Provided by: esorex_3.13.7+ds-1_amd64 
NAME
esorex - ESO Recipe Execution Tool
SYNOPSIS
esorex [esorex-options] recipe [recipe-options] sof
DESCRIPTION
EsoRex is the ESO Recipe Execution Tool. It can list, configure and execute CPL-based
recipes from the command line.
One of the features provided by the CPL is the ability to create data-reduction algorithms
that run as plugins (dynamic libraries). These are called recipes and are one of the main
aspects of the CPL data-reduction development environment.
As these recipes are dynamic libraries, it is not possible to run them directly from the
command line. However, ESO provides several tools to do this, thus saving recipe
developers the need to write such an application themselves. One of these is GASGANO (a
GUI-based tool) and the other is EsoRex (which runs from the command line) and is
described here.
OPTIONS
--help Display this help and exit. If a recipe name is also given, then help will be given
for it as well. [TRUE]
--version
Display version information and exit. [FALSE]
--check-sof-exist
When TRUE, all the input files must exist and be readable before calling the
recipe. This option may also be set using the environment variable
ESOREX_CHECK_SOF_EXIST. [FALSE]
--config
Configuration file to be used for EsoRex. This option may also be set using the
environment variable ESOREX_CONFIG. []
--create-config
Creates a configuration file for Esorex. If set to TRUE a config file 'esorex.rc'
is created in the '.esorex' directory in $HOME of the user.If a filename is
specified, a config file will be created accordingly. If a recipe is specified in
the command line, then the configuration file will be created for the recipe
instead (called 'recipename.rc') Note that an existing file will be overwritten,
but a backup file will be copied to 'filename.rc.bak' in the same directory. If the
filename ends with extension .json then a machine-readable JSON format will be
used. This option may also be set using the environment variable
ESOREX_CREATE_CONFIG. [FALSE]
--link-dir
The directory in which a symbolic link to each of the product files should be
written. The enable/disable switch to control whether the link is actually made is
the '--suppress-link' option. This option may also be set using the environment
variable ESOREX_LINK_DIR. [/tmp]
--log-dir
Directory where to place the logfile. This option may also be set using the
environment variable ESOREX_LOG_DIR. [.]
--log-file
Filename of logfile. This option may also be set using the environment variable
ESOREX_LOG_FILE. [esorex.log]
--log-level
Controls the severity level of messages that will be printed to the logfile. This
option may also be set using the environment variable ESOREX_LOG_LEVEL. <debug |
info | warning | error | off> [info]
--no-datamd5
Disables the computation of the MD5 data hash for FITS product files. This option
may also be set using the environment variable ESOREX_NO_DATAMD5. [FALSE]
--no-checksum
Disables the computation of the standard FITS product checksums. This option may
also be set using the environment variable ESOREX_NO_CHECKSUM. [FALSE]
--man-page
Display a manual page for the specified recipe, and then exit. Note that this
option only applies to recipes, and that it does nothing for esorex by itself. See
also the '--help' option. This option may also be set using the environment
variable ESOREX_MAN_PAGE. [FALSE]
--mem-check
Report on memory status at completion of recipe execution. This option may also be
set using the environment variable ESOREX_MEM_CHECK. [FALSE]
--msg-level
Controls the severity level of messages that will be printed to the terminal. This
option may also be set using the environment variable ESOREX_MSG_LEVEL. <debug |
info | warning | error | off> [info]
--output-dir
The directory where the product files should be finally moved to (all products are
first created in the current dir). This option may also be set using the
environment variable ESOREX_OUTPUT_DIR. [.]
--output-prefix
Prefix applied to any output file. For example, specifying 'pre' would translate
'filename.fits' to 'pre_0000.fits'. See also the '--suppress-prefix' option. This
option may also be set using the environment variable ESOREX_OUTPUT_PREFIX. [out]
--output-readonly
When TRUE, any existing product files in the specified output directory will be set
to read-only, for user, group and other. If FALSE, then EsoRex will use the default
permissions for that account/directory. destroy any pre-existing files. This
option exists for the Paranal operations environment. This option can additionally
be used to prevent EsoRex from overwriting pre-existing files. This option may also
be set using the environment variable ESOREX_OUTPUT_READONLY. [FALSE]
--paf-config
Configuration file for creation of PAF files. This option may also be set using the
environment variable ESOREX_PAF_CONFIG. []
--params
List the input parameters and their current settings (whether from the command line
or a configuration file) for the esorex application. Parameters are labelled using
the parameter's alias. If a recipe is also specified, then the list of its
parameters will also be generated in the same way. This option may also be set
using the environment variable ESOREX_PARAMS. [FALSE]
--products-sof
Output file which contains the FITS files created by the recipe. If the filename
ends with extension .json then a machine-readable JSON formatwill be used. This
option may also be set using the environment variable ESOREX_PRODUCTS_SOF. []
--recipes
Display a list of all available recipes (that are available in the directory tree
specified with '--recipe-dir'). This option may also be set using the environment
variable ESOREX_RECIPES. [FALSE]
--recipe-config
Configuration file for any selected recipe. This option may also be set using the
environment variable ESOREX_RECIPE_CONFIG. []
--recipe-dir
Directory containing recipe libraries. Note that esorex will recursively search not
only the specified directory, but all sub-directories below it as well. Multiple
directory heads may be specified, by separating the starting paths with colons (:).
This option may also be set using the environment variable ESOREX_PLUGIN_DIR. [.]
--show-hidden
When TRUE recipe parameters which are declared as hidden by the recipe are shown in
the output of help and man page options. [FALSE]
--suppress-link
When TRUE, no symbolic link is created to the output product. However, if FALSE,
then a symbolic link is created in the directory specified with the option
'--link-dir' for each product that is created by the recipe. This option may also
be set using the environment variable ESOREX_SUPPRESS_LINK. [TRUE]
--suppress-prefix
When TRUE, the original name of the output product, as produced by the recipe, is
maintained. If FALSE, then the name of the output file is changed to the
"prefix_number" format. The prefix can be altered using the '--output-prefix'
option. This option may also be set using the environment variable
ESOREX_SUPPRESS_PREFIX. [FALSE]
--time Measure and show the recipe's execution time. This option may also be set using the
environment variable ESOREX_TIME. [FALSE]
--unload-plugin
When TRUE, the plugin is unloaded after execution. If FALSE, the plugin is not
unloaded after processing, so that a software like, e.g. valgrind, can be used for
debugging the executed recipe. This option may also be set using the environment
variable ESOREX_UNLOAD_PLUGIN. [TRUE]
ENVIRONMENT
All options can be set as environment parameters as well. See the previous
paragraph for details.
FILES
/etc/esorex.rc $HOME/.esorex/esorex.rc
Default configuration files
The configuration file contains the EsoRex options, less the `--´ switch, but
prefixed with `esorex.caller.´. Blank lines are ignored and lines beginning with
`#´ are treated as comments.
Here is an example configuration file.
# Example EsoRex configuration file
#
esorex.caller.recipe-dir=/home/username/EsoRex/Plugins
esorex.caller.log-dir=.
esorex.caller.log-file=esorex.log
esorex.caller.log-file=esorex.log
esorex.caller.output-dir=.
esorex.caller.output-prefix=out_
filename.sof
A sof file contains a list of the input data. This data is specified in an sof file
(which is just a text file), where each input file is specified with its associated
classification and category. The format of each line in the sof file is as follows:
full-path-to-file classification
Optionally, a third column may be provided. Permitted values are either RAW or
CALIB. This is for when a recipe does not identify the type of input file, but as
all ESO recipes are required to do so, this column is typically not needed.
An example sof file, for the mythological "ZIMOS" instrument, might look like this:
/data/mos/ZIMOS.03-12-26T01:05:06.fits MOS_SCIENCE
/data/mos/ZIMOS.03-12-26T01:26:00.fits MOS_SCIENCE
/data/mos/ZIMOS.03-12-26T01:47:04.fits MOS_SCIENCE
/data/cal/master_bias4.fits MASTER_BIAS
/data/cal/grs_LR_red.3.tfits GRISM_TABLE
/data/gasgano/extract_table2.fits EXTRACT_TABLE
/data/cal/badpixel.3.tfits CCD_TABLE
For an concrete example for a specific instrument, check the documentation for that
instrument.
HINTS
File permissions
When a recipe is used with the --suppress-prefix option, and the --output-dir is
set to the current working directory, then the first execution of a recipe will
work correctly, but subsequent executions may fail. This is due to output products
being given `read-only´ permission (to avoid the potential inadvertent loss of
products). The recipe itself is unable to modify the permissions, and thus it fails
when attempting to create the file. The solution (other than using a different
output directory or prefixes) is to change the permission of these output files or
delete them prior to any subsequent execution of that recipe.
This problem is less likely to occur in EsoRex v2+, due to the replacement of the
--output-overwrite option with the --output-readonly (which is disabled by
default). However, a determined user can still reach this situation, in which case
the non-readable products must have their permissions changed, as described above.
Configuration files
When creating configuration files, if the the recipe is provided on the command
line, then EsoRex will generate the configuration file for this recipe. If no
recipe name is given, then EsoRex will generate a configuration file for EsoRex
itself. All configuration files are written in the $HOME/.esorex/ directory.
Memory checking
It is possible to get EsoRex to check for memory leaks in the recipe that it is
running, by enabling the --mem-check option. Then, at the conclusion of the recipe
execution, and after memory deallocation, a list of all remaining allocated memory
will be printed to screen. If there are no memory leaks, then no addition output is
displayed.
REPORTING BUGS
Report bugs to <cpl-help@eso.org>.
COPYRIGHT
Copyright 2003-2018, European Southern Observatory.