cal_apriori_pang_uvfits.py

#!/usr/bin/env python2

#hops2uvfits.py
#take data from all fringe files in a directory and put them in a uvfits file
import numpy as np
import mk4 # part of recent HOPS install, need HOPS ENV variables
import datetime
import ctypes
import astropy.io.fits as fits
import astropy.time as at
from astropy.time import Time
from argparse import Namespace
import glob
import os, sys
#import eat.hops.util
#from eat.io import util
#from eat.plots import util as putil
#from astropy.time import Time
import numpy.matlib
import scipy.interpolate
import itertools as it
from hops2uvfits import *
import pandas as pd
import datetime
from datetime import timedelta

# For Andrew:
#DATADIR_DEFAULT = '/home/achael/EHT/hops/data/3554/' #/098-0924/'
DAY=str(3600)
CALDIR_DEFAULT = '/home/achael/Desktop/imaging_workshop/HOPS_Rev1/SEFDs/SEFD_HI/'+DAY
DATADIR_DEFAULT = '/home/achael/Desktop/imaging_workshop/HOPS_Rev1/er1-hops-hi/6.uvfits_new/'+DAY
OUTDIR_DEFAULT = '/home/achael/Desktop/imaging_workshop/HOPS_Rev1/er1-hops-hi/7.apriorical'

#For Katie
#CALDIR_DEFAULT = '/Users/klbouman/Research/vlbi_imaging/software/hops/eat/SEFDs/SEFD_HI/3601'
#DATADIR_DEFAULT =  '/Users/klbouman/Research/vlbi_imaging/software/hops/tmpout2' #'/Users/klbouman/Research/vlbi_imaging/software/hops/er1-hops-hi/6.uvfits/3601'
#OUTDIR_DEFAULT = '/Users/klbouman/Research/vlbi_imaging/software/hops/tmpout'


#conversion factors and data types
#station_dic = {'ALMA':'AA', 'APEX':'AP', 'SMTO':'AZ', 'JCMT':'JC', 'LMT':'LM', 'PICOVEL':'PV', 'SMAP':'SM', 'SMAR':'SR', 'SPT':'SP'}
station_dic = {'ALMA':'AA', 'A':'AA','AA':'AA',
           'APEX':'AP', 'X':'AP','AP': 'AP',
            'LMT':'LM','L':'LM','LM':'LM',
            'PICOVEL':'PV','P':'PV','IRAM30': 'PV','PV':'PV',
            'SMTO':'AZ','Z': 'AZ','SMT':'AZ','AZ':'AZ',
            'SPT':'SP','Y':'SP','SP':'SP',
            'JCMT':'JC','J':'JC','JC':'JC',
            'SMAP':'SM','S':'SM','SMAR':'SM','SMA':'SM','SM':'SM',
            'SMAR':'SR','R':'SR','SMR':'SR','SR':'SR'}

station_frot = {'PV':(1,-1,0),'AZ':(1,1,0),'SM':(1,-1,np.pi/4.),'LM': (1,-1,0),'AA':(1,0,0),'SP':(1,0,0),'AP':(1,1,0),'JC':(1,0,0),'SR':(1,-1,np.pi/4.)}

BLTYPE = [('time','f8'),('t1','a32'),('t2','a32')]
DTARR = [('site', 'a32'), ('x','f8'), ('y','f8'), ('z','f8')]
DTCAL = [('time','f8'), ('rscale','c16'), ('lscale','c16')]
DTPOL = [('time','f8'),('freq','f8'),('tint','f8'),
            ('t1','a32'),('t2','a32'),
            ('u','f8'),('v','f8'),
            ('rr','c16'),('ll','c16'),('rl','c16'),('lr','c16'),
            ('rrweight','f8'),('llweight','f8'),('rlweight','f8'),('lrweight','f8')]
EP = 1.e-5
CORRCOEFF = 10000.0
DEGREE = np.pi/180.0
HOUR = 15.0*DEGREE
C = 299792458.0
MHZ2HZ = 1e6
MJD_0 = 2400000.5
RADPERARCSEC = (np.pi / 180.) / 3600.

##################################################################################################
# Caltable object
##################################################################################################
# ANDREW TODO copied from caltable.py in ehtim
# load directly instead?
class Caltable(object):
    """
       Attributes:
    """

    def __init__(self, ra, dec, rf, bw, datatables, tarr, source='NONE', mjd=0, timetype='UTC'):
        """A polarimetric VLBI observation of visibility amplitudes and phases (in Jy).

           Args:

           Returns:
               caltable (Caltable): an Caltable object
        """

        if len(datatables) == 0:
            raise Exception("No data in input table!")

        # Set the various parameters
        self.source = str(source)
        self.ra = float(ra)
        self.dec = float(dec)
        self.rf = float(rf)
        self.bw = float(bw)
        self.mjd = int(mjd)

        if timetype not in ['GMST', 'UTC']:
            raise Exception("timetype must by 'GMST' or 'UTC'")
        self.timetype = timetype
        self.tarr = tarr

        # Dictionary of array indices for site names
        self.tkey = {self.tarr[i]['site']: i for i in range(len(self.tarr))}

        # Save the data
        self.data = datatables

    def copy(self):
        """Copy the caltable object.

           Args:

           Returns:
               (Caltable): a copy of the Caltable object.
        """
        new_caltable = Caltable(self.ra, self.dec, self.rf, self.bw, self.data, self.tarr, source=self.source, mjd=self.mjd, timetype=self.timetype)
        return new_caltable


def load_caltable_ds(datastruct, tabledir, sqrt_gains=False ):
    """Load apriori cal tables
    """

    if datastruct.dtype != "EHTIM":
        raise Exception("datastruct must be in EHTIM format in load_caltable!")
    tarr = datastruct.antenna_info
    source = datastruct.obs_info.src
    mjd = int(np.min(datastruct.data['time'] - MJD_0))
    ra = datastruct.obs_info.ra
    dec = datastruct.obs_info.dec
    rf = datastruct.obs_info.ref_freq
    bw = datastruct.obs_info.ch_bw

    datatables = {}
    for s in range(0, len(tarr)):

        site = tarr[s]['site']

        # AIPS can only handle 8-character source name so "source" may
        # be truncated.  Therefore, we match a pattern (note the "*")
        # and proceed only if there is one match
        pattern   = tabledir + "/" + source + '*_' + site + '.txt'
        filenames = glob.glob(pattern)
        if len(filenames) == 1:
            try:
                data = np.loadtxt(filenames[0], dtype=bytes).astype(str)
            except IOError:
                print("CORRUPTED FILE: " + filenames[0])
                continue

            filename_source = filenames[0].\
                replace(tabledir+'/', '').\
                replace('_'+site+'.txt', '')
            if source != filename_source:
                print('WARNING: the filename indicates a different source name')
                if filename_source.startswith(source):
                    print('which is probably due to AIPS source name truncation,'+
                          ' use the full name "'+filename_source+'"instead')
                    source = filename_source
        elif len(filenames) == 0:
            print("NO FILE MATCHING: " + pattern)
            continue
        else:
            print("MULTIPLE FILES MATCHING: " + pattern)
            continue

        datatable = []

        # ANDREW HACKY WAY TO MAKE IT WORK WITH ONLY ONE ENTRY
        onerowonly=False
        try: data.shape[1]
        except IndexError:
            data = data.reshape(1,len(data))
            onerowonly = True
        for row in data:

            time = (float(row[0]) - mjd) * 24.0 # time is given in mjd

 #            # Maciek's old convention had a square root
 #           rscale = np.sqrt(float(row[1])) # r
 #           lscale = np.sqrt(float(row[2])) # l

            if len(row) == 3:
                rscale = float(row[1])
                lscale = float(row[2])
            elif len(row) == 5:
                rscale = float(row[1]) + 1j*float(row[2])
                lscale = float(row[3]) + 1j*float(row[4])
            else:
                raise Exception("cannot load caltable -- format unknown!")
            if sqrt_gains:
                rscale = rscale**.5
                lscale = lscale**.5
            #ANDREW THERE ARE ZERO VALS IN THE CALTABLE
            if rscale==0. and lscale==0.:
                continue
            else:
                datatable.append(np.array((time, rscale, lscale), dtype=DTCAL))
            #ANDREW HACKY WAY TO MAKE IT WORK WITH ONLY ONE ENTRY
            if onerowonly:
                datatable.append(np.array((1.1*time, rscale, lscale), dtype=DTCAL))

        datatables[site] = np.array(datatable)

    if len(datatables)>0:
        caltable = Caltable(ra, dec, rf, bw, datatables, tarr, source=source, mjd=mjd, timetype='UTC')
    else:
        caltable=False
    return caltable

def xyz_2_latlong(obsvecs):
    """Compute the (geocentric) latitude and longitude of a site at geocentric position x,y,z
       The output is in radians
    """
    if len(obsvecs.shape)==1:
        obsvecs=np.array([obsvecs])
    out = []
    for obsvec in obsvecs:
        x = obsvec[0]
        y = obsvec[1]
        z = obsvec[2]
        lon = np.array(np.arctan2(y,x))
        lat = np.array(np.arctan2(z, np.sqrt(x**2+y**2)))
        out.append([lat,lon])
    out = np.array(out)
    #if out.shape[0]==1: out = out[0]
    return out

def apply_caltable_uvfits(caltable, datastruct, filename_out, interp='linear', extrapolate=True,frotcal=True,elev_function='astropy',interp_dt=1.,elev_interp_kind='cubic',err_scale=1.):
    """apply a calibration table to a uvfits file
       Args:
        caltable (Caltable) : a caltable object
        datastruct (Datastruct) :  input data structure in EHTIM format
        filename_out (str) :  uvfits output file name
        frotcal (bool): whether apply field rotation angle correction
        elev_function (string): 'ehtim' for ehtim's function of calculating elevation, anything else
        for astropy functions
    """

    if datastruct.dtype != "EHTIM":
        raise Exception("datastruct must be in EHTIM format in apply_caltable_uvfits!")

    if not (caltable.tarr == datastruct.antenna_info).all():
        raise Exception("The telescope array in the Caltable is not the same as in the Datastruct")

    if extrapolate is True: # extrapolate can be a tuple or numpy array
        fill_value = "extrapolate"
    else:
        fill_value = extrapolate

    # interpolate the calibration  table
    rinterp = {}
    linterp = {}
    skipsites = []

    #PREPARE INTERPOLATION DATA
    xyz={}
    latitude={}
    longitude={}
    ra = caltable.ra*np.pi*2./24.#rad
    dec = caltable.dec*np.pi*2./360.#rad
    sourcevec = np.array([np.cos(dec), 0, np.sin(dec)])
    PAR={}
    ELE={}
    OFF={}
    elevfit={}
    gmst_function= lambda time_mjd: Time(time_mjd, format='mjd').sidereal_time('mean','greenwich').hour*2.*np.pi/24.


    #FIND MAX RANGE OF MJD TIMES FOR INTERPOLATION
    if (frotcal==True)&(interp_dt>0):
        dt_mjd = interp_dt*1./24./60./60. #interp_dt in sec
        mjd_max=-1
        mjd_min=1e10
        for s in range(0, len(caltable.tarr)):
            site = caltable.tarr[s]['site']
            try:
                #sometimes station reported but no calibration
                time_mjd = caltable.data[site]['time']/24.0 + caltable.mjd
                mjd_max_foo = np.max(time_mjd)
                mjd_min_foo = np.min(time_mjd)
                if (mjd_max_foo > mjd_max):
                    mjd_max = mjd_max_foo
                if (mjd_min_foo < mjd_min):
                    mjd_min = mjd_min_foo
            except KeyError: continue
        #MAKE TIME GRIDS FOR INTERPOLATION
        time_mjd_fake = np.arange(mjd_min,mjd_max,dt_mjd)
        gmst_fake = gmst_function(time_mjd_fake)
        datetimes_fake = Time(time_mjd_fake, format='mjd').to_datetime()
        strtime_fake = [str(round_time(x)) for x in datetimes_fake]
        thetas_fake = np.mod((gmst_fake - ra), 2.*np.pi)

    for s in range(0, len(caltable.tarr)):
        site = caltable.tarr[s]['site']
        xyz_foo = np.asarray((caltable.tarr[s]['x'],caltable.tarr[s]['y'],caltable.tarr[s]['z']))
        xyz[site] = xyz_foo
        latlong = xyz_2_latlong(xyz_foo)
        latitude[site] = latlong[0][0]#rad
        longitude[site] = latlong[0][1]#rad
        PAR[site] = station_frot[site][0]
        ELE[site] = station_frot[site][1]
        OFF[site] = station_frot[site][2]

        # This is only if we interpolate elevation
        if (frotcal==True)&(interp_dt>0):
            if elev_function=='ehtim':
                elev_fake_foo = get_elev_2(earthrot(xyz[site], thetas_fake), sourcevec)#ehtim
            else:
                elev_fake_foo = get_elev(ra, dec, xyz[site], strtime_fake)##astropy

            elevfit[site] = scipy.interpolate.interp1d(time_mjd_fake, elev_fake_foo,
                                                kind=elev_interp_kind)

        try:
            caltable.data[site]
        except KeyError:
            skipsites.append(site)
            print ("No Calibration  Data for %s !" % site)
            continue

        time_mjd = caltable.data[site]['time']/24.0 + caltable.mjd

        rinterp[site] = scipy.interpolate.interp1d(time_mjd, caltable.data[site]['rscale'],
                                                   kind=interp, fill_value=fill_value)
        linterp[site] = scipy.interpolate.interp1d(time_mjd, caltable.data[site]['lscale'],
                                                   kind=interp, fill_value=fill_value)



    #-------------------------------------------
    # sort by baseline
    data =  datastruct.data
    idx = np.lexsort((data['t2'], data['t1']))
    bllist = []
    for key, group in it.groupby(data[idx], lambda x: set((x['t1'], x['t2'])) ):
        bllist.append(np.array([obs for obs in group]))
    bllist = np.array(bllist)

    # apply the  calibration

    datatable = []
    coub=0
    for bl_obs in bllist:
        t1 = bl_obs['t1'][0]
        t2 = bl_obs['t2'][0]
        coub=coub+1
        print('Calibrating {}-{} baseline, {}/{}'.format(t1,t2,coub,len(bllist)))
        time_mjd = bl_obs['time'] - MJD_0 #dates are in mjd in Datastruct
        if frotcal==True:
            gmst = gmst_function(time_mjd)
            thetas = np.mod((gmst - ra), 2*np.pi)
            hangle1 = gmst + longitude[t1] - ra #HOUR ANGLE FIRST TELESCOPE
            hangle2 = gmst + longitude[t2] - ra #HOUR ANGLE SECOND TELESCOPE
            par1I_t1 = np.sin(hangle1)
            par1I_t2 = np.sin(hangle2)
            par1R_t1 = np.cos(dec)*np.tan(latitude[t1]) - np.sin(dec)*np.cos(hangle1)
            par1R_t2 = np.cos(dec)*np.tan(latitude[t2]) - np.sin(dec)*np.cos(hangle2)
            parangle1 = np.angle(par1R_t1 + 1j*par1I_t1 ) #PARALACTIC ANGLE T1
            parangle2 = np.angle(par1R_t2 + 1j*par1I_t2 ) #PARALACTIC ANGLE T2
            if interp_dt<=0:
                if elev_function=='ehtim':
                    elev1 = get_elev_2(earthrot(xyz[t1], thetas), sourcevec)
                    elev2 = get_elev_2(earthrot(xyz[t2], thetas), sourcevec)
                else:
                    datetimes = Time(time_mjd, format='mjd').to_datetime()
                    strtime = [str(round_time(x)) for x in datetimes]
                    elev1 = get_elev(ra, dec, xyz[t1], strtime) #ELEVATION T1
                    elev2 = get_elev(ra, dec, xyz[t2], strtime) #ELEVATION T2
            else:
                elev1 = elevfit[t1](time_mjd)
                elev2 = elevfit[t2](time_mjd)

            fran1 = PAR[t1]*parangle1 + ELE[t1]*elev1 + OFF[t1]
            fran2 = PAR[t2]*parangle2 + ELE[t2]*elev2 + OFF[t2]
            fran_R1 = np.exp(1j*fran1)
            fran_L1 = np.exp(-1j*fran1)
            fran_R2 = np.exp(1j*fran2)
            fran_L2 = np.exp(-1j*fran2)


        if t1 in skipsites:
            rscale1 = lscale1 = np.array(1.)
        else:
            if frotcal==False:
                rscale1 = rinterp[t1](time_mjd)
                lscale1 = linterp[t1](time_mjd)
            else:
                rscale1 = rinterp[t1](time_mjd)*fran_R1
                lscale1 = linterp[t1](time_mjd)*fran_L1
        if t2 in skipsites:
            rscale2 = lscale2 = np.array(1.)
        else:
            if frotcal==False:
                rscale2 = rinterp[t2](time_mjd)
                lscale2 = linterp[t2](time_mjd)
            else:
                rscale2 = rinterp[t2](time_mjd)*fran_R2
                lscale2 = linterp[t2](time_mjd)*fran_L2


#        if force_singlepol == 'R':
#            lscale1 = rscale1
#            lscale2 = rscale2
#        if force_singlepol == 'L':
#            rscale1 = lscale1
#            rscale2 = lscale2

        rrscale = rscale1 * rscale2.conj()
        llscale = lscale1 * lscale2.conj()
        rlscale = rscale1 * lscale2.conj()
        lrscale = lscale1 * rscale2.conj()

        bl_obs['rr'] = (bl_obs['rr']) * rrscale
        bl_obs['ll'] = (bl_obs['ll']) * llscale
        bl_obs['rl'] = (bl_obs['rl']) * rlscale
        bl_obs['lr'] = (bl_obs['lr']) * lrscale

        bl_obs['rrweight'] = (bl_obs['rrweight']) / (np.abs(rrscale)**2)
        bl_obs['llweight'] = (bl_obs['llweight']) / (np.abs(llscale)**2)
        bl_obs['rlweight'] = (bl_obs['rlweight']) / (np.abs(rlscale)**2)
        bl_obs['lrweight'] = (bl_obs['lrweight']) / (np.abs(lrscale)**2)

        if len(datatable):
            datatable = np.hstack((datatable, bl_obs))
        else:
            datatable = bl_obs

    # put in uvfits format datastruct
    # telescope arrays
    tarr = datastruct.antenna_info
    tkeys = {tarr[i]['site']: i for i in range(len(tarr))}
    tnames = tarr['site']
    tnums = np.arange(1, len(tarr) + 1)
    xyz = np.array([[tarr[i]['x'],tarr[i]['y'],tarr[i]['z']] for i in np.arange(len(tarr))])

    # uvfits format output data table
    bl_list = []
    for i in xrange(len(datatable)):
        entry = datatable[i]
        t1num = entry['t1']
        t2num = entry['t2']
        rl = entry['rl']
        lr = entry['lr']
        if tkeys[entry['t2']] < tkeys[entry['t1']]: # reorder telescopes if necessary
            #print entry['t1'], tkeys[entry['t1']], entry['t2'], tkeys[entry['t2']]
            entry['t1'] = t2num
            entry['t2'] = t1num
            entry['u'] = -entry['u']
            entry['v'] = -entry['v']
            entry['rr'] = np.conj(entry['rr'])
            entry['ll'] = np.conj(entry['ll'])
            entry['rl'] = np.conj(lr)
            entry['lr'] = np.conj(rl)
            datatable[i] = entry
        bl_list.append(np.array((entry['time'],entry['t1'],entry['t2']),dtype=BLTYPE))
    _, unique_idx_anttime, idx_anttime = np.unique(bl_list, return_index=True, return_inverse=True)
    _, unique_idx_freq, idx_freq = np.unique(datatable['freq'], return_index=True, return_inverse=True)

    # random group params
    u = datatable['u'][unique_idx_anttime]
    v = datatable['v'][unique_idx_anttime]
    t1num = [tkeys[scope] + 1 for scope in datatable['t1'][unique_idx_anttime]]
    t2num = [tkeys[scope] + 1 for scope in datatable['t2'][unique_idx_anttime]]
    bls = 256*np.array(t1num) + np.array(t2num)
    jds = datatable['time'][unique_idx_anttime]
    tints = datatable['tint'][unique_idx_anttime]

    # data table
    nap = len(unique_idx_anttime)
    nsubchan = 1
    nstokes = 4
    nchan = datastruct.obs_info.nchan

    outdat = np.zeros((nap, 1, 1, nchan, nsubchan, nstokes, 3))
    outdat[:,:,:,:,:,:,2] = -1.0

    vistypes = ['rr','ll','rl','lr']
    for i in xrange(len(datatable)):
        row_freq_idx = idx_freq[i]
        row_dat_idx = idx_anttime[i]

        for j in range(len(vistypes)):
            outdat[row_dat_idx,0,0,row_freq_idx,0,j,0] = np.real(datatable[i][vistypes[j]])
            outdat[row_dat_idx,0,0,row_freq_idx,0,j,1] = np.imag(datatable[i][vistypes[j]])
            outdat[row_dat_idx,0,0,row_freq_idx,0,j,2] = datatable[i][vistypes[j]+'weight']

    # package data for saving
    obsinfo_out = datastruct.obs_info
    antennainfo_out = Antenna_info(tnames, tnums, xyz)
    uvfitsdata_out = Uvfits_data(u,v,bls,jds, tints, outdat)
    datastruct_out = Datastruct(obsinfo_out, antennainfo_out, uvfitsdata_out)

    # save final file
    save_uvfits(datastruct_out, filename_out)
    return

def get_elev(ra_source, dec_source, xyz_antenna, time):
    #this one is by Michael Janssen
    """
    given right ascension and declination of a sky source [ICRS: ra->(deg,arcmin,arcsec) and dec->(hour,min,sec)]
    and given the position of the telescope from the vex file [Geocentric coordinates (m)]
    and the time of the observation (e.g. '2012-7-13 23:00:00') [UTC:yr-m-d],
    returns the elevation of the telescope.
    Note that every parameter can be an array (e.g. the time)
    """
    from astropy import units as u
    from astropy.coordinates import EarthLocation, AltAz, ICRS, Angle
    #angle conversions:
    ra_src      = Angle(ra_source, unit=u.rad)
    dec_src      = Angle(dec_source, unit=u.rad)

    source_position  = ICRS(ra=ra_src, dec=dec_src)
    antenna_position = EarthLocation(x=xyz_antenna[0]*u.m, y=xyz_antenna[1]*u.m, z=xyz_antenna[2]*u.m)
    altaz_system     = AltAz(location=antenna_position, obstime=time)
    trans_to_altaz   = source_position.transform_to(altaz_system)
    elevation        = trans_to_altaz.alt
    return elevation.rad

def round_time(t,round_s=1.):

    """rounding time to given accuracy

    Args:
        t: time
        round_s: delta time to round to in seconds

    Returns:
        round_t: rounded time
    """
    t0 = datetime.datetime(t.year,1,1)
    foo = t - t0
    foo_s = foo.days*24*3600 + foo.seconds + foo.microseconds*(1e-6)
    foo_s = np.round(foo_s/round_s)*round_s
    days = np.floor(foo_s/24/3600)
    seconds = np.floor(foo_s - 24*3600*days)
    microseconds = int(1e6*(foo_s - days*3600*24 - seconds))
    round_t = t0+datetime.timedelta(days,seconds,microseconds)
    return round_t


def earthrot(vecs, thetas):
    """Rotate a vector / array of vectors about the z-direction by theta / array of thetas (radian)
    """
    if len(vecs.shape)==1:
        vecs = np.array([vecs])
    if np.isscalar(thetas):
        thetas = np.array([thetas for i in range(len(vecs))])

    # equal numbers of sites and angles
    if len(thetas) == len(vecs):
        rotvec = np.array([np.dot(np.array(((np.cos(thetas[i]),-np.sin(thetas[i]),0),(np.sin(thetas[i]),np.cos(thetas[i]),0),(0,0,1))), vecs[i])
                       for i in range(len(vecs))])

    # only one rotation angle, many sites
    elif len(thetas) == 1:
        rotvec = np.array([np.dot(np.array(((np.cos(thetas[0]),-np.sin(thetas[0]),0),(np.sin(thetas[0]),np.cos(thetas[0]),0),(0,0,1))), vecs[i])
                       for i in range(len(vecs))])
    # only one site, many angles
    elif len(vecs) == 1:
        rotvec = np.array([np.dot(np.array(((np.cos(thetas[i]),-np.sin(thetas[i]),0),(np.sin(thetas[i]),np.cos(thetas[i]),0),(0,0,1))), vecs[0])
                       for i in range(len(thetas))])
    else:
        raise Exception("Unequal numbers of vectors and angles in earthrot(vecs, thetas)!")

    return rotvec

def get_elev_2(obsvecs, sourcevec):
    """Return the elevation of a source with respect to an observer/observers in radians
       obsvec can be an array of vectors but sourcevec can ONLY be a single vector
    """

    if len(obsvecs.shape)==1:
        obsvecs=np.array([obsvecs])

    anglebtw = np.array([np.dot(obsvec,sourcevec)/np.linalg.norm(obsvec)/np.linalg.norm(sourcevec) for obsvec in obsvecs])
    el = 0.5*np.pi - np.arccos(anglebtw)

    return el

##################################################################################################################################
##########################  Main FUNCTION ########################################################################################
##################################################################################################################################
def main(datadir=DATADIR_DEFAULT, caldir=CALDIR_DEFAULT, outdir=DATADIR_DEFAULT,
         interp='linear', extrapolate=True, ident='',sqrt_gains=False, frotcal=True,elev_function='astropy',interp_dt=1.,elev_interp_kind='cubic',err_scale=1.):

    print("********************************************************")
    print("*********************CALUVFITS**************************")
    print("********************************************************")

    print("Applying calibration tables from directory", caldir)
    print("to uvfits files in directory: ", datadir)
    print(' ')

    uvfitsfiles = glob.glob(datadir + '/*.uvfits')
    for uvfitsfile in sorted(uvfitsfiles):
        print(' ')
        print("A priori calibrating: ", uvfitsfile)

        tok = uvfitsfile.replace('.uvfits', '').split('_', 2)
        print("pipeline: "+tok[0])
        print("expr no:  "+tok[1])
        print("source:   "+tok[2])

        datastruct_ehtim = load_and_convert_hops_uvfits(uvfitsfile)

        source = datastruct_ehtim.obs_info.src
        if len(source) <= 8 and source != tok[2]:
            print('WARNING: source specified inside the uvfits file, "'+
                  source+'", does not match file name "'+tok[2]+'"')
            print('Guess real source name by using the file name')
            source = tok[2]
            datastruct_ehtim.obs_info.src = tok[2]

        tarr = datastruct_ehtim.antenna_info
        caltable = load_caltable_ds(datastruct_ehtim, caldir,sqrt_gains=sqrt_gains)
        if caltable==False:
            print("couldn't find caltable in " + caldir + " for " + source + "!!")
            continue

        outname = outdir + '/' + os.path.basename(uvfitsfile).replace('.uvfits', ident+'.apriori.uvfits')
        apply_caltable_uvfits(caltable, datastruct_ehtim, outname, interp=interp, extrapolate=extrapolate,frotcal=frotcal,elev_function=elev_function,interp_dt=interp_dt,elev_interp_kind=elev_interp_kind,err_scale=err_scale)
        print("Saved calibrated data to ", outname)
    print("---------------------------------------------------------")
    print("---------------------------------------------------------")
    print("---------------------------------------------------------")
    print(' ')
    return 0

if __name__=='__main__':
    if len(sys.argv) == 1:
        datadir = DATADIR_DEFAULT
    else: datadir = sys.argv[-1]
    if datadir[0] == '-': datadir=DATADIR_DEFAULT

    if ("-h" in sys.argv) or ("--h" in sys.argv):
        print("usage: caluvfits.py datadir \n" +
              "options: \n" +
              "   --caldir caldir : specify directory with cal tables \n" +
              "   --outdir outdir : specifiy output directory for calibrated files \n" +
              "   --ident : specify identifying tag for uvfits files \n"
              "   --interp : specify interpolation order \n" +
              "   --no-extrapolate : specify to not calibrate outside interval in cal tables \n"
              "   --sqrt_gains : specify to take sqrt of gains before applying")
        sys.exit()


    frotcal = True
    if "--no-frotcal"  in sys.argv: frotcal = False

    extrapolate = True
    if "--no-extrapolate" in sys.argv: extrapolate = False

    sqrt_gains = False
    if "--sqrt_gains" in sys.argv: sqrt_gains = True

    elev_function = 'astropy'
    if "--elev_function" in sys.argv:
        for a in range(0, len(sys.argv)):
            if(sys.argv[a] == '--elev_function'):
                elev_function = (sys.argv[a+1])

    interp_dt = 1.
    if "--interp_dt" in sys.argv:
        for a in range(0, len(sys.argv)):
            if(sys.argv[a] == '--interp_dt'):
                interp_dt = float(sys.argv[a+1])

    err_scale = 1.
    if "--err_scale" in sys.argv:
        for a in range(0, len(sys.argv)):
            if(sys.argv[a] == '--err_scale'):
                err_scale = float(sys.argv[a+1])

    interp = "linear"
    if "--interp" in sys.argv:
        for a in range(0, len(sys.argv)):
            if(sys.argv[a] == '--interp'):
                interp = (sys.argv[a+1])

    elev_interp_kind='cubic'
    if "--elev_interp_kind" in sys.argv:
        for a in range(0, len(sys.argv)):
            if(sys.argv[a] == '--elev_interp_kind'):
                elev_interp_kind = (sys.argv[a+1])

    ident = ""
    if "--ident" in sys.argv:
        for a in range(0, len(sys.argv)):
            if(sys.argv[a] == '--ident'):
                ident = "_" + sys.argv[a+1]

    caldir = CALDIR_DEFAULT
    if "--caldir" in sys.argv:
        for a in range(0, len(sys.argv)):
            if(sys.argv[a] == '--caldir'):
                caldir = sys.argv[a+1]

    outdir = datadir
    if "--outdir" in sys.argv:
        for a in range(0, len(sys.argv)):
            if(sys.argv[a] == '--outdir'):
                outdir = sys.argv[a+1]
    else:
        outdir = OUTDIR_DEFAULT

    main(datadir=datadir, outdir=outdir, caldir=caldir, ident=ident, interp=interp, extrapolate=extrapolate,sqrt_gains=sqrt_gains,frotcal=frotcal,elev_function=elev_function,interp_dt=interp_dt,elev_interp_kind=elev_interp_kind,err_scale=1.)