Feature/add separatrix and magnetic axes in plotequilibrium

[prasad-sawantdesai]

plotequilibrium -u imas:hdf5?path=/work/imas/shared/imasdb/ITER/3/135014/1

[SimonPinches]

This doesn't look correct. In this configuration the separatrix should connect to the lower X-point which it doesn't. Can we also plot the two X-points in this figure?

[ksunhee8]

The sepratrix plotted from the boundary.r/z is not real separatrix, it is rather last closed flux surface. Therefore it would be useful to check if boundary_separatrix.r/z and boundary_second_separatrix.r/z are available and try to plot all three of them. The boundary_separatrix and boundary_second_separatrix can contain x_point.r/z, for more specific indication of x-points. These would be good to be plotted when they are available in the IDSs.

[MireilleSchneider]

I suggest then to just rename 'speratrix' into 'LCFS' such that everyone is happy. Ideally it would be good to also display the separatrix but my guess is that the data is simply not filled in the IDS.

[SimonPinches]

It's not the last closed flux surface, that would be the separatrix. It might be the last closed flux surface according to some discretisation of flux values, but that seems a bit arbitrary.

[olivhoenen]

We should decide what we want here:

• DD3 vs DD4 or both? (boundary/contour structures have changed)
• what to plot: x-points, magnetic center, separatrix (if present, boundary if not), secondary_separatrix (and x_point)? (these are DD3-related structures/names, for DD4 you should look into contour_tree/node and node/levelset)

[prasad-sawantdesai]

This doesn't look correct. In this configuration the separatrix should connect to the lower X-point which it doesn't. Can we also plot the two X-points in this figure?

Thanks.. added separatrix and x-points

[prasad-sawantdesai]

The sepratrix plotted from the boundary.r/z is not real separatrix, it is rather last closed flux surface. Therefore it would be useful to check if boundary_separatrix.r/z and boundary_second_separatrix.r/z are available and try to plot all three of them. The boundary_separatrix and boundary_second_separatrix can contain x_point.r/z, for more specific indication of x-points. These would be good to be plotted when they are available in the IDSs.

Thank you.. I could not find any IMAS entry with boundary_second_separatrix.r/z . I used boundary_separatrix.r/z and it looks like this -> #20 (comment)

[prasad-sawantdesai]

Thanks for the comments @SimonPinches
plotequilibrium -u imas:mdsplus?path=/work/imas/shared/imasdb/ITER/3/100507/2 --md "imas:hdf5?path=/work/imas/shared/imasdb/ITER_MD/3/116000/4#wall"

[olivhoenen]

• strike points are not present at the moment in DD4, so either we re-introduce them or we can decide not to add them in this plot overlay (cf. feat(equilibrium): enhance contour_tree for advanced plasma topologies IMAS-Data-Dictionary#243 (comment))

[prasad-sawantdesai]

$ plotequilibrium -u  imas:hdf5?path=/work/imas/shared/imasdb/ITER/3/100507/5 --md "imas:hdf5?path=/work/imas/shared/imasdb/ITER_MD/3/116000/5#wall"

[prasad-sawantdesai]

• strike points are not present at the moment in DD4, so either we re-introduce them or we can decide not to add them in this plot overlay (cf. feat(equilibrium): enhance contour_tree for advanced plasma topologies IMAS-Data-Dictionary#243 (comment))

We shall keep implementation of strike points from DD3.. Once we have addition of fields for strike points in DD4 we will add implementation for the same..

[olivhoenen]

Last round of comments:

• please allow to remove provenance info with an extra option --no-provenance
• when printing provenance about machine description, please also show a single URI per group of subsystems that are sharing the same data-entry (it works when it is the same as the equilibrium one, but not when it is different), and please print this in the same line, only return for printing the time ref
• please make sure you plot boundary/outline if present
• please rename -p option (confusing for users of idsprint -p/--plot) as --profiles, and in these 1D plots do not label the y axis (this is redundant with legend) + use square brackets for units (legend and x-axis title) + use [1] as unit for normalized data and [s] for time (or simply use the unit metadata you get from imas-python)
• make sure we can still plot machine description with psi when using --no-overlay -md
• is the --rho option useful / correct? if not, please remove

[paulotex]

LGTM. I tried on 2 data entries from efitpp (predictMagnetics + efitpp, from scenarios 105027/2 and 135011/7).

[prasad-sawantdesai]

Last round of comments:

1. please allow to remove provenance info with an extra option --no-provenance
   Added a06d803

2. when printing provenance about machine description, please also show a single URI per group of subsystems that are sharing the same data-entry (it works when it is the same as the equilibrium one, but not when it is different), and please print this in the same line, only return for printing the time ref
   Updated aaec5d8

3. please make sure you plot boundary/outline if present
   2595404

4. please rename -p option (confusing for users of idsprint -p/--plot) as --profiles, and in these 1D plots do not label the y axis (this is redundant with legend) + use square brackets for units (legend and x-axis title) + use [1] as unit for normalized data and [s] for time (or simply use the unit metadata you get from imas-python)
   301de7f

5. make sure we can still plot machine description with psi when using --no-overlay -md
   7745398

6. is the --rho option useful / correct? if not, please remove
   Yes, this is useful to plot toroidal flux if exists.

idsprint -u  imas:mdsplus?path=/work/imas/shared/imasdb/TEST/3/134173/2326#equilibrium/time_slice[0]/profiles_2d[0]/phi
09:53:03 INFO     Parsing data dictionary version 3.40.0 @dd_zip.py:89
╭─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ <class 'imas.ids_primitive.IDSNumericArray'>                                                                                                                                                                    │
│ └── numpy.ndarray|(101, 101)|float64: <IDSNumericArray (IDS:equilibrium, time_slice[0]/profiles_2d[0]/phi, FLT_2D)>                                                                                             │
│                                       numpy.ndarray([[-69.5883, -69.5883, -69.5883, ..., -69.5883, -69.5883, -69.5883],                                                                                         │
│                                              [-69.5883, -69.5883, -69.5883, ..., -69.5883, -69.5883, -69.5883],                                                                                                 │
│                                              [-69.5883, -69.5883, -69.5883, ..., -69.5883, -69.5883, -69.5883],                                                                                                 │
│                                              ...,                                                                                                                                                               │
│                                              [-69.5883, -69.5883, -69.5883, ..., -69.5883, -69.5883, -69.5883],                                                                                                 │
│                                              [-69.5883, -69.5883, -69.5883, ..., -69.5883, -69.5883, -69.5883],                                                                                                 │
│                                              [-69.5883, -69.5883, -69.5883, ..., -69.5883, -69.5883, -69.5883]])

[olivhoenen]

6. is the --rho option useful / correct? if not, please remove
   Yes, this is useful to plot toroidal flux if exists.

idsprint -u  imas:mdsplus?path=/work/imas/shared/imasdb/TEST/3/134173/2326#equilibrium/time_slice[0]/profiles_2d[0]/phi
09:53:03 INFO     Parsing data dictionary version 3.40.0 @dd_zip.py:89
╭─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ <class 'imas.ids_primitive.IDSNumericArray'>                                                                                                                                                                    │
│ └── numpy.ndarray|(101, 101)|float64: <IDSNumericArray (IDS:equilibrium, time_slice[0]/profiles_2d[0]/phi, FLT_2D)>                                                                                             │
│                                       numpy.ndarray([[-69.5883, -69.5883, -69.5883, ..., -69.5883, -69.5883, -69.5883],                                                                                         │
│                                              [-69.5883, -69.5883, -69.5883, ..., -69.5883, -69.5883, -69.5883],                                                                                                 │
│                                              [-69.5883, -69.5883, -69.5883, ..., -69.5883, -69.5883, -69.5883],                                                                                                 │
│                                              ...,                                                                                                                                                               │
│                                              [-69.5883, -69.5883, -69.5883, ..., -69.5883, -69.5883, -69.5883],                                                                                                 │
│                                              [-69.5883, -69.5883, -69.5883, ..., -69.5883, -69.5883, -69.5883],                                                                                                 │
│                                              [-69.5883, -69.5883, -69.5883, ..., -69.5883, -69.5883, -69.5883]])

Ok fair enough, but if we plot profiles_2d/phi why do we say show rho overlay in help?
--rho Show rho overlay on the plot

[olivhoenen]

Great, let's merge