Spitzer Documentation & Tools
IRAC Instrument Handbook
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8.4.4        Source Extraction

The Spitzer source extractor, APEX, may be used to fit point sources in IRAC data. This software can be run in two modes, in a single frame mode (apex_1frame) which can be run on an individual BCD, CBCD or a mosaic, and in a multi-frame mode which uses the mosaic to detect sources, but the individual BCDs or CBCDs to measure their fluxes. Note that PRF fitting is not recommended to be performed on IRAC mosaics, but on (C)BCDs only.       Noise Estimation

The BCD uncertainty files are rough uncertainty estimations and do not include all of the systematic effects associated with IRAC detectors, nor do they include the absolute flux uncertainty. These uncertainty images are generated as follows. They begin as an estimate of the read noise (one number in electrons for the whole image) and the shot-noise due to the sky (proportional to the square-root of the number of electrons in the image as calculated in Section 2.5.1). Then each module propagates the uncertainty image forward, including the uncertainties in dark and flat calibration files. The pipeline modules used the uncertainty image as a way to quantitatively estimate the quality of the sky estimate given by the value of a pixel. In the end, the uncertainty images overestimate the formal uncertainty of the image, because the net propagated uncertainty is much higher than the observed pixel-to-pixel fluctuations in the images. We therefore recommend that the uncertainty images only be used for relative weights between pixels, for example when performing outlier rejection or making a weighted mosaic that combines multiple input frames that view the same sky mosaic pixel.


The accuracy of the fluxes from APEX is very sensitive to the noise estimates, as these affect the fitted background value. For crowded fields, it is essential to include an estimate of the confusion noise (not included in the BCD uncertainty image). This can be estimated by measuring the difference between the actual image RMS and the estimated RMS in the uncertainty image, and then either adding it to the uncertainty image, or using it as the confusion noise value when generating uncertainty images with the post-BCD software (see Section       PRF Estimation

The PRFs released with MOPEX should be fairly good matches to the data and a significant improvement on the previous versions. We do not recommend using the prf_estimate.pl script to generate PRFs from the mosaics.       Background Estimation

For point source fitting the parameter use_background_subtracted_image_for_fitting = 1 is the default and self-explanatory. An additional option Background_Fit is available in the Source Estimate block. This lets a background level to be one of the point source fit parameters. The default is off - the background subtracted image is assumed to have had a robust measure of the background removed. But Background_Fit may be useful in crowded regions or with structured backgrounds. Aperture photometry (done on the mosaics in multi-frame APEX) by default uses a background annulus on non-background subtracted data.       Source Extraction

Source detection and extraction are controlled by the parameters Detection max/min area and detection threshold. APEX will frequently try to split bright sources into several components. This tendency can be controlled by setting the Max_Number_PS parameter in &SOURCESTIMATE to a low number (2 – 3). Two files are output: extract_raw.tbl contains all detections, and extract.tbl, which is a subset of extract_raw.tbl, contains the objects and fields which are selected by select conditions and select columns. Source extraction from the BCDs or CBCDs (multiframe mode) is recommended for IRAC data.       Outlier Rejection

By default, APEX will not perform outlier rejection. This can be gotten around by running the mosaicker with outlier rejection turned on and keeping the intermediate products (delete_intermediate files = 0).   

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