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Writing a Table with a SkyCoord mixin fails when SkyCoord is created from a list of SkyCoord #6446
Description
This fails:
from astropy.coordinates import SkyCoord
from astropy.table import Table
c1 = SkyCoord(1, 3, unit='deg')
c2 = SkyCoord(2, 4, unit='deg')
sc1 = SkyCoord([c1, c2])
t = Table([sc1])
t.write('mixin.ecsv', format='ascii.ecsv', overwrite=True)But this works fine:
from astropy.coordinates import SkyCoord
from astropy.table import Table
sc2 = SkyCoord([1, 2], [3, 4], unit='deg')
t2 = Table([sc2])
t2.write('mixin.ecsv', format='ascii.ecsv', overwrite=True)So, sc1 and sc2 are different(!) in some way for the Table writer. I tracked this down to
sc1 somehow having its galcen_v_sun attribute set(?!):
>>> sc1.galcen_v_sun
<CartesianDifferential (d_x, d_y, d_z) in km / s
( 11.1, 232.24, 7.25)>
>>> sc2.galcen_v_sunSo it appears that the Table writer cannot serialize SkyCoord objects with galcen_v_sun attributes, and I don't know why this attribute is set when initializing a SkyCoord object from a list of SkyCoord objects. Are these both bugs?
Here's the traceback for the first example, showing the galcen_v_sun values in the raised error message
(RepresenterError: cannot represent an object: ( 11.1, 232.24, 7.25) km / s):
---------------------------------------------------------------------------
RepresenterError Traceback (most recent call last)
<ipython-input-68-df4a66266376> in <module>()
6 sc1 = SkyCoord([c1, c2])
7 t = Table([sc1])
----> 8 t.write('mixin.ecsv', format='ascii.ecsv', overwrite=True)
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/astropy/table/table.py in write(self, *args, **kwargs)
2548 passed through to the underlying data reader (e.g. `~astropy.io.ascii.write`).
2549 """
-> 2550 io_registry.write(self, *args, **kwargs)
2551
2552 def copy(self, copy_data=True):
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/astropy/io/registry.py in write(data, *args, **kwargs)
579
580 writer = get_writer(format, data.__class__)
--> 581 writer(data, *args, **kwargs)
582
583
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/astropy/io/ascii/connect.py in io_write(format, table, filename, **kwargs)
43 from .ui import write
44 format = re.sub(r'^ascii\.', '', format)
---> 45 return write(table, filename, format=format, **kwargs)
46
47
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/astropy/io/ascii/ui.py in write(table, output, format, Writer, fast_writer, **kwargs)
733 return
734
--> 735 lines = writer.write(table)
736
737 # Write the lines to output
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/astropy/io/ascii/core.py in write(self, table)
1310 # Write header and data to lines list
1311 lines = []
-> 1312 self.write_header(lines, table.meta)
1313 self.data.write(lines)
1314
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/astropy/io/ascii/core.py in write_header(self, lines, meta)
1269 def write_header(self, lines, meta):
1270 self.header.write_comments(lines, meta)
-> 1271 self.header.write(lines)
1272
1273 def write(self, table):
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/astropy/io/ascii/ecsv.py in write(self, lines)
72 header_yaml_lines = (['%ECSV {0}'.format(ECSV_VERSION),
73 '---']
---> 74 + meta.get_yaml_from_header(header))
75
76 lines.extend([self.write_comment + line for line in header_yaml_lines])
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/astropy/table/meta.py in get_yaml_from_header(header)
288 del header['cols']
289
--> 290 lines = yaml.dump(header, Dumper=TableDumper).splitlines()
291 return lines
292
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/yaml/__init__.py in dump(data, stream, Dumper, **kwds)
198 If stream is None, return the produced string instead.
199 """
--> 200 return dump_all([data], stream, Dumper=Dumper, **kwds)
201
202 def safe_dump_all(documents, stream=None, **kwds):
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/yaml/__init__.py in dump_all(documents, stream, Dumper, default_style, default_flow_style, canonical, indent, width, allow_unicode, line_break, encoding, explicit_start, explicit_end, version, tags)
186 dumper.open()
187 for data in documents:
--> 188 dumper.represent(data)
189 dumper.close()
190 finally:
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/yaml/representer.py in represent(self, data)
24
25 def represent(self, data):
---> 26 node = self.represent_data(data)
27 self.serialize(node)
28 self.represented_objects = {}
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/yaml/representer.py in represent_data(self, data)
45 data_types = type(data).__mro__
46 if data_types[0] in self.yaml_representers:
---> 47 node = self.yaml_representers[data_types[0]](self, data)
48 else:
49 for data_type in data_types:
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/yaml/representer.py in represent_dict(self, data)
203
204 def represent_dict(self, data):
--> 205 return self.represent_mapping('tag:yaml.org,2002:map', data)
206
207 def represent_set(self, data):
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/astropy/table/meta.py in represent_mapping(self, tag, mapping, flow_style)
268 for item_key, item_value in mapping:
269 node_key = self.represent_data(item_key)
--> 270 node_value = self.represent_data(item_value)
271 if not (isinstance(node_key, yaml.ScalarNode) and not node_key.style):
272 best_style = False
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/yaml/representer.py in represent_data(self, data)
45 data_types = type(data).__mro__
46 if data_types[0] in self.yaml_representers:
---> 47 node = self.yaml_representers[data_types[0]](self, data)
48 else:
49 for data_type in data_types:
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/astropy/table/meta.py in _repr_odict(dumper, data)
145 '!!omap [foo: bar, mumble: quux, baz: gorp]\\n'
146 """
--> 147 return _repr_pairs(dumper, u'tag:yaml.org,2002:omap', six.iteritems(data))
148
149
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/astropy/table/meta.py in _repr_pairs(dump, tag, sequence, flow_style)
120 best_style = True
121 for (key, val) in sequence:
--> 122 item = dump.represent_data({key: val})
123 if not (isinstance(item, yaml.ScalarNode) and not item.style):
124 best_style = False
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/yaml/representer.py in represent_data(self, data)
45 data_types = type(data).__mro__
46 if data_types[0] in self.yaml_representers:
---> 47 node = self.yaml_representers[data_types[0]](self, data)
48 else:
49 for data_type in data_types:
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/yaml/representer.py in represent_dict(self, data)
203
204 def represent_dict(self, data):
--> 205 return self.represent_mapping('tag:yaml.org,2002:map', data)
206
207 def represent_set(self, data):
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/astropy/table/meta.py in represent_mapping(self, tag, mapping, flow_style)
268 for item_key, item_value in mapping:
269 node_key = self.represent_data(item_key)
--> 270 node_value = self.represent_data(item_value)
271 if not (isinstance(node_key, yaml.ScalarNode) and not node_key.style):
272 best_style = False
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/yaml/representer.py in represent_data(self, data)
45 data_types = type(data).__mro__
46 if data_types[0] in self.yaml_representers:
---> 47 node = self.yaml_representers[data_types[0]](self, data)
48 else:
49 for data_type in data_types:
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/yaml/representer.py in represent_dict(self, data)
203
204 def represent_dict(self, data):
--> 205 return self.represent_mapping('tag:yaml.org,2002:map', data)
206
207 def represent_set(self, data):
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/astropy/table/meta.py in represent_mapping(self, tag, mapping, flow_style)
268 for item_key, item_value in mapping:
269 node_key = self.represent_data(item_key)
--> 270 node_value = self.represent_data(item_value)
271 if not (isinstance(node_key, yaml.ScalarNode) and not node_key.style):
272 best_style = False
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/yaml/representer.py in represent_data(self, data)
45 data_types = type(data).__mro__
46 if data_types[0] in self.yaml_representers:
---> 47 node = self.yaml_representers[data_types[0]](self, data)
48 else:
49 for data_type in data_types:
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/yaml/representer.py in represent_dict(self, data)
203
204 def represent_dict(self, data):
--> 205 return self.represent_mapping('tag:yaml.org,2002:map', data)
206
207 def represent_set(self, data):
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/astropy/table/meta.py in represent_mapping(self, tag, mapping, flow_style)
268 for item_key, item_value in mapping:
269 node_key = self.represent_data(item_key)
--> 270 node_value = self.represent_data(item_value)
271 if not (isinstance(node_key, yaml.ScalarNode) and not node_key.style):
272 best_style = False
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/yaml/representer.py in represent_data(self, data)
55 node = self.yaml_multi_representers[None](self, data)
56 elif None in self.yaml_representers:
---> 57 node = self.yaml_representers[None](self, data)
58 else:
59 node = ScalarNode(None, str(data))
~/local/conda/envs/photutils-dev/lib/python3.6/site-packages/yaml/representer.py in represent_undefined(self, data)
227
228 def represent_undefined(self, data):
--> 229 raise RepresenterError("cannot represent an object: %s" % data)
230
231 SafeRepresenter.add_representer(type(None),
RepresenterError: cannot represent an object: ( 11.1, 232.24, 7.25) km / s
CC: @eteq, @taldcroft
Activity
eteq commentedon Aug 15, 2017
This one's a doozy, bit I figured it out. PR incoming shortly! (#6448)
eteq commentedon Aug 15, 2017
Oh and note this is effectively 2 separate bugs:
galcen_v_sunis getting set at all in this casegalcen_v_sundoes not get represented properly in ecsvI'm going to decide that this issue is about 1 (which is a lot easier to fix), but make a separate issue for 2.
regression test for astropy#6446
regression test for astropy#6446