reduce command is the DRAGONS Recipe System command line interface.
The Recipe System also provides an application programming interface (API),
whereby users and developers can programmatically invoke
Reduce and set
parameters on an instance of that class (see The Reduce Class).
Both interfaces allow users to configure and launch a Recipe System processing
pipeline on one or more similar input datasets. Control of the Recipe System
reduce command line is provided by a variety of options and
switches which we will introduce in this chapter.
4.2. Usage Examples¶
Below we show examples that a user might typically want to do when using
reduce. The command offers a lot of flexibility though, these examples
are just a small subset of the possibilities. The objective here is to help
the user get started.
4.2.1. Nominal usage¶
Because the Recipe System is automated, in many cases all that is needed is the command and a filename.
The system defaults to the “sq” mode, ie. science quality recipes. The best match recipe will be used with the best match primitive set. The required processed calibrations will be fetched from the local calibration manager.
The system defaults to using the Gemini Astrodata configuration package and
the Gemini data reduction package,
4.2.2. Overriding Primitive Parameters¶
The primitives for each set are given default values that have been found to
give good results in most cases. Depending on the data and the science
objectives, it might be necessary to tweak the primitive parameters to
optimize the reduction. The
-p, or in long form
--param option allows
the user to override the defaults.
reduce S20161025S0111.fits -p stackFrames:operation=median \ stackFrames:reject_method=minmax
This sets the
stackFrames input parameters
As one can see that, if several parameters are to be modified, the command can grow rather long. There is a way to keep it clean, see the section below on the @file facility.
4.2.3. Calling Specific Recipes and Primitives¶
The Recipe System’s default behavior is to select the best recipe automatically. It is however possible, and sometimes required, to override this.
126.96.36.199. Override the default recipe¶
The first case where the recipe selection can be overridden is to select a recipe in the library different from the default. A recipe library can contain more than one recipe. Only one is set as the default. To let the Recipe System select the most appropriate recipe library, but then request the use of recipe within that library other than the default, simply state the name of the desired recipe. A good example is when making a bad pixel mask (BPM) for NIRI:
reduce @flats @darks -r makeProcessedBPM
Here the Recipes System will find the recipe library for NIRI flats (because
the flats are first in the list), and then instead of running the default
recipe which would in this case make a processed flat, it will run the
For information about the
@ format, see The @file Facility below.
188.8.131.52. User recipe¶
It is possible for the user to force the use of a custom recipe. This is
done with the
-r flag again. The structure “recipe library containing
recipes” must still be obeyed. Here is how the request is made:
reduce S20161025S0111.fits -r myrecipelibrary.myspecialrecipe
Both the name of the recipe library and, after the dot, the name of the recipe function are required. The path to the library can be prepended.
184.108.40.206. Calling a single primitive¶
Single primitives can be called directly from the command line bypassing the
recipes entirely. A useful case is when one wants to display dataset. There
is a primitive named
display. The Recipe System will find the best-match
primitive set, and then run the
display primitive it contains.
reduce S20161025S0111.fits -r display
4.2.4. Manually Setting Calibrations¶
When the calibration manager is not available or if working on a new type of data not yet coded in the calibration association rules, it will be necessary to specify the processed calibration to use on the command line.
Another situation would be if one wanted to try various version of a calibration or different calibrations altogether to try to optimize a reduction. In such a case, one needs full control on which calibration is being used rather than always using the “best-match” returned by the local calibration manager.
reduce S20161025S0111.fits --user_cal processed_bias:S20161025S0200_bias.fits
4.3. Command Line Options and Switches¶
reduce command help is provided by the
--help option. This help is
also available as a manual page as (
man reduce). The options and switches
are described further here.
4.3.1. Information Switches¶
- -h, –help
- show the help message and exit
- -v, –version
- show program’s version number and exit
- -d, –displayflags
Display all parsed option flags and exit.
The table provides a convenient view of all passed and default values for
reduce. This can be useful when wanting to verify the syntax of a
reducecall and to make sure everything has been parsed as expected.
Note that when not specified, recipename indicates ‘None’ because at this point in the execution the Recipe System has not yet been invoked and a default recipe not yet been determined. Eg.,
$ reduce -d --logmode quiet fitsfile.fits Literals var 'dest' Value ----------------------------------------------------------------- ['-d', '--displayflags'] :: displayflags :: True ['-p', '--param'] :: userparam :: None ['--logmode'] :: logmode :: quiet ['--ql'] :: mode :: sq ['--qa'] :: mode :: sq ['--upload'] :: upload :: None ['-r', '--recipe'] :: recipename :: None ['--adpkg'] :: adpkg :: None ['--suffix'] :: suffix :: None ['--drpkg'] :: drpkg :: geminidr ['--user_cal'] :: user_cal :: None
- [‘-c’, ‘–config’] :: config_file :: None
Input fits file(s): fitsfile.fits
4.3.2. Configuration Switches and Options¶
- –adpkg <ADPKG>
Specify an external AstroData configuration package. This is used for non-Gemini instruments or during development of a new Gemini instrument. The package must be importable. The default AstroData configuration package is
gemini_instrumentsand it is distributed with DRAGONS.
- –drpkg DRPKG
Specify an external data reduction package. This is used for non-Gemini instruments or during development of a new Gemini instrument. The package must be importable. The default data reduction package is
geminidrand it is distributed with DRAGONS.
- –logfile <LOGFILE>
- Set the log file name. The default is
reduce.logand it is written in the current directory.
- –logmode <LOGMODE>
Set logging mode. One of
“quiet” writes only to the log file. The other modes writes information to the screen and to the log file. The default is “standard”.
- -p <USERPARAM [USERPARAM …]>, –param <USERPARAM [USERPARAM …]>
Set a primitive input parameter from the command line. The form is
This sets the parameter such that it applies only for the primitive “primitivename”. To set multiple parameter-value pairs, separate them with whitespace, eg.
-p par1=val1 par2=val2
-p parametername=valueis also allowed but beware, that will sets any parameter with that name from any primitives to that value. It is somewhat dangerous and of limited use. It is to be seen as a global setting.
- Set the mode of operation to “qa”, “quality assessment”. When no “qa” or “ql” flag are specified the default mode is “sq”. The “qa” mode is use internally at Gemini. Recipes differ depending on the mode.
- Set the mode of operation to “ql”, “quicklook”. When no “qa” or “ql” flag are specified the default mode is “sq”. The “ql” mode is use for quick, near science quality reduction. Science quality is not guaranteed. Recipes differ depending on the mode. This mode is not yet implemented. “ql” recipes are not yet available.
- -r <RECIPENAME>, –recipe <RECIPENAME>
Specify a recipe by name. Users can request a non-default system recipe by names, e.g.,
-r makeProcessedBPM, or may specify their own recipe library and recipe function within. A user-defined recipe function must be “dotted” with the recipe file.
For a recipe file in the current working directory, the path can be omitted:
A recipe library can contain more than one recipe. The recipe library must be a Python module, eg.
recipelibrary.py. The recipes are Python functions within that module.
Finally, instead of specifying a recipe, it is possible to specify a primitive:
- –suffix <SUFFIX>
- Add “suffix” to output filenames at the end of the reduction.
Currently used internally (Gemini) only.
Send specific pipeline products to internal database. The default is None.
--upload metrics calibs
- –user_cal <USER_CAL [USER_CAL …]>
Specify which processed calibration to use for the reduction. This override the selection from the local calibration manager. The syntax is:
The recognized calibration types are currently:
- -c <CONFIGFILE>, –config <CONFIGFILE>
- Specify a configuration file for DRAGONS. By default, the file indicated
$DRAGONSRCenvironment variable will be used or, if that variable is not defined, then the default
~/.dragons/dragonsrc. This switch will take priority to use the specified configuration file.
4.4. The @file Facility¶
The reduce command line interface supports an “at-file” facility.
@file allows users to provide any and all command line options and flags
reduce in an acsii text file. This tool is very useful to keep the
command line to a reasonable length and also to keep a record of the
configurations that are applied. Here we illustrate how to use it.
4.4.1. Basic @file Usage¶
In a previous section we had an example where we were modifying a primmitive’s input parameter values.
reduce S20161025S0111.fits -p stackFrames:operation=median \ stackFrames:reject_method=minmax
Instead of typing the parameter settings on the command line, it might be
more convenient to use an “at-file”. We can write the parameter information
in the “at-file” and add it to our
reduce call. Let us have a file
named “myreduction.par” with this content:
-p stackFrames:operation=median stackFrames:reject_method=minmax
Now we can call
reduce as follow:
reduce S20161025S0111.fits @myreduction.par
By passing an
reduce on the command line, users can encapsulate
all the options and positional arguments they may wish to specify in a single
@file. It is possible to use multiple
@file and even to embed one or
@file in another (see Recursive @file Usage). The parser opens all files
sequentially and parses all arguments in the same manner as if they were
specified on the command line.
To further illustrate the convenience provided by an
@file, we’ll continue
with an example
reduce command line that has even more arguments. We will
also include new positional arguments, i.e., file names:
$ reduce -p stackFrames:operation=median stackFrames:reject_method=minmax \ -r myrecipelib.myrecipe S20161025S0200.fits S20161025S0201.fits \ S20161025S0202.fits S20161025S0203.fits S20161025S0204.fits
Here, two user parameters are being specified with
-p, a recipe with
-r, and a list of input datasets. We can write all this into a plain text
@file, let’s name it “reduce_args.par”:
# input data files S20161025S0200.fits S20161025S0201.fits S20161025S0202.fits S20161025S0203.fits S20161025S0204.fits # primitive parameters optimization --param # stackFrames stackFrames:operation=median stackFrames:reject_method=minmax # recipe -r myrecipelib.myrecipe
Now we can call
reduce this way:
The order of the arguments in an
@file is irrelevant, as is the file name.
Also, the parser sees no difference across white space characters, such as
space, tabs, newlines, etc. Comments are accommodated, both full line and
in-line with the
Finally, the “at-file” does not need to be in the current directory. A path can be given. For example:
4.4.2. Recursive @file Usage¶
As implemented, the
@file facility will recursively handle and process
@file specifications that appear in a
on the command line. For example, we may have another file containing a
list of input files, let’s call it “bias.lis”:
# raw biases S20161025S0200.fits S20161025S0201.fits S20161025S0202.fits S20161025S0203.fits S20161025S0204.fits
Then, we can add this list as an “at-file” in the
# input files @bias.lis # primitive parameters optimization --param # stackFrames stackFrames:operation=median stackFrames:reject_method=minmax # recipe -r myrecipelib.myrecipe
reduce call becomes:
The parser will open and read the @bias.lis, consuming those lines in the same way as any other command line arguments. Indeed, such a file need not only contain fits files (positional arguments), but other arguments as well. This is recursive. That is, the @fitsfiles can contain other “at-files”, which can contain other “at-files”, which can contain …, etc. These will be processed serially.
Or one might want to keep the input files and the parameter settings separate.
Then if we remove the
@bias.lis from the “reduce_args.par” files, we can
use it explicitly on the
reduce command line:
reduce @bias.lis @reduce_args.par
4.4.3. Overriding @file Values¶
reduce application employs a customized command line parser such that
the command line option given in the
@file can be modified on the command
line after the
@file has been processed.
--param will accumulate a set of parameters or override a
particular parameter. This may be seen when a parameter is specified in a
@file and then specified on the command line. See Example 1 and 2
For unitary value arguments, the command line value will override the
@file value. See Example 3 below.
It is further specified that if one or more datasets (i.e. positional arguments) are passed on the command line, all files appearing as positional arguments in the “at-file” will be replaced by the one(s) on the command line. See Example 4 below.
In all cases, remember to use the
-d option to verify the parsing if you
are not sure.
@file used in the examples, “reducepar”, contains:
# input data files S20161025S0200.fits S20161025S0201.fits S20161025S0202.fits S20161025S0203.fits S20161025S0204.fits # primitive parameters optimization --param # stackFrames stackFrames:operation=median # recipe -r myrecipelib.myrecipe
Example 1: Accumulate a new parameter:
reduce @reducepar --param stackFrames:hsigma=5.0 Summary of parsed options: -------------------------- Input files: no changes Parameters: ['stackFrames:operation=median', 'stackFrames:hsigma=5.0'] Recipe: no changes
Example 2: Override a parameter defined in the
reduce @reducepar --param stackFrames:operation=wtmean Summary of parsed options: -------------------------- Input files: no changes Parameters: ['stackFrames:operation=wtmean'] Recipe: no changes
Example 3: Override the recipe:
reduce @reducepar -r myrecipelib.different_recipe Summary of parsed options: -------------------------- Input files: no changes Parameters: no changes Recipe: myrecipelib.different_recipe
Example 4: Override the input files. All the files in the
reduce @reducepar S20161025S0111.fits Summary of parsed options: -------------------------- Input files: S20161025S0111.fits Parameters: no changes Recipe: no changes