Installation Notes
Contents
1. OpenGENIE Commands to write data files The PROCESS routine is available to automate the writing of data files in GSAS FULLPROF or CCSL formats gt gt process a first run number last run number will generate GSAS format files for data collected in the Polaris A bank detectors for the series of runs from first run number to last run number Use B C or E qualifiers to process data from the B C and E detector banks respectively Files are written to the current OpenGENIE default directory with filename Xnnnnn gsa where X is the detector bank letter and nnnnn is the 5 digit run number Note if the first and last run numbers are omitted the routine will prompt the user for them To generate FULLPROF Ins 10 format data files add the F qualifier gt gt process c f first run number last run number will generate both FULLPROF and GSAS format files for data collected in the Polaris C detector bank The FULLPROF format files have filename Xnnnnn dat where X is the detector bank letter and nnnnn 1s the 5 digit run number To generate CCSL format data files add the T qualifier gt gt process e t first run number last run number will generate both CCSL and GSAS format files for data collected in the Polaris E detector bank The CCSL format files have filename Xnnnnn xye where X is the detector bank letter and nnnnn is the 5 digit run number Absorption Correction During Processing of Multiple Data Sets To apply the same ab2. use the cd command in OpenGENIE 2 gt Qd MCE Userdata user gt gt cd newuser To check the current default directory use the pwd command in OpenGENIE gt gt pwd Appendix Using user specified background and vanadium files to normalise data During normalisation of Polaris data using the AFOCUS etc commands OpenGENIE will use default instrument calibration files which contain the standard background empty instrument and vanadium data sets These files are called aback dat and avan dat and bback dat bvan dat etc for the other detector banks and are stored in the calibration folder Generally these files will be appropriate to the most recent ISIS running cycle at the time of downloading the files from the ISIS ftp site In most cases using calibration files from the wrong cycle will make negligible difference to the normalisation of your data Nevertheless the calibration folder also contains data files from previous cycles these are easily identified as their file names include a run number e g cb53876 dat 1s a background data set from the Polaris C bank ev55556 dat is a vanadium data set from the E bank To normalise RAW data files using specified background and or vanadium calibration files use the POLFOCUS routine gt gt lt wksp gt POLFOCUS A nrun 55970 back 54974 van 54975 this will normalise Polaris A bank data from run number 55970 using the background file created from run number 54974
3. Setting Up OpenGENIE to Analyse Polaris Data Ron Smith ISIS Crystallography Group June 2009 updated February 2010 OpenGENIE can be downloaded from the web e Go to www opengenie org select the Download OpenGENIE hyperlink and choose the appropriate version e An auto installer guides you through the installation process proceeding with the default options when offered a choice will work perfectly well After installing OpenGENIE there are a few quick steps to follow so that you can work on your Polaris data on your own PC These steps are all described in detail below 1 Create a PolOpenGenie folder on your C drive and download a set of Polaris specific OpenGENIE scripts and data files into this folder 2 Modify the default OpenGENIE startup file so that it loads commands for processing Polaris data 3 Modify the Genieinit_pol gcl file which you have downloaded in step 1 above so that it knows where on your computer to look for the RAW data files 4 Change the default working directory to something more suitable optional 5 Download your Polaris RAW data files from the ISIS web site 1 Create a PolOpenGenie Folder First create a PolOpenGenie folder on your C drive and then use a web brower to navigate to ftp ftp nd rl ac uk and download a set of Polaris specific OpenGENIE scripts and data files into this folder in Internet Explorer 7 select Page Open FTP Site in Windows Explorer to enable d
4. and the vanadium file created from run number 54975 Zo SwkSp gt POLEOCUS C nrun 52 9 0 bfile c polopengenie calibration cb52980 dat viile c polopengenie calibration cv52931 46 dat this will normalise Polaris C bank data from run number 52978 using the background file cb52980 dat and the vanadium file cv52931 46 dat the same background file could have been specified by using the option back 52980 however because the vanadium file name does not conform to the standard Polaris naming convention use of the v ile option allowed its full name to be specified Note also the requirement to use double backslash characters in the file name specifications The data in the workspace may then be corrected for absorption and GSAS Fullprof etc format data files written using the correct gsasgen fullprofgen etc commands described above Alternatively instead of using the POLFOCUS command to use specific background and vanadium runs simply rename the run number specific files you wish to use these are all in the _ calibration folder to aback dat and avan dat etc and use the AFOCUS etc commands as described above it s probably a good idea to make a copy of the files first and then rename them
5. ci fdir polopengenie inst pol fext raw ed c polopengenie The first searchpath line creates a label called pol_data which points to the current default directory and a folder C data again note the use of double backslash characters which are required in OpenGENIE to indicate the single backslash character used in labelling Windows folders and directories The second searchpath line tells OpenGENIE to look for RAW data files in pol_data first If it can t find them there it then looks in the path Sdiskdir then looks in the path Sarchive e Sdiskdir is an OpenGENIE defined label for the disk and directory path defined by the set disk and set dir commands see the lines in the screen capture above e Sarchive is a label pointing to network drives at ISIS Once you have decided on a suitable location on your PC to store the RAW data files simply replace C data in the first searchpath line with your chosen location and delete the Sarchive text from the second searchpath line It s probably a good idea to keep the Sdiskdir option on the second line 4 Default Working Directory Finally it may be a good idea to change the default startup working directory where OpenGENIE will write any files created To do this simply right click on the OpenGENIE desktop icon select Properties then select the Shortcut tab and you ll see something like this Open GENIE Properties General Shortc
6. commands OpenGENIE Commands To Inspect Polaris Data Data normalisation focusing 2 SWKSD CLOCUS Tul number Or arocus biocus erocus where lt wksp gt is a user defined name for the workspace and run number is the run number If run number is omitted the user will be prompted for the number On the Polaris instrument control computer ndxpolaris ONLY the right hand screen displaying the remote desktop session use run_number Q to specify the current run gt gt lt wksp gt cfocus 0 Or aroc s DEOecusS focus To display the workspace use the display command gt gt display lt wksp gt may be abbreviated to gt gt d lt wksp gt An alternative command ALLFOCUS will normalise all 4 detector banks into consecutive entries in the workspace array w The workspace array w is dimensioned to 100 entries once this number has been filled the array index reverts back to 1 gt gt allfocus run n umber To display the diffraction data use the display command gt gt display w n where n is an integer between 1 and 100 Note the ALLFOCUS command will not work if a variable or workspace with the name w has already been created as OpenGENIE will not be able to determine if the variable workspace or the array is being referenced To add together several consecutive runs into a single data set e g if data collection from a sample has been split into a series of shorter runs such as in a time resolve
7. d study use the ADDRUNS command gt gt lt WKSP gt addunita Lrt run number Jase run number will add together data collected in the Polaris A bank detectors for the series of runs from first run number to last run number Use B C or E qualifiers to process data from the B C and E detector banks respectively Use the qualifier P for data collected from samples contained in the Paris Edinburgh pressure cell this will apply a correction to account for attenuation of the beam by the WC anvils and TiZr gasket and omit the instrument background subtraction Absorption correction of data in OpenGENIE The CORRECT routine is available to carry out an absorption correction for cylindrical sample geometry gt gt lt wout gt correct lt win gt where lt win gt is the name of the OpenGENIE workspace containing the normalised data The corrected data are written to the workspace lt wout gt To calculate quantities required such as number of scattering units per unit volume and the total scattering and attenuation cross sections use the utility SETUP_CORRECT oP SSeTUp COrrecCt SETUP_CORRECT also has an optional AUTO qualifier which will write the quantities required for the absorption correction to a global variable correct_global to enable a single attenuation correction to be applied to a sequence of runs from the same sample e g a temperature scan in a furnace or cryostat the procedure for this is described below
8. elected your files will either be assembled into a ZIP file and you will be prompted to save this to your local disk or you will be offered a page of links from where you can download them individually Note that there is a limit on the number of files 100 and in the case of the ZIP file total size 300Mb that can be downloaded in one go If you are accessing large e g MAPS RAW files you may need to use the individual file links method for the RAW files and then download all the relevant LOG files in a single ZIP file The catalogue index was last updated at 12 00 BST files created after that time will not yet be available for download RAW Data File Access This form gives you access to both the RAW data files e g GEM12345 RAW and sample environment log files e g GEM12345_Temp1 TXT collected at ISIS you just need to select the instrument name type of files RAW LOG and then enter the numbers of the first and last runs you collected Instrument POLARIS First Run Number 12345 Last Run Number 12356 Contents RAW files ILOG files SAV SO files Download via ZIP file ZIP file uncompressed Web links to individual data files Display Windows explorer links to folders ISIS only Transfer to VMS cluster ISISA SESHAT All VMS instruments files placed in directory SCRATCHSDISK ISISDATA Begin Raw Data Download Processed Data File Access e g GEM Xpress access This f
9. he line load c polopengenie genieinit_pol gcl to it default_genieinit gcl Notepad C Id default_genieinit gcl y 1 5 2003 12 05 09 58 52 cmm Exp Joad cA polopengeniegenieinit_ pol gel printr printn printn Open GENIE successfully started at now note the use of double backslash characters which are required in OpenGENIE to indicate the single backslash character used in labelling Windows folders and directories This will ensure all the focusing setup_correct correct process etc commands and scripts which are needed to analyse Polaris data are defined when OpenGenie starts you may want to make a backup copy of the original version of default_genieinit gcl first 3 Modify the C PolOpenGenie genieinit_pol gcl file The genieinit_pol gcl file which you will have downloaded along with the Polaris specific files in step instructs OpenGENIE to look for Polaris RAW data files in various folders on the Polaris instrument PCs and other network drives at ISIS You won t be able to access these locations remotely so you ll need to change a line in this file to tell OpenGENIE where on your own PC you have stored your Polaris RAW data files The relevant section of the file is near the top and is shown below P genieinit_pol gcl Notepad i Ii toggle into searchpath pol data ciw data searchpathdefault pol_data diskdir archive dae ndxpolaris fdisk
10. iles used when normalising Polaris data It also contains files giving details of detector positions which are required to focus the data The _command folder holds gcl script files containing OpenGENIE procedures to focus normalise apply attenuation corrections write GSAS format files etc note some of these gcl files contain more than one procedure The _modules folder holds the Fortran executable files used in some of these procedures e g setup_correct correct and routines to write GSAS Fullprof etc format data files The RIS OpenGenie notes doc file has now been replaced by this file Installation Notes pdf and contains these installation instructions along with notes on the commands available in OpenGENIE for processing your Polaris data 2 Modify default_genieint gcl file A startup file default_genieinit gcl is run every time OpenGENIE is started This file is in the location C Program Files CCLRC ISIS Facility Open GENIE src gcl default_genieinit gcl The file that installs with OpenGENIE is shown below P default_genieinit gcl Notepad File Edit Format View Help C I Id default_genieinit gecl y 1 5 2003 12 05 09 58 52 cmm Exp open GENIE successfully started at nowt This file needs to have an extra line added to it so that it loads a file which defines all the commands which are needed to analyse Polaris data Open the file in Notepad or any other text editor and add t
11. orm gives you access to processed data created at ISIS following e g a GEM Xpress experiment You need to supply the proposal number of the experiment leaving out any RB or XB prefix and the name of the instrument used Instrument GEM Eryneriment Drannacal Nambher RR XR vi 4 Local intranet 100 A dialogue box will open telling you that the process may take a few minutes press OK and depending on what browser you are using you may get a security certificate warning chose whatever option is needed to enable you to continue to the web site to download the files A second dialogue box should then open where you will be prompted for a username and password This is where you need to enter your Federal id and password At this point you may get an error message saying that the site 1s not available Internet Explorer 7 but if you click OK to this message the new web page displayed contains a hyperlink to the zipped folder containing your RAW data files Clicking on this hyperlink should allow you to download the zipped folder to your own computer from where you can extract the RAW files to the location you chose in step 3 above If you have any problems contact a Polaris Instrument Scientist we may be able to get the files to you some other way e g via the ISIS ftp site One last thing a copy of the relevant pages from the Polaris User Manual the green folder in the Polaris cabin which tells you how to use some of the
12. rag and drop copying of files folders e select folder directory Scratch e select folder directory RonSmith e select folder directory PolOpenGenie You will now have the view shown below note the file names and dates you see may differ from those in the screen captures below as programs or data files are updated or new ones added File Edit View Favorites Tools Help gt Back amp 2 ae PP Search Folders a s G x MD E Size Type Modified File Folder 19 06 2009 16 05 command File Folder 19 06 2009 16 05 3 modules File Folder 19 06 2009 16 05 E genieinit_pol gel L34EKB Tkgenies Comman 08 06 2009 14 03 Wh RIS OpenGenie notes doc 320 KB Microsoft Office Wo 27 03 2009 14 14 User Anonymous a Local intranet Copy these folders and files into the C PolOpenGenie folder you have just created You should then have the directory folder structure shown below on your own PC f C PolOpenGENIE Seles File Edit View Favorites Tools Help Back cal a r Search Kea Folders a F x w Hab Address 9y C PolOpenGENIe w Mame Size Type Date Modified C calibration File Folder 1 05 2009 11 22 command File Folder Os 06 2009 14 34 C modules File Folder Os f06f2009 14 34 genieinit_pol gel 2KB Tkgenie3 Comman 08 06 2009 14 03 MRIS OpenGenie notes doc S20 KB Microsoft Office Wo 27 03 2009 14 14 P My Computer 5 objects The _calibration folder holds standard background and vanadium data f
13. rst and last run numbers required in the appropriate fields If you only want RAW files remove the tick from the LOG files check box Select your preferred download route by pressing the appropriate Download via radio button Finally press the Begin Raw Data Download button to start the process ISIS Data Access Windows Internet Explorer DER 6 yy E http fidata isis rl ac uk 4 X le Pe 2 a w one i Data Access fap gt aah v Page iG Tools a ISIS PC Controlled Instrument Data File Access This page allows you to access data files created on the ISIS PC controlled instruments data for VMS controlled instruments must currently be obtained in the usual way by logging onto ISISA and using the RESTISIS command as detailed at http2 www isis rlac_uk computing archiver htm Once you have entered details of the files you require you will be redirected to a secure connection where e You will need to reply Yes to the question of do you want to accept a certificate e When prompted you will need to enter a username and password that was issued to you at ISIS you may use either a Federal ID or VMS account If you do not have an account you should contact the ISIS User Office isisuo rl ac uk and request a Federal ID please quote your experiment number also known as the RB or proposal number when requesting the account If everything is correct then depending on the option you s
14. sorption correction to a large number of normalised data sets e g following temperature scans in a furnace or cryostat before writing GSAS etc format files add the ATT qualifier to the PROCESS command gt gt process c att first run number last run number will first launch the SETUP_CORRECT routine to acquire the necessary sample information before normalising correcting and writing the data files automatically using the routines described above The parameters required in the absorption correction are written to named fields in the global variable correct_global and are copied to the correct field in the workspace storing the normalised diffraction pattern To generate data files in GSAS FULLPROF or CCSL format from normalised diffraction patterns in an OpenGENIE workspace use the commands gt gt GSASGEN lt wksp gt gt gt FULLPROFGEN lt wksp gt gt gt CCSLGEN lt wksp gt where lt wksp gt is the name of the OpenGENIE workspace containing the normalised data This will generate data files with the same file name construction and default time of flight limits as generated using the PROCESS command above To force these routines to prompt for file names time of flight limits etc add the NODEFAULT qualifier gt gt GSASGEN NODEFAULT lt wksp gt gt gt FULLPROFGEN NODEFAULT lt wksp gt gt gt CCSLGEN NODEFAULT lt wksp gt Miscellaneous OpenGENIE Commands To change the current default directory
15. ut Security Open GENIE Ed Target type Application T arget location Target Start in C polopengenie Shortcut key None Rur Normal window Comment The Start in field probably points several sub folders down within the C Program Files folder sO you may want to change this so that when you start writing data files they will be easy to find In the example above this has been set to C polopengenie If you don t change this setting you can always use the cd command in OpenGENIE at any time to set or change your preferred working directory folder Note this step isn t actually necessary if you look at the screen capture of the genieinit_pol gcl file step 3 above you ll see it contains the line cd c polopengenie which does exactly the same thing If you want OpenGENIE to work in a different location simply change this line in the genieinit_pol gcl file 5 Download your Polaris RAW data files In order to access your RAW data files you will need a valid user id called a Federal id and password which will have been issued to you by the STFC FBU IT group If you do not have a Federal id or have forgotten it please contact either the ISIS User Office or a Polaris Instrument Scientist Using a web browser go to http data isis rl ac uk Half way down the page you ll see a section labelled RAW Data File Access below From the Instrument pull down menu select Polaris Enter the fi
Download Pdf Manuals
Related Search