From b9a6cb229b7c976563f148d1393e483fc12fb389 Mon Sep 17 00:00:00 2001
From: Olivier Sauter <olivier.sauter@epfl.ch>
Date: Wed, 9 Apr 2025 20:15:41 +0200
Subject: [PATCH 1/4] add new call to read/write from/to IMAS database
including backend
---
matlab/IMAS/gdat_imas.m | 13 +++++++--
matlab/{TCV_IMAS => IMAS}/ids2database.m | 34 +++++++++++++-----------
2 files changed, 29 insertions(+), 18 deletions(-)
rename matlab/{TCV_IMAS => IMAS}/ids2database.m (79%)
diff --git a/matlab/IMAS/gdat_imas.m b/matlab/IMAS/gdat_imas.m
index d2b06fef..a65df0e9 100644
--- a/matlab/IMAS/gdat_imas.m
+++ b/matlab/IMAS/gdat_imas.m
@@ -7,7 +7,7 @@ function [gdat_data,gdat_params,error_status,varargout] = gdat_imas(shot,data_re
%
% If no inputs are provided, return the list of available pre-defined data_request in gdat_data and default parameters gdat_params
%
-% IMAS means assume access data from IDS database ala IMAS with run_number, database_user, tokamak_name, data_major_version and using imas_open_env and ids_get calls
+% IMAS means assume access data from IDS database ala IMAS with run_number, database_user, tokamak_name, data_major_version and using imas_open_env and ids_get calls (added backend choice as well, default hdf5 (13), otherwise 12 for mdsplus)
% Should be the same on ITER hpc and gateway, to be checked
%
% At first only "ids" request implemented, but keywords like ip etc should relate to specific IDS as for any machine
@@ -270,6 +270,10 @@ if ~isfield(gdat_data.gdat_params,'data_major_version')
gdat_data.gdat_params.data_major_version = '3';
if gdat_data.gdat_params.nverbose >= 3; disp('set data_major_version to ''3'' as default since not provided'); end
end
+if ~isfield(gdat_data.gdat_params,'backend')
+ gdat_data.gdat_params.backend = 13;
+ if gdat_data.gdat_params.nverbose >= 3; disp('set backend to 13 as default since not provided'); end
+end
error_status = 6; % at least reached this level
gdat_params = gdat_data.gdat_params;
@@ -285,8 +289,13 @@ if do_mdsopen_mdsclose
return
end
try
- gdat_data.gdat_params.idx_imas_open_env = imas_open_env('ids', shot, gdat_data.gdat_params.run,gdat_data.gdat_params.database_user, ...
+ if exist('imas_open_env_backend') > 0
+ gdat_data.gdat_params.idx_imas_open_env = imas_open_env_backend(shot, gdat_data.gdat_params.run,gdat_data.gdat_params.database_user, ...
+ gdat_data.gdat_params.tokamak_name,gdat_data.gdat_params.data_major_version,gdat_data.gdat_params.backend);
+ else
+ gdat_data.gdat_params.idx_imas_open_env = imas_open_env('ids', shot, gdat_data.gdat_params.run,gdat_data.gdat_params.database_user, ...
gdat_data.gdat_params.tokamak_name,gdat_data.gdat_params.data_major_version);
+ end
disp('')
catch ME
warning('could not imas_open_env with following gdat_data.gdat_params:');
diff --git a/matlab/TCV_IMAS/ids2database.m b/matlab/IMAS/ids2database.m
similarity index 79%
rename from matlab/TCV_IMAS/ids2database.m
rename to matlab/IMAS/ids2database.m
index eb2c2ed7..75ccc26f 100644
--- a/matlab/TCV_IMAS/ids2database.m
+++ b/matlab/IMAS/ids2database.m
@@ -1,13 +1,13 @@
function [ids_put_status] = ids2database(shot,run,occurence,ids2put,tree_user,tree_tokamak,tree_majorversion,imas_backend,varargin);
%
-% [ids_put_status] = ids2database(shot,run,occurence,ids2put,varargin);
+% [ids_put_status] = ids2database(shot,run,occurence,ids2put,tree_user,tree_tokamak,tree_majorversion,imas_backend,varargin);
%
% open/create shot,run and put the ids from ids2put.idsnames (names from fieldnames(ids2put) && within IDS_list)
-% from new ..._env routines, now user/publi database name, tokamak name and major UAL version (3 or 4 at this stage) need to be specified
+% from new ..._env routines, now user/public database name, tokamak name and major UAL version (3 or 4 at this stage) need to be specified
% tree_name: getenv('USER') by default, can be 'public'
-% tree_tokamak: 'tcv' by default
+% tree_tokamak: '' no default, typically tcv, TCV, ITER, etc (case will appear in folder name)
% tree_majorversion: '3' by default
-% imas_backend: "MDSplus" or "HDF5"
+% imas_backend: "MDSplus" or "HDF5" or 12 or 13
%
% varargin{1}: tbd
%
@@ -15,9 +15,9 @@ function [ids_put_status] = ids2database(shot,run,occurence,ids2put,tree_user,tr
ids_put_status = 0;
tree_user_default = getenv('USER');
-tree_tokamak_default = 'tcv';
+tree_tokamak_default = '';
tree_majorversion_default = '3';
-imas_backend_default = 'MDSplus';
+imas_backend_default = 'HDF5';
% initialize input parser
p = inputParser;
@@ -28,9 +28,9 @@ p.addOptional('run', [], @(x) (isnumeric(x) && isscalar(x) && (x == round(x))));
p.addOptional('occurence', 0, @(x) isempty(x) || (isnumeric(x) && isscalar(x) && (x == round(x)))); % integer
p.addOptional('ids2put', struct([]), @(x) (isstruct(x)));
p.addOptional('tree_user', tree_user_default, @(x) (isempty(x) || ischar(x)));
-p.addOptional('tree_tokamak', tree_tokamak_default, @(x) (isempty(x) || ischar(x)));
+p.addOptional('tree_tokamak', tree_tokamak_default, @(x) (~isempty(x) && ischar(x)));
p.addOptional('tree_majorversion', tree_majorversion_default, @(x) (ischar(x)));
-p.addOptional('imas_backend', imas_backend_default, @(x) (isempty(x) || ischar(x)));
+p.addOptional('imas_backend', imas_backend_default, @(x) (isempty(x) || ischar(x) || (isnumeric(x) && any(x==[12,13]))));
p.parse;
defaults_ids2database = p.Results; % to keep track of defaults
@@ -86,9 +86,9 @@ end
params_ids2database = params;
% check ids_names
ids_names=fieldnames(ids2put);
-[dummy1]=which('ids_list');
+[dummy1]=which('IDS_list');
if isempty(dummy1)
- ids_full_list = tcv_available_ids;
+ ids_full_list = eval([lower(tree_tokamak) '_available_ids']);
warning(['IDS_list not available, quick fix introducing list of ids available for TCV: ' fprintf('%s ',ids_full_list{:}) char(10)]);
else
% get effective function between ids_list and IDS_list (which or exist not sufficient)
@@ -106,17 +106,19 @@ if isempty(ids_names_ok)
return
end
-if ~ismember(params_ids2database.imas_backend, {'MDSplus', 'HDF5'})
- warning(['Unknown imas_backend: ', imas_backend, ', selecting default: ',imas_backend_default]);
- params_ids2database.imas_backend = imas_backend_default;
+if ischar(params_ids2database.imas_backend) && ~ismember(params_ids2database.imas_backend, {'MDSplus', 'HDF5'})
+ warning(['Unknown imas_backend: ', imas_backend, ', selecting default: ',imas_backend_default]);
+ params_ids2database.imas_backend = imas_backend_default;
end
% Get IMAS backend ID
switch params_ids2database.imas_backend
- case "HDF5"
+ case 'HDF5'
backendid=13;
- case "MDSplus"
+ case 'MDSplus'
backendid=12;
+ otherwise
+ backendid = params_ids2database.imas_backend;
end
try
@@ -128,7 +130,7 @@ try
shot_is_new = 0;
end
if shot_is_new
- idx = imas_create_env_backend(shot, run, params_ids2database.tree_user,params_ids2database.tree_tokamak, params_ids2database.tree_majorversion, backendid)
+ idx = imas_create_env_backend(shot, run, params_ids2database.tree_user,params_ids2database.tree_tokamak, params_ids2database.tree_majorversion, backendid);
else
idx = imas_open_env_backend(shot,run,params_ids2database.tree_user,params_ids2database.tree_tokamak,params_ids2database.tree_majorversion,backendid); %
end
--
GitLab
From 7ffc93dcad66e62e7cbff7a9d6bb73ea603b253d Mon Sep 17 00:00:00 2001
From: Olivier Sauter <olivier.sauter@epfl.ch>
Date: Wed, 9 Apr 2025 22:53:03 +0200
Subject: [PATCH 2/4] simplify getting IDS_list
---
matlab/IMAS/ids2database.m | 17 +++++------------
matlab/TCV_IMAS/tcv2ids2database.m | 2 +-
2 files changed, 6 insertions(+), 13 deletions(-)
diff --git a/matlab/IMAS/ids2database.m b/matlab/IMAS/ids2database.m
index 75ccc26f..deecfcb2 100644
--- a/matlab/IMAS/ids2database.m
+++ b/matlab/IMAS/ids2database.m
@@ -5,9 +5,9 @@ function [ids_put_status] = ids2database(shot,run,occurence,ids2put,tree_user,tr
% open/create shot,run and put the ids from ids2put.idsnames (names from fieldnames(ids2put) && within IDS_list)
% from new ..._env routines, now user/public database name, tokamak name and major UAL version (3 or 4 at this stage) need to be specified
% tree_name: getenv('USER') by default, can be 'public'
-% tree_tokamak: '' no default, typically tcv, TCV, ITER, etc (case will appear in folder name)
+% tree_tokamak: 'tcv' by default, typically tcv, TCV, ITER, etc (case will appear in folder name)
% tree_majorversion: '3' by default
-% imas_backend: "MDSplus" or "HDF5" or 12 or 13
+% imas_backend: 'MDSplus' or 'HDF5' or 12 or 13
%
% varargin{1}: tbd
%
@@ -15,7 +15,7 @@ function [ids_put_status] = ids2database(shot,run,occurence,ids2put,tree_user,tr
ids_put_status = 0;
tree_user_default = getenv('USER');
-tree_tokamak_default = '';
+tree_tokamak_default = 'tcv';
tree_majorversion_default = '3';
imas_backend_default = 'HDF5';
@@ -86,15 +86,8 @@ end
params_ids2database = params;
% check ids_names
ids_names=fieldnames(ids2put);
-[dummy1]=which('IDS_list');
-if isempty(dummy1)
- ids_full_list = eval([lower(tree_tokamak) '_available_ids']);
- warning(['IDS_list not available, quick fix introducing list of ids available for TCV: ' fprintf('%s ',ids_full_list{:}) char(10)]);
-else
- % get effective function between ids_list and IDS_list (which or exist not sufficient)
- [dummy2,ids_list_eff]=fileparts(dummy1);
- ids_full_list = feval(ids_list_eff);
-end
+aa=gdat([],'ids');
+ids_full_list = aa.gdat_params.sources_available;
ids_names_notok = setdiff(ids_names,ids_full_list);
if ~isempty(ids_names_notok)
disp(['these subfields are not ids names, so not used: ' sprintf('%s ',ids_names_notok{:})])
diff --git a/matlab/TCV_IMAS/tcv2ids2database.m b/matlab/TCV_IMAS/tcv2ids2database.m
index fd9b711a..916ec438 100644
--- a/matlab/TCV_IMAS/tcv2ids2database.m
+++ b/matlab/TCV_IMAS/tcv2ids2database.m
@@ -10,7 +10,7 @@ function [ids_from_tcv,varargout] = tcv2ids2database(shot,run_out,varargin);
% varargin: 'occurence': occurence value
% varargin: 'ids_names': cell, ids to load, by default all defined so far (if empty or empty string or not given)
% see tcv_available_ids for the list of IDSs available for TCV
-% varargin: 'imas_backend': "MDSplus" or "HDF5"
+% varargin: 'imas_backend': 'MDSplus' or 'HDF5'
% varargin: 'error_bar': type (string)
% 'delta' or empty (default): meaning difference in upper is set (standard error_bar
% 'added': errorbar is added: upper=data+delta and lower=data-delta
--
GitLab
From 88a314d5dac96b4ab69534777627417ac812d468 Mon Sep 17 00:00:00 2001
From: Luke Simons <luke.simons@epfl.ch>
Date: Mon, 14 Apr 2025 13:27:56 +0000
Subject: [PATCH 3/4] Fixed comment about tcv imas in gdat_imas.m
---
matlab/IMAS/gdat_imas.m | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/matlab/IMAS/gdat_imas.m b/matlab/IMAS/gdat_imas.m
index a65df0e9..f0190f2e 100644
--- a/matlab/IMAS/gdat_imas.m
+++ b/matlab/IMAS/gdat_imas.m
@@ -7,7 +7,7 @@ function [gdat_data,gdat_params,error_status,varargout] = gdat_imas(shot,data_re
%
% If no inputs are provided, return the list of available pre-defined data_request in gdat_data and default parameters gdat_params
%
-% IMAS means assume access data from IDS database ala IMAS with run_number, database_user, tokamak_name, data_major_version and using imas_open_env and ids_get calls (added backend choice as well, default hdf5 (13), otherwise 12 for mdsplus)
+% IMAS assumes data access from IDS database ala IMAS with run_number, database_user, tokamak_name, data_major_version and using imas_open_env and ids_get calls (added backend choice as well, default hdf5 (13), otherwise 12 for mdsplus)
% Should be the same on ITER hpc and gateway, to be checked
%
% At first only "ids" request implemented, but keywords like ip etc should relate to specific IDS as for any machine
--
GitLab
From 8867989de46a78f70515efdefa7b41214c98714d Mon Sep 17 00:00:00 2001
From: Luke Simons <luke.simons@epfl.ch>
Date: Mon, 14 Apr 2025 13:42:14 +0000
Subject: [PATCH 4/4] Clarified comment on imas_backend in ids2database.m
---
matlab/IMAS/ids2database.m | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/matlab/IMAS/ids2database.m b/matlab/IMAS/ids2database.m
index deecfcb2..b98deef0 100644
--- a/matlab/IMAS/ids2database.m
+++ b/matlab/IMAS/ids2database.m
@@ -7,7 +7,7 @@ function [ids_put_status] = ids2database(shot,run,occurence,ids2put,tree_user,tr
% tree_name: getenv('USER') by default, can be 'public'
% tree_tokamak: 'tcv' by default, typically tcv, TCV, ITER, etc (case will appear in folder name)
% tree_majorversion: '3' by default
-% imas_backend: 'MDSplus' or 'HDF5' or 12 or 13
+% imas_backend: string, numeric input for imas_backend data type. Can be 'MDSplus' (== 12) or 'HDF5' (== 13)
%
% varargin{1}: tbd
%
--
GitLab