#
#hifidemo_FitHifiFringe_apr2010.py: instructions to run FitHifiFringe
#    Task.
#
# v0.0 ACAB 02/Dec/2009: created for Caltech group demo
# v0.1 ACAB 07/Dec/2009: adapted for Madrid DPWS Dec 2009
# v0.2 ACAB 07/Mar/2010: adapted to HIPE 3.0, with a different example
# v0.3 ACAB 03/Apr/2010: adapted to HIPE 2.6 for ESTEC DPWS Apr 2010
#

#load band 4B SScan LChop observation 
#from ~/.hcss/lstore/
#It  has a short-period standing wave in some scans,
#and a long-period one in others.
obs=getObservation("1342180554",poolName="pool_1342180554")

storage= ProductStorage(poolname)
query=herschel.ia.pal.query.AttribQuery(herschel.ia.obs.ObservationContext,"p","1")
result = storage.select(query)
obs = storage.load(result[0].urn).product

#run fitHifiFringe using the GUI....
#This will process all SpectrumDataSets. It generates 2 plots
#per scan, so don't forget to set plot=0 if the observation
#contains many scans....!
#note that if one runs the GUI, the input ObservationContext is overwritten,
#so for this demo, read it again
obs = storage.load(result[0].urn).product

#Or work on DataSet level. 
#Select  a level 2 spectrumdataset
sds_lev2=obs.refs["level2"].product.refs["WBS-H-USB"].product.refs["60"].product["dataset"]

#Run fitHifiFringe using the GUI....
#Drag sds_lev2 to the sds1 button.

#or on the command line, using default settings
fhf = FitHifiFringe()
sds_lev2_out = fhf(sds1=sds_lev2,nfringes=1,plot=1,start_period=20,end_period=3000.,typical_period=150.,averscan=False,doglue=True)

#Notes on previous fit:
#
# -the mask (orange line) 'detects' lines that do not seem to be present
#  This is not seriously affecting the fit, as the masked regions are small.
#
# -the baseline (blue line) may not be reasonable, as long-period standing waves
#  might be present. Baseline curvatures can be controlled with the 'typical_period'
#  parameter. Higher values mean less curvature. In the following example,
#  midcycle was increased to 650 MHz, and as one can see the SW baseline is 
#  much smoother and any deviations from that will be fitted with sine waves

fhf = FitHifiFringe()
sds_lev2_out = fhf(sds1=sds_lev2,nfringes=1,plot=1,start_period=50,end_period=3000.,typical_period=650.,averscan=False,doglue=True)

#In case the period vs. Chi^2 plot shows multiple peaks, increase
#the number of standing waves to fit accordingly.

fhf = FitHifiFringe()
sds_lev2_out = fhf(sds1=sds_lev2,nfringes=2,plot=1,start_period=50,end_period=3000.,typical_period=650.,averscan=False,doglue=True)

#if a line was not fully masked, add mask by hand
#note that not the entire region is masked--> solved in HIPE 3
fhf = FitHifiFringe()
sds_lev2_out = fhf(sds1=sds_lev2,nfringes=2,plot=1,start_period=50,end_period=3000.,typical_period=650.,averscan=False,doglue=True,usermask=[(1113.,1114.)])


#If you know pretty well the period, narrow the search range
#(speeds up processing)

fhf = FitHifiFringe()
sds_lev2_out = fhf(sds1=sds_lev2,nfringes=2,plot=1,start_period=80,end_period=110.,typical_period=650.,averscan=False,doglue=True)

#If you like to work on WBS sub-bands.
#Useful if there are strong WBS sub-band jumps, or getting better
#solutions for narrow lines.

sds_lev2_out = fhf(sds1=sds_lev2,nfringes=2,plot=1,start_period=80,end_period=110.,typical_period=650.,averscan=False,doglue=False)