5. Tips and Tricks

This is a collection of tips and tricks that can be useful for reducing different data, or to do it slightly differently from what is presented in the example.

5.1. Getting Bad Pixel Masks from the archive

Starting with DRAGONS v3.1, the static bad pixel masks (BPMs) are now handled as calibrations. They are downloadable from the archive instead of being packaged with the software. There are various ways to get the BPMs.

Note that at this time there no static BPMs for Flamingos-2 data.

5.1.2. Associated calibrations

The BPMs are now handled like other calibrations. This means that they are also downloaded from the archive. From the archive search form, once you have identified your science data, select the “Load Associated Calibrations” (which turns to “View Calibrations” once the table is loaded). The BPM will show up with the green background.

_images/bpmassociated.png


This will be the case for new data (from late March 2023). For old data, until we fix an issue recently discovered, they will not show up as associated calibration and you will have to find them manual as explained in the previous section, Manual search. We understand the issue and are working on a fix.

5.1.3. Calibration service

The calibration service in DRAGONS 3.1 adds several new features. One of them is the ability to search multiple databases in a serial way, including online database, like the Gemini archive.

The system will look first in your local database for processed calibration and BPMs. If it does not find anything that matches, it will look in the next database. To activate this feature, in ~/.dragons/, create or edit the configuration file dragonsrc as follows:

[calibs]
databases = ${path_to_my_data}/niriimg_tutorial/playground/cal_manager.db get store
            https://archive.gemini.edu get

If you know that you will be connected to the internet when you reduce the data, you do not need to pre-download the BPM, DRAGONS will find it for you in the archive.

If you want to pre-download the BPM without having to search for it, like in the previous two sections, you can let DRAGONS find it and download it for you:

$ reduce -r getBPM <file_for_which_you_need_bpm>
$ caldb add calibrations/processed_bpm/<the_bpm>

5.2. Create Master Fringe Frame

The reduction of some datasets requires a master fringe frame. The filters that need a fringe frame are shown in the appendix Fringe Correction Tables.

To create the master fringe frame from the dithered science observations and add it to the calibration database:

$ reduce @list_of_science.txt -r makeProcessedFringe

This command line will produce an image with the _fringe suffix in the current working directory.

Again, note that this step is only needed for images obtained with some detector and filter combinations. Make sure you checked the Fringe Correction Tables.

The above can be done with the API as follows:

1reduce_fringe = Reduce()
2reduce_fringe.files.extend(list_of_science)
3reduce_fringe.recipename = 'makeProcessedFringe'
4reduce_fringe.runr()

5.3. Bypass automatic calibration association

We can think of two reasons why a user might want to bypass the calibration manager and the automatic processed calibration association. The first is to override the automatic selection, to force the use of a different processed calibration than what the system finds. The second is if there is a problem with the calibration manager and it is not working for some reason.

Whatever the specific situation, the following syntax can be used to bypass the calibration manager and set the input processed calibration yourself.

$ reduce @sci_images.list --user_cal processed_bias:S20001231S0001_bias.fits processed_flat:S20001231S0002_flat.fits

The list of recognized processed calibration is:

  • processed_arc

  • processed_bias

  • processed_dark

  • processed_flat

  • processed_fringe

  • processed_standard

5.4. Browse Recipes and Primitives

“reduce”, either the command line or the API class, is the tool that selects and run a “recipe”. A recipe is a sequence of operations called “primitives”. Each primitives has a defined set of input parameters with default values that can be overriden by the user.

The “showrecipes” command line is used to show the default recipe for a file, a specific recipe for that file, or all the recipes associated with the file.

Once you know the recipe and primitives it is calling, you can explore the primitives’ parameters using the “showpars” command line.

The tools are fully documented in the Recipe System Users Manual.

5.5. Customizing input parameters

From the command line, setting the value of a primitive input parameter is done as follows:

$ reduce @sci.lis -p stackFrames:scale=True

The -p flag indicates that the following items are parameter changes. The syntax is <primitive_name>:<parameter_name>=<value>

From the API, the uparms attribute to the Reduce instance is used.

1reduce_science.uparms.append(("stackFrames:scale", True))

5.6. Setting the output suffix

When troubleshooting an issue or trying various settings to optimize a reduction, it might be useful to name the final recipe output differently for each attempt.

Only the suffix of the final output file can be changed, not its full name.

From the command line:

$ reduce @sci.lis --suffix='newsuffix'

From the API:

1reduce_science.suffix = "newsuffix"
2reduce_science.runr()