Command-line interface¶
Every step can be run with sub-commands of the musered command. By default
it supposes that the command is run in the directory containing the settings
file, named settings.yml. Otherwise this settings file can be specified
with --settings.
It is also possible to setup completion, or to run the
subcommands in a REPL with musered repl (after installing click-repl).
Contents
musered¶
Main MuseRed command.
See the help of the sub-commands for more details.
By default musered tries to read a settings file (settings.yml) in the
current directory. This file can also be set with --settings, or with
the MUSERED_SETTINGS environment variable.
The logging level can be set in the settings file, and overridden with
--loglevel.
musered [OPTIONS] COMMAND [ARGS]...
Options
- --version¶
Show the version and exit.
- --redversion <redversion>¶
version of the reduction (overrides the version in settings
- --loglevel <loglevel>¶
log level (debug, info, warning, etc.)
- --drslevel <drslevel>¶
log level for the DRS
- --settings <settings>¶
settings file, default to settings.yml
- --pdb¶
run pdb if an exception occurs
- --debug¶
debug log level + pdb
Environment variables
- MUSERED_SETTINGS
Provide a default for
--settings
check-integrity¶
Test raw files checksum.
musered check-integrity [OPTIONS]
Options
- --report¶
report integrity checks
clean¶
Remove data and database entries for a given recipe and dates.
musered clean [OPTIONS]
Options
- -r, --recipe <recipe>¶
- -d, --date <date>¶
- -n, --night <night>¶
- --force¶
nothing is done if this is not set
- --keep-files¶
do not delete files
exp-align¶
Compute offsets between exposures.
musered exp-align [OPTIONS] DATASET
Options
- --method <method>¶
method to use: drs (default) or imphot
- --name <name>¶
output name, default to method
- --params <params>¶
name of the parameters block
- --filter <filter>¶
filter to use for the images (drs only): white (default), Johnson_V, Cousins_R, Cousins_I
- --date <date>¶
exposure to process, by default all exposures are used
- -f, --force¶
force re-processing (imphot only)
- --dry-run¶
do not run the recipe
- --njobs <njobs>¶
number of parallel process (imphot)
Arguments
- DATASET¶
Required argument
exp-combine¶
Compute offsets between exposures.
musered exp-combine [OPTIONS] DATASET
Options
- --params <params>¶
name of the parameters block
- --method <method>¶
method to use: drs (default) or mpdaf. This can be overridden in the settings file.
- --name <name>¶
output name, default to “{dataset}_{recipe}”
- --dry-run¶
do not run the recipe
- -f, --force¶
force re-processing
Arguments
- DATASET¶
Required argument
info¶
Print info about raw and reduced data, or night or exposure.
musered info [OPTIONS]
Options
- --datasets¶
list all datasets
- --nights¶
list all nights
- --runs¶
list all runs
- --calibs¶
list calibration sequences
- --exps¶
list all exposures
- --qc <qc>¶
show QC keywords
- --date <date>¶
show info for a given date
- --run <run>¶
show info for a given run
- --excluded¶
show excluded exps (for the main info report)
- --tables <tables>¶
tables to show, comma-separated list, allowed values are raw, calib, and science. By default all tables are displayed.
- --no-header¶
hide header
info-exp¶
Show reduction log for a night or exposure.
Example:
$ musered info-exp 2017-06-16T01:34:56.867
$ musered info-exp --night --short 2017-06-17
musered info-exp [OPTIONS] [EXP]...
Options
- --night¶
show reduction log for a night
- --short¶
shortened output for –exp
- -r, --recipe <recipe>¶
recipe name to show
Arguments
- EXP¶
Optional argument(s)
info-raw¶
Print a table with raw exposures.
The displayed files can be limited to the result of a query, with key:value items passed as arguments. Example:
$ musered info-raw DPR_CATG:CALIB night:2017-06-18
musered info-raw [OPTIONS] [SELECT]...
Arguments
- SELECT¶
Optional argument(s)
info-warnings¶
Print warnings.
--mode summaryprints a table with the number of warnings per recipe and exposure name.--mode listprints the list of exposures with warnings, with the log filename.--mode detailprints all warnings for each exposure.
musered info-warnings [OPTIONS]
Options
- -m, --mode <mode>¶
display mode
- Options
summary | list | detail
- -d, --date <date>¶
show info for a given date
- -r, --recipe <recipe>¶
recipe name to show
process-calib¶
Process calibrations (bias, dark, flat, etc.) for given nights.
By default, process calibrations for all nights, and all types except dark.
Already processed calibrations are skipped unless using --force.
musered process-calib [OPTIONS] [DATE]...
Options
- -f, --force¶
force re-processing nights
- --dry-run¶
do not run the recipe
- --bias¶
run muse_bias
- --dark¶
run muse_dark
- --flat¶
run muse_flat
- --wavecal¶
run muse_wavecal
- --lsf¶
run muse_lsf
- --twilight¶
run muse_twilight
Arguments
- DATE¶
Optional argument(s)
process-exp¶
Run recipes for science exposures.
By default, run scibasic, standard, and scipost, for all exposures.
Already processed exposures are skipped unless using --force.
musered process-exp [OPTIONS] [DATE]...
Options
- -f, --force¶
force re-processing exposures
- --dry-run¶
do not run the recipe
- --scibasic¶
run muse_scibasic
- --standard¶
run muse_standard
- --scipost¶
run muse_scipost
- --makecube¶
run muse_scipost_make_cube
- --superflat¶
run superflat
- --zap¶
run zap
- --fsf¶
run fsf for individual exposures
- --params <params>¶
name of the parameters block
- --dataset <dataset>¶
process exposures for a given dataset
Arguments
- DATE¶
Optional argument(s)
retrieve-data¶
Retrieve files and/or calibrations from the ESO archive.
By default this will retrieve science files and associated calibrations, with the filters defined in the settings files. It is also possible to retrieve all the calibration files for a list of nights (with –calib) and for an instrument mode (–ins-mode).
Note that the definition of nights is different for MuseRed and for ESO:
for MuseRed, the 2017-06-19 night corresponds to the day calibrations of 2017-06-20
for ESO, the 2017-06-19 night corresponds to the day calibrations of 2017-06-19
Examples:
$ musered retrieve-data --start 2017-06-19 IC4406
$ musered retrieve-data --calib 2017-06-19 --ins-mode WFM-AO-N
musered retrieve-data [OPTIONS] [DATASET]...
Options
- --username <username>¶
username for the ESO archive
- --help-query¶
print query options
- --dry-run¶
don’t retrieve files
- --force¶
request all objects
- --no-update-db¶
don’t update the database
- --calib <calib>¶
retrieve only calibrations for a list of comma-separated nights (YYYY MM(M) DD)
- --ins-mode <ins_mode>¶
instrument mode for calib retrieval
- --start <start>¶
start date, to limit query results
- --end <end>¶
end date, to limit query results
Arguments
- DATASET¶
Optional argument(s)
shell¶
Starts an IPython shell.
musered shell [OPTIONS]
std-combine¶
Combine std exposures for a given run.
musered std-combine [OPTIONS] [RUN]...
Options
- --params <params>¶
name of the parameters block
- -f, --force¶
force re-processing
Arguments
- RUN¶
Optional argument(s)
update-db¶
Create or update the database containing FITS keywords.
musered update-db [OPTIONS]
Options
- -f, --force¶
force update for existing rows
update-qa¶
Update QA databases (qa_raw and qa_reduced).
musered update-qa [OPTIONS] [DATE]...
Options
- --sky¶
update qa_reduced table with sky flux in B,V,R
- --fsf¶
update qa_reduced table with FSF values
- --sparta¶
update qa_raw table with average sparta seeing and GL
- --imphot¶
update qa_reduced table with imphot values
- --psfrec¶
run PSF reconstruction and update qa_raw table
- --recipe <recipe>¶
recipe name
- --band <band>¶
band to use for –imphot, default to F775W
- --force¶
force update of database
- --dry-run¶
don’t update the database
Arguments
- DATE¶
Optional argument(s)
update-qc¶
Create or update the database containing QC keywords.
musered update-qc [OPTIONS]
Options
- --type <type>¶
type of file to parse (DPR.TYPE)
- --recipe <recipe>¶
recipe for which files are parsed
- -f, --force¶
force update for existing rows