Tohban EOVSA Imaging Tutorial A-Z

Connection details to pipeline server

Step 1: Downloading raw data (IDB) on Pipeline machine

On CASA of the Pipeline machine, which has the complete EOVSA SQL database.

If you are not using mobaxterm, directly SSH to Pipeline through your Linux or Mac computer and start tcsh to run CASA.

from astropy.time import Time
import os
trange = Time(['2017-08-21 20:15:00', '2017-08-21 20:25:00'])             #Change accordingly
#### (Optional) change output path, default current directory "./" #####
outpath = './msdata/'
if not os.path.exists(outpath):
    os.makedirs(outpath)
######################################################
msfiles = importeovsa(idbfiles=trange, ncpu=1, visprefix=outpath)

OR (for a time range longer than 10 minutes)

from suncasa.tasks import task_calibeovsa as calibeovsa
from suncasa.tasks import task_importeovsa as timporteovsa
from split_cli import split_cli as split
import dump_tsys as dt
from util import Time
import numpy as np
import os
from glob import glob
from eovsapy import util


trange = Time(['2017-08-21 20:15:00', '2017-08-21 20:35:00'])     #Change accordingly
idbdir = util.get_idbdir(trange[0])

info = dt.rd_fdb(trange[0])
for k, v in info.iteritems():
    info[k] = info[k][~(info[k] == '')]

sidx = np.where(
    np.logical_and(info['SOURCEID'] == 'Sun', info['PROJECTID'] == 'NormalObserving') & np.logical_and(
        info['ST_TS'].astype(np.float) >= trange[0].lv,
        info['ST_TS'].astype(np.float) <= trange[
            1].lv))
filelist = info['FILE'][sidx]

outpath = './msdata/'
if not os.path.exists(outpath):
    os.makedirs(outpath)
inpath = idbdir + '{}/'.format(trange[0].datetime.strftime("%Y%m%d"))
ncpu = 1

msfiles = timporteovsa.importeovsa(idbfiles=[inpath + ll for ll in filelist], ncpu=ncpu, timebin="0s", width=1,
                                   visprefix=outpath,
                                   nocreatms=False, doconcat=False,
                                   modelms="", doscaling=False, keep_nsclms=False, udb_corr=True)

If you come across errors with calibeovsa, add following lines to your ~/.casa/init.py file.

import sys
sys.path.append('/common/python')
sys.path.append('/common/python/packages/pipeline_casa')
execfile('/common/python/suncasa/tasks/mytasks.py')

Step 2: Concatenate all the 10 mins data, if there are any

Follow this step if there are more than one .ms files, if not run step 3 directly.

# This is to set the path/name for the concatenated files
concatvis = os.path.basename(msfiles[0])[:11] + '_concat.ms'
vis = calibeovsa(msfiles, doconcat=True, concatvis=concatvis, msoutdir=outpath)

Step 3: Calibration

This will calibrate the input visibility, write out calibration tables under /data1/eovsa/caltable/, and apply the calibration. If doimage=True, a quicklook image will be produced (by integrating over the entire time).

calibeovsa(vis='IDB20170821202020.ms', caltype=['refpha','phacal'], doimage=True)        #Change the vis filename accordingly

One needs to transfer the created ms data files from pipeline to inti server, which has all the casatasks installed, in order to run the rest of the imaging steps.

Connection details to Inti server

For Windows, on Mobaxterm,

1. With your NJIT VPN connected, connect to one of the afsconnect servers (for example, afsaccess3.njit.edu) using your UCID and password.
2. ssh -X UCID@inti.hpcnet.campus.njit.edu

To avoid typing the full inti address each time you attempt for ssh, you may wish to add the following lines with your username to C:\Program Files\Git\etc\ssh\ssh_config on Windows and /.ssh/config on Mac and Linux machines.

Host inti
Hostname inti.hpcnet.campus.njit.edu
User USERNAME

To have sufficient disk space with EOVSA data analysis over Inti, use your dedicated directory YOURDIRECTORY at the location given below. If you do not have a directory, Please take help from Sijie in creating one.

cd /inti/data/users/YOURDIRECTORY     

For Linux or Mac machine, ssh -X UCID@inti.hpcnet.campus.njit.edu

Transferring data files between servers

A direct transfer between the servers is possible, but with some issues (this method will be updated soon).

Alternatively, one can follow the below procedure to do the transfer.

For Windows, on mobaxterm, drag and drop the ms file to your local machine or use scp command as given below.

scp -r -C userid@pipeline:/your/folder/msfile /localmachine/destination/folder/

On mobaxterm and on your local terminal, use the following command to finally copy the ms file to Inti.

scp -r -C /localmachine/destination/folder/msfile UCID@inti.hpcnet.campus.njit.edu:/inti/data/users/YOURDIRECTORY

For Mac and Linux, SCP can be used in the same way. Add the following lines to your SSH config file, to bypass ovsa.njit.edu from copying. vi ~/.ssh/config

Host ovsa
        HostName ovsa.njit.edu
        User guest
Host pipeline
        Hostname pipeline.solar.pvt
        User userid
        ProxyCommand ssh -W %h:%p guest@ovsa.njit.edu

Software details on the servers

On Inti, when logging in for the first time, please add the following lines to your accounts ~/.bashrc file.

>>vi ~/.bashrc Insert the text given below and save it.

#### setting start ####
if [ $HOSTNAME == "baozi.hpcnet.campus.njit.edu" ]; then
    source /srg/.setenv_baozi
fi
if [ $HOSTNAME == "inti.hpcnet.campus.njit.edu" ]; then
    source /inti/.setenv_inti
fi
if [ $HOSTNAME == "guko.resource.campus.njit.edu" ]; then
    source /data/data/.setenv_guko
fi
#### setting end ####

Both CASA 5 and 6 are available on Inti.

Enter the bash environment on inti, and load the desired casa environment. To load CASA 5, enter bash environment by giving >>bash

>> loadcasa5
>> suncasa              #This should load the software making you ready for the analysis

Or to load CASA 6, enter bash environment by giving >>bash

>> loadcasa6
>> ipython              #This should load the software making you ready for the analysis

Here, for example, to use clean, first start ipython as given above, then type in >>from casatasks import tclean

Step 4: Self-calibration on Inti server

https://github.com/binchensun/casa-eovsa/blob/master/slfcal_example.py

from suncasa.utils import helioimage2fits as hf
import os
import numpy as np
import pickle
from matplotlib import gridspec as gridspec
from sunpy import map as smap
from matplotlib import pyplot as plt
from split_cli import split_cli as split
import time

# =========== task handlers =============
dofullsun=0 # initial full-sun imaging             ##Change accordingly
domasks=1 # get masks                              ##Change accordingly
doslfcal=1 # main cycle of doing selfcalibration   ##Change accordingly
doapply=1 # apply the results                           ##Change accordingly
doclean_slfcaled=1 # perform clean for self-calibrated data        ##Change accordingly

# ============ declaring the working directories ============
workdir = os.getcwd()+'/' #main working directory. Using current directory in this example
slfcaldir = workdir+'slfcal/' #place to put all selfcalibration products
imagedir = slfcaldir+'images/' #place to put all selfcalibration images
maskdir = slfcaldir+'masks/' #place to put clean masks
imagedir_slfcaled = slfcaldir+'images_slfcaled/' #place to put final self-calibrated images
caltbdir = slfcaldir+'caltbs/' # place to put calibration tables
# make these directories if they do not already exist
dirs = [workdir, slfcaldir, imagedir, maskdir, imagedir_slfcaled, caltbdir]
for d in dirs:
    if not os.path.exists(d):
        os.makedirs(d)

# ============ Split a short time for self-calibration ===========
# input visibility
ms_in = workdir + 'IDB20170821_concat_original.ms'             ##Change accordingly
# output, selfcaled, visibility
ms_slfcaled = workdir + os.path.basename(ms_in).replace('original','slfcaled') 
# intermediate small visibility for selfcalbration 
# selected time range for generating self-calibration solutions
trange='2017/08/21/20:21:10~2017/08/21/20:21:30'               ##Change accordingly
slfcalms = slfcaldir+'slfcalms.XX.slfcal'
slfcaledms = slfcaldir+'slfcalms.XX.slfcaled'
if not os.path.exists(slfcalms):
    split(vis=ms_in,outputvis=slfcalms,datacolumn='data',timerange=trange,correlation='XX')

# ============ Prior definitions for spectral windows, antennas, pixel numbers =========
spws=[str(s+1) for s in range(30)]
antennas='0~12' 
npix=512
nround=3 #number of slfcal cycles
# parameters specific to the event (found from step 1)
phasecenter='J2000 10h02m59 11d58m14'        ##Change accordingly
xran=[280,480]                               ##Change accordingly
yran=[-50,150]                               ##Change accordingly

# =========== Step 1, doing a full-Sun image to find out phasecenter and appropriate field of view =========
if dofullsun:
    #initial mfs clean to find out the image phase center
    im_init='fullsun_init'
    os.system('rm -rf '+im_init+'*')
    tclean(vis=slfcalms,
            antenna='0~12',
            imagename=im_init,
            spw='1~15',
            specmode='mfs',
            timerange=trange,
            imsize=[npix],
            cell=['5arcsec'],
            niter=1000,
            gain=0.05,
            stokes='I',
            restoringbeam=['30arcsec'],
            interactive=False,
            pbcor=True)

    hf.imreg(vis=slfcalms,imagefile=im_init+'.image.pbcor',fitsfile=im_init+'.fits',
             timerange=trange,usephacenter=False,verbose=True)
    clnjunks = ['.flux', '.mask', '.model', '.psf', '.residual','.sumwt','.pb','.image']
    for clnjunk in clnjunks:
        if os.path.exists(im_init + clnjunk):
            os.system('rm -rf '+im_init + clnjunk)

    from sunpy import map as smap
    from matplotlib import pyplot as plt
    fig = plt.figure(figsize=(6,6))
    ax = fig.add_subplot(111)
    eomap=smap.Map(im_init+'.fits')
    #eomap.data=eomap.data.reshape((npix,npix))
    eomap.plot_settings['cmap'] = plt.get_cmap('jet')
    eomap.plot(axes = ax)
    eomap.draw_limb()
    plt.show()
    viewer(im_init+'.image.pbcor')

# =========== Step 2 (optional), generate masks =========
# if skipped, will not use any masks
if domasks:
    clearcal(slfcalms)
    delmod(slfcalms)
    antennas='0~12' 
    pol='XX'
    imgprefix=maskdir+'slf_t0'

    # step 1: set up the clean masks
    img_init=imgprefix+'_init_ar_'
    os.system('rm -rf '+img_init+'*')
    #spwrans_mask=['1~5','6~12','13~20','21~30']
    spwrans_mask=['1~12']
    #convert to a list of spws
    spwrans_mask_list = [[str(i) for i in (np.arange(int(m.split('~')[0]),int(m.split('~')[1])))] for m in spwrans_mask]
    masks=[]
    imnames=[]
    for spwran in spwrans_mask:
        imname=img_init+spwran.replace('~','-')
        try:
            tclean(vis=slfcalms,
                    antenna='0~12',
                    imagename=imname,
                    spw=spwran,
                    specmode='mfs',
                    timerange=trange,
                    imsize=[npix],
                    cell=['2arcsec'],
                    niter=1000,
                    gain=0.05,
                    stokes='XX',
                    restoringbeam=['20arcsec'],
                    phasecenter=phasecenter,
                    weighting='briggs',
                    robust=1.0,
                    interactive=True,
		    datacolumn='data',
                    pbcor=True,
                    savemodel='modelcolumn')
            imnames.append(imname+'.image')
            masks.append(imname+'.mask')
            clnjunks = ['.flux', '.model', '.psf', '.residual']
            for clnjunk in clnjunks:
                if os.path.exists(imname + clnjunk):
                    os.system('rm -rf '+ imname + clnjunk)
        except:
            print('error in cleaning spw: '+spwran)

    pickle.dump(masks,open(slfcaldir+'masks.p','wb'))

# =========== Step 3, main step of selfcalibration =========
if doslfcal:
    if os.path.exists(slfcaldir+'masks.p'):
        masks=pickle.load(open(slfcaldir+'masks.p','rb'))
    if not os.path.exists(slfcaldir+'masks.p'):
        print 'masks do not exist. Use default mask'
        masks=[]
    os.system('rm -rf '+imagedir+'*')
    os.system('rm -rf '+caltbdir+'*')
    #first step: make a mock caltable for the entire database
    print('Processing ' + trange)
    slftbs=[]
    calprefix=caltbdir+'slf'
    imgprefix=imagedir+'slf'
    tb.open(slfcalms+'/SPECTRAL_WINDOW')
    reffreqs=tb.getcol('REF_FREQUENCY')
    bdwds=tb.getcol('TOTAL_BANDWIDTH')
    cfreqs=reffreqs+bdwds/2.
    tb.close()
    # starting beam size at 3.4 GHz in arcsec
    sbeam=40.
    strtmp=[m.replace(':','') for m in trange.split('~')]
    timestr='t'+strtmp[0]+'-'+strtmp[1]
    refantenna='0'
    # number of iterations for each round
    niters=[100, 300, 500]
    # roburst value for weighting the baselines
    robusts=[1.0, 0.5, 0.0]
    # apply calibration tables? Set to true for most cases
    doapplycal=[1,1,1]
    # modes for calibration, 'p' for phase-only, 'a' for amplitude only, 'ap' for both
    calmodes=['p','p','a']
    # setting uvranges for model image (optional, not used here)
    uvranges=['','',''] 
    for n in range(nround):
        slfcal_tb_g= calprefix+'.G'+str(n)
        fig = plt.figure(figsize=(8.4,7.))
        gs = gridspec.GridSpec(5, 6)
        for s,sp in enumerate(spws):
            print 'processing spw: '+sp
            cfreq=cfreqs[int(sp)]
            # setting restoring beam size (not very useful for selfcal anyway, but just to see the results)
            bm=max(sbeam*cfreqs[1]/cfreq, 6.)
            slfcal_img = imgprefix+'.spw'+sp.zfill(2)+'.slfcal'+str(n)
            # only the first round uses nearby spws for getting initial model
            if n == 0:
                spbg=max(int(sp)-2,1)
                sped=min(int(sp)+2,30)
                spwran=str(spbg)+'~'+str(sped)
                print('using spw {0:s} as model'.format(spwran))
                if 'spwrans_mask' in vars():
                    for m, spwran_mask in enumerate(spwrans_mask):
                        if sp in spwran_mask:
                            mask = masks[m]
                            print('using mask {0:s}'.format(mask))
                            findmask = True
                    if not findmask:
                        print('mask not found. Do use any masks')
            else:
                spwran = sp
                if 'spwrans_mask' in vars():
                    for m, spwran_mask in enumerate(spwrans_mask):
                        if sp in spwran_mask:
                            mask = masks[m]
                            print 'using mask {0:s}'.format(mask)
                            findmask = True
                    if not findmask:
                        print('mask not found. Do use any masks')
            try:
                tclean(vis=slfcalms,
                        antenna=antennas,
                        imagename=slfcal_img,
                        uvrange=uvranges[n],
                        spw=spwran,
                        specmode='mfs',
                        timerange=trange,
                        imsize=[npix],
                        cell=['2arcsec'],
                        niter=niters[n],
                        gain=0.05,
                        stokes='XX', #use pol XX image as the model
                        weighting='briggs',
                        robust=robusts[n],
                        phasecenter=phasecenter,
                        mask=mask,
                        restoringbeam=[str(bm)+'arcsec'],
                        pbcor=False,
                        interactive=False,
                        savemodel='modelcolumn')
                if os.path.exists(slfcal_img+'.image'):
                    fitsfile=slfcal_img+'.fits'
                    hf.imreg(vis=slfcalms,imagefile=slfcal_img+'.image',fitsfile=fitsfile,
                             timerange=trange,usephacenter=False,toTb=True,verbose=False,overwrite=True)
                clnjunks = ['.mask','.flux', '.model', '.psf', '.residual', '.image','.pb','.image.pbcor','.sumwt']
                for clnjunk in clnjunks:
                    if os.path.exists(slfcal_img + clnjunk):
                        os.system('rm -rf '+ slfcal_img + clnjunk)
                ax = fig.add_subplot(gs[s])
                eomap=smap.Map(fitsfile)
                eomap.plot_settings['cmap'] = plt.get_cmap('jet')
                eomap.plot(axes = ax)
                eomap.draw_limb()
                #eomap.draw_grid()
                ax.set_title(' ')
		ax.get_xaxis().set_visible(False)
		ax.get_yaxis().set_visible(False)
                ax.set_xlim(xran)
                ax.set_ylim(yran)
                os.system('rm -f '+ fitsfile)

            except:
                print 'error in cleaning spw: '+sp
                print 'using nearby spws for initial model'
                sp_e=int(sp)+2
                sp_i=int(sp)-2
                if sp_i < 1:
                    sp_i = 1
                if sp_e > 30:
                    sp_e = 30
                sp_=str(sp_i)+'~'+str(sp_e)
                try:
                    tget(tclean)
                    spw=sp_
                    print('using spw {0:s} as model'.format(sp_))
                    tclean()
                except:
                    print 'still not successful. abort...'
                    break

            gaincal(vis=slfcalms, refant=refantenna,antenna=antennas,caltable=slfcal_tb_g,spw=sp, uvrange='',\
                    gaintable=[],selectdata=True,timerange=trange,solint='inf',gaintype='G',calmode=calmodes[n],\
                    combine='',minblperant=4,minsnr=2,append=True)
            if not os.path.exists(slfcal_tb_g):
                print 'No solution found in spw: '+sp
        figname=imagedir+'slf_t0_n{:d}.png'.format(n)
	plt.subplots_adjust(left=0, bottom=0, right=1, top=1, wspace=0, hspace=0)
        plt.savefig(figname)
        time.sleep(10)
        plt.close()

        if os.path.exists(slfcal_tb_g):
            slftbs.append(slfcal_tb_g)
            slftb=[slfcal_tb_g]
            os.chdir(slfcaldir)
            if calmodes[n] == 'p': 
                plotcal(caltable=slfcal_tb_g,antenna='1~12',xaxis='freq',yaxis='phase',\
                        subplot=431,plotrange=[-1,-1,-180,180],iteration='antenna',figfile=slfcal_tb_g+'.png',showgui=False)
            if calmodes[n] == 'a':
                plotcal(caltable=slfcal_tb_g,antenna='1~12',xaxis='freq',yaxis='amp',\
                        subplot=431,plotrange=[-1,-1,0,2.],iteration='antenna',figfile=slfcal_tb_g+'.png',showgui=False)
            os.chdir(workdir)


        if doapplycal[n]:
            clearcal(slfcalms)
            delmod(slfcalms)
            applycal(vis=slfcalms,gaintable=slftb,spw=','.join(spws),selectdata=True,\
                     antenna=antennas,interp='nearest',flagbackup=False,applymode='calonly',calwt=False)

        if n < nround-1: 
            prompt=raw_input('Continuing to selfcal?')
            #prompt='y'
            if prompt.lower() == 'n':
                if os.path.exists(slfcaledms):
                    os.system('rm -rf '+slfcaledms)
                split(slfcalms,slfcaledms,datacolumn='corrected')
                print 'Final calibrated ms is {0:s}'.format(slfcaledms)
                break
            if prompt.lower() == 'y':
                slfcalms_=slfcalms+str(n)
                if os.path.exists(slfcalms_):
                    os.system('rm -rf '+slfcalms_)
                split(slfcalms,slfcalms_,datacolumn='corrected')
                slfcalms=slfcalms_
        else:
            if os.path.exists(slfcaledms):
                os.system('rm -rf '+slfcaledms)
            split(slfcalms,slfcaledms,datacolumn='corrected')
            print 'Final calibrated ms is {0:s}'.format(slfcaledms)

# =========== Step 4: Apply self-calibration tables =========
if doapply:
    import glob
    os.chdir(workdir)
    clearcal(ms_in)
    clearcal(slfcalms)
    applycal(vis=slfcalms,gaintable=slftbs,spw=','.join(spws),selectdata=True,\
             antenna=antennas,interp='linear',flagbackup=False,applymode='calonly',calwt=False)
    applycal(vis=ms_in,gaintable=slftbs,spw=','.join(spws),selectdata=True,\
             antenna=antennas,interp='linear',flagbackup=False,applymode='calonly',calwt=False)
    if os.path.exists(ms_slfcaled):
        os.system('rm -rf '+ms_slfcaled)
    split(ms_in, ms_slfcaled,datacolumn='corrected')

# =========== Step 5: Generate final self-calibrated images (optional) =========
if doclean_slfcaled:
    import glob
    pol='XX'
    print('Processing ' + trange)
    img_final=imagedir_slfcaled+'/slf_final_{0}_t0'.format(pol)
    vis = ms_slfcaled
    spws=[str(s+1) for s in range(30)]
    tb.open(vis+'/SPECTRAL_WINDOW')
    reffreqs=tb.getcol('REF_FREQUENCY')
    bdwds=tb.getcol('TOTAL_BANDWIDTH')
    cfreqs=reffreqs+bdwds/2.
    tb.close()
    sbeam=30.
    from matplotlib import gridspec as gridspec
    from sunpy import map as smap
    from matplotlib import pyplot as plt
    fitsfiles=[]
    for s,sp in enumerate(spws):
        cfreq=cfreqs[int(sp)]
        bm=max(sbeam*cfreqs[1]/cfreq,4.)
        imname=img_final+'_s'+sp.zfill(2)
        fitsfile=imname+'.fits'
        if not os.path.exists(fitsfile):
            print 'cleaning spw {0:s} with beam size {1:.1f}"'.format(sp,bm)
            try:
                tclean(vis=vis,
                        antenna=antennas,
                        imagename=imname,
                        spw=sp,
                        specmode='mfs',
                        timerange=trange,
                        imsize=[npix],
                        cell=['1arcsec'],
                        niter=1000,
                        gain=0.05,
                        stokes=pol,
                        weighting='briggs',
                        robust=2.0,
                        restoringbeam=[str(bm)+'arcsec'],
                        phasecenter=phasecenter,
                        mask='',
                        pbcor=True,
                        interactive=False)
            except:
                print 'cleaning spw '+sp+' unsuccessful. Proceed to next spw'
                continue
            if os.path.exists(imname+'.image.pbcor'):
                imn = imname+'.image.pbcor'
                hf.imreg(vis=vis,imagefile=imn,fitsfile=fitsfile,
                         timerange=trange,usephacenter=False,toTb=True,verbose=False)
            fitsfiles.append(fitsfile)
            junks=['.flux','.model','.psf','.residual','.mask','.image','.pb','.image.pbcor','.sumwt']
            for junk in junks:
                if os.path.exists(imname+junk):
                    os.system('rm -rf '+imname+junk)
        else:
            print('fits file '+fitsfile+' already exists, skip clean...')
            fitsfiles.append(fitsfile)

    fig = plt.figure(figsize=(8.4,7.))
    gs = gridspec.GridSpec(5, 6)
    for s,sp in enumerate(spws):
        cfreq=cfreqs[int(sp)]
        ax = fig.add_subplot(gs[s])
        eomap=smap.Map(fitsfiles[s])
        eomap.plot_settings['cmap'] = plt.get_cmap('jet')
        eomap.plot(axes = ax)
        eomap.draw_limb()
        ax.set_title(' ')
        ax.get_xaxis().set_visible(False)
        ax.get_yaxis().set_visible(False)
        ax.set_xlim(xran)
        ax.set_ylim(yran)
        plt.text(0.98,0.85,'{0:.1f} GHz'.format(cfreq/1e9),transform=ax.transAxes,ha='right',color='w',fontweight='bold')
    plt.subplots_adjust(left=0, bottom=0, right=1, top=1, wspace=0, hspace=0)
    plt.show()