## I-TRAIN #1 Imaging with the ALMA Pipeline
## D Tafoya, LT Maud, E Moravec, MC Toribio
## contact@nordic-alma.se
## This file provides general commands to follow the tutorial. Most lines have been commented out. Use at your convenience.
## References: https://casaguides.nrao.edu/index.php/ALMA_Imaging_Pipeline_Reprocessing

##=================================================
##Preparations
##Extract your tar file
#tar -xvf 2018.1.01201.S.PLtutorial.tar.gz

##Descend the folder tree:
#cd 2018.1.01201.S/science_goal.uid___A001_X133d_X2c85/group.uid___A001_X133d_X2c86/member.uid___A001_X133d_X2c8b/calibrated/working



#==================================================
##Launch CASA from your terminal:
#casapy -- pipeline  # depends on your alias setup




import glob
import os

##Set up environment for the pipeline:
__rethrow_casa_exceptions = True
context = h_init()

## Delete uid*_target.ms and flagversions if it exists
os.system('rm -rf uid*_target.ms')
os.system('rm -rf uid*_target.ms.flagversions')


##List all MS in folder:
#MyVis=glob.glob('*ms')


##Imaging Pipeline steps:
try:
    #hifa_importdata(vis=MyVis,dbservice=False)
    
    #hif_mstransform(pipelinemode="automatic")
    
    ##OPTIONAL: If you want to use existing target flags, run the next line:
    #os.system('cp ../../calibration/*.flagtargetstemplate.txt ./*.flagtargetstemplate.txt)
    #hifa_flagtargets(pipelinemode="automatic")

    ##Calculate effective beams and theoretical noise for different robust parameters before imaging:    
    #hifa_imageprecheck(pipelinemode="automatic")
    
    ##Generate image parameters:
    #hif_makeimlist(specmode='mfs')

    ##Continuum
    ##OPTIONAL: If you want to use the existing continuum selection, run the next line:
    #os.system('cp ../../calibration/cont.dat ./cont.dat')
    #hif_findcont(pipelinemode="automatic")  ##Finds continuum
    #hif_uvcontfit(pipelinemode="automatic") ##Fits continuum
    #hif_uvcontsub(pipelinemode="automatic") ##Subtracts continuum

    ##Imaging
    #hif_makeimages(pipelinemode="automatic")
    #hif_makeimlist(specmode='cont')
    #hif_makeimages(pipelinemode="automatic")
    #hif_makeimlist(specmode='cube')
    #hif_makeimages(pipelinemode="automatic")

    #Export images to FITS
    #hifa_exportdata(imaging_products_only=True)

finally:
    #Save pipeline environment: 
    h_save()