FPS Updates

bin/plot_sdss_sky

@@ -7,6 +7,7 @@ from matplotlib import pyplot as plt
 from astropy.visualization import hist
 from astropy.io import fits as pyf
 import os
+from astropy.table import Table
 matplotlib.style.use('default')
 import warnings
 warnings.filterwarnings("ignore")
@@ -17,13 +18,14 @@ run2d = os.getenv('RUN2D')
 redux = os.getenv('BOSS_SPECTRO_REDUX')
 
 file_c=redux+'/'+run2d+'/fieldlist-'+run2d+'.fits'
-hdu_list = pyf.open(file_c)
-table_hdu = hdu_list[1]
-table_data = table_hdu.data
+if os.path.exists(file_c):
+	hdu_list = pyf.open(file_c)
+	table_hdu = hdu_list[1]
+	table_data = table_hdu.data
+else: table_data=Table(names=('RACEN','DECCEN', 'PROGRAMNAME'))
 RA=table_data.field('RACEN')
 DEC=table_data.field('DECCEN')
 prog=table_data.field('PROGRAMNAME')
-
 PROG_N=np.zeros(len(prog))
 PROG_C=[]
 for i in range(0, len(prog)):
@@ -48,7 +50,9 @@ for i in range(0, len(prog)):
     elif 'OFFSET' in prog[i]:
         PROG_N[i]=7.0
         PROG_C.extend(['black'])
-
+    else: 
+        PROG_N[i]=0.0
+        PROG_C.extend(['saddlebrown']) 
 
 
 PROG_C=np.array(PROG_C)
@@ -58,6 +62,8 @@ c3=0
 c4=0
 c5=0
 c6=0
+c7=0
+c0=0
 
 # convert coordinates to degrees
 RA *= np.pi / 180
@@ -92,6 +98,8 @@ for i in range(0, len(RA)):
     elif PROG_C[i] == 'green' and c6== 0:
         ax.plot(x, y, color=PROG_C[i],label='eFEDS')
         c6=1
+    elif PROG_C[i] == 'black' and c7==0:
+        ax.plot(x, y, color=PROG_C[i],label='Offset')
     else:
         ax.plot(x, y, color=PROG_C[i])
 plt.legend(loc=1,fontsize=10)
@@ -106,6 +114,9 @@ c2=0
 c3=0
 c4=0
 c5=0
+c6=0
+c7=0
+c0=0
 
 fig, ax = plt.subplots(figsize=(9.5*1.0,5.5*1.0))
 ax = plt.axes(projection='mollweide')
@@ -131,12 +142,15 @@ for i in range(0, len(RA)):
     elif PROG_C[i] == 'orange' and c4== 0:
         ax.plot(x, y, color=PROG_C[i],label='AQMES-Wide')
         c4=1
-    elif PROG_C[i] == 'magenta' and c4== 0:
+    elif PROG_C[i] == 'magenta' and c5== 0:
         ax.plot(x, y, color=PROG_C[i],label='AQMES-Bonus')
         c5=1
-    elif PROG_C[i] == 'green' and c5== 0:
+    elif PROG_C[i] == 'green' and c6== 0:
         ax.plot(x, y, color=PROG_C[i],label='eFEDS')
         c6=1
+    elif PROG_C[i] == 'black' and c7== 0:
+        ax.plot(x, y, color=PROG_C[i],label='eFEDS')
+        c7=1
     else:
         ax.plot(x, y, color=PROG_C[i])
 plt.legend(loc=1,fontsize=10)
@@ -147,9 +161,11 @@ plt.savefig(redux+'/'+run2d+'/SDSSV.png',dpi=500)
 plt.close()
 
 file_c=redux+'/'+run2d+'/spAll-'+run2d.replace('/','-')+'.fits'
-hdu_list = pyf.open(file_c)
-table_hdu = hdu_list[1]
-table_data = table_hdu.data
+if os.path.exists(file_c):
+	hdu_list = pyf.open(file_c)
+	table_hdu = hdu_list[1]
+	table_data = table_hdu.data
+else: table_data=Table(names=('PLUG_RA','PLUG_DEC', 'PROGRAMNAME','NSPECOBS'))
 RA1=table_data.field('PLUG_RA')
 DEC1=table_data.field('PLUG_DEC')
 prog1=table_data.field('PROGRAMNAME')

bin/run_PyXCSAO.py

@@ -53,8 +53,10 @@ def get_fiber(flux, PlugMap, hdr, i):
     #meta['objid']=PlugMap['OBJID'][i]
     meta['program']=PlugMap['PROGRAM'][i]
     meta['objtype']=PlugMap['OBJTYPE'][i]
-    meta['SOURCETYPE']=PlugMap['SOURCETYPE'][i]
-
+    if 'SOURCETYPE' in hdr:meta['SOURCETYPE']=PlugMap['SOURCETYPE'][i]
+    elif 'CATEGORY' in hdr:meta['SOURCETYPE']=PlugMap['CATEGORY'][i]
+    else:meta['SOURCETYPE']=PlugMap['OBJTYPE'][i]
+
     if 'PLATEID' in hdr: meta['FIELDID']=hdr['PLATEID']
     elif 'FIELDID' in hdr: meta['FIELDID']=hdr['FIELDID']
     else: meta['FIELDID']=np.nan
@@ -77,9 +79,15 @@ def get_fiber(flux, PlugMap, hdr, i):
     meta['sdss_r']=PlugMap['MAG'][i][2]
     meta['sdss_i']=PlugMap['MAG'][i][3]
     meta['sdss_z']=PlugMap['MAG'][i][4]
-    meta['gaia_G']=PlugMap['GAIA_G'][i]
-    meta['BP']=PlugMap['GAIA_BP'][i]
-    meta['RP']=PlugMap['GAIA_RP'][i]
+    if 'GAIA_G' in hdr:meta['gaia_G']=PlugMap['GAIA_G'][i]
+    elif 'GAIA_G_MAG' in hdr:meta['gaia_G']=PlugMap['GAIA_G_MAG'][i]
+    else: meta['gaia_G']=np.NaN
+    if 'GAIA_BP' in hdr:meta['BP']=PlugMap['GAIA_BP'][i]
+    elif 'BP_MAG' in hdr:meta['BP']=PlugMap['BP_MAG'][i]
+    else: meta['BP']=np.NaN
+    if 'GAIA_RP' in hdr:meta['RP']=PlugMap['GAIA_RP'][i]
+    elif 'RP_MAG' in hdr:meta['RP']=PlugMap['RP_MAG'][i]
+    else: meta['RP']=np.NaN
     meta['J']=PlugMap['TWOMASS_MAG'][i][0]
     meta['H']=PlugMap['TWOMASS_MAG'][i][1]
     meta['K']=PlugMap['TWOMASS_MAG'][i][2]
@@ -97,8 +105,7 @@ def get_fiber(flux, PlugMap, hdr, i):
                         default=os.getenv('RUN1D'))
     args = parser.parse_args()
 
-    platemjd=os.path.basename(args.fitsfile)[8:19]
-
+    platemjd='-'.join(os.path.basename(args.fitsfile).split('-')[1:]).split('.')[0]
 
     # Open a file with access mode 'a'
     logfile = args.run1d+'/spXCSAO-' + platemjd + '.log'
@@ -112,7 +119,7 @@ def get_fiber(flux, PlugMap, hdr, i):
     splog.write('idlutils version ' + os.popen('idlutils_version').read())
     splog.write('Python version ' + python_version())
     try:
-        #splog.write('pyxcsao version ' + pyxcsao.__path__[0].split('/')[-2][:-4])
+    #splog.write('pyxcsao version ' + pyxcsao.__path__[0].split('/')[-2][:-4])
         splog.write('pyxcsao version ' +os.getenv('PYXCSAO_VER'))
         c=PyXCSAO(st_lambda=5000,end_lambda=10000)
         templates=os.getenv('PYXCSAO_DIR')+'/../grids/phoenix_full1.p'
@@ -137,5 +144,5 @@ def get_fiber(flux, PlugMap, hdr, i):
         test.write(args.run1d+'/spXCSAO-' + platemjd + '.fits',overwrite=True)
 
         splog.write('CPU time to compute RVs = '+ str(datetime.now()-t0))
-    except: splog.write('WARNING: Python package pyxcsao not installed\n')
+    except: splog.write('WARNING: Failed run of pyXCSAO\n')
     splog.close()

pro/fpsconfig/field_to_string.pro

@@ -5,10 +5,10 @@ function field_to_string, field
     for i=0, n_elements(field)-1 do sfield[i] = field_to_string(field[i])
     return, sfield
   endif
-
-  if field lt 10000 then $
-    return, strtrim(string(field,f='(i5.5)'),2) $
-  else $
-    return, strtrim(field,2)
+    return, strtrim(string(field,f='(i6.6)'),2) 
+  ;if field lt 10000 then $
+  ;  return, strtrim(string(field,f='(i6.6)'),2) $
+  ;else $
+  ;  return, strtrim(field,2)
 
 end

pro/rm/rm_combine_script.pro

@@ -14,7 +14,7 @@ if keyword_set(legacy) then begin
    ;fieldstr = strmid(planfile,11,4)
    fieldstr = strsplit(repstr(repstr(planfile,'spPlancomb',''),'.par', ''),'-',/extract)
 endif else begin
-   fieldstr = strmid(planfile,11,5)
+   fieldstr = (strsplit(repstr(repstr(planfile,'spPlancomb',''),'.par', ''),'-',/extract))[0]
 endelse
 
 if not keyword_set(finaldir) then finaldir = '';'recalib/' ; 'recalib/test20/'

pro/rm/rm_spcoadd_v5.pro

@@ -1139,7 +1139,8 @@ pro rm_spcoadd_v5, spframes, outputname, $
    ;----------
    ; Remove header cards that were specific to this first exposure
    ; (where we got the header).
-   sxaddpar, bighdr, 'FIELDID', strmid(outputname,8,5)
+   sxaddpar, bighdr, 'FIELDID', (strsplit(outputname,'-',/EXTRACT))[1]
+   ;sxaddpar, bighdr, 'FIELDID', strmid(outputname,8,5)
    ncoeff = sxpar(bighdr, 'NWORDER')
    for i=2, ncoeff-1 do sxdelpar, bighdr, 'COEFF'+strtrim(string(i),2)
 
@@ -1474,7 +1475,7 @@ pro rm_spcoadd_v5, spframes, outputname, $
      ;coaddname = repstr(repstr(outputname,'spField','spSpec'),'.fits', $ 
      ; '-'+string(itarget,format='(i3.3)')+'.fits')
      coaddname = repstr(repstr(outputname,'spField','spSpec'),'.fits', $
-      '-'+targid_tar+'.fits') 
+      '-'+strtrim(targid_tar,2)+'.fits') 
      fulloutname_coadd = djs_filepath(coaddname, root_dir=coadddir)
      ; HDU # 0 header
      mwrfits, junk_d, fulloutname_coadd, bighdr, /create

pro/rm/rm_spcombine_v5.pro

@@ -151,10 +151,10 @@ pro rm_spcombine_v5, planfile, docams=docams, adderr=adderr, xdisplay=xdisplay,
   if (NOT keyword_set(thismjd)) then $
    thismjd = max(allseq.mjd)
   if keyword_set(legacy) or keyword_set(plates) then begin
-    fieldmjd = string(yanny_par(hdr,'plateid'),format='(i5.5)') $
+    fieldmjd = field_to_string(yanny_par(hdr,'plateid')) $
       + '-' + string(thismjd,format='(i5.5)')
   endif else begin
-    fieldmjd = string(yanny_par(hdr,'fieldid'),format='(i5.5)') $
+    fieldmjd = field_to_string(yanny_par(hdr,'fieldid')) $
       + '-' + string(thismjd,format='(i5.5)') 
   endelse
   for i=0, n_elements(allseq.mjd)-1 do begin

pro/rm/spreduce1d_empca.pro

@@ -120,8 +120,9 @@ CPU, TPOOL_NTHREADS = 1
 
    ;----------
    ; Determine names of output files
-
-   platemjd = strmid(fileandpath(platefile), 8, 11)
+   platemjd=(strsplit(repstr(platefile,".fits",""), '-',/extract))[1:2]
+   platemjd=strjoin(platemjd, '-')
+   ;platemjd = strmid(fileandpath(platefile), 8, 11)
    if platemjd eq '15013-59165' or platemjd eq '15014-59165' then begin
       chop_data = [3600., 9000.]
       splog, 'Setting wavelength coverage as:'+string(chop_data[0])+' to '+string(chop_data[1])+' for plate-mjd '+platemjd
@@ -946,7 +947,7 @@ endif
    endif
 
    plottitle = string(zans[0].field, zans[0].mjd, $
-    format='("Flux-Calibration Errors Field=", i4, " MJD=", i5)')
+    format='("Flux-Calibration Errors Field=", i4 ," MJD=", i5)')
    qaplot_fcalibvec, objloglam, objflux, objivar, synflux, plugmap, zans, $
     plottitle=plottitle
 

pro/spec1d/conflist.pro

@@ -635,7 +635,7 @@ pro conflist, plist=plist, create=create, $
          'data'         , ' ', $
          'plots'        , ' ', $
          'fieldquality' , ' ', $
-         'platesn2'     , 0.0, $
+         'fieldsn2'     , 0.0, $
          'deredsn2'     , 0.0, $
          'qsurvey'      , 0L,  $
          'mjdlist'      , ' ', $
@@ -998,8 +998,13 @@ pro conflist, plist=plist, create=create, $
         hdr=hdrcomb,/anonymous))[0].mjd
       ;if jdtemp ge 59309 and run2d ne 'master' then begin
       ;if jdtemp ge 59309 then begin
-      plate_temp = (yanny_readone(combparfile[ifile], 'SPEXP', $
-        hdr=hdrcomb,/anonymous))[0].plateid
+      if keyword_set(plates) then begin
+        plate_temp = (yanny_readone(combparfile[ifile], 'SPEXP', $
+            hdr=hdrcomb,/anonymous))[0].plateid
+      endif else begin
+        plate_temp = (yanny_readone(combparfile[ifile], 'SPEXP', $
+            hdr=hdrcomb,/anonymous))[0].fieldid
+      endelse
       epoch_temp = (yanny_readone(combparfile[ifile], 'SPEXP', $
         hdr=hdrcomb,/anonymous))[0].epoch_combine
       plist[ifile].mapname=strtrim(string(plate_temp),2)+'-'+strtrim(string(epoch_temp),2)
@@ -1224,7 +1229,19 @@ pro conflist, plist=plist, create=create, $
         plist[ifile].epoch = cinfo.epoch
         plist[ifile].chunkhtml='<a href="https://platedesign.sdss.org/runs/'+cinfo.chunk+'/'+cinfo.chunk+'.html">'+cinfo.chunk+'</a>'
       endif else begin
-        splog, 'Empty or missing platePlans.par file'
+	if keyword_set(plates) or keyword_set(legacy) then begin
+          splog, 'Empty or missing platePlans.par file'
+	endif else begin
+	  splog, 'Empty or missing configPlans.par file'
+          fibermap='fibermap-'+strtrim(yanny_par(hdrp,'fieldid'),2)+'.fits'
+          fibermap=djs_filepath(fibermap, root_dir=topdir + '/' + run2d, subdir=field_to_string(yanny_par(hdrp,'fieldid')))
+          if FILE_TEST(fibermap) then begin
+              plughead=headfits(fibermap,EXTEN=1)
+              plist[ifile].racen = sxpar(plughead,'RACEN')
+              plist[ifile].deccen = sxpar(plughead,'DECCEN')
+              ;if strtrim(sxpar(plughead,'OBS'),2) EQ 'APO'
+          endif else splog, 'Empty or missing fibermap: '+fibermap
+	endelse
       endelse
 
       ;----------

pro/spec1d/fieldmerge.pro

@@ -106,7 +106,7 @@ pro fieldmerge1, field=field, mjd=mjd, except_tags1=except_tags1, $
    endif else begin
       outroot = ['spAll','spAllLine']
       if (keyword_set(field) and keyword_set(mjd)) then begin
-        outroot='spectra/full/'+strtrim(string(field),2)+'/'+strtrim(string(mjd),2)+'/'+outroot+'-'+strtrim(string(field),2)+'-'+strtrim(string(mjd),2)
+        outroot='spectra/full/'+field_to_string(field)+'/'+strtrim(string(mjd),2)+'/'+outroot+'-'+field_to_string(field)+'-'+strtrim(string(mjd),2)
       endif else begin
         if (keyword_set(run2d)) then outroot = outroot + '-' + repstr(run2d,'/','-')
       endelse
@@ -315,10 +315,11 @@ pro fieldmerge1, field=field, mjd=mjd, except_tags1=except_tags1, $
    for ifile=0L, nfile-1 do begin
       print, 'Reading ZANS file ',ifile+1, ' of ', nfile
       if keyword_set(legacy) or keyword_set(plates) then begin
-         field_plate=plist[ifile].field
+         field_plate=field_to_string(plist[ifile].field)
       endif else begin
-         field_plate=plist[ifile].field
+         field_plate=field_to_string(plist[ifile].field)
       endelse
+
       readspec, field_plate, mjd=plist[ifile].mjd, $
        run2d=strtrim(plist[ifile].run2d), run1d=strtrim(plist[ifile].run1d), $
        zans=zans, objhdr=objhdr, $  ;; zmanual=zmanual, 
@@ -475,9 +476,12 @@ pro fieldmerge1, field=field, mjd=mjd, except_tags1=except_tags1, $
       ; Get PRIMTARGET+SECTARGET with those values from
       ; the plug-map structure in spfield file.
       ; HJIM decoment the next three lines for the final version
-      outdat[indx].primtarget = plugmap.primtarget
-      outdat[indx].sectarget = plugmap.sectarget
-      outdat[indx].lambda_eff = plugmap.lambda_eff
+      if (tag_exist(plugmap,'primtarget')) then $
+        outdat[indx].primtarget = plugmap.primtarget
+      if (tag_exist(plugmap,'sectarget')) then $
+        outdat[indx].sectarget = plugmap.sectarget
+      if (tag_exist(plugmap,'lambda_eff')) then $
+        outdat[indx].lambda_eff = plugmap.lambda_eff
       if (tag_exist(plugmap,'zoffset')) then $
        outdat[indx].zoffset = plugmap.zoffset
       if (tag_exist(plugmap,'xfocal')) then $
@@ -636,7 +640,7 @@ pro fieldmerge1, field=field, mjd=mjd, except_tags1=except_tags1, $
                     '-' + string(plugmap[fid].catalogid,format='(i11.11)')+'.fits'
             endfor
           endif else begin
-            if not keyword_keyword_set(legacy) then begin
+            if not keyword_set(legacy) then begin
                 for fid = 0L, n_elements(zans)-1 do begin
                     healpix_dir_t[fid]=mwm_root + $
                         strtrim(string(healp[fid].healpixgrp),2) + '/' + $

pro/spec1d/plate_spec_image.pro

@@ -78,15 +78,20 @@ for i=0L, n_elements(zans)-1L do begin
     if keyword_set(legacy) then begin
        pmjdf= pmjd+'-'+string(f='(i4.4)', fiber)
     endif else begin
-       catalogid=plug[i].catalogid
-       if catalogid eq 0 then begin
-          pmjdf= pmjd+'-'+string(f='(i11.11)', fiber)
-       endif else begin
-         if plug[i].program.contains('offset', /FOLD_CASE ) then begin
-           pmjdf= pmjd+'-'+strtrim(string(catalogid),1)
+       if keyword_set(plates) then begin
+         catalogid=plug[i].catalogid
+         if catalogid eq 0 then begin
+            pmjdf= pmjd+'-'+string(f='(i11.11)', fiber)
          endif else begin
-           pmjdf= pmjd+'-'+string(f='(i11.11)', catalogid)
+           if plug[i].program.contains('offset', /FOLD_CASE ) then begin
+             pmjdf= pmjd+'-'+strtrim(string(catalogid),1)
+           endif else begin
+             pmjdf= pmjd+'-'+string(f='(i11.11)', catalogid)
+           endelse
          endelse
+       endif else begin
+         catalogid=plug[i].catalogid
+         pmjdf=pmjd+'-'+strtrim(string(catalogid),2)
        endelse
     endelse
     stamp='http://skyserver.sdss.org/dr16/SkyServerWS/ImgCutout/getjpeg?TaskName=Skyserver.Chart.Image&ra='+strtrim(string(f='(f40.5)', ra),2)+'&dec='+strtrim(string(f='(f40.5)', dec),2)+'&scale=0.1&width=512&height=512&opt=G&query=&Grid=on'

pro/spec1d/readspec.pro

@@ -166,8 +166,9 @@ pro readspec1, plate, rownums, mjd=mjd, flux=flux, flerr=flerr, invvar=invvar, $
  align=align, silent=silent, qread=qread, sdss=sdss, unsigned=unsigned, $
  legacy=legacy, plates=plates
 
+   platestr = field_to_string(plate)
    ;platestr = plate_to_string(plate)
-   platestr = string(plate, format='(i5.5)')
+;   platestr = string(plate, format='(i5.5)')
    if (NOT keyword_set(mjd)) then mjdstr = '*' $
     else mjdstr = string(mjd,format='(i5.5)')
    if (keyword_set(path)) then begin