;+ ; Plot the molecular line frequencies for previously detected ; molecular lines stored in !g.molecules on the currently displayed ; plot at the appropriate location given the current x-axis. ; ;

Note: The display is changed to show frequency as the x-axis ; if it is not already doing so. ; ;

Note: It is assumed that you want them shown ; at their rest frequency in the frequency reference frame current in ; use on the plotter adjusted for any source velocity. If the source ; velocity has already been used to adjust the x-axis display then ; this routine will plot the molecule lines at their rest frequencies ; without any offset. Use the /novsource keyword to turn off ; any consideration of the source velocity - lines are simply plotted ; at their rest frequencies no matter what the source velocity is or ; what the displayed x-axis is. ; ;

The set of lines to be search can be narrowed by supplying a formula ; or name. Wildcards are allowed and arrays of formula and names can ; be supplied. ; ;

Only lines with an upper state energy less than or equal to the ; elimit value (in K) are shown. The default value for this keyword is 50 K. ; ;

To show fewer lines use a lower elimit value or select specific ; lines using the formula or name keywords. ; ;

The indices keyword can be used to return the set of indices in the ; !g.molecules array of molecule_struct structures. This can be used ; to get access to full information if desired. See moleculeread ; for a description of the contents of the molecule_struct structure. ; ;

The line information was extracted from the Database for ; Astronomical Spectroscopy - Splatalogue available at www.splatalogue.net ; specifically tailored for the available spectral line coverage of ; the GBT. Splatalogue is a fully rationalized and extended ; compilation of existing spectroscopic resources for use by the ; astronomical community including, but not limited too, the JPL, ; CDMS, Lovas/NIST, Frank Lovas' own Spectral Line Atlas of ; Interstellar Molecules (SLAIM) catalogs. ; ;

Splatalogue is maintained at the North American ALMA Science Center ; with cooperation from the East Asian and European ALMA Regional ; Centers. The Splatalogue Subsystem Scientist is Anthony Remijan. ; ;

For questions, comments, suggestions or concerns about Splatalogue ; please submit a Helpdesk ticket through the ALMA Science Portal at ; help.almascience.org. ; ;

The text file containing the line information is found at ; $GBT_IDL_DIR/pro/guide/GBTIDL_RFF.csv ; ; @keyword formula {in}{optional}{type=string(s)}{default=''} optionally ; filter the list of molecules to those whose formula matches this ; string. Wildcards are allowed following the rules of the IDL ; STRMATCH function. If formula is array of strings, each element is ; used separately and the final list is the set of all lines with ; a formula matching any of the strings on that list. If not supplied, ; the entire list is used. The filter is case insensitive. ; @keyword name {in}{optional}{type=string(s)}{default=''} optionally ; filter the list of molecules to those whose name matches this ; string. Wildcards are allowed following the rules of the IDL ; STRMATCH function. If name is array of strings, each element is ; used separately and the final list is the set of all lines with ; a name matching any of the strings on that list. If not supplied, ; the entire list is used. The filter is case-insensitive. ; @keyword doprint {in}{optional}{type=boolean}{default=0} optionally print ; the line frequencies. The printed frequencies are the line ; frequencies in the frame being displayed on the plotter. ; @keyword elimit {in}{optional}{type=double}{default=50.0} Only lines ; with an upper state energy less than or equal to this limit will be ; plotted. The units are Kelvin. Lowering this limit reduces the ; number of lines plotted. ; @keyword indices {out}{optional}{type=integer} The list of indices ; in !g.molecules of the lines that were plotted. This can be used to ; get the original information (e.g. rest frequency) of the lines ; marked on the plot. This has a value of -1 when no lines were ; plotted. ; @keyword novsource {in}{optional}{type=boolean} Optionally set this ; to turn off any consideration of the source velocity when marking ; the locations of any molecule lines. ; ; @examples ; 

;  ;    All instances of ammonia
;  molecule,formula='NH3*'
;  ;    Two formulas to match
;  molecule,formula=['NH3*','HCCCHO*']
;  ;    Alternatively
;  molecule,name=['ammonia','2-propynal']
;  ; lower the upper state energy cutoff to 20 K
;  molecule,elimit=20
;  ; get the indices of the species plotted
;  molecule,indices=indices
;  ; print out their names
;  print,!g.molecules[indices].name
;
; ; @uses moleculeread ; @uses freq ; @uses veltovel ; @uses shiftvel ; @uses shiftfreq ; @uses decode_veldef ; @uses show ; @uses vline ; @uses getxrange ; @uses getyrange ; @uses getxvoffset ; @uses getxunits ; @uses getxoffset ; @uses getplotterdc ; @uses textoidl ; ; @version $Id$ ;- pro molecule, formula=formula, name=name, doprint=doprint, elimit=elimit, indices=indices, novsource=novsource compile_opt idl2 on_error,2 if n_elements(doprint) eq 0 then doprint = 0 indices = -1 if not !g.line then begin message,'This only works with spectral line data.',/info return endif ; check on user error in specifying formula or name ; this is common: formula=H2CCNH instead of "H2CCNH" ; the former likely results in an undefined value being ; sent in so the usual n_elements test sees it as unset ; by the user and shows all lines. Instead, use arg_present ; and n_elements to warn the user they probably didn't ; mean to do that. Suggest that they forgot to use quotes. if n_elements(name) eq 0 and arg_present(name) then begin message,'name keyword was supplied but is empty.',/info message,'Did you forget to put the name within quotes?',/info return endif if n_elements(formula) eq 0 and arg_present(formula) then begin message,'formula keyword was supplied but is empty.',/info message,'Did you forget to put the formula within quotes?',/info return endif ; if they are supplied, they must be strings if n_elements(name) gt 0 and size(name,/type) ne 7 then begin message,'name keyword must be a string',/info return endif if n_elements(name) gt 0 and size(name,/type) ne 7 then begin message,'formula keyword must be a string',/info return endif if n_elements(elimit) le 0 then elimit = 50.0 freq ; set x axis to frequency yrange = getyrange(empty=empty) if empty then begin message,'Nothing in the plotter',/info return endif ; use full values of x, not just xrange, so that if we are zoomed ; when unzoom happens, the currently hidden lines will be shown x = getxarray() xmax = x[n_elements(x)-1] xmin = x[0] if xmax lt xmin then begin tmp = xmax xmax = xmin xmin = tmp endif ymax = yrange[1] ymin = yrange[0] ; check for lines in range yrange = ymax - ymin yincr=0.04 ; compute reason-able tag posion offsets yOffset= -4.0*yincr ; start from bottom most position nShow = 0 ; count number of lines shown moleculeRead ; read in molecule frequencies ; will not duplicate any effort if ; already read ; select by formula count = 0 indx = -1 matches = -1 if n_elements(formula) gt 0 then begin for i=0,n_elements(formula)-1 do begin thisMatch = strmatch(!g.molecules.formula,formula[i],/fold_case) if count eq 0 then begin matches = thisMatch endif else begin matches = matches + thisMatch endelse count = count + 1 endfor endif if n_elements(name) gt 0 then begin for i=0,n_elements(name)-1 do begin thisMatch = strmatch(!g.molecules.name,name[i],/fold_case) if count eq 0 then begin matches = thisMatch endif else begin matches = matches + thisMatch endelse count = count + 1 endfor endif if count gt 0 then begin indx = where(matches gt 0,count) if count le 0 then begin message,'No molecules matching formula(s) and name(s)',/info return endif endif else begin ; everything through !g,nmol indx = lindgen(!g.nmol) endelse ; final filter on energy eLimIndx = where(!g.molecules[indx].upperStateE le elimit,count) if count le 0 then begin if n_elements(name) gt 0 or n_elements(formula) gt 0 then begin message,'No molecules matching formula(s) and name(s) with upper state energies less than elimit',/info endif else begin message,'No molecules with upper state energies less than elimit',/info endelse return endif indx = indx[eLimIndx] plotted = lonarr(n_elements(indx)) if keyword_set(novsource) then begin dopplerFactor = 1.0 endif else begin ; get source velocity as a true velocity, use DC in the plotter pdc = getplotterdc() vdef = pdc.velocity_definition ok = decode_veldef(vdef, veldef, vframe) ; this is the TRUE velocity in vframe vsrel = veltovel(pdc.source_velocity, 'TRUE',veldef) ; this is the current velocity offset that the user has set in ; the plotter - that is a real velocity offset. vxOffset = getxvoffset() ; the velocity offset to actually shift the rest frequencies vshift = shiftvel(-vsrel,+vxoffset,veldef='TRUE') ; use this to get the doppler factor, just pick any frequency ; use observed_frequency - easy to get dopplerFactor = shiftfreq(pdc.observed_frequency, vshift, veldef='TRUE') / pdc.observed_frequency endelse ; xoffset - this is a simple linear offset, applied last xoffset = getxoffset() xunits = getxunits() ; find scale from xunits to MHz fscale = 1.d case xunits of 'Hz': fscale = 1.d6 'kHz': fscale = 1.d3 'MHz': fscale = 1.d 'GHz': fscale = 1.d-3 endcase ; clear any previously displayed molecule vertical lines clearvlines,idstring='__molecule',/noshow ;For all selected molecular lines for i = 0, (n_elements(indx)-1) do begin ; get frequency in appropriate frame thisMol = !g.molecules[indx[i]] xf = thisMol.freq ; xf = xf * dopplerFactor ; still in MHz xf = xf * fscale ; now in plotter units xf = xf - xoffset ; now with correct offset ; if line is in the plotted range if ((xf gt xmin) and (xf lt xmax)) then begin plotted[i] = 1 textLabel = textoidl( strtrim(string(thisMol.formula))) ; actually mark line location, with formula vline, xf,label=textLabel, ylabel=yOffset+1.0,/noshow,/ynorm, idstring='__molecule' nShow = nShow + 1 ; count lines plotted yOffset = yOffset + yincr ; move to next text position if (yOffset ge -yincr) then yOffset = -4.*yincr ; cycle back to first if (doprint) then print, thisMol.formula,' nu = ', xf endif ; if past both x end points, exit endfor reshow plIndx = where(plotted,plCount) if plCount gt 0 then indices = indx[plIndx] return end ; end of molecule