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Q2: During the 8 Feb 2024 WOH, he asked Q3: "What causes the black dots in the MIRI MRS channel 2 image below?". Experts suggested it was likely due to bad pixels. The bad pixel map was recently updated so their guidance was to rerun the pipeline using the updated files. The user was able to get rid of most of the weird spots with that advice; however, some were still appearing in the data. Then, when extracting spectra from regions with low SNR, they were finding spectra with negative flux (specifically in channel 1, which doesn't have many lines for their source). Their science and background data were equally deep, so they used pixel-wise background subtraction, but even using master background subtraction, they are still seeing a negative flux. Is this potentially caused by the way the mask was applied?
A2: If you're not detecting continuum, it's possible you're just in the error levels. The region has low flux and it's very diffuse. Pixel-wise background subtraction is a good idea when you have diffuse extended emission and you're trying to eliminate any other noise errors (especially if it's the same depth as your science data). The spectrum looks reasonable in that you're getting down into the detector nosie. MIRI dark current is variable with time, which makes it complicated because you can't have a dark reference file to subtract that would give you an exact zero. One of the pipeline steps looks at a central region in the middle of the detector and computes the median effective residual dark, and subtracts that off. It assumes the delta dark current is constant across the detector. Within some fraction of the pixel uncertainty, it may not be exactly zero on average, so that could explain what you're seeing here. If it was multiple sigma below zero, it would be more concerning, but this spectrum seems reasonable.
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Q3: There are times when users want to do an aperture extraction over all channels and they want the aperture to be the same across every channel to extract from the same region in space. This data is for a bright cluster galaxy (BCG) with a CGM extended tail. The user selects some regions and plots them, so they have a BCG circular region to use for spectral extraction with the cubeviz extraction tool, and they want to use this for all channels; however, there's a problem where in some channels, the BCG falls outside the mosaic (specifically for channel 1) . For channel 1, – the BCG isn't centered in the same place, so there are NaN pixels. To extract the spectrum from this region with the cubeviz tool, if the user wants to do a sum, it won't work due to the presence of NaN pixels. Is it possible to eventually change the code to use, e.g., numpy.nansum? It would make it easier to use the spectral extraction tool (rather than using a manual method).
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