The GALFA HI User`s Guide
Contents
1. Command file to go and browse for a file you want to run Click on file command galfasre then click on Start Command Line Observation This will load the IFLO setup file and perform the calibration pattern It takes about 3 minutes to complete this step Please WATCH the AO Observer Display for a few minutes It should show updated messages every few seconds If you notice that observing is hanging you don t see updated messages every few seconds try re starting WAPPs or call Snezana c At any time during observing you can open Quick Look Data Display on dataview to make sure the spectra are being updated d OPTIONAL STEP You can also view data using GALSPECT s display i Open a new xterm on dataview and type guest dataview guest vncviewer galfal ii This brings up a plot window entitled TightVNC Pixmap framebuffer With the cursor on this window type h this will blow up the plot and make it easier to inspect spectra iii G ALFA folder in the control room explains how to change different display options 3 Running the calibration script at the end At the end of a2010 observing run the calibration script should be run at the position where the last drift scan was finished Same as at the start just with using the file command_galfacurpos 4 Stopping GALSPECT at the end of the run On dataview s galfal window the one which prints numbers all the time press Control C2. 4 Return to the previous step and type again var levels in the galfal window 17 A 2 Sample checklist for commensal TOGS observing updated on Dec 7 2005 These are instructions for running GALSPECT commensally with a2010 The procedure consists of 1 Starting GALSPECT before a2010 starts TO 2 Running the calibration script at the start of a2010 observer 3 Running the calibration script at the end of a2010 observer 4 Stopping GALSPECT TO For each TOGS run there is a contact person on duty To find out who to call in case of problems please check the TOGS Contact Schedule in the control room located in GALFA s folder 1 Starting GALSPECT A few minutes before a2010 starts the TO should login to GALSPECT and start the datataking script with the following a Check that ALFA is uncovered and its amplifiers are ON b Login to dataview as user guest password is naic305m and open an xterm window c In this window login to galfal computer by typing guest dataview guest ssh i galfa_key galfaQ galfal The prompt appears d In the same window type var diag Let it run for some time like 30 sec you will see lots of messages GALSPECT is warming up Stop this by typing Control C e Then type var levels_togs If this gives the message LO2 Set failed got back ERROR setting freq follow the procedure given in the footnote Typically we want RMS values to be around 10 However as w
3. One of the reasons why it was decided not to use one of the equal area WCS coordinate schemes is that the available FITS file viewing software often time does not read in the input properly or two different viewers may interpret the same fits file differently when using anything but the most basic WCS schemes If you d like to convince yourself of this pick up a copy of ds9 and a copy of Karma and try opening up a fits file which uses the Samson Flamsteed SFS projection CALLING SEQUENCE 21 plotobserved ra dec pixelsize outputfilename EXAMPLE Running the following command in IDL plotobserved 1 5 5 10 40 3 5 home mkrco GALFAobserved fits will generate a fits file covering an RA range from 1 5 to 5 hrs and a DEC range of 10 to 40 degrees and a pixelsize of 3 5 arcminutes as specified above 22
4. a is lower case Click on Line then Accept d On the window Choose Receiver click on ALFA then click on Disable Quick Tsys then click on Select Receiver Now This will start rotating the turret to ALFA e Re start WAPPs with On the CIMA Observer s Interface window click on Pulsar Observing Then on the WAPP Wideband Arecibo Pulsar Processor Datataking Control GUI window click on More This will open a new window called more click on Restart ALL WAPPs You can now dismiss the last two windows From CIMA Observer s Interface window select Command File Observing g A new window CIMA command file observing window will pop up Click on Load to go and browse for a file you want to run Click on file pt1 click on Open Then back on the CIMA command file observing window click on Run This will load the IFLO setup file and start driving the telescope to the desired source 5 Starting GALSPECT a While the telescope is driving to the desired position Login to dataview as user guest password is naic305m b Open an xterm and login to galfal computer by typing guest dataview guest ssh i galfa_key galfaQgalfal The prompt appears c In the same window type var diag Let it run you will see lots of messages as GALSPECT is warming up d Once you get on the source in the same w
5. and exit from this window B Logging into GALSPECT To log in into the GALSPECT machine you must have access to a gal fa_key file This file serves as authentication for your access to the spectrometer You should obtain a copy of the file from share galfa scripts The appropriate command to log in into GALSPECT using the gal fa_key file is ssh i galfakey galfa galfal This will provide you with access to write in the var directory and to launch diagnostics as well as observing commands For detailed documentation consult the GALFA Spectrometer Setup Operation Basics document from the GALFA website 19 C C 1 Description of GALFA codes and their usage BW_fm BW_fm pro is a program used for designing observing files The latest version of this program can be found on Josh Goldston s web page http astro berkeley edu goldston BW fm pro The main inputs to BW_fm are the location and size of the region one is interested in mapping BW_fm then produces three files that can be fed to CIMA to produce over a series of days a well sampled and calibrated map of the desired region A call to BW_fm can be rather complex IDL gt BW_fm sourcename RA dec wait_time dra ddec late out_exp out_exp out_cat out_cat end_time end_time start_lsts start_lsts end_lsts end_lsts gear gear file file days_done days_done redst redst loops loops ifloname ifloname restfreq restfreq azwag azwag sfsradec sfsra
6. examined to figure our which exact scan was run and if satisfactory all entries for this scan can then be deleted from the pt2 file Alternatively a new set of files could be created by specifying which scans those ones that run successfully should be excluded It is wise to keep track of all scans that run successfully and make sure that by the end of the observing run all scans were completed with the desired number of repetitions This way you will avoid having annoying gaps in your map An example of running BW_fm is given here BW_fm ms 22 73 13 9 13 0 80 5 8 7 oe oc et slst elst gear 5 file days_done 0 1 2 3 loops 2 ifloname galfa_iflo gui but see Appendix C 1 for the explanation of all input parameters 2 3 3 GALSPECT files Before you start observing you also need to command GALSPECT to start taking data This involves giving several input parameters and can be done manually However using a simple script for this purpose is more efficient and less error prone For instructions on how to log in into GALSPECT please refer to the Appendix B It is highly recommended that you consult the GALFA Spectrometer Setup Operation Basics document from the GALFA website for detailed documentation on running the spectrometer before writing any scripts to GALSPECT Besides your project s name the only other important parameter is the central sky frequency for your observations A selected central
7. full header information The archive itself is stored entirely in simple ascii text files to allow for versatility and simplicity These files are located within sub directories of the main archive directory see Section 5 however it is expected that most users will not need to look at the archive files directly but instead can rely on codes already developed by others such as plotobserved for example Contributions of codes which utilize the archive are welcome and contributors should contact Marko Kr o The following is only a concise description of the archive s functionality and some of the useful end user programs which have been built to take advantage of it Due to the complexity of the archive and the need for precise documentation a separate archive specific document will be written in the near future The archive consists of three main components e The positionarchive is a directory with 96 different ascii files It is designed for fast searching based on a given sky position There are 24 files for 24 RA hours times 4 files 8 These files are located in the positionarchive sub directory of the main archive directory see Section 5 Each file contains records each record represents one 1 second dump from the spectrometer including all 7 beams in each record For each record there is a pointer directing to its location within the BIGarchive e The SM ALLarchive is where we organize the information based on each galfa fits file Th
8. list and short description of currently available end user codes and procedures which utilize the archive More detailed descriptions and usage can be found in the Appendix plotobserved pro This IDL procedure will take a given RA and DEC range along with a pixel size and will generate a fits file containing a map of the specified region where the value of each pixel represents the total integration time in seconds of all GALFA observation within that pixel divided by the pixel s area on the sky in square arcminutes This code is located within the planning codes sub directory see Section 5 15 A Quick Observing Checklists A 1 Sample Basket weave Observing Checklist This is a sample observing checklist for basketweave mapping using scripts generated by BW_fm pro This can be easily expanded and adapted to any particular project 1 Before your observations begin place the appropriate pt1 pt2 and sources files generated by BW_fm pro into your project directory share obs4 usr aXXX 2 place the appropriate GALSPECT scripts for your project into the var directory on galfal 3 FIRST MAKE SURE THAT THE ALFA COVER IS OFF when you start observing 4 Starting CIMA and pointing the telescope a On observer login as dtusr t b Open an xterm and type cima If it asks which version choose normal v 2 1 c On the center window entitled Start New CIMA Session enter your name and project number aXXX NOTE
9. sampled map are GEAR Integration Time sec ALFA angle deg 6 2 4 0 5 4 1 30 4 8 3 30 3 9 6 0 2 12 0 0 1 12 4 30 If the fastest gear is insufficient for a particular project then it is possible to use a lower gear or to re observe the region multiple times at faster gears Due to the nature of basket weave scanning the former solution requires fewer days with more hours of observing per day while the latter requires more days with fewer hours per day It will be necessary to provide this information on an observing proposal It should be noted that it is rather inefficient to use basketweaving to map regions which are smaller in R A The preferred method for obtaining a reference spectrum for GALFA observations is based on the Smart Frequency Switching SFS technique SFS observations should be obtained before and after each day s basket weave or a drift scan As eventually all GALFA observations will be combined together to produce a large map it is necessary to complement GALFA observations with the SFS calibration With the usual setup once on source the SFS calibration takes only 3 4 minutes The need for this additional observing time should be accounted for when applying for observing time As a general rule of thumb the needed observing time for each day will be equal to the R A extent of the map and one day of observing will be required for every half degree in Declination using the fastest gear However the best and eas
10. to provide a complete understanding of the GALFA projects nor GALSPECT More detailed information on many aspects of GALFA is located on the GALFA websitet Some of the more commonly used documents from the website are listed here e GALFA Spectrometer Setup Operation Basics Heiles Tang Mock 2004 e GALFA Spectrometer Operating Manual Jeff Mock 2004 e GALFA Consortium Guidelines e GALFA HI Data Reduction Software Page For more general information on observing with the Arecibo telescope check User s Manual for Arecibo Ob servations The Control Interface Module for Arecibo CIMA and Remote Observing with the Arecibo Telescope available at http www naic edu astro All GALFA s memos including the latest version of this document are located at http www naic edu alfa galfa galfadocs shtml If you notice outdated information in this document please e mail Sne ana Stanimirovi sstanimi astro wisc edu 1 1 Nomenclature In this document we adopt the following font styles for various files directories commonly referred to directory names are given in italics codes as well as computers are given in bold e simulated typed text is given in typewriter fonts e names of particular sample observing files are given with Sans Serif fonts Thttp www naic edu alfa galfa http www naic edu alfa galfa docs galspect_jun06 pdf Shttp www naic edu alfa galfa docs galspect http www naic ed
11. you start as remote is very slow 4 2 Quickly plotting spectra Make sure you have source ed the right idlenv file see Section 5 Start IDL An example of how to quickly open a fits file and plot spectra is IDL gt file share galfa galfa 20050817 togs 0011 fits IDL gt m1 mrdfits file 1 hdr1 IDL gt plot m1 300 data m1 will be an idl data structure and this will plot the 300th spectrum 4 3 Checking if everything worked properly Several diagnostic IDL codes exist that can examine fits files Document Does everything work properly Do these tests on every day s data written by Carl Heiles and available at http astron berkeley edu sstanimi GALFA galfa_page html under GALFA Software explains how to use these codes On the same web page you can find the basic document describing data reduction steps GALFA HI Data Reduction Pipeline written by Josh Goldston 5 Software setup and paths All GALFA related data codes and documentation available in Arecibo are located within the share galfa directory and its subdirectories In order to access data files you must have your own user account at Arecibo Once you have an account set up you should source the appropriate share galfa idlenv file from your bashrc or cshre or whatever you use file This will appropriately configure all the IDL paths and variables so that you may use all the GALFA related IDL procedures with ease At the moment t
12. CIMA is capable of loading a pre existing gui file which can then be easily modified Several sample gui files can be found in share galfa scripts CIMAguifiles Most likely you will be able to simply copy one of these files into your observing directory the only parameter that matters is the central frequency for your observations e For GALFA projects doing basket weave scanning the appropriate central frequency to use is 1445 4057 MHz and the appropriate setup file is galfa_iflo gui e For projects doing commensal observing with an E ALFA project the appropriate central frequency is 1385 MHz and the appropriate setup file is togs gui In the case you wish to examine the setup files and or make some changes please remember that you can run CIMA off line harmlessly from any Arecibo machine Here are some basic instructions on how to do this 1 Copy over a sample gui file from share galfa scripts CIMAguifiles to your project directory share obs4 usr aXXXX 2 Start CIMA by typing cima at the command prompt on any Arecibo machine without logging in as the observer 3 On the window titled Start New CIMA Session fill in the project number observer name select Line Observing mode and click Accept 4 To load the sample gui file a On the window titled CIMA Observer s Inter face click on Load Save State b In the CIMA Generic Save Load State window click on Load a Saved State and select the sample gui file you copied to your
13. For instructions on how to get this going go to Remote Observing with the Arecibo Telescope web page which has instructions for both Windows and Macs Concerning data monitoring the general program at Arecibo is Quickview however it is at the moment too slow to display remotely Using GALSPECT s display is easier however it requires having VNC Viewer installed on your computer Important note it is recommended to run VNC Viewer only for a few minutes at the beginning of your remote session as this program may affect datataking e For a Mac laptop desktop computer you can download a free version of VNC Viewer from http homepage mac com kedoin VNC VNCViewer In order to provide a proper channeling of information for VNC a slightly more complicated command has to be used when logging to galfa1 ssh L 5900 galfail 5900 username remote naic edu This will bring you to remote naic edu then you need to get to galfal with ssh i galfa_key galfa galfal When you start observing start your VNC Viewer and open the Display window Make sure that the first line in this window shows Hostname display localhost 0 the rest should be set with default parameters Then click on OK If the datataking has already started you will see a spectrum on your screen You can then use usual keys to change this display check GALFA Spectrometer Setup Operation Basics for available options For closing the display close the window
14. The GALFA HI User s Guide Marko Kr o Sne ana Stanimirovi Josh Goldston September 7 2006 Contents 1 Introduction 1 1 Nomenclature 2 Before observing 2 1 Planning your observations 2 1 1 As primary observer 2 1 2 As a commensal observer 2 2 Observing modes 2 3 Preparing observing files 2 3 1 CIMA gui files a a 2 3 2 Basketweave files 2 0 2 3 3 GALSPECT files 3 Observing 3 1 Observing in Arecibo 3 1 1 As a primary GALFA user 3 1 2 As a commensal GALFA user 3 2 Remote Observing 4 Quick Data Checks 4 2 Quickly plotting spectra 4 3 Checking if everything worked properly 5 Software setup and paths 6 The GALFA Archive draft 10 10 10 10 11 13 13 13 13 13 14 6 1 Archive dependent codes A Quick Observing Checklists A 1 Sample Basket weave Observing Checklist A 2 Sample checklist for commensal TOGS observing updated on Dec 7 2005 B Logging into GALSPECT C Description of GALFA codes and their usage 16 16 18 19 1 Introduction The purpose of this document is to serve as a concise how to guide for observations using Arecibo s GALFA spec trometer GALSPECT The information here is limited to the basics which are needed to operate the telescope and how to prepare observing files This document is not intended
15. alactic HI right in the center of this band If the line is not positioned properly then something is not right with your LO2 setup Also watch the CIMA log display window for error messages If you notice that information in this window is not regularly updated you may need to re start WAPP units Appendix A 1 shows how to do this 3 1 2 As a commensal GALFA user At the moment there is one large commensal project going on TOGS running commensally with ALFALFA a2010 The observing procedure consists of 10 1 Starting GALSPECT by the Telescope Operator 2 Running the 1st calibration script at the start of the E ALFA run by the current observer 3 Running the 2nd calibration script at the end of the E ALFA run by the observer 4 Stopping GALSPECT at the end by the Telescope Operator A more detailed checklist can be found in Appendix A 2 3 2 Remote Observing General instructions for remote observing with the Arecibo telescope apply also for remote GALFA observations The latest instructions general can be found at http www naic edu 7Eastro under Observing Remember that it is required to always call the Arecibo control room 15 30 min before your observing run to let the telescope operator know your plans Typically you will ssh X username remote naic edu then login to observer2 and start CIMA This may be very slow though as CIMA has very complex graphics A better and faster way is by using a vnc server
16. ariable It will also not list scans for days that are done in the late starting commands in the files REDST If set is a structure that the data reduction software can use to find start times end times and cycle times LOOPS Loops per WAPP fits file Default is 4 This is mostly irrelevant to GALSPECT operation but keeps the WAPPS happy 20 IFLONAME the name of the iflo gui file to load default is galfa_iflo gui RESTFREQ The rest frequency to use if not set assumed to be 1420 405750 SFSRADEC If you wish to give a position to do the sfs calibration other than the starting point of 00_00 enter it here in ra dec decimal format e OUT_EXP Set this to a variable that will contain the expressions that can be entered into the the command file Use OUT_EXP N M for day N delay M e OUT_CAT Set this to a variable that will contain the the catalog of all starting places for all scans e END_TIME Set this to a variable that will contain the time in hhmmss s form that the scan ends e START_LSTS Set this to a variable that will contain the start times for all the possible starting positons in decimal LST e g 21 7312 e END_LSTS Set this to a variable that will contain the end times for each day in decimal LST C 2 Using plotobserved to query GALFA Archive By inputing a range of RA and Dec values and a pixelsize you can create a plot of all positions observed with GALFSPECT INPUTS ra A vector conta
17. d in detail in Giovanelli et al 2005 astro ph 0508301 The preferred way for obtaining a reference spectrum for GALFA HI observations is the SFS technique details can be found in Heiles 2005 GALFA Technical Memo 2005 01 2 3 Preparing observing files In general you will need four observing files and they should be placed in your project s directory in Arecibo share obs4 usr aXXXX The first file provides the IFLO setup information we call it gui file the second file provides source coordinates and velocity information so called catalog file when scanning source information refers to coordinates of the starting positions for basket weave drift scans and the last two files are command scripts for running the SFS calibration and basket weave drift scans 2 3 1 CIMA gui files This is a simple IFLO setup file that specifies the central frequency for your observations At the moment GAL SPECT can be operated only together with the Wideband Arecibo Pulsar Processor WAPP the traditional spectral line backend at Arecibo The CIMA gui file gives the central frequency for all WAPP units one for each ALFA beam sets their bandwidth to 100 MHz and the maximum number of channels allowed 4096 However all that really matters here for GALSPECT is the central frequency Remember that GALSPECT has a fixed configuration a bandwidth of 7 MHz and 8192 channels and you do not need to worry about setting these parameters
18. dec Below is listed a complete description of each input and output variable as well as all keywords INPUTS SOURCENAME An arbitrary name for the region e g blw RA The center of the region you wish to observe in RA decimal hours e g 22 85 DEC The center of the region you wish to observe in dec decimal degrees e g 3 85 WAIT_TIME The requested time for turning around in seconds 13 seconds seems to be the best time to choose DRA The size of the region you wish to observe in RA decimal hours e g 1 85 DDEC The size of the region you wish to observe in dec decimal degrees e g 3 85 LATE The number of places you wish to compute a late start time These are useful if your observations get screwed up and you wish to do part of a day s worth of scans A typical number here would be 3 KEYWORD PARAMETERS GEAR The style in terms of dec attack angle to scan the sky There are 6 different viable styles gears to use ranging from 1 to 6 6 is the default and fastest gear If we take a Nyquist pixel to be 1 8 arcminutes on a side then GEAR Integration time per Nyquist pixel ALFA angle 6 2 4 0 5 4 1 30 4 8 3 30 3 9 60 2 12 0 O 1 12 4 30 FILE If this keyowrd is set BW_fm writes 3 files for use as inputs to CIMA at AO NB In older versions BW fm used to write many files now it just writes 3 DAYS_DONE If this keyword set then BW fm will only produce files for days that are not listed in the DAYS_DONE v
19. e have not loaded the iflo setup yet the RMS values most likely won t be close to 10 Do not worry about this Once the observer starts the galfa calibration script everything will be fine In the same window type var togs This will start taking data with GALSPECT You will see a lot of numbers being printed every second or so This will run the entire observing session 2 Running the calibration script at the start Once the primary a2010 observer has logged in and started cima she he should run the galfa calibration script The starting position for this calibration is listed in the a2010 cat file and is called galfasrc galfasrc should be approximately the mean of the drift scan positions in a2010 cat and can be kept fixed over a period of 7 10 days Of course this position should be updated sooner if the positions of the a2010 observations change significantly e g a completely different region is begun a From CIMA Observer s Interface window select Command File Observing 11 1 Open a new xterm on dataview 2 Login to wappserv as user wapp password wappme by typing ssh wapp wappserv It will ask for password type wappme 3 Type source home cima Wapp Bin Progs Start start_gpib 4 Return to the previous step and type again var levels_togs in the galfal window If this doesn t work call the contact person 18 b A new window Command File Observing will pop up Click on
20. frequency results in the selection of a particular LO1 frequency and this reflects on the required LO2 frequency that needs to be given to GALSPECT to position its narrow band window exactly on the hydrogen line Remember that GALSPECT takes two spectra simultaneously a wide calibration spectrum covering 100 MHz with 512 channels and a science spectrum covering 7 14 MHz with 8192 frequency channels For a given central frequency you can calculate the LO2 frequency from LO1 central_freq 250 MHz LO2 L01 1420 405 18 75 MHz The LO2 frequency is needed to start datataking as well as for setting levels on GALSPECT For example if your central frequency is 1385 MHz then GALSPECT s LO2 is 195 845 MHz To set levels you will need to type in an xterm window on galfa1 gdiag newdac 10 102 195 845 To start taking data for example for project togs you will need gdiag galfa vnc scram 102 195 845 sdiv 600 proj togs These command can be given as scripts the above lines can be found as var levelstogs and var togs respectively on the galfal computer Other sample scripts can be found in var samples directory You may modify these short scripts and place your own versions in the var directory on galfal GALFA Spectrometer Setup Operation Basics document explains what all other parameters mean although you most likely will not need to change them For example sdiv 600 specifies that a new fits file will be writte
21. here are several versions updates of the data reduction software The latest information is given on http astron berkeley edu sstanimi GALFA galfa_page html under GALFA Software The latest software is invoked by source ing share galfa idlenv2 0 A short description of the directory structure within share galfa follows e share galfa Main Directory contains all GALFA raw data files and the current idlenv file e share galfa archive The GALFA Archive and related codes e share galfa galfamh mh files containing modified headers for all archived data e share galfa gsrX X GALFA HI date reduction codes X X is the version number version 2 0 is currently the latest 6For setting up an account contact Arun Venkataraman at arun naic edu 13 e share galfa scripts Various sample scripts and files e share galfa planningcode Codes and routines used in planning and preparation for observing runs All files that are to be used during observations should be placed in the relevant project directory For any approved project the project directory is share obs4 usr lt projnum gt where lt projnum gt has a form aX XXX This is the directory where CIMA will look to find all project related files and scripts 6 The GALFA Archive For future uses and storage of GALFA observations we have developed the data archive GALFA Archive Currently the Archive contains all data files obtained with GALSPECT since Nov 4 2004 7 with a
22. iest way to get the time requirements for a particular basketweave project is to use an IDL program called BW_fm see Appendix for full desription This program will provide starting and ending LST times for each day s observations and the total number of days required to cover a certain region 2 1 2 As a commensal observer When observing commensally with another ALFA project we may not have control over the pointing of the telescope It may be necessary to coordinate with the primary observer on a few issues e The selection of the central frequency will effect the LO1 frequency and respectively GALSPECT s LO2 frequency This LO2 frequency is determined and specified when starting datataking in order to center the HI line properly within the GALSPECT s narrow science band An example of how to calculate GALSPECT s LO2 frequency based on the selected central sky frequency is given in Section 2 3 3 A more detailed discussion on GALSPECT can be found in the document GALFA spectrometer Setup Operation Basics e GALFA observations require SFS calibration This takes additional 5 mins and both primary and commensal observers should remind the Telescope Scheduler of this need 9 0 i j l 8 0 i ON Y hh Declination decimal degrees J2004 f fi Ll f fi L L f li f f L L f L L fi 2545 23 40 23 35 23 30 23 25 RA decimal hours J2004 Figure 1 Example basket weave
23. indow type var levels 9 Adapted from a2060 s checklist last updated on March 9 2006 16 If this gives the message LO2 Set failed got back ERROR setting freq follow the procedure given in the footnote This will finish quickly and give you a short summary Check RMS values they should all be around 10 Now in the same window start the data taking script by type var a2060 This will mean you are starting to write data files with the GALSPECT You should start to see numbers tick by 5s 10s 15s etc You may also see some error messages this is OK The only serious problem is if this window does not print new things of some kind every 5 seconds or so If the window is completely frozen no new text type CTRL C in the window and type var a2060novnc This mode should again give you numbers that tick by NOTE If you end up using this mode the OPTIONAL STEP below that allows you to view what GALSPECT is doing will not work This is OK 6 Running the calibration and observations a b c Return to cima on observer2 and to the CIMA command file observing window Click on Load to go and browse for a file you want to run Click on file pt2 click on Open Then back on the CIMA command file observing window click on Run This will start a series of steps it will run a calibration routine first then a basket weave scan Please WATCH the CIMA log display window f
24. ining the minimum and maximum ra values to be plotted in decimal values ex 12 5 20 Make sure that the first value is the minimum dec Same as RA just for DEC in degrees ex 1 5 34 pixelsize The width in arcminutes of each box in the final image ex 3 5 The RA width of each pixel in the map will then be the same as the corresponding width for a pixel a pixel at 0 degrees DEC outputfilename String containing the full path and name of the FITS map to be generated OUTPUT This code will generate a standard fits file covering the given RA and DEC ranges Each pixel is a square of width pixelsize arcminutes In order to avoid possible confusion with the various different world coordinate systems this map is NOT equal areas More specifically each pixel has a DEC width of pixelsize and RA width of pixelsize assuming you re doing the conversion to from hours to arcminutes at the celestial equator a k a Lhr 15 deg 900 arcmin The value of each pixel corresponds to the total integration time in seconds per unit area on the sky squared arcminutes The area is calculated by solving the integral in spherical coordinates so that pixels at higher DECs cover less area than those at lower DEC values NOTE This code is dependent on the GALFA archive therefore it must be run on an Arecibo machine NOTE Crossing the 24 0 hr point in RA is currently not supported by this code you can instead try to make two smaller maps NOTE
25. is allows you quick searches for particular groups of observations covering a particular RA and Dec range time of observation or a project number Due to its small size there is only one SM ALLarchive file It is located within the main archive directory see Section 5 Each line in the SMALLarchive contains information regarding one 10 minute GALFA fits file e The BIGarchive is the meat of the archive The other smaller archives are essentially meant as pointers to the big one Each one second dump is assigned a BIGRECNUM Big archive record number For each one second dump we store full header and position information we could ever possibly want This archive is going to become very big really fast To avoid having to read in one huge file the BIG archive is subdivided by months These files are located within the BIGarchive sub directory IMPORTANT NOTE The archive is still considered to be a work in progress As such it may occasionally need to be reset and reconstructed If you try using one of the archive related codes and find that the archive is not entirely up to date then wait a day or two and try again TThere were precursor observations prior to this date but the fits files generated by GALSPECT at that time were in a different format which at this time is not supported by the archive 8for 4 sets of Dec ranges lt 10 10 20 20 30 gt 40 covering the whole Arecibo sky 14 6 1 Archive dependent codes This is a
26. n every 600 sec IMPORTANT NOTE There is no off line method for testing your scripts without actually executing the commands contained within them You should not test your scripts while another user may be using the spectrometer An easy way to check whether someone else is using GALSPECT is to issue the ps command and watch for any gdiag processes 3 Observing You can conduct your observations in several ways The most common way is by being present in Arecibo and operating the telescope from the control room Another frequently used way is by operating the telescope remotely Remote GALFA observations are undertaken commonly and with a great success Once your program has started and you are for example doing a different basket scan day after day it is possible to continue running observations in absentee This way telescope operators will be operating the telescope and GALSPECT for you while you can monitor data remotely If you decide to observe in this way you should providing detailed instructions as well as some training for telescope operators Also it is important that you call before the start of each observing run to make sure everything is working smoothly All three methods have been used for GALFA observations frequently and successfully 3 1 Observing in Arecibo 3 1 1 Asa primary GALFA user Before you start check with the telescope operator that the ALFA cover has been removed The observing consists of several steps 1 L
27. never press q inside this window as this will stop the datataking script e For a Linux laptop desktop ask your system administrator how to download and install VNC Viewer In an xterm type ssh t username remote naic edu ssh t galfa galfal to connect to galfal To start VNC Viewer in another xterm type vnceviewer via username remote naic edu galfal 0 11 e If you do not have VNC Viewer installed on your computer you can still run it remotely from Arecibo This will be a bit slow but it will work fine In an additional xterm window connect to Arecibo with ssh X username remote naic edu then simply type vncviewer galfai once you start observing If all fail and you can not get the display on your screen you can ask the telescope operator to open GALSPECT s display in Arecibo for you and make sure the hydrogen line is positioned in the right place In the near future an IDL program will be provided as an alternative way to monitor data A useful program to run during a remote observing session is monpnt In an xterm window on observer just type monpnt to start it This will show current telescope pointing and time information 12 4 Quick Data Checks 4 1 Where are data files All data files obtained with GALSPECT are stored in Arecibo in directory share galfa If you are examining your data in Arecibo locally or remotely you will login to remote naic edu first Make sure to ssh to fusion00 or fusion02 before
28. og in to the main computer observer2 and start CIMA in the usual way 2 Run the first command file pt1 this will load the IFLO setup file gui and drive the telescope close to the starting position 3 In the meantime log in to GALSPECT this really means galfal computer run the diagnostic script var diag then run the script to set GALSPECT s levels e g var levels and then start the datataking script for example with var togs 4 On CIMA load and run the 2nd command script pt2 this will run the calibration first SFS and then start the first available basket weave scan 5 Monitor data through either the general Arecibo s monitoring program called Quickview or by using GAL SPECT s display software 6 When observing is finished stop the datataking script on GALSPECT s xterm window by typing Control C and exit from CIMA More detailed steps are given in the Appendix A 1 sample observing checklists What to look for in the display Quickview will show spectra coming from all 7 beams and having a bandwidth of 100 MHz There are a lot of clickable options for changing display that are easy to understand on line The GALSPECT s display can show either wide or narrow band spectra In the wide spectrum display you will see a gray band emphasizing the part of the spectrum where narrow band is centered This gray window should be positioned at about 1 4 of the wide band and you should be able to see the G
29. or a few minutes It should show updated messages every few seconds If the telescope is waiting at to begin the basketweave scan for some number of seconds that is OK At any time during observing you can open Quick Look Data Display on dataview to make sure the spectra are being updated OPTIONAL STEP You can also view data using GALSPECT s display i Open a new xterm on dataview and type guestQ dataview guest vncviewer galfal ii This brings up a plot window entitled TightVNC Pixmap framebuffer With the cursor on this window type h this will blow up the plot and make it easier to inspect spectra iii G ALFA folder in the control room explains how to change different display options 7 Stopping at the end of the run a b c On observer2 on the CIMA log display window click on Abort Wait a moment until everything stops If it doesn t stop keep typing Abort until it does On dataview s galfal window the one which prints numbers all the time press Control C and exit from this window If you forget to do this GALSPECT will take data all night On observer2 on CIMA Observer s Interface click on Exit CIMA to exit from cima Close all windows 101 Open a new xterm on dataview 2 login to wappserv as user wapp password wappme by typing ssh wappQ wappserv It will ask for password type wappme 3 Type source home cima Wapp Bin Progs Start start_gpib
30. project directory 5 Make whatever changes need to be made in CIMA as you would for a real observing run a Likely the most common change that will need to be made is to the IF LO parameters which can be reached by CIMA Observer s Inter face Receiver IF LO Control NEW Improved IF LO Setup b Remember to click on Apply this Setup to apply the changes 6 Save the new configuration to a new gui file a On the window titled CIMA Observer s Interface click on Load Save State b In the CIMA Generic Save Load State window click on Save Selected Choices c In the new Save Correlator Configuration window select a new filename and Comment and click on Save Configuration 7 Exit CIMA by clicking on the Exit CIMA button in the CIMA Observer s Inter face window 2 3 2 Basketweave files Program BW_fm creates two CIMA command files called pt1 and pt2 and the catalog file called _sources In order to optimize observing time BW _fm produces several starting positions at different LSTs for each basket weave scan You can run this program at the start of your observing run create these three files and copy them to your observing directory share obs4 usr aXXXX When called within CIMA the script pt2 checks the current LST when it is ready to start scanning and then chooses the most appropriate scan to observe as well as the most appropriate starting position for the chosen scan After each day s run the cima log file should be
31. scans 2 2 Observing modes The preferred observing mode is basket weave scanning or meridian nodding This observing mode consists of observing at the meridian and moving the telescope only in zenith angle with a given rate covering a zig zag pattern on the sky as the Earth rotates On consecutive days adjacent shifted scans are obtained and the whole region of interest is slowly covered The main advantages of the basket weave scanning technique over other more traditional scanning techniques are fast coverage of a large area of the sky the elliptical ALFA beams always have the same orientation inter woven scans have many crossing points that allow a fine gain adjustment and transit observations limit contamination from variable sidelobes Figure 1 shows an example of two basket weave scans The ALFA rotation angle is chosen to keep the equidistant separation between ALFA beams while scanning A list of possible scanning rates and appropriate ALFA rotation angles is given in Section 2 1 1 While scanning spectra are recorded every second The separation between ALFA beams is about 1 79 arcmins close to Nyquist sampling and it does not depend on the scanning speed Another observing mode used often especially when observing commensally with E ALFA projects is drift scanning The User s Manual for Arecibo Observations explains the traditional drift scanning mode The type of drift scans used for E ALFA s ALFALFA project is explaine
32. u alfa galfa consortium 5http astron berkeley edu sstanimi GALFA galfa_page html 2 Before observing 2 1 Planning your observations 2 1 1 As primary observer The first step in planning a set of observations is to consult the GALFA Archive in order to determine whether the de sired region to be observed or a portion of it has been observed already In the near future it will be possible to query the Archive directly see program plotobserved in Appendix C for now the best is to check GALFA s web page at UC Berkeley http astron berkeley edu sstanimi GALFA galfa_page html under GALFA Status for a list of observed projects and positions Alternatively send an e mail to Sne ana Stanimirovi sstanimi astro wisc edu Mary Putman mputman umich edu or Carl Heiles heiles vermi berkeley edu The next thing to decide is the observing mode The preferred mode for GALFA observations is the basket weave scanning However for sources that span over a small RA range or for commensal observing with various E ALFA projects a drift scanning observing mode can be used A more detailed discussion of different observing modes can be found in Section 2 3 For the basket weave scanning there are 6 viable gears speeds that can be used Each gear will scan the sky at a different rate If we take a Nyquist pixel to be 1 8 on a side then the equivalent per pixel integration time and required rotation angle for ALFA to produce a regularly
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