Документ взят из кэша поисковой машины. Адрес оригинального документа : http://www.mrao.cam.ac.uk/projects/OAS/oi_data/oi_fits.py Дата изменения: Fri Jan 11 15:22:07 2008 Дата индексирования: Fri Feb 28 13:42:23 2014 Кодировка: Поисковые слова: apod

# $Id: oi_fits.py,v 1.6 2004/03/01 10:35:33 jsy1001 Exp $

"""Example python module for FITS optical interferometry exchange format.

Implements April 2003 release of the Standard.

This module is structured as a set of python classes, instances of
which provide object-oriented access to data from an OI-FITS file
(which may not exist on disk yet!). The classes are as follows:

OI_FITS -- Instance stores data for entire OI-FITS file

The data attributes of the OI_FITS instance are instances of other
classes, or lists/dictionaries of these. Each of the these 'table classes'
corresponds to one of the FITS binary tables defined in the Standard:

Array -- OI_ARRAY table

Target -- OI_TARGET table

Wavelength -- OI_WAVELENGTH table

Vis -- OI_VIS table

Vis2 -- OI_VIS2 table

T3 -- OI_T3 table

The table classes typically have data attributes that are instances of
lower-level classes, corresponding to rows of the FITS table. These
'row classes' generally don't have any method attributes.

The entire FITS file corresponding to an OI_FITS instance may be read
from/written to disk using the instance's FromHDUList() and
ToHDUList() methods. These convert from/to a pyfits.HDUList instance
(which represents data from a generic FITS file), as defined in the
third-party pyfits module. pyfits provides many functions that can
operate on HDUList instances (see the pyfits manual).

A script to write an OI-FITS file would be structured as follows:

import oi_fits
oi = oi_fits.OI_FITS()
# insert code to assign to data attributes
oi.ToHDUList().writeto('output.fits')

A script to read from an OI-FITS file would be structured like this:

import oi_fits, pyfits
hlist = pyfits.open('input.fits')
oi = oi_fits.OI_FITS()
oi.FromHDUList(hlist)
hlist.close()
# insert code to do something with oi's data attributes

The _test function at the end of this file is a trivial example of
reading and writing an OI-FITS file.

Instances of table classes have FromTable() and ToTable() methods, which
convert between the table class instance and a pyfits.BinTableHDU
instance. These methods may be used when reading/writing individual
tables, rather than the whole file.

"""

from numarray import *
import pyfits, string


# Exceptions raised by methods of these classes
class OI_FITSError(Exception):
"""Base Exception class."""
pass

class OI_FITSConformError(OI_FITSError):
"""Raised if pyfits.BinTableHDU does not conform to OI-FITS spec."""
pass

class OI_FITSEmptyTableError(OI_FITSError):
"""Raised by ToTable() methods when table would have zero rows."""


class OI_FITS:
"""Data for entire OI_FITS file.

Data attributes are:

arrays -- Dictionary of Array instances, indexed by arrname

target -- Target instance

wavelengths -- Dictionary of Wavelength instances, indexed by insname

vis -- List of Vis instances

vis2 -- List of Vis2 instances

t3 -- List of T3 instances


Methods are:

ToHDUList() -- return pyfits.HDUList instance

FromHDUList(hlist) -- assign to data attributes from pyfits.HDUList instance

verify() -- would ToHDUList().writeto() give a standard-conforming FITS file?

"""

def __init__(self):
self.arrays = {}
self.target = None
self.wavelengths = {}
self.vis = []
self.vis2 = []
self.t3 = []

def ToHDUList(self):
"""Return pyfits.HDUList instance."""
hlist = pyfits.HDUList()
# Add primary HDU
pri = pyfits.PrimaryHDU()
hlist.append(pri)
# Add binary table HDUs
hlist.append(self.target.ToTable())
for i in range(len(self.wavelengths)):
hlist.append(self.wavelengths.values()[i].ToTable(extver=i+1))
for i in range(len(self.arrays)):
hlist.append(self.arrays.values()[i].ToTable(extver=i+1))
for i in range(len(self.vis)):
hlist.append(self.vis[i].ToTable(extver=i+1))
for i in range(len(self.vis2)):
hlist.append(self.vis2[i].ToTable(extver=i+1))
for i in range(len(self.t3)):
hlist.append(self.t3[i].ToTable(extver=i+1))
return hlist

def FromHDUList(self, hlist):
"""Assign to data attributes from pyfits.HDUList instance.

May raise OI_FITSConformError.

"""
for hdu in hlist[1:]:
extname = hdu.header['EXTNAME']
if extname == 'OI_WAVELENGTH':
wavelength = Wavelength()
wavelength.FromTable(hdu)
if wavelength.insname in self.wavelengths.keys():
raise OI_FITSConformError, "wavelength table has non-unique insname"
self.wavelengths[wavelength.insname] = wavelength
elif extname == 'OI_ARRAY':
array = Array()
array.FromTable(hdu)
if array.arrname in self.arrays.keys():
raise OI_FITSConformError, "array table has non-unique arrname"
self.arrays[array.arrname] = array
elif extname == 'OI_TARGET':
self.target = Target()
self.target.FromTable(hdu)
elif extname == 'OI_VIS':
vis = Vis()
vis.FromTable(hdu)
self.vis.append(vis)
elif extname == 'OI_VIS2':
vis2 = Vis2()
vis2.FromTable(hdu)
self.vis2.append(vis2)
elif extname == 'OI_T3':
t3 = T3()
t3.FromTable(hdu)
self.t3.append(t3)
else:
print 'Skipping non-standard %s table' % extname
if not self.verify():
raise OI_FITSConformError, "Missing table or bad insname"

def verify(self):
"""Would ToHDUList().writeto() give a standard-conforming FITS file?

Checks tables present.

"""
data = self.vis+self.vis2+self.t3
if self.target is None or len(data) == 0:
return 0
for obj in data:
if not self.wavelengths.has_key(obj.insname):
return 0
return 1


class Element:
"""Array element, corresponds to one row of an OI_ARRAY FITS table.

Data attributes are:

tel_name -- (string) Telescope name

sta_name -- (string) Station name

sta_index -- (int) Station number

diameter -- (float) Element diameter (meters)

staxyz -- (float 3-tuple) Station coords relative to array center (meters)

"""
pass


class Array:
"""Data for OI_ARRAY FITS table.

Data attributes are:

revision -- (int) Revision number of the table definition

arrname -- (string) Array name

frame -- (string) Coordinate frame (always 'GEOCENTRIC')

arrayx, arrayy, arrayz -- (float) Array center coordinates (meters)

elements -- *Dictionary* of Element instances, indexed by sta_index


Methods are:

ToTable() -- Return pyfits.BinTableHDU instance

FromTable() -- Copy to data attributes from pyfits.BinTableHDU instance

"""

def __init__(self):
self.revision = 1
self.frame = 'GEOCENTRIC'
self.elements = {}

def ToTable(self, extver=1):
"""Return pyfits.BinTableHDU instance."""
if len(self.elements) == 0:
raise OI_FITSEmptyTableError, "No elements in OI_ARRAY"
cols = []
cols.append(pyfits.Column(name='TEL_NAME', format='16A'))
cols.append(pyfits.Column(name='STA_NAME', format='16A'))
cols.append(pyfits.Column(name='STA_INDEX', format='I'))
cols.append(pyfits.Column(name='DIAMETER', format='E', unit='m'))
cols.append(pyfits.Column(name='STAXYZ', format='3D', unit='m'))
tabhdu = pyfits.new_table(cols, nrows=len(self.elements))
# Make list of Element instances, ordered by sta_index
els = self.elements.values()
els.sort(lambda a, b: cmp(a.sta_index, b.sta_index))
# Insert data
irow = 0
for r in els:
vals = [r.tel_name, r.sta_name, r.sta_index, r.diameter,
array(r.staxyz)]
for icol in range(len(cols)):
tabhdu.data.field(icol)[irow] = vals[icol]
irow += 1
tabhdu.name = 'OI_ARRAY'
hdr = tabhdu.header
hdr.update('EXTVER', extver,
comment='ID number of this OI_ARRAY')
hdr.update('OI_REVN', self.revision,
comment='Revision number of the table definition')
hdr.update('ARRNAME', self.arrname,
comment='Array name')
hdr.update('FRAME', self.frame,
comment='Coordinate frame')
hdr.update('ARRAYX', self.arrayx,
comment='[m] Array center X coordinate')
hdr.update('ARRAYY', self.arrayy,
comment='[m] Array center Y coordinate')
hdr.update('ARRAYZ', self.arrayz,
comment='[m] Array center Z coordinate')
return tabhdu

def FromTable(self, tabhdu):
"""Copy to data attributes from pyfits.BinTableHDU instance.

Values from non-standard columns get assigned to extra data
attributes.

"""
try:
self.revision = tabhdu.header['OI_REVN']
for keyword in ['ARRNAME', 'FRAME', 'ARRAYX', 'ARRAYY', 'ARRAYZ']:
self.__dict__[string.lower(keyword)] = tabhdu.header[keyword]
except KeyError:
raise OI_FITSConformError, "Missing keyword"
cols = tabhdu.get_coldefs()
self.elements = {}
for irow in range(len(tabhdu.data)):
el = Element()
for name in cols.names:
el.__dict__[string.lower(name)] = tabhdu.data[irow].field(name)
try:
el.staxyz = tuple(el.staxyz)
if self.elements.has_key(el.sta_index):
raise OI_FITSConformError, "Duplicate sta_index"
except AttributeError:
raise OI_FITSConformError, "Missing column"
self.elements[el.sta_index] = el


class TargetRecord:
"""Info on an observing target.

Corresponds to one row of an OI_TARGET FITS table.

Data attributes are:

target_id -- (int) Index number

target -- (string) Target name

raep0 -- (float) RA at mean equinox (degrees)

decep0 -- (float) DEC at mean equinox (degrees)

equinox -- (float) Equinox

ra_err -- (float) Error in RA at mean equinox (degrees)

dec_err -- (float) Error in RA at mean equinox (degrees)

sysvel -- (float) Systemic radial velocity (meters per second)

veltyp -- (string) Reference for radial velocity

veldef -- (string) Definition of radial velocity

pmra -- (float) Proper motion in RA (degrees per year)

pmdec -- (float) Proper motion in DEC (degrees per year)

pmra_err -- (float) Error of proper motion in RA (degrees per year)

pmdec_err -- (float) Error of proper motion in DEC (degrees per year)

parallax -- (float) Parallax (degrees)

para_err -- (float) Error in parallax (degrees)

spectyp -- (string) Spectral type

"""
pass


class Target:
"""Data for OI_TARGET FITS table.

Data attributes are:

revision -- (int) Revision number of the table definition

records -- *Dictionary* of TargetRecord instances, indexed by target_id


Methods are:

ToTable() -- Return pyfits.BinTableHDU instance

FromTable() -- Copy to data attributes from pyfits.BinTableHDU instance

"""

def __init__(self):
self.revision = 1
self.records = {}

def ToTable(self):
"""Return pyfits.BinTableHDU instance."""
if len(self.records) == 0:
raise OI_FITSEmptyTableError, "No records in OI_TARGET"
cols = []
cols.append(pyfits.Column(name='TARGET_ID', format='I'))
cols.append(pyfits.Column(name='TARGET', format='16A'))
cols.append(pyfits.Column(name='RAEP0', format='D', unit='deg'))
cols.append(pyfits.Column(name='DECEP0', format='D', unit='deg'))
cols.append(pyfits.Column(name='EQUINOX', format='E', unit='yr'))
cols.append(pyfits.Column(name='RA_ERR', format='D', unit='deg'))
cols.append(pyfits.Column(name='DEC_ERR', format='D', unit='deg'))
cols.append(pyfits.Column(name='SYSVEL', format='D', unit='m/s'))
cols.append(pyfits.Column(name='VELTYP', format='8A'))
cols.append(pyfits.Column(name='VELDEF', format='8A'))
for name in ['PMRA', 'PMDEC', 'PMRA_ERR', 'PMDEC_ERR']:
cols.append(pyfits.Column(name=name, format='D', unit='deg/yr'))
cols.append(pyfits.Column(name='PARALLAX', format='E', unit='deg'))
cols.append(pyfits.Column(name='PARA_ERR', format='E', unit='deg'))
cols.append(pyfits.Column(name='SPECTYP', format='16A'))
tabhdu = pyfits.new_table(cols, nrows=len(self.records))
# Make list of TargetRecord instances, ordered by target_id
recs = self.records.values()
recs.sort(lambda a, b: cmp(a.target_id, b.target_id))
# Insert data
irow = 0
for r in recs:
vals = [r.target_id, r.target, r.raep0, r.decep0, r.equinox,
r.ra_err, r.dec_err, r.sysvel,
r.veltyp, r.veldef, r.pmra, r.pmdec,
r.pmra_err, r.pmdec_err, r.parallax, r.para_err, r.spectyp]
for icol in range(len(cols)):
tabhdu.data.field(icol)[irow] = vals[icol]
irow += 1
tabhdu.name = 'OI_TARGET'
hdr = tabhdu.header
hdr.update('EXTVER', 1)
hdr.update('OI_REVN', self.revision,
comment='Revision number of the table definition')
return tabhdu

def FromTable(self, tabhdu):
"""Copy to data attributes from pyfits.BinTableHDU instance.

Values from non-standard columns get assigned to extra data
attributes.

"""
try:
self.revision = tabhdu.header['OI_REVN']
except KeyError:
raise OI_FITSConformError, "Missing keyword OI_REVN"
cols = tabhdu.get_coldefs()
self.records = {}
for irow in range(len(tabhdu.data)):
rec = TargetRecord()
for name in cols.names:
rec.__dict__[string.lower(name)] = tabhdu.data[irow].field(name)
try:
if self.records.has_key(rec.target_id):
raise OI_FITSConformError, "Duplicate target_id"
except AttributeError:
raise OI_FITSConformError, "Missing column"
self.records[rec.target_id] = rec


class Wavelength:
"""Data for OI_WAVELENGTH FITS table.

Data attributes are:

revision -- (int) Revision number of the table definition

insname -- (string) Name of detector

eff_wave -- (float list) Effective wavelength of each channel (meters)

eff_band -- (float list) Effective bandpass of each channel (meters)


Methods are:

ToTable() -- Return pyfits.BinTableHDU instance

FromTable() -- Copy to data attributes from pyfits.BinTableHDU instance

"""

def __init__(self):
self.revision = 1
self.eff_wave = []
self.eff_band = []

def ToTable(self, extver=1):
"""Return pyfits.BinTableHDU instance."""
if len(self.eff_wave) == 0 or len(self.eff_band) == 0:
raise OI_FITSEmptyTableError, "No channels in OI_WAVELENGTH"
col1 = pyfits.Column(name='EFF_WAVE', format='E', unit='m',
array=array(self.eff_wave))
col2 = pyfits.Column(name='EFF_BAND', format='E', unit='m',
array=array(self.eff_band))
tabhdu = pyfits.new_table([col1, col2])
tabhdu.name = 'OI_WAVELENGTH'
hdr = tabhdu.header
hdr.update('EXTVER', extver,
comment='ID number of this OI_WAVELENGTH')
hdr.update('OI_REVN', self.revision,
comment='Revision number of the table definition')
hdr.update('INSNAME', self.insname,
comment='Name of detector')
return tabhdu

def FromTable(self, tabhdu):
"""Copy to data attributes from pyfits.BinTableHDU instance."""
try:
self.revision = tabhdu.header['OI_REVN']
self.insname = tabhdu.header['INSNAME']
except KeyError:
raise OI_FITSConformError, "Missing keyword"
try:
self.eff_wave = tabhdu.data.field('EFF_WAVE').tolist()
self.eff_band = tabhdu.data.field('EFF_BAND').tolist()
except NameError:
raise OI_FITSConformError, "Missing column"


class VisRecord:
"""Complex visibility record.

Corresponds to one row of an OI_VIS FITS table.

Data attributes are:

target_id -- (int) Target number as index into Target.records

time - (float) UTC time of observation (seconds)

mjd -- (float) Modified Julian Day

int_time -- (float) Integration time (seconds)

visamp -- (float list, length nwave) Visibility amplitude

visamperr -- (float list, length nwave) Error in visibility amplitude

visphi -- (float list, length nwave) Visibility phase (degrees)

visphierr -- (float list, length nwave) Error in visibility phase (degrees)

ucoord -- (float) U coordinate of the data (meters)

vcoord -- (float) V coordinate of the data (meters)

sta_index -- (int 2-tuple) Station numbers contributing to the data

flag -- (boolean list, length nwave) Flag

"""
pass


class Vis:
"""Data for OI_VIS FITS table.

Data attributes are:

revision -- (int) revision number of the table definition

date_obs -- (int 3-tuple: y, m, d) UTC start date of observations
(or may be None)

arrname -- (string) Identifies corresponding Array instance (may be None)

insname -- (string) Identifies corresponding Wavelength instance

records -- list of VisRecord instances

nwave -- length of visamp, visamperr, visphi, visphierr, flag attributes
of records


Methods are:

ToTable() -- Return pyfits.BinTableHDU instance

FromTable() -- Copy to data attributes from pyfits.BinTableHDU instance

"""

def __init__(self):
self.revision = 1
self.arrname = None
self.nwave = 0
self.records = []

def ToTable(self, extver=1):
"""Return pyfits.BinTableHDU instance."""
if len(self.records) == 0:
raise OI_FITSEmptyTableError, "No records in OI_VIS"
# Define table structure
cols = []
cols.append(pyfits.Column(name='TARGET_ID', format='I'))
cols.append(pyfits.Column(name='TIME', format='D', unit='s'))
cols.append(pyfits.Column(name='MJD', format='D', unit='day'))
cols.append(pyfits.Column(name='INT_TIME', format='D', unit='s'))
cols.append(pyfits.Column(name='VISAMP', format='%dD' % self.nwave))
cols.append(pyfits.Column(name='VISAMPERR', format='%dD' % self.nwave))
cols.append(pyfits.Column(name='VISPHI', format='%dD' % self.nwave,
unit='deg'))
cols.append(pyfits.Column(name='VISPHIERR', format='%dD' % self.nwave,
unit='deg'))
cols.append(pyfits.Column(name='UCOORD', format='D', unit='m'))
cols.append(pyfits.Column(name='VCOORD', format='D', unit='m'))
cols.append(pyfits.Column(name='STA_INDEX', format='2I'))
cols.append(pyfits.Column(name='FLAG', format='%dL' % self.nwave))
tabhdu = pyfits.new_table(cols, nrows=len(self.records))
# Insert data
irow = 0
for r in self.records:
if self.nwave == 1:
vals = [r.target_id, r.time, r.mjd, r.int_time,
r.visamp[0], r.visamperr[0],
r.visphi[0], r.visphierr[0],
r.ucoord, r.vcoord, array(r.sta_index, type=Int16),
r.flag[0]]
else:
vals = [r.target_id, r.time, r.mjd, r.int_time,
array(r.visamp), array(r.visamperr), array(r.visphi),
array(r.visphierr), r.ucoord, r.vcoord,
array(r.sta_index, type=Int16),
array(r.flag, type=Bool)]
for icol in range(len(cols)):
tabhdu.data.field(icol)[irow] = vals[icol]
irow += 1
# Workaround for probable pyfits bug
true = array([ord('T')]*self.nwave, type=UInt8)
false = array([ord('F')]*self.nwave, type=UInt8)
tabhdu.data._parent.field('FLAG')[:] = where(tabhdu.data.field('FLAG'),
true, false)
# Insert header records
tabhdu.name = 'OI_VIS'
hdr = tabhdu.header
hdr.update('EXTVER', extver,
comment='ID number of this OI_VIS')
hdr.update('OI_REVN', self.revision,
comment='Revision number of the table definition')
hdr.update('DATE-OBS', '%04d-%02d-%02d' % self.date_obs,
comment='UTC Start date of observations')
if self.arrname is not None:
hdr.update('ARRNAME', self.arrname,
comment='Identifies corresponding OI_ARRAY')
hdr.update('INSNAME', self.insname,
comment='Identifies corresponding OI_WAVELENGTH')
return tabhdu

def FromTable(self, tabhdu):
"""Copy to data attributes from pyfits.BinTableHDU instance."""
try:
self.revision = tabhdu.header['OI_REVN']
self.date_obs = tuple(
map(int, string.split(tabhdu.header['DATE-OBS'], '-')))
# ARRNAME is optional
try:
self.arrname = tabhdu.header['ARRNAME']
except KeyError:
self.arrname = None
self.insname = tabhdu.header['INSNAME']
except KeyError:
raise OI_FITSConformError, "Missing keyword"
cols = tabhdu.get_coldefs()
try:
i = cols.names.index('VISAMP')
except ValueError:
raise OI_FITSConformError, "Missing column VISAMP"
end = 0
while cols.formats[i][end] in string.digits: end += 1
if end != 0:
self.nwave = int(cols.formats[i][:end])
else:
self.nwave = 1
self.records = []
for irow in range(len(tabhdu.data)):
row = tabhdu.data[irow]
rec = VisRecord()
try:
rec.target_id = row.field('TARGET_ID')
rec.time = row.field('TIME')
rec.mjd = row.field('MJD')
rec.int_time = row.field('INT_TIME')
if self.nwave > 1:
rec.visamp = row.field('VISAMP').tolist()
rec.visamperr = row.field('VISAMPERR').tolist()
rec.visphi = row.field('VISPHI').tolist()
rec.visphierr = row.field('VISPHIERR').tolist()
rec.flag = row.field('FLAG').tolist()
else:
rec.visamp = [row.field('VISAMP')]
rec.visamperr = [row.field('VISAMPERR')]
rec.visphi = [row.field('VISPHI')]
rec.visphierr = [row.field('VISPHIERR')]
rec.flag = [row.field('FLAG')]
rec.ucoord = row.field('UCOORD')
rec.vcoord = row.field('VCOORD')
rec.sta_index = tuple(row.field('STA_INDEX').tolist())
except NameError:
raise OI_FITSConformError, "Missing column"
self.records.append(rec)


class Vis2Record:
"""Visibility squared record.

Corresponds to one row of an OI_VIS2 FITS table.

Data attributes are:

target_id -- (int) Target number as index into Target.records

time - (float) UTC time of observation (seconds)

mjd -- (float) Modified Julian Day

int_time -- (float) Integration time (seconds)

vis2data -- (float list, length nwave) Squared visibility

vis2err -- (float list, length nwave) Error in squared visibility

ucoord -- (float) U coordinate of the data (meters)

vcoord -- (float) V coordinate of the data (meters)

sta_index -- (int 2-tuple) Station numbers contributing to the data

flag -- (boolean list, length nwave) Flag

"""
pass


class Vis2:
"""Data for OI_VIS2 FITS table.

Data attributes are:

revision -- (int) revision number of the table definition

date_obs -- (int 3-tuple: y, m, d) UTC start date of observations
(or may be None)

arrname -- (string) Identifies corresponding Array instance (may be None)

insname -- (string) Identifies corresponding Wavelength instance

records -- list of Vis2Record instances

nwave -- length of vis2data, vis2err, flag attributes of records


Methods are:

ToTable() -- Return pyfits.BinTableHDU instance

FromTable() -- Copy to data attributes from pyfits.BinTableHDU instance

"""

def __init__(self):
self.revision = 1
self.arrname = None
self.nwave = 0
self.records = []

def ToTable(self, extver=1):
"""Return pyfits.BinTableHDU instance."""
if len(self.records) == 0:
raise OI_FITSEmptyTableError, "No records in OI_VIS2"
# Define table structure
cols = []
cols.append(pyfits.Column(name='TARGET_ID', format='I'))
cols.append(pyfits.Column(name='TIME', format='D', unit='s'))
cols.append(pyfits.Column(name='MJD', format='D', unit='day'))
cols.append(pyfits.Column(name='INT_TIME', format='D', unit='s'))
cols.append(pyfits.Column(name='VIS2DATA', format='%dD' % self.nwave))
cols.append(pyfits.Column(name='VIS2ERR', format='%dD' % self.nwave))
cols.append(pyfits.Column(name='UCOORD', format='D', unit='m'))
cols.append(pyfits.Column(name='VCOORD', format='D', unit='m'))
cols.append(pyfits.Column(name='STA_INDEX', format='2I'))
cols.append(pyfits.Column(name='FLAG', format='%dL' % self.nwave))
tabhdu = pyfits.new_table(cols, nrows=len(self.records))
# Insert data
irow = 0
for r in self.records:
if self.nwave == 1:
vals = [r.target_id, r.time, r.mjd, r.int_time,
r.vis2data[0], r.vis2err[0],
r.ucoord, r.vcoord, array(r.sta_index, type=Int16),
r.flag[0]]
else:
vals = [r.target_id, r.time, r.mjd, r.int_time,
array(r.vis2data), array(r.vis2err),
r.ucoord, r.vcoord, array(r.sta_index, type=Int16),
array(r.flag, type=Bool)]
for icol in range(len(cols)):
tabhdu.data.field(icol)[irow] = vals[icol]
irow += 1
# Workaround for probable pyfits bug
true = array([ord('T')]*self.nwave, type=UInt8)
false = array([ord('F')]*self.nwave, type=UInt8)
tabhdu.data._parent.field('FLAG')[:] = where(tabhdu.data.field('FLAG'),
true, false)
# Insert header records
tabhdu.name = 'OI_VIS2'
hdr = tabhdu.header
hdr.update('EXTVER', extver,
comment='ID number of this OI_VIS2')
hdr.update('OI_REVN', self.revision,
comment='Revision number of the table definition')
if self.date_obs is not None:
hdr.update('DATE-OBS', '%04d-%02d-%02d' % self.date_obs,
comment='UTC Start date of observations')
if self.arrname is not None:
hdr.update('ARRNAME', self.arrname,
comment='Identifies corresponding OI_ARRAY')
hdr.update('INSNAME', self.insname,
comment='Identifies corresponding OI_WAVELENGTH')
return tabhdu

def FromTable(self, tabhdu):
"""Copy to data attributes from pyfits.BinTableHDU instance."""
try:
self.revision = tabhdu.header['OI_REVN']
self.date_obs = tuple(
map(int, string.split(tabhdu.header['DATE-OBS'], '-')))
# ARRNAME is optional
try:
self.arrname = tabhdu.header['ARRNAME']
except KeyError:
self.arrname = None
self.insname = tabhdu.header['INSNAME']
except KeyError:
raise OI_FITSConformError, "Missing keyword"
cols = tabhdu.get_coldefs()
try:
i = cols.names.index('VIS2DATA')
except ValueError:
raise OI_FITSConformError, "Missing column"
end = 0
while cols.formats[i][end] in string.digits: end += 1
if end != 0:
self.nwave = int(cols.formats[i][:end])
else:
self.nwave = 1
self.records = []
for irow in range(len(tabhdu.data)):
row = tabhdu.data[irow]
rec = Vis2Record()
try:
rec.target_id = row.field('TARGET_ID')
rec.time = row.field('TIME')
rec.mjd = row.field('MJD')
rec.int_time = row.field('INT_TIME')
if self.nwave > 1:
rec.vis2data = row.field('VIS2DATA').tolist()
rec.vis2err = row.field('VIS2ERR').tolist()
rec.flag = row.field('FLAG').tolist()
else:
rec.vis2data = [row.field('VIS2DATA')]
rec.vis2err = [row.field('VIS2ERR')]
rec.flag = [row.field('FLAG')]
rec.ucoord = row.field('UCOORD')
rec.vcoord = row.field('VCOORD')
rec.sta_index = tuple(row.field('STA_INDEX').tolist())
except NameError:
raise OI_FITSConformError, "Missing column"
self.records.append(rec)


class T3Record:
"""Triple product record. Corresponds to one row of an OI_T3 FITS table.

Data attributes are:

target_id -- (int) Target number as index into Target.records

time - (float) UTC time of observation (seconds)

mjd -- (float) Modified Julian Day

int_time -- (float) Integration time (seconds)

t3amp -- (float list, length nwave) Visibility amplitude

t3amperr -- (float list, length nwave) Error in visibility amplitude

t3phi -- (float list, length nwave) Visibility phase (degrees)

t3phierr -- (float list, length nwave) Error in visibility phase (degrees)

u1coord -- (float) U coordinate of baseline AB of the triangle (meters)

v1coord -- (float) V coordinate of baseline AB of the triangle (meters)

u2coord -- (float) U coordinate of baseline BC of the triangle (meters)

v2coord -- (float) V coordinate of baseline BC of the triangle (meters)

sta_index -- (int 3-tuple) Station numbers contributing to the data

flag -- (boolean list, length nwave) Flag

"""
pass


class T3:
"""Data for OI_T3 FITS table.

Data attributes are:

revision -- (int) revision number of the table definition

date_obs -- (int 3-tuple: y, m, d) UTC start date of observations
(or may be None)

arrname -- (string) Identifies corresponding Array instance (may be None)

insname -- (string) Identifies corresponding Wavelength instance

records -- list of T3Record instances

nwave -- length of t3amp, t3amperr, t3phi, t3phierr, flag attributes
of records


Methods are:

ToTable() -- Return pyfits.BinTableHDU instance

FromTable() -- Copy to data attributes from pyfits.BinTableHDU instance

"""

def __init__(self):
self.revision = 1
self.arrname = None
self.nwave = 0
self.records = []

def ToTable(self, extver=1):
"""Return pyfits.BinTableHDU instance."""
if len(self.records) == 0:
raise OI_FITSEmptyTableError, "No records in OI_T3"
# Define table structure
cols = []
cols.append(pyfits.Column(name='TARGET_ID', format='I'))
cols.append(pyfits.Column(name='TIME', format='D', unit='s'))
cols.append(pyfits.Column(name='MJD', format='D', unit='day'))
cols.append(pyfits.Column(name='INT_TIME', format='D', unit='s'))
cols.append(pyfits.Column(name='T3AMP', format='%dD' % self.nwave))
cols.append(pyfits.Column(name='T3AMPERR', format='%dD' % self.nwave))
cols.append(pyfits.Column(name='T3PHI', format='%dD' % self.nwave,
unit='deg'))
cols.append(pyfits.Column(name='T3PHIERR', format='%dD' % self.nwave,
unit='deg'))
cols.append(pyfits.Column(name='U1COORD', format='D', unit='m'))
cols.append(pyfits.Column(name='V1COORD', format='D', unit='m'))
cols.append(pyfits.Column(name='U2COORD', format='D', unit='m'))
cols.append(pyfits.Column(name='V2COORD', format='D', unit='m'))
cols.append(pyfits.Column(name='STA_INDEX', format='3I'))
cols.append(pyfits.Column(name='FLAG', format='%dL' % self.nwave))
tabhdu = pyfits.new_table(cols, nrows=len(self.records))
# Insert data
irow = 0
for r in self.records:
if self.nwave == 1:
vals = [r.target_id, r.time, r.mjd, r.int_time,
r.t3amp[0], r.t3amperr[0], r.t3phi[0],
r.t3phierr[0], r.u1coord, r.v1coord,
r.u2coord, r.v2coord, array(r.sta_index, type=Int16),
r.flag[0]]
else:
vals = [r.target_id, r.time, r.mjd, r.int_time,
array(r.t3amp), array(r.t3amperr), array(r.t3phi),
array(r.t3phierr), r.u1coord, r.v1coord,
r.u2coord, r.v2coord, array(r.sta_index, type=Int16),
array(r.flag, type=Bool)]
for icol in range(len(cols)):
tabhdu.data.field(icol)[irow] = vals[icol]
irow += 1
# Workaround for probable pyfits bug
true = array([ord('T')]*self.nwave, type=UInt8)
false = array([ord('F')]*self.nwave, type=UInt8)
tabhdu.data._parent.field('FLAG')[:] = where(tabhdu.data.field('FLAG'),
true, false)
# Insert header records
tabhdu.name = 'OI_T3'
hdr = tabhdu.header
hdr.update('EXTVER', extver,
comment='ID number of this OI_T3')
hdr.update('OI_REVN', self.revision,
comment='Revision number of the table definition')
if self.date_obs is not None:
hdr.update('DATE-OBS', '%04d-%02d-%02d' % self.date_obs,
comment='UTC Start date of observations')
if self.arrname is not None:
hdr.update('ARRNAME', self.arrname,
comment='Identifies corresponding OI_ARRAY')
hdr.update('INSNAME', self.insname,
comment='Identifies corresponding OI_WAVELENGTH')
return tabhdu

def FromTable(self, tabhdu):
"""Copy to data attributes from pyfits.BinTableHDU instance."""
try:
self.revision = tabhdu.header['OI_REVN']
self.date_obs = tuple(
map(int, string.split(tabhdu.header['DATE-OBS'], '-')))
# ARRNAME is optional
try:
self.arrname = tabhdu.header['ARRNAME']
except KeyError:
self.arrname = None
self.insname = tabhdu.header['INSNAME']
except KeyError:
raise OI_FITSConformError, "Missing keyword"
cols = tabhdu.get_coldefs()
try:
i = cols.names.index('T3AMP')
except ValueError:
raise OI_FITSConformError, "Missing column"
end = 0
while cols.formats[i][end] in string.digits: end += 1
if end != 0:
self.nwave = int(cols.formats[i][:end])
else:
self.nwave = 1
self.records = []
for irow in range(len(tabhdu.data)):
row = tabhdu.data[irow]
rec = Vis2Record()
try:
rec.target_id = row.field('TARGET_ID')
rec.time = row.field('TIME')
rec.mjd = row.field('MJD')
rec.int_time = row.field('INT_TIME')
if self.nwave > 1:
rec.t3amp = row.field('T3AMP').tolist()
rec.t3amperr = row.field('T3AMPERR').tolist()
rec.t3phi = row.field('T3PHI').tolist()
rec.t3phierr = row.field('T3PHIERR').tolist()
rec.flag = row.field('FLAG').tolist()
else:
rec.t3amp = [row.field('T3AMP')]
rec.t3amperr = [row.field('T3AMPERR')]
rec.t3phi = [row.field('T3PHI')]
rec.t3phierr = [row.field('T3PHIERR')]
rec.flag = [row.field('FLAG')]
rec.u1coord = row.field('U1COORD')
rec.v1coord = row.field('V1COORD')
rec.u2coord = row.field('U2COORD')
rec.v2coord = row.field('V2COORD')
rec.sta_index = tuple(row.field('STA_INDEX').tolist())
except NameError:
raise OI_FITSConformError, "Missing column"
self.records.append(rec)


def _test(inputName='bigtest.fits', outputName='junk.fits'):
"""Test code.

Reads an existing OI-FITS file, writes it out again, then reads the copy.

"""
# Read file
hlist = pyfits.open(inputName)
oi = OI_FITS()
oi.FromHDUList(hlist)
hlist.close()
# Check tables present
oi.verify()
# Write file
oi.ToHDUList().writeto(outputName)
# Read last output
hlist = pyfits.open(outputName)
oi2 = OI_FITS()
oi2.FromHDUList(hlist)
hlist.close()


if __name__ == '__main__':
_test()