def gridGalaxy(galaxy='IC0342', setup='13CO_C18O',
datadir='/lustre/pipeline/scratch/DEGAS/',
overwrite=True, release='QA1', edgetrim = 100,
basebuff = 64, plotTimeSeries=True, PostprocOnly=False,
scanblorder=11, posblorder=7, pipeversion=None,
**kwargs):
# Override automatic version; needed for development sometimes.
if pipeversion is None:
pipeversion = pkg_resources.get_distribution("degas").version
setup_dict = {'13CO_C18O':'13co_c18o',
'HCN_HCO+':'hcn_hcop',
'12CO':'12co'}
filelist = glob.glob(os.path.join(datadir,galaxy,setup,"*.fits"))
OutputDirectory = os.path.join(datadir,galaxy,"images")
if not os.access(OutputDirectory, os.W_OK):
try:
os.mkdir(OutputDirectory)
os.chdir(OutputDirectory)
except OSError:
raise
else:
os.chdir(OutputDirectory)
if '12CO' in setup:
filename = galaxy + '_' + setup + '_v{0}'.format(pipeversion)
maskfile= (datadir + '/masks/BOOLEAN_MASKS/' + galaxy
+ '.' + setup_dict[setup]
+ '.mask.fits')
if not PostprocOnly:
gbtpipe.griddata(filelist,
startChannel=edgetrim,
endChannel=1024-edgetrim,
outdir=OutputDirectory,
flagSpike=True, spikeThresh=3,
flagRMS=True, plotTimeSeries=plotTimeSeries,
flagRipple=True, rippleThresh=1.2,
pixPerBeam=4.0,
rmsThresh=1.1,
robust=False,
blorder=scanblorder,
plotsubdir='timeseries/',
windowStrategy='cubemask',
maskfile=maskfile,
outname=filename, **kwargs)
postprocess.cleansplit(filename + '.fits',
spectralSetup=setup,
HanningLoops=1,
spatialSmooth=1.3,
maskfile=maskfile,
blorder=posblorder,
**kwargs)
else:
filename = galaxy + '_' + setup + '_v{0}'.format(pipeversion)
maskfile= (datadir + '/masks/BOOLEAN_MASKS/' + galaxy
+ '.' + setup_dict[setup]
+ '.mask.fits')
if not PostprocOnly:
if os.path.exists(maskfile):
warnings.warn("Processing with mask {0}".format(maskfile))
gbtpipe.griddata(filelist,
startChannel=edgetrim,
endChannel=1024-edgetrim,
outdir=OutputDirectory,
flagSpike=True, spikeThresh=3,
flagRMS=True, plotTimeSeries=plotTimeSeries,
flagRipple=True, rippleThresh=1.2,
pixPerBeam=4.0,
rmsThresh=1.1,
robust=False,
blorder=scanblorder,
plotsubdir='timeseries/',
windowStrategy='cubemask',
maskfile=maskfile,
outname=filename, **kwargs)
else:
warnings.warn("Mask file not found. Proceeding to grid without mask file")
gbtpipe.griddata(filelist,
startChannel=edgetrim,
endChannel=1024-edgetrim,
outdir=OutputDirectory,
flagSpike=True, spikeThresh=3,
flagRMS=True, plotTimeSeries=plotTimeSeries,
flagRipple=True, rippleThresh=1.2,
pixPerBeam=4.0,
rmsThresh=1.1,
robust=False,
blorder=scanblorder,
plotsubdir='timeseries/',
outname=filename, **kwargs)
if os.path.exists(maskfile):
warnings.warn("Processing with mask {0}".format(maskfile))
postprocess.cleansplit(filename + '.fits',
spectralSetup=setup,
HanningLoops=1, blorder=posblorder,
spatialSmooth=1.3,
maskfile=maskfile,
**kwargs)
else:
warnings.warn("Processing without mask")
postprocess.cleansplit(filename + '.fits',
spectralSetup=setup,
HanningLoops=1, blorder=posblorder,
spatialSmooth=1.3,
**kwargs)
def gridGalaxy(galaxy='IC0342',
setup='13CO_C18O',
datadir='/lustre/pipeline/scratch/DEGAS/',
overwrite=True,
release='QA1',
edgetrim=100,
basebuff=64,
plotTimeSeries=True,
PostprocOnly=False,
**kwargs):
pipeversion = pkg_resources.get_distribution("degas").version
origDir = os.getcwd()
filelist = glob.glob(os.path.join(datadir, galaxy, setup, "*.fits"))
OutputDirectory = os.path.join(datadir, galaxy, "images")
if not os.access(OutputDirectory, os.W_OK):
try:
os.mkdir(OutputDirectory)
except OSError:
raise
os.chdir(OutputDirectory)
if '12CO' in setup:
filename = galaxy + '_' + setup + '_v{0}'.format(pipeversion)
if not PostprocOnly:
gbtpipe.griddata(filelist,
startChannel=edgetrim,
endChannel=1024 - edgetrim,
baselineRegion=[
slice(edgetrim, edgetrim + basebuff, 1),
slice(1024 - edgetrim - basebuff,
1024 - basebuff, 1)
],
outdir=OutputDirectory,
flagRMS=True,
plotTimeSeries=plotTimeSeries,
flagRipple=True,
pixPerBeam=4.0,
plotsubdir='timeseries',
outname=filename,
**kwargs)
postprocess.cleansplit(os.path.join(OutputDirectory,
filename + '.fits'),
spectralSetup=setup,
HanningLoops=1,
spatialSmooth=1.3,
**kwargs)
else:
filename = galaxy + '_' + setup + '_v{0}'.format(pipeversion)
if not PostprocOnly:
gbtpipe.griddata(
filelist,
startChannel=edgetrim,
endChannel=1024 - edgetrim,
# do whole region. May not work for
# strong lines like 12CO.
baselineRegion=[slice(edgetrim, 1024 - edgetrim, 1)],
#baselineRegion = [slice(edgetrim,
# edgetrim+basebuff,1),
# slice(448,576,1),
# slice(1024-edgetrim-basebuff,
# 1024-edgetrim,1)],
outdir=OutputDirectory,
blorder=5,
flagSpike=True,
spikeThresh=3.0,
flagRMS=True,
rippleThresh=2.0,
plotTimeSeries=plotTimeSeries,
flagRipple=True,
pixPerBeam=4.0,
plotsubdir='timeseries',
outname=filename,
**kwargs)
postprocess.cleansplit(os.path.join(OutputDirectory,
filename + '.fits'),
spectralSetup=setup,
HanningLoops=1,
spatialSmooth=1.3,
**kwargs)
os.chdir(origDir)
def gridGalaxy(galaxy='IC0342',
setup='13CO_C18O',
datadir='/lustre/pipeline/scratch/DEGAS/',
overwrite=True,
release='QA1',
edgetrim=100,
basebuff=64,
plotTimeSeries=True,
PostprocOnly=False,
**kwargs):
pipeversion = pkg_resources.get_distribution("degas").version
# Note that we also use a few channels in the middle.
filelist = glob.glob(datadir + galaxy + '/' + setup + '/*fits')
OutputDirectory = datadir + galaxy + '/images/'
if not os.access(OutputDirectory, os.W_OK):
try:
os.mkdir(OutputDirectory)
os.chdir(OutputDirectory)
except OSError:
raise
if '12CO' in setup:
filename = galaxy + '_' + setup + '_v{0}'.format(pipeversion)
if not PostprocOnly:
gbtpipe.griddata(filelist,
startChannel=edgetrim,
endChannel=1024 - edgetrim,
baselineRegion=[
slice(edgetrim, edgetrim + basebuff, 1),
slice(1024 - edgetrim - basebuff,
1024 - basebuff, 1)
],
outdir=OutputDirectory,
flagRMS=True,
plotTimeSeries=plotTimeSeries,
flagRipple=True,
pixPerBeam=4.0,
plotsubdir='timeseries',
outname=filename,
**kwargs)
postprocess.cleansplit(OutputDirectory + filename + '.fits',
spectralSetup=setup,
HanningLoops=1,
spatialSmooth=1.3,
**kwargs)
else:
filename = galaxy + '_' + setup + '_v{0}'.format(pipeversion)
if not PostprocOnly:
gbtpipe.griddata(filelist,
startChannel=edgetrim,
endChannel=1024 - edgetrim,
baselineRegion=[
slice(edgetrim, edgetrim + basebuff, 1),
slice(448, 576, 1),
slice(1024 - edgetrim - basebuff,
1024 - basebuff, 1)
],
outdir=OutputDirectory,
blorder=5,
flagRMS=True,
plotTimeSeries=plotTimeSeries,
flagRipple=True,
pixPerBeam=4.0,
plotsubdir='timeseries',
outname=filename,
**kwargs)
postprocess.cleansplit(OutputDirectory + filename + '.fits',
spectralSetup=setup,
HanningLoops=1,
spatialSmooth=1.3,
**kwargs)
filelist = glob.glob('testdir/*fits')
# Trim 100 channels from the end of each spectrum
# (which is 1024 channels long, in total)
edgetrim = 100
# Use a 64 channel window for baselining on each end of the spectrum.
basebuff = 64
# Note that we also use a few channels in the middle.
# Grid them dataz.
gbtpipe.griddata(filelist,
startChannel=edgetrim,
endChannel=1024 - edgetrim,
baselineRegion=[
slice(edgetrim, edgetrim + basebuff, 1),
slice(448, 576, 1),
slice(1024 - edgetrim - basebuff, 1024 - basebuff, 1)
],
flagRMS=True,
flagRipple=True,
pixPerBeam=4.0)
# Postprocess the data
degas.cleansplit('ngc1068.fits')
# Now, we have a calibrated cube. Let's make pictures.
mpl.rcParams['font.family'] = 'serif'
mpl.rcParams['font.serif'] = 'FreeSerif'
hcn = SpectralCube.read('NGC1068_HCN_rebase3_smooth1.fits')