MIVOT (pyvo.mivot)¶
This module contains the new feature of annotations in VOTable. Astropy version >= 6.0 is required.
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.
Model Instances in VOTables is a VO standard
Requires Astropy>=6.0
pyvo.mivotis a prototype feature which must be activated withactivate_features("MIVOT")
Implementation Scope¶
This implementation is totally model-agnostic.
It does not operate any validation against specific data models.
It just requires the annotation syntax being compliant with the standards.
However, many data samples used for the test suite and provided as examples
are based on the EpochPropagation class of the Mango data model
that is still a draft.
This class collects all the parameters we need to compute the epoch propagation of moving sky objects.
Some of the examples have been provided by a special end-point of the Vizier cone-search service
(https://cdsarc.cds.unistra.fr/beta/viz-bin/mivotconesearch) that maps query results to this model.
It is to be noted that the Vizier service does not annotate errors at the time of writing (Q1 2024)
The implementation uses the Astropy read/write annotation module (6.0+), which allows to get (and set) Mivot blocks from/into VOTables as an XML element serialized as a string.
Not all MIVOT features are supported by this implementation, which mainly focuses on the epoch propagation use case:
JOINfeatures are not supported.
TEMPLATESwith more than oneINSANCEnot supported.
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, resulting from a cone-search query which data are mapped
to the ``EpochPosition class, can be consumed.
>>> 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://cdsarc.cds.unistra.fr/beta/viz-bin/mivotconesearch/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
... )
... )
>>> mivot_instance = m_viewer.dm_instance
>>> print(mivot_instance.dmtype)
mango:EpochPosition
>>> print(mivot_instance.coordSys.spaceRefFrame.value)
ICRS
>>> while m_viewer.next():
... 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 to_dict() method of MivotInstance.
from pyvo.mivot import MivotViewer
from pyvo.mivot.utils.dict_utils import DictUtils
m_viewer = MivotViewer(path_to_votable)
mivot_instance = m_viewer.dm_instance
mivot_object_dict = mivot_object.to_dict()
DictUtils.print_pretty_json(mivot_object_dict)
{
"dmtype": "mango: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"},
"coordSys": {
"dmtype": "coords:SpaceSys",
"dmid": "ICRS",
"dmrole": "coords:Coordinate.coordSys",
"spaceRefFrame": {"value": "ICRS"},
},
}
It is recommended to use a copy of the dictionary as it will be rebuilt each time the
to_dict()method is invoked.The default representation of
MivotInstanceinstances is made with a pretty string serialization of this dictionary (method__repr__()).An extended version of the object dictionary e.g. with information about where the values were picked from from, is available using the method
to_hk_dict().
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.
Get a SkyCoord Instance Directly From the Annotations¶
Once you get a MivotInstance representing the last row read, you can use it to create an astropy.SkyCoord object.
from pyvo.mivot import MivotViewer
m_viewer = MivotViewer(path_to_votable)
mivot_instance = m_viewer.dm_instance
print(mivot_instance.get_SkyCoord())
<SkyCoord (ICRS): (ra, dec) in deg(52.26722684, 59.94033461)
(pm_ra_cosdec, pm_dec) in mas / yr(-0.82, -1.85)>
This feature works under the condition that the annotations contain a valid instance of mango:EPochPosition, otherwise
a NoMatchingDMTypeError is thrown.
Although not a standard at the time of writing, the class structure supported by this implementation must match the figure above.
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():
xml_view = mivot_viewer.xml_view
# do whatever you want with this XML element
It 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:
INSTANCEfor the objectsATTRIBUTEfor the attributesCOLLECTIONfor 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:
INSTANCEare represented by Python classesATTRIBUTEare represented by Python class fieldsCOLLECTIONare 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
@dmtypeare kept as attributes of generated Python objects.The structure of the
MivotInstanceobjects can be inferred from the mapped model in 2 different ways:From the MIVOT instance property
MivotInstance.to_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).
Reference/API¶
pyvo.mivot Package¶
Classes¶
|
MivotViewer is a PyVO table wrapper aiming at providing a model view on VOTable data read with usual tools. |
Class Inheritance Diagram¶
pyvo.mivot.viewer Package¶
pyvo.mivot.seekers Package¶
seekers package contains utilities for retrieving
components of VOTales or of Mivot blocks