3. Example 1-A: Dithered Point Source Longslit - Using the “reduce” command line

In this example we will reduce a GMOS longslit observation of a DB white dwarf candidate using the “reduce” command that is operated directly from the unix shell. Just open a terminal and load the DRAGONS conda environment to get started.

This observation dithers along the slit and along the dispersion axis.

3.1. The dataset

If you have not already, download and unpack the tutorial’s data package. Refer to Downloading the tutorial datasets for the links and simple instructions.

The dataset specific to this example is described in:

Here is a copy of the table for quick reference.


S20171022S0087,89 (515 nm)
S20171022S0095,97 (530 nm)

Science biases


Science flats

S20171022S0088 (515 nm)
S20171022S0096 (530 nm)

Science arcs

S20171022S0092 (515 nm)
S20171022S0099 (530 nm)

Standard (LTT2415)

S20170826S0160 (515 nm)

Standard biases


Standard flats

S20170826S0161 (515 nm)

Standard arc

S20170826S0162 (515 nm)

3.2. Set up the Local Calibration Manager

DRAGONS comes with a local calibration manager and a local light weight database that uses the same calibration association rules as the Gemini Observatory Archive. This allows “reduce” to make requests for matching processed calibrations when needed to reduce a dataset.

Let’s set up the local calibration manager for this session.

In ~/.geminidr/, create or edit the configuration file rsys.cfg as follow:

standalone = True
database_dir = <where_the_data_package_is>/gmosls_tutorial/playground

This simply tells the system where to put the calibration database, the database that will keep track of the processed calibrations we are going to send to it.


~ in the path above refers to your home directory. Also, don’t miss the dot in .geminidr.

Then initialize the calibration database:

caldb init

That’s it. It is ready to use.

You can add processed calibrations with caldb add <filename> (we will later), list the database content with caldb list, and caldb remove <filename> to remove a file from the database (it will not remove the file on disk.) (See the “caldb” documentation for more details.)

3.3. Create file lists

This data set contains science and calibration frames. For some programs, it could contain different observed targets and different exposure times depending on how you like to organize your raw data.

The DRAGONS data reduction pipeline does not organize the data for you. You have to do it. However, DRAGONS provides tools to help you with that.

The first step is to create input file lists. The tool “dataselect” helps with that. It uses Astrodata tags and “descriptors” to select the files and send the filenames to a text file that can then be fed to “reduce”. (See the Astrodata User Manual for information about Astrodata.)

First, navigate to the playground directory in the unpacked data package:

cd <path>/gmosls_tutorial/playground

3.3.1. Two lists for the biases

The science observations and the spectrophotometric standard observations were obtained using different regions-of-interest (ROI). So we will need two master biases, one “Full Frame” for the science and one “Central Spectrum” for the standard.

We can use dataselect to select biases for each ROIs.

Given the data that we have in the playdata directory, we can create our GMOS-S bias list using the tags and expression using the ROI settings. Remember, this will always depend on what you have in your raw data directory. For easier selection criteria, you might want to keep raw data from different programs in different directories.

First, let’s see which biases we have for in our raw data directory.

dataselect ../playdata/*.fits --tags BIAS | showd -d detector_roi_setting

filename                          detector_roi_setting
../playdata/S20170825S0347.fits       Central Spectrum
../playdata/S20170825S0348.fits       Central Spectrum
../playdata/S20170825S0349.fits       Central Spectrum
../playdata/S20170825S0350.fits       Central Spectrum
../playdata/S20170825S0351.fits       Central Spectrum
../playdata/S20170826S0224.fits       Central Spectrum
../playdata/S20170826S0225.fits       Central Spectrum
../playdata/S20170826S0226.fits       Central Spectrum
../playdata/S20170826S0227.fits       Central Spectrum
../playdata/S20170826S0228.fits       Central Spectrum
../playdata/S20171021S0265.fits             Full Frame
../playdata/S20171021S0266.fits             Full Frame
../playdata/S20171021S0267.fits             Full Frame
../playdata/S20171021S0268.fits             Full Frame
../playdata/S20171021S0269.fits             Full Frame
../playdata/S20171023S0032.fits             Full Frame
../playdata/S20171023S0033.fits             Full Frame
../playdata/S20171023S0034.fits             Full Frame
../playdata/S20171023S0035.fits             Full Frame
../playdata/S20171023S0036.fits             Full Frame

We can see the two groups that differ on their ROI.

dataselect ../playdata/*.fits --tags BIAS --expr='detector_roi_setting=="Central Spectrum"' -o biasesstd.lis
dataselect ../playdata/*.fits --tags BIAS --expr='detector_roi_setting=="Full Frame"' -o biasessci.lis

3.3.2. A list for the flats

The GMOS longslit flats are not normally stacked. The default recipe does not stack the flats. This allows us to use only one list of the flats. Each will be reduced individually, never interacting with the others.

If you have multiple programs and you want to reduce only the flats for that program, you might want to use the program_id descriptor

Or, like here, we have only one set of flats, so we will just gather them all together.

dataselect ../playdata/*.fits --tags FLAT -o flats.lis

3.3.3. A list for the arcs

The GMOS longslit arcs are not normally stacked. The default recipe does not stack the arcs. This allows us to use only one list of arcs. Each will be reduce individually, never interacting with the others.

The arcs normally share the program_id with the science observations if you find that you need more accurate sorting. We do not need it here.

dataselect ../playdata/*.fits --tags ARC -o arcs.lis

3.3.4. A list for the spectrophotometric standard star

If a spectrophotometric standard is recognized as such by DRAGONS, it will receive the Astrodata tag STANDARD. All spectrophotometric standards normally used at Gemini are in the DRAGONS list of recognized standards.

dataselect ../playdata/*.fits --tags STANDARD -o std.lis

3.3.5. A list for the science observation

The science observations are what is left, anything that is not a calibration or assigned the tag CAL.

If we had multiple targets, we would need to split them into separate list. To inspect what we have we can use dataselect and showd together.

dataselect ../playdata/*.fits --xtags CAL | showd -d object

filename                              object
../playdata/S20171022S0087.fits   J2145+0031
../playdata/S20171022S0089.fits   J2145+0031
../playdata/S20171022S0095.fits   J2145+0031
../playdata/S20171022S0097.fits   J2145+0031

Here we only have one object from the same sequence. We would not need any expression, just exclusing calibrations would be sufficient. But we demonstrate here how one would specify the object name for a more surgical selection.

dataselect ../playdata/*.fits --xtags CAL --expr='object=="J2145+0031"' -o sci.lis

3.4. Master Bias

We create the master biases with the “reduce” command, then add them to the local calibration manager with the caldb command.

reduce @biasesstd.lis
reduce @biasessci.lis
caldb add *_bias.fits

The master biases are S20170825S0347_bias.fits and S20171021S0265_bias.fits; this information is in both the terminal log and the log file. The @ character before the name of the input file is the “at-file” syntax. More details can be found in the "at-file" Facility documentation.


The file name of the output processed bias is the file name of the first file in the list with _bias appended as a suffix. This the general naming scheme used by “reduce”.

3.5. Master Flat Field

GMOS longslit flat field are normally obtained at night along with the observation sequence to match the telescope and instrument flexure. The matching flat nearest in time to the target observation is used to flat field the target. The central wavelength, filter, grating, binning, gain, and read speed must match.

Because of the flexure, GMOS longslit flat field are not stacked. Each is reduced and used individually. The default recipe takes that into account.

We can send all the flats, regardless of characteristics, to reduce and each will be reduce individually. When a calibration is needed, in this case, a master bias, the best match will be obtained automatically from the local calibration manager.

reduce @flats.lis --ql
caldb add *_flat.fits

We can bulk-add the master flats to the local calibration manager as shown above.


GMOS longslit reduction is currently available only for quicklook reduction. The science quality recipes do not exist, hence the use of the --ql flag to activate the “quicklook” recipes.

3.6. Processed Arc - Wavelength Solution

GMOS longslit arc can be obtained at night with the observation sequence, if requested by the program, but are often obtained at the end of the night or the following afternoon instead. Like the spectroscopic flats, they are not stacked which means that they can be sent to reduce all to together and will be reduced individually.

The wavelength solution is automatically calculated and has been found to be quite reliable. There might be cases where it fails; inspect the *_mosaic.pdf plot and the RMS of determineWavelengthSolution in the logs to confirm a good solution.

reduce @arcs.lis --ql
caldb add *_arc.fits


Failures of the wavelength solution calculation are not easy to fix in quicklook mode. It might be better to simply not use the arc at all and rely on the approximate solution instead. When the science quality package is released, there will be interactive tools to fix a bad solution. Remember, this version only offers quicklook reduction for GMOS longslit.

3.7. Processed Standard - Sensitivity Function

The GMOS longslit spectrophotometric standards are normally taken when there is a hole in the queue schedule, often when the weather is not good enough for science observations. One standard per configuration, per program is the norm. If you dither along the dispersion axis, most likely only one of the positions will have been used for the spectrophotometric standard. This is normal for baseline calibrations at Gemini. The standard is used to calculate the sensitivity function. It has been shown that a difference of 10 or so nanometers in central wavelength setting does not significantly impact the spectrophotometric calibration.

The reduction of the standard will be using a master bias, a master flat, and a processed arc. If those have been added to the local calibration manager, they will be picked up automatically.

reduce @std.lis --ql
caldb add *_standard.fits

To inspect the spectrum:

dgsplot S20170826S0160_ql_standard.fits 1

To learn how to plot a 1-D spectrum with matplotlib using the WCS from a Python script, see Tips and Tricks Plot a 1-D spectrum.

The sensitivity function is stored within the processed standard spectrum. To learn how to plot it, see Tips and Tricks Inspect the sensitivity function.

3.8. Science Observations

The science target is a DB white dwarf candidate. The sequence has four images that were dithered spatially and along the dispersion axis. DRAGONS will register the four images in both directions, align and stack them before extracting the 1-D spectrum.


In this observation, there is only one source to extract. If there were multiple sources in slits, regardless of whether they are of interest to the program, DRAGONS will locate them, trace them, and extract them automatically. Each extracted spectrum is stored in an individual extension in the output multi-extension FITS file.

This is what one raw image looks like.

raw science image

With the master bias, the master flat, the processed arcs (one for each of the grating position, aka central wavelength), and the processed standard in the local calibration manager, to reduce the science observations and extract the 1-D spectrum, one only needs to do as follow.

reduce @sci.lis --ql

This produces a 2-D spectrum (S20171022S0087_2D.fits) which has been bias corrected, flat fielded, QE-corrected, wavelength-calibrated, corrected for distortion, sky-subtracted, and stacked. It also produces the 1-D spectrum (S20171022S0087_1D.fits) extracted from that 2-D spectrum. The 1-D spectrum is flux calibrated with the sensitivity function from the spectrophotometric standard. The 1-D spectra are stored as 1-D FITS images in extensions of the output Multi-Extension FITS file.

This is what the 2-D spectrum looks like.

reduce -r display S20171022S0087_2D.fits
2D stacked spectrum

The apertures found are list in the log for the findApertures just before the call to traceApertures. Information about the apertures are also available in the header of each extracted spectrum: XTRACTED, XTRACTLO, XTRACTHI, for aperture center, lower limit, and upper limit, respectively.

This is what the 1-D flux-calibrated spectrum of our sole target looks like.

dgsplot S20171022S0087_1D.fits 1
1D spectrum

To learn how to plot a 1-D spectrum with matplotlib using the WCS from a Python script, see Tips and Tricks Plot a 1-D spectrum.

If you need an ascii representation of the spectum, you can use the primitive write1DSpectra to extra the values from the FITS file.

reduce -r write1DSpectra S20171022S0087_1D.fits

The primitive outputs in the various formats offered by astropy.Table. To see the list, use showpars.

showpars S20171022S0087_1D.fits write1DSpectra

To use a different format, set the format parameters.

reduce -r write1DSpectra -p format=ascii.ecsv extension='ecsv' S20171022S0087_1D.fits