def run(self):
""" The run method creates the BDP.
Parameters
----------
None
Returns
-------
None
"""
dt = utils.Dtime("ContinuumSub") # tagging time
self._summary = {} # an ADMIT summary will be created here
contsub = self.getkey("contsub")
pad = self.getkey("pad")
fitorder = self.getkey("fitorder")
# x.im -> x.cim + x.lim
# b1 = input spw BDP
# b1a = optional input {Segment,Line}List
# b1b = optional input Cont Map (now deprecated)
# b2 = output line cube
# b3 = output cont map
b1 = self._bdp_in[0]
f1 = b1.getimagefile(bt.CASA)
b1a = self._bdp_in[1]
# b1b = self._bdp_in[2]
b1b = None # do not allow continuum maps to be input
f2 = self.mkext(f1, 'lim')
f3 = self.mkext(f1, 'cim')
f3a = self.mkext(f1, 'cim3d') # temporary cube name, map is needed
b2 = SpwCube_BDP(f2)
b3 = Image_BDP(f3)
self.addoutput(b2)
self.addoutput(b3)
taskinit.ia.open(self.dir(f1))
s = taskinit.ia.summary()
nchan = s['shape'][
2] # ingest has guarenteed this to the spectral axis
if b1a != None: # if a LineList was given, use that
if len(b1a.table) > 0:
# this section of code actually works for len(ch0)==0 as well
#
ch0 = b1a.table.getFullColumnByName("startchan")
ch1 = b1a.table.getFullColumnByName("endchan")
if pad != 0: # can widen or narrow the segments
if pad > 0:
logging.info("pad=%d to widen the segments" % pad)
else:
logging.info("pad=%d to narrow the segments" % pad)
ch0 = np.where(ch0 - pad < 0, 0, ch0 - pad)
ch1 = np.where(ch1 + pad >= nchan, nchan - 1, ch1 + pad)
s = Segments(ch0, ch1, nchan=nchan)
ch = s.getchannels(
True) # take the complement of lines as the continuum
else:
ch = range(
nchan
) # no lines? take everything as continuum (probably bad)
logging.warning(
"All channels taken as continuum. Are you sure?")
elif len(contsub) > 0: # else if contsub[] was supplied manually
s = Segments(contsub, nchan=nchan)
ch = s.getchannels()
else:
raise Exception, "No contsub= or input LineList given"
if len(ch) > 0:
taskinit.ia.open(self.dir(f1))
taskinit.ia.continuumsub(outline=self.dir(f2),
outcont=self.dir(f3a),
channels=ch,
fitorder=fitorder)
taskinit.ia.close()
dt.tag("continuumsub")
casa.immoments(
self.dir(f3a), -1,
outfile=self.dir(f3)) # mean of the continuum cube (f3a)
utils.remove(self.dir(f3a)) # is the continuum map (f3)
dt.tag("immoments")
if b1b != None:
# this option is now deprecated (see above, by setting b1b = None), no user option allowed
# there is likely a mis-match in the beam, given how they are produced. So it's safer to
# remove this here, and force the flow to smooth manually
print "Adding back in a continuum map"
f1b = b1b.getimagefile(bt.CASA)
f1c = self.mkext(f1, 'sum')
# @todo notice we are not checking for conforming mapsize and WCS
# and let CASA fail out if we've been bad.
casa.immath([self.dir(f3), self.dir(f1b)], 'evalexpr',
self.dir(f1c), 'IM0+IM1')
utils.rename(self.dir(f1c), self.dir(f3))
dt.tag("immath")
else:
raise Exception, "No channels left to determine continuum. pad=%d too large?" % pad
# regression
rdata = casautil.getdata(self.dir(f3)).data
logging.regression("CSUB: %f %f" % (rdata.min(), rdata.max()))
# Create two output images for html and their thumbnails, too
implot = ImPlot(ptype=self._plot_type,
pmode=self._plot_mode,
abspath=self.dir())
implot.plotter(rasterfile=f3, figname=f3, colorwedge=True)
figname = implot.getFigure(figno=implot.figno, relative=True)
thumbname = implot.getThumbnail(figno=implot.figno, relative=True)
b2.setkey("image", Image(images={bt.CASA: f2}))
b3.setkey("image", Image(images={bt.CASA: f3, bt.PNG: figname}))
dt.tag("implot")
if len(ch) > 0:
taskargs = "pad=%d fitorder=%d contsub=%s" % (pad, fitorder,
str(contsub))
imcaption = "Continuum map"
self._summary["continuumsub"] = SummaryEntry(
[figname, thumbname, imcaption], "ContinuumSub_AT",
self.id(True), taskargs)
dt.tag("done")
dt.end()
]
###############
#### input ####
###############
rms_val = 2.3e-2 #rms from casa viewer
sigma = 2.5
infile = 'data/HZ7_Centered.fits'
emissionChannels = '51~75' #channels from casa viewer
###########################################################
#### Option 1: Using the includpix to make moment maps ####
###########################################################
casa.immoments(axis='spec',
imagename=infile,
moments=[0, 1, 2],
outfile='HZ7_mom_includepix',
includepix=[sigma * rms_val, 100],
chans=emissionChannels)
######################################################################################################
#### Option 2: Making a mask from the -1 map and choosing everything above 0.0001 Janskys as real ####
######################################################################################################
#using a mask created by collapsing the line in casaviewer. Here I manually select that everything above 0.1 mJy is real.
casa.immoments(axis='spec',
imagename=infile,
moments=[-1],
outfile='HZ7_avg',
chans=emissionChannels) # make the HZ7_avg file
casa.immoments(axis='spec',
imagename='HZ7_mom_includepix',
moments=[0, 1, 2],
def run(self):
""" The run method creates the BDP
Parameters
----------
None
Returns
-------
None
"""
dt = utils.Dtime("CubeSum") # tagging time
self._summary = {} # an ADMIT summary will be created here
numsigma = self.getkey("numsigma") # get the input keys
sigma = self.getkey("sigma")
use_lines = self.getkey("linesum")
pad = self.getkey("pad")
b1 = self._bdp_in[0] # spw image cube
b1a = self._bdp_in[1] # cubestats (optional)
b1b = self._bdp_in[2] # linelist (optional)
f1 = b1.getimagefile(bt.CASA)
taskinit.ia.open(self.dir(f1))
s = taskinit.ia.summary()
nchan = s['shape'][2]
if b1b != None:
ch0 = b1b.table.getFullColumnByName("startchan")
ch1 = b1b.table.getFullColumnByName("endchan")
s = Segments(ch0,ch1,nchan=nchan)
# @todo something isn't merging here as i would have expected,
# e.g. test0.fits [(16, 32), (16, 30), (16, 29)]
if pad > 0:
for (c0,c1) in s.getsegmentsastuples():
s.append([c0-pad,c0])
s.append([c1,c1+pad])
s.merge()
s.recalcmask()
# print "PJT segments:",s.getsegmentsastuples()
ns = len(s.getsegmentsastuples())
chans = s.chans(not use_lines)
if use_lines:
msum = s.getmask()
else:
msum = 1 - s.getmask()
logging.info("Read %d segments" % ns)
# print "chans",chans
# print "msum",msum
# from a deprecated keyword, but kept here to pre-smooth the spectrum before clipping
# examples are: ['boxcar',3] ['gaussian',7] ['hanning',5]
smooth= []
sig_const = False # figure out if sigma is taken as constant in the cube
if b1a == None: # if no 2nd BDP was given, sigma needs to be specified
if sigma <= 0.0:
raise Exception,"Neither user-supplied sigma nor CubeStats_BDP input given. One is required."
else:
sig_const = True # and is constant
else:
if sigma > 0:
sigma = b1a.get("sigma")
sig_const = True
if sig_const:
logging.info("Using constant sigma = %f" % sigma)
else:
logging.info("Using varying sigma per plane")
infile = b1.getimagefile(bt.CASA) # ADMIT filename of the image (cube)
bdp_name = self.mkext(infile,'csm') # morph to the new output name with replaced extension 'csm'
image_out = self.dir(bdp_name) # absolute filename
args = {"imagename" : self.dir(infile)} # assemble arguments for immoments()
args["moments"] = 0 # only need moments=0 (or [0] is ok as well)
args["outfile"] = image_out # note full pathname
dt.tag("start")
if sig_const:
args["excludepix"] = [-numsigma*sigma, numsigma*sigma] # single global sigma
if b1b != None:
# print "PJT: ",chans
args["chans"] = chans
else:
# @todo in this section bad channels can cause a fully masked cubesum = bad
# cubestats input
sigma_array = b1a.table.getColumnByName("sigma") # channel dependent sigma
sigma_pos = sigma_array[np.where(sigma_array>0)]
smin = sigma_pos.min()
smax = sigma_pos.max()
logging.info("sigma varies from %f to %f" % (smin,smax))
maxval = b1a.get("maxval") # max in cube
nzeros = len(np.where(sigma_array<=0.0)[0]) # check bad channels
if nzeros > 0:
logging.warning("There are %d NaN channels " % nzeros)
# raise Exception,"need to recode CubeSum or use constant sigma"
dt.tag("grab_sig")
if len(smooth) > 0:
# see also LineID and others
filter = Filter1D.Filter1D(sigma_array,smooth[0],**Filter1D.Filter1D.convertargs(smooth))
sigma_array = filter.run()
dt.tag("smooth_sig")
# create a CASA image copy for making the mirror sigma cube to mask against
file = self.dir(infile)
mask = file+"_mask"
taskinit.ia.fromimage(infile=file, outfile=mask)
nx = taskinit.ia.shape()[0]
ny = taskinit.ia.shape()[1]
nchan = taskinit.ia.shape()[2]
taskinit.ia.fromshape(shape=[nx,ny,1])
plane = taskinit.ia.getchunk([0,0,0],[-1,-1,0]) # convenience plane for masking operation
dt.tag("mask_sig")
taskinit.ia.open(mask)
dt.tag("open_mask")
count = 0
for i in range(nchan):
if sigma_array[i] > 0:
if b1b != None:
if msum[i]:
taskinit.ia.putchunk(plane*0+sigma_array[i],blc=[0,0,i,-1])
count = count + 1
else:
taskinit.ia.putchunk(plane*0+maxval,blc=[0,0,i,-1])
else:
taskinit.ia.putchunk(plane*0+sigma_array[i],blc=[0,0,i,-1])
count = count + 1
else:
taskinit.ia.putchunk(plane*0+maxval,blc=[0,0,i,-1])
taskinit.ia.close()
logging.info("%d/%d channels used for CubeSum" % (count,nchan))
dt.tag("close_mask")
names = [file, mask]
tmp = file + '.tmp'
if numsigma == 0.0:
# hopefully this will also make use of the mask
exp = "IM0[IM1<%f]" % (0.99*maxval)
else:
exp = "IM0[abs(IM0/IM1)>%f]" % (numsigma)
# print "PJT: exp",exp
casa.immath(mode='evalexpr', imagename=names, expr=exp, outfile=tmp)
args["imagename"] = tmp
dt.tag("immath")
casa.immoments(**args)
dt.tag("immoments")
if sig_const is False:
# get rid of temporary files
utils.remove(tmp)
utils.remove(mask)
# get the flux
taskinit.ia.open(image_out)
st = taskinit.ia.statistics()
taskinit.ia.close()
dt.tag("statistics")
# report that flux, but there's no way to get the units from casa it seems
# ia.summary()['unit'] is usually 'Jy/beam.km/s' for ALMA
# imstat() does seem to know it.
if st.has_key('flux'):
rdata = [st['flux'][0],st['sum'][0]]
logging.info("Total flux: %f (sum=%f)" % (st['flux'],st['sum']))
else:
rdata = [st['sum'][0]]
logging.info("Sum: %f (beam parameters missing)" % (st['sum']))
logging.regression("CSM: %s" % str(rdata))
# Create two output images for html and their thumbnails, too
implot = ImPlot(ptype=self._plot_type,pmode=self._plot_mode,abspath=self.dir())
implot.plotter(rasterfile=bdp_name,figname=bdp_name,colorwedge=True)
figname = implot.getFigure(figno=implot.figno,relative=True)
thumbname = implot.getThumbnail(figno=implot.figno,relative=True)
dt.tag("implot")
thumbtype = bt.PNG # really should be correlated with self._plot_type!!
# 2. Create a histogram of the map data
# get the data for a histogram
data = casautil.getdata(image_out,zeromask=True).compressed()
dt.tag("getdata")
# get the label for the x axis
bunit = casa.imhead(imagename=image_out, mode="get", hdkey="bunit")
# Make the histogram plot
# Since we give abspath in the constructor, figname should be relative
myplot = APlot(ptype=self._plot_type,pmode=self._plot_mode,abspath=self.dir())
auxname = bdp_name + "_histo"
auxtype = bt.PNG # really should be correlated with self._plot_type!!
myplot.histogram(columns = data,
figname = auxname,
xlab = bunit,
ylab = "Count",
title = "Histogram of CubeSum: %s" % (bdp_name),
thumbnail=True)
auxname = myplot.getFigure(figno=myplot.figno,relative=True)
auxthumb = myplot.getThumbnail(figno=myplot.figno,relative=True)
images = {bt.CASA : bdp_name, bt.PNG : figname}
casaimage = Image(images = images,
auxiliary = auxname,
auxtype = auxtype,
thumbnail = thumbname,
thumbnailtype = thumbtype)
if hasattr(b1,"line"): # SpwCube doesn't have Line
line = deepcopy(getattr(b1,"line"))
if type(line) != type(Line):
line = Line(name="Undetermined")
else:
line = Line(name="Undetermined") # fake a Line if there wasn't one
self.addoutput(Moment_BDP(xmlFile=bdp_name,moment=0,image=deepcopy(casaimage),line=line))
imcaption = "Integral (moment 0) of all emission in image cube"
auxcaption = "Histogram of cube sum for image cube"
taskargs = "numsigma=%.1f sigma=%g smooth=%s" % (numsigma, sigma, str(smooth))
self._summary["cubesum"] = SummaryEntry([figname,thumbname,imcaption,auxname,auxthumb,auxcaption,bdp_name,infile],"CubeSum_AT",self.id(True),taskargs)
dt.tag("done")
dt.end()
def run(self):
""" The run method creates the BDP.
Parameters
----------
None
Returns
-------
None
"""
dt = utils.Dtime("ContinuumSub") # tagging time
self._summary = {} # an ADMIT summary will be created here
contsub = self.getkey("contsub")
pad = self.getkey("pad")
fitorder = self.getkey("fitorder")
# x.im -> x.cim + x.lim
# b1 = input spw BDP
# b1a = optional input {Segment,Line}List
# b1b = optional input Cont Map (now deprecated)
# b2 = output line cube
# b3 = output cont map
b1 = self._bdp_in[0]
f1 = b1.getimagefile(bt.CASA)
b1a = self._bdp_in[1]
# b1b = self._bdp_in[2]
b1b = None # do not allow continuum maps to be input
f2 = self.mkext(f1,'lim')
f3 = self.mkext(f1,'cim')
f3a = self.mkext(f1,'cim3d') # temporary cube name, map is needed
b2 = SpwCube_BDP(f2)
b3 = Image_BDP(f3)
self.addoutput(b2)
self.addoutput(b3)
taskinit.ia.open(self.dir(f1))
s = taskinit.ia.summary()
nchan = s['shape'][2] # ingest has guarenteed this to the spectral axis
if b1a != None: # if a LineList was given, use that
if len(b1a.table) > 0:
# this section of code actually works for len(ch0)==0 as well
#
ch0 = b1a.table.getFullColumnByName("startchan")
ch1 = b1a.table.getFullColumnByName("endchan")
if pad != 0: # can widen or narrow the segments
if pad > 0:
logging.info("pad=%d to widen the segments" % pad)
else:
logging.info("pad=%d to narrow the segments" % pad)
ch0 = np.where(ch0-pad < 0, 0, ch0-pad)
ch1 = np.where(ch1+pad >= nchan, nchan-1, ch1+pad)
s = Segments(ch0,ch1,nchan=nchan)
ch = s.getchannels(True) # take the complement of lines as the continuum
else:
ch = range(nchan) # no lines? take everything as continuum (probably bad)
logging.warning("All channels taken as continuum. Are you sure?")
elif len(contsub) > 0: # else if contsub[] was supplied manually
s = Segments(contsub,nchan=nchan)
ch = s.getchannels()
else:
raise Exception,"No contsub= or input LineList given"
if len(ch) > 0:
taskinit.ia.open(self.dir(f1))
taskinit.ia.continuumsub(outline=self.dir(f2),outcont=self.dir(f3a),channels=ch,fitorder=fitorder)
taskinit.ia.close()
dt.tag("continuumsub")
casa.immoments(self.dir(f3a),-1,outfile=self.dir(f3)) # mean of the continuum cube (f3a)
utils.remove(self.dir(f3a)) # is the continuum map (f3)
dt.tag("immoments")
if b1b != None:
# this option is now deprecated (see above, by setting b1b = None), no user option allowed
# there is likely a mis-match in the beam, given how they are produced. So it's safer to
# remove this here, and force the flow to smooth manually
print "Adding back in a continuum map"
f1b = b1b.getimagefile(bt.CASA)
f1c = self.mkext(f1,'sum')
# @todo notice we are not checking for conforming mapsize and WCS
# and let CASA fail out if we've been bad.
casa.immath([self.dir(f3),self.dir(f1b)],'evalexpr',self.dir(f1c),'IM0+IM1')
utils.rename(self.dir(f1c),self.dir(f3))
dt.tag("immath")
else:
raise Exception,"No channels left to determine continuum. pad=%d too large?" % pad
# regression
rdata = casautil.getdata(self.dir(f3)).data
logging.regression("CSUB: %f %f" % (rdata.min(),rdata.max()))
# Create two output images for html and their thumbnails, too
implot = ImPlot(ptype=self._plot_type,pmode=self._plot_mode,abspath=self.dir())
implot.plotter(rasterfile=f3,figname=f3,colorwedge=True)
figname = implot.getFigure(figno=implot.figno,relative=True)
thumbname = implot.getThumbnail(figno=implot.figno,relative=True)
b2.setkey("image", Image(images={bt.CASA:f2}))
b3.setkey("image", Image(images={bt.CASA:f3, bt.PNG : figname}))
dt.tag("implot")
if len(ch) > 0:
taskargs = "pad=%d fitorder=%d contsub=%s" % (pad,fitorder,str(contsub))
imcaption = "Continuum map"
self._summary["continuumsub"] = SummaryEntry([figname,thumbname,imcaption],"ContinuumSub_AT",self.id(True),taskargs)
dt.tag("done")
dt.end()
def run(self):
""" The run method, calculates the moments and creates the BDP(s)
Parameters
----------
None
Returns
-------
None
"""
self._summary = {}
momentsummary = []
dt = utils.Dtime("Moment")
# variable to track if we are using a single cutoff for all moment maps
allsame = False
moments = self.getkey("moments")
numsigma = self.getkey("numsigma")
mom0clip = self.getkey("mom0clip")
# determine if there is only 1 cutoff or if there is a cutoff for each moment
if len(moments) != len(numsigma):
if len(numsigma) != 1:
raise Exception("Length of numsigma and moment lists do not match. They must be the same length or the length of the cutoff list must be 1.")
allsame = True
# default moment file extensions, this is information copied from casa.immoments()
momentFileExtensions = {-1: ".average",
0: ".integrated",
1: ".weighted_coord",
2: ".weighted_dispersion_coord",
3: ".median",
4: "",
5: ".standard_deviation",
6: ".rms",
7: ".abs_mean_dev",
8: ".maximum",
9: ".maximum_coord",
10: ".minimum",
11: ".minimum_coord",
}
logging.debug("MOMENT: %s %s %s" % (str(moments), str(numsigma), str(allsame)))
# get the input casa image from bdp[0]
# also get the channels the line actually covers (if any)
bdpin = self._bdp_in[0]
infile = bdpin.getimagefile(bt.CASA)
chans = self.getkey("chans")
# the basename of the moments, we will append _0, _1, etc.
basename = self.mkext(infile, "mom")
fluxname = self.mkext(infile, "flux")
# beamarea = nppb(self.dir(infile))
beamarea = 1.0 # until we have it from the MOM0 map
sigma0 = self.getkey("sigma")
sigma = sigma0
ia = taskinit.iatool()
dt.tag("open")
# if no CubseStats BDP was given and no sigma was specified, find a
# noise level via casa.imstat()
if self._bdp_in[1] is None and sigma <= 0.0:
raise Exception("A sigma or a CubeStats_BDP must be input to calculate the cutoff")
elif self._bdp_in[1] is not None:
sigma = self._bdp_in[1].get("sigma")
# immoments is a bit peculiar. If you give one moment, it will use
# exactly the outfile you picked for multiple moments, it will pick
# extensions such as .integrated [0], .weighted_coord [1] etc.
# we loop over the moments and will use the numeric extension instead.
# Might be laborious loop for big input cubes
#
# arguments for immoments
args = {"imagename" : self.dir(infile),
"moments" : moments,
"outfile" : self.dir(basename)}
# set the channels if given
if chans != "":
args["chans"] = chans
# error check the mom0clip input
if mom0clip > 0.0 and not 0 in moments:
logging.warning("mom0clip given, but no moment0 map was requested. One will be generated anyway.")
# add moment0 to the list of computed moments, but it has to be first
moments.insert(0,0)
if not allsame:
numsigma.insert(0, 2.0*sigma)
if allsame:
# this is only executed now if len(moments) > 1 and len(cutoff)==1
args["excludepix"] = [-numsigma[0] * sigma, numsigma[0] * sigma]
casa.immoments(**args)
dt.tag("immoments-all")
else:
# this is execute if len(moments)==len(cutoff) , even when len=1
for i in range(len(moments)):
args["excludepix"] = [-numsigma[i] * sigma, numsigma[i] * sigma]
args["moments"] = moments[i]
args["outfile"] = self.dir(basename + momentFileExtensions[moments[i]])
casa.immoments(**args)
dt.tag("immoments-%d" % moments[i])
taskargs = "moments=%s numsigma=%s" % (str(moments), str(numsigma))
if sigma0 > 0:
taskargs = taskargs + " sigma=%.2f" % sigma0
if mom0clip > 0:
taskargs = taskargs + " mom0clip=%g" % mom0clip
if chans == "":
taskargs = taskargs + " chans=all"
else:
taskargs = taskargs + " chans=%s" % str(chans)
taskargs += ' <span style="background-color:white"> ' + basename.split('/')[0] + ' </span>'
# generate the mask to be applied to all but moment 0
if mom0clip > 0.0:
# get the statistics from mom0 map
# this is usually a very biased map, so unclear if mom0sigma is all that reliable
args = {"imagename": self.dir(infile)}
stat = casa.imstat(imagename=self.dir(basename + momentFileExtensions[0]))
mom0sigma = float(stat["sigma"][0])
# generate a temporary masked file, mask will be copied to other moments
args = {"imagename" : self.dir(basename + momentFileExtensions[0]),
"expr" : 'IM0[IM0>%f]' % (mom0clip * mom0sigma),
"outfile" : self.dir("mom0.masked")
}
casa.immath(**args)
# get the default mask name
ia.open(self.dir("mom0.masked"))
defmask = ia.maskhandler('default')
ia.close()
dt.tag("mom0clip")
# loop over moments to rename them to _0, _1, _2 etc.
# apply a mask as well for proper histogram creation
map = {}
myplot = APlot(pmode=self._plot_mode,ptype=self._plot_type,abspath=self.dir())
implot = ImPlot(pmode=self._plot_mode,ptype=self._plot_type,abspath=self.dir())
for mom in moments:
figname = imagename = "%s_%i" % (basename, mom)
tempname = basename + momentFileExtensions[mom]
# rename and remove the old one if there is one
utils.rename(self.dir(tempname), self.dir(imagename))
# copy the moment0 mask if requested; this depends on that mom0 was done before
if mom0clip > 0.0 and mom != 0:
#print "PJT: output=%s:%s" % (self.dir(imagename), defmask[0])
#print "PJT: inpmask=%s:%s" % (self.dir("mom0.masked"),defmask[0])
makemask(mode="copy", inpimage=self.dir("mom0.masked"),
output="%s:%s" % (self.dir(imagename), defmask[0]),
overwrite=True, inpmask="%s:%s" % (self.dir("mom0.masked"),
defmask[0]))
ia.open(self.dir(imagename))
ia.maskhandler('set', defmask)
ia.close()
dt.tag("makemask")
if mom == 0:
beamarea = nppb(self.dir(imagename))
implot.plotter(rasterfile=imagename,figname=figname,
colorwedge=True,zoom=self.getkey("zoom"))
imagepng = implot.getFigure(figno=implot.figno,relative=True)
thumbname = implot.getThumbnail(figno=implot.figno,relative=True)
images = {bt.CASA : imagename, bt.PNG : imagepng}
thumbtype=bt.PNG
dt.tag("implot")
# get the data for a histogram (ia access is about 1000-2000 faster than imval())
map[mom] = casautil.getdata(self.dir(imagename))
data = map[mom].compressed()
dt.tag("getdata")
# make the histogram plot
# get the label for the x axis
bunit = casa.imhead(imagename=self.dir(imagename), mode="get", hdkey="bunit")
# object for the caption
objectname = casa.imhead(imagename=self.dir(imagename), mode="get", hdkey="object")
# Make the histogram plot
# Since we give abspath in the constructor, figname should be relative
auxname = imagename + '_histo'
auxtype = bt.PNG
myplot.histogram(columns = data,
figname = auxname,
xlab = bunit,
ylab = "Count",
title = "Histogram of Moment %d: %s" % (mom, imagename), thumbnail=True)
casaimage = Image(images = images,
auxiliary = auxname,
auxtype = auxtype,
thumbnail = thumbname,
thumbnailtype = thumbtype)
auxname = myplot.getFigure(figno=myplot.figno,relative=True)
auxthumb = myplot.getThumbnail(figno=myplot.figno,relative=True)
if hasattr(self._bdp_in[0], "line"): # SpwCube doesn't have Line
line = deepcopy(getattr(self._bdp_in[0], "line"))
if not isinstance(line, Line):
line = Line(name="Unidentified")
else:
# fake a Line if there wasn't one
line = Line(name="Unidentified")
# add the BDP to the output array
self.addoutput(Moment_BDP(xmlFile=imagename, moment=mom,
image=deepcopy(casaimage), line=line))
dt.tag("ren+mask_%d" % mom)
imcaption = "%s Moment %d map of Source %s" % (line.name, mom, objectname)
auxcaption = "Histogram of %s Moment %d of Source %s" % (line.name, mom, objectname)
thismomentsummary = [line.name, mom, imagepng, thumbname, imcaption,
auxname, auxthumb, auxcaption, infile]
momentsummary.append(thismomentsummary)
if map.has_key(0) and map.has_key(1) and map.has_key(2):
logging.debug("MAPs present: %s" % (map.keys()))
# m0 needs a new mask, inherited from the more restricted m1 (and m2)
m0 = ma.masked_where(map[1].mask,map[0])
m1 = map[1]
m2 = map[2]
m01 = m0*m1
m02 = m0*m1*m1
m22 = m0*m2*m2
sum0 = m0.sum()
vmean = m01.sum()/sum0
# lacking the full 3D cube, get two estimates and take the max
sig1 = math.sqrt(m02.sum()/sum0 - vmean*vmean)
sig2 = m2.max()
#vsig = max(sig1,sig2)
vsig = sig1
# consider clipping in the masked array (mom0clip)
# @todo i can't use info from line, so just borrow basename for now for grepping
# this also isn't really the flux, the points per beam is still in there
loc = basename.rfind('/')
sum1 = ma.masked_less(map[0],0.0).sum() # mom0clip
# print out: LINE,FLUX1,FLUX0,BEAMAREA,VMEAN,VSIGMA for regression
# the linechans parameter in bdpin is not useful to print out here, it's local to the LineCube
s_vlsr = admit.Project.summaryData.get('vlsr')[0].getValue()[0]
s_rest = admit.Project.summaryData.get('restfreq')[0].getValue()[0]/1e9
s_line = line.frequency
if loc>0:
if basename[:loc][0:2] == 'U_':
# for U_ lines we'll reference the VLSR w.r.t. RESTFREQ in that band
if abs(vmean) > vsig:
vwarn = '*'
else:
vwarn = ''
vlsr = vmean + (1.0-s_line/s_rest)*utils.c
msg = "MOM0FLUX: %s %g %g %g %g %g %g" % (basename[:loc],map[0].sum(),sum0,beamarea,vmean,vlsr,vsig)
else:
# for identified lines we'll assume the ID was correct and not bother with RESTFREQ
msg = "MOM0FLUX: %s %g %g %g %g %g %g" % (basename[:loc],map[0].sum(),sum0,beamarea,vmean,vmean,vsig)
else:
msg = "MOM0FLUX: %s %g %g %g %g %g %g" % ("SPW_FULL" ,map[0].sum(),sum0,beamarea,vmean,vmean,vsig)
logging.regression(msg)
dt.tag("mom0flux")
# create a histogram of flux per channel
# grab the X coordinates for the histogram, we want them in km/s
# restfreq should also be in summary
restfreq = casa.imhead(self.dir(infile),mode="get",hdkey="restfreq")['value']/1e9 # in GHz
# print "PJT %.10f %.10f" % (restfreq,s_rest)
imval0 = casa.imval(self.dir(infile))
freqs = imval0['coords'].transpose()[2]/1e9
x = (1-freqs/restfreq)*utils.c
#
h = casa.imstat(self.dir(infile), axes=[0,1])
if h.has_key('flux'):
flux0 = h['flux']
else:
flux0 = h['sum']/beamarea
flux0sum = flux0.sum() * abs(x[1]-x[0])
# @todo make a flux1 with fluxes derived from a good mask
flux1 = flux0
# construct histogram
title = 'Flux Spectrum (%g)' % flux0sum
xlab = 'VLSR (km/s)'
ylab = 'Flux (Jy)'
myplot.plotter(x,[flux0,flux1],title=title,figname=fluxname,xlab=xlab,ylab=ylab,histo=True)
dt.tag("flux-spectrum")
self._summary["moments"] = SummaryEntry(momentsummary, "Moment_AT",
self.id(True), taskargs)
# get rid of the temporary mask
if mom0clip > 0.0:
utils.rmdir(self.dir("mom0.masked"))
dt.tag("done")
dt.end()
def blankcube(image,
dummyMS,
smooth=True,
verbose=True,
region='centerbox[[10h21m45s,18.05.14.9],[15arcmin,15arcmin]]',
ruthless=False,
extension='.image',
beamround='int',
blankThreshold=2.5,
moments=[0]):
'''
Parameters
----------
image : string
Base name of image. If target image has extension other than '.image',
change the extension keyword.
dummyMS : string
MS file required for blanking process in CASA
smooth : bool, optional
Smooth the image to a circular beam before blanking?
Default True
verbose : bool, optional
region : string, optional
region parameter featured in CASA
ruthless : bool, optional
Delete previous outputs from blankcube
extension : string, optional
Extension of the target image. Must include the '.', e.g., '.restored'
Default '.image'
beamround : string,float
P
blankThreshold : float, optional
Initial blanking threshold of all pixels scaled by the standard
deviation times the blankingthreshold
Default = 2.5 (Walter et al. 2008)
moments : list, optional
Moments to calculate from cube. Options are 0,1,2.
Example: [0,1,2]
Default: [0]
Returns
-------
out : null
Examples
--------
'''
from casa import immath, imsmooth, immoments
from casa import image as ia
from casa import imager as im
from casa import quanta as qa
import os
import numpy as np
# Delete files associated with previous runs
if ruthless:
os.system('rm -rf ' + image + '.smooth.blk.image')
os.system('rm -rf ' + image + '.smooth.image')
os.system('rm -rf ' + image + '.blk.image')
os.system('rm -rf ' + image + '.mask')
imageDir = './'
# Create moment maps
mom0, mom1, mom2 = False, False, False
if len(moments) > 0:
for i, moment in enumerate(moments):
if moment == 0:
mom0 = True
if moment == 1:
mom1 = True
if moment == 2:
mom2 = True
if mom1 == True or mom2 == True:
beamScale = 1.01
elif mom0 == True:
beamScale = 2.
# determine beamsize of cube
ia.open(imageDir + image + extension)
beamsizes = np.zeros(ia.shape()[2])
for i in range(ia.shape()[2]):
beamsizes[i] = ia.restoringbeam(channel=i)['major']['value']
beamsizeUnit = ia.restoringbeam(channel=i)['major']['unit']
beamsize = qa.convert(str(beamsizes.max()) + beamsizeUnit,
'arcsec')['value']
if type(beamround) == float:
beamsize_smooth = beamround * beamsize
else:
beamsize_smooth = np.ceil(beamsize) #beamsize_smooth = 1.01 * beamsize
ia.close()
if verbose:
print 'Max beamsize is ' + str(beamsize) + '"'
if not os.path.exists(image + '.blk.image'):
# create cube for blanking
if smooth: # smooth to a larger beam if the user desires
if verbose:
print 'Convolving to ' + str(beamsize_smooth) + '"'
imsmooth(imagename=image + extension,
outfile=image + '.blk.image',
major=str(beamsize_smooth) + 'arcsec',
minor=str(beamsize_smooth) + 'arcsec',
region=region,
pa='0deg',
targetres=True)
else: # do no smooth
immath(imagename=image + extension,
outfile=image + '.blk.image',
mode='evalexpr',
region=region,
expr='IM0')
if not os.path.exists(image + '.smooth.image'):
# convolve cube to 2X beam for blanking
imsmooth(imagename=image + extension,
outfile=image + '.smooth.image',
major=str(beamsize * beamScale) + 'arcsec',
minor=str(beamsize * beamScale) + 'arcsec',
pa='0deg',
region=region,
targetres=True)
# determine threshold of cube
ia.open(image + '.smooth.image')
threshold = ia.statistics()['sigma'][0] * blankThreshold
ia.close()
# blank the cube at threshold*sigma
ia.open(image + '.smooth.image')
ia.calcmask(mask=image + '.smooth.image > ' + str(threshold), name='mask1')
wait = 'waits for calcmask to close'
ia.close()
# hand blank the cube
im.open(dummyMS)
pause = None
while pause is None:
im.drawmask(image=image + '.smooth.image', mask=image + '.mask')
pause = 0
im.close
# mask contains values of 0 and 1, change to a mask with only values of 1
ia.open(image + '.mask')
ia.calcmask(image + '.mask' + '>0.5')
ia.close()
# apply mask on smoothed image
immath(imagename=image + '.smooth.image',
outfile=image + '.smooth.blk.image',
mode='evalexpr',
mask='mask(' + image + '.mask)',
expr='IM0')
# apply mask on image
ia.open(imageDir + image + '.blk.image')
ia.maskhandler('copy', [image + '.smooth.blk.image:mask0', 'newmask'])
ia.maskhandler('set', 'newmask')
ia.done()
cube = '.blk.image' # specify name of cube for moment calculation
# create moment 0 map
if mom0:
if ruthless:
os.system('rm -rf ' + image + '.mom0.image')
immoments(imagename=image + cube,
moments=[0],
axis='spectra',
chans='',
mask='mask(' + image + cube + ')',
outfile=image + '.mom0.image')
# create moment 1 map
if mom1:
if ruthless:
os.system('rm -rf ' + image + '.mom1.image')
immoments(imagename=image + cube,
moments=[1],
axis='spectra',
chans='',
mask='mask(' + image + cube + ')',
outfile=image + '.mom1.image')
# create moment 2 map
if mom2:
if ruthless:
os.system('rm -rf ' + image + '.mom2.image')
immoments(imagename=image + cube,
moments=[2],
axis='spectra',
chans='',
mask='mask(' + image + cube + ')',
outfile=image + '.mom2.image')
if verbose and mom0:
from casa import imstat
flux = imstat(image + '.mom0.image')['flux'][0]
ia.open(image + '.mom0.image')
beammaj = ia.restoringbeam(channel=0)['major']['value']
beammin = ia.restoringbeam(channel=0)['minor']['value']
beamsizeUnit = ia.restoringbeam(channel=0)['major']['unit']
ia.close()
print 'Moment Image: ' + str(image) + '.mom0.image'
print 'Beamsize: ' + str(beammaj) + '" X ' + str(beammin) + '"'
print 'Flux: ' + str(flux) + ' Jy km/s'
def blankcube(image,
dummyMS,
smooth=True,
verbose=True,
region='centerbox[[10h21m45s,18.05.14.9],[15arcmin,15arcmin]]',
ruthless=False,
extension='.image',
beamround='int',
blankThreshold=2.5,
moments=[0]):
'''
Parameters
----------
image : string
Base name of image. If target image has extension other than '.image',
change the extension keyword.
dummyMS : string
MS file required for blanking process in CASA
smooth : bool, optional
Smooth the image to a circular beam before blanking?
Default True
verbose : bool, optional
region : string, optional
region parameter featured in CASA
ruthless : bool, optional
Delete previous outputs from blankcube
extension : string, optional
Extension of the target image. Must include the '.', e.g., '.restored'
Default '.image'
beamround : string,float
P
blankThreshold : float, optional
Initial blanking threshold of all pixels scaled by the standard
deviation times the blankingthreshold
Default = 2.5 (Walter et al. 2008)
moments : list, optional
Moments to calculate from cube. Options are 0,1,2.
Example: [0,1,2]
Default: [0]
Returns
-------
out : null
Examples
--------
'''
from casa import immath,imsmooth,immoments
from casa import image as ia
from casa import imager as im
from casa import quanta as qa
import os
import numpy as np
# Delete files associated with previous runs
if ruthless:
os.system('rm -rf ' + image + '.smooth.blk.image')
os.system('rm -rf ' + image + '.smooth.image')
os.system('rm -rf ' + image + '.blk.image')
os.system('rm -rf ' + image + '.mask')
imageDir = './'
# Create moment maps
mom0,mom1,mom2 = False,False,False
if len(moments) > 0:
for i, moment in enumerate(moments):
if moment == 0:
mom0 = True
if moment == 1:
mom1 = True
if moment == 2:
mom2 = True
if mom1 == True or mom2 == True:
beamScale = 1.01
elif mom0 == True:
beamScale = 2.
# determine beamsize of cube
ia.open(imageDir + image + extension)
beamsizes = np.zeros(ia.shape()[2])
for i in range(ia.shape()[2]):
beamsizes[i] = ia.restoringbeam(channel=i)['major']['value']
beamsizeUnit = ia.restoringbeam(channel=i)['major']['unit']
beamsize = qa.convert(str(beamsizes.max()) + beamsizeUnit,'arcsec')['value']
if type(beamround) == float:
beamsize_smooth = beamround*beamsize
else:
beamsize_smooth = np.ceil(beamsize) #beamsize_smooth = 1.01 * beamsize
ia.close()
if verbose:
print 'Max beamsize is ' + str(beamsize) + '"'
if not os.path.exists(image + '.blk.image'):
# create cube for blanking
if smooth: # smooth to a larger beam if the user desires
if verbose:
print 'Convolving to ' + str(beamsize_smooth) + '"'
imsmooth(imagename=image + extension,
outfile=image + '.blk.image',
major=str(beamsize_smooth) + 'arcsec',
minor=str(beamsize_smooth) + 'arcsec',
region=region,
pa='0deg',
targetres=True)
else: # do no smooth
immath(imagename=image + extension,
outfile=image + '.blk.image',
mode='evalexpr',
region=region,
expr='IM0')
if not os.path.exists(image + '.smooth.image'):
# convolve cube to 2X beam for blanking
imsmooth(imagename=image + extension,
outfile=image + '.smooth.image',
major=str(beamsize*beamScale) + 'arcsec',
minor=str(beamsize*beamScale) + 'arcsec',
pa='0deg',
region=region,
targetres=True)
# determine threshold of cube
ia.open(image + '.smooth.image')
threshold = ia.statistics()['sigma'][0] * blankThreshold
ia.close()
# blank the cube at threshold*sigma
ia.open(image + '.smooth.image')
ia.calcmask(mask=image + '.smooth.image > ' + str(threshold),
name='mask1')
wait = 'waits for calcmask to close'
ia.close()
# hand blank the cube
im.open(dummyMS)
pause = None
while pause is None:
im.drawmask(image=image + '.smooth.image',
mask=image + '.mask')
pause = 0
im.close
# mask contains values of 0 and 1, change to a mask with only values of 1
ia.open(image + '.mask')
ia.calcmask(image + '.mask' + '>0.5')
ia.close()
# apply mask on smoothed image
immath(imagename=image + '.smooth.image',
outfile=image + '.smooth.blk.image',
mode='evalexpr',
mask='mask(' + image + '.mask)',
expr='IM0')
# apply mask on image
ia.open(imageDir + image + '.blk.image')
ia.maskhandler('copy',[image + '.smooth.blk.image:mask0', 'newmask'])
ia.maskhandler('set','newmask')
ia.done()
cube = '.blk.image' # specify name of cube for moment calculation
# create moment 0 map
if mom0:
if ruthless:
os.system('rm -rf ' + image + '.mom0.image')
immoments(imagename=image + cube,
moments=[0],
axis='spectra',
chans='',
mask='mask(' + image + cube + ')',
outfile=image + '.mom0.image')
# create moment 1 map
if mom1:
if ruthless:
os.system('rm -rf ' + image + '.mom1.image')
immoments(imagename=image + cube,
moments=[1],
axis='spectra',
chans='',
mask='mask(' + image + cube + ')',
outfile=image + '.mom1.image')
# create moment 2 map
if mom2:
if ruthless:
os.system('rm -rf ' + image + '.mom2.image')
immoments(imagename=image + cube,
moments=[2],
axis='spectra',
chans='',
mask='mask(' + image + cube + ')',
outfile=image + '.mom2.image')
if verbose and mom0:
from casa import imstat
flux = imstat(image + '.mom0.image')['flux'][0]
ia.open(image + '.mom0.image')
beammaj = ia.restoringbeam(channel=0)['major']['value']
beammin = ia.restoringbeam(channel=0)['minor']['value']
beamsizeUnit = ia.restoringbeam(channel=0)['major']['unit']
ia.close()
print 'Moment Image: ' + str(image) + '.mom0.image'
print 'Beamsize: ' + str(beammaj) + '" X ' + str(beammin) + '"'
print 'Flux: ' + str(flux) + ' Jy km/s'
def run(self):
""" The run method creates the BDP
Parameters
----------
None
Returns
-------
None
"""
dt = utils.Dtime("CubeSum") # tagging time
self._summary = {} # an ADMIT summary will be created here
numsigma = self.getkey("numsigma") # get the input keys
sigma = self.getkey("sigma")
use_lines = self.getkey("linesum")
pad = self.getkey("pad")
b1 = self._bdp_in[0] # spw image cube
b1a = self._bdp_in[1] # cubestats (optional)
b1b = self._bdp_in[2] # linelist (optional)
f1 = b1.getimagefile(bt.CASA)
taskinit.ia.open(self.dir(f1))
s = taskinit.ia.summary()
nchan = s['shape'][2]
if b1b != None:
ch0 = b1b.table.getFullColumnByName("startchan")
ch1 = b1b.table.getFullColumnByName("endchan")
s = Segments(ch0, ch1, nchan=nchan)
# @todo something isn't merging here as i would have expected,
# e.g. test0.fits [(16, 32), (16, 30), (16, 29)]
if pad > 0:
for (c0, c1) in s.getsegmentsastuples():
s.append([c0 - pad, c0])
s.append([c1, c1 + pad])
s.merge()
s.recalcmask()
# print "PJT segments:",s.getsegmentsastuples()
ns = len(s.getsegmentsastuples())
chans = s.chans(not use_lines)
if use_lines:
msum = s.getmask()
else:
msum = 1 - s.getmask()
logging.info("Read %d segments" % ns)
# print "chans",chans
# print "msum",msum
# from a deprecated keyword, but kept here to pre-smooth the spectrum before clipping
# examples are: ['boxcar',3] ['gaussian',7] ['hanning',5]
smooth = []
sig_const = False # figure out if sigma is taken as constant in the cube
if b1a == None: # if no 2nd BDP was given, sigma needs to be specified
if sigma <= 0.0:
raise Exception, "Neither user-supplied sigma nor CubeStats_BDP input given. One is required."
else:
sig_const = True # and is constant
else:
if sigma > 0:
sigma = b1a.get("sigma")
sig_const = True
if sig_const:
logging.info("Using constant sigma = %f" % sigma)
else:
logging.info("Using varying sigma per plane")
infile = b1.getimagefile(bt.CASA) # ADMIT filename of the image (cube)
bdp_name = self.mkext(
infile, 'csm'
) # morph to the new output name with replaced extension 'csm'
image_out = self.dir(bdp_name) # absolute filename
args = {
"imagename": self.dir(infile)
} # assemble arguments for immoments()
args["moments"] = 0 # only need moments=0 (or [0] is ok as well)
args["outfile"] = image_out # note full pathname
dt.tag("start")
if sig_const:
args["excludepix"] = [-numsigma * sigma,
numsigma * sigma] # single global sigma
if b1b != None:
# print "PJT: ",chans
args["chans"] = chans
else:
# @todo in this section bad channels can cause a fully masked cubesum = bad
# cubestats input
sigma_array = b1a.table.getColumnByName(
"sigma") # channel dependent sigma
sigma_pos = sigma_array[np.where(sigma_array > 0)]
smin = sigma_pos.min()
smax = sigma_pos.max()
logging.info("sigma varies from %f to %f" % (smin, smax))
maxval = b1a.get("maxval") # max in cube
nzeros = len(np.where(sigma_array <= 0.0)[0]) # check bad channels
if nzeros > 0:
logging.warning("There are %d NaN channels " % nzeros)
# raise Exception,"need to recode CubeSum or use constant sigma"
dt.tag("grab_sig")
if len(smooth) > 0:
# see also LineID and others
filter = Filter1D.Filter1D(
sigma_array, smooth[0],
**Filter1D.Filter1D.convertargs(smooth))
sigma_array = filter.run()
dt.tag("smooth_sig")
# create a CASA image copy for making the mirror sigma cube to mask against
file = self.dir(infile)
mask = file + "_mask"
taskinit.ia.fromimage(infile=file, outfile=mask)
nx = taskinit.ia.shape()[0]
ny = taskinit.ia.shape()[1]
nchan = taskinit.ia.shape()[2]
taskinit.ia.fromshape(shape=[nx, ny, 1])
plane = taskinit.ia.getchunk(
[0, 0, 0],
[-1, -1, 0]) # convenience plane for masking operation
dt.tag("mask_sig")
taskinit.ia.open(mask)
dt.tag("open_mask")
count = 0
for i in range(nchan):
if sigma_array[i] > 0:
if b1b != None:
if msum[i]:
taskinit.ia.putchunk(plane * 0 + sigma_array[i],
blc=[0, 0, i, -1])
count = count + 1
else:
taskinit.ia.putchunk(plane * 0 + maxval,
blc=[0, 0, i, -1])
else:
taskinit.ia.putchunk(plane * 0 + sigma_array[i],
blc=[0, 0, i, -1])
count = count + 1
else:
taskinit.ia.putchunk(plane * 0 + maxval, blc=[0, 0, i, -1])
taskinit.ia.close()
logging.info("%d/%d channels used for CubeSum" % (count, nchan))
dt.tag("close_mask")
names = [file, mask]
tmp = file + '.tmp'
if numsigma == 0.0:
# hopefully this will also make use of the mask
exp = "IM0[IM1<%f]" % (0.99 * maxval)
else:
exp = "IM0[abs(IM0/IM1)>%f]" % (numsigma)
# print "PJT: exp",exp
casa.immath(mode='evalexpr',
imagename=names,
expr=exp,
outfile=tmp)
args["imagename"] = tmp
dt.tag("immath")
casa.immoments(**args)
dt.tag("immoments")
if sig_const is False:
# get rid of temporary files
utils.remove(tmp)
utils.remove(mask)
# get the flux
taskinit.ia.open(image_out)
st = taskinit.ia.statistics()
taskinit.ia.close()
dt.tag("statistics")
# report that flux, but there's no way to get the units from casa it seems
# ia.summary()['unit'] is usually 'Jy/beam.km/s' for ALMA
# imstat() does seem to know it.
if st.has_key('flux'):
rdata = [st['flux'][0], st['sum'][0]]
logging.info("Total flux: %f (sum=%f)" % (st['flux'], st['sum']))
else:
rdata = [st['sum'][0]]
logging.info("Sum: %f (beam parameters missing)" % (st['sum']))
logging.regression("CSM: %s" % str(rdata))
# Create two output images for html and their thumbnails, too
implot = ImPlot(ptype=self._plot_type,
pmode=self._plot_mode,
abspath=self.dir())
implot.plotter(rasterfile=bdp_name, figname=bdp_name, colorwedge=True)
figname = implot.getFigure(figno=implot.figno, relative=True)
thumbname = implot.getThumbnail(figno=implot.figno, relative=True)
dt.tag("implot")
thumbtype = bt.PNG # really should be correlated with self._plot_type!!
# 2. Create a histogram of the map data
# get the data for a histogram
data = casautil.getdata(image_out, zeromask=True).compressed()
dt.tag("getdata")
# get the label for the x axis
bunit = casa.imhead(imagename=image_out, mode="get", hdkey="bunit")
# Make the histogram plot
# Since we give abspath in the constructor, figname should be relative
myplot = APlot(ptype=self._plot_type,
pmode=self._plot_mode,
abspath=self.dir())
auxname = bdp_name + "_histo"
auxtype = bt.PNG # really should be correlated with self._plot_type!!
myplot.histogram(columns=data,
figname=auxname,
xlab=bunit,
ylab="Count",
title="Histogram of CubeSum: %s" % (bdp_name),
thumbnail=True)
auxname = myplot.getFigure(figno=myplot.figno, relative=True)
auxthumb = myplot.getThumbnail(figno=myplot.figno, relative=True)
images = {bt.CASA: bdp_name, bt.PNG: figname}
casaimage = Image(images=images,
auxiliary=auxname,
auxtype=auxtype,
thumbnail=thumbname,
thumbnailtype=thumbtype)
if hasattr(b1, "line"): # SpwCube doesn't have Line
line = deepcopy(getattr(b1, "line"))
if type(line) != type(Line):
line = Line(name="Undetermined")
else:
line = Line(name="Undetermined") # fake a Line if there wasn't one
self.addoutput(
Moment_BDP(xmlFile=bdp_name,
moment=0,
image=deepcopy(casaimage),
line=line))
imcaption = "Integral (moment 0) of all emission in image cube"
auxcaption = "Histogram of cube sum for image cube"
taskargs = "numsigma=%.1f sigma=%g smooth=%s" % (numsigma, sigma,
str(smooth))
self._summary["cubesum"] = SummaryEntry([
figname, thumbname, imcaption, auxname, auxthumb, auxcaption,
bdp_name, infile
], "CubeSum_AT", self.id(True), taskargs)
dt.tag("done")
dt.end()
def run(self):
""" The run method, calculates the moments and creates the BDP(s)
Parameters
----------
None
Returns
-------
None
"""
self._summary = {}
momentsummary = []
dt = utils.Dtime("Moment")
# variable to track if we are using a single cutoff for all moment maps
allsame = False
moments = self.getkey("moments")
numsigma = self.getkey("numsigma")
mom0clip = self.getkey("mom0clip")
# determine if there is only 1 cutoff or if there is a cutoff for each moment
if len(moments) != len(numsigma):
if len(numsigma) != 1:
raise Exception("Length of numsigma and moment lists do not match. They must be the same length or the length of the cutoff list must be 1.")
allsame = True
# default moment file extensions, this is information copied from casa.immoments()
momentFileExtensions = {-1: ".average",
0: ".integrated",
1: ".weighted_coord",
2: ".weighted_dispersion_coord",
3: ".median",
4: "",
5: ".standard_deviation",
6: ".rms",
7: ".abs_mean_dev",
8: ".maximum",
9: ".maximum_coord",
10: ".minimum",
11: ".minimum_coord",
}
logging.debug("MOMENT: %s %s %s" % (str(moments), str(numsigma), str(allsame)))
# get the input casa image from bdp[0]
# also get the channels the line actually covers (if any)
bdpin = self._bdp_in[0]
infile = bdpin.getimagefile(bt.CASA)
chans = self.getkey("chans")
# the basename of the moments, we will append _0, _1, etc.
basename = self.mkext(infile, "mom")
fluxname = self.mkext(infile, "flux")
# beamarea = nppb(self.dir(infile))
beamarea = 1.0 # until we have it from the MOM0 map
sigma0 = self.getkey("sigma")
sigma = sigma0
dt.tag("open")
# if no CubseStats BDP was given and no sigma was specified, find a
# noise level via casa.imstat()
if self._bdp_in[1] is None and sigma <= 0.0:
raise Exception("A sigma or a CubeStats_BDP must be input to calculate the cutoff")
elif self._bdp_in[1] is not None:
sigma = self._bdp_in[1].get("sigma")
# immoments is a bit peculiar. If you give one moment, it will use
# exactly the outfile you picked for multiple moments, it will pick
# extensions such as .integrated [0], .weighted_coord [1] etc.
# we loop over the moments and will use the numeric extension instead.
# Might be laborious loop for big input cubes
#
# arguments for immoments
args = {"imagename" : self.dir(infile),
"moments" : moments,
"outfile" : self.dir(basename)}
# set the channels if given
if chans != "":
args["chans"] = chans
# error check the mom0clip input
if mom0clip > 0.0 and not 0 in moments:
logging.warning("mom0clip given, but no moment0 map was requested. One will be generated anyway.")
# add moment0 to the list of computed moments, but it has to be first
moments.insert(0,0)
if not allsame:
numsigma.insert(0, 2.0*sigma)
if allsame:
# this is only executed now if len(moments) > 1 and len(cutoff)==1
args["excludepix"] = [-numsigma[0] * sigma, numsigma[0] * sigma]
casa.immoments(**args)
dt.tag("immoments-all")
else:
# this is execute if len(moments)==len(cutoff) , even when len=1
for i in range(len(moments)):
args["excludepix"] = [-numsigma[i] * sigma, numsigma[i] * sigma]
args["moments"] = moments[i]
args["outfile"] = self.dir(basename + momentFileExtensions[moments[i]])
casa.immoments(**args)
dt.tag("immoments-%d" % moments[i])
taskargs = "moments=%s numsigma=%s" % (str(moments), str(numsigma))
if sigma0 > 0:
taskargs = taskargs + " sigma=%.2f" % sigma0
if mom0clip > 0:
taskargs = taskargs + " mom0clip=%g" % mom0clip
if chans == "":
taskargs = taskargs + " chans=all"
else:
taskargs = taskargs + " chans=%s" % str(chans)
taskargs += ' <span style="background-color:white"> ' + basename.split('/')[0] + ' </span>'
# generate the mask to be applied to all but moment 0
if mom0clip > 0.0:
# get the statistics from mom0 map
# this is usually a very biased map, so unclear if mom0sigma is all that reliable
args = {"imagename": self.dir(infile)}
stat = casa.imstat(imagename=self.dir(basename + momentFileExtensions[0]))
mom0sigma = float(stat["sigma"][0])
# generate a temporary masked file, mask will be copied to other moments
args = {"imagename" : self.dir(basename + momentFileExtensions[0]),
"expr" : 'IM0[IM0>%f]' % (mom0clip * mom0sigma),
"outfile" : self.dir("mom0.masked")
}
casa.immath(**args)
# get the default mask name
taskinit.ia.open(self.dir("mom0.masked"))
defmask = taskinit.ia.maskhandler('default')
taskinit.ia.close()
dt.tag("mom0clip")
# loop over moments to rename them to _0, _1, _2 etc.
# apply a mask as well for proper histogram creation
map = {}
myplot = APlot(pmode=self._plot_mode,ptype=self._plot_type,abspath=self.dir())
implot = ImPlot(pmode=self._plot_mode,ptype=self._plot_type,abspath=self.dir())
for mom in moments:
figname = imagename = "%s_%i" % (basename, mom)
tempname = basename + momentFileExtensions[mom]
# rename and remove the old one if there is one
utils.rename(self.dir(tempname), self.dir(imagename))
# copy the moment0 mask if requested; this depends on that mom0 was done before
if mom0clip > 0.0 and mom != 0:
#print "PJT: output=%s:%s" % (self.dir(imagename), defmask[0])
#print "PJT: inpmask=%s:%s" % (self.dir("mom0.masked"),defmask[0])
makemask(mode="copy", inpimage=self.dir("mom0.masked"),
output="%s:%s" % (self.dir(imagename), defmask[0]),
overwrite=True, inpmask="%s:%s" % (self.dir("mom0.masked"),
defmask[0]))
taskinit.ia.open(self.dir(imagename))
taskinit.ia.maskhandler('set', defmask)
taskinit.ia.close()
dt.tag("makemask")
if mom == 0:
beamarea = nppb(self.dir(imagename))
implot.plotter(rasterfile=imagename,figname=figname,colorwedge=True)
imagepng = implot.getFigure(figno=implot.figno,relative=True)
thumbname = implot.getThumbnail(figno=implot.figno,relative=True)
images = {bt.CASA : imagename, bt.PNG : imagepng}
thumbtype=bt.PNG
dt.tag("implot")
# get the data for a histogram (ia access is about 1000-2000 faster than imval())
map[mom] = casautil.getdata(self.dir(imagename))
data = map[mom].compressed()
dt.tag("getdata")
# make the histogram plot
# get the label for the x axis
bunit = casa.imhead(imagename=self.dir(imagename), mode="get", hdkey="bunit")
# object for the caption
objectname = casa.imhead(imagename=self.dir(imagename), mode="get", hdkey="object")
# Make the histogram plot
# Since we give abspath in the constructor, figname should be relative
auxname = imagename + '_histo'
auxtype = bt.PNG
myplot.histogram(columns = data,
figname = auxname,
xlab = bunit,
ylab = "Count",
title = "Histogram of Moment %d: %s" % (mom, imagename), thumbnail=True)
casaimage = Image(images = images,
auxiliary = auxname,
auxtype = auxtype,
thumbnail = thumbname,
thumbnailtype = thumbtype)
auxname = myplot.getFigure(figno=myplot.figno,relative=True)
auxthumb = myplot.getThumbnail(figno=myplot.figno,relative=True)
if hasattr(self._bdp_in[0], "line"): # SpwCube doesn't have Line
line = deepcopy(getattr(self._bdp_in[0], "line"))
if not isinstance(line, Line):
line = Line(name="Unidentified")
else:
# fake a Line if there wasn't one
line = Line(name="Unidentified")
# add the BDP to the output array
self.addoutput(Moment_BDP(xmlFile=imagename, moment=mom,
image=deepcopy(casaimage), line=line))
dt.tag("ren+mask_%d" % mom)
imcaption = "%s Moment %d map of Source %s" % (line.name, mom, objectname)
auxcaption = "Histogram of %s Moment %d of Source %s" % (line.name, mom, objectname)
thismomentsummary = [line.name, mom, imagepng, thumbname, imcaption,
auxname, auxthumb, auxcaption, infile]
momentsummary.append(thismomentsummary)
if map.has_key(0) and map.has_key(1) and map.has_key(2):
logging.debug("MAPs present: %s" % (map.keys()))
# m0 needs a new mask, inherited from the more restricted m1 (and m2)
m0 = ma.masked_where(map[1].mask,map[0])
m1 = map[1]
m2 = map[2]
m01 = m0*m1
m02 = m0*m1*m1
m22 = m0*m2*m2
sum0 = m0.sum()
vmean = m01.sum()/sum0
# lacking the full 3D cube, get two estimates and take the max
sig1 = math.sqrt(m02.sum()/sum0 - vmean*vmean)
sig2 = m2.max()
#vsig = max(sig1,sig2)
vsig = sig1
# consider clipping in the masked array (mom0clip)
# @todo i can't use info from line, so just borrow basename for now for grepping
# this also isn't really the flux, the points per beam is still in there
loc = basename.rfind('/')
sum1 = ma.masked_less(map[0],0.0).sum() # mom0clip
# print out: LINE,FLUX1,FLUX0,BEAMAREA,VMEAN,VSIGMA for regression
# the linechans parameter in bdpin is not useful to print out here, it's local to the LineCube
s_vlsr = admit.Project.summaryData.get('vlsr')[0].getValue()[0]
s_rest = admit.Project.summaryData.get('restfreq')[0].getValue()[0]/1e9
s_line = line.frequency
if loc>0:
if basename[:loc][0:2] == 'U_':
# for U_ lines we'll reference the VLSR w.r.t. RESTFREQ in that band
if abs(vmean) > vsig:
vwarn = '*'
else:
vwarn = ''
vlsr = vmean + (1.0-s_line/s_rest)*utils.c
msg = "MOM0FLUX: %s %g %g %g %g %g %g" % (basename[:loc],map[0].sum(),sum0,beamarea,vmean,vlsr,vsig)
else:
# for identified lines we'll assume the ID was correct and not bother with RESTFREQ
msg = "MOM0FLUX: %s %g %g %g %g %g %g" % (basename[:loc],map[0].sum(),sum0,beamarea,vmean,vmean,vsig)
else:
msg = "MOM0FLUX: %s %g %g %g %g %g %g" % ("SPW_FULL" ,map[0].sum(),sum0,beamarea,vmean,vmean,vsig)
logging.regression(msg)
dt.tag("mom0flux")
# create a histogram of flux per channel
# grab the X coordinates for the histogram, we want them in km/s
# restfreq should also be in summary
restfreq = casa.imhead(self.dir(infile),mode="get",hdkey="restfreq")['value']/1e9 # in GHz
# print "PJT %.10f %.10f" % (restfreq,s_rest)
imval0 = casa.imval(self.dir(infile))
freqs = imval0['coords'].transpose()[2]/1e9
x = (1-freqs/restfreq)*utils.c
#
h = casa.imstat(self.dir(infile), axes=[0,1])
if h.has_key('flux'):
flux0 = h['flux']
else:
flux0 = h['sum']/beamarea
flux0sum = flux0.sum() * abs(x[1]-x[0])
# @todo make a flux1 with fluxes derived from a good mask
flux1 = flux0
# construct histogram
title = 'Flux Spectrum (%g)' % flux0sum
xlab = 'VLSR (km/s)'
ylab = 'Flux (Jy)'
myplot.plotter(x,[flux0,flux1],title=title,figname=fluxname,xlab=xlab,ylab=ylab,histo=True)
dt.tag("flux-spectrum")
self._summary["moments"] = SummaryEntry(momentsummary, "Moment_AT",
self.id(True), taskargs)
# get rid of the temporary mask
if mom0clip > 0.0:
utils.rmdir(self.dir("mom0.masked"))
dt.tag("done")
dt.end()