.. reduce.rst .. _reduce: ********************** The ``reduce`` command ********************** Introduction ============ The ``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 :ref:`reduceapi`). 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 on the ``reduce`` command line is provided by a variety of options and switches which we will introduce in this chapter. .. todo: say that the caldb is a vital companion of reduce and refer to the chapter dedicated to it. 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. Nominal usage ------------- Because the Recipe System is automated, in many cases all that is needed is the command and a filename. :: reduce S20161025S0111.fits 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 :ref:`caldb`. The system defaults to using the Gemini Astrodata configuration package and the Gemini data reduction package, ``gemini_instruments`` and ``geminidr``, respectively. Overriding Primitive Parameters ------------------------------- The primitives in 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 ``operation`` and ``reject_method`` to ``median`` and ``minmax``, respectively. 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 :ref:`@file facility`. 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. 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 ``makeProcessedBPM`` recipe. For information about the ``@`` format, see :ref:`atfile` below. 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. 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 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 Command Line Options and Switches ================================= The ``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. 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 ``reduce`` call 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 ['--logfile'] :: logfile :: reduce.log --------------------------------------------------------------------- Input fits file(s): fitsfile.fits Configuration Switches and Options ---------------------------------- **--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_instruments`` and it is distributed with DRAGONS. E.g., ``--adpkg scorpio_instruments`` **--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 ``geminidr`` and it is distributed with DRAGONS. E.g., ``--drpkg scorpiodr`` **--logfile ** Set the log file name. The default is ``reduce.log`` and it is written in the current directory. **--logmode ** Set logging mode. One of * standard * quiet * debug "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 , --param ** Set a primitive input parameter from the command line. The form is ``-p primitivename:parametername=value`` 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`` The form ``-p parametername=value`` is 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. **--qa** 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. **--ql** 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. **-r , --recipe ** 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. :: -r /path/to/recipes/recipelibrary.recipename For a recipe file in the current working directory, the path can be omitted:: -r recipelibrary.recipename 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:: -r display **--suffix ** Add "suffix" to output filenames at the end of the reduction. **--upload** **Currently used internally (Gemini) only.** Send specific pipeline products to internal database. The default is None. :: --upload metrics calibs or equivalently:: --upload=metrics,calibs **--user_cal ** Specify which processed calibration to use for the reduction. This override the selection from the local calibration manager. The syntax is:: --user_cal calibrationtype:path/calibrationfilename Eg.:: --user_cal processed_bias:somepath/processed_bias.fits The recognized calibration types are currently: * processed_arc * processed_bias * processed_dark * processed_flat * processed_fringe * processed_slitillum * processed_standard **-c , --config ** Specify a configuration file for DRAGONS. By default, the file indicated by the ``$DRAGONSRC`` environment 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. .. _atfile: The @file Facility ================== The reduce command line interface supports an "at-file" facility. An ``@file`` allows users to provide any and all command line options and flags to ``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. Basic @file Usage ----------------- In a previous section we had an example where we were modifying a primitive'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 ``@file`` to ``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 more ``@file`` in another (see :ref:`recursive`). 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:: reduce @reduce_args.par 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 ``#`` character. Finally, the "at-file" does not need to be in the current directory. A path can be given. For example:: reduce @../reduce_args.par .. _recursive: Recursive @file Usage --------------------- As implemented, the ``@file`` facility will recursively handle and process other ``@file`` specifications that appear in a ``@file`` or 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 ``reduce_args.par`` file:: # input files @bias.lis # primitive parameters optimization --param # stackFrames stackFrames:operation=median stackFrames:reject_method=minmax # recipe -r myrecipelib.myrecipe The ``reduce`` call becomes:: reduce @reduce_args.par 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 Overriding @file Values ----------------------- The ``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. The ``-p`` or ``--param`` will accumulate a set of parameters *or* override a particular parameter. This may be seen when a parameter is specified in a user ``@file`` and then specified on the command line. See Example 1 and 2 below. 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. Examples ++++++++ The ``@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 ``@file``:: 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 ``@files`` will be ignored:: reduce @reducepar S20161025S0111.fits Summary of parsed options: -------------------------- Input files: S20161025S0111.fits Parameters: no changes Recipe: no changes