2. Full API Example

Here we put together several of the tools to show how it can all work, from beginning to end.

Import everything we will need.

>>> import glob

>>> from recipe_system.reduction.coreReduce import Reduce

>>> from gempy.utils import logutils
>>> from gempy.adlibrary import dataselect

Create the file lists. One for the darks, one for the flats, one for the science target.

>>> all_files = glob.glob('../raw/*.fits')

# 20 second darks.
>>> expression = 'exposure_time==20'
>>> parsed_expr = dataselect.expr_parser(expression)
>>> darks20s = dataselect.select_data(all_files, ['DARK'], [], parsed_expr)

# all the flats
>>> flats = dataselect.select_data(all_files, ['FLAT'])

# the science data
>>> expression = 'object=="SN2014J"'
>>> parsed_expr = dataselect.expr_parser(expression)
>>> target = dataselect.select_data(all_files, expression=parsed_expr)

Set up the calibration manager and database, by creating or editing the ~/.dragons/dragonsrc file as indicated below.
```
[calibs]
databases = <path_to>/redux_dir/dragons.db get store
```
In principle, if you configure the database to automatically store calibrations as they are produced, there is no need for you to interact with it, as it will automatically be initialized when the reduction starts. [1] However, you may want to inspect its contents, or possibly delete files from it, in which case you should create a python object to allow you to interact directly with it, as follows (the final init() call is optional unless you want to add calibrations to the database before running reduce).
```
>>> from recipe_system import cal_service
>>> caldb = cal_service.set_local_database()
>>> caldb.init()
```

Set up the logger.

>>> logutils.config(file_name='example.log')

Reduce the darks and add the master dark to the calibration database.
```
>>> reduce_darks = Reduce()
>>> reduce_darks.files.extend(darks20s)
>>> reduce_darks.runr()
```
The resultant processed dark will automatically be added to the database provided the store flag is set. The log will indicate whether the file was added or not. If not, it can be manually added:
```
>>> caldb.add_cal(reduce_darks.output_filenames[0])
```

Reduce the flats and add the master flat to the calibration database.

>>> reduce_flats = Reduce()
>>> reduce_flats.files.extend(flats)
>>> reduce_flats.runr()

Again, the processed flat need only be added manually if the store flag was not set:

>>> caldb.add_cal(reduce_flats.output_filenames[0])

Reduce the science target, with some input parameter override.

>>> reduce_target = Reduce()
>>> reduce_target.files.extend(target)
>>> reduce_target.uparms.append(('skyCorrect:scale', False))
>>> reduce_target.runr()

Footnotes