ANALYZ instruction sequences HI in galaxies

For use with data taken AFTER January 1, 2000 and BEFORE August 15, 2001
(For other data, see Appendix - Old analyz routines)

This appendix contains example analyz sequences used to look at HI spectra.

These routines presently only work for the L-band receivers, since presently I don't have gain curves for the other receivers integrated into the routines. sorry.

This routine takes the average of the (gain/za/az corrected) dumps in each scan, and analysis is done on the individual correlator sections. Thus if you have the correlators overlapping in frequency, and the galaxy therefore shows up in more than one correlator this routine will only look at one `detection' at a time. The commands to by typed are in boldface, followed by a description of the command. For help with these routines contact Karen O'Neil (koneil@naic.edu). All this assume you have run once analyz before. If you have not, please go to http://www.naic.edu/$\sim$astro/spectral_line/analyz and load hi_now.cmd, mjsr.o, and baseh.o into you analyz directories. Additionally, if you have not run analyz before, instruction (2) should read:

(2)	analyz
		$<proj\:name>$ $<num\:chan>$ 800	Type your project name,
			"num chan" = total no. of channels needed.
		corv2	This chooses the correct correlator libraries
		$\sim$hi_now.cmd	This puts the libraries you need into your analyz directory
		autoexecute
(1)	cd analyz		change to your ANALYZ directory
(2)	analyz		starts the analyz program
		$<proj\:name>$	Type your project name
		corv2	This insures the correct correlator libraries are attached
(3)	attach $<data>$ data		attaches the desired data file
(4)	redata $<scan>$ $<n>$ $<cal\_value>$		scans n records, starting with rec, corrects for
			gain/za/az variations, ultimately stores the data in reg. 43
			The cal value is available in the control room at AO
(5)	s $<s1>$ $<s2>$;hor;plot		selects the region of interest (i.e. where a galaxy
			images lies), plots the data
(6)	getres $<low>$ $<high>$		gets vel widths, etc.
			$low$ & $high$ are the channel numbers which
			encompass the galaxy

DESCRIPTION of the above commands:

• (1) cd analyz: By changing into your "analyz" directory, you are insuring that analyz will be able to find your libraries, any necessary fortran files, etc.

• (2) analyz...: Entering the correct project name here ($<proj\:name>$) insures that analyz recognizes the correct number of store/recall registers and that analyz finds the libraries associated with your work. These files are located in your analyz directory, and are labeled, i.e. a9999anz.anz and a9999lib.anz, respectively.

• (3) attach $<data>$ data: This attaches the (old) data to analyz. After you "mvdata" while observing, your data is typically placed in a files called "/share/olcor/corfile.$<data$>.$<proj>$.n", i.e. if the data for project a9999 was taken on March 21, 2000, the file would be "/share/olcor/corfile.21mar00.a9999.1.

• (4) redata $<scan>$ $<n>$ $<cal\_value>$: This first stores the individual ON/OFF - 1 data dumps into registers 100 - 100+$<num\:rec>$ - 1. It then does a rough baseline correction, corrects each ON/OFF - 1 for gain/za/az variations and converts temperature to Janskies (using the standard gain curves and your cals), and stores those in registers 100+$<num\:rec>$ - 100+2*$<num\:rec>$ - 1. Next, the average of all the (ON/OFF-1) records is found, and stored in register 100+2*$<num\:rec>$. Finally, the A & B polarizations are averaged, and those results are stored both in register 100+2*$<num\:rec>$+1, and in register 43 (where the next set of routines expects to find the data. (NOTE: Make your you have 100+2*$<num\:rec>$+1 registers available!) The cal values are obtained in the control room. At the time this is written (18 Sept 00), the cal values are approx. 1.88 for the L-narrow and 9.17 for the L-wide (high cal). These values can change, and you really should get the correct value for your observations.

• (5) s....: At this point, you need to figure out what range of channel numbers you wish to use to analyz your data. You need a range big enough so that you can obtain an accurate baseline, yet small enough that you can readily determine the sides of your galaxy.

• (6) getres $<low>\:<high>$: $<low>$ & $<high>$ are the channel number range chosen in the last step. This routine does the following:
  • setvel: Uses the "optical" definition to convert frequencies to velocity, and then stores the velocities in register 41. The data is then "sectioned" for the rest of the analysis.
  • baseh -5: This runs the baseline reduction routine, allowing you to choose which order fit you would like (from 1 to 5). The baseline is then subtracted from the data, and the results are stored in register 47.
  • msrtest: This runs the msrj program, and outputs the following results:
    Line 1 - The area, central velocity, and width at 50% of the mean flux.
    Line 2 - The area, central velocity, and width at 20% of the mean flux.
    Line 3 - The area, central velocity, and width at 50% of the peak flux.
    Line 4 - The area, central velocity, and width at 20% of the peak flux.
    Line 5 - The area, central velocity, and width at 20% of each of the two horns,
    searched from the inside out.
    NOTE: Ignore the minus signs on the widths and areas - they come about because the data is flipped from what the msrj program expects (so the high velocity is subtracted from the low, instead of vice-versa.)

------------------ EXAMPLE using NEW routines (this data will be available for public use): (please note that these routines were run with fcidisp 0;fciprint 0; and the echo off (TOGGLE 'ECHO)

FIRST time:

        % cd analyz
        % analyz
        Enter your initials  [array size and number of STO/RCL registers optional]
        > temp 16284 800
        File ANZ_BASE/site/syslib.anz attached as SYSLIB.

        Enter <CR> or select an FLIB from the following:
         corv1    CORLIB for data prior to:07mar00
         corv2    CORLIB for data after   :06mar00
        FLIB> corv2
        File ANZ_BASE/site/corv2lib.anz attached as FLIB.

        >>> Creating a file for the stack and sto/rcl registers <<<
        Attaching temppanz.anz as STO/RCL file.
        Your arrays are 16384 elements long, and you have 800 sto/rcl registers.
        None of your sto/rcl registers are kept in main memory.
        Loading... PL X Y Z T HDR 
        File templib.anz attached as ULIB1
 
        Welcome to Analyz, version 5.16 patchlevel 2
 
 
        >~hi_now.cmd
        Error 144: ANALYZ fault: unrecognized command structure

        >exit

        STOP: ANALYZ exit
         Note: Following IEEE floating-point traps enabled; see ieee_handler(3M): 
         Overflow;  Division by Zero;  Invalid Operand; 
         Sun's implementation of IEEE arithmetic is discussed in 
         the Numerical Computation Guide.

        %analyz

        Enter your initials  [array size and number of STO/RCL registers optional]
        >temp

        Enter <CR> or select an FLIB from the following:
         corv1    CORLIB for data prior to:07mar00
         corv2    CORLIB for data after   :06mar00
        FLIB>corv2

        File ANZ_BASE/site/corv2lib.anz attached as FLIB.
 
        Attaching tempanz.anz as STO/RCL file.
        Your arrays are 16384 elements long, and you have 800 sto/rcl registers.
        None of your sto/rcl registers are kept in main memory.
        Loading... PL X Y Z T HDR 
        File templib.anz attached as ULIB1.
 
        Welcome to Analyz, version 5.16 patchlevel 2
 
 
        File /usr/local/phil/philib.anz attached as ULIB2.
        Created new array named @calv

        > attach "/proj/a1366/corfile.21mar00.a1366.1" data
        File /proj/a1366/corfile.21mar00.a1366.1 attached as DATA.
        Status = OLD; access = SEQUENTIAL; form = UNFORMATTED

        > redata 13 50 1.88
        loading via: ANZ_BASE/tools/ld -N -x -A /usr/local/bin/analyz.exe -T 037bc00 -o a.out
        ANZ_BASE/external/extern_main.o  ANZ_BASE/external/libextern.a -LANZ_BASE/external -lF77 -lm -lc
        New program text loaded successfully.

                .....

	Created new array named @ci
	on/off -1 raw in 100 -   149.0
	Created new array named @tmp2
	Created new array named @tmp3
	Created new array named @tmp4

	on/off -1 corr in   150.0     -   199.0
	on/off -1 corrected average in   202.0
	CAL (in K) in reg   200.0
	Calibrated data in register   203.0
	Temperature is   31.08
	on/off -1 corr, AB avg'd in   204.0        42.00
	rms subtracted data in 43

        > rcl 43;ver -0.02 0.01;plot 
 
        > hor 0 600;plot

        > getres 0 600

        loading via: ANZ_BASE/tools/ld -N -x -A /usr/local/bin/analyz.exe -T 0579400 -o a.out baseh.o
          -LANZ_BASE/external -lF77 -lm -lc
        New program text loaded successfully.

         Set base regions, with crosshair:
         Hit space key after each positioning,
         DO NOT touch mouse button!
         Hit Q after last (rightmost) limit.
         Limits are:   10  583  186  389  0  0  0  0  0  0
        Are limits OK? (y/n) [y] y
 
         Order     rms    Ftest
           1      0.001    27.985
           2      0.001     1.258
           3      0.001    11.416
           4      0.001    10.127
           5      0.001     2.408
        What order do you want?  2
        loading via: ANZ_BASE/tools/ld -N -x -A /usr/local/bin/analyz.exe -T 059e000 -o a.out msrj.o
          -LANZ_BASE/external -lF77 -lm -lc
        New program text loaded successfully.
        ow flag LEFT side chan for area bounds.
         Hit any key.
         Flag RIGHT side channel.
         Hit any key.
        Happy with the choice of bounds?  (y/n) [y] y
	 area(232, 339) =-.3657E+01 Center = 9438.65884    Width(239, 338) = -546.33510
	 area(232, 339) =-.3657E+01 Center = 9440.86550    Width(238, 338) = -556.47625
	 area(232, 339) =-.3657E+01 Center = 9453.49903    Width(241, 330) = -493.37126
	 area(232, 339) =-.3657E+01 Center = 9440.68466    Width(239, 338) = -548.14477
	 area(232, 339) =-.3558E+01 Center = 9458.75213    Width(239, 338) = -528.72213
	 	area = -.3657E+01 Ok? (y/n or e (for exit))e
        MSR Done...
        > 

________________________________________________

NOTE:

• If RFI is a problem with your data, one way of reducing its effects is to take have a large number of dumps and take the median, rather than the average of the dumps (i.e. set the dumplength to 6s and still take 5 minute scans). In this case you can replace "(7) doit $<$rec$>$ $<$num$>$" with "(7) mednf $<$reg num$>$ $<$rec$>$ $<$num$>$", where register number should be above 100. This will dump the median (rather than the average) of the $<$num$>$ scans into the correct registers. Another alternative, which only works for the l-wide receiver, is to run "(7) medlwf $<$reg num$>$ $<$rec$>$ $<$num$>$", which will output the data in Jy into the appropriate registers. In this case the results given after the "getfcts" command are already in Jy and do not need to be converted.

• If you want to save your data and come back to it later, you need to not only save the data (which is in register 43, after the "redata" commad), but also save your frequency information (which is in register 8), as headers are not preserved. This means if, for example, you want to save your data to register 500, you need to type:

  > rcl 43;sto 500
  >rcl 8;sto 501
  

  To begin working on your data again, you must the restore both the data and frequency info:

  >rcl 500;sto 43;rcl 501;sto 8
  

• If you have more than one scan of the same object, you can recall them by:
  • Run "redata"
  • rcl the data from 43 ad save it in a safe register (i.e. 70) $\rightarrow$ rcl 43;sto 70
  • repeat the first two steps for all your data, saving the data in subsequent registers,
  • rcl all the data ad average it. I.e. if you have 5 data sets which you placed in registers 70 - 74, you would type:

    > rcl 70;rcl 71;+;rcl 72;+;rcl 73;+;rcl 74;+;/ 5
    

  • store the averaged data back into 43 $\rightarrow$ sto 43

• If you want to smooth your data and work with the smoothed version, just recall your data from 43, smooth it, ad store it back in 43. I.e.

  >rcl 43;smo 19;sto 43
  

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