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Commit a4b0f603 authored by David Rafferty's avatar David Rafferty
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Fix handling of LogarithmicSI and OrientationIsAbsolute columns

parent 84ab38d2
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1 merge request!43Fix handling of LogarithmicSI and OrientationIsAbsolute columns
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with 157 additions and 103 deletions
lsmtool/tableio.py
+ 157
− 103
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......@@ -38,6 +38,7 @@ except AttributeError:
# Python 3
def itervalues(d):
return iter(d.values())
def iteritems(d):
return iter(d.items())
numpy_type = "U"
......@@ -45,6 +46,7 @@ else:
# Python 2
def itervalues(d):
return d.itervalues()
def iteritems(d):
return d.iteritems()
numpy_type = "S"
......@@ -70,7 +72,8 @@ except NameError:
# https://www.astron.nl/lofarwiki/doku.php?id=public:user_software:documentation:makesourcedb
allowedColumnNames = {'name': 'Name', 'type': 'Type', 'patch': 'Patch',
'ra': 'Ra', 'dec': 'Dec', 'i': 'I', 'q': 'Q', 'u': 'U', 'v': 'V',
'majoraxis':'MajorAxis', 'minoraxis':'MinorAxis', 'orientation':'Orientation', 'orientationisabsolute': 'OrientationIsAbsolute',
'majoraxis': 'MajorAxis', 'minoraxis': 'MinorAxis',
'orientation': 'Orientation', 'orientationisabsolute': 'OrientationIsAbsolute',
'ishapelet': 'IShapelet', 'qshapelet': 'QShapelet', 'ushapelet': 'UShapelet',
'vshapelet': 'VShapelet', 'category': 'Category', 'logarithmicsi': 'LogarithmicSI',
'rotationmeasure': 'RotationMeasure', 'polarizationangle': 'PolarizationAngle',
......@@ -79,18 +82,20 @@ allowedColumnNames = {'name':'Name', 'type':'Type', 'patch':'Patch',
allowedColumnUnits = {'name': None, 'type': None, 'patch': None, 'ra': 'degree',
'dec': 'degree', 'i': 'Jy', 'i-apparent': 'Jy', 'q': 'Jy', 'u': 'Jy', 'v': 'Jy',
'majoraxis':'arcsec', 'minoraxis':'arcsec', 'orientation':'degree', 'orientationisabsolute':None,
'majoraxis': 'arcsec', 'minoraxis': 'arcsec', 'orientation': 'degree',
'orientationisabsolute': None,
'ishapelet': None, 'qshapelet': None, 'ushapelet': None,
'vshapelet': None, 'category': None, 'logarithmicsi': None,
'rotationmeasure': 'rad/m^2', 'polarizationangle': 'rad',
'polarizedfraction':'PolarizedFraction', 'referencewavelength':'ReferenceWavelength',
'polarizedfraction': 'PolarizedFraction',
'referencewavelength': 'ReferenceWavelength',
'referencefrequency': 'Hz', 'spectralindex': None}
allowedColumnDefaults = {'name': 'N/A', 'type': 'N/A', 'patch': 'N/A', 'ra': 0.0,
'dec': 0.0, 'i': 0.0, 'q': 0.0, 'u': 0.0, 'v': 0.0, 'majoraxis': 0.0,
'minoraxis':0.0, 'orientation':0.0, 'orientationisabsolute': False,
'minoraxis': 0.0, 'orientation': 0.0, 'orientationisabsolute': 'false',
'ishapelet': 'N/A', 'qshapelet': 'N/A', 'ushapelet': 'N/A',
'vshapelet':'N/A', 'category':2, 'logarithmicsi': True,
'vshapelet': 'N/A', 'category': 2, 'logarithmicsi': 'true',
'rotationmeasure': 0.0, 'polarizationangle': 0.0,
'polarizedfraction': 0.0, 'referencewavelength': 'N/A',
'referencefrequency': 0.0, 'spectralindex': [0.0]}
......@@ -102,6 +107,63 @@ allowedVOServices = {
'wenss': 'http://vizier.u-strasbg.fr/viz-bin/votable/-A?-source=VIII/62A&'}
def raformat(val):
"""
Column formatter for RA values.
Parameters
----------
val : float
Input RA value in deg
Returns
-------
valstr : str
Formatted string as 'hh:mm:ss.s'
"""
return Angle(val, unit='degree').to_string(unit='hourangle', sep=':')
def decformat(val):
"""
Column formatter for Dec values.
Parameters
----------
val : float
Input Dec value in deg
Returns
-------
valstr : str
Formatted string as 'dd.mm.ss.s'
"""
return Angle(val, unit='degree').to_string(unit='degree', sep='.')
def fluxformat(val):
"""
Column formatter for flux density values.
Parameters
----------
val : float
Input flux density value in Jy
Returns
-------
valstr : str
Formatted string to 3 digits
"""
if type(val) is ma.core.MaskedConstant:
return '{}'.format(val)
else:
return '{0:0.3f}'.format(val)
def skyModelReader(fileName):
"""
Reads a makesourcedb sky model file into an astropy table.
......@@ -132,7 +194,7 @@ def skyModelReader(fileName):
# Read format line
formatString = None
for l, line in enumerate(modelFile):
for line in modelFile:
if 'format' in line.lower():
formatString = line
break
......@@ -182,25 +244,37 @@ def createTable(outlines, metaDict, colNames, colDefaults):
log = logging.getLogger('LSMTool.Load')
# Before loading table into an astropy Table object, set lengths of Name,
# Patch, and Type columns to 100 characters. Due to a change in the astropy
# table API with v4.1, we have to check the version and use the appropriate
# column names
# Patch, and Type columns to 100 characters to ensure long names are not
# truncated. The LogarithmicSI and OrientationIsAbsolute columns are set
# to 5 characters to allow true/false values to be stored as strings without
# truncation. Due to a change in the astropy table API with v4.1, we have to
# check the version and use the appropriate column names
if LooseVersion(astropy.__version__) < LooseVersion('4.1'):
# Use the input column names for the converters
nameCol = 'col{0}'.format(colNames.index('Name')+1)
typeCol = 'col{0}'.format(colNames.index('Type')+1)
if 'Patch' in colNames:
patchCol = 'col{0}'.format(colNames.index('Patch')+1)
if 'LogarithmicSI' in colNames:
logSICol = 'col{0}'.format(colNames.index('LogarithmicSI')+1)
if 'OrientationIsAbsolute' in colNames:
orienCol = 'col{0}'.format(colNames.index('OrientationIsAbsolute')+1)
else:
# Use the output column names for the converters
nameCol = 'Name'
typeCol = 'Type'
patchCol = 'Patch'
logSICol = 'LogarithmicSI'
orienCol = 'OrientationIsAbsolute'
converters = {}
converters[nameCol] = [ascii.convert_numpy('{}100'.format(numpy_type))]
converters[typeCol] = [ascii.convert_numpy('{}100'.format(numpy_type))]
if 'Patch' in colNames:
converters[patchCol] = [ascii.convert_numpy('{}100'.format(numpy_type))]
if 'LogarithmicSI' in colNames:
converters[logSICol] = [ascii.convert_numpy('{}5'.format(numpy_type))]
if 'OrientationIsAbsolute' in colNames:
converters[orienCol] = [ascii.convert_numpy('{}5'.format(numpy_type))]
log.debug('Creating table...')
table = Table.read('\n'.join(outlines), guess=False, format='ascii.no_header', delimiter=',',
......@@ -213,12 +287,12 @@ def createTable(outlines, metaDict, colNames, colDefaults):
specVec = []
maskVec = []
maxLen = 0
for l in specOld:
for entry in specOld:
try:
if type(l) is float or type(l) is int:
if type(entry) is float or type(entry) is int:
maxLen = 1
else:
specEntry = [float(f) for f in l.split(';')]
specEntry = [float(f) for f in entry.split(';')]
if len(specEntry) > maxLen:
maxLen = len(specEntry)
except:
......@@ -227,14 +301,14 @@ def createTable(outlines, metaDict, colNames, colDefaults):
if defSpeclen > maxLen:
maxLen = defSpeclen
log.debug('Maximum number of spectral-index terms in model: {0}'.format(maxLen))
for l in specOld:
for entry in specOld:
try:
# Take existing entry and fix type
if type(l) is float or type(l) is int:
specEntry = [float(l)]
if type(entry) is float or type(entry) is int:
specEntry = [float(entry)]
specMask = [False]
else:
specEntry = [float(f) for f in l.split(';')]
specEntry = [float(f) for f in entry.split(';')]
specMask = [False] * len(specEntry)
except:
# No entry in table, so use default value
......@@ -256,8 +330,6 @@ def createTable(outlines, metaDict, colNames, colDefaults):
log.debug('Converting RA...')
RARaw = table['Ra'].data.tolist()
RACol = Column(name='Ra', data=RA2Angle(RARaw))
def raformat(val):
return Angle(val, unit='degree').to_string(unit='hourangle', sep=':')
RACol.format = raformat
RAIndx = table.keys().index('Ra')
table.remove_column('Ra')
......@@ -266,18 +338,11 @@ def createTable(outlines, metaDict, colNames, colDefaults):
log.debug('Converting Dec...')
DecRaw = table['Dec'].data.tolist()
DecCol = Column(name='Dec', data=Dec2Angle(DecRaw))
def decformat(val):
return Angle(val, unit='degree').to_string(unit='degree', sep='.')
DecCol.format = decformat
DecIndx = table.keys().index('Dec')
table.remove_column('Dec')
table.add_column(DecCol, index=DecIndx)
def fluxformat(val):
if type(val) is ma.core.MaskedConstant:
return '{}'.format(val)
else:
return '{0:0.3f}'.format(val)
table.columns['I'].format = fluxformat
# Set column units and default values
......@@ -744,8 +809,8 @@ def ds9RegionWriter(table, fileName):
log.debug('Writing ds9 region file to {0}'.format(fileName))
outLines = []
outLines.append('# Region file format: DS9 version 4.0\nglobal color=green '\
'font="helvetica 10 normal" select=1 highlite=1 edit=1 '\
outLines.append('# Region file format: DS9 version 4.0\nglobal color=green '
'font="helvetica 10 normal" select=1 highlite=1 edit=1 '
'move=1 delete=1 include=1 fixed=0 source\nfk5\n')
# Make sure all columns have the correct units
......@@ -761,20 +826,17 @@ def ds9RegionWriter(table, fileName):
if row['Type'].lower() == 'gaussian':
a = row['MajorAxis'] / 3600.0 # deg
b = row['MinorAxis'] / 3600.0 # deg
pa = row['Orientation'] # degree
pa = row['Orientation'] # deg
# ds9 can't handle 1-D Gaussians, so make sure they are 2-D
if a < 1.0 / 3600.0:
a = 1.0 / 3600.0 # deg
if b < 1.0 / 3600.0:
b = 1.0 / 3600.0 # deg
stype = 'GAUSSIAN'
region = 'ellipse({0}, {1}, {2}, {3}, {4}) # text={{{5}}}\n'.format(ra,
dec, a, b, pa+90.0, name)
region = 'ellipse({0}, {1}, {2}, {3}, {4}) # text={{{5}}}\n'.format(ra, dec, a, b,
pa+90.0, name)
else:
stype = 'POINT'
region = 'point({0}, {1}) # point=cross width=2 text={{{2}}}\n'.format(ra,
dec, name)
region = 'point({0}, {1}) # point=cross width=2 text={{{2}}}\n'.format(ra, dec, name)
outLines.append(region)
regionFile.writelines(outLines)
......@@ -854,7 +916,6 @@ def casaRegionWriter(table, fileName):
for row in table:
ra = row['Ra']
dec = row['Dec']
name = row['Name']
if row['Type'].lower() == 'gaussian':
a = row['MajorAxis'] / 3600.0 # degree
......@@ -932,10 +993,9 @@ def factorDirectionsWriter(table, fileName):
gRA = Angle(0.0)
gDec = Angle(0.0)
outLines.append('{0} {1},{2} {3} {4} {5} {6} {7} {8} {9} {10} {11} {12} '
'{13} {14}\n'.format(patchName,
gRA.to_string(unit='hourangle', sep='hms'), gDec.to_string(sep='dms'),
'empty', 'empty', 0, 0, 0, 'LD', 'empty', 'empty', 'empty', False,
size, flux))
'{13} {14}\n'.format(patchName, gRA.to_string(unit='hourangle', sep='hms'),
gDec.to_string(sep='dms'), 'empty', 'empty', 0, 0, 0,
'LD', 'empty', 'empty', 'empty', False, size, flux))
regionFile.writelines(outLines)
regionFile.close()
......@@ -951,7 +1011,7 @@ def broadcastTable(fileName):
Name of sky model file to broadcast
"""
from astropy.vo.samp import SAMPHubServer, SAMPIntegratedClient, SAMPHubError
from astropy.vo.samp import SAMPIntegratedClient
import urlparse
client = SAMPIntegratedClient()
......@@ -1068,8 +1128,6 @@ def convertExternalTable(table, columnMapping, fluxUnits='mJy'):
log.debug('Converting RA...')
RARaw = table['Ra'].data.tolist()
RACol = Column(name='Ra', data=RA2Angle(RARaw))
def raformat(val):
return Angle(val, unit='degree').to_string(unit='hourangle', sep=':')
RACol.format = raformat
RAIndx = table.keys().index('Ra')
table.remove_column('Ra')
......@@ -1078,8 +1136,6 @@ def convertExternalTable(table, columnMapping, fluxUnits='mJy'):
log.debug('Converting Dec...')
DecRaw = table['Dec'].data.tolist()
DecCol = Column(name='Dec', data=Dec2Angle(DecRaw))
def decformat(val):
return Angle(val, unit='degree').to_string(unit='degree', sep='.')
DecCol.format = decformat
DecIndx = table.keys().index('Dec')
table.remove_column('Dec')
......@@ -1120,8 +1176,6 @@ def convertExternalTable(table, columnMapping, fluxUnits='mJy'):
table.add_column(col)
# Set column units and default values
def fluxformat(val):
return '{0:0.3f}'.format(val)
for i, colName in enumerate(table.colnames):
log.debug("Setting units for column '{0}' to {1}".format(
colName, allowedColumnUnits[colName.lower()]))
......
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