### mv the cubes to the working directory
os.system("mkdir "+dir_data+galname)
os.system("mv "+dir_data+"data/"+galname+"*32*smooth "\
+dir_data+galname+"/"+galname+"_co32_"+suffix+".cube")
### step 6/10: create CO(2-1) cube mask
print("### step 6/10: create CO(2-1) cube mask")
cube_co32 = glob.glob(dir_data+galname+"/"\
+galname+"*_co32_"+suffix+".cube")[0]
thres_co32 = rms_co32 * increment_mask * thres_masking
outmask_co32=cube_co32.replace(".cube",".mask")
myim2.createmask(cube_co32,thres_co32,outmask_co32)
beamarea = myim2.beam_area(image_co32,increment_mask)
myim2.remove_smallmask(outmask_co32,beamarea,pixelmin)
### mv to working directory
os.system("rm -rf "+cube_co32)
os.system("mv "+image_co32+" "+cube_co32)
print("### step 9/10: immoments")
myim2.moment_maps(cube_co32,chans,outmask_co32,rms_co32*thres_mom)
beam_mask = beam_size * increment_mask # beam size for the masking
myim2.easy_imsmooth(image_co21, beam_mask, False) # co21
### mv the cubes to the working directory
os.system("mkdir " + dir_data + galname)
os.system("mv "+dir_data+"data/"+galname+"*smooth "\
+dir_data+galname+"/"+galname+"_"+suffix+".cube")
### step 6/10: create CO(2-1) cube mask
print("### step 6/10: create CO(2-1) cube mask")
cube_co21 = glob.glob(dir_data+galname+"/"\
+galname+"_"+suffix+".cube")[0]
thres_co21 = rms_co21 * increment_mask * thres_masking
outmask_co21 = cube_co21.replace(".cube", ".mask")
myim2.createmask(cube_co21, thres_co21, outmask_co21)
beamarea = myim2.beam_area(image_co21, increment_mask)
myim2.remove_smallmask(outmask_co21, beamarea, pixelmin)
### mv to working directory
os.system("rm -rf " + cube_co21)
os.system("mv " + image_co21 + " " + cube_co21)
print("### step 9/10: immoments")
myim2.moment_maps(cube_co21, chans, outmask_co21, rms_co21 * thres_mom)
### pbmask
print("### step 10/10: pb mask at " + str(pbcut))
#mask_pb = dir_data+galname+"/"+galname+"_pb_"+suffix+".mask"
beam_mask = beam_size * increment_mask # beam size for the masking
myim2.easy_imsmooth(image_co10, beam_mask, False) # co10
### mv the cubes to the working directory
os.system("mkdir " + dir_data + galname)
os.system("mv "+dir_data+"data/"+galname+"*10*smooth "\
+dir_data+galname+"/"+galname+"_co10_"+suffix+".cube")
### step 6/10: create CO(2-1) cube mask
print("### step 6/10: create CO(2-1) cube mask")
cube_co10 = glob.glob(dir_data+galname+"/"\
+galname+"*_co10_"+suffix+".cube")[0]
thres_co10 = rms_co10 * increment_mask * thres_masking
outmask_co10 = cube_co10.replace(".cube", ".mask")
myim2.createmask(cube_co10, thres_co10, outmask_co10)
beamarea = myim2.beam_area(image_co10, increment_mask)
myim2.remove_smallmask(outmask_co10, beamarea, pixelmin)
### mv to working directory
os.system("rm -rf " + cube_co10)
os.system("mv " + image_co10 + " " + cube_co10)
print("### step 9/10: immoments")
myim2.moment_maps(cube_co10, chans, outmask_co10, rms_co10 * thres_mom)
### pbmask
print("### step 10/10: pb mask at " + str(pbcut))
#mask_pb = dir_data+galname+"/"+galname+"_pb_"+suffix+".mask"
beam_mask = beam_size * increment_mask # beam size for the masking
myim2.easy_imsmooth(image_ci10, beam_mask, False) # ci10
### mv the cubes to the working directory
os.system("mkdir " + dir_data + galname)
os.system("mv "+dir_data+"fits/"+galname+"*10*smooth "\
+dir_data+galname+"/"+galname+"_ci10_"+suffix+".cube")
### step 5/10: create CO(1-0) cube mask
print("### step 5/10: create CI(1-0) cube mask")
cube_ci10 = glob.glob(dir_data+galname+"/"\
+galname+"*_ci10_"+suffix+".cube")[0]
thres_ci10 = rms_ci10 * increment_mask * thres_masking
outmask_ci10 = cube_ci10.replace(".cube", ".mask")
myim2.createmask(cube_ci10, thres_ci10, outmask_ci10)
beamarea = myim2.beam_area(image_ci10, increment_mask)
myim2.remove_smallmask(outmask_ci10, beamarea, pixelmin)
### step 8/10: imsmooth
print("### step 8/10: imsmooth")
myim2.easy_imsmooth(image_ci10, beam_size, True) # ci10
### mv to working directory
os.system("rm -rf " + cube_ci10)
os.system("mv " + dir_data + "fits/" + galname + "*10*smooth " + cube_ci10)
print("### step 9/10: immoments")
myim2.moment_maps(cube_ci10, chans, outmask_ci10, rms_ci10 * thres_mom)
multiplier_co10 = 0.05 # peak * multiplier
multiplier_co21 = 0.05 # peak * multiplier
#####################
### Main Procedure
#####################
### setup
dir_data1 = dir_data + galname + "/"
im_co10 = glob.glob(dir_data1 + galname + "*co10*" + suffix + "*m*0.fits")[0]
im_co21 = glob.glob(dir_data1 + galname + "*co21*" + suffix + "*m*0.fits")[0]
outmask_co10 = im_co10.replace(".moment0.fits", "_mom.mask")
outmask_co21 = im_co21.replace(".moment0.fits", "_mom.mask")
### create mask for each moment map
peak = imstat(im_co10)["max"][0]
myim2.createmask(im_co10, peak * multiplier_co10, outmask_co10)
peak = imstat(im_co21)["max"][0]
myim2.createmask(im_co21, peak * multiplier_co21, outmask_co21)
outfile = dir_data1 + galname + "_r21_" + suffix + ".mask"
os.system("rm -rf " + outfile)
immath(imagename=[outmask_co10, outmask_co21],
mode="evalexpr",
expr="IM0*IM1",
outfile=outfile)
makemask(mode="copy",
inpimage=outfile,
inpmask=outfile,
output=outfile + ":mask0",
overwrite=True)