MIRI Time Series Observation Pipeline Caveats

Unique features of the JWST calibration pipeline for time-series observations (TSOs) with the MIRI instrument, and caveats for users, are described in this article. Users should also refer to the TSO pipeline overview for characteristics and caveats that are common to all instruments. This information reflects the status for the JWST pipeline version 1.4.6. 

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This article highlights some aspects of the JWST calibration pipeline for MIRI, in particular those where the treatment of TSO exposures differs from "regular" MIRI exposures. It is important also to highlight that early in the mission our understanding of the observatory performance is evolving quite rapidly, and changes to calibration procedures are expected. 

The information presented covers all 3 of MIRI's modes that are available for TSOs: imaging, slitless low-resolution spectroscopy, and medium-resolution spectroscopy. 

Stage 1 processing for LRS, MRS and imaging

First and last frames

The mid-infrared detectors in MIRI have a wider variety of response behaviours than is typically seen in the optical or near-infrared. The first and last frames in an integration are known to show deviations from their expected response, and they are therefore marked as "DO NOT USE" for linearity correction, jump detection and ramp fitting. The last frame in particular is problematic, as it displays a "pull-down" effect whose magnitude varies between odd and even rows. Including this frame in the ramp fit pulls down the calculated rate, and thus impacts the flux calibration of the target. 

For TSOs, where stability is considered more important than the absolute flux calibration, the first and last frames are included in the ramp fitting step, as for a given exposure the effects are observed to be stable over time. Particularly for bright targets where the number of groups per integration is small, the added value of 2 extra reads in the ramp can outweigh the impact of the anomalous response in the first and last frames. However, it is important to highlight that the absolute flux calibration of the target may be affected by not rejecting these frames. 

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Users can always study the impact of including these frames by toggling the firstframe and lastframe steps of the Detector 1 pipeline. Changing the execution status of pipeline steps is demonstrated in this TSO Webbinar excerpt. (Additional information is available for the full "JWebbinar-11" on time-series observations under the "Materials and Videos" tab at the JWebbinar webpage). Note that these pipeline steps flag the frames as "DO NOT USE", so skipping the steps includes the frames in subsequent steps.  

Reference pixel correction

The MIRI detectors have 4 columns of reference pixels on each side of the detector (8 columns in total). These pixels are read out despite not being part of the illuminated section of the array. The measured signal from these reference pixels can be used to clean up their illuminated counterparts along the same rows. 

However, many of the MIRI subarrays are not connected to the array edges; therefore, the reference pixel signals are not available for many subarray exposures. Insufficient data were available from ground testing to optimize a reference pixel correction method for subarray exposures. For this reason, the reference pixel step is skipped for all subarray exposures (TSO or non-TSO). For full frame imaging or MRS TSOs, the reference pixel step is applied. 

Stage 2 processing

World Coordinate System assignment (imaging, LRS, MRS)

The first step in running Spec2Pipeline or Image2Pipeline is the assignment of the world coordinate system parameters for the data based on the telescope pointing information. For the spectroscopic modes, this includes the wavelength information. This step assumes that the target is perfectly placed at the nominal position in the science aperture (the center of the imaging or MRS fields, the nominal pointing position in the SLITLESSPRISM subarray). Depending on the execution of target acquisition (TA) or the accuracy of the TA procedure, or in the case of offsets specified in the special requirements, there may be small offsets of the target from that nominal position. This may introduce noise or errors at later pipeline stages. Note also that pointing jitter may add to pointing-related noise in the final science product. LRS slitless observations have mandatory TA, accompanied by a TA verification image taken after the telescope moves the target to the nominal position in the subarray. This allows the target placement to be visualized before the light is dispersed. 

The spectral extraction step in Spec2Pipeline also accesses positional header keywords to locate the target in the subarray. In case of WCS registration issues, the extraction aperture may not be placed in the optimal location. Therefore, verifying the placement of the target in the subarray, and performing a custom extraction manually to ensure the correct placement of the aperture, is recommended.

Note that in Cycle 1, MIRI imaging with target acquisition has not yet been implemented. 

Spectral leak (LRS only)

The spectral dispersion profile of the double prism that is used by the LRS mode turns over on itself around 4 µm. The theoretical curve is shown in Figure 1 and ground testing has shown the as-built instrument to be close to the optical model. This means wavelengths below 4 µm are dispersed back onto the longer wavelengths. For the case of LRS slit spectroscopy, a filter is mounted on the slit mask blocking all radiation below ~4.5 µm, but for slitless operation, i.e., for all LRS TSOs, this is not the case.

The issue is mitigated by the sharp drop in prism transmission below 5 µm (see Figure 2); however, a leak is present between 3 and 4 µm that allows short wavelength flux to "contaminate" the spectrum. This is not currently modeled by the ETC, nor is it corrected in the pipeline. Calibration strategies and reference files will be updated as more in-flight data is gathered, but observers with early observations in Cycle 1 should be aware of this issue. 

Figure 1. Nominal  spectral dispersion of the MIRI low-resolution spectrometer 

The nominal (as-designed) spectral dispersion of the MIRI low-resolution spectrometer, showing the spectral fold over around 4 µm. (© Kendrew et al. 2015).
Figure 2. MIRI LRS prism transmission for slit and slitless operation

For slitted operation, the slit mask is fitted with a blocking filter, specifically to block radiation below 4.5 µm. The overall transmission for slitless operation is therefore higher, but also includes a spectral leak between 3 and 4 µm (© Kendrew et al. 2015).

Background subtraction (LRS)

For slitless LRS observations, background subtraction has not yet been implemented in the automated pipeline. The recommended approach based on pre-flight information is to use the background-only columns of the subarray to derive a mean background spectrum, and subtract it manually. The spectral extraction step (extract_1d) can also be configured to perform background subtraction as part of the extraction. This is demonstrated in the TSO JWebbinar materials. 

For TSO imaging, background subtraction is performed in stage 3 of the pipeline, as part of the tso_photometry step. 

Photometric calibration (LRS)

The photometric calibration reference file provides calibration factors as a function of wavelength, which are then attached to the data in the photom step using the wavelength information assigned in the assign_wcs step of the Spec2 pipeline. This means that any inaccuracies in the initial target placement, or pointing drifts of jitter over the course of the exposure, will result in an inaccurate calibration, or in the case of jitter or drifts, an additional noise source. To test for this issue, or avoid this source of error, the step can be skipped. The subsequent pipeline steps are able to process the data based on DN/s units. 

Cube build and spectral extraction (MRS)

When performing TSOs with the medium resolution spectrometer, pipeline processing ends before the cube building and spectral extraction steps. The final output product are the 2-D, photometrically calibrated spectral images produced by the photom step. Spectral extraction directly from the 2-D focal plane array is not yet supported in the pipeline. Support for MRS TSOs will continue to be improved during early science operations. 

Stage 3 processing

TSO photometry (imaging)

The CalTSO3 pipeline produces a photometric time series for MIRI imaging TSOs. This step assumes that the target was placed perfectly at the nominal pointing location in the array or subarray, and does not move between integrations. Time-series imaging with MIRI, however, is not performed with target acquisition. In addition, pointing jitter or drifts can cause further inaccuracies in the placement of the photometric aperture in this step. Target placement should always be checked for each integration for time-series imaging, and it may be beneficial to perform the time-series construction manually. 


Kendrew, S., et al. 2015, PASP, 127, 623
The Mid-Infrared Instrument for the James Webb Space Telescope, IV: The Low-Resolution Spectrometer

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Originally published