[AstroPy] Problem reading VOTable produced by HLA
Andy Ptak
andrew.f.ptak at nasa.gov
Tue Feb 26 09:51:01 EST 2013
Hello,
I am trying out reading VOTables using and am having trouble. Specifically reading tables returned by the Hubble Legacy Archive. The query was:
http://hla.stsci.edu/cgi-bin/hlaSIAP.cgi?inst=ACS&pos=11.888333,-25.288056&size=0.001389
which I attached.
I am using astropy installed by pip on the enthought distribution on a mac, so its version 0.2 and numpy got upgraded to 1.7.0 (if that matters).
First, is there a way to have a votable imported directly from query without saving it to a physical file first? Maybe its best practice to save VO queries to a file to trace errors, in case the votable is very large, etc. but when you know you are getting something back that is small and (as in this case) you mainly want a list of fields for further work, saving the full votable seams like an unnecessary extra step.
The errors I am getting are below. I got similar errors when using a different votable call I found on the HLA website (basically the same except using acsSIAP.cgi?strict=1
Is this a problem with the Votable being returned by stsci, a bug or am I doing something wrong?
Thanks,
Andy Ptak
In [4]: from astropy.io.votable import parse
In [6]: votable = parse("test1.xml")
WARNING: W42: test1.xml:3:0: W42: No XML namespace specified [astropy.io.votable.exceptions]
WARNING: W03: test1.xml:7:4: W03: Implictly generating an ID from a name 'INPUT:POS' -> 'INPUT_POS' [astropy.io.votable.exceptions]
WARNING: W03: test1.xml:8:4: W03: Implictly generating an ID from a name 'INPUT:SIZE' -> 'INPUT_SIZE' [astropy.io.votable.exceptions]
WARNING: W03: test1.xml:9:4: W03: Implictly generating an ID from a name 'INPUT:FORMAT' -> 'INPUT_FORMAT' [astropy.io.votable.exceptions]
WARNING: W03: test1.xml:10:4: W03: Implictly generating an ID from a name 'INPUT:imagetype' -> 'INPUT_imagetype' [astropy.io.votable.exceptions]
WARNING: W03: test1.xml:11:4: W03: Implictly generating an ID from a name 'INPUT:inst' -> 'INPUT_inst' [astropy.io.votable.exceptions]
WARNING: W03: test1.xml:12:4: W03: Implictly generating an ID from a name 'INPUT:hrcmatch' -> 'INPUT_hrcmatch' [astropy.io.votable.exceptions]
WARNING: W03: test1.xml:13:4: W03: Implictly generating an ID from a name 'INPUT:zoom' -> 'INPUT_zoom' [astropy.io.votable.exceptions]
WARNING: W03: test1.xml:14:4: W03: Implictly generating an ID from a name 'INPUT:autoscale' -> 'INPUT_autoscale' [astropy.io.votable.exceptions]
WARNING: W03: test1.xml:15:4: W03: Implictly generating an ID from a name 'INPUT:asinh' -> 'INPUT_asinh' [astropy.io.votable.exceptions]
WARNING: W06: test1.xml:16:4: W06: Invalid UCD 'VOX:STC_CoordRefFrame': UCD has invalid character ':' in 'VOX:STC_CoordRefFrame' [astropy.io.votable.exceptions]
WARNING: W06: test1.xml:17:4: W06: Invalid UCD 'VOX:WCS_CoordProjection': UCD has invalid character ':' in 'VOX:WCS_CoordProjection' [astropy.io.votable.exceptions]
WARNING: W06: test1.xml:19:6: W06: Invalid UCD 'VOX:Image_AccessReference': UCD has invalid character ':' in 'VOX:Image_AccessReference' [astropy.io.votable.exceptions]
WARNING: W06: test1.xml:82:6: W06: Invalid UCD 'VOX:Image_Format': UCD has invalid character ':' in 'VOX:Image_Format' [astropy.io.votable.exceptions]
WARNING: W06: test1.xml:91:6: W06: Invalid UCD 'VOX:Image_Title': UCD has invalid character ':' in 'VOX:Image_Title' [astropy.io.votable.exceptions]
WARNING: W06: test1.xml:94:6: W06: Invalid UCD 'VOX:Image_Naxis': UCD has invalid character ':' in 'VOX:Image_Naxis' [astropy.io.votable.exceptions]
WARNING: W06: test1.xml:97:6: W06: Invalid UCD 'VOX:Image_Scale': UCD has invalid character ':' in 'VOX:Image_Scale' [astropy.io.votable.exceptions]
WARNING: W06: test1.xml:100:6: W06: Invalid UCD 'VOX:Image_Naxes': UCD has invalid character ':' in 'VOX:Image_Naxes' [astropy.io.votable.exceptions]
WARNING: W06: test1.xml:103:6: W06: Invalid UCD 'VOX:WCS_CoordRefPixel': UCD has invalid character ':' in 'VOX:WCS_CoordRefPixel' [astropy.io.votable.exceptions]
WARNING: W06: test1.xml:106:6: W06: Invalid UCD 'VOX:WCS_CoordRefValue': UCD has invalid character ':' in 'VOX:WCS_CoordRefValue' (suppressing further warnings of this type...) [astropy.io.votable.exceptions]
ERROR: OverflowError: Python int too large to convert to C long [numpy.ma.core]
---------------------------------------------------------------------------
OverflowError Traceback (most recent call last)
/Volumes/Apps_and_Docs/aptak/Dropbox/HLA/<ipython-input-6-61a1dc44cf49> in <module>()
----> 1 votable = parse("test1.xml")
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/astropy/io/votable/table.pyc in parse(source, columns, invalid, pedantic, chunk_size, table_number, table_id, filename, _debug_python_based_parser)
114 _debug_python_based_parser=_debug_python_based_parser) as iterator:
115 return tree.VOTableFile(
--> 116 config=config, pos=(1, 1)).parse(iterator, config)
117
118
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/astropy/io/votable/tree.pyc in parse(self, iterator, config)
3084 if start:
3085 tag_mapping.get(tag, self._add_unknown_tag)(
-> 3086 iterator, tag, data, config, pos)
3087 elif tag == 'DESCRIPTION':
3088 if self.description is not None:
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/astropy/io/votable/tree.pyc in _add_resource(self, iterator, tag, data, config, pos)
3015 resource = Resource(config=config, pos=pos, **data)
3016 self.resources.append(resource)
-> 3017 resource.parse(self, iterator, config)
3018
3019 def _add_coosys(self, iterator, tag, data, config, pos):
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/astropy/io/votable/tree.pyc in parse(self, votable, iterator, config)
2871 if start:
2872 tag_mapping.get(tag, self._add_unknown_tag)(
-> 2873 iterator, tag, data, config, pos)
2874 elif tag == 'DESCRIPTION':
2875 if self.description is not None:
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/astropy/io/votable/tree.pyc in _add_table(self, iterator, tag, data, config, pos)
2828 table = Table(self._votable, config=config, pos=pos, **data)
2829 self.tables.append(table)
-> 2830 table.parse(iterator, config)
2831
2832 def _add_info(self, iterator, tag, data, config, pos):
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/astropy/io/votable/tree.pyc in parse(self, iterator, config)
2212 'TABLEDATA', data.iterkeys(), config, pos)
2213 self.array = self._parse_tabledata(
-> 2214 iterator, colnumbers, fields, config)
2215 break
2216 elif tag == 'BINARY':
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/astropy/io/votable/tree.pyc in _parse_tabledata(self, iterator, colnumbers, fields, config)
2357
2358 array = _resize(array, alloc_rows)
-> 2359 array[numrows:] = array_chunk
2360 if alloc_rows != 0:
2361 array.mask[numrows:] = mask_chunk
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc in __setslice__(self, i, j, value)
3067
3068 """
-> 3069 self.__setitem__(slice(i, j), value)
3070
3071
/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/ma/core.pyc in __setitem__(self, indx, value)
3031 _mask = ndarray.__getattribute__(self, '_mask')
3032 # Set the data, then the mask
-> 3033 ndarray.__setitem__(_data, indx, dval)
3034 ndarray.__setitem__(_mask, indx, mval)
3035 elif hasattr(indx, 'dtype') and (indx.dtype == MaskType):
OverflowError: Python int too large to convert to C long
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/astropy/attachments/20130226/0f83a413/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: test1.xml
Type: application/xml
Size: 17588 bytes
Desc: not available
URL: <http://mail.python.org/pipermail/astropy/attachments/20130226/0f83a413/attachment.xml>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/astropy/attachments/20130226/0f83a413/attachment-0001.html>
More information about the AstroPy
mailing list