MIVOT (pyvo.mivot
): Annotation Viewer - Public API¶
Introduction¶
Model Instances in VOTables (MIVOT) defines a syntax to map VOTable data to any model serialized in VO-DML. The annotation operates as a bridge between the data and the model. It associates the column/param metadata from the VOTable to the data model elements (class, attributes, types, etc.) […]. The data model elements are grouped in an independent annotation block complying with the MIVOT XML syntax. This annotation block is added as an extra resource element at the top of the VOTable result resource. The MIVOT syntax allows to describe a data structure as a hierarchy of classes. It is also able to represent relations and composition between them. It can also build up data model objects by aggregating instances from different tables of the VOTable (get more in MIVOT (pyvo.mivot)).
Using the API¶
Integrated Readout¶
The ModelViewer
module manages access to data mapped to a model through dynamically
generated objects (MivotInstance
class).
The example below shows how a VOTable result of a cone-search query can be parsed and data
mapped to the EpochPosition
class.
>>> import astropy.units as u
>>> from astropy.coordinates import SkyCoord
>>> from pyvo.dal.scs import SCSService
>>> from pyvo.utils.prototype import activate_features
>>> from pyvo.mivot.version_checker import check_astropy_version
>>> from pyvo.mivot.viewer.mivot_viewer import MivotViewer
>>> activate_features("MIVOT")
>>> if check_astropy_version() is False:
... pytest.skip("MIVOT test skipped because of the astropy version.")
>>> scs_srv = SCSService("https://vizier.cds.unistra.fr/viz-bin/conesearch/V1.5/I/239/hip_main")
>>> m_viewer = MivotViewer(
... scs_srv.search(
... pos=SkyCoord(ra=52.26708 * u.degree, dec=59.94027 * u.degree, frame='icrs'),
... radius=0.05
... ),
... resolve_ref=True
... )
>>> mivot_instance = m_viewer.dm_instance
>>> print(mivot_instance.dmtype)
mango:EpochPosition
>>> print(mivot_instance.spaceSys.frame.spaceRefFrame.value)
ICRS
>>> while m_viewer.next_row_view():
... print(f"position: {mivot_instance.latitude.value} {mivot_instance.longitude.value}")
position: 59.94033461 52.26722684
In this example, the data readout is totally managed by the MivotViewer
instance.
The astropy.io.votable
API is encapsulated in this module.
Model leaves (class attributes) are complex types that provide additional information:
value
: attribute valuedmtype
: attribute type such as defined in the Mivot annotationsunit
: attribute unit such as defined in the Mivot annotationsref
: identifier of the table column mapped on the attribute
The model view on a data row can also be passed as a Python dictionary
using the dict
property of MivotInstance
.
from pyvo.mivot.utils.dict_utils import DictUtils
mivot_instance = m_viewer.dm_instance
mivot_object_dict = mivot_object.dict
DictUtils.print_pretty_json(mivot_object_dict)
{
"dmtype": "EpochPosition",
"longitude": {"value": 359.94372764, "unit": "deg"},
"latitude": {"value": -0.28005255, "unit": "deg"},
"pmLongitude": {"value": -5.14, "unit": "mas/yr"},
"pmLatitude": {"value": -25.43, "unit": "mas/yr"},
"epoch": {"value": 1991.25, "unit": "year"},
"Coordinate_coordSys": {
"dmtype": "SpaceSys",
"dmid": "SpaceFrame_ICRS",
"dmrole": "coordSys",
"spaceRefFrame": {"value": "ICRS"},
},
}
It is recommended to use a copy of the dictionary as it will be rebuilt each time the
dict
property is invoked.The default representation of
MivotInstance
instances is made with a pretty string serialization of this dictionary.
Per-Row Readout¶
The annotation schema can also be applied to table rows read outside of the MivotViewer
with the astropy.io.votable
API:
votable = parse(path_to_votable)
table = votable.resources[0].tables[0]
# init the viewer
mivot_viewer = MivotViewer(votable, resource_number=0)
mivot_object = mivot_viewer.dm_instance
# and feed it with the table row
read = []
for rec in table.array:
mivot_object.update(rec)
read.append(mivot_object.longitude.value)
# show that the model retrieve the correct data values
assert rec["RAICRS"] == mivot_object.longitude.value
assert rec["DEICRS"] == mivot_object.latitude.value
In this case, it is up to the user to ensure that the read data rows are those mapped by the Mivot annotations.
For XML Hackers¶
The model instances can also be serialized as XML elements that can be parsed with XPath queries.
with MivotViewer(path_to_votable) as mivot_viewer:
while mivot_viewer.next_row_view():
xml_view = mivot_viewer.xml_view
# do whatever you want with this XML element
It is to be noted that mivot_viewer.xml_view
is a shortcut
for mivot_viewer.xml_view.view
where mivot_viewer.xml_view
is is an instance of pyvo.mivot.viewer.XmlViewer
.
This object provides many functions facilitating the XML parsing.
Class Generation in a Nutshell¶
MIVOT reconstructs model structures with 3 elements:
INSTANCE
for the objectsATTRIBUTE
for the attributesCOLLECTION
for the elements with a cardinality greater than 1
The role played by each of these elements in the model hierarchy is defined
by its @dmrole
XML attribute. Types of both INSTANCE
and ATTRIBUTE
are defined by
their @dmtype
XML attributes.
MivotInstance
classes are built by following MIVOT annotation structure:
INSTANCE
are represented by Python classesATTRIBUTE
are represented by Python class fieldsCOLLECTION
are represented by Python lists ([])
@dmrole
and @dmtype
cannot be used as Python keywords as such, because they are built from VO-DML
identifiers, which have the following structure: model:a.b
.
Only the last part of the path is kept for attribute names.
For class names, forbidden characters (
:
or.
) are replaced with_
.Original
@dmtype
are kept as attributes of generated Python objects.The structure of the
MivotInstance
objects can be inferred from the mapped model in 2 different ways:From the MIVOT instance property
MivotInstance.dict
a shown above. This is a pure Python dictionary but its access can be slow because it is generated on the fly each time the property is invoked.
From the internal class dictionary
MivotInstance.__dict__
(see the Python data model).
Exploring the MivotInstance structure with the internal dictionaries¶mivot_instance = mivot_viewer.dm_instance print(mivot_instance.__dict__.keys()) dict_keys(['dmtype', 'longitude', 'latitude', 'pmLongitude', 'pmLatitude', 'epoch', 'Coordinate_coordSys']) print(mivot_instance.Coordinate_coordSys.__dict__.keys()) dict_keys(['dmtype', 'dmid', 'dmrole', 'spaceRefFrame']) print(mivot_instance.Coordinate_coordSys.spaceRefFrame.__dict__.keys()) dict_keys(['dmtype', 'value', 'unit', 'ref'])
Reference/API¶
pyvo.mivot.viewer Package¶
Classes¶
|
MivotInstance holds the dictionary (__dict__) similar with the mapped model structure where the references have been resolved. |
|
MivotViewer is a PyVO table wrapper aiming at providing a model view on VOTable data read with usual tools. |