;+
; :Description:
;    Extract CoMP Intensity image from closest to line center.
;
; :Params:
;   date_dir        day of year to process, in YYYYMMDD format
;   wave_type       name of line for set of wavelengths
;
;
; :Author: sitongia
;-
pro extract_intensity, date_dir, wave_type

  common comp_paths, bias_dir, flat_dir, mask_dir, inventory_basedir, binary_dir, $
    defered_file, hot_file, $
    ldm_basedir, usb_basedir, raw_synoptic_basedir, raw_usb_basedir, process_synoptic_basedir, process_usb_basedir, $
    archive_dir, movie_dir, fullres_dir, log_dir

  common comp_constants, nx, ny, $
    center1074, center1079, center1083, $
    stokes, n_stokes, $
    debug, logFileUnit

;; ADDED BY JAMES MICHAELIS
;; ADD COMMON BLOCKS FOR EACH LOGGER
  common logBlock_artifact,         Counter_1, NameRegistry_1, IDRegistry_1, LUN_1
  common logBlock_process,          Counter_2, NameRegistry_2, IDRegistry_2, LUN_2
  common logBlock_activity,         Counter_3, NameRegistry_3, IDRegistry_3, LUN_3
  common logBlock_observation,      Counter_4, NameRegistry_4, IDRegistry_4, LUN_4
  common logBlock_entity,           Counter_5, NameRegistry_5, IDRegistry_5, LUN_5
  common logBlock_dataset,          Counter_6, NameRegistry_6, IDRegistry_6, LUN_6
  common logBlock_qualityAssertion, Counter_7, NameRegistry_7, IDRegistry_7, LUN_7
  common logBlock_qualityEvidence,  Counter_8, NameRegistry_8, IDRegistry_8, LUN_8
  common logBlock_fitsHeader,       Counter_9, LUN_9    
;; END

;; ADDED BY JAMES MICHAELIS
;; RESTORE VARIABLE STATE FROM PRIOR EXECUTION (allows logBlock values to be carried over)
  Restore,'CoMP_commonBlocks.sav'
;; END


  COMPILE_OPT IDL2
  
  ; Configure
  comp_paths
  comp_initialize, date_dir
  
  printf, logFileUnit, 'extract_intensity'
  
  ; Check keywords
  uselist = 0
  if n_elements(list_file) eq 1 then uselist = 1
  
  process_dir = process_usb_basedir + date_dir
  
  cd, process_dir
  
  ; Line center
  case wave_type of
    '1074' : begin
      lineCenter = center1074
      ScaleMax = 20.0
      gifMin = 0.0
      gifMax = 5.0
    end
    '1079' : begin
      lineCenter = center1079
      ScaleMax = 20.0
      gifMin = 0
      gifMax = 3.5
    end
    '1083' : begin
      lineCenter = center1083
      ScaleMax = 200000.0
      gifMin = 0
      gifMax = 200000.0
    end
  endcase
  
  ; Read in the field mask
  fits_read, mask_dir+'fieldmask1.fits', fieldmask1
  fits_read, mask_dir+'fieldmask2.fits', fieldmask2
  
  ; The FITS image files
  files = file_search('*.comp.' + wave_type + '.fts.gz', COUNT=count)
  
  for filesIndex = 0L, count-1 do begin
    if debug eq 1 then print, "File " + files[filesIndex] + " " + systime()
    
    fits_read, files[filesIndex], data, primary_header, exten_no=0
    fits_read, files[filesIndex], data, header, exten_no=1

    extract_intensity_cube, files[filesIndex], images, waves
    
    ; Determine index of wavelength closest to line center
    waveDiff = abs(waves - lineCenter)
    lineCenterIndex = where(waveDiff eq min(waveDiff))
    lineCenterIndex = lineCenterIndex[0]
    if debug eq 1 then print, "Using wavelength ", waves[lineCenterIndex]
    
    ; Intensity simple by extracting image near line center
    intensity = images[*, *, lineCenterIndex]
    ; Clip
    ;intensity = 0 > intensity < ScaleMax ; larger of 0 and image, then smaller of image and ScaleMax.
    ; Set the processing level
    sxaddpar,primary_header,'LEVEL   ','L1'
    ; Write files
    sxaddpar, primary_header, 'METHOD  ', 'EXTRACT', ' Method used: extract filtergram at line center'
    fits_write, strmid(files[filesIndex],0,15) + '.comp.' + wave_type+'.intensity.fts', intensity, primary_header    
  endfor

  ; Compress files
  if debug eq 1 then print, "Compressing FITS files."
  spawn, 'gzip -f *.comp.' + wave_type + '.intensity.fts'
    
  ; Make GIF files from Intensity
  files = file_search('*.comp.' + wave_type + '.intensity.fts.gz', COUNT=count)
  if debug eq 1 then print, "Make GIFs"
  for filesIndex = 0L, count-1 do begin   
    ; Make GIF from I file
    make_gif, files[filesIndex], nx, 'Intensity', wave_type, gifMin, gifMax
    
;; ADDED BY JAMES MICHAELIS
;; ADD LOG STATEMENTS 
    newNameFITS = strmid(files[filesIndex],0,15) + '.comp.' + wave_type+'.intensity.fts'  
    newNameGIF = strmid(files[filesIndex],0,15) + '.comp.' + wave_type+'.intensity.gif'  
    newName = strmid(files[filesIndex],0,15)+'.comp.'+wave_type+'.fts.gz'
    
    ID_Process_1 = log_process('Extract Intensity','Extract CoMP Intensity image from closest to line center.', $    
    'extract_intensity.pro','https://subversion.ucar.edu/HAO/MLSO/CoMP/Pipeline/extract_intensity.pro','3798','Interactive Data Language (IDL)','Steve Tomczyk',[loggedID('artifact',name)],[],[])
    ID_Artifact_1 = log_artifact(newNameFITS,'','FITS','http://path/to/FITS/' + newNameFITS,[],newNameFITS)
    ID_Artifact_2 = log_artifact(newNameGIF,'','GIF','http://path/to/GIF/' + newNameGIF,[],newNameGIF)
    ID_Entity_1 = log_entity(newName,'CoMP intensity record processed by extract intensity routine',[ID_Dataset_1],[ID_Artifact_1, ID_Artifact_2])
    ID_FitsHeader_1 = log_fitsheader(newNameFITS, [ID_Artifact_1])
    print, ID_Entity_1
    ID_Observation_1 = log_observation('CoMP intensity observation','CoMP intensity observation','StokesIntensityObservation','2011-06-29T21:49:38','2011-06-29T21:49:38','StokesParameterI','Stokes Intensity','SunCorona','Sun Corona',[ID_Entity_1])
;; END
    
    
  endfor
  
  printf, logFileUnit, "done ", systime()
  free_lun, logFileUnit
  if debug eq 1 then print, "Done all ", systime()

;; ADDED BY JAMES MICHAELIS  
  stop_logger ; closes LUNs for each log
  Save, /ALL, filename='CoMP_commonBlocks.sav' ; save all variables (including common blocks) to file to be opened later.  this preserves logging blocks for upcoming IDL scripts
;; END

end

; Main program for testing

extract_intensity, '20110504', '1083'
end