Added profiles from CAKE #236

AreWeDreaming · 2023-03-08T06:53:42Z

Ripped out other references to profiles needs to be reviewed carefully

- Ripped out other references to profiles needs to be reviewed carefully

…mapping_for_d3d

AreWeDreaming · 2023-03-08T06:57:05Z

omas/machine_mappings/d3d.json

- "core_profiles.global_quantities.v_loop": {
-  "COCOSIO": 11,
-  "PYTHON": "core_profiles_global_quantities_data(ods, {pulse})"
- },


I had to rip this out to make it work. Putting it back in causes:
``core_profiles.profiles_1d.0.grid.rho_pol_norm has no data

@orso82 Do you understand why @AreWeDreaming would get this error, if this is not removed?

Maybe core_profiles_global_quantities_data looks at core_profiles.profiles_1d.0.grid.rho_pol_norm for some reason, and that mapping was not in place?

AreWeDreaming · 2023-03-08T06:57:42Z

omas/machine_mappings/d3d.json

 },
 "core_profiles.profiles_1d.:.electrons.temperature": {
-  "TDI": "\\{PROFILES_tree}::TOP.PROFILES.ETEMPFIT",
-  "treename": "{PROFILES_tree}"


Same here, but not because of errors but because of multiple sources for the same field. I don't know how to resolve this.

@orso82 How does one specify in the machine mappings when the same quantity is available via a variety of MDSplus trees? Maybe passing an argument to ods.open that gets passed to the underlying new core_profiles_profile_1d?

smithsp

Looks promising.

smithsp · 2023-03-08T15:50:34Z

omas/machine_mappings/d3d.json

- "core_profiles.global_quantities.v_loop": {
-  "COCOSIO": 11,
-  "PYTHON": "core_profiles_global_quantities_data(ods, {pulse})"
- },


@orso82 Do you understand why @AreWeDreaming would get this error, if this is not removed?

smithsp · 2023-03-08T15:52:24Z

omas/machine_mappings/d3d.json

 },
 "core_profiles.profiles_1d.:.electrons.temperature": {
-  "TDI": "\\{PROFILES_tree}::TOP.PROFILES.ETEMPFIT",
-  "treename": "{PROFILES_tree}"


@orso82 How does one specify in the machine mappings when the same quantity is available via a variety of MDSplus trees? Maybe passing an argument to ods.open that gets passed to the underlying new core_profiles_profile_1d?

orso82 · 2023-03-08T17:30:55Z

See the "options" section in the "*.json" files to see how options can be passed to mapping functions. For example, you should be able to do:

"__options__": {
  "EFIT_tree": "EFIT01",
  "PROFILES_tree": "ZIPFIT01",
  "analysis_type": "CERQUICK",
  "default_tree": "D3D",
  "fast_ece": false,
  "nref": 0,
  "revision": "BLESSED"
 },
...
"core_profiles.profiles_1d.:.electrons.density": {
  "PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree})"
 }

which can then be passed with

with ods.open("d3d", 133221, PROFILES_tree="mytree")
    plot(ods['core_profiles.profiles_1d.0.electrons.density'])

orso82 · 2023-03-08T17:32:08Z

Should the ability to read ZIPFITS be retained? Are you sure there is nothing that depends on that?

AreWeDreaming · 2023-03-08T17:40:02Z

@orso82 Thanks for the example. I am not suggesting to removed anything, I was just confused about what to do and wanted to have an example for what I was struggling with when asking for help. I didn't realize that I need to move the zipfit mapping out of the .json file and into my new routine. I'll add an if-clause and the tree name as an argument.
The Omas viewer should be able to show whatever Omas can load from zip fits.

- The use of coniditionals seems to cause problems for the .json - Code could probably use some refactoring

AreWeDreaming · 2023-03-08T19:36:05Z

The last commit has several problems:

The "PROFILES_tree" extra argument has to include \', e.g. "\'ZIPFIT01\'" in order to not loose its string nature. This is not the case for "EFIT_tree" which is a very similar extra argument.
PROFILES_tree="\'OMFIT_PROFS\'"and PROFILES_tree="\'ZIPFIT01\'" do not provide the same fields. This seems to confuse the .json file that wants to have a fixed set of fields for each mapping function regardless of its input argument.
I also need uncertainties. I learned from Sean that the TDI function is error_of but I am not sure how to do this for all fields without explicitly looping. I am not sure if explicitly looping over each field might cause separate MDS+ requests for each quantity. I guess I could just create a query like this:

query = {
            "electrons.density.data_error_upper": "error_of(\\TOP.n_e)",
            "electrons.temperature.data_error_upper": "error_of(\\TOP.T_e)",
            "ion[0].density.data_error_upper": "error_of(\\TOP.n_D)",
            "ion[0].temperature.data_error_upper": "error_of(\\TOP.T_i)",
            "ion[0].velocity.toroidal.data_error_upper": "error_of(\\TOP.V_tor_C)",
            "ion[0].density.data_error_upper": "error_of(\\TOP.n_C)"
        }

orso82 · 2023-03-09T04:46:18Z

see how it's done for charge_exchange.channel for example
I need to see the error, if there is an error
Indeed you'll have to query the uncertainties separately and then assign them to the ODS

AreWeDreaming · 2023-03-09T06:09:26Z

Ok, so I managed to sort out all the problems I think. It seems that there were some minor errors that then became several weird problems. Now I can switch between ZIPFIT/OMFIT_PROFS without issues and the tree specification works without \".
I also added the uncertainties.
We'll have to revisit this when the fields for *_fit have data in MDS+. For now, I am happy with this.

- Removed GS error evolution plot

- Also added labels for ion

- Load missing equilibrium quantities via OMFIT - Added functions for improved unit and scale handling in plots - Added extra optional argument `omas_viewer` to equilibrium summary - It plots `p`, `q`, `j_tor`, and `chi^2` for diagnostics - Creates annotations for the `chi^2` plot with identifiers - Shows contraints for `j_tor` and `p` from `code.paramters`

- Moved functions needed by mappings to seprate file - Moved the machine mapping decorator to a utilities file - Moved MDS+ related routines into their own file - Added extra argument to pass `update_mapping` as an argument - Removed `compile` statement as it was causing trouble for the debugger

…mfit_profiles_mapping_for_d3d

github-actions · 2023-07-16T02:13:21Z

Stale pull request message

smithsp · 2023-07-21T19:36:14Z

@AreWeDreaming should remove the no-pr-activity label if this PR is still valid. If it needs further testing, let's work on it. The last automatic test failed.

github-actions · 2023-09-21T01:44:52Z

Stale pull request message

…kfile times

AreWeDreaming added 2 commits March 7, 2023 21:19

Added profiles from CAKE

e1da058

- Ripped out other references to profiles needs to be reviewed carefully

Merge remote-tracking branch 'origin/master' into add_omfit_profiles_…

039f0ec

…mapping_for_d3d

AreWeDreaming requested a review from orso82 March 8, 2023 06:53

AreWeDreaming commented Mar 8, 2023

View reviewed changes

AreWeDreaming self-assigned this Mar 8, 2023

AreWeDreaming added WIP Work in progress help needed labels Mar 8, 2023

smithsp reviewed Mar 8, 2023

View reviewed changes

Re-added support for ZIPFITS.

7f2063d

- The use of coniditionals seems to cause problems for the .json - Code could probably use some refactoring

AreWeDreaming added 2 commits March 8, 2023 21:17

Fixed issues with treenames and ZIPFIT

33ded7f

Added errors, minor refactpring

98eccb2

AreWeDreaming removed help needed WIP Work in progress labels Mar 9, 2023

AreWeDreaming added 10 commits March 13, 2023 11:37

Updated equilibrium_summary for oams_viewer

b33081c

Some refactoring and clean-up

3355078

- Removed GS error evolution plot

Added homogeneous_time=1 for core_profiles

acbb984

Removed stale entry in d3d.json

4450aed

- Also added labels for ion

Fixed profile loading, added pressure and current

82f36e4

Fixes for test_machine_mapping_functions test

98c1080

Fix mds_value import in omas-machine

92ec163

Merged changes from the ring inclusion fix

a8bb83e

AreWeDreaming and others added 10 commits March 24, 2023 08:08

Added fit data to profile plots

37ce0f3

Fix bug for profiles w/o errors

183c500

Adding new equilibrium_quality to omas_plot

d67c543

Merge branch 'omas_viewer_dev' of github.com:gafusion/omas into add_o…

1fb13aa

…mfit_profiles_mapping_for_d3d

Added E_r plot, fixed machine mapping test

0c3297b

Some error handling for empty MDS trees

72088fe

Separated time fetching for better performance

09aee93

More plotting tweaks

b4b2ecf

Some bugfixes for caching working in omas_viewer

c1149de

Enabled ece to be used by machine_to_omas

7fa7ea8

github-actions bot added the no-pr-activity label Jul 16, 2023

github-actions bot removed the no-pr-activity label Jul 22, 2023

github-actions bot added the no-pr-activity label Sep 21, 2023

github-actions bot closed this Sep 28, 2023

smithsp reopened this Oct 25, 2024

machine_mappings:d3d:Get equilibrium times from the gfile times, not …

0ca0f7f

…kfile times

github-actions bot removed the no-pr-activity label Oct 26, 2024

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Added profiles from CAKE #236

Added profiles from CAKE #236

AreWeDreaming commented Mar 8, 2023

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smithsp Mar 8, 2023

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Added profiles from CAKE #236

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Added profiles from CAKE #236

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