imodenv(1)                  General Commands Manual                 imodenv(1)



NAME
       Description of IMOD environment variables


DESCRIPTION
       This page describes all of the environment variables that can be set
       for use with IMOD programs.


   User-level variables
       ANALYZEDM3_DEBUG
              Set this variable (no value needed) to get debugging output from
              the function that analyzes DigitalMicrograph dm3 or dm4 files
              for header data.

       AUTODOC_DIR
              Alternative directory to search for an autodoc file when a
              program uses PIP for input.

       ETOMO_LOG_DIR
              Directory into which Etomo will place error log files named by
              date and time, instead of into $HOME/.etomologs.  Set this to a
              non-existent name (e.g., stuffAndNonsense) to have sequentially
              numbered error logs kept in the directory from which Etomo was
              started.

       ETOMO_LOGS_TO_RETAIN
              Set this to the number of log files named by date and time to
              retain in the directory where they are kept.  The default is 31
              if this variable is not set.

       ETOMO_MEM_LIM
              Memory limit for running etomo.  Define this as a number of
              megabytes followed by the letter "m".  The default of 128m is
              set in the etomo startup script.  Larger values will allow
              larger final alignment logs to be displayed.

       FINDWARP_LEGACY_RATIOS
              Set to 1 to force Findwarp to use an older method of
              computing the ratio of measurements to unknown values even for
              new data, or -1 to make it use the newer method even with older
              data.

       IMOD_ALL_BIG_TIFF
              Set to 1 to make all new TIFF files be opened in the newer
              format that allows files bigger than 4 GB, even when it is not
              known at the time of opening that the file will be large.
              Currently only Mrc2tif and Newstack will write a multi-
              image TIFF file bigger than 4 GB in the correct format.  This
              variable would need to be set to get other other programs to
              write large TIFF files correctly.  However, with it set, smaller
              TIFF files written by those programs (except 3dmod snapshots)
              will be unreadable by other software that does not read large
              files.

       IMOD_AUTOSAVE
              Interval at which 3dmod should autosave the model, in minutes
              (superceded by setting in 3dmod preferences).

       IMOD_AUTOSAVE_DIR
              Directory into which 3dmod should autosave the model (superceded
              by setting in 3dmod preferences).

       IMOD_BRIEF_HEADER
              If this variable is set, all Fortran programs except header
              will output a brief header with the dimensions, pixel size,
              mode, minimum, maximum, and mean value, and the first and last
              title.

       IMOD_CALIB_DIR
              Directory in which IMOD-related information can live, unaffected
              by upgrading the main IMOD directory.  Set by startup scripts to
              /usr/local/ImodCalib.

       IMOD_DIR
              The path to the top IMOD directory; set by startup scripts, or
              can be set before startup script is run.

       IMOD_DUMP_FSCACHE
              Makes 3dmod tell the system to dismiss the file system cache
              while loading a file on Linux.  This behavior was originally the
              default because, on early 64-bit systems with files bigger than
              about half of the system memory capacity, the system would swap
              out data within 3dmod while loading.  This bad system behavior
              was no longer observed in testing on FC4, RHEL4 and RHEL5.  Set
              this variable (no value needed) for working on systems that show
              this problem or to clear the cache in order to experiment with
              file access times.

       IMOD_JAVADIR
              Location of Java to be used to run Etomo; $IMOD_JAVADIR/bin is
              put on the front of the path in the etomo startup script.

       IMOD_JPEG_QUALITY
              Sets the quality level for JPEG output from programs other than
              Mrc2tif and 3dmod; values between 25 and 100 are meaningful.

       IMOD_JPEG_RESOLUTION
              Sets the resolution in dots per inch stored in JPEG files
              produced by programs other than Mrc2tif and 3dmod.  This is
              limited to a 16-bit integer (65535) and cannot encode pixel
              sizes below 400 nm.

       IMOD_NO_IMAGE_BACKUP
              If this variable is set (no value needed), virtually all
              programs that create image files will no longer back up an
              existing file by adding ~ to the name.  Instead, they will
              overwrite the file.

       IMOD_OUTPUT_FORMAT
              Sets the default file format for new files created by virtually
              all IMOD programs.  Possible settings are MRC, HDF, TIFF (or
              TIF), and JPEG (or JPG).  TIFF and JPEG output will work only
              for programs that output data as whole images instead of in
              chunks; JPEG output must be byte or RGB mode and will only work
              when writing a single section to the output file.

       IMOD_PLUGIN_DIR
              Main directory for IMOD plugins; set by startup scripts to be
              inside IMOD.

       IMOD_PROCESSORS
              Number of processors in the computer; used by slicer to decide
              how many threads to run in parallel.  Also used to create a
              parallel processing table when cpu.adoc is not found.

       IMOD_PS_FONT
              Name of a font (instead of Helvetica) to use in the Postscript
              output from various graphics programs; Arial is good for going
              to Illustrator.

       IMOD_QTLIBDIR
              Directory in which IMOD's copy of Qt lives, if any.  Set by IMOD
              startup scripts.


       IMOD_STEREO_COMMAND
              When using obsolete hardware stereo, system command for
              switching the monitor to display left and right buffers in
              overlapping fashion.

       IMOD_STEREO_RESTORE
              System command for switching the monitor back to normal mode.

       IMOD_STEREO_TBOFFSET
              Default value of vertical offset when using top/bottom stereo
              display.

       IMOD_TIFF_COMPRESSION
              Sets the type of compression for TIFF files output by programs
              other than Mrc2tif.  Must be set to an integer value: 1 for
              none, 5 for LZW, 7 for JPEG, 8 for ZIP, or other values listed
              in the Mrc2tif manpage.

       IMOD_TIFF_QUALITY
              Sets the quality level for TIFF compressed files output by
              programs other than Mrc2tif.  Values should be between 1 and 9
              for ZIP compression and between 25 and 100 for JPEG compression.

       IMOD_NO_TIFF_MEM_MAP
              Set this variable to any value to disable memory mapping when
              reading TIFF files, which can greatly increase the memory usage
              for large files.

       IMOD_TMPDIR
              Path for temporary directory used by scripts.  On Windows, this
              can be in Cygwin or Windows format, with forward or back
              slashes.

       IMOD_USE_GPU

       IMOD_USE_GPU2
              These variables will tell the Tilt program (and eventually
              perhaps other programs) to use the GPU on a CUDA-capable NVIDIA
              graphics card.  Set the variable to 0 to use the best available
              GPU, or to a positive number to specify the GPU to use.  If
              there is only one GPU, 0 and 1 have the same effect.  The
              setting with IMOD_USE_GPU is overridden by the UseGPU entry to
              Tilt, if any, while a setting with IMOD_USE_GPU2 overrides the
              UseGPU entry.

       INVERT_MRC_ORIGIN
              This variable can be used to override the default setting for
              whether origin values are written to an MRC file with the
              internal IMOD convention, in which subareas have more negative
              origin values, or with an inverted sign that corresponds to the
              MRC standard.  Set the variable to 1 to have origins written
              with the MRC standard sign, or 0 to have them written with the
              internal IMOD sign.  Currently the default is to write with the
              internal IMOD sign.

       PARALLEL_BOUNDARY_SIZE
              Set this buffer with the default number of pixels to use for the
              boundary region when writing in parallel to an MRC file.  This
              value will override the built-in default of 2048 provided that
              it is greater than that default; options to Splittilt,
              Sirtsetup(10), Splitcorrection, and Splitblend for setting
              the size of the boundary region will in turn override this
              value.

       PARALLEL_HDF_BUF_SIZE
              Set this variable with the number of megabytes to allocate for
              buffering data when writing to an HDF file in parallel from
              multiple processes.  The default is 20.

       PIP_PRINT_ENTRIES
              Set this variable to 1 to enable printing of all options entered
              into a program using PIP input or 0 to disable it.  The variable
              is automatically set to 1 when running programs through command
              files (i.e., vmstocsh and vmstopy both add lines to their output
              to set the variable to 1).  Thus, if you leave the variable
              unset in your environment, entries will be printed in programs
              run through "subm" but not when programs are run at the command
              line.  If you want the output when running at the command line,
              set the variable to 1 in your environment.  To avoid this output
              when running a command file, add a line
                  $setenv PIP_PRINT_ENTRIES 0
              at the beginning of the file.

       PLAX_REDRAWS
              If there is trouble with the "plax" window used by Fortran
              graphics programs not updating properly, set this variable to
              the number of times for it be drawn (try 2 or 3).  These
              programs include nda, sda, mtk, genhstplt, mtoverlap, mtpairing,
              avgstatplot, and filterplot.

       RAPTOR_BIN
              Directory where alternative RAPTOR executables are located;
              leave this undefined to run the executables in IMOD.

       READ_MODE0_SIGNED
              Set this variable non-zero to override the default for whether
              an MRC file in mode 0 should be read as signed or unsigned
              bytes.  Potential values are:
                 -2   to read all mode 0 files as unsigned, even ones with an
              IMOD stamp
                 -1   to read mode 0 files lacking an IMOD stamp as unsigned
                 1    to read mode 0 files lacking an IMOD stamp as signed
                 2   to read all mode 0 files as signed, even ones with an
              IMOD stamp
              The values of -1 and 1 could be useful if a file header has
              incorrect entries for the minimum and maximum.  Values of -2 or
              2 would be needed if other software changed the representation
              of bytes in a file without modifying the IMOD stamp and flag
              values.

       RUNCMD_VERBOSE
              Set this variable to 1 to have the runcmd function called by
              Python programs print each command, input to the command, and
              the output of the command unless the output was already printed
              on standard out.

       SUBM_LOG_TYPE
              Set this variable to a positive value up to 4 to have subm
              (submfg) produce sequentially numbered log files with the given
              number of digits, or to -1 to -3 to have a date-time stamp
              attached the log file name.

       SUBM_MESSAGE
              Set this variable to an alternative message to be used when subm
              (submfg) completes execution of a command file.

       TIFF_RES_PIXEL_LIMIT
              This variable sets an upper limit on the pixel size, in microns,
              that is set when reading a TIFF file that has resolution tags in
              it.  This setting affects whether tif2mrc automatically puts
              a pixel size from the TIFF input into the output file, and
              whether 3dmod thinks that a read-in TIFF file has a pixel
              size other than 1.  The default value is 3.0 microns.

       TILECACHE_LIMIT_MB
              The variable sets the default limit on the size of the
              tile/strip cache in 3dmod when an image pyramid is displayed
              and the cache size is not specified with the -C or -CT option.
              The value should be an integer specifying the size in megabytes.
              The default in 3dmod is 20000.

       WRITE_MODE0_SIGNED
              Set this variable to 0 to have all MRC files in mode 0 written
              as unsigned bytes, which was the convention used by IMOD prior
              to 4.8.24 but is contrary to the current MRC standard.


   Build and Test Variables
       BRT_TEST_OPTIONS
              When the Batchruntomo test is run in the nightly ImodTests, this
              variable can be set to provide options in place of "-cpu 2".

       BRT_TEST_SOURCE_DIR
              If this environment variable is set to a location where the
              stacks BBa.st and BBb.st are located, the nightly tests in
              ImodTests will include a reconstruction of this data set with
              Batchruntomo.

       CUDA_DIR
              Directory with CUDA toolkit, must be defined to enable building
              with CUDA.

       CUDA_BIN_PATH
              On Windows, this must be defined as the location of CUDA
              binaries if they are not in $CUDA_DIR/bin

       CUDA_LIB_PATH
              On Windows, this must be defined as the location of CUDA
              libraries if they are not in $CUDA_DIR/lib

       IMOD_FFTW_TIMING
              If defined, enables output from the FFTW wrapper routine about
              the number of threads used and the time consumed.

       IMOD_REPORT_CORES
              If defined, enables output from the numOPMthreads routine about
              the number of physical and logical processors and its decision
              on how to limit the number of threads.

       IMOD_SETUP_USE_MKL
              Make the default for IMOD setup to be to use MKL.

       IMOD_TEST_SECTION
              This is passed to the uitest script when running Etomo tests.
              It is used to choose one of the tests in uitest.adoc.

       IMOD_UITEST_DATA
              When running Etomo tests, the root directory for data files.

       IMOD_UITEST_SCRIPT
              This is used in uitest.make.  It should be set to the location
              of the uitest script

       IMOD_UITEST_SOURCE
              When running Etomo tests, the location of the uitest.adoc and
              all autodocs it refers to.

       JAVA_DIR
              Location of Java SDK to be used by the IMOD build and test
              script.

       MSVCREDIST
              Location of Microsoft Visual C redistributable run-time
              libraries that are to be copied when building a distribution.
              When this is defined, manifests are also added to all
              executables.

       QTDIR  Location of Qt, or at least of Qt bin directory if include is
              elsewhere.

       SCRIPT_TEST_DIR
              An alternate location for Python source scripts run by the tests
              in ImodTests/scriptTests.

       SOLVEMATCH_TEST
              Set this variable to prevent Solvematch from exiting with error
              when given a data set with relative coordinates.

       TEST_ALIGNFRAMES_GPU
              Set this variable to run the Alignframes test
              ImodTests/xformTests with GPU.



IMOD                                4.10.10                         imodenv(1)