and original stacks, then delete the original stack.  A man-
       ual replacement model can be specified.  It is suggested that object 1
       contain patches specified in the default way, by a point on each pixel;
       object 2 contain lines, if any; object 3 contain patches specified by
       boundary contours, if any; and that directives be added to specify
       these choices and that objects 1-3 are all-section objects.  These sug-
       gestions will be enforced when there is a GUI for setting up batch
       directives.  If the manual replacement model is located elsewhere, it
       will be copied to the dataset and renamed to the standard name for such
       models, so that the model can be opened and added to when running in
       Etomo.

       Detection of blank images and images with large dark regions at the
       highest tilt angles can be done before further processing by including
       the preprocessing directive "endExcludeCriterion" with a fractional
       value such as 0.5.  (The directive is ignored for montaged tilt
       series.)  The program will look at the standard deviation (SD) of
       images at each end of the tilt series and find ones whose SD is less
       that the criterion times the mean SD of the five adjacent less-tilted
       images.  Up to three images can be excluded on each end of the series
       by this analysis.  The program will then do a histogram analysis with
       Clip to see whether the intensity distribution has two peaks and how
       much of the area falls in the lower peak.  A view is excluded if inten-
       sity at the lower peak is less than 0.17 times that at the upper peak
       and more than 0.33 of the pixels are in the lower peak (these defaults
       can be modified with "darkExcludeRatio" and "darkExcludeFraction"
       directives).  Views can be eliminated up to 6 tilts from either end in
       this way, but with either analysis, only consecutive views will be
       eliminated.  View skipping/exclusion lists will be added or adjusted in
       xcorr.com, track.com, align.com, and tilt.com.

       Coarse alignment is always performed.  The binning of a prealigned
       stack can be specified.

       Fiducialless alignment can be chosen, in which case tomogram thickness
       must be specified.  The tomogram will not be reoriented at all (no
       angle offset or X-axis tilt applied).

       Patch tracking can be chosen.  Again, tomogram thickness must be speci-
       fied, but in this case the tomogram will be reoriented based on angles
       found by Tiltalign.  Also, if you specify gold erasing after 3D bead
       finding, the thickness must be specified for the tomogram used to find
       the beads.

       Gold fiducial tracking can be done either with automatic seed-finding
       then bead tracking, or with RAPTOR followed by optional bead tracking.
       For a second axis, Transferfid can be run, followed by automatic
       seed-finding to fill in the resulting model.  RAPTOR can be run instead
       for the second axis (unlike in Etomo), although there will then be no
       list of corresponding fiducials.  Beadtrack can be run more than
       once, because this completes a model more reliably than selecting fur-
       ther rounds of tracking in a single run.

       Fine alignment with Tiltalign can include local alignments in all
       cases.  There is a directive to enable the stretching (distortion)
       solution.  When enabled, stretching will be solved for only if there
       are gold fiducials on two surfaces, and if there are enough on the
       minority surface overall and relative to the total number.  Stretching
       may be solved for in the global solution but not in the local one if
       there are too few fiducials on the minority surface per local area.  In
       addition to making these decisions, Batchruntomo also calls the program
       Restrictalign, which will reduce the number of variables being
       solved for when in a systematic way when the number of fiducials is
       small.  The fine alignment produces an angle offset and an X-axis tilt
       that is applied when building the tomogram, unless there are too few
       gold.  In addition, if there is gold on two surfaces, the distance
       between the gold particles provides an estimate of thickness that can
       be used as one basis for the tomogram thickness.  Otherwise, if gold is
       to be erased after 3D bead finding, the thickness for the required
       tomogram must be specified.

       Tomogram positioning can be done for both plastic sections and cryosam-
       ples by setting the "Positioning.sampleType" directive to 1 or 2,
       respectively.  Plastic section positioning is done with a binned-down
       whole tomogram for now.  If there is no "Positioning.binByFactor"
       directive, the program will pick a binning up to 4 that brings the
       binned size under 512 in its largest dimension.  If there is no "Posi-
       tioning.thickness" directive, the program will pick a thickness based
       on the largest dimension: 250 if size under 512, 400 if size under
       1024, 500 if size under 2048, and 600 otherwise.  The program will run
       Findsection and try to make a model for Tomopitch with 5 pairs of
       sample lines. Cryosample positioning is done with the script Cryoposi-
       tion(1).  In this case, the "Positioning.thickness" directive is
       required.  Cryoposition picks an appropriate binning, but if you do
       want to set this binning, it can be done with a "cryoposition.Binning-
       ToApply" directive instead of the runtime "Positioning.binByFactor"
       directive.  By default, 25 unbinned pixels will be added on each sur-
       face by Tomopitch; this can be changed with a "tomopitch.ExtraThick-
       ness" directive.

       When there is no positioning, angles are set from the Tiltalign out-
       put.  The Z height of the specimen in the tomogram will be whatever
       location results from the coarse alignment; thus the specimen will be
       centered in Z if features contributing to the cross-correlations are
       evenly distributed in depth.  If the correlations are dominated by fea-
       tures near one surface, the specimen will not be centered in Z.  If
       there are fiducials on two surfaces, one can use a "Position.centerOn-
       Gold" directive to apply the Z shift computed by Tiltalign for cen-
       tering on the range of fiducials in Z.  Another side-effect of using
       this directive is that the estimated thickness from alignment will be
       larger so that the tomogram will then contain all of the gold included
       as fiducials.

       The aligned stack can have specified binning and size.  Optional modi-
       fications of the aligned stack are performed in the standard order, or
       with gold erasing first if the -erase option is entered.  CTF correc-
       tion can be done with a single nominal defocus value.  Alternatively,
       Ctfplotter can be used to find the defocus automatically if the
       "autofitRangeAndStep" directive is present.  When Ctfphaseflip is
       run, it will use a "setname.defocus" file if it is present; otherwise
       it will use a "setname_simple.defocus" file created with the nominal
       defocus from the "setupset.copyarg.defocus" directive.  (The "set-
       name.defocus" file could derive from manual or automatic running of
       Ctfplotter, or could be created by other means).  Gold erasing can
       be done with automatic finding of beads in a tomogram, or by transform-
       ing the fiducial model (or the model put out by Tiltalign that has
       gaps filled in, if available).  For finding beads in the tomogram, the
       "GoldErasing.thickness" directive must be supplied unless there are
       beads on two surfaces.  As of IMOD 4.8.39, the binning is set as the
       unbinned bead size divided by 5 and rounded to an integer, as in Etomo;
       thus, the "GoldErasing.binning" directive is no longer required.  Both
       the automatic finding of beads in 3D, and the detection of defocus, are
       steps that one might want to check before proceeding.  To allow inter-
       vention at a single stopping place, CTF correction and gold erasing
       steps are interleaved: defocus is detected, beads are found, CTF is
       corrected, then beads are erased.  2D filtering can be specified.

       The tomogram can be computed with weighted backprojection, with SIRT,
       or with both methods.  The iterations to leave can be specified for
       SIRT.  The thickness can be chosen automatically if there are gold
       beads on both surfaces or if tomogram positioning was done, otherwise
       it must be specified with a directive.  The "Reconstruction.fallback-
       Thickness" directive is the most useful one because it can be used to
       specify a thickness to be used when there is no thickness available
       from either fine alignment or positioning.  The fallback thickness will
       also be used if the thickness from either is less than 40% of the fall-
       back thickness, which would be the case if there are gold on only one
       surface and no positioning was done.

       Tomogram combination for a dual-axis dataset is possible with all kinds
       of alignments and will proceed automatically.  The program first uses
       Findsection to find the Z limits, and decides whether to get the
       initial registration between volumes with Solvematch or Dualvol-
       match(1).  The patch correlations and fitting are done with Autopatch-
       fit(1); by default, it will try medium to extra-large patches and add
       target residual values of 0.4,0.45 for Findwarp on the final trial.
       There are "runtime.Combine" directives to control this behavior and to
       set a few other parameters for tomogram combination; also, "comparam"
       directives can be used to modify parameters in solvematch.com, patch-
       corr.com, and matchorwarp.com. If both SIRT and back-projection recon-
       structions are available, the latter will be combined unless the com-
       bine "doSIRTifBoth" directive specifies otherwise.  The decision of
       whether to match A to B instead of B to A is made based on the ratio of
       the B to A thicknesses determined from their Z limits.  This ratio is
       compared to a criterion that can be set with the "matchAtoBThickRatio"
       directive and whose default is 0.9.  With this criterion, A will be
       matched to B if B is thinner than A by more than ~10%.  Lowering the
       criterion would make it match A to B only when the thickness difference
       is more extreme.  Raising the criterion toward 1 would make it match A
       to B with less thickness difference.  It can be set to a very low num-
       ber (0.2) to guarantee that B is always matched to A, or a very high
       number (5) to have A always matched to B.

       Postprocessing can be done with Trimvol, and should be selected with
       the directive "runtime.Postprocess.any.doTrimvol".  For compatibility
       with old behavior, Trimvol will still be run if any of the "run-
       time.Trimvol" directives "findSecAddThickness", "reorient", "thick-
       ness", "sizeInX", "sizeInY", "scaleFromX", "scaleFromY", or "scale-
       FromZ" are present.  Findsection will be used to find the section
       limits if the "findSecAddThickness" directive is present.  The output
       file for a final reconstruction will have the usual name, setname.rec.
       For a dual-axis data set, it is possible to trim one or both of the
       single axis reconstructions; here the output file will be named with
       "_trim.rec".  If both SIRT and back-projection were used, the postpro-
       cessing "doSIRTifBoth" directive controls whether to trim one or both
       reconstructions; in the latter case the file for the back-projection
       will be named "_BP.rec".  Whenever a SIRT reconstruction is trimmed,
       the result on the final iteration will be used.  By default, the
       trimmed volume will be reoriented by rotating around X.  The entire
       volume will be used unless the "findSecAddThickness", "thickness",
       "sizeInX", or "sizeInY" directive is present.  If one of the "scale-
       From" directives or the "scaleToMeanSD" directive is present, the vol-
       ume will be scaled to bytes.  If "scaleFromX" or "scaleFromY" is not
       present, the area used for scaling in X or Y will be the Trimvol
       default of 80% of the range; if "scaleFromZ" is not present, the cen-
       tral one-third of slices will be used.  All of these size and scaling
       directives may be specified either as a number of pixels, or as a frac-
       tion between 0.02 and 1.

       Nonlinear anisotropic diffusion (NAD) with Nad_eed_3d can be run if
       both "runtime.NAD" directives are present for specifying the number of
       iterations and the K value.


   Stopping and Restarting
       The -start and -end options allow datasets to be started and stopped at
       chosen steps in the sequence.  The most useful step to stop at would be
       10, to check CTF plotting and/or gold detection, then restart at 11.
       To check fine alignment before going on, stop and restart at 6.

       If you are setting up a situation where parameters are being changed
       before restarting in an existing dataset, you should experiment to make
       sure the changes have the desired effect and are not overridden.  Here
       are some general guidelines on that point:
       1) Changes in "comparam" directives will generally have no effect once
       a command file is created, because they are processed generically dur-
       ing command file creation.  In most cases, creation occurs during tomo-
       gram setup, but some files are created with Makecomfile just when
       needed, so it would be possible to change "comparam" directives for a
       file still to be created.  Some exceptions to this are "align.tiltal-
       ign.SurfacesToAnalyze" and "tilt.tilt.THICKNESS", for which the current
       directive value will be used instead of the value in the command file.
       2) Changes in "setupset" directives will also generally have no effect
       because they are interpreted during setup; the use of the defocus value
       mentioned above is an exception.
       3) Changes in "runtime" directives will generally have the desired
       effect.
       4) Changes in parameters in the command files will generally have the
       desired effect, unless that parameter is managed by Batchruntomo on the
       basis of "runtime" directives and other information.  The biggest exam-
       ple of this is the treatment of "align.com" when Tiltalign is rerun;
       the -use option is provided specifically to avoid rerunning Tiltal-
       ign(1).


   Resource Usage
       The CPU list provided with the -cpus option is passed directly to Pro-
       cesschunks(1) for running operations that are divided into multiple
       chunks.  However, other operations that run from a single command file
       will generally be run on the local machine, unless the -single option
       is used to direct them to the first machine in the CPU list.  The
       exceptions are two time-consuming steps in dual-axis combination,
       Matchvol and Autopatchfit, which benefit from using multiple
       threads and are sent to the machine with the highest number of CPUs.
       When running single command files, the program sets a limit on the num-
       ber of threads equal to the number of CPUs designated in the CPU list
       for the machine being used, if it is known (-limit can be entered if
       this is not otherwise known for the local machine).


   Running External Commands
       It is possible to specify an arbitrary external command to run either
       instead of a step or after one has run, with "runtime.ReplaceS-
       tep.any.#" or "runtime.RunAfterStep.any.#", respectively, where "#" is
       the step number given below for the -end option.  So far this is possi-
       ble only for CTF determination (step 9) and aligned stack filtering
       (step 13), but more steps can be added easily if needed.  The directive
       value must consist of a single line to run one command-line operation
       without piping or redirection.  The program will place this command
       after a "$" in a command file named "replaceStep.#.com" or "runAfter-
       Step.#.com", and a log will be created when it is run.  The command can
       contain %{setname}, which will be substituted with the root name of the
       data set plus the axis letter, if any.  A replacement command will be
       run even if there are no directives to activate the normal running of
       that step.  However, a command to be run after a step will be run only
       if the normal step is run.


OPTIONS
       Batchruntomo 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.

       -directive (-di) OR -DirectiveFile       File name
              Input file with directives for automating one or more data sets.
              The filename must end in .adoc.  All non-option arguments will
              be taken as such input files.  (Successive entries accumulate)

       -root (-ro) OR -RootName       File name
              A data set name can be provided with this option to override the
              name contained in the directive file, thus allowing directive
              files to be reused without editing.  If this option is used, the
              number of directive files must be either one or the same as the
              number of root names.  The current location of the tilt series
              must be indicated with the -current option if only one directive
              file is entered with multiple root names.  (Successive entries
              accumulate)

       -current (-cu) OR -CurrentLocation       File name
              Directory where tilt series is currently located, or where it
              was originally located if it has already been delivered.  This
              entry overrides the data set directory contained in the direc-
              tive file.  It can be used in two different ways.  If the
              -deliver or -make option is entered, this option specifies the
              directory where a tilt series will be moved from, and it must be
              entered either once (if all data sets are in the same place) or
              once for each data set. If neither of those options are entered,
              then this option specifies the directory where the data set will
              be processed and must be entered once for each data set or not
              at all.  If the program is being rerun with the -deliver option
              and the data set has already been delivered on a previous run,
              the entry here can be either the original location of the stack
              or its current location; the program will recognize that its
              current location is under the delivery directory.  However, if
              the -make option was used and the data set was already deliv-
              ered, this entry must be the original location of the stack
              rather than its new location; otherwise the program will move it
              into a subdirectory of its data set directory.  (Successive
              entries accumulate)

       -deliver (-de) OR -DeliverToDirectory    File name
              Make a subdirectory of the specified directory for each data
              set, named with the root name of the data set, and move the tilt
              series into the subdirectory.  This option can be entered either
              once, or once for each data set to deliver to more than one
              location.  Several other files with the same root name as the
              tilt series will be moved from the current location of the data
              set: an associated metadata file with extension ".mdoc", a log
              of acquisition with extension ".log", and a file of tilt angles
              with extension ".rawtlt".  A raw boundary model for patch track-
              ing or autoseeding will also be delivered.  The -current option
              must be entered either once, or once for each data set.  (Suc-
              cessive entries accumulate)

       -make (-m) OR -MakeSubDirectory
              Make a subdirectory for each data set at its current location,
              named with the root name of the data set, and move the tilt
              series into the subdirectory.  Other files will be moved there
              as well, just as for the -deliver option.  With this option, you
              can sort data sets into multiple top-level directories, and the
              program will take care of putting each one into its own subdi-
              rectory.  This option cannot be entered with the -deliver
              option.  The -current option must be entered either once, or
              once for each data set, and must specify the original location
              of the stack if the program is being rerun and the stack has
              already been delivered.

       -one (-o) OR -ProcessOneAxis   Integer
              Enter 1 to do setup and process A axis, or 2 to skip setup and
              process only B axis.  This entry applies to all dual-axis data
              sets being run.

       -cpus (-cp) OR -CPUMachineList      Text string
              Machines to use in parallel processing, or number of local
              cores.  Each machine name can be followed by a ":" (colon), fol-
              lowed by the number of CPUs to use in that machine; e.g.,
              druid:4,tubule:4.  Prior to IMOD 4.8.25, a "#" sign was used
              instead of ":".  Using the "#" sign will now result in a warning
              when entering options on the command line and an error when
              entering options through standard input, because in the latter
              case it cannot be distinguished from the start of a comment.

       -single (-si) OR -SingleOnFirstCPU
              Run single command files on the first machine in the CPU list,
              instead of on the local machine.  The matchvol and autopatchfit
              steps in combine are not affected by this entry; they are always
              run on the machine with the most CPUs.

       -gpus (-g) OR -GPUMachineList       Text string
              Machines to use for parallel processing with a GPU, or 1 for
              local GPU.  As when running processchunks with the -G option,
              multiple or specific GPUs can be specified by colon-separated
              numbers after a machine name, e.g., druid:2,tubule:1:2.

       -nice (-n) OR -NiceValue       Integer
              Priority level or niceness for running jobs.  Note that this
              applies to all computations, not just those run with parallel
              processing.  The default is 15.

       -limit (-l) OR -LimitLocalThreads   Integer
              Limit on the number of threads when running a single command
              file on the local machine.  By default, this limit is set to the
              number of CPUs on the local machine indicated by the entry to
              -cpus.  If that entry consists only of remote machines, then the
              program has no information about this limit, and single command
              files containing programs parallelized with OpenMP will use all
              available cores.  This option allows one to enter a limit in
              this case, as well as to set a different limit than the number
              of CPUs in the CPU list.

       -remote (-re) OR -RemoteDirectory   File name
              Path on remote machines to directory from which this program is
              started.

       -check (-ch) OR -CheckFile     File name
              File to check for quit and finish signals.  The default is
              batchruntomo.###.input in the directory where this program is
              started, where ### is the process ID.  This file should not have
              the same name as the file used by Batchruntomo to control Pro-
              cesschunks when it runs jobs, which is "processchunks.cmds" in
              the data set directory.  If a Q is placed in this file, it will
              terminate any running jobs and stop all processing.  If an F is
              placed in the file, the program will stop after finishing the
              current data set.  Termination will usually be quicker if a Q is
              placed into "processchunks.cmds" as well, with no delay between
              that action and writing Q to this check file.  Thus, it should
              be done by a program or by entering a single command line with
              two commands on it.

       -email (-em) OR -EmailAddress       Text string
              Address for sending email messages either when a set is aborted
              or when the run completes.

       -SMTP (-SM) OR -SMTPserver     Text string
              An SMTP server for sending email messages.  The default is
              "localhost", but if the local host cannot send email, a server
              can be entered with this option.

       -validation (-v) OR -ValidationType      Integer
              By default, the program will check all directives in the direc-
              tive and template files against the master list of directives in
              IMOD_DIR/com/directives.csv.  Enter 1 to run the program just to
              check a directive file and exit, 2 to check a template file and
              exit, or -1 to skip this step.  When checking a directive file,
              the directive file is first processed to find certain required
              values, and an error in that step will prevent the checking of
              directives.  Template files referenced by the directive file
              will be checked as well.  With an entry of 2, the file will be
              checked right after reading.  A batch directive file is required
              to contain only directives with a Y in the "Batch" column of the
              master directives file, and a template file must contain only
              directives with a Y in the "Tmplt" column.

       -end (-en) OR -EndingStep      Floating point
              Step to end processing with in each set and axis.  Steps are
              numbered as follows:
                 0: Setup
                 1: Preprocessing
                 2: Cross-correlation alignment
                 3: Prealigned stack
                 4: Patch tracking, autoseeding, or RAPTOR
                 5: Bead tracking
                 6: Alignment
                 7: Positioning
                 8: Aligned stack generation
                 9: CTF plotting
                 10: 3D gold detection
                 11: CTF correction
                 12: Gold erasing after transforming fiducial model or
                     projecting 3D model
                 13: 2D filtering
                 14: Reconstruction
                 14.5: Postprocessing on a/b axis reconstruction
                 15: Combine setup
                 16: Solvematch
                 17: Initial matchvol
                 18: Autopatchfit
                 19: Volcombine
                 20: Postprocessing with Trimvol
                 21: NAD (Nonlinear anistropic diffusion)
                These numbers can be relied on not to change again since this
              is now a floating point entry; fractional values will be used if
              necessary to insert more steps without renumbering.

       -start (-st) OR -StartingStep       Floating point
              Step to start processing with.  Steps are numbered as described
              for -end.  Each set will start at this step unless the -first
              option is entered, in which case only the first set will start
              with this step and others will start from the beginning.  In the
              latter case, add 100 to start with this step in the second axis
              of a dual-axis data set.

       -first (-f) OR -StartForFirstSetOnly
              Skip to starting step only for the first set; the following sets
              will be run from the beginning.

       -use OR -UseExistingAlignment
              This option can be used to rerun Tiltalign instead of using the
              existing fine alignment when the -start option is used with a
              value over 6 and the program will be running any steps that
              involve the aligned stack or reconstruction.  With an entry of 0
              in this situation, the program reruns Tiltalign iteratively
              in the usual fashion before proceeding (this can only be done
              with input on sequential lines, not from command line).  The
              default is not to do this, to keep the program from overwriting
              an alignment based on manually adjusted parameters.  Rerunning
              alignment in this situation was a necessity in early versions of
              the program but should no longer be needed; this option is being
              kept just for backwards compatibility.

       -exit (-ex) OR -ExitOnError
              Exit on error instead of going on to next axis or data set

       -etomo (-et) OR -EtomoDebug    Integer
              Run etomo with the given debug level

       -PID   Print process ID

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

       -StandardInput
              Read parameter entries from standard input


FILES
       Batch and template files must have the extension ".adoc".  The tilt
       series file must have an extension ".st" or ".mrc".  When Etomo is run
       to set up the data set, it copies the batch directive file to the
       dataset directory with the name "batchDirective.adoc".  If there are
       any template files, they are copied to the dataset with the the names
       "scopeTemplate.adoc", "systemTemplate.adoc", and "userTemplate.adoc".
       However, if any feature is used that requires modification of the batch
       directive file, namely use of the -root or -current option or template
       files listed without paths, Batchruntomo writes the modified file to
       the dataset directory as "batchDirective.adoc" and runs Etomo with this
       file.

AUTHOR
       David Mastronarde

BUGS
       Email bug reports to mast at colorado dot edu

SEE ALSO
       etomo

HISTORY
IMOD                                4.10.10                    batchruntomo(1)