ID

This code is defunct, but the xpa commands it uses are still (mostly) useful.
See this link to see how to use xpa commands.

ID (Image Display) displays an image with ds9+xpa and allows the user to create and store markers. These markers may, for example, be used by down-stream codes to identify elliptical (galaxy) apertures, a column of mirrors in a hexburst image, or a set of stars to be used for constructing a mean stellar PSF for the image.

Simple mode:

Go to the id test directory (use gotr) and choose a subdirectory for testing. In the simplest mode, after invoking ID, just type in the name of the FITS image you want to view and mark up.

%  pwd   
/home/sco/sco/projects/Test_Data_for_Codes/T_runs/id/generic
%  ls
S/
%  S/GRAB 

You can now run ID
Local test image = m51.fits
.  ..  m51.fits  S
%  ID
 No local file: id.input

Enter name of input file to use:  m51.fits

 ANSWER QUERIES UNTIL DONE

At the end of the ID, there may be a number of files present but the most important ones are:

 
id.objects  == an ASCII file storing the marker info 
               in formats that SCO codes understand 

m51.info    == the *.info for the image you processed. This 
               file will contains the ID marker info (the 
               id.objects) and other output files as you 
               process them with other codes.

I usually use ID to mark objects to be photometered. Below is a sample image, an image that is dumped by ID to a JPEG file while it is running!

FIGURE 1: A sample image marked up with ID.

Sometimes, I run ID from other programs and do not want to always manually specify the name of the input image. If you create a local file called "id.input" that contains the name of the image file to be processed, then the interactive query is skipped. Finally, I have a little script called "run_id" that will build "id.input" and run ID. To use it just type soemthing like:

run_id name_of_image.fits

This will get you pretty much anything you want for image mark-up. Maybe not.

Notes on ds9 region files.

As of Apr2014 I have begun to move away from using ID because of a variety of reasons. For one thing, it is getting harder and harder to maintain f77 codes, and some of the tasks that ID performs are actually better suited to bash scripting anyway. Another significant point is that for reasons I do not understand, the behaviour of ds9 seems to be changing with markers, both for Ubuntu and RHEL6 installations. In particular, when a marker color is changed (from the default value of "green") I can make a green marker, but when I make the next marker, the color has reverted back to green! In some cases, the marker type also changes. Hence, I have been writing things that construct the desired region files (with type, color, text, etc.. specified) and then I write them to the gui. It is far quicker to then simply change the position and other properties rather than spend time using menus to change things like color etc... BEFORE I set the region marker. Finally, a pretty clear description of ds9 region parameters can be found in this SAORD webdoc.

I am also writing a number of scripts for catalog production, matching, mergeing, etc... One very useful thing is to be able to overplot the catalog sources on a ds9 display of an image. In SCOLIB.xpadisp.f I have a lot of tools for constructing region files. However, I am finding that python and bash scripting may, again, prove more versatile and easier t control than f77. This seems like a good time to summarize properties of the region file formats. I have used ds9 to make the figure below that uses a variety of region marker properties. I then generated the region file for this set and display that file just below the figure.

FIGURE 2: A variety of ds9 region markers.

Below I show three versions of saving the region files for the ds9 markers above.

 
% cat ds9_image.reg
# Region file format: DS9 version 4.1
# Filename: dss.fits
global color=green dashlist=8 3 width=1 font="helvetica 10 normal roman" select=1 highlite=1 dash=0 fixed=0 edit=1 move=1 delete=1 include=1 source=1
image
circle(591,674,8.0682613)
circle(553.00319,734.00065,15.91123) # color=red text={This is a name string}
box(830.50069,674.4987,76.999999,64.999999,3.7329666e-07) # color=yellow text={a box is here}
box(811.50235,509.00281,47.000001,44,3.7329666e-07) # text={green box, but!?!}
ellipse(406.99729,788.99714,26.000001,34.000001,328.65585) # color=cyan text={NGC 4625}
line(290.99788,628.00014,358.00043,690.00181) # line=0 0 color=white text={line_marker}
# vector(381.99825,569.99892,86.277293,55.388852) vector=1 color=magenta text={vector001}


% cat ds9_fk5_sex.reg
# Region file format: DS9 version 4.1
# Filename: dss.fits
global color=green dashlist=8 3 width=1 font="helvetica 10 normal roman" select=1 highlite=1 dash=0 fixed=0 edit=1 move=1 delete=1 include=1 source=1
fk5
circle(12:41:24.062,+41:13:10.87,13.7166")
circle(12:41:29.923,+41:14:51.92,27.0502") # color=red text={This is a name string}
box(12:40:47.979,+41:13:17.35,130.905",110.52",0.871148) # color=yellow text={a box is here}
box(12:40:50.513,+41:08:35.56,79.9032",74.8136",0.871148) # text={green box, but!?!}
ellipse(12:41:52.063,+41:16:21.57,44.2018",57.8105",329.527) # color=cyan text={NGC 4625}
line(12:42:09.142,+41:11:44.62,12:41:59.205,+41:13:31.92) # line=0 0 color=white text={line_marker}
# vector(12:41:55.295,+41:10:08.57,146.677",56.26) vector=1 color=magenta text={vector001}

% cat ds9_fk5_fp.reg
# Region file format: DS9 version 4.1
# Filename: dss.fits
global color=green dashlist=8 3 width=1 font="helvetica 10 normal roman" select=1 highlite=1 dash=0 fixed=0 edit=1 move=1 delete=1 include=1 source=1
fk5
circle(190.35026,41.219686,13.716598")
circle(190.37468,41.247756,27.050184") # color=red text={This is a name string}
box(190.19991,41.221486,130.90528",110.52013",0.871148) # color=yellow text={a box is here}
box(190.21047,41.143211,79.903228",74.813627",0.871148) # text={green box, but!?!}
ellipse(190.46693,41.272658,44.201786",57.810532",329.527) # color=cyan text={NGC 4625}
line(190.53809,41.195728,190.49669,41.225533) # line=0 0 color=white text={line_marker}
# vector(190.4804,41.169047,146.67732",56.26) vector=1 color=magenta text={vector001}

A Special Addition (Oct24,2013)

I have been researching contour algorithms. I wanted a way to plot sets of contours, and when desired, I wanted to plot these segments in small user-defined sets. It occurred to me that this task could be easily added to ID. The ID code will now, after completing its usual tasks, will seach for a local file called extra_ds9.reg. This file is just an ordinary ds9 regions file. When this file is recognized to be present, the user is queried for the size of the plot set desired. The code then steps through the plotting of all regions listed in this file.

Image scaling

I have modified the run_id script so that is calls the cih (compute image histogram) code (via cih.sh) to derive a backgound level and noise level (sigma). A local file called "zrange.from_cih" is generated by this call, and the -1sigma and +5sigma values from this file. The ID code uses them to set the image grey-scale limits (z1,z2). Moreover, if a local file called "galaxy.scale" is present, then the scaling levels (a1,a2) are read from there and used to set:


   z1 = bkg + a1*sigma  
   z2 = bkg + a2*sigma  

For PFC galaxies, I typically use  a1=-1.0 , a2=100.0

I find that these auto-scaled levels tend to save time by avoiding a lot of recourse to the Scale option in ds9.

DS9 Region Position Angles

A number of regions that I frequently use (ellipse, vector) have an Angle value associated with them. For ds9 ellipse and vector markers, the position angle of the major axis (or the line) is measured from the POSITIVE-X axis (Angle=0) in a counter-clockwise sense in units of degrees. An example is shown below in Figure 3.

FIGURE 3: An example of Angle for ellipse and vector regions in ds9.

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