def exportData( dataTuple ,name): dataK, labelK, data_errorK, dataL, labelL = dataTuple # concatenate all arrays from dataTuple and add labels for errors data_full = np.concatenate( (np.concatenate( ( dataK, data_errorK ) , axis = 1 ), dataL), axis = 1 ) error_label = [] for i in labelK: error_label += [i + "_error"] label_full = labelK + error_label + labelL votable = VOTableFile() resource = Resource() votable.resources.append(resource) table = Table(votable) resource.tables.append(table) fields = [] for i in range( data_full.shape[1] ): fields += [Field( votable, name = label_full[i], datatype='float' )] table.fields.extend( fields ) table.create_arrays( data_full.shape[0] ) for i in range( data_full.shape[0] ): table.array[i] = tuple( data_full[i,:] ) votable.to_xml(name +".xml")
def test_exec_sync():
# save results in a file
# create the VOTable result
# example from http://docs.astropy.org/en/stable/io/votable/
votable = VOTableFile()
resource = Resource()
votable.resources.append(resource)
table = Table(votable)
resource.tables.append(table)
table.fields.extend([
Field(votable, name="filename", datatype="char", arraysize="*"),
Field(votable, name="matrix", datatype="double", arraysize="2x2")])
table.create_arrays(2)
table.array[0] = ('test1.xml', [[1, 0], [0, 1]])
table.array[1] = ('test2.xml', [[0.5, 0.3], [0.2, 0.1]])
buffer = BytesIO()
votable.to_xml(buffer)
cadc = Cadc(auth_session=requests.Session())
response = Mock()
response.to_table.return_value = buffer.getvalue()
cadc.cadctap.search = Mock(return_value=response)
output_file = '{}/test_vooutput.xml'.format(tempfile.tempdir)
cadc.exec_sync('some query', output_file=output_file)
actual = parse(output_file)
assert len(votable.resources) == len(actual.resources) == 1
assert len(votable.resources[0].tables) ==\
len(actual.resources[0].tables) == 1
actual_table = actual.resources[0].tables[0]
try:
# TODO remove when astropy LTS upgraded
from astropy.utils.diff import report_diff_values
assert report_diff_values(table, actual_table, fileobj=sys.stdout)
except ImportError:
pass
def table_from_scratch():
from astropy.io.votable.tree import VOTableFile, Resource, Table, Field
# Create a new VOTable file...
votable = VOTableFile()
# ...with one resource...
resource = Resource()
votable.resources.append(resource)
# ... with one table
table = Table(votable)
resource.tables.append(table)
# Define some fields
table.fields.extend([
Field(votable, ID="filename", datatype="char"),
Field(votable, ID="matrix", datatype="double", arraysize="2x2")])
# Now, use those field definitions to create the numpy record arrays, with
# the given number of rows
table.create_arrays(2)
# Now table.array can be filled with data
table.array[0] = ('test1.xml', [[1, 0], [0, 1]])
table.array[1] = ('test2.xml', [[0.5, 0.3], [0.2, 0.1]])
# Now write the whole thing to a file.
# Note, we have to use the top-level votable file object
out = io.StringIO()
votable.to_xml(out)
def createTableFromObject(data, path="", names=[], dtypes=[], sizes=[]):
path_tmp = "/Users/cjimenez/Documents/PHD/data/tmp/"
# Create a new VOTable file...
votable = VOTableFile()
# ...with one resource...
resource = Resource()
votable.resources.append(resource)
# ... with one table
table = Table(votable)
resource.tables.append(table)
# Define some fields
fields = []
for idx, val in enumerate(names):
fields.append(Field(votable, name=val, datatype=dtypes[idx]))
table.fields.extend(fields)
# Now, use those field definitions to create the numpy record arrays, with
# the given number of rows
table.create_arrays(len(data))
# Now table.array can be filled with data
for idx, val in enumerate(data):
table.array[idx] = val
# Now write the whole thing to a file.
# Note, we have to use the top-level votable file object
votable.to_xml(path_tmp + path)
def write_set(self, filename, votype='ascii', overwrite=False):
'''
Write all tables to a VOT file
Required Arguments:
*filename*: [ string ]
The VOT file to write the tables to
Optional Keyword Arguments:
*votype*: [ 'ascii' | 'binary' ]
Whether to write the tables as ASCII or binary tables
'''
if os.path.exists(filename):
if overwrite:
os.remove(filename)
else:
raise Exception("File exists: %s" % filename)
vo_table = VOTableFile()
resource = Resource()
vo_table.resources.append(resource)
for table_key in self.tables:
resource.tables.append(_to_table(self.tables[table_key], vo_table))
if votype is 'binary':
vo_table.get_first_table().format = 'binary'
vo_table.set_all_tables_format('binary')
vo_table.to_xml(filename)
def votable_xml_string(version):
votable_file = VOTableFile(version=version)
votable_file.resources.append(Resource())
xml_bytes = io.BytesIO()
votable_file.to_xml(xml_bytes)
xml_bytes.seek(0)
bstring = xml_bytes.read()
s = bstring.decode("utf-8")
return s
print np.array(table[sys.argv[2]])[i_r]
print i_r
from astropy.io.votable.tree import VOTableFile, Resource, Table, Field
# Create a new VOTable file...
votable = VOTableFile()
# ...with one resource...
resource = Resource()
votable.resources.append(resource)
# ... with one table
table_out = Table(votable)
resource.tables.append(table_out)
table_out.fields.extend(fields)
table_out.create_arrays(len(i_r))
for n in col_names:
table_out.array[n] = table[n][i_r]
votable.to_xml (sys.argv[4])
#table = vot.get_first_table().to_table(use_names_over_ids=True)
#print table
f3 = Field(t,
name='intensity_err',
datatype=fits_pixel_type,
ucd='stat.error;phot.flux.density;em.MIR',
unit='erg.s-1.cm-1.sr-1')
f3.description = 'error (standard deviation)'
f4 = Field(t,
name='transmission_reference',
datatype=fits_pixel_type,
ucd='phys.transmission;em.MIR',
unit='')
f4.description = 'reference modeled atmospheric transmission spectrum'
# Add the fields to the table
t.fields.extend([f1, f2, f3, f4])
# Allocate the space for the four columns in the table
t.create_arrays(pixel_data.shape[1])
# Copy over each row of the table. Is there a better way?
for i in range(pixel_data.shape[1]):
values = tuple(pixel_data[:, i])
t.array[i] = values
# Output the XML VOTable file
with open(outputfile, mode) as f:
vt.to_xml(f)
sys.exit(0)
def save_table(table, tabname):
results = VOTableFile()
resource = Resource()
results.resources.append(resource)
resource.tables.append(from_table(table).get_first_table())
results.to_xml(tabname)
def sort_write(sortname, spect, fitsdict, filesort, space=3):
"""
Write out an xml and ascii file that contains the details of the file sorting.
By default, the filename is printed first, followed by the filetype.
After these, all parameters listed in the 'keyword' item in the
settings file will be printed
Parameters
----------
sortname : str
The filename to be used to save the list of sorted files
spect : dict
Properties of the spectrograph.
fitsdict : dict
Contains relevant information from fits header files
filesort : dict
Details of the sorted files
space : int
Keyword to set how many blank spaces to place between keywords
"""
msgs.info("Preparing to write out the data sorting details")
nfiles = fitsdict['filename'].size
# Specify which keywords to print after 'filename' and 'filetype'
prord = ['filename', 'frametype', 'target', 'exptime', 'naxis0', 'naxis1', 'filter1', 'filter2']
prdtp = ["char", "char", "char", "double", "int", "int", "char", "char"]
# Now insert the remaining keywords:
fkey = spect['keyword'].keys()
for i in fkey:
if i not in prord:
prord.append(i)
# Append the type of value this keyword holds
typv = type(fitsdict[i][0])
if typv is int or typv is np.int_:
prdtp.append("int")
elif isinstance(fitsdict[i][0], basestring) or typv is np.string_:
prdtp.append("char")
elif typv is float or typv is np.float_:
prdtp.append("double")
else:
msgs.bug("I didn't expect useful headers to contain type {0:s}".format(typv).replace('<type ', '').replace('>', ''))
# Open a VOTable for writing
votable = VOTableFile()
resource = Resource()
votable.resources.append(resource)
table = Table(votable)
resource.tables.append(table)
# Define VOTable fields
tabarr=[]
# Insert the filename and filetype first
for i in xrange(len(prord)):
tabarr.append(Field(votable, name=prord[i], datatype=prdtp[i], arraysize="*"))
table.fields.extend(tabarr)
table.create_arrays(nfiles)
filtyp = filesort.keys()
for i in xrange(nfiles):
values = ()
for pr in prord:
if pr == 'frametype':
addval = ""
for ft in filtyp:
if i in filesort[ft]:
if len(addval) != 0: addval += ","
addval += ft
addval = (addval,)
else: addval = (fitsdict[pr][i],)
values = values + addval
table.array[i] = values
#osspl = sortname.split('.')
#if len(osspl) > 1:
# fname = sortname
#else:
fname = sortname+'.xml'
votable.to_xml(fname)
msgs.info("Successfully written sorted data information file:"+msgs.newline() +
"{0:s}".format(fname))
# ASCII file (JXP)
jxpord = ['filename', 'date', 'frametype', 'target', 'exptime', 'binning',
'dichroic', 'disperser', 'cdangle', 'decker']
# Generate the columns
clms = []
for pr in jxpord:
try:
lidx = prord.index(pr)
except ValueError:
msgs.warn('{:s} keyword not used'.format(pr))
else:
clm = []
for i in xrange(nfiles):
clm.append(table.array[i][lidx])
clms.append(Column(clm, name=pr))
# Create Table
jxp_tbl = tTable(clms)
# Write
jxp_name = fname.replace('.xml', '.lst')
jxp_tbl.write(jxp_name, format='ascii.fixed_width')
return
for i in firstdata, nvssdata, wenssdata, sumssdata:
if len(i.rawcatdata) > 0:
externalsurveys.append(i)
#VO output..
if keepvo > 0:
votable = VOTableFile()
resource = Resource()
votable.resources.append(resource)
resource.tables.append(
catalogue.makevo(votable, description=telescope + ' Data'))
for surveydata in externalsurveys:
resource.tables.append(
surveydata.makevo(votable,
description=surveydata.survey.name + ' Data'))
votable.to_xml(options.outputdir + '/' + inname + '.vo')
outfiles.append(options.outputdir + '/' + inname + '.vo')
print '**** vo catalogue containg all available source lists is in ' + inname + '.vo'
#Make the required plots for each survey.
for surveydata in externalsurveys:
outfiles = outfiles + surveydata.docomparison(options.outputdir + '/' +
inname + '_')
#Print out the best flux comparison (and attempt 2 frequency flux compare)
outfiles = outfiles + fluxcompare(externalsurveys, options.outputdir + '/')
#Output image stats
outfiles = outfiles + [
catalogue.getimstats(options.outputdir + '/' + inname + '_STATS.txt',
externalsurveys, [localdr, numsources])
c = SkyCoord(x[2] + 'h' + x[3] + 'm' + x[4] + 's',
x[5] + x[6] + 'd' + x[7] + 'm' + x[8] + 's', 'icrs')
island_id = ""
ra_deg_cont = c.ra.deg
dec_deg_cont = c.dec.degree
freq = 1408
flux_peak_err = 0
flux_int_err = 0
maj_axis = maj_axis_deconv
min_axis = min_axis_deconv
pos_ang = pos_ang_deconv
maj_axis_err = 0
min_axis_err = 0
pos_ang_err = 0
chi_squared_fit = -1
rms_fit_gauss = -1
spectral_index = 0
spectral_curvature = 0
flag_c1 = 0
flag_c2 = 0
flag_c3 = 0
flag_c4 = 0
z=island_id,component_id,component_name,ra_hms_cont,dec_dms_cont,ra_deg_cont,dec_deg_cont,ra_err,dec_err,freq,flux_peak, \
flux_peak_err,flux_int,flux_int_err,maj_axis,min_axis,pos_ang,maj_axis_err,min_axis_err,pos_ang_err, \
maj_axis_deconv,min_axis_deconv,pos_ang_deconv,chi_squared_fit,rms_fit_gauss,spectral_index,spectral_curvature, \
rms_image,flag_c1,flag_c2,flag_c3,flag_c4,comment
table.array[r] = z
votable.to_xml(XMLFilename)
def visibility(request):
now = datetime.datetime.now()
html = "<html><body>It is now %s.</body></html>" % now
# Create a new VOTable file...
votable = VOTableFile()
# ...with one resource...
resource = Resource()
votable.resources.append(resource)
# ... with one table
table = Table(votable)
resource.tables.append(table)
resource.description ="European Space Astronomy Centre. INTEGRAL SOC - " \
"Object Visibility Simple Access Protocol (ObjVisSAP)"
resource.infos.append(Info(name="QUERY_STATUS", value="OK"))
resource.infos.append(Info(name="SERVICE PROTOCOL", value="1.0"))
resource.infos.append(Info(name="REQUEST", value="queryData"))
resource.infos.append(
Info(name="s_ra", value="%s" % request.GET.get("s_ra")))
resource.infos.append(
Info(name="s_dec", value="%s" % request.GET.get("s_dec")))
resource.infos.append(
Info(name="t_min", value="%s" % request.GET.get("t_min")))
resource.infos.append(
Info(name="t_max", value="%s" % request.GET.get("t_max")))
# Define some fields
# table.fields.extend([
# Field(votable, name="filename", datatype="char", arraysize="*"),
# Field(votable, name="matrix", datatype="double", arraysize="2x2")])
table.fields.extend([
Field(votable,
name="t_start",
datatype="double",
ucd="time.start",
utype="Char.TimeAxis.Coverage.Bounds.Limits.StartTime"),
Field(votable,
name="t_stop",
datatype="double",
ucd="time.start",
utype="Char.TimeAxis.Coverage.Bounds.Limits.StartTime"),
Field(votable,
name="t_visibility",
datatype="double",
ucd="time.start",
utype="Char.TimeAxis.Coverage.Bounds.Limits.StartTime"),
])
results = VisibilityCalculator.getVisibilityIntervals(
request.GET.get("s_ra"), request.GET.get("s_dec"),
request.GET.get("t_min"), request.GET.get("t_max"))
number_of_intervals = len(results)
table.create_arrays(number_of_intervals)
for i in range(0, number_of_intervals):
table.array[i] = (results[i][0], results[i][1], results[i][2])
# Now write the whole thing to a file to be streamed
# Note, we have to use the top-level votable file object
xml_now = "/tmp/new_votable_%s.xml" % now
votable.to_xml(xml_now)
stream = open(xml_now).read()
os.remove(xml_now)
return HttpResponse(stream, content_type='text/xml')
