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.

5.1.1. Manual search

Ideally, the BPMs will show up in the list of associated calibrations, the “Load Associated Calibration” tab on the archive search form (next section). This will happen of all new data. Yet, it is also possible to search for them manually.

On the archive search form, set the “Instrument” to match your data, set the “Obs.Type” to “BPM”, if relevant for the instrument, set the “Binning”. Hit “Search” and the list of BPMs will show up as illustrated in the figure below.

The date in the BPM file name is a “Valid-from” date. It is valid for data taken on or after that date. Find the most recent BPM that is valid for your date and download (click on “D”) it. Then follow the instructions found in the tutorial examples.

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.

If a BPM does not show up, see if you find one using the manual search explained in the previous section, Manual search.

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:

reduce_fringe = Reduce()
reduce_fringe.files.extend(list_of_science)
reduce_fringe.recipename = 'makeProcessedFringe'
reduce_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 (a dict) to the Reduce instance is used.

reduce_science.uparms["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:

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

5.7. Useful parameters

5.7.1. skip_primitive

I might happen that you will want or need to not run a primitive in a recipe. You could copy the recipe over and edit it. Or you could invoke the skip_primitive parameter to tell DRAGONS to completely skip that step.

Let’s say that you want the data aligned but not stacked. You would do:

reduce @sci.lis -p stackFrames:skip_primitive=True

5.7.2. write_outputs

When debugging or when there’s a need to inspect intermediate products, you might want to write the output of a specific primitive to disk. This is done with the write_outputs parameter.

For example, to write the mosaiced frames before alignment and stacking, you would do:

reduce @sci.lis -p mosaicDetectors:write_outputs=True