GNU Astronomy Utilities

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2.2.4 Dataset inspection and cropping

First, let’s visually inspect the datasets we downloaded in Setup and data download. Let’s take F160W image as an example. Do the steps below with the other image(s) too (and later with any dataset that you want to work on). It is very important to get a good visual feeling of the dataset you intend to use. Also, note how SAO DS9 (used here for visual inspection of FITS images) doesn’t follow the GNU style of options where “long” and “short” options are preceded by -- and - respectively (for example --width and -w, see Options).

Run the command below to see the F160W image with DS9. Ds9’s -zscale scaling is good to visually highlight the low surface brightness regions, and as the name suggests, -zoom to fit will fit the whole dataset in the window. If the window is too small, expand it with your mouse, then press the “zoom” button on the top row of buttons above the image. Afterwards, in the bottom row of buttons, press “zoom fit”. You can also zoom in and out by scrolling your mouse or the respective operation on your touch-pad when your cursor/pointer is over the image.

$ ds9 download/hlsp_xdf_hst_wfc3ir-60mas_hudf_f160w_v1_sci.fits     \
      -zscale -zoom to fit

As you hover your mouse over the image, notice how the “Value” and positional fields on the top of the ds9 window get updated. The first thing you might notice is that when you hover the mouse over the regions with no data, they have a value of zero. The next thing might be that the dataset actually has two “depth”s (see Quantifying measurement limits). Recall that this is a combined/reduced image of many exposures, and the parts that have more exposures are deeper. In particular, the exposure time of the deep inner region is larger than 4 times of the outer (more shallower) parts.

To simplify the analysis in this tutorial, we’ll only be working on the deep field, so let’s crop it out of the full dataset. Fortunately the XDF survey web page (above) contains the vertices of the deep flat WFC3-IR field. With Gnuastro’s Crop program29, you can use those vertices to cutout this deep region from the larger image. But before that, to keep things organized, let’s make a directory called flat-ir and keep the flat (single-depth) regions in that directory (with a ‘xdf-’ suffix for a shorter and easier filename).

$ mkdir flat-ir
$ astcrop --mode=wcs -h0 --output=flat-ir/xdf-f105w.fits \
          --polygon="53.187414,-27.779152 : 53.159507,-27.759633 : \
                     53.134517,-27.787144 : 53.161906,-27.807208" \

$ astcrop --mode=wcs -h0 --output=flat-ir/xdf-f125w.fits \
          --polygon="53.187414,-27.779152 : 53.159507,-27.759633 : \
                     53.134517,-27.787144 : 53.161906,-27.807208" \

$ astcrop --mode=wcs -h0 --output=flat-ir/xdf-f160w.fits \
          --polygon="53.187414,-27.779152 : 53.159507,-27.759633 : \
                     53.134517,-27.787144 : 53.161906,-27.807208" \

The only thing varying in the three calls to Gnuastro’s Crop program is the filter name! Note how everything else is the same. In such cases, you should generally avoid repeating a command manually, it is prone to many bugs, and as you see, it is very hard to read (didn’t you suddenly write a 7 as an 8?). To simplify the command, and later allow work on more filters, we can use the shell’s for loop as shown below. Notice how the place where the filter names (f105w, f125w and f160w) are used above, have been replaced with $f (the shell variable that for will update in every loop) below.

$ rm flat-ir/*.fits
$ for f in f105w f125w f160w; do \
    astcrop --mode=wcs -h0 --output=flat-ir/xdf-$f.fits \
            --polygon="53.187414,-27.779152 : 53.159507,-27.759633 : \
                       53.134517,-27.787144 : 53.161906,-27.807208" \
            download/hlsp_xdf_hst_wfc3ir-60mas_hudf_"$f"_v1_sci.fits; \

Please open these images and inspect them with the same ds9 command you used above. You will see how it is nicely flat now and doesn’t have varying depths. In the example above, the polygon vertices are in degrees, but you can also replace them with sexagesimal coordinates (for example using 03h32m44.9794 or 03:32:44.9794 instead of 53.187414 instead of the first RA and -27d46m44.9472 or -27:46:44.9472 instead of the first Dec). To further simplify things, you can even define your polygon visually as a DS9 “region”, save it as a “region file” and give that file to crop. But we need to continue, so if you are interested to learn more, see Crop.

Another important result of this crop is that regions with no data now have a NaN (Not-a-Number, or a blank value) value. In the downloaded files, such regions had a value of zero. However, zero is a number, and is thus meaningful, especially when you later want to NoiseChisel30. Generally, when you want to ignore some pixels in a dataset, and avoid higher-level ambiguities or complications, it is always best to give them blank values (not zero, or some other absurdly large or small number). Gnuastro has the Arithmetic program for such cases, and we’ll introduce it later in this tutorial.



To learn more about the crop program see Crop.


As you will see below, unlike most other detection algorithms, NoiseChisel detects the objects from their faintest parts, it doesn’t start with their high signal-to-noise ratio peaks. Since the Sky is already subtracted in many images and noise fluctuates around zero, zero is commonly higher than the initial threshold applied. Therefore not ignoring zero-valued pixels in this image, will cause them to part of the detections!

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