NIRCam Time Series Observation Pipeline Caveats

Unique features of the JWST calibration pipeline for time-series observations (TSOs) with the NIRCam instrument, and caveats for users, are covered in this article. Users should also refer to JWST Time Series Observations Pipeline Caveats for characteristics and caveats common to all instrument. This information reflects the status for the JWST pipeline version 1.4.6. 

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Some aspects of the JWST Science Calibration Pipeline for NIRCam are highlighted below, in particular those where the treatment of TSO exposures differs from non-TSO exposures. It is also important 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 here covers both of NIRCam's modes that are available for TSOs: imaging time series and grism time-series spectroscopy.


Stage 1 processing

The pre-amplifier reset noise and 1/f noise can be the dominant noise source for some NIRCam modes, so it is important to apply some corrections to reduce these noise contributions.

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In particular, the SUBGRISM128 and SUBGRISM64 subarrays (which allow bright sources without saturation) do not have bottom reference pixels on the short wavelength detectors to subtract pre-amplifier reset noise. It is beneficial to use background pixels to subtract the average counts in a given 512 pixel or 2048 pixel wide amplifier region (for Noutputs = 4 and Noutputs = 1, respectively) to remove amplifier offsets. After removing pre-amplifier reset noise, the 1/f noise is still significant. Row-by-row subtraction (which is the fast read direction) for each 512 pixel or 2048 pixel wide amplifier region (for Noutputs = 4 and Noutputs = 1, respectively) can improve the precision (Schlawin et al. 2020). Note that if one is using Noutputs = 4 (the recommended mode), the PSF for the F322W2 grism position spans 2 amplifiers so the row-by-row subtraction must be performed on the different amplifiers.

Failing to correct for pre-amplifier reset noise and 1/f noise can result in more than just excess noise. The jump step of the pipeline can erroneously flag this noise as jumps from cosmic rays. The excess flags can generate additional problems by discarding a majority of scientifically useful pixels. This excess flagging can be mitigated by skipping the jump detection step of the pipeline but this has the disadvantage of not flagging real cosmic rays. Therefore, the best solution is a row-by-row subtraction per amplifier at the reference pixel correction step of the pipeline and with normal jump step flagging to identify real cosmic rays.

Stage 3 processing

JWST target acquisition is designed to accurately center the source at the subpixel level with a small angle maneuver (SAM). This means that the source should land in a repeatable and predictable location. However, there may be offsets from a perfect centering so it is worth checking the whether the XREF_SCI and YREF_SCI keywords in the header match the location of the source. Additionally, JWST pipeline version 1.4.6 does not adjust the aperture position as a function of time.  If motions of the telescope caused by jitter and/or High Gain Antenna moves occur, the position of the aperture used to extract photometric signal needs to be moved. Fortunately, the expected jitter and motion of high gain antenna moves is expected to be small, below the 3 mas level, except for a 1 minute period following a High Gain Antenna move (Schlawin et al. 2021).

In-flight measurements show that the jitter is smaller than predicted at 1 mas and that the HGA moves settle quickly.

The Weak Lens point spread function can span a significant size (2.2") so the target star can blend with nearby sources. To calculate the contamination overlap, one can use WebbPSF to simulate background stars and scale the transit depth accordingly.


Stage 1 processing

1/f noise has considerable impact on grism time series because there are no background pixels for a given row on two to three amplifiers depending on the filter and position. Thus, the noise can be highly correlated along the dispersion (i.e. wavelength) direction. Binning N wavelengths together, therefore, may not decrease the noise by the square root of N as would be expected if each pixel is independent. While 1/f noise cannot be eliminated, it can be reduced by using small aperture sizes and reference pixel correction and row-by-row correction on amplifiers that have background pixels in the horizontal/fast-read direction. This should be performed at the reference pixel correction step of the pipeline after removing the pre-amplifier resets. The pre-amplifier resets can be estimated from either the average reference pixel or average background pixel in each 512 pixel or 2048 pixel wide amplifier region (for Noutputs = 4 and Noutputs = 1, respectively).

Stage 2 processing

The second stage of the pipeline truncates the array to an immediate region surrounding the source. This step can be skipped or adjusted so that more pixels are available for background subtraction. The pipeline parameters for NIRCam grism time series are described in Read The Docs. As of this writing, the value is 64 pixels tall so it will not affect the SUBGRISM64 subarray. For the SUBGRISM128 (128 pixels tall) and SUBGRISM256 (256 pixels tall) subarrays or full frame, the extract2D step will use a 2048 × 64 cutout region. It can be advantageous to include 128 pixels for the SUBGRISM128 and 256 pixels for the SUBGRISM256 and full frame images for background subtraction, identifying possible neighboring sources and evaluating the 1/f noise in background regions. This can be changed with the tsgrism_extract_height parameter. Spectral extraction is performed in pixel coordinates without tracing the spectrum or taking partial pixels. For each column the target flux is summed after a median background subtraction using pre-defined aperture extraction and background regions in the "_extract1d.json" file. Additionally, the photometric calibration step will convert from DN/s to MJy/sr. If there is significant jitter, this step can introduce additional noise especially near sharp gradients such as the shortest and longest wavelengths of the grism spectrum.


Schlawin, E., et al. 2020, AJ, 160, 231
JWST Noise Floor. I. Random Error Sources in JWST NIRCam Time Series

Schlawin, E., et al. 2021, AJ, 161, 115
JWST Noise Floor. II. Systematic Error Sources in JWST NIRCam Time Series

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