To make this easier on yourself, I suggest making a sticky-note with the following information for the sequence on which you'll be working: Sequence Number Observation ID Rootname Source Name GBM File Number Redshift Galactic Column Most of the above info can be found on the list for sequence numbers which need to be done; the last two numbers can be found on the by clicking on the appropriate sequence number and observation id combo at http://hotgas.pha.jhu.edu/hetg_seq.html \end{center} \normalsize 1. Type: ciao321 at the unix prompt. 2. On web, go to http://cda.harvard.edu/chaser/mainEntry.do 3. Type in Sequence Number and ObsID in appropriate boxes. 4. Click on "search" button in top left of page. 5. Click on boxes "Primary Products" and "Secondary Products"; click "Add to Retrieval List". 6. Click on "Retrieve Products". 7. Type in your email address. 8. In unix window, type in: cd $DATA1 9. Make a directory for your data; type in: mkdir sequencenumber_obsID (e.g. mkdir 700006_1802). 10. cd into the directory you just created. (e.g. type: cd 700006_1802). 11. type: ftp cda.harvard.edu 12. Type anonymous for User Name and your email address as the password. 13. cd into the directory name given in the email they sent you. (e.g. cd /pub/srftp/f@P4jzM1). 14. type: ls 15. Note the file name shown. 16. type: get filenameshown (e.g. get package_144_0451200241546.tar) 17. On web, go to http://cxc.harvard.edu/cgi-gen/cda/get_bias 18. Type in ObsID; click on "submit". 19. This will take you to a website which will tell you how to get the data. 20. In unix window, still logged into cda.harvard.edu, type: bin 21. type: cd directorygivenonwebsite (e.g. cd /pub/srftp/f890xm2). 22. type: ls 23. Note the file name shown. 24. type: mget filenameshown (e.g. mget B8967.tar). Answer "y" at the prompt. 25. Close the website. 26. In the unix window, type: exit (e.g. exit from cda.harvard.edu) 27. You should now be in /data1/magnetar/yourusername/hetgreproc/sequencenumber_obsid 28. type: ls 29. type: tar -xvf packageseenabove (e.g. tar -xvf package_144_0451200241546.tar) 30. type: ls 31. type: tar -xvf Bseenabove (e.g. tar -xvf B8967.tar). 32. type: cd obsID# (e.g. cd 1802). 33. type: mv *bias* primary/ 34. type: mv *pbk* primary/ 35. type: mkdir analysis 36. type: mkdir aux 37. type: cd analysis 38. type: ciao321 39. type: reproc1_ciao321.perl rootnameofyourdata (e.g. reproc1_ciao321.perl q0836_700006_1802; the correct rootname can be found on the chart of data to be processed). 40. This will take more than 20 minutes to run. 41. When this is done (e.g. when the unix prompt comes back up), type: ls 42. You should see three files, which end in bpix1.fits.gz, evt2.fits.gz, and pha2.fits.gz. 43. type: hetgrmfs.perl rootnameofyourdata (e.g. hetgrmfs.perl q8036_700006_1802). 44. type: ls /home/yourusername/cxcds_param/fullgarf_nocorr.par 45. If the computer can't find this, type: cp $ASCDS_INSTALL/contrib/param/fullgarf.par /home/yourusername/cxcds_param/fullgarf_nocorr.par 46. type: idl 47. At the idl prompt, type: rootname='rootnameofyourdata' (e.g. rootname='q0836_700006_1802'). 48. At the idl prompt, type: hetgarfs_ciao321,rootname,/cdir 49. exit idl (e.g. at the idl prompt, type: exit). 50. type: ls 51. You should see a file that ends in _mkgarf 52. type: source filenamethatendsin_mkgarf (e.g. type: source q8036_700006_1802_mkgarf). 53. This will take more than 30 minutes to run. 54. When this is done (e.g. when the unix prompt comes back up), type: gzip * 55. type: cd ../ 56. IF YOU HAVE DONE THIS BEFORE, AND ARE CONFIDENT YOU'VE DONE EVERYTHING RIGHT, type: rm -fr *.tar 57. IF YOU HAVE DONE THIS BEFORE, AND ARE CONFIDENT YOU'VE DONE EVERYTHING RIGHT, type: rm -fr primary 58. IF YOU HAVE DONE THIS BEFORE, AND ARE CONFIDENT YOU'VE DONE EVERYTHING RIGHT, type: rm -fr secondary 59. IF YOU HAVE DONE THIS BEFORE, AND ARE CONFIDENT YOU'VE DONE EVERYTHING RIGHT, type: rm -fr supporting 60. IF YOU HAVE DONE THIS BEFORE, AND ARE CONFIDENT YOU'VE DONE EVERYTHING RIGHT, type: rm -fr oif.fits 61. IF YOU HAVE DONE THIS BEFORE, AND ARE CONFIDENT YOU'VE DONE EVERYTHING RIGHT, type: rm -fr vv* 62. type: cd $DATA1 63. type: mkdir gdb_backup 64. type: cd gdb_backup 65. type: mkdir sequencenumber_obsID (e.g. type: mkdir 700006_1802). 66. type: cd sequencenumber_obsID (e.g. type: cd 700006_1802). 67. type: cp ../../sequencenumber_obsID/obsID/analysis/*evt2* . (e.g. type: cp ../../700006_1802/1802/analysis/*evt2* .) 68. type: cp ../../sequencenumber_obsID/obsID/analysis/*pha2* . (e.g. type: cp ../../700006_1802/1802/analysis/*pha2* .) 69. type: cp ../../sequencenumber_obsID/obsID/analysis/*1_garf* . (e.g. type: cp ../../700006_1802/1802/analysis/*1_garf* .) 70. type: gzip * 71. type: oldftools 72. Make sure you are in the analysis sub-directory of the data you are working on. (e.g. your prompt should read /data1/magnetar/yourusername/hetgreproc/sequencenumber_obsID/obsID/analysis). 73. type: ls *evt2* 74. One file should show up. 75. type: ls *m1.rmf* 76. Two files should show up. 77. type: ls *p1.rmf* 78. Two files should show up. 79. type: ls *1_garf* 80. Eight files should show up. 81. type: *nqe*1_garf* 82. Four files should show up. 83. type: idl 84. At the idl prompt, type: rootname='whateveryouusedbefore' (e.g. rootname='q0836_700006_1802'). 85. At the idl prompt, type: mkhetgarchspec,rootname,/nqe,/clnfile 86. At the idl prompt, type: exit 87. type: ls -1 *.pha|wc -l 88. Pay careful attention to which of the characters in the above command are Ls and which are 1s. The in caps, it would read: LS -1 *.PHA|WC -L 89. The number 52 should show up. 90. type: ls -1 *.rsp|wc -l 91. The number 48 should show up. 92. type: mkdir fits_spectra 93. type: cp *pha2* fits_spectra 94. type: mv *.pha fits_spectra 95. type: mv *.rsp fits_spectra 96. type: mv fits_spectra/*1.pha . 97. type: gzip fits_spectra/* 98. type: tar -cvf rootnameyouhavebeenusing_hetg_fitspec.tar fits_spectra (e.g. type: tar -cvf q0836_700006_1802_hetg_fitspec.tar fits_spectra). 99. type: gzip *.tar 100. Make sure you are in the analysis sub-directory of the data you are working on. (e.g. your prompt should read /data1/magnetar/yourusername/hetgreproc/sequencenumber_obsID/obsID/analysis). 101. type: mkdir lcxd 102. type: cd lcxd 103. type: idl 104. At the idl prompt, type: rootname='whateveryouusedbefore' (e.g. rootname='q0836_700006_1802'). 105. At the idl prompt, type: $pwd 106. This will return a directory address. 107. At the idl prompt, type: evtdir='thedirectoryaddressjustreturnedendingatanalysis' (e.g. type: evtdir='/data1/magnetar/yourusername/hetgreproc/700006_1802/1802/analysis'). 108. At the idl prompt, type: label1='SourceName [Sequencenumber, ObsID]' (e.g. type: label1='Q0836 [700006, 1802]'). 109. At the idl prompt, type: mkhetglcxdjr,rootname,evtdir=evtdir,label1=label1 110. When this has completed running, at the idl prompt, type: exit 111. type: ls 112. This should show a file ending in _mkgif 113. type: source filenameendingin_mkgif (e.g. type: source q0836_700006_1802_mkgif). 114. When this has finished, open a webpage 115. In the webpage address space, type: file:///data1/magnetar/yourusername/hetgreproc/sequencenumber_obsID/obsID/analysis/lcxd (e.g. open the website file:///data1/magnetar/yourusername/hetgreproc/700006_1802/1802/analysis/lcxd). 116. Click on each .gif file, looking for correct label at top, evenly spaced graph, and correct x and y axis labels. 117. Back in the unix window, type: gzip * 118. type: cd ../ 119. type: tar -cvf rootnameyouhavebeenusing_hetg_lc.tar lcxd/ (e.g. type: tar -cvf q0836_700006_1802_hetg_lc.tar lcxd/). 120. type: tar -cvf rootnameyouhavebeenusing_hetg_xdisp.tar lcxd/ (e.g. type: tar -cvf q0836_700006_1802_hetg_xdisp.tar lcxd/). 121. type: gunzip lcxd/* 122. type: gzip rootnameyouhavebeenusing_hetg_lc.tar (e.g. type: gzip q0836_700006_1802_hetg_lc.tar). 123. type: gzip rootnameyouhavebeenusing_hetg_xdisp.tar (e.g. type: gzip q0836_700006_1802_hetg_xdisp.tar). 124. type: mkdir ascii_spectra 125. type: cd ascii_spectra 126. type: gunzip ../* 127. type: cp ../*obsID_*1_garf*.fits . (e.g. type: cp ../*1802_*1_garf*.fits .) 128. type: ls 129. Four files should show. 130. type: idl 131. At the idl prompt, type: rootname='rootnameyouhavebeenusing' (e.g. type: rootname='q0836_700006_1802'). 132. At the idl prompt, type: $pwd 133. This will return a directory address. 134. At the idl prompt, type: evtdir='thedirectoryaddressjustreturnedendingatanalysis' (e.g. type: evtdir='/data1/magnetar/yourusername/hetgreproc/700006_1802/1802/analysis'). 135. At the idl prompt, type: label1='SourceName [Sequencenumber, ObsID]' (e.g. type: label1='Q0836 [700006, 1802]'). 136. Open the website: http://hotgas.pha.jhu.edu/hetg_seq.html Click on your sequence number and look for the redshift in the upper left hand portion. 137. At the idl prompt, type: redshift='redshiftnumberfoundonhotgaswebsite' (e.g. type: redshift='2.172000'). 138. At the idl prompt, type: mkgdbasciispectra,rootname,evtdir=evtdir,redshift=redshift,label1=label1 139. When this process has finished running, at the idl prompt, type: exit 140. type: ls 141. This will show a file ending in _invspec_mkgif 142. type: source filenameendingin_invspec_mkgif (e.g. type: source q0836_700006_1802_invspec_mkgif). 143. When this has finished, open a webpage 144. In the webpage address space, type: file:///data1/magnetar/yourusername/hetgreproc/sequencenumber_obsID/obsID/analysis/ascii_spectra (e.g. open the website file:///data1/magnetar/yourusername/hetgreproc/700006_1802/1802/analysis/ascii_spectra). Click on each .gif file, looking for correct label at top, evenly spaced graph, and correct x and y axis labels. 145. Back in the unix window, type: gzip * 146. type: cd ../ 147. type: tar -cvf rootnameyouhavebeenusing_hetg_asciispec.tar ascii_spectra/ (e.g. type: tar -cvf q0836_700006_1802_hetg_asciispec.tar ascii_spectra/) 148. type: gunzip ascii_spectra/* 149. type: gzip rootnameyouhavebeenusing_hetg_asciispec.tar (e.g. type: gzip q0836_700006_1802_hetg_asciispec.tar) 150. type: ls -1 *1_garf.fits |wc -l 151. This should return the number 8. 152. type: idl 153. At the idl prompt, type: rootname='sameoldthing' (e.g. type: rootname='q0836_700006_1802'). 154. At the idl prompt, type: label1='SourceName [Sequencenumber, ObsID]' (e.g. type: label1='Q0836 [700006, 1802]'). 155. At the idl prompt, type: mkgdbarfplots,rootname,label1=label1 156. At the idl prompt, type: exit 157. type: ls 158. There should be a file that ends in _mkeffarea 159. type: source filethatendsin_mkeffarea (e.g. type: source q0836_700006_1802). 160. type: mkdir effarea 161. type: mv *_ev_* effarea/ 162. type: tar -cvf rootnameyouhavebeenusing_hetg_effarea.tar effarea (e.g. type: tar -cvf q0836_700006_1802_hetg_effarea.tar effarea). 163. type: gzip rootnameyouhavebeenusing_hetg_effarea.tar (e.g. type: gzip q0836_700006_1802_hetg_effarea.tar). 164. When this has finished, open a webpage 165. In the webpage address space, type: file:///data1/magnetar/yourusername/hetgreproc/sequencenumber_obsID/obsID/analysis/effarea (e.g. open the website file:///data1/magnetar/yourusername/hetgreproc/700006_1802/1802/analysis/effarea). 166. Click on each .gif file, looking for correct label at top, evenly spaced graph, and correct x and y axis labels. 167. type: cd $DATA1 168. type: cd ../ 169. type: mkdir gdbfitting 170. type: cd gdbfitting 171. Download file from website at http://lheawww.gsfc.nasa.gov/~yaqoob/gdbfit.tar 172. Download file from website at http://lheawww.gsfc.nasa.gov/~yaqoob/hetg_archive_02aug04_sy1sy2.txt 173. In unix window, type: tar -xvf gdbfit.tar 174. type: cp ../hetgreproc/sequencenumber_obsID/obsID/analysis/fits_spectra/*meg*m1p1*0800*.* . (e.g. type: cp ../hetgreproc/700006_1802/1802/analysis/fits_spectra/*meg*m1p1*0800*.* .) 174. type: cp ../hetgreproc/sequencenumber_obsID/obsID/analysis/fits_spectra/*heg*m1p1*0400*.* . (e.g. type: cp ../hetgreproc/700006_1802/1802/analysis/fits_spectra/*heg*m1p1*0400*.* .) 175. type: rm -fr *nqe* 176. type: gunzip * 177. type: xspec 178. t the xspec prompt, type: sy ls *pha* 179. This will return two files with your rootname; one with "meg" in the name, one with "heg" in the name. Do the following process with the "meg" file first. 180. At the xspec prompt, type: da fileendinginmeg (e.g. type: da q0836_700006_1802_meg_m1p1_b0800.pha). 181. This will print a few lines to the screen; note the one that begins with "Net count rate". 182. Multiply this number by 2 and round to 4 decimal places. 183. Open the file hetg_archive_02aug04_sy1sy2.txt that you saved in gdbfitting. 184. Look for the sequence number and observation id that you are working on. 185. In the fourth to last column, enter the number you got in instruction #182. 186. Look at the table of sequences to be done, and note the number under GBM file. 187. At the xspec prompt, type: @gdbm01.xcm (e.g. type: @gdbmthenumberrecommendedforyoursequence.xcm). 188. Open the website: http://hotgas.pha.jhu.edu/hetg_seq.html Click on your sequence number and look for the Galactic Column in the upper left hand portion. 189. Divide this Galactic Column Number by 100. 190. At the xspec prompt, type: newp 1 numberreachedwithinstruction#189 -1 (e.g. type: newp 1 0.0292 -1). 191. at the xspec prompt, type: @gdb_meg_fit.xcm 192. This will bring up the plt prompt. 193. At the plt prompt, type: @gdb_meg_clean_ufspec.pco 194. At the plt prompt, type: la t "SourceName [SequenceNumber, ObsID] MEG (-1,+1)" (e.g. type: la t "Q0836 [700006, 1802] MEG (-1,+1)"). 195. At the plt prompt, type: cpd /xw 196. At the plt prompt, type: p 197. This should show you what the graph currently looks like. If the y-axis doesn't look good, you can change it by typing: r y newynumber (e.g. by typing: r y 10E-5). 198. At the plt prompt, type: wenv sameoldrootname_meg_m1p1_b0800_uf_xe (e.g. type: wenv q0836_700006_1802_meg_m1p1_b0800_uf_xe). 199. At the plt prompt, type: hard /gif 200. At the plt prompt, type: $mv pgplot.gif sameoldrootname_meg_m1p1_b0800_uf_xe.gif (e.g. type: $mv pgplot.gif q0836_700006_1802_meg_m1p1_b0800_uf_xe.gif). 201. At the plt prompt, type: exit 202. At the xspec prompt, type: flux 0.5 2.0 203. This will print a line to the screen; the number in parantheses is the one you want. 204. Multiply this number by 1E11 (i.e. add 11 to the exponent) and round up to 2 significant figures. 205. Go back to the window where the hetg_archive_02aug04_sy1sy2.txt file is open. 206. Enter the number you found in instruction #204 in the second to last column of the line for your sequence number and observation ID. 207. At the xspec prompt, type: save mo sameoldrootname_meg_m1p1_b0800_uf_xe.xcm (e.g. type: save mo q0836_700006_1802_meg_m1p1_b0800_uf_xe.xcm). 208. At the xspec prompt, type: sy ls *pha* 209. This will return two files with your rootname; one with "meg" in the name, one with "heg" in the name. Now do the following process with the "heg" file. 210. At the xspec prompt, type: da fileendinginheg (e.g. type: da q0836_700006_1802_heg_m1p1_b0400.pha). 211. This will print a few lines to the screen; note the one that begins with "Net count rate". 212. Multiply this number by 2 and round to 4 decimal places. 213. Go back to the window with the file hetg_archive_02aug04_sy1sy2.txt that you saved in gdbfitting. 214. Look for the sequence number and observation id that you are working on. 215. In the third to last column, enter the number you got in instruction #212. 216. Look at the table of sequences to be done, and note the number under GBM file. 217. At the xspec prompt, type: @gdbm01.xcm (e.g. type: @gdbmthenumberrecommendedforyoursequence.xcm). 218. Open the website: http://hotgas.pha.jhu.edu/hetg_seq.html Click on your sequence number and look for the Galactic Column in the upper left hand portion. 219. Divide this Galactic Column Number by 100. 220. At the xspec prompt, type: newp 1 numberreachedwithinstruction#189 -1 (e.g. type: newp 1 0.0292 -1). 221. at the xspec prompt, type: @gdb_heg_fit.xcm 222. This will bring up the plt prompt. 223. At the plt prompt, type: @gdb_heg_clean_ufspec.pco 224. At the plt prompt, type: la t "SourceName [SequenceNumber, ObsID] HEG (-1,+1)" (e.g. type: la t "Q0836 [700006, 1802] HEG (-1,+1)"). 225. At the plt prompt, type: cpd /xw 226. At the plt prompt, type: p 227. This should show you what the graph currently looks like. If the y-axis doesn't look good, you can change it by typing: r y newynumber (e.g. by typing: r y 10E-5). 228. At the plt prompt, type: wenv sameoldrootname_heg_m1p1_b0400_uf_xe (e.g. type: wenv q0836_700006_1802_heg_m1p1_b0400_uf_xe). 229. At the plt prompt, type: hard /gif 230. At the plt prompt, type: $mv pgplot.gif sameoldrootname_heg_m1p1_b0400_uf_xe.gif (e.g. type: $mv pgplot.gif q0836_700006_1802_heg_m1p1_b0400_uf_xe.gif). 231. At the plt prompt, type: exit 232. At the xspec prompt, type: flux 2 10 233. This will print a line to the screen; the number in parantheses is the one you want. 234. Multiply this number by 1E11 (i.e. add 11 to the exponent) and round up to 2 significant figures. 235. Go back to the window where the hetg_archive_02aug04_sy1sy2.txt file is open. 236. Enter the number you found in instruction #204 in the last column of the line for your sequence number and observation ID. 237. At the xspec prompt, type: save mo sameoldrootname_heg_m1p1_b0400_uf_xe.xcm (e.g. type: save mo q0836_700006_1802_heg_m1p1_b0400_uf_xe.xcm). 238. At the xspec prompt, type: exit type "y" at prompt. 239. type: ls sameoldrootname*xe.xcm (e.g. type: ls q0836_700006_1802_*xe.xcm). 240. This should show two files. 241. type: ls sameoldrootname*xe.gif (e.g. type: ls q0836_700006_1802_*xe.gif). 242. This should show two files. 243. Make sure you are in the analysis sub-directory of the sequence you are working on. 244. type: mkdir ufspec 245. type: cd ufspec 246. type: cp /data1/magnetar/yourusername/gdbfitting/sameoldrootname*xe.xcm . (e.g. type: cp /data1/magnetar/yourusername/gdbfitting/q0836_700006_1802_*xe.xcm .) 247. type: cp /data1/magnetar/yourusername/gdbfitting/sameoldrootname*xe.gif . (e.g. type: cp /data1/magnetar/yourusername/gdbfitting/q0836_700006_1802_*xe.gif .) 248. type: xv /data1/magnetar/yourusername/gdbfitting/sameoldrootname*xe.gif (e.g. type: cp /data1/magnetar/yourusername/gdbfitting/q0836_700006_1802_*xe.gif). 249. This should bring up a graph; make sure that the title is correct, as well as the axis titles and the placement on the axis. 250. Check off the sequence number and obsID on the list of sequences to be done.