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MCD implementation of Native Frames case
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lmichel authored Mar 2, 2021
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125 changes: 125 additions & 0 deletions usecases/native_frames/mcd-implementation/README.md
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# Implementation of 'Native-Frame' case

# Overview
This case involves data extracted from the Chandra Source Catalog, Release 2.0
containing Source ID and Position in 2 reference frames (ICRS, GALACTIC).

The primary goals of the case appear to be
* Illustrate that the model allows for >1 instance of any given Property
+ Positions in multiple reference frames
+ Flux in multiple bands
* Illustrate ability to reconcile Positions in different Frames

The data has been annotated using IVOA VO-DML Mapping syntax
* one Position using the Measurment model Position with Point coordinate,
which rama automatically converts to an AstroPy SkyCoord.
* one Position using the Mango model LonLatSkyPosition with LonLatPoint coordinate.

Annotation was produced using the 'Jovial' modeling toolset (Java). Jovial
was written by Omar Laurino, and updated by me to the current data model content.
It provides utilities to help define and create instances of (annotations)
IVOA VO-DML compliant data models.

Uses the 'rama' python package to parse annotated data file and instantiate
instances of VO Data Model Classes. The package also applies Adapters which
translate certain VO Data Model Classes to corresponding AstroPY types.
eg: meas:Point -> astropy:SkyCoord
eg: meas:Time -> astropy:Time
This package was developed by Omar Laurino, and updated by me to the current
data model content.

## Resources Used
* Mapping Syntax
+ Working Draft document:
https://volute.g-vo.org/svn/trunk/projects/dm/vo-dml-mapping/doc/VO-DML_mapping_WD.pdf

* Jovial Library
+ version used in this project:
https://github.com/mcdittmar/jovial
+ master repository:
https://github.com/olaurino/jovial

* Rama module
+ version used in this project:
https://github.com/mcdittmar/rama
+ master repository:
https://github.com/olaurino/rama

## Details
* Load Annotated VOTable
```
doc = Reader( Votable(infile) )
```
* **Goal: Find/Identify Positions (the long way)**
Note: LonLatSkyPosition|Point should be integrated with Position|Point
Note: rama auto-converts coords:Point to astropy:SkyCoord while mango:LonLatPoint remains in model representation
```
catalog = doc.find_instances(Source)[0]
positions = []
for param in ( catalog.parameter_dock ):
if type(param.measure) in [ Position, LonLatSkyPosition ]:
if isinstance( param.measure.coord, SkyCoord ):
frame = param.measure.coord.frame.name
else:
frame = param.measure.coord.coord_sys.frame.space_ref_frame
sys.stdout.write("o Found Position in '%s' frame\n"%(frame))
sys.stdout.write(" + coord type = %s\n"%str(type(param.measure.coord) ))
positions.append(param.measure)
```
o Found Position in 'icrs' frame
+ coord type = <class 'astropy.coordinates.sky_coordinate.SkyCoord'>
o Found Position in 'GALACTIC' frame
+ coord type = <class 'rama.models.mango.LonLatPoint'>
* **Goal: Create AstroPy SkyCoord from LonLatPosition**
Note: - the following can form an adapter on LonLatPoint to enable auto-convertion
```
coords1 = positions[0].coord
coords2 = SkyCoord( positions[1].coord.longitude,
positions[1].coord.latitude,
frame=positions[1].coord.coord_sys.frame.space_ref_frame.lower(),
equinox=positions[1].coord.coord_sys.frame.equinox,
unit=positions[1].coord.longitude.unit )
sys.stdout.write("o coords1: type=%s, frame=%s\n"%(str(type(coords1)), coords1.frame.name ))
sys.stdout.write("o coords2: type=%s, frame=%s\n"%(str(type(coords2)), coords2.frame.name ))
```
o coords1: type=<class 'astropy.coordinates.sky_coordinate.SkyCoord'>, frame=icrs
o coords2: type=<class 'astropy.coordinates.sky_coordinate.SkyCoord'>, frame=galactic
* **Goal: Convert both to common Frame - client's preferred frame**
```
coords1_user = coords1.transform_to(FK5(equinox="J2015.5"))
coords2_user = coords2.transform_to(FK5(equinox="J2015.5"))
sys.stdout.write("o coords1: type=%s, frame=%s\n"%(str(type(coords1_user)), coords1_user.frame.name ))
sys.stdout.write("o coords2: type=%s, frame=%s\n"%(str(type(coords2_user)), coords2_user.frame.name ))
```
o coords1: type=<class 'astropy.coordinates.sky_coordinate.SkyCoord'>, frame=fk5
o coords2: type=<class 'astropy.coordinates.sky_coordinate.SkyCoord'>, frame=fk5
* **Goal: Plot the data**
Note: Since the original data are positions of the same source in different frames, these should overlap.
```
plt.figure( figsize=(6.5,6.5) )
plt.suptitle("Plots of Source Data")
plt.subplots_adjust(top=0.90,bottom=0.1)
ax1 = plt.subplot(211, projection="aitoff")
ax1.grid(True)
ra_rad = coords1_user.ra.wrap_at(180 * u.deg).radian
dec_rad = coords1_user.dec.radian
plt.plot(ra_rad, dec_rad, 'o', markersize=3, color="blue")
ax2 = plt.subplot(212)
ax2.set_title("Overlay coordinates converted to common frame")
ax2.grid(True)
ax2.set_xlabel("RA [%s]"%coords1_user.ra.unit)
ax2.set_ylabel("DEC [%s]"%coords1_user.dec.unit)
plt.plot( coords1_user.ra, coords1_user.dec,'o', markersize=3, color='blue')
plt.plot( coords2_user.ra, coords2_user.dec,'x', markersize=3, color='red')
plt.show()
```
![Figure_1](https://user-images.githubusercontent.com/14201994/109700688-1be4fa00-7b60-11eb-9ea0-a34e46b386b1.png)
237 changes: 237 additions & 0 deletions usecases/native_frames/mcd-implementation/csc2_annotated.vot
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<?xml version="1.0" encoding="UTF-8"?><VOTABLE xmlns="http://www.ivoa.net/xml/VOTable/v1.4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<DESCRIPTION>
VizieR Astronomical Server vizier.u-strasbg.fr
Date: 2021-01-21T13:05:40 [V1.99+ (14-Oct-2013)]
Explanations and Statistics of UCDs: See LINK below
In case of problem, please report to: [email protected]
In this version, NULL integer columns are written as an empty string
&lt;TD&gt;&lt;/TD&gt;, explicitely possible from VOTable-1.3
</DESCRIPTION>
<!-- VOTable description at http://www.ivoa.net/Documents/latest/VOT.html -->
<INFO ID="VERSION" name="votable-version" value="1.99+ (14-Oct-2013)" />
<INFO ID="Ref" name="-ref" value="VIZ60097b26a189" />
<INFO ID="MaxTuples" name="-out.max" value="10" />
<INFO name="queryParameters" value="15">
-oc.form=dec
-out.max=10
-nav=cat:IX/57&amp;tab:{IX/57/csc2master}&amp;key:source=IX/57&amp;HTTPPRM:&amp;
-c.eq=J2000
-c.r= 2
-c.u=arcmin
-c.geom=r
-source=IX/57/csc2master
-order=I
-out.orig=standard
-out=2CXO
-out=RAICRS
-out=DEICRS
-out=GLON
-out=GLAT
</INFO>

<VODML>
<MODEL>
<NAME>mango</NAME>
<URL>file:/Users/sao/Documents/IVOA/GitHub/ivoa-dm-examples/tmp/Mango-v1.0.vo-dml.xml</URL>
</MODEL>
<MODEL>
<NAME>meas</NAME>
<URL>https://www.ivoa.net/xml/Meas/20200908/Meas-v1.0.vo-dml.xml</URL>
</MODEL>
<MODEL>
<NAME>coords</NAME>
<URL>https://www.ivoa.net/xml/STC/20200908/Coords-v1.0.vo-dml.xml</URL>
</MODEL>
<MODEL>
<NAME>ivoa</NAME>
<URL>https://www.ivoa.net/xml/VODML/IVOA-v1.vo-dml.xml</URL>
</MODEL>
<GLOBALS>
<INSTANCE dmtype="coords:SpaceSys" ID="_coosys1">
<COMPOSITION dmrole="coords:PhysicalCoordSys.frame">
<INSTANCE dmtype="coords:SpaceFrame">
<ATTRIBUTE dmrole="coords:SpaceFrame.spaceRefFrame">
<LITERAL value="ICRS" dmtype="ivoa:string"/>
</ATTRIBUTE>
</INSTANCE>
</COMPOSITION>
</INSTANCE>
<INSTANCE dmtype="mango:coordinates.LonLatCoordSys" ID="_coosys2">
<COMPOSITION dmrole="coords:PhysicalCoordSys.frame">
<INSTANCE dmtype="coords:SpaceFrame">
<ATTRIBUTE dmrole="coords:SpaceFrame.spaceRefFrame">
<LITERAL value="GALACTIC" dmtype="ivoa:string"/>
</ATTRIBUTE>
<ATTRIBUTE dmrole="coords:SpaceFrame.equinox">
<LITERAL value="J2000" dmtype="coords:Epoch"/>
</ATTRIBUTE>
</INSTANCE>
</COMPOSITION>
</INSTANCE>
</GLOBALS>
<TEMPLATES tableref="Results">
<INSTANCE dmtype="mango:Source">
<ATTRIBUTE dmrole="mango:Source.identifier">
<COLUMN dmtype="ivoa:string" ref="_col1"/>
</ATTRIBUTE>
<COMPOSITION dmrole="mango:Source.parameterDock">
<INSTANCE dmtype="mango:Parameter">
<ATTRIBUTE dmrole="mango:Parameter.ucd">
<LITERAL value="pos.eq" dmtype="ivoa:string"/>
</ATTRIBUTE>
<COMPOSITION dmrole="mango:Parameter.measure">
<INSTANCE dmtype="meas:Position">
<ATTRIBUTE dmrole="meas:Position.coord">
<INSTANCE dmtype="coords:Point">
<ATTRIBUTE dmrole="coords:Point.axis1">
<COLUMN dmtype="ivoa:RealQuantity" ref="_col2"/>
</ATTRIBUTE>
<ATTRIBUTE dmrole="coords:Point.axis2">
<COLUMN dmtype="ivoa:RealQuantity" ref="_col3"/>
</ATTRIBUTE>
<REFERENCE dmrole="coords:Coordinate.coordSys">
<IDREF>_coosys1</IDREF>
</REFERENCE>
</INSTANCE>
</ATTRIBUTE>
</INSTANCE>
</COMPOSITION>
</INSTANCE>
<INSTANCE dmtype="mango:Parameter">
<ATTRIBUTE dmrole="mango:Parameter.ucd">
<LITERAL value="pos.galactic" dmtype="ivoa:string"/>
</ATTRIBUTE>
<COMPOSITION dmrole="mango:Parameter.measure">
<INSTANCE dmtype="mango:measures.LonLatSkyPosition">
<ATTRIBUTE dmrole="mango:measures.LonLatSkyPosition.coord">
<INSTANCE dmtype="mango:coordinates.LonLatPoint">
<ATTRIBUTE dmrole="mango:coordinates.LonLatPoint.longitude">
<COLUMN dmtype="ivoa:RealQuantity" ref="_col5"/>
</ATTRIBUTE>
<ATTRIBUTE dmrole="mango:coordinates.LonLatPoint.latitude">
<COLUMN dmtype="ivoa:RealQuantity" ref="_col4"/>
</ATTRIBUTE>
<REFERENCE dmrole="coords:Coordinate.coordSys">
<IDREF>_coosys2</IDREF>
</REFERENCE>
</INSTANCE>
</ATTRIBUTE>
</INSTANCE>
</COMPOSITION>
</INSTANCE>
</COMPOSITION>
</INSTANCE>
</TEMPLATES>
</VODML>

<!-- Execution Reports -->

<RESOURCE ID="yCat_9057" name="IX/57">
<DESCRIPTION>The Chandra Source Catalog (CSC), Release 2.0 (Evans+, 2019)</DESCRIPTION>
<COOSYS ID="H" system="ICRS" />
<TABLE ID="Results" name="IX/57/csc2master">
<DESCRIPTION>Chandra Source Catalog, V2.0; master sources</DESCRIPTION>
<!-- Chandra Source Catalog, V2.0; master sources (\originalcolumnnames) -->

<!-- Definitions of GROUPs and FIELDs -->

<!-- +++No column could be found to attach a LINK in table: IX/57/csc2master -->
<FIELD ID="_col1" name="2CXO" ucd="meta.id;meta.main" datatype="char" arraysize="18"><!-- ucd="ID_MAIN" -->
<DESCRIPTION>Source name (Jhhmmss.s+ddmmssX) (name)</DESCRIPTION>
</FIELD>
<FIELD ID="_col2" name="RAICRS" ucd="pos.eq.ra;meta.main" ref="H" datatype="double" width="11" precision="7" unit="deg"><!-- ucd="POS_EQ_RA_MAIN" -->
<DESCRIPTION>Source position, ICRS right ascension (ra)</DESCRIPTION>
</FIELD>
<FIELD ID="_col3" name="DEICRS" ucd="pos.eq.dec;meta.main" ref="H" datatype="double" width="11" precision="7" unit="deg"><!-- ucd="POS_EQ_DEC_MAIN" -->
<DESCRIPTION>Source position, ICRS declination (dec)</DESCRIPTION>
</FIELD>
<FIELD ID="_col4" name="GLON" ucd="pos.galactic.lon" datatype="double" width="12" precision="E5" unit="deg"><!-- ucd="POS_GAL_LON" -->
<DESCRIPTION>[-90/90] Source position, Galactic latitude (equinox J2000, epoch J2000) (gal_b)</DESCRIPTION>
</FIELD>
<FIELD ID="_col5" name="GLAT" ucd="pos.galactic.lat" datatype="double" width="12" precision="E5" unit="deg"><!-- ucd="POS_GAL_LAT" -->
<DESCRIPTION>[0/360] Source position, Galactic longitude (gal_l)</DESCRIPTION>
</FIELD>
<DATA>
<TABLEDATA>
<TR>
<TD> J165541.6-424937</TD>
<TD>253.9235440</TD>
<TD>-42.8271581</TD>
<TD>3.34360e-01</TD>
<TD>3.42863e+02</TD>
</TR>
<TR>
<TD> J165643.7-424532</TD>
<TD>254.1822020</TD>
<TD>-42.7589867</TD>
<TD>2.29009e-01</TD>
<TD>3.43035e+02</TD>
</TR>
<TR>
<TD> J165650.6-423812</TD>
<TD>254.2110170</TD>
<TD>-42.6366900</TD>
<TD>2.88859e-01</TD>
<TD>3.43143e+02</TD>
</TR>
<TR>
<TD> J165655.8-423816</TD>
<TD>254.2327631</TD>
<TD>-42.6379642</TD>
<TD>2.75568e-01</TD>
<TD>3.43152e+02</TD>
</TR>
<TR>
<TD> J165649.7-423849</TD>
<TD>254.2074791</TD>
<TD>-42.6470446</TD>
<TD>2.84426e-01</TD>
<TD>3.43134e+02</TD>
</TR>
<TR>
<TD> J165659.9-423630</TD>
<TD>254.2496619</TD>
<TD>-42.6083618</TD>
<TD>2.84331e-01</TD>
<TD>3.43183e+02</TD>
</TR>
<TR>
<TD> J165658.8-423732</TD>
<TD>254.2452153</TD>
<TD>-42.6257554</TD>
<TD>2.76031e-01</TD>
<TD>3.43168e+02</TD>
</TR>
<TR>
<TD> J165703.7-425442</TD>
<TD>254.2655991</TD>
<TD>-42.9116713</TD>
<TD>8.59080e-02</TD>
<TD>3.42954e+02</TD>
</TR>
<TR>
<TD> J165719.8-425620</TD>
<TD>254.3329099</TD>
<TD>-42.9390771</TD>
<TD>3.02880e-02</TD>
<TD>3.42963e+02</TD>
</TR>
<TR>
<TD> J170103.4-404053</TD>
<TD>255.2642189</TD>
<TD>-40.6814190</TD>
<TD>8.82591e-01</TD>
<TD>3.45166e+02</TD>
</TR>
</TABLEDATA>
</DATA>
</TABLE>
<INFO name="matches" value="10">matching records</INFO>

<INFO name="Warning" value="No center provided++++" />
<INFO name="Warning" value="+++No column for LINK to a row in table: IX/57/csc2master" />
<INFO name="Warning" value="truncated result (maxtup=10)" />
<INFO name="QUERY_STATUS" value="OVERFLOW">truncated result (maxtup=10)</INFO>

</RESOURCE>
</VOTABLE>

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