[Issue335] description_2d propagated and set to 1 by default by Didou09 · Pull Request #336 · ToFuProject/tofu

Didou09 · 2020-01-27T14:38:27Z

Main changes:

The input keyword argument 'description_2d', used to choosed the wall geometry from an imas wall IDS, is now available from all methods of MultiIDSLoader that call to_Config() in the background. These include in particular to_Plasma2D(), to_Cam(), to_Data() and calc_signal()
When not set (description_2d=None), the variable is now automatocally set to 1 if possible (to 0 otherwise)

Example (on IRFM Intra only):

In [1]: import tofu as tf
/Home/DV226270/ToFu_All/tofu_git/tofu/tofu/imas2tofu/__init__.py:83: UserWarning: 
You do not seem to be using the latest IMAS version:
'module list' vs 'module av IMAS' suggests:
	- Current version: 3.23.1-4.0.3
	- Latest version : 3.25.0-4.4.0
  warnings.warn(msg)
/Home/DV226270/ToFu_All/tofu_git/tofu/tofu/__init__.py:95: UserWarning: 
The following subpackages are not available:
    - tofu.mag
  => see print(tofu.dsub[<subpackage>]) for details.
  warnings.warn(msg)

In [2]: multi = tf.imas2tofu.MultiIDSLoader(ids=['bolometer'], shot=55983, ids_base=True)
Getting ids     [occ]  tokamak  user         version  shot   run  refshot  refrun
--------------  -----  -------  -----------  -------  -----  ---  -------  ------
bolometer       [0]    west     imas_public  3        55983  0    -1       -1    
pulse_schedule  [0]    "        "            "        "      "    "        "     
wall            [0]    "        "            "        "      "    "        "     

In [3]: bolo = multi.to_Data('bolometer')

In [4]: bolo = multi.to_Data('bolometer', description_2d=0)
/Home/DV226270/ToFu_All/tofu_git/tofu/tofu/imas2tofu/_core.py:2350: UserWarning: 
ids wall has same number of limiter / mobile units
	- len(wall.description_2[0].limiter.unit) = 1
	- len(wall.description_2[0].mobile.unit) = 1
  => Choosing limiter by default
  warnings.warn(msg)

Issues:

Fixes, in devel, Issue #335

…_Data(), and set to 1 when possible by default

…(), to_Cam(), to_Data() and calc_signal()

pep8speaks · 2020-01-28T10:04:06Z

Hello @Didou09! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2020-01-28 12:42:09 UTC

lasofivec

Awesome ! :)

lasofivec · 2020-01-28T10:31:20Z

                  description_2d=None, mobile=None, plot=True):
+        """ Export the content of wall ids as a tofu Config object
+
+        Choose the occurence (occ), and index (description_2d, cf. dd_doc) to


what is dd_doc ?

It is an IMAS-specific documentation
Users of IMAS will know it, others won't, but anyway, this sub-package imas2tofu is to be used by IMAS users only, so they will know ;-)

Basically, to get the documentation on IMAS on the ITER clusters for example, you typically type dd_doc in a terminal (with the ritgh modules pre-loaded), and a web browser opens ndirectly on an IMAS documentation page

lasofivec · 2020-01-28T10:34:49Z

+        plot_sig:   None / str
+            shortcut of the signal to be plotted, if any
+        plot_X:     None / str
+            shortcut of the abscissa against which to plot the signal, if any


what does shortcut means here ?

All data fields can be accessed by shortcuts, they are available via the method get_shortcuts() that displays them all, ordered by ids and signal.

For example:

In [1]: import tofu as tf /Home/DV226270/ToFu_All/tofu_git/tofu/tofu/imas2tofu/__init__.py:83: UserWarning: You do not seem to be using the latest IMAS version: 'module list' vs 'module av IMAS' suggests: - Current version: 3.23.1-4.0.3 - Latest version : 3.25.0-4.4.0 warnings.warn(msg) /Home/DV226270/ToFu_All/tofu_git/tofu/tofu/__init__.py:95: UserWarning: The following subpackages are not available: - tofu.mag => see print(tofu.dsub[<subpackage>]) for details. warnings.warn(msg) In [2]: multi = tf.imas2tofu.MultiIDSLoader(ids=['bolometer'], shot=55983, synthdiag=True) Getting ids [occ] tokamak user version shot run refshot refrun -------------- ----- ------- ----------- ------- ----- --- ------- ------ bolometer [0] west imas_public 3 55983 0 -1 -1 core_sources [0] " " " " " " " equilibrium [0] " " " " " " " ual_begin_arraystruct_action: %TREE-W-NNF, Node Not Found (ual_lowlevel.cpp:719) => failed ! pulse_schedule [0] " " " " " " " wall [0] " " " " " " " /Home/DV226270/ToFu_All/tofu_git/tofu/tofu/imas2tofu/_core.py:1200: UserWarning: ERROR: ual_begin_arraystruct_action failed for "grids_ggd" warnings.warn(str(err)) In [3]: multi.get_shortcuts() ids shortcut long version -------------- ------------ ------------------------------------------------------------------------- bolometer etendue channel[chan].etendue bolometer los_pt1Phi channel[chan].line_of_sight.first_point.phi bolometer los_pt1R channel[chan].line_of_sight.first_point.r bolometer los_pt1Z channel[chan].line_of_sight.first_point.z bolometer los_pt2Phi channel[chan].line_of_sight.second_point.phi bolometer los_pt2R channel[chan].line_of_sight.second_point.r bolometer los_pt2Z channel[chan].line_of_sight.second_point.z bolometer los_ptsRZPhi f( los_pt1R, los_pt1Z, los_pt1Phi, los_pt2R, los_pt2Z, los_pt2Phi ) bolometer names channel[chan].name bolometer power channel[chan].power.data bolometer prad power_radiated_total bolometer pradbulk power_radiated_inside_lcfs bolometer t channel[chan].power.time bolometer tpower time core_sources 1dbrem source[identifier.name=bremsstrahlung].profiles_1d[time].electrons.energy core_sources 1dline source[identifier.name=lineradiation].profiles_1d[time].electrons.energy core_sources 1dprad f( 1dbrem, 1dline ) core_sources 1dpsi source[identifier.name=lineradiation].profiles_1d[time].grid.psi core_sources 1drhopn f( 1dpsi ) core_sources 1drhotn source[identifier.name=lineradiation].profiles_1d[time].grid.rho_tor_norm core_sources t time equilibrium 1djT time_slice[time].profiles_1d.j_tor equilibrium 1dpe time_slice[time].profiles_1d.pressure equilibrium 1dphi time_slice[time].profiles_1d.phi equilibrium 1dpsi time_slice[time].profiles_1d.psi equilibrium 1dq time_slice[time].profiles_1d.q equilibrium 1drhopn f( 1dpsi, psiaxis, psisep ) equilibrium 1drhotn time_slice[time].profiles_1d.rho_tor_norm equilibrium 2dB f( 2dBT, 2dBR, 2dBZ ) equilibrium 2dBR time_slice[time].ggd[0].b_field_r[0].values equilibrium 2dBT time_slice[time].ggd[0].b_field_tor[0].values equilibrium 2dBZ time_slice[time].ggd[0].b_field_z[0].values equilibrium 2djT time_slice[time].ggd[0].j_tor[0].values equilibrium 2dmeshFaces grids_ggd[0].grid[0].space[0].objects_per_dimension[2].object[].nodes equilibrium 2dmeshNodes grids_ggd[0].grid[0].space[0].objects_per_dimension[0].object[].geometry equilibrium 2dmeshR time_slice[0].profiles_2d[0].r equilibrium 2dmeshZ time_slice[0].profiles_2d[0].z equilibrium 2dphi time_slice[time].ggd[0].phi[0].values equilibrium 2dpsi time_slice[time].ggd[0].psi[0].values equilibrium 2drhopn f( 2dpsi, psiaxis, psisep ) equilibrium 2drhotn f( 2dphi ) equilibrium 2dtheta f( axR, axZ, 2dmeshNodes ) equilibrium BT0 time_slice[time].global_quantities.magnetic_axis.b_field_tor equilibrium ax f( axR, axZ ) equilibrium axR time_slice[time].global_quantities.magnetic_axis.r equilibrium axZ time_slice[time].global_quantities.magnetic_axis.z equilibrium ip time_slice[time].global_quantities.ip equilibrium psiaxis time_slice[time].global_quantities.psi_axis equilibrium psisep time_slice[time].global_quantities.psi_boundary equilibrium q0 time_slice[time].global_quantities.q_axis equilibrium q95 time_slice[time].global_quantities.q_95 equilibrium qmin time_slice[time].global_quantities.q_min.value equilibrium sep f( sepR, sepZ ) equilibrium sepR time_slice[time].boundary_separatrix.outline.r equilibrium sepZ time_slice[time].boundary_separatrix.outline.z equilibrium strike0 f( strike0R, strike0Z ) equilibrium strike0R time_slice[time].boundary.strike_point[0].r equilibrium strike0Z time_slice[time].boundary.strike_point[0].z equilibrium strike1 f( strike1R, strike1Z ) equilibrium strike1R time_slice[time].boundary.strike_point[1].r equilibrium strike1Z time_slice[time].boundary.strike_point[1].z equilibrium t time equilibrium volume time_slice[time].global_quantities.volume equilibrium x0 f( x0R, x0Z ) equilibrium x0R time_slice[time].boundary.x_point[0].r equilibrium x0Z time_slice[time].boundary.x_point[0].z equilibrium x1 f( x1R, x1Z ) equilibrium x1R time_slice[time].boundary.x_point[1].r equilibrium x1Z time_slice[time].boundary.x_point[1].z pulse_schedule events f( events_names, events_times ) pulse_schedule events_names event[].identifier pulse_schedule events_times event[].time_stamp wall wall f( wallR, wallZ ) wall wallR description_2d[0].limiter.unit[0].outline.r wall wallZ description_2d[0].limiter.unit[0].outline.z

I implemented this because accessing data in an IMAS ids can be cumbersome since the path to it can be long and not always intuitive.
So each long path has a shortcut.
Most are predefined but the user can customize them if he wants to define his/her own shortcuts. Koyo did it for example in issue #218

ok, I imagined it was this but I rather keep a record of the answer. Plus I didn't know shortcuts were also for the abscissa for example

codecov-io · 2020-01-28T10:38:16Z

Codecov Report

Merging #336 into devel will decrease coverage by <.01%.
The diff coverage is 12.5%.

@@            Coverage Diff             @@
##            devel     #336      +/-   ##
==========================================
- Coverage   40.02%   40.02%   -0.01%     
==========================================
  Files          79       79              
  Lines       24132    24134       +2     
==========================================
  Hits         9659     9659              
- Misses      14473    14475       +2

Impacted Files	Coverage Δ
tofu/imas2tofu/_core.py	`0.67% <0%> (-0.01%)`	⬇️
tofu/version.py	`100% <100%> (ø)`	⬆️

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 822c9da...5b11c7b. Read the comment docs.

[Issue335] descriptio_2d propagated to to_Plasma2D(), to_Cam() and to…

e4c7c24

…_Data(), and set to 1 when possible by default

Didou09 added the imas interfacing - improve label Jan 27, 2020

Didou09 requested a review from lasofivec January 27, 2020 14:38

Didou09 self-assigned this Jan 27, 2020

lasofivec approved these changes Jan 27, 2020

View reviewed changes

lasofivec suggested changes Jan 27, 2020

View reviewed changes

Comment thread tofu/imas2tofu/_core.py

[Issue335] Added docstr to Multi.get_data(), to_Config(), to_Plasma2D…

375c9f3

…(), to_Cam(), to_Data() and calc_signal()

[Issue335] PEP8 compliance

038ef35

lasofivec approved these changes Jan 28, 2020

View reviewed changes

[Issue335] Typos

5b11c7b

Didou09 merged commit 0840bdc into devel Jan 28, 2020

Didou09 mentioned this pull request Jan 28, 2020

imas2tofu: propagate description2d to Data and calc_signal and choose when possible #335

Closed

Didou09 deleted the Issue335_description2d branch January 28, 2020 13:21

Didou09 mentioned this pull request Jan 30, 2020

tofu 1.4.2 preparation #339

Merged

Didou09 mentioned this pull request Mar 10, 2020

Preparing 1.4.3 #364

Merged

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

[Issue335] description_2d propagated and set to 1 by default#336

[Issue335] description_2d propagated and set to 1 by default#336
Didou09 merged 4 commits intodevelfrom
Issue335_description2d

Didou09 commented Jan 27, 2020

Uh oh!

Uh oh!

pep8speaks commented Jan 28, 2020 •

edited

Loading

Uh oh!

lasofivec left a comment

Uh oh!

lasofivec Jan 28, 2020

Uh oh!

Didou09 Jan 28, 2020

Uh oh!

Uh oh!

lasofivec Jan 28, 2020

Uh oh!

Didou09 Jan 28, 2020

Uh oh!

Didou09 Jan 28, 2020

Uh oh!

lasofivec Jan 28, 2020

Uh oh!

codecov-io commented Jan 28, 2020 •

edited

Loading

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

Conversation

Didou09 commented Jan 27, 2020

Main changes:

Example (on IRFM Intra only):

Issues:

Uh oh!

Uh oh!

pep8speaks commented Jan 28, 2020 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Comment last updated at 2020-01-28 12:42:09 UTC

Uh oh!

lasofivec left a comment

Choose a reason for hiding this comment

Uh oh!

lasofivec Jan 28, 2020

Choose a reason for hiding this comment

Uh oh!

Didou09 Jan 28, 2020

Choose a reason for hiding this comment

Uh oh!

Uh oh!

lasofivec Jan 28, 2020

Choose a reason for hiding this comment

Uh oh!

Didou09 Jan 28, 2020

Choose a reason for hiding this comment

For example:

Uh oh!

Didou09 Jan 28, 2020

Choose a reason for hiding this comment

Uh oh!

lasofivec Jan 28, 2020

Choose a reason for hiding this comment

Uh oh!

codecov-io commented Jan 28, 2020 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

pep8speaks commented Jan 28, 2020 •

edited

Loading

codecov-io commented Jan 28, 2020 •

edited

Loading