ISISUserManualWrittenbyMicahWoodard,MollyVitale-Sullivan,andNickLotspeich,

TheCollegeofIdahoJanuary2019

1) Renamefilesa) IntheBulkRenameUtilityprogramselectwhichfilesyouwouldliketorename.b) Inthe‘Replace(3)’section,replacezerosandunneededhyphenstotheformat‘starname-sequence#.fit’c) Therenamingprocessisthesameforflatsandcal

2) CopyMastersintofoldera) M_Bias_2x2-15C.fitb) M_Dark10s2x2-15C.fitc) M_Dark600s2x2-15C.fitd) Hot_Pix_Map.lste) response_starname_mm-dd-yyf) 6532start.lst

3) SettingsTaba) IntheSettingstabandchoose‘...’belowWorkingdirectorytochoosethedesiredfolder.

4) MastersTab

a) IntheMasterstab,clicktheboxnexttoimagenumbertodoublecheckthatISISisreadingthecorrectnumberofflats.

b) Click‘Go’andtheM_Flat.fitfilewillbeaddedtothefolder

5) ImageTaba) Choosethecorrectfolderandselectthefirstimage.b) Gothroughalltheimagestomakesuretheyareallappearingcorrectly.Removeanyoutcasts.c) Canadjust‘Hi:’forbetterqualityofthespectra.d) ClickNexttogotogeneral.

6) GeneralTaba) MakesuretheRootnameandtheObjectnamematchthestarnameb) Insertcal_1fileintocalibrationboxc) Inthe“Filesnameprefixandsuffix”sectionmakesuretoputahyphenintheobjectsuffixboxd) Inthe“SpectralCalibration”boxiswhereyouchoosewhichwavelengthsyou’respectrawillinclude.The

predefinedmode:2400grooves/mm(3lines)willstartyouatthehydrogenalpha

e) Ifyouwanttodocustommode,youwillhavetomakeaDispersionnumber.lstfileinnotepadandinsertthenameofthefile(omit.lst)intheboxbeside

i) Thedispersionnumberconveyshowwavelengthchangesasyougoacrosspixels.Youhavetomanuallychangethepartofspectrayouwanttolookat(betweenwhichwavelengthsyoucollect),takethespectra,andthentellISISwhatwavelengths.MakesuretotypethestartingwavelengthintheXCoordinateofLineatWavelengthboxinCalibrationTab.Todothis,yougottamakeanotepaddocumentwiththefollowing

ii) Subtractthethird(highest)wavelengthfromthefirst(lowest)wavelengthiii) Gotocalibrationtabasdisplaythecalibrationphotofromthespectraiv) Putcursoroverthemiddleofthefirstlineontheredlinetofindthexcoordinateofthemiddle

pixelv) Putcursoroverthemiddleofthethirdlineontheredlinetofindthexcoordinateofthemiddle

pixelvi) Subtractthethirdpixelcoordinatefromthefirstpixelcoordinatevii) Dividethechangeinwavelengthbythechangeinpixels.Thiswillbeyourdispersionnumber

ChangeinWavelength/ChangeinPixels

viii) Opennotepadandputthefollowing(1) 2(Thisnumberisthepolynomial.Sincewehave3wavelengths,polynomialis2)(2) Dispersionnumber(3) Listthethreedifferentwavelengthnumbers

ix) Saveasa.lstfile(Justtypenameandthen.lst)

7) CalibrationTaba) Clickonthecenterofthespectratosettheverticalcoordinate

b) Drawaboxaroundthecenterlinesaboveandbelowthespectra,thenclickTiltc) NexttoCalibrationImage,clickDisplay.Thecalibrationlinesshouldappeard) ScrolltotheleftmostcalibrationlineandslidetheSeuilhauttotheleftenoughtodecreasethewidthof

thecalibrationline.e) ClickonthecenterofthecalibrationlinetosettheXcoordinateatwavelength___toA:___(pixels)f) DrawaboxaroundthecalibrationlinejustinsidetheouterBinningZoneAdjustmentlines,thenclick

Slantg) ClickNext

8) GoTab

a) ClickGo!

b) DisplayProfile.ThiswillgototheProfileTabanddisplaytheplot.

c) Titletheplot-withthestandardnamingconventions

9) GnuplotTab

a) Renametheplotto‘starname,dateandtime’orsomethingtothisidea.

b) ClickPlotandDONE!Thereshouldbea.pngimageinthefoldernow

i) YOUDIDIT�� Cheers! ��

10) Converting to Radial Velocity

a) Under the Profile tab click on FWHM (full-width half max)

b) If it is an absorption peak, choose absorption

c) Double click on both sides of the peak at the same height

d) Record the Position value and check the signal to noise ratio SNR (3)

e) Under the Misc tab and under the Wavelength to Velocity section type profile name into Input Spectrum box, input starting wavelength you got from FWHM, and then title your output spectrum

f) Turn this .dat file into .fit file by going to the Tools Tab under the Spectra 3 subtab in the convert file format of a spectra sequence and convert it. Put name in input file and the name you want in the output file

g) You can display this new .fit file on profile. The radial velocity is now in place of the wavelength at the bottom of the screen.

h) Figure out how to label the x-axis with the radial velocity (instead of Angstroms)