Spitzer Documentation & Tools
IRS Instrument Handbook



7.4  High Resolution (SH and LH) Spectral Modules

7.4.1              LH Tilts from Residual Dark

During observations with the Long-High (LH) module, the dark current may have anomalously high values in the first 100-200 seconds of a series of exposures. Depending on the integration time and the number of cycles selected, data in the first exposure (or first nod position) may be affected. The "excess flux" is not evenly distributed over the LH array, being brightest on the blue end of each echelle order. The faint excess flux is seen as a bright band stretching across the bottom of the array, both on and between the orders, as illustrated in Figure 7.16.


Figure 7.16  Illustration of excess LH dark current, which is distributed unevenly over the array with the brightest region towards the blue end (bottom) of the array.

This phenomenon manifests itself in extracted spectra of relatively faint sources as a "scalloping" or order tilting, wherein the slopes of affected orders are made bluer (flatter), inducing order-to-order discontinuities. The order-to-order discontinuities are typically 30-50 mJy. The magnitude of the effect does not seem to be related to source brightness. In Figure 7.17 we show two extracted LH spectra of a faint point source. The top spectrum has the source at the nod 1 position, while the bottom spectrum has the source at the nod 2 position. A background sky spectrum has not been subtracted in either case, but the edges of the (color-coded) orders have been trimmed. The order mismatches are obvious in the nod 1 data, but vanish in the nod 2 data.

Figure 7.17 Nod 1 and nod 2 spectra.  Notice the blue tilts in the nod 1 spectrum.

If you have observations of faint point sources with LH, and you are seeing these order tilts in your spectra, we recommend that you check your LH BCDs in the first nod position (or during the first few hundred seconds of a series of exposures), to see if this effect is more apparent. If order discontinuities such as described above are evident in the first few exposures or the first nod position, observers should consider not including these data during co-addition. If your LH data do not show this effect, you can include all the data in your final co-added spectrum.

Alternatively, users may wish to correct the effect using the DARKSETTLE software. An example is given in the DARKSETTLE recipe in the Spitzer Data Analysis Cookbook.

No similar effect has been conclusively identified in SL, LL, or SH modules.  RED tilts of up to 10% have been seen in the longest wavelength LH orders 11 and 12, for bright red sources. This effect appears to be unrelated to dark current variations.

7.4.2             LH Orders 1-3 Red Tilts

LH orders 1-3 (at 29-37 micron) are sometimes mismatched and show red tilts with respect to shorter wavelength orders. The mismatch increases from 2% (order 3-4) to 10% (order 1-2). This effect appears to be most prominent for bright red sources (e.g., Mrk 231 in Figure 7.18). It does not appear for bright blue stars, such as the primary LH calibration standard star ksiDra. The cause of these LH red tilts is unknown.

Figure 7.18 The LH spectrum of Mrk 231 shows red tilts in orders 1-3 (29-37 micron).


7.4.3             High-res vs. Low-res spectral slope difference

There is a small tilt of 2% over the 9-35 micron range of high-resolution spectra, relative to low-resolution spectra. Spectra match at 9 micron but LH is 2% higher at 35 micron than LL. Different standard stars and Decin models are used to calibrate LL and LH. HR 7341 (0.97 Jy at 12.0 microns) is used to calibrate LL. Ksi Dra (11.2 Jy at 12.0 microns) is used to calibrate LH.  The 2% difference may be attributed to uncertainties in the fluxes of these two standard stars, which are of this order.  Users may want to use broad band photometry to scale their spectra to the correct level.

7.4.4             SH Spectral Ghosts

"Ghosts" of extremely bright spectral lines can sometimes be seen in SH data, as illustrated in Figure 7.19. These ghosts have an integrated flux of about 0.5% of the primary line in spectra extracted over the full slit. In the 2D spectra, the ghosts can have peak pixels that are about 1% of that seen in the primary feature. The ghost lines are off center to the left in the blue direction and to the right in the red direction, and partially overlap the slit edges. The separation of the ghosts from the line of origin increases with wavelength should not be mistaken for physical velocity structure in the target (the implied velocity if the ghosts were a physical structure ranges from 1800 km/s in order 20 to 2900 km/s in order 13 in the example shown in the figure). The ghosts are easiest to see in the 2D spectra, because they have a "tell-tale" spatial offset along the slit bracketing strong emission lines. Users who see very faint satellite lines around their emission features should inspect the sky-subtracted 2D spectra to determine if they are ghosts.

Ghost features are not seen in LH, and would be detectable if they had peak pixel values a few tenths of a percent of that in the primary feature.

Figure 7.19 A bcd from AOR 16921344 of the planetary nebula J900. Red circles highlight the locations of the spectral ghost features.


Mitigation: Users concerned about removing these ghosts from their spectrum can easily do so by masking the pixels in the 2D image before extracting the spectrum.

7.5  Solved Issues

We include here issues that may be relevant for users that have data processed with older pipeline versions.

7.5.1             Bug in S18.7 High-resolution IRS Post-BCD products (Solved in S18.18)

As part of the standard IRS post-BCD data processing, all the BCDs associated with a given pointing are co-added. A bug in the pipeline sometimes causes incorrect weights to be used in the co-addition for S18.7 and earlier IRS high-resolution data. The problem occurs most frequently for SH data.

The affected files are all found in the pbcd/ directory of data sets downloaded from the Spitzer Heritage Archive. Any of the co-added files (coa2d.fits, c2msk.fits, c2unc.fits) may be incorrect. If a coa2d.fits file is found to be incorrect, any files generated from it will be also. The affected files have the following suffixes: tune.fits, tune.tbl. The BCDs are unaffected by this problem, so these files can be used to extract spectra and/or assemble spectral maps without cause for concern. To determine if your data are affected, please examine the 2dcoad.txt files in the pbcd/ directory of your data set. The first column of this file contains the weights used in the co-addition. The weights should all be close to unity. If you see low and/or negative weights, then your co-added files may be corrupted.

The IRS team plans to reprocess all data in mid 2010, and this will rectify the problem. In the meantime, if desired, users can create their own coa2d.fits files by combining the appropriate bcd.fits files. The associated 1D spectra can then be extracted using SPICE. While it is possible to use a variety of software packages to create the co-added images, we are providing an IDL procedure for this purpose. This procedure, coad.pro, can be found on the Data Analysis & Tools portion of the Spitzer Heritage Archive. Alternatively, users may co-add 1D spectra which have been extracted from the BCDs, which are unaffected by the bug.

7.5.2             Low-Res Nod 1 vs. Nod 2 Flux Offset (solved in S15)

SL Nod 2 fluxes are consistently 4% lower than Nod 1. This is the result of a spatial tilt in the flat field. LL2 Nod 1 fluxes are 4% lower than Nod 2 at 14-18 microns, decreasing to 1% at 21 microns. As a result, Nod 2 and Nod 1 are tilted relative to one another.

Users should average the nods to compute the source flux and determine the flux calibration. After S15, the flat field has been adjusted to remove the Nod1-Nod2 difference.

7.5.3             LL Nonlinearity Correction Too Large (solved in S14)

Slopes are overestimated at high count levels in LL. The effect is >5% for a 1 Jy source, and >20% for a 2 Jy source. The effect is worst for long exposure-times. The SL nonlinearity correction appears to be OK.

Red sources appear redder and blue sources appear bluer due to this effect. However, curvature and other high order effects can also appear, reflecting the detector response. For example, fringes in the flat-field may be amplified, leading to extra 'noise' in LL spectra. The primary LL calibration source, HR 7341 (0.97 Jy at 12 microns) is affected by this problem at a low level. Reducing the nonlinearity coefficient causes a 5% drop in flux at 14-17 microns (LL2). The effect is <2% at 17-21 microns (LL2) and <1% at 26-36 microns (LL1).

To mitigate this problem, the non-linearity coefficient was adjusted for S14, resulting in a 5% drop in flux at 17-21 microns (LL2).  This last effect was corrected by revised flux calibration in S15.

7.5.4             Tilted SH and LH Flatfields (solved in S14)

Before applying the fluxcon, the SH and LH orders appear tilted to the red. This is due to a difference between the standard extraction, which forces the wavsamp rectangle height to 1.0 pixels, and the custom extraction used to make the flatfield, which uses a variable height rectangle as defined by the wavsamp.

Pre-S15, the tilts were removed by applying the fluxcon table. From S15 onward, the variable height rectangles defined via the wavsamp are used for all extractions. This has the added benefit of matching the instrumental resolution.

7.5.5             Bumps in LH Near 20 Microns (solved in S15)

Bumps are seen in LH orders 19 and 20, at ~19, 20, and 21 microns (see Figure 7.20). They are attributable to bright features at the order edges which are accentuated by the S13-S14 LH flatfield. Features were not present pre-S13, and were fixed in the S15 flatfield. The pipeline S13.2 reduction shows three new peaks around 20 microns that are spurious. The features show in a full slit extraction but when the extraction aperture is shrunk to 2 pixels, the feature vanishes in one nod position but remains in the other. This is due to pixels X=13, Y=12 to 22 which all look unusually bright in the 2D frame even when the source is off on the other side of the slit.

To mitigate this problem, a new LH flat field was created for S15, with bad regions suppressed. For S13, trimming the orders can remove the strongest of the three peaks but not its two weaker neighbors.



Figure 7.20 LH spectrum. Notice the peaks at 19, 20, and 21 microns in the S13.2 spectrum.

7.5.6             Mismatched LH Orders (solved in S17)

For pipeline version S15.0, before flux calibration (in extract.tbl spectra), LH orders are mismatched and appear tilted to the red. This is caused by the increasing wavsamp height with wavelength in each order to accommodate the spectrograph resolution. The effect is not apparent in the flux calibrated (spect.tbl) spectra, as it is corrected by the fluxcon polynomial.

For S17 onward, this effect is corrected at the spectral extraction stage. The flux in each wavelength bin is normalized to a wavsamp height of 1 pixel.

Note that this issue should not be confused with the LH blue tilts and red tilts discussed in Section 7.4.1, which still may be seen in some spectra.

7.5.7             LL Salt and Pepper Rogues (solved in S17)

In S15, LL 'Super Darks' averaged over many campaigns were used to subtract off the instrumental bias signature. Due to the variable nature of rogue pixels, this introduced salt (new rogues not in the super dark), and pepper (rogues in the super dark, but not in the current campaign) into the data.

From S17 onward, campaign-dependent 'moving window darks' are used to better match the rogues in each campaign and to track the changing minimum zodiacal light level. The salt and pepper in S15 BCDs can be very effectively removed by subtracting an appropriate background observation.