Automated sorting of LRIS frames by instrument configuration

Version History






Debora Pelliccia

6 Sep 2023


To prepare for the data reduction, PypeIt, first, automatically associates fits files to specific Frame Types (see Automated typing of LRIS (BLUE and RED) frames) and, then, collects groups of frames in unique instrument configurations (see below). This is performed by the pypeit_setup script, which sorts the frames and writes a PypeIt Reduction File for each unique configuration. See Setup.

LRIS configuration identification

The LRIS instrument configurations are determined, in the same way for keck_lris_red, keck_lris_red_orig, keck_lris_red_mark4, keck_lris_blue, and keck_lris_blue_orig (unless otherwise noted), by the function pypeit.metadata.PypeItMetaData.unique_configurations(), which finds unique combinations of the following keywords:

fitstbl key

Header Key










NUMAMPS (TAPLINES for keck_lris_red_mark4)





The unique configurations are determined by collating the relevant metadata from the headers of all frames found by a run of pypeit_setup, except those that are designated as bias frames. The reason is that bias frames can have header data (e.g., dispangle) that do not match the instrument configuration that an observer intended for their use; e.g., the frames were taken before the instrument was fully configured for the night’s observations. Therefore, PypeIt uses the dateobs, binning, amp keys to match the bias frames to the configurations with frames taken on the same date, with the same binning and on the same amplifier.

After that, pypeit.metadata.PypeItMetaData.set_configurations() associates each frame to the relevant unique configuration (“setup”), by assigning a setup identifier (e.g., A,B,C,D…) to every frames for which the values of the above keywords match the values of the specific unique configuration.

LRIS calibration groups

PypeIt uses the concept of a “calibration group” to define a complete set of calibration frames (e.g., arcs, flats) and the science frames to which these calibration frames should be applied.

By default, pypeit_setup uses the setup identifier to assign frames to a single calibration group. Frames that are in the same calibration group will have the same PypeIt keyword calib. No automated procedure exists to do anything except this. However, the user can edit the PypeIt Reduction File to, within a given configuration, assign specific calibration frames to specific science frames using the data in the calib column of the Data Block.


Requirement PLL-17 states: “As a user, I expect the pipeline to automatically and correctly associate calibrations with science frames.”

PypeIt meets this requirement in the majority of use cases, as shown by the tests below.

Note that the tests described in Automated typing of LRIS (BLUE and RED) frames are also relevant here since they show that PypeIt correctly identifies LRIS data and associates them with a single configuration, all written to a single pypeit file.

To test that PypeIt can successfully identify multiple configurations among a set of files, we have added five tests ${PYPEIT_DEV}/unit_tests/ They are:

  • test_setup_keck_lris_blue_multiconfig(),

  • test_setup_keck_lris_blue_orig_multiconfig()

  • test_setup_keck_lris_red_multiconfig()

  • test_setup_keck_lris_red_orig_multiconfig()

  • test_setup_keck_lris_red_mark4_multiconfig()

Here is an example of how to run the tests:

cd ${PYPEIT_DEV}/unit_tests
pytest -W ignore

The tests require that you have downloaded the PypeIt PypeIt Development Suite and defined the PYPEIT_DEV environmental variable that points to the relevant directory.

The algorithm for all these tests is the same and is as follows:

  1. Collect the names of all files in selected LRIS directories (separately for keck_lris_blue, keck_lris_blue_orig, keck_lris_red, keck_lris_red_orig, keck_lris_red_mark4).

  2. Use PypeItSetup to automatically identify the configurations for these files.

  3. Check that the code found two configurations and wrote the pypeit files for each.

  4. For each configuration:

    1. Read the pypeit file

    2. Check that the name for the setup is correct (‘A’ or ‘B’)

    3. Check that the calibration group is the same for all frames (‘0’ or ‘1’)

Because these tests are now included in the PypeIt Unit Tests (GitHub CI), these configuration checks are performed by the developers for every new version of the code.