The GALFA HI User`s Guide
Contents
1. 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 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 galfal 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 respec tively on the galfal computer Other sample scripts can be found in var samples directory You may mod ify these short sc2. 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 jproj number 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 On observer2 login as dtusr b c On the window that appears choose the EXPANDED version of CIMA d On the window titled Welcome to CIMA enter your name and project number case sensitive Then under Select Observing Mode select Line e On the window Available Receivers click on ALFA then click on Disable Quick Tsys then click on Select Receiver Now This will start rotating the turret to ALFA Click on DISMISS to get rid of this window Re start the WAPPs with On the CIMA Observer s Interface window click on Pulsar Observing Then on the WAPP Wideband Arecibo Pulsar Processor Dataking Control GUI window click on More This will open a new window in which you may click on Restart ALL WAPPs You may now dismiss the last two windows a Right click an
3. run to let the telescope operator know your plans All observing scripts will be used in the same way as if you are observing in Arecibo The only difference is concerning data monitoring The general Arecibo s monitoring program Quickview is at the moment too slow to display remotely Using GALSPECT 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 galfal ssh L 5900 galfa1 5900 username remote naic edu This will bring you to remoteQnaic 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 O 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 never p
4. the project name that GALSPECT used to write the fits files names are the names of the different areas done in the one project can be a single entry and days are the number of days each one takes The directory structure it generates is shown graphically in Fig 2 The fits files will be automatically transferred into the fits directory 4 2 2 Stage O data reduction The stage 0 data reduction takes the data in raw form removes the IF bandpass see Heiles 2005 GALFA Technical Memo 2005 01 on how exactly this is done does a rough gain calibration to put the data into temperature units does a doppler correction to the LSR finds the data that are during your BW scan and saves them to an appropriate folder The data are organized by day numbers if there are 11 days in your scan pattern your days will go from 00 to 10 and the data for each day will reside in folders in this is my directory proj regxz regz n As a byproduct each fits file will have a corresponding mh file that will live in this is my directory proj mh and each day will 13 this is my directory proj fits rega regb regc A xing rega_00 rega_01 rega_02 lsfs Figure 2 The file structure generated by make_dirs this is my directory proj rega regb regc 5 6 8 have Isfs file that will live in this s my directory proj regx lsfs The reduction of the data does not require you to know where all these th
5. to average them if averaging is desired See the code for exact usage The code can take a very long time to run there is a lot of matrix multiplication and so forth The code makes a file in the region directory that contains the final data cube In future versions this will be in a fits format as well but currently is an idl sav file 4 3 Data reduction for drift scans Coming in the near future 16 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 share galfa idlenv file from your bashrc or cshrc 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 The share galfa idlenv file will always point to the most recent stable versions of the reduction codes however older versions can be found within the subdirectories in which those procedures are located 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 g
6. 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 6 1 Archive dependent codes This is a 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 18 A Quick Checklists
7. C The center of the region you wish to observe in dec decimal degrees e g 3 85 e WAIT_TIME The requested time for turning around in seconds 13 seconds seems to be the best time to choose e DRA The size of the region you wish to observe in RA decimal hours e g 1 85 e DDEC The size of the region you wish to observe in dec decimal degrees e g 3 85 e 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 e 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 6 0 2 12 0 0 1 12 4 30 e FILE If this keyowrd is set BW_fm writes a bunch of files for use as inputs to CIMA at AO e DAYS_DONE If this keyword set then BW_fm will only produce files for days that are not listed in the DAYS_DONE variable It will also not list scans for days that are done in the late starting commands in the files 22 e NON_EXTENDED If this keyword is set BW_fm will write files compatible ONLY with CIMA versions before the Extended release June 05 Otherwise it will write files compatible ONLY with The Exten
8. PP 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 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
9. 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 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 Interface gt gt Receiver IF LO Control gt gt 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 Inter face click on Load Save State b In the CIMA Generic Save LoadState window click on Save Selected Choices c In the new Save Correlator Configuration window select a new filename and Comment and click on Save Con figuration 7 Exit CIMA by clicking on the Exit Normally 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 You will have to run this program for each observing day separately create these three files and copy them to your observing directory share obs4 usr aX XXX In order to optimize obse
10. The GALFA HI User s Guide Marko Kr o Snezana Stanimirovi Josh Goldston September 2 2005 draft Contents 1 Introduction ibd Nomenclatures zy AE ae a A O E A OR A AAA 2 Before observing 2 1 Planning your observations s sa a aha la OA ee RE a oda ley DLL As primary observer mc A a a ee a 2 1 2 Asa commensal Observer uoni ata ea ar oa e eel e EE Ea 2 2 OBServine modes o A A acl hs A ad A A A a ala ator age Bake Bes 2 3 Preparing observing filesi atas g sles ee RAR ee EA a e a Pee a ee 2al CIMA aurea 2 3 2 Basketweavediles 2 402 da A di a la aida Br da ll 2 3 3 GALSPEC TALES ote ey ii a A e a ae 3 Observing Sul Observing inArecibO 2 2 A Bh is Be ook SG Se ee eae ee EE 3 1 1 Asa primary GALFA User 2 65 54 ra ti AA A OCR Eee 3 1 2 Asacommensal GALFA user ee e a a E A E A e E A 32 Remote Observing oia A a le lene a a ds dde a dd id 4 Data Reduction 4 1 Quick examination plotting of data 4 2 Data reduction for basket weave scans ooa 4 210 Preparing your data os la a bt oe AA A A Be ES aS 4 2 2 Stage Q data reduction i ek e e ao he RO ee Oe a a A a 4 2 3 Crossing point calibration 2 h e A ea a a a a a E e a h A A ls a eaid ahs aa a TR ken ee a A ete i a ee Son te ode Ge EAA E ore a a a da i 4 3 Data reduction for drift scans Software setup and paths The GALFA Archive 6 1 Archive dependent codes Quick Checklists A 1 Sample Basket weave Observing Che
11. alfa gsrX X GALFA HI date reduction codes X X is the version number 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 with a 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 t
12. based on the same input parameters as BW_fm and its usage will be described here in the very near future C 3 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 the observations obtained with the GALFA spectromer INPUTS ra A vector containing 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 23 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 1hr 15 deg 900 arcmin The value of each pixel corresponds to the total integration seconds time per unit area on the sky squared arcminutes The area is calculated by solving the integral in spherica
13. cklist ooa aa e A 2 Sample checklist for commensal TOGS observing oaa a Logging into GALSPECT Description of GALFA codes and their usage CE BW mir eia A Ne A ee SA A SA A A a E eo Ena C 2 Optimizing your observing with GALF Aschedule 2 o o C 3 Using plotobserved to query GALFA Archive e 17 17 18 19 19 20 21 1 Introduction The purpose of this document is to serve as a concise how to guide for observations and data reduction using Arecibo s GALFA spectrometer GALSPECT The information here is limited to the basics which are needed to operate the telescope and to reduce the data from your observations This document is not intended 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 For more general information on observing with the Arecibo telescope check User s Manual for Arecibo Ob servations and The Control Interface Module for Arecibo CIMA both documents can be found at http www naic edu 7Eastro All GALFA s memos including the latest version of this document are located at http alfa naic edu galactic docs 1 1 Nomenclature In t
14. d 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 please call Snezana The same script should be run at the end of a2010 run no need to drive the telescope to a special position just run the calibration script at the place where the last scan was finished 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 Same as at the start just with using the file command_galfacurpos 4 Stopping at the end of the run On dataview s galfal window the one which prints numbers all the time press Control C 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
15. ded CIMA release and later e REDST If set is a structure that the data reduction software can use to find start times end times and cycle times e LOOPS Loops per fits file Default is 4 Only functions in extended mode 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 MHz OUTPUTS e OUT_EXP These are the expressions that can be entered into the the command file Use OUT_EXP N M for day N delay M e OUT_CAT The catalog of all starting places for all scans Put these strigns int he catalog file called by the command line file e END_TIME The time in hhmmss s form that the scan ends e START_LSTS The start times for all the possible starting positons in decimal LST e g 21 7312 e END_LSTS The end times for each day in decimal LST C 2 Optimizing your observing with GALF Aschedule For basket weave scans our primary sense of time is LST Unfortunately time at Arecibo is scheduled based on 15 minute AST intervals This can have the effect of producing a significant amount of unused time that we may be scheduled for Once time has been assigned to a particular project it is useful to use GALF Aschedule to try and maximize the efficient use of the assigned time when performing basket weave scans GALF Aschedule overplots the time scheduled for a project versus the time required for a certain set of basketweave observations
16. ector to produce a map with any binning or channel range desired in make_grid pro IDL gt gridzalfa indata FWHM fwhm XGRID xgrid GRID grid IMSIZEX imsizex IMSIZEY imsizey REFRA refra REFDEC refdec GEOMETRY geo OUTNAME outname ASSOC assoc GFUNC func OBSERVER observer Clearly there are many important parameters here in terms of defining the area of your map the type of beam shape you wish to use and so forth An example call might look like IDL gt gridzalfa mht fwhm 3 2 xgrid 1 1 grid 1 5 imsizex 1024 imsizey 512 refra 2 15 0 refdec 9 45 0 geo sin outname export dzd4 heiles gsrdata A2011 lwa sprslwa sav gfunc gau observer josh Where the mht parameter is the data stored by todarr pro The details of what each of the parameters means are detailed in the code itself and exactly which to choose to have the best maps is yet to be optimized The code has been optimized for speed 11 hours of data takes about 30 seconds to run Once this has been run it is time for the final gridding step make_grid pro IDL gt make_grid root region proj mhtin spmatin spcen sprng spavg gridfile corin corin mhtin is the file name for the results of todarr pro and corin is the equivalent for xingarr pro Spmatin sparse matrix in is the sparse matrix file from gridzalfa The spcen sprng and spavg determine which channels to grid and how
17. ed xg_assn pro IDL gt xg_assn root region scans proj fitsvars The first four options here are very straight forward and fitsvars is an output of all the diagnostic information for the SVD matrix inversion It is not an essential data product of the reduction process This code can take a long time as it needs to invert a sometimes very large equations of condition matrix 4 2 4 Gridding NB Gridding is currently in an Alpha release The code does not yet have all of the desired functionality and may have outstanding bugs 15 Finally we reach the end the gridding process The gridding process has two major parts the assignment of intensity from time ordered data to grid points and the construction of a data cube from the raw data given this assignment This process in total consists of four routines First two preliminary routines xingarr and todarr just compile the correction data and the pointing data into two simple files to be read by the other routines IDL gt todarr root region scans proj IDL gt xingarr root region scans proj Run these two before running gridzalfa pro and make_grid pro Gridzalfa has a storied lineage gridzilla AO_gridzilla ao gridzilla GALFA and now the somewhat more sonorous gridzalfa The basic product of gridzalfa is a sparse matrix that relates time ordered data points TODs to grid pixels without loading in any actual data This matrix can then be multiplied by a data v
18. 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 Galactic 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 AO Observer 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 Asa 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
19. es 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 explained 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 spectral line backend commonly used for observations with the Arecibo telescope The CIMA gui file gives the central frequency for all WA
20. file serves as authentication The appropriate command to log in into GALSPECT using the gal fa key file is ssh i lt GALFA_KEY PATH gt galfa key gal faQgal fal 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 21 C Description of GALFA codes and their usage C l 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 site http astron 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 a series of 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_cat end_time start_lsts end_lsts gear gear file file days _done days_done non_extended non_extended redst redst loops loops ifloname ifloname restfreq restfreq 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 e RA The center of the region you wish to observe in RA decimal hours e g 22 85 e DE
21. h 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 easiest 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 GALF Aspectrometer Setup Opera
22. he 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 7 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 5For setting up an account contact Arun Venkataraman at arun naic edu 6There 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 for 4 sets of Dec ranges lt 10 10 20 20 30 gt 40 covering the whole Arecibo sky 17 e The SM ALLarchive is where we organize the information based on each galfa fits file This 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 SMALLarchive file It is located within the main archive directory see Section 5 Each line in the SMALLarchive contains information regarding one
23. his document we adopt the following type styles for various files directories commonly referred to e directory names are given in italics e 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 http alfa naic edu galactic al fa_galactic html http alfa naic edu galactic docs galspect3 ps 3http al fa naic edu hardware backend gal fa http al fa naic edu galactic meeting3 Gal fa Guidelines_Aug17 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 desired 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 for a list of observed projects and positions Alternatively send an e mail to Snezana Stanimirovi sstanimi astro berkeley 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
24. hly 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 Log 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 normally from CIMA More detailed steps are given in the Appendix A 1 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
25. ings are this is only for enrichment There are 2 ways to run the stage zero reduction process stg0 pro and stg0_st pro stg0_st pro is by far the easier of the two as it relies upon a structure output from BW fm for much of the information If you are in a more complicated circumstance or you do not have this structure available use stg0 pro IDL gt stg_0 year month day proj source maindir startn endn slst elst scan cyc_time lfn 1fn nomh nomh calfile calfile stops stops Most of these inputs are either self explanatory or can be read about by using IDL gt doc_library stg_0 but some are a little subtle sist are the starting LSTs of the observation as predicted by BW _fm pro elst is the ending lst of the observation and in most circumstances can just be found from the output of BW fm as is explained in the comments of the code If though the observations were terminated early but the spectrometer was left running for some time it is best to put in the LST at which the BW was terminated to avoid adding data to your map taken in some alien observing mode The inputs to stg0_st are simpler because a lot of the information is handled by the data in the outputs of BW fm IDL gt stg0_st year month day proj scan maindir redst nomh nomh delay delay redst is the output of BW_fm by the same name and delay allows one to specify if this particular scan was started not on
26. l 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 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 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 24
27. m and open an xterm window b In this window 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 for some time like 30 sec you will see lots of messages GALSPECT is warming up Stop this by typing Control C d 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 9 1 Open a new xterm on dataview 2 login to wappserv as user wapp password wappme by typing ssh wappQwappserv It will ask for password type wappme 3 Type source share wappsrc bin start_gpib 4 Return to the previous step and type again var levels_togs in the galfa1 window If this doesn t work call Snezana 20 e 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 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 a From CIMA Observer s Interface window select Command File Observing b A new window Command File Observing will pop up Click on Command file to go and browse WN for a file you want to run Click on file command galfasrc then click on Start Command Line Observation This will loa
28. onrem conrem conrem would only be set if the data had not had their continuum subtracted in the previous stages and noauto would only be set if for some reason one did not want to compute the fit for crossing points within a single file Both of these should be considered engineering modes that should never need to be invoked Then all of these gains must be put into a giant least squares matrix by a code called Isfxpt pro IDL gt lsfxpt root region scans proj degree mra dra xarrall yarrall fourier fourier daygain daygain There are a few major options in Isfxpt pro including the choice of the degree of polynomial to fit to the varying gains in time and whether to explicitly include a day to day gain change for all beams It is not yet known what degree of polynomial is best to choose a reasonable range might be 2 8 although it does seem desirable to allow day to day wholesale gain changes with the daygain flag We have also implemented Fourier decomposition of the gain variations to supplant or compliment the polynomial modes To use this feature set the fourier flag to n m where n is the lowest fourier mode of interest and m is the highest fourier mode of interest This code should run rather quickly Once Isfxpt pro has been run the code must determine the coefficents by inverting the equations of condition matrix and determine the correction factors for each data point This is done with a code call
29. ress 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 vncviewer via username remote naic edu galfal 0 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 11 ssh X username remote naic edu then simply type vncviewer galfal 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 observer2 just type monpnt to start it This will show current telescope pointing and time information 12 4 Data Reduction All data files obtained with GALSPECT are stored in Arecibo in share galfa If you are doing data reduction in Arecibo locally or remotely you will log in to remote naic edu first Make sure to ssh to fusion00 or fusion02 before you start as remote is very slow 4 1 Quick e
30. ripts 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 written 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 smoot
31. rving time BW fm produces several starting positions at different LSTs for each basket weave scan 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 examined to figure our which exact scan was run and if satisfactory this scan can be excluded when making observing scripts for the following days 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 This way you will avoid having annoying gaps in your map In order to avoid clutter and possible confusion it may be smart to only place the files necessary for any given day on that day 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 testfile days_done 0 1 2 3 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
32. the first up down nod Lambda but at the beginning of a later scan Note that if one had the scan truncated as described above and needs to choose an appropriate elst one should use stg0 not stg0 _st 14 4 2 3 Crossing point calibration Crossing point calibration exists to gauge the gain of each beam for each day as a function of time for each day At present crossing point calibration can only be done on a contiguous number of scans starting at day 0 though this quirk may be fixed in future releases of the software The crossing point code referred to as xing has a few phases First all the crossing points must be found with a code called xgen pro This is a relatively fast procedure xgen pro takes a standard set of inputs IDL gt xgen root region scans dates proj and works on an entire region rather than a day at a time as in stg0 Again the details of how the inputs are formatted can be found with doc_library but they are pretty simple After xgen is run all of the spectra must be loaded into the crossing point files with a code called lxw pro lxw pro is called similarly IDL gt l1xw root region scans proj with all the inputs identically formatted This takes a significant chunk of time because each sav file must be read a few times to load all of the spectra The relative point to point gains must then be determined with a code called xfit pro IDL gt xfit root region scans proj noauto noauto c
33. tion 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 oO o Declination decimal degrees J2004 i RA decimal hours J2004 Figure 1 Example basket weave 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 do
34. u may now start the pt2 script Unless you have modified the scripts from their original version created by BW_fm the telescope should start an SFS and then begin your basketweaves b To check the data as it s coming in from the WAPPS you may open Quick Look Data Display on dataview to make sure the spectra are being updated c Optionally you may monitor the data written by GALSPECT NOTE this should be avoided if you re observing remotely due to network latency i Open a new xterm on dataview and type vncviewer galfal ii This brings up a display window titled Tight VNC Pixmap framebuffer Instructions for how to operate this window are located in the GALFA spectrometer Setup Operation Basics document mentioned in section 1 A 2 Sample checklist for commensal TOGS observing These are instructions for running GALSPECT commensally with a2010 so call project TOGS The latest version of instructions can be found in Arecibo in share galfa X XXX The procedure consists of 1 Starting GALSPECT before a2010 project 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 Here are some basic steps 1 Starting GALSPECT A few minutes before a2010 starts the TO should login to GALSPECT and start the datataking script with the following a Login to dataview as user guest password is naic305
35. 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 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 wit
36. xamination plotting of data Make sure you have source ed the right idlenv file Start idl An example of how you can quickly open a fits file and plot spectra is IDL gt file share galfa galfa 20050817 togs 0011 fits IDL gt mi mrdfits file 1 hdri IDL gt plot m1 300 data m1 will be an idl data structure and this will plot the 300th spectrum In the near future several other tools for quick data examination will be provided 4 2 Data reduction for basket weave scans This document makes a few assumptions about the data you are interested in reducing You must have access to an updated gsr directory currently available in Arecibo and UC Berkeley and have your IDL setup correct for data reduction see Section 5 The data you are interested in reducing must have been taken with ALFA and GALSPECT and must have been accompanied by a SFS calibration scan The data must be taken with the basket weave CIMA technique The data are significantly easier to reduce if CIMA command files were generated with BW fm see Section 2 1 2 2 but this is not crucial 4 2 1 Preparing your data To simplify the reduction process we set up a directory structure this helps the code be sure where everything is The directory structure is regularized via a piece of code called make_dirs which is run as follows IDL gt make_dirs maindir project names days maindir is the directory the whole thing falls under project is
37. ywhere on the screen and select Start CIMA g From CIMA Observer s Interface window select Command File Observing h A new window Command File Observing will appear Click on Command File to go and browse for a file you want to run At this point in time you want to run the pt1 file for the source and day you wish to observe NOTE this is one of the files generated by BW_fm pro The pt1 script will setup all the IFLO parameters 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 guest password is naic305m b Open an xterm and log in to galfal by typing ssh i galfa key galfa galfal The prompt appears c In the same window type var gdiag patt This will run for about 15 seconds you will see lots of messages but so long as none are errors you re ok d Once the telescope has reached the source in the same window you man now launch your script for setting the levels on the spectrometer ex var a2004 levels Check the RMS levels in the final summary they should be near the levels you set in your script usually 10 e Now you may start taking data by running your script for data taking 8 Adapted from Snezana Stanimirovic s a2032 checklist 19 6 STARTING THE OBSERVATIONS AND CHECKING THE DATA a Go back to CIMA Following the same procedures as for running the pt1 script yo
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