cmd = "%s/nomagic in=%s out=%s repval=%d %s" % (kapdir, thresh, magic, 0, "> /dev/null")
os.system(cmd)
### recreate mask of clump i - mask0
cmd = "%s/thresh in=%s out=%s thrlo=%d thrhi=%d newlo=%d newhi=%d %s" % (
kapdir,
magic,
mask,
0,
0,
0,
1,
"> /dev/null",
)
os.system(cmd)
ndf2fits.ndf2fits(mask)
Fig1.show_contour(maskFITS, levels=(0.5, 1000), linewidth=3, colors=("black"))
Fig2.show_contour(maskFITS, levels=(0.5, 1000), linewidth=3, colors=("black"))
Fig3.show_contour(maskFITS, levels=(0.5, 1000), linewidth=3, colors=("black"))
cmd = "rm %s %s %s" % (thresh, mask, magic)
os.system(cmd)
# PLOT FW contours
# OPEN up the region specific clump list
data = pyfits.open(clumpcatb)
DATA = data[1].data
for j in DATA:
I = int(j[0])
def Z(CD): #OB star checking
Fig = aplpy.FITSFigure(CD)
Fig.show_colorscale(vmax=8.5E22,vmin=2.5E21, stretch='linear',cmap='afmhot_r')
Fig.add_colorbar()
Fig.colorbar.set_axis_label_text('Column Density (H$_{2}$ cm$^{-2}$)')
#Plot YSOs
#YSO.c2dGBS_v2(Fig)
#PLOT FW contours
#OPEN up the region specific clump list
clumpcat = '/data/damian/run31/FW/cat/OrionA_20150227_clump_cat.fit'
clumps = '/data/damian/run31/FW/clumps/OrionA_20150227_clumps.sdf'
data = pyfits.open(clumpcat)
DATA = data[1].data
for j in DATA:
I = int(j[0])
print str(I)+'/'+str(len(DATA))
### SETUP temp. file names
thresh = '/data/damian/run31/mask/thresh'+str(I)+'.sdf'
mask = '/data/damian/run31/mask/mask_'+str(I)+'.sdf'
maskFITS = '/data/damian/run31/mask/mask_'+str(I)+'.fits'
magic = '/data/damian/run31/mask/magic'+str(I)+'.sdf'
### isolate clump i ###
cmd = '%s/thresh in=%s out=%s thrlo=%d thrhi=%d newlo=%s newhi=%s %s'%(kapdir,clumps,thresh,I,I,'bad','bad','> /dev/null')
os.system(cmd)
### process 2 - remove 0value data
cmd = '%s/nomagic in=%s out=%s repval=%d %s'%(kapdir,thresh,magic,0,'> /dev/null')
os.system(cmd)
### recreate mask of clump i - mask0
cmd = '%s/thresh in=%s out=%s thrlo=%d thrhi=%d newlo=%d newhi=%d %s'%(kapdir,magic,mask,0,0,0,1,'> /dev/null')
os.system(cmd)
ndf2fits.ndf2fits(mask)
Fig.show_contour(maskFITS, levels=(0.5,1000), linewidth=3, colors=('black'))
cmd = 'rm %s %s %s'%(thresh,mask,magic)
os.system(cmd)
#Deffine OB star data
data1 = np.loadtxt('/data/damian/run27/OBstars_list.txt')
RA_OB = data1[:,0]
DEC_OB = data1[:,1]
data2 = np.loadtxt('/data/damian/run27/OBstars.txt',dtype='string')
RA_OBx = map(float, data2[:,2])
DEC_OBx = map(float, data2[:,3])
data1 = np.loadtxt('/data/damian/data/OBstars/obcatalog_deg.txt')
RA_OB_R = data1[:,0]
DEC_OB_R = data1[:,1]
Fig.show_markers(RA_OB,DEC_OB, edgecolor='k', facecolor='none', marker='*',s=100, alpha=1)
Fig.show_markers(RA_OBx,DEC_OBx, edgecolor='k', facecolor='cyan', marker='*',s=100, alpha=1)
Fig.show_markers(RA_OB_R,DEC_OB_R, edgecolor='r', facecolor='none', marker='*',s=100, alpha=1)
Fig.tick_labels.set_xformat('hh:mm:ss')
return
p = PARGET(YSO,'fpixscale','ndftrace')
smooth = sig/p[0]
cmd = '%s/gausmooth in=%s fwhm=%f out=%s'%(kapdir,YSO,smooth,YSOsurface)
os.system(cmd)
cmd = '%s/gausmooth in=%s fwhm=%f out=%s'%(kapdir,proto,smooth,protosurface)
os.system(cmd)
cmd = '%s/gausmooth in=%s fwhm=%f out=%s'%(kapdir,PMS,smooth,PMSsurface)
os.system(cmd)
#scale up units
scale850 = 18909
cmult = '%s/cmult in=%s scalar=%s out=%s'%(kapdir,YSOsurface,scale850,YSOsurfaceunits)
os.system(cmult)
cmult = '%s/cmult in=%s scalar=%s out=%s'%(kapdir,protosurface,scale850,protosurfaceunits)
os.system(cmult)
cmult = '%s/cmult in=%s scalar=%s out=%s'%(kapdir,PMSsurface,scale850,PMSsurfaceunits)
os.system(cmult)
#convert to fits file
ndf2fits.ndf2fits(PMSsurfaceunits)
ndf2fits.ndf2fits(protosurfaceunits)
ndf2fits.ndf2fits(YSOsurfaceunits)
#print surfaceunits
#clean up
cmd1 = 'rm YSO/temp/*'
os.system(cmd1)
break
elif '450' in myfile:
print "=============="
print '450 micron map'
print myfile
p450 = PARGET(myfile,'fpixscale','ndftrace')
#p850 = PARGET(input_dir+'/'+file850+'.sdf','fpixscale','ndftrace')
print "Pixel sizes are "+str(p450[0])
p450 = p450[0]
cunits = (p450**2.)/1000
old_units = '.sdf'
nu_units = 'Jypix.sdf'
col_units = 'Jypix_col.sdf'
prefix = string.split(myfile,old_units)[0]
print 'Converting %s to %s...'%(old_units,nu_units)
nu_file = prefix+nu_units
nu_2dfile = prefix+col_units
cmd = '%s/cmult in=%s scalar=%f out=%s QUIET'%(kapdir,myfile,cunits,nu_file)
os.system(cmd)
cmd = '%s/setunits ndf=%s units=%s'%(kapdir,nu_file,'Jy/pix')
os.system(cmd)
cmd = '%s/collapse in=%s out=%s axis=%s'%(kapdir,nu_file,nu_2dfile,3)
os.system(cmd)
ndf2fits.ndf2fits(nu_2dfile)
##############################
#### CALCULATE PROPERTIES ####
##############################
#use NOMAGIC to remove the blanks
nm850 = 'SMM/'+region+'/temp/s850_NMclump'+str(I)+'.sdf'
nmtemp = 'SMM/'+region+'/temp/temp_NMclump'+str(I)+'.sdf'
nmtemp_err = 'SMM/'+region+'/temp/temp_NMclump_err'+str(I)+'.sdf'
nnoise = 'SMM/'+region+'/temp/s850noiseNM'+str(I)+'.sdf'
nomagic(c850,nm850)
nomagic(cnoise,nnoise)
nomagic(THtemp,nmtemp)
nomagic(THtemp_err,nmtemp_err)
#from individual clump maps
ndf2fits.ndf2fits(nm850)
ndf2fits.ndf2fits(nnoise)
ndf2fits.ndf2fits(nmtemp)
ndf2fits.ndf2fits(nmtemp_err)
#deffine FITS files
#existing files#
nm850FITS = 'SMM/'+region+'/temp/s850_NMclump'+str(I)+'.fits'
cnoise = 'SMM/'+region+'/temp/s850noiseNM'+str(I)+'.fits'
nmtempFITS = 'SMM/'+region+'/temp/temp_NMclump'+str(I)+'.fits'
nmtempFITS_err = 'SMM/'+region+'/temp/temp_NMclump_err'+str(I)+'.fits'
#new files#
massFITS = 'SMM/'+region+'/Mass'+str(I)+'.fits'
masserrFITS = 'SMM/'+region+'/masserr'+str(I)+'.fits'
#copy existing clump file to act as a base on to which calculations will be writen.
copy(cnoise,massFITS)
import ndf2fits
import numpy as np
data = np.loadtxt('maps.txt',dtype='string')
for i in data:
ndf2fits.ndf2fits(i)
for i in maps:
#Make directory
if not os.path.exists('CDmaps/CDpart'):
os.makedirs('CDmaps/CDpart')
#split INPUT file
s850,temp,dtemp,alpha,proto,YSO,clumps,clumpcat = string.split(i,',')
prefix1 = string.split(s850,'.sdf')[0]
prefix2 = string.split(temp,'.sdf')[0]
file = string.split(prefix1,'/')[0]
#deffine region name
name = string.split(clumps,'/')[2]
region = string.split(name,'_2')[0]
#Convert maps to fits
ndf2fits.ndf2fits(s850)
ndf2fits.ndf2fits(temp)
s850FITS = prefix1+'.fits'
tempFITS = prefix2+'.fits'
massFITS = 'CDmaps/mass/'+region+'_mass.fits'
mass15FITS = 'CDmaps/mass/'+region+'_mass15K.fits'
#print massFITS
print temp
cmd = 'cp %s %s'%(s850FITS,massFITS)
os.system(cmd)
cmd = 'cp %s %s'%(s850FITS,mass15FITS)
os.system(cmd)
#Open files
##############################
#### CALCULATE PROPERTIES ####
##############################
#use NOMAGIC to remove the blanks
nm850 = 'SMM/'+region+'/temp/s850_NMclump'+str(I)+'.sdf'
nmtemp = 'SMM/'+region+'/temp/temp_NMclump'+str(I)+'.sdf'
nmtemp_err = 'SMM/'+region+'/temp/temp_NMclump_err'+str(I)+'.sdf'
nnoise = 'SMM/'+region+'/temp/s850noiseNM'+str(I)+'.sdf'
nomagic(c850,nm850)
nomagic(cnoise,nnoise)
nomagic(THtemp,nmtemp)
nomagic(THtemp_err,nmtemp_err)
#from individual clump maps
nm850FITS =ndf2fits.ndf2fits(nm850)
cnoise = ndf2fits.ndf2fits(nnoise)
nmtempFITS =ndf2fits.ndf2fits(nmtemp)
nmtempFITS_err = ndf2fits.ndf2fits(nmtemp_err)
#deffine FITS files
#existing files#
#nm850FITS = 'SMM/'+region+'/temp/s850_NMclump'+str(I)+'.fits'
#cnoise = 'SMM/'+region+'/temp/s850noiseNM'+str(I)+'.fits'
#nmtempFITS = 'SMM/'+region+'/temp/temp_NMclump'+str(I)+'.fits'
#nmtempFITS_err = 'SMM/'+region+'/temp/temp_NMclump_err'+str(I)+'.fits'
#new files#
massFITS = 'SMM/'+region+'/temp/Mass'+str(I)+'.fits'
masserrFITS = 'SMM/'+region+'/temp/masserr'+str(I)+'.fits'
#copy existing clump file to act as a base on to which calculations will be writ
copy(cnoise,massFITS)
# all free-free mask1 = "%s/mult in1=%s in2=%s out=%s" % (kapdir, sub450, mask, mask450FF) mask2 = "%s/mult in1=%s in2=%s out=%s" % (kapdir, sub850, mask, mask850FF) os.system(mask1) os.system(mask2) ############################ # make ratio and temp maps # original div1 = "%s/div in1=%s in2=%s out=%s" % (kapdir, mask450, mask850, ratio) os.system(div1) # freefree div2 = "%s/div in1=%s in2=%s out=%s" % (kapdir, mask450FF, mask850FF, ratioFF) os.system(div2) ndf2fits.ndf2fits(ratio) ndf2fits.ndf2fits(ratioFF) temperature(ratio, ratio_fits, ratio_fits, 1.8, "FALSE") temperature(ratioFF, ratioFF_fits, ratioFF_fits, 1.8, "FALSE") mv1 = "mv %s %s" % (ratio_fits, temp_fits) mv2 = "mv %s %s" % (ratioFF_fits, tempFF_fits) os.system(mv1) os.system(mv2) ndf2fits.fits2ndf(temp_fits) ndf2fits.fits2ndf(tempFF_fits) # compare temp maps submap = "maps/s21/submap.sdf"
#all free-free mask1 = '%s/mult in1=%s in2=%s out=%s'%(kapdir,sub450,mask,mask450FF) mask2 = '%s/mult in1=%s in2=%s out=%s'%(kapdir,sub850,mask,mask850FF) os.system(mask1) os.system(mask2) ############################ #make ratio and temp maps #original div1 = '%s/div in1=%s in2=%s out=%s'%(kapdir,mask450,mask850,ratio) os.system(div1) #freefree div2 = '%s/div in1=%s in2=%s out=%s'%(kapdir,mask450FF,mask850FF,ratioFF) os.system(div2) ndf2fits.ndf2fits(ratio) ndf2fits.ndf2fits(ratioFF) temperature(ratio,ratio_fits,ratio_fits,1.8,'FALSE') temperature(ratioFF,ratioFF_fits,ratioFF_fits,1.8,'FALSE') mv1 = 'mv %s %s'%(ratio_fits,temp_fits) mv2 = 'mv %s %s'%(ratioFF_fits,tempFF_fits) os.system(mv1) os.system(mv2) ndf2fits.fits2ndf(temp_fits) ndf2fits.fits2ndf(tempFF_fits) #compare temp maps submap = 'maps/s21/submap.sdf'
