Spitzer Documentation & Tools
Spitzer Data Analysis Cookbook


Recipe 25.            MOPEX: MIPS 70 micron mosaic of HII 173

In this recipe, we mosaic the FEPS Legacy Science program MIPS 70 microns small-field photometry observation of the Pleiades star HII 173. This recipe continues in a source extraction step.

25.1            Requirements

You will need to download MOPEX (http://irsa.ipac.caltech.edu/data/SPITZER/docs/dataanalysistools/tools//mopex), in order to run the script mosaic.pl. You will need to use this namelist: http://irsa.ipac.caltech.edu/data/SPITZER/docs/dataanalysistools/cookbook/files/mosaic_70um.nl. Download the 70 microns BCD and post-BCD data for AOR 5315584. See Recipe 1 for instructions on downloading data via the Spitzer Archive interface.

25.2            Have a quick look at the data

The online (=automatically produced) 70 microns mosaics may not be good enough to start analyzing for science right away, but they are good enough to quickly assess your data - did you see something bright or not? For an initial look at your data, use ds9 or your favorite image viewer to examine the on-line mosaics that came with your data.

unix% cd /where/you/unpacked_data/r5315584/ch1/pbcd/

unix% ds9 SPITZER_M1_5315584_0000_1_E429953_msaic.fits &

Note that, unlike for 24 micron observations, there are no "non-prime" data here. However, under pipeline version S11 onward, there are two mosaics - filtered and unfiltered. No source is apparent at the center, but off-center, there seems to be one. For completeness, we note that there are no 160 microns mosaics at all, because this array was never "prime," so all of these data are ancillary.

25.3            Set up lists of filenames and namelist files in preparation to remosaic data

Personally, I like to have just one copy of the cal/ directory into which I can put the latest pmasks and the PRF (http://irsa.ipac.caltech.edu/data/SPITZER/docs/mips/calibrationfiles/) I want to start from. Also copy the cdf namelist files for this example into a cdf/ subdirectory.

unix% cd r5315584/ch1/bcd/

unix% ln -s /where/you/unpacked_data/cal ./cal

unix% mkdir cdf

unix% mv /where/you/downloaded/mosaic_70um.nl ./cdf/


Lists that contain all of the BCDs, masks, and uncertainty files are needed as input to the mosaic.pl script.

unix% cd r5315584/ch2/bcd/

unix% ls *_bcd.fits > InputImageList.txt

unix% ls *bmask.fits > DmaskList.txt

unix% ls *bunc.fits > SigmaList.txt

unix% wc *.txt

unix% nedit cdf/mosaic_70um.nl

Here you don't need to worry about serendipitous data or the first frame effect. You might want to check the length of each file (wc *.txt) to be sure that each list has the same number of files. If you find that that file has a lot more lines than the others, the following is probably what happened. Because the filtered and unfiltered BCDs have similar filename extensions, be sure that you are only putting the unfiltered (or just the filtered) into the InputImageList.txt file.


Edit the namelist to reflect where your cal files are located -- be sure to use absolute pathnames!

25.4            Remosaic the data

unix% mosaic.pl -n mosaic_70um.nl


unix% mkdir pbcd70

unix% mosaic.pl -n mosaic_70um.nl > pbcd70/mosaic.log


Note that the namelist is assumed to be in the cdf/ subdirectory, not in your current directory. If desired, redirect the output to a log file for your records. (actual mosaic log file: http://irsa.ipac.caltech.edu/data/SPITZER/docs/dataanalysistools/cookbook/files/mosaic70.log)


Common errors:

  • "mosaic.pl: Command not found." means you have not sourced the csh when setting up the mopex package in your current shell (window).
  • other "files not found" -- make sure you set all the paths correctly in the namelist, and that you're sitting in the correct directory when you call mosaic.pl.
  • Error with "PSUtils" -- mopex_script_env.csh is not properly set up.

Check the mosaic.

unix% ds9 pbcd70/Combine/mosaic.fits &

Check the mosaic for anything that looks 'odd.' It should look similar to the unfiltered mosaic shown below (which came with your data, in the pbcd directory).