redu.ima

! Reduction pipeline for COMPASS line and continuum observations

begin procedure redu_init

    ! Define user parameters
    
    if .not.exist(redu) then

	define structure redu /global
	
	define char*16 redu%basename /global
	define char*8 redu%setting /global
	define char*8 redu%spws[4] /global
	define char*16 redu%subdir /global

	define integer redu%drop_edge_channels /global
	define real redu%uv_preview_clip /global
	define integer redu%uv_preview_smooth /global
	define integer redu%uv_preview_taper /global
	define logical redu%uv_preview_save_plot /global
	define real redu%map_robust /global
	define real redu%map_size[2] /global
	define real redu%map_cell[2] /global
	define real redu%primary_truncate /global
	
	define logical redu%extract_continuum /global
	define logical redu%self_calibrate /global
	define logical redu%uv_restore /global
	define logical redu%jvm_correction /global
	define logical redu%primary_beam_correction /global
	define logical redu%subtract_baseline /global
	define logical redu%delete_intermediate_files /global
	define logical redu%interactive /global

	let redu%drop_edge_channels 5
	let redu%spws 25 27 29 31
	let redu%subdir ""
	let redu%uv_preview_clip 3
	let redu%uv_preview_smooth 3
	let redu%uv_preview_taper 3
	let redu%uv_preview_save_plot .false.
	let redu%map_robust 1
	let redu%map_size 0 0
	let redu%map_cell 0 0
	let redu%primary_truncate .2

	let redu%extract_continuum .true.
	let redu%self_calibrate .true.
	let redu%uv_restore .true.
	let redu%jvm_correction .false.
	let redu%primary_beam_correction .false.
	let redu%subtract_baseline .false.
	let redu%delete_intermediate_files .true.
	let redu%interactive .false.
	
    endif
    
end procedure redu_init	


begin procedure redu_run

    ! Run the reduction pipeline

    define char*32 datadir
    define char*16 image_ext

    let datadir "../../data/"
    let map_robust redu%map_robust
    let map_size redu%map_size
    let map_cell redu%map_cell
    
    for spw /in redu%spws

	say 'ANSI%YELLOW'"Reducing data for "'redu%basename'", setting "'redu%setting'", spectral window "'spw''ANSI%NONE'
	let name 'redu%basename'"-set"'redu%setting'"-spw"'spw'
	
	! Convert the UVFITS files to UVT
	sic mkdir 'datadir'"/reduced/"'redu%subdir'"/"'redu%basename'"/uvtables/"
	@ fits_to_uvt 'datadir'"/calibrated/uvfits/"'name'".uvfits" 'datadir'"/reduced/"'redu%subdir'"/"'redu%basename'"/uvtables/"'name'".uvt"
	let name 'datadir'"/reduced/"'redu%subdir'"/"'redu%basename'"/uvtables/"'name'
	read uv 'name' /range redu%drop_edge_channels -1*redu%drop_edge_channels CHANNEL
	if redu%interactive pause 'ANSI%YELLOW'"UV table loaded. You can check the result with UV_STAT, or type C to continue."'ANSI%NONE'
	
	! Self-calibration
	if redu%self_calibrate then
	    let self_display .false.
	    let self_flag .true.
	    let self_times 10 10 /resize
	    symbol stop continue ! avoid pauses at each self-calibration loop
	    selfcal phase
	    symbol stop pause
	    if redu%interactive pause 'ANSI%YELLOW'"Done with the self-calibration. You can adjust the self-calibration parameters, or type C to continue."'ANSI%NONE'
	    selfcal apply
	endif
	
	! Time-average
	uv_time
	
	! Save the UV table
	write uv 'name'
	
	! Create a UV table for the continuum
	if redu%extract_continuum then
	    uv_preview clip 'redu%uv_preview_clip' smooth 'redu%uv_preview_smooth' taper 'redu%uv_preview_taper'
	    if redu%uv_preview_save_plot hardcopy 'name'"-uv_preview.png" /device png /overwrite
	    if redu%interactive pause 'ANSI%YELLOW'"Done with the line-free channels identification. You can check that the results are reasonable, or type C to continue."'ANSI%NONE'
	    uv_filter
	    uv_compress /continuum
	    let name 'datadir'"/reduced/"'redu%subdir'"/"'redu%basename'"/uvtables/"'redu%basename'"-set"'redu%setting'"-spw"'spw'"-cont"
	    write uv 'name'
	endif
	
	! Make a continuum map and clean it
	if redu%extract_continuum then
	    uv_map /continuum
	    clean
	    if redu%uv_restore then
		if redu%jvm_correction fit /jvm
		uv_restore
	    endif
	    if redu%interactive pause 'ANSI%YELLOW'"Done with the imaging of the continuum. You can check it with the VIEW command, or type C to continue."'ANSI%NONE'
	    if redu%primary_beam_correction then
		primary /truncate redu%primary_truncate
		if redu%interactive pause 'ANSI%YELLOW'"Done with the primary beam correction. You can check it with the VIEW command, or type C to continue."'ANSI%NONE'
		stat clean /noise sky%rms ! store the noise computed from the clean image
	    else
		stat clean
	    endif
	    sic mkdir 'datadir'"/reduced/"'redu%subdir'"/"'redu%basename'"/cubes/"
	    let name 'datadir'"/reduced/"'redu%subdir'"/"'redu%basename'"/cubes/"'redu%basename'"-set"'redu%setting'"-spw"'spw'"-cont"
	    if redu%primary_beam_correction then
		write sky 'name'
	    else
		write clean 'name'
	    endif
	endif

	! Make a UV table for the lines
	let name 'datadir'"/reduced/"'redu%subdir'"/"'redu%basename'"/uvtables/"'redu%basename'"-set"'redu%setting'"-spw"'spw'
	sic rename 'name'".uvt" 'name'"-lines.uvt"
	let name 'name'"-lines"
	read uv 'name'
	if redu%subtract_baseline then
	    uv_preview clip 'redu%uv_preview_clip' smooth 'redu%uv_preview_smooth' taper 'redu%uv_preview_taper'
	    uv_baseline ! substract a baseline
	    write uv 'name'
	endif

	! Make a line datacube cube and clean it
	uv_map
	clean
	if redu%uv_restore then
	    if redu%jvm_correction fit /jvm
	    uv_restore
	endif
	if redu%interactive pause 'ANSI%YELLOW'"Done with the line imaging. You can check it with the VIEW command, or type C to continue."'ANSI%NONE'
	if redu%primary_beam_correction then
	    primary /truncate redu%primary_truncate
	    stat clean /noise sky%rms
	else
	    stat clean
	endif
	sic mkdir 'datadir'"/reduced/"'redu%subdir'"/"'redu%basename'"/cubes/"
	let name 'datadir'"/reduced/"'redu%subdir'"/"'redu%basename'"/cubes/"'redu%basename'"-set"'redu%setting'"-spw"'spw'"-lines"
	if redu%primary_beam_correction then
	    write sky 'name'
	    let image_ext "lmv-sky"
	else
	    write clean 'name'
	    let image_ext "lmv-clean"
	endif
	
	! Export the continuum UV table and image to FITS
	if redu%extract_continuum then
	    let name 'datadir'"/reduced/"'redu%subdir'"/"'redu%basename'"/uvtables/"'redu%basename'"-set"'redu%setting'"-spw"'spw'"-cont"
	    fits 'name'.uvfits from 'name'.uvt /over
	    let name 'datadir'"/reduced/"'redu%subdir'"/"'redu%basename'"/cubes/"'redu%basename'"-set"'redu%setting'"-spw"'spw'"-cont"
	    fits 'name'.fits from 'name'.'image_ext' /over
	endif
	
	! Export the line UV table and datacube to FITS
	let name 'datadir'"/reduced/"'redu%subdir'"/"'redu%basename'"/uvtables/"'redu%basename'"-set"'redu%setting'"-spw"'spw'"-lines"
	fits 'name'.uvfits from 'name'.uvt /over
	let name 'datadir'"/reduced/"'redu%subdir'"/"'redu%basename'"/cubes/"'redu%basename'"-set"'redu%setting'"-spw"'spw'"-lines"
	fits 'name'.fits from 'name'.'image_ext' /over

	! Remove intermediate files
	if redu%delete_intermediate_files then
	    let name 'datadir'"/reduced/"'redu%subdir'"/"'redu%basename'"/uvtables/"'redu%basename'"-set"'redu%setting'"-spw"'spw'
	    sic delete 'name'"-cont.uvt"
	    sic delete 'name'"-lines.uvt"
	    let name 'datadir'"/reduced/"'redu%subdir'"/"'redu%basename'"/cubes/"'redu%basename'"-set"'redu%setting'"-spw"'spw'
	    sic delete 'name'"-cont."'image_ext'
	    sic delete 'name'"-lines."'image_ext'
	endif
    next

    say 'ANSI%YELLOW'"All done."'ANSI%NONE'
    
end procedure redu_run


begin procedure redu_cleanup

    ! Cleanup files and variables
    
    sic delete selfcal-PHASE.last
    sic delete selfcal-PHASE.last~
    sic delete selfcal.tmp
    sic delete test.gdf
    delete /var redu

end procedure redu_cleanup


! Main program

if "x&1".eq."xinit" then
    @ redu_init
else if "x&1".eq."xrun" then
    @ redu_run
else if "x&1".eq."xclean" then
    @ redu_cleanup
else
    message e redu "Usage: redu COMMAND"
    return base
endif