5. The Reduce Class

The Reduce class provides the underlying structure of the reduce command. This section describes and discusses the programmatic interface available on the class Reduce. This section is for users wanting to use the Reduce class programmatically.

The reduce application introduced in the previous chapter is a user interface script providing a command line access to the Reduce class. The reduce application parses the arguments and initialize the Reduce class and its runr method. It is possible to bypass the reduce command and sets attributes directly on an instance of Reduce, as the following discussion illustrates.

5.1. Using Reduce

The Reduce class is defined in the recipe_system.reduction.coreReduce module. The Reduce class provides a set of attributes and one public method, runr that launches a reduction. This is the only public method on the class.

5.1.1. Very Basic Usage

The most basic usage involves importing the class, instantiating it, assigning a file to reduce and then launching the runr method.

>>> from recipe_system.reduction.coreReduce import Reduce
>>> myreduce = Reduce()
>>> myreduce.files.append('S20161025S0111.fits')
>>> myreduce.runr()

5.1.2. Typical Usage for Reduction

A more typical usage for reducing data can involve setting other options and can include setting up a logger. When using the Gemini data reduction primitives, the logger is highly recommended.

Normal usage will also likely involve the use of the calibration database facility, caldb. We will ignore caldb here and rather fully describe it and its usage in a subsequent chapter, Local Calibration Database. See Full API Example where we put it all together.

>>> from recipe_system.reduction.coreReduce import Reduce
>>> from gempy.utils import logutils
>>>
>>> logutils.config(file_name='example.log')
>>>
>>> inputfiles = ['S20161025S0200.fits', 'S20161025S0201.fits']
>>> myreduce = Reduce()
>>> myreduce.files = inputfiles
>>> myreduce.runr()

Neither coreReduce nor the Reduce class initializes any logging activity. This is the responsibility of the programmer. The Recipe System does not require a logger but the Gemini primitives do. The absence of a logger when using the Gemini data reduction package leads to double the reporting on the screen. More an annoyance than a problem, admittedly.

You are free to provide your own logger, or you can use the fully defined logger provided in DRAGONS. It is recommended that you use the system logger as Reduce is tuned to use the DRAGONS logger.

Returning to the example above, we could also set the recipe to a custom recipe, override a primitive parameters, set a data reduction package, etc. The attributes that can be set are discussed in Public Attributes to Reduce below.

>>> myreduce.recipename = 'myrecipelib.myrecipe'
>>> myreduce.uparms = [('stackFrames:operation', 'median')]
>>> myreduce.dkpkg = 'thirdpartydr'
>>> # rerun with the modified recipe and parameter
>>> myreduce.runr()

A notable quirk is how to set the adpkg that is defined in the reduce command line interface. The Reduce class does not have an attribute for it. Instead, the programmer must import any third party AstroData instrument configuration files explicitely before launching runr.

>>> import astrodata
>>> import thirdparty_instruments
>>>
>>> myreduce.Reduce()
>>> myreduce.drpkg = 'thirdpartydr'
>>> myreduce.files.append('filename.fits')
>>> myreduce.runr()

5.2. Public Attributes to Reduce

Public Attribute Python type Default
files <type ‘list’ of ‘str’> []
output_filenames <type ‘list’ of ‘str’> None
mode <type ‘str’> ‘sq’
recipename <type ‘str’> ‘_default’
drpkg <type ‘str’> ‘geminidr’
suffix <type ‘str’> None
ucals <type ‘dict’> None
uparms <type ‘list’ of ‘tuple’> None
upload <type ‘list’ of ‘str’> None
files

A list of input file names to reduce. Only the first file in the list will be used for the recipe and primitive selection.

myreduce.files.extend(['S20161025S0200.fits', 'S20161025S0201.fits'])

output_filenames

A list of output file names. This cannot be set. It is a return value. It is used after the recipe has run to collect the names of the files that were created.

output_stack = myreduce.output_filenames[0]

mode

The reduction mode. The Gemini data reduction package currently supports ‘sq’ and ‘qa’, with ‘ql’ in the works. [‘sq’: Science Quality, ‘qa’: Quality Assessment, ‘ql’: Quick Look Reduction.]

myreduce.mode = 'qa'

recipename

The name of the recipe to use. If left to “_default”, the Recipe System will invoke the mappers and select the best matching recipe library and use its default recipe.

If only the name of a recipe is provided, the mappers will be invoked to find the best matching recipe library and use the named recipe rather than the default.

If a “module.recipe” string is provided, the user’s “module” will be imported and the user’s “recipe” will be used. No mapping will be done.

myreduce.recipename = 'myrecipelib.myrecipe'

If the name of a primitive is given, the Recipe System will find the best match primitive set and run the specified primitives from that set.

suffix

The suffix to add the final outputs of a recipe. In the Gemini primitives, default suffixes are assigned to each primitives. Setting suffix will override the default suffix of the last primitive in the recipe.

myreduce.suffix = '_flatBfilter'

drpkg

The name of the data reduction package to use. The default is geminidr. If using a third-party package, or during new instrument development, set this attributes to import the correct suite of recipes and primitives.

myreduce.drpkg = 'scorpiodr'

ucals

Set the processed calibration to be used. This overrides the automatic selection done by the calibration manager, if one is being used. This setting must be used if no calibration manager is used or available, or when, for example, the calibrations association rules are not yet implemented. It is also useful for testing and for getting full control of the calibrations being used.

The format for this attribute’s value needs to looks like this:

{'processed_bias': '/path/master_bias.fits'}

There must be one entry for each type of calibrations.

The recognized calibration types are currently:

  • processed_arc
  • processed_bias
  • processed_dark
  • processed_flat
  • processed_fringe
  • processed_slitillum
  • processed_standard

The normalize_ucals function in the recipe_system.utils.reduce_utils module will convert a list of strings (in the format required for the command-line interface) into the appropriate dictionary and check that the specified calibrations files are readable and have the required tags. However, it is not necessary to make use of this function.

Here’s how to use normalize_ucals:

from recipe_system.utils.reduce_utils import normalize_ucals

mycalibrations = ['processed_bias:/path/master_bias.fits',
                  'processed_flat:/path/master_Bflat.fits']

myreduce.ucals = normalize_ucals(mycalibrations)
uparms

Set primitive parameter values. This will override the primitive defaults. This is a list of tuples with the primitive name and parameter in the first element, and the value in the second one.

myreduce.uparms = [('stackFrames:operation', 'median')]

If the primitive name is omitted all parameters with that name, in any primitives will be reset. Be careful.

upload
Internal use only. Specify which types of product to upload to the Gemini internal database. Allowed values are “metrics”, “calibs”, and “science”.