GNU Astronomy Utilities


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2.1.21 Marking objects for publication

In FITS images in a publication we created a ready-to-print visualization of the FITS image used in this tutorial. However, you rarely want to show a naked image like that! You usually want to highlight some objects (that are the target of your science) over the image and show different marks for the various types of objects you are studying. In this tutorial, we will do just that: select a sub-set of the full catalog of clumps, and show them with different marks shapes and colors, while also adding some text under each mark. To add coordinates on the edges of the figure in your paper, see Annotations for figure in paper.

To start with, let’s put a red plus sign over the sub-sample of reddest clumps similar to Reddest clumps, cutouts and parallelization. First, we will need to make the table of marks. We will choose those with a color stronger than 1.5 magnitudes and a signal-to-noise ratio (in F160W) larger than 5. We also only need the RA, Dec, color and magnitude (in F160W) columns.

$ asttable cat/mags-with-color.fits --range=F105W-F160W,1.5:inf \
           --range=sn-f160w,5:inf -cRA,DEC,MAG-F160w,F105W-F160W \
           -oreport-image/reddest-cat.fits

To keep the rest of the code easier to read, let’s move to the report-image directory:

$ cd report-image

Gnuastro’s ConvertType program also has features to add marks over the finally produced PDF. Below, we will start with the same astconvertt command of the previous section. The positions of the marks should be given as a table to the --marks option. Two other options are also mandatory: --markcoords identifies the columns that contain the coordinates of each mark and --mode specifies if the coordinates are in image or WCS coordinates.

$ astconvertt sb.fits --output=reddest.pdf --fluxlow=20 \
              --marks=reddest-cat.fits --mode=wcs \
              --markcoords=RA,DEC

Open the output reddest.pdf and see the result. You will see relatively thick red circles placed over the given coordinates. In your PDF browser, zoom-in to one of the regions, you will see that while the pixels of the background image become larger, the lines of these regions do not degrade! This is the concept/power of Vector Graphics: ideal for publication! For more on raster (pixelated) and vector (infinite-resolution) graphics, see Raster and Vector graphics.

We had planned to put a plus-sign on each object. However, because we did not explicitly ask for a certain shape, ConvertType put a circle. Each mark can have its own separate shape. Shapes can be given by a name or a code. The full list of available shapes names and codes is given in the description of --markshape option of Drawing with vector graphics.

To use a different shape, we need to add a new column to the base table, containing the identifier of the desired shape for each mark. For example, the code for the plus sign is 2. With the commands below, we will add a new column with this fixed value. With the first AWK command we will make a single-column file, where all the rows have the same value. We pipe our base table into AWK, so it has the same number of rows. With the second command, we concatenate (or append) the new column with Table, and give this new column the name SHAPE (to easily refer to it later and not have to count). With the third command, we clean-up behind our selves (deleting the extra params.txt file). Finally, we use the --markshape option to tell ConvertType which column to use for the shape identifier.

$ asttable reddest-cat.fits | awk '{print 2}' > params.txt

$ asttable reddest-cat.fits --catcolumnfile=params.txt \
           --colmetadata=5,SHAPE,id,"Shape of mark" \
           --output=reddest-marks.fits
$ rm params.txt

$ astconvertt sb.fits --output=reddest.pdf --fluxlow=20 \
              --marks=reddest-marks.fits --mode=wcs \
              --markcoords=RA,DEC --markshape=SHAPE

Open the PDF and have a look! You do see red signs over the coordinates, but the thick plus-signs only become visible after you zoom-in multiple times! To make them larger, you can give another column to specify the size of each mark. Let’s set the full width of the plus sign to extend 3 arcseconds. The commands are similar to above, try to follow the difference (in particular, how we use --sizeinarcsec).

$ asttable reddest-cat.fits | awk '{print 2, 3}' > params.txt

$ asttable reddest-cat.fits --catcolumnfile=params.txt \
           --colmetadata=5,SHAPE,id,"Shape of mark" \
           --colmetadata=6,SIZE,arcsec,"Size in arcseconds" \
           --output=reddest-marks.fits
$ rm params.txt

$ astconvertt sb.fits --output=reddest.pdf --fluxlow=20 \
              --marks=reddest-marks.fits --mode=wcs \
              --markcoords=RA,DEC --markshape=SHAPE \
              --marksize=SIZE --sizeinarcsec

The power of this methodology is that each mark can be completely different! For example, let’s show the objects with a color less than 2 magnitudes with a circle, and those with a stronger color with a plus (recall that the code for a circle was 1 and that of a plus was 2). You only need to replace the first command above with the one below. Afterwards, run the rest of the commands in the last code-block.

$ asttable reddest-cat.fits -cF105W-F160W \
           | awk '{if($1<2) shape=1; else shape=2; print shape, 3}' \
           > params.txt

Have a look at the resulting reddest.pdf. You see that the circles are much larger than the plus signs. This is because the “size” of a cross is defined to be its full width, but for a circle, the value in the size column is the radius. The way each shape interprets the value of the size column is fully described under --markshape of Drawing with vector graphics. To make them more comparable, let’s set the circle sizes to be half of the cross sizes.

$ asttable reddest-cat.fits -cF105W-F160W \
           | awk '{if($1<2) {shape=1; size=1.5} \
                   else     {shape=2; size=3} \
                   print shape, size}' \
           > params.txt

Let’s make things a little more complex (and show more information in the visualization) by using color. Gnuastro recognizes the full extended web colors, for their full list (containing names and codes) see Vector graphics colors. But like everything else, an even easier way to view and select the color for your figure is on the command-line! If your terminal supports 24-bit true-color, you can see all the colors by running this command (supported on modern GNU/Linux distributions):

$ astconvertt --listcolors

we will give a “Sienna” color for the objects that are fainter than 29th magnitude and a “deeppink” color to the brighter ones (while keeping the same shapes definition as before) Since there are many colors, using their codes can make the table hard to read by a human! So let’s use the color names instead of the color codes in the example below (this is useful in other columns require strings-only, like the font name).

The only intricacy is in the making of params.txt. Recall that string columns need column metadata (Gnuastro text table format). In this particular case, since the string column is the last one, we can safely use AWK’s print command. But if you have multiple string columns, to be safe it is better to use AWK’s printf and explicitly specify the number of characters in the string columns.

$ asttable reddest-cat.fits -cF105W-F160W,MAG-F160W \
           | awk 'BEGIN{print "# Column 3: COLOR [name, str8]"}\
                  {if($1<2)  {shape=1; size=1.5} \
                   else      {shape=2; size=3} \
                   if($2>29) {color="sienna"} \
                   else      {color="deeppink"} \
                   print shape, size, color}' \
           > params.txt

$ asttable reddest-cat.fits --catcolumnfile=params.txt \
           --colmetadata=5,SHAPE,id,"Shape of mark" \
           --colmetadata=6,SIZE,arcsec,"Size in arcseconds" \
           --output=reddest-marks.fits
$ rm params.txt

$ astconvertt sb.fits --output=reddest.pdf --fluxlow=20 \
              --marks=reddest-marks.fits --mode=wcs \
              --markcoords=RA,DEC --markshape=SHAPE \
              --marksize=SIZE --sizeinarcsec --markcolor=COLOR

As one final example, let’s write the magnitude of each object under it. Since the magnitude is already in the marks.fits that we produced above, it is very easy to add it (just add --marktext option to ConvertType):

$ astconvertt sb.fits --output=reddest.pdf --fluxlow=20 \
              --marks=reddest-marks.fits --mode=wcs \
              --markcoords=RA,DEC --markshape=SHAPE \
              --marksize=SIZE --sizeinarcsec \
              --markcolor=COLOR --marktext=MAG-F160W

Open the final PDF (reddest.pdf) and you will see the magnitudes written under each mark in the same color. In the case of magnitudes (where the magnitude error is usually much larger than 0.01 magnitudes, four decimals is not too meaningful. By default, for printing floating point columns, we use the compiler’s default precision (which is about 4 digits for 32-bit floating point numbers). But you can over-write this (to only show two digits after the decimal point) with the --marktextprecision=2 option.

You can customize the written text by specifying a different line-width (for the text, different from the main mark), or even specifying a different font for each mark! You can see the full list of available fonts for the text under a mark with the first command below and with the second, you can actually see them in a custom PDF (to only show the fonts).

$ astconvertt --listfonts
$ astconvertt --showfonts

As you see, there are many ways you can customize each mark! The above examples were just the tip of the iceburg! But this section has already become long so we will stop it here (see the box at the end of this section for yet another useful example). Like above, each feature of a mark can be controlled with a column in the table of mark information. Please see in Drawing with vector graphics for the full list of columns/features that you can use.

Drawing ellipses: With the commands below, you can measure the elliptical properties of the objects and visualized them in a ready-to-publish PDF (we will only show the ellipses of the largest clumps):

$ astmkcatalog ../seg/xdf-f160w.fits --ra --dec --semimajor \
               --axisratio --positionangle --clumpscat \
               --output=ellipseinfo.fits
$ asttable ellipseinfo.fits -hCLUMPS | awk '{print 4}' > params.txt
$ asttable ellipseinfo.fits -hCLUMPS --catcolumnfile=params.txt \
           --range=SEMI_MAJOR,10,inf -oellipse-marks.fits \
           --colmetadata=6,SHAPE,id,"Shape of mark"
$ astconvertt sb.fits --output=ellipse.pdf --fluxlow=20 \
              --marks=ellipse-marks.fits --mode=wcs \
              --markcoords=RA,DEC --markshape=SHAPE \
              --marksize=SEMI_MAJOR,AXIS_RATIO --sizeinpix \
              --markrotate=POSITION_ANGLE

To conclude this section, let us highlight an important factor to consider in vector graphics. In ConvertType, things like line width or font size are defined in units of points. In vector graphics standards, 72 points correspond to one inch. Therefore, one way you can change these factors for all the objects is to assign a larger or smaller print size to the image. The print size is just a meta-data entry, and will not affect the file’s volume in bytes! You can do this with the --widthincm option. Try adding this option and giving it very different values like 5 or 30.


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