From 726cf9d45f584b89e37cedd5fc92c3f5bda104de Mon Sep 17 00:00:00 2001
From: Olivier Sauter <Olivier.Sauter@epfl.ch>
Date: Sun, 13 Oct 2019 20:06:46 +0200
Subject: [PATCH] bpol and ec_antennas according to latest IMAS update,
grid_type transform all except tensors
---
matlab/TCV_IMAS/tcv_get_ids_core_profiles.m | 23 +++++++--
matlab/TCV_IMAS/tcv_get_ids_ec_antennas.m | 7 ++-
matlab/TCV_IMAS/tcv_get_ids_equilibrium.m | 19 ++++++-
matlab/TCV_IMAS/tcv_get_ids_magnetics.m | 7 ++-
matlab/TCV_IMAS/tcv_get_ids_nbi.m | 7 ++-
matlab/TCV_IMAS/tcv_get_ids_pf_active.m | 6 ++-
matlab/TCV_IMAS/tcv_get_ids_tf.m | 6 ++-
matlab/TCV_IMAS/tcv_get_ids_wall.m | 6 ++-
matlab/TCV_IMAS/tcv_ids_bpol_probe.m | 2 +-
matlab/TCV_IMAS/tcv_ids_headpart.m | 57 +++++++++++++++++++--
10 files changed, 123 insertions(+), 17 deletions(-)
diff --git a/matlab/TCV_IMAS/tcv_get_ids_core_profiles.m b/matlab/TCV_IMAS/tcv_get_ids_core_profiles.m
index a3ddde24..b0d2703e 100644
--- a/matlab/TCV_IMAS/tcv_get_ids_core_profiles.m
+++ b/matlab/TCV_IMAS/tcv_get_ids_core_profiles.m
@@ -21,7 +21,11 @@ machine = 'tcv';
tens_time = -1;
tens_rho = -0.1;
-[ids_core_profiles, params_cores_profiles] = tcv_ids_headpart(shot,ids_equil_empty,'cores_profiles',varargin{:});
+if exist('gdat_params')
+ [ids_core_profiles, params_cores_profiles] = tcv_ids_headpart(shot,ids_equil_empty,'cores_profiles','gdat_params',gdat_params,varargin{:});
+else
+ [ids_core_profiles, params_cores_profiles] = tcv_ids_headpart(shot,ids_equil_empty,'cores_profiles',varargin{:});
+end
ids_core_profiles_description = [];
% base all from times fro nete_rho (which should be conf by default)
@@ -269,11 +273,20 @@ for ir=1:length(temp_1d.q.x)
q_cpt(ir,:) = interpos(temp_1d.q.t,temp_1d.q.data(ir,:),ids_core_profiles.time,tens_time);
end
for it=1:length(ids_core_profiles.time)
- [ids_core_profiles.profiles_1d{it}.q] = interpos(temp_1d.q.x,q_cpt(:,it),temp_1d.fit.te_rho.grids_1d.rhopolnorm, ...
+ ij=isfinite(q_cpt(:,it));
+ if sum(ij) >= 5
+ [ids_core_profiles.profiles_1d{it}.q] = interpos(temp_1d.q.x(ij),q_cpt(ij,it),temp_1d.fit.te_rho.grids_1d.rhopolnorm, ...
tens_rho,[1 0],[0 0]);
- [qfit,dqdrhotor] = interpos(ids_core_profiles.profiles_1d{it}.grid.rho_tor,ids_core_profiles.profiles_1d{it}.q,tens_rho,[1 0],[0 0]);
- ids_core_profiles.profiles_1d{it}.magnetic_shear = ids_core_profiles.profiles_1d{it}.grid.rho_tor./ids_core_profiles.profiles_1d{it}.q ...
- .* dqdrhotor;
+ [qfit,dqdrhotor] = interpos(ids_core_profiles.profiles_1d{it}.grid.rho_tor,ids_core_profiles.profiles_1d{it}.q,tens_rho,[1 0],[0 0]);
+ ids_core_profiles.profiles_1d{it}.magnetic_shear = ids_core_profiles.profiles_1d{it}.grid.rho_tor./ids_core_profiles.profiles_1d{it}.q ...
+ .* dqdrhotor;
+ elseif sum(ij) > 0
+ ids_core_profiles.profiles_1d{it}.q = interp1(temp_1d.q.x(ij),q_cpt(ij,it),temp_1d.fit.te_rho.grids_1d.rhopolnorm);
+ ids_core_profiles.profiles_1d{it}.magnetic_shear = -9.e40;
+ else
+ ids_core_profiles.profiles_1d{it}.q = -9.e40;
+ ids_core_profiles.profiles_1d{it}.magnetic_shear = -9.e40;
+ end
end
if nargin <= 2
diff --git a/matlab/TCV_IMAS/tcv_get_ids_ec_antennas.m b/matlab/TCV_IMAS/tcv_get_ids_ec_antennas.m
index b7a15132..353aac4a 100644
--- a/matlab/TCV_IMAS/tcv_get_ids_ec_antennas.m
+++ b/matlab/TCV_IMAS/tcv_get_ids_ec_antennas.m
@@ -6,7 +6,12 @@ function [ids_ec_antennas,ids_ec_antennas_description,varargout] = tcv_get_ids_e
% gdat_params: gdat_data.gdat_params to get all params passed from original call, in particular error_bar options
%
-[ids_ec_antennas, params_ec_antennas] = tcv_ids_headpart(shot,ids_ec_antennas_empty,'ec_antennas','homogeneous_time',0,varargin{:});
+if exist('gdat_params')
+ [ids_ec_antennas, params_ec_antennas] = tcv_ids_headpart(shot,ids_ec_antennas_empty,'ec_antennas','homogeneous_time',0, ...
+ 'gdat_params',gdat_params,varargin{:});
+else
+ [ids_ec_antennas, params_ec_antennas] = tcv_ids_headpart(shot,ids_ec_antennas_empty,'ec_antennas','homogeneous_time',0,varargin{:});
+end
% As a general rule, for a new substructure under the main ids, construct a local structure like:
% "global_quantities" with subfields being the relevant data to get and a local structure:
diff --git a/matlab/TCV_IMAS/tcv_get_ids_equilibrium.m b/matlab/TCV_IMAS/tcv_get_ids_equilibrium.m
index f283c6db..6abbae2f 100644
--- a/matlab/TCV_IMAS/tcv_get_ids_equilibrium.m
+++ b/matlab/TCV_IMAS/tcv_get_ids_equilibrium.m
@@ -6,7 +6,11 @@ function [ids_equilibrium,ids_equilibrium_description,varargout] = tcv_get_ids_e
% gdat_params: gdat_data.gdat_params to get all params passed from original call, in particular error_bar and cocos_out options
%
-[ids_equilibrium, params_equilibrium] = tcv_ids_headpart(shot,ids_equil_empty,'equilibrium',varargin{:});
+if exist('gdat_params')
+ [ids_equilibrium, params_equilibrium] = tcv_ids_headpart(shot,ids_equil_empty,'equilibrium','gdat_params',gdat_params,varargin{:});
+else
+ [ids_equilibrium, params_equilibrium] = tcv_ids_headpart(shot,ids_equil_empty,'equilibrium',varargin{:});
+end
% As a general rule, for a new substructure under the main ids, construct a local structure like:
% "global_quantities" with subfields being the relevant data to get and a local structure:
@@ -352,7 +356,6 @@ for it=1:numel(ids_equilibrium.time)
global_quantities.psi_boundary.data(it);
end
-
% make arrays not filled in empty:
ids_equilibrium.grids_ggd = {};
for it=1:numel(ids_equilibrium.time_slice)
@@ -373,6 +376,18 @@ for it=1:numel(ids_equilibrium.time_slice)
ids_equilibrium.time_slice{it}.constraints.x_point = {};
end
+% special test matrix cocos transform
+% $$$ ldim1=129;
+% $$$ ldim2=257;
+% $$$ it=1;
+% $$$ ids_equilibrium.time_slice{it}.coordinate_system.grid_type.index = 13;
+% $$$ ids_equilibrium.time_slice{it}.coordinate_system.grid.dim1 = linspace(0,1,ldim1)';
+% $$$ ids_equilibrium.time_slice{it}.coordinate_system.grid.dim2 = linspace(0,2*pi,ldim2);
+% $$$ ids_equilibrium.time_slice{it}.coordinate_system.tensor_contravariant = 2.*ones(ldim1,ldim2,3,3);
+% $$$ ids_equilibrium.time_slice{it}.coordinate_system.tensor_covariant = 2.*ones(ldim1,ldim2,3,3);
+% $$$ ids_equilibrium.time_slice{it}.coordinate_system.g11_contravariant = 2.*ones(ldim1,ldim2,3,3);
+
+
% cocos automatic transform
if exist('ids_generic_cocos_nodes_transformation_symbolic') == 2
[ids_equilibrium,cocoscoeff]=ids_generic_cocos_nodes_transformation_symbolic(ids_equilibrium,'equilibrium',gdat_params.cocos_in, ...
diff --git a/matlab/TCV_IMAS/tcv_get_ids_magnetics.m b/matlab/TCV_IMAS/tcv_get_ids_magnetics.m
index cecb76c6..bf1ea850 100644
--- a/matlab/TCV_IMAS/tcv_get_ids_magnetics.m
+++ b/matlab/TCV_IMAS/tcv_get_ids_magnetics.m
@@ -5,7 +5,12 @@ function [ids_magnetics,ids_magnetics_description,varargout] = tcv_get_ids_magne
% gdat_params: gdat_data.gdat_params to get all params passed from original call, in particular error_bar options
%
-[ids_magnetics, params_magnetics] = tcv_ids_headpart(shot, ids_magnetics_empty,'magnetics','homogeneous_time',0,varargin{:});
+if exist('gdat_params')
+ [ids_magnetics, params_magnetics] = tcv_ids_headpart(shot, ids_magnetics_empty,'magnetics','homogeneous_time',0, ...
+ 'gdat_params',gdat_params,varargin{:});
+else
+ [ids_magnetics, params_magnetics] = tcv_ids_headpart(shot, ids_magnetics_empty,'magnetics','homogeneous_time',0,varargin{:});
+end
[ids_magnetics.bpol_probe,ids_magnetics_description.bpol_probe]= tcv_ids_bpol_probe(params_magnetics.shot, ids_magnetics.bpol_probe(1),gdat_params);
[ids_magnetics.flux_loop,ids_magnetics_description.flux_loop]= tcv_ids_flux_loop(params_magnetics.shot, ids_magnetics.flux_loop(1),gdat_params);
diff --git a/matlab/TCV_IMAS/tcv_get_ids_nbi.m b/matlab/TCV_IMAS/tcv_get_ids_nbi.m
index 073bf1d4..8da3b80b 100644
--- a/matlab/TCV_IMAS/tcv_get_ids_nbi.m
+++ b/matlab/TCV_IMAS/tcv_get_ids_nbi.m
@@ -6,7 +6,12 @@ function [ids_nbi,ids_nbi_description,varargout] = tcv_get_ids_nbi(shot,ids_nbi_
% gdat_params: gdat_data.gdat_params to get all params passed from original call, in particular error_bar options
%
-[ids_nbi, params_nbi] = tcv_ids_headpart(shot,ids_nbi_empty,'nbi','homogeneous_time',0,varargin{:});
+if exist('gdat_params')
+ [ids_nbi, params_nbi] = tcv_ids_headpart(shot,ids_nbi_empty,'nbi','homogeneous_time',0,'gdat_params',gdat_params,varargin{:});
+else
+ [ids_nbi, params_nbi] = tcv_ids_headpart(shot,ids_nbi_empty,'nbi','homogeneous_time',0,varargin{:});
+end
+
ids_nbi_description='';
% As a general rule, for a new substructure under the main ids, construct a local structure like:
% "global_quantities" with subfields being the relevant data to get and a local structure:
diff --git a/matlab/TCV_IMAS/tcv_get_ids_pf_active.m b/matlab/TCV_IMAS/tcv_get_ids_pf_active.m
index 4ffa647c..8d3ef3e2 100644
--- a/matlab/TCV_IMAS/tcv_get_ids_pf_active.m
+++ b/matlab/TCV_IMAS/tcv_get_ids_pf_active.m
@@ -4,7 +4,11 @@ function [ids_pf_active,ids_pf_active_description,varargout] = tcv_get_ids_pf_ac
%
% Input pharser
-[ids_pf_active, params] = tcv_ids_headpart(shot, ids_pf_active_empty,'pf_active','homogeneous_time',0,varargin{:});
+if exist('gdat_params')
+ [ids_pf_active, params] = tcv_ids_headpart(shot, ids_pf_active_empty,'pf_active','homogeneous_time',0,'gdat_params',gdat_params,varargin{:});
+else
+ [ids_pf_active, params] = tcv_ids_headpart(shot, ids_pf_active_empty,'pf_active','homogeneous_time',0,varargin{:});
+end
% Get subfield
[ids_pf_active.coil,ids_pf_active_description.coil]= tcv_ids_coil(params.shot, ids_pf_active.coil(1),gdat_params);
diff --git a/matlab/TCV_IMAS/tcv_get_ids_tf.m b/matlab/TCV_IMAS/tcv_get_ids_tf.m
index 03650ac4..2a5774ec 100644
--- a/matlab/TCV_IMAS/tcv_get_ids_tf.m
+++ b/matlab/TCV_IMAS/tcv_get_ids_tf.m
@@ -11,7 +11,11 @@ function [ids_tf,ids_tf_description] = tcv_get_ids_tf(shot, ids_tf_empty, gdat_
ids_tf = ids_tf_empty;
-[ids_tf, params_tf] = tcv_ids_headpart(shot, ids_tf_empty,'tf','homogeneous_time',0,varargin{:});
+if exist('gdat_params')
+ [ids_tf, params_tf] = tcv_ids_headpart(shot, ids_tf_empty,'tf','homogeneous_time',0,'gdat_params',gdat_params,varargin{:});
+else
+ [ids_tf, params_tf] = tcv_ids_headpart(shot, ids_tf_empty,'tf','homogeneous_time',0,varargin{:});
+end
tmp = gdat_tcv(shot, 'b0');
if ~ischar(tmp.data)
diff --git a/matlab/TCV_IMAS/tcv_get_ids_wall.m b/matlab/TCV_IMAS/tcv_get_ids_wall.m
index 506dc5c7..fca0dfa2 100644
--- a/matlab/TCV_IMAS/tcv_get_ids_wall.m
+++ b/matlab/TCV_IMAS/tcv_get_ids_wall.m
@@ -5,7 +5,11 @@ function [ids_wall,ids_wall_description,varargout] = tcv_get_ids_wall(shot, ids_
%
% Input pharser
-[ids_wall, params] = tcv_ids_headpart(shot, ids_wall_empty,'wall','homogeneous_time',0,varargin{:});
+if exist('gdat_params')
+ [ids_wall, params] = tcv_ids_headpart(shot, ids_wall_empty,'wall','homogeneous_time',0,'gdat_params',gdat_params,varargin{:});
+else
+ [ids_wall, params] = tcv_ids_headpart(shot, ids_wall_empty,'wall','homogeneous_time',0,varargin{:});
+end
% Get data of outline
[ids_wall.description_2d,ids_wall_description.description_2d]= tcv_ids_wall_description_2d(params.shot, ids_wall.description_2d(1));
diff --git a/matlab/TCV_IMAS/tcv_ids_bpol_probe.m b/matlab/TCV_IMAS/tcv_ids_bpol_probe.m
index 1eef311b..5027b8e8 100644
--- a/matlab/TCV_IMAS/tcv_ids_bpol_probe.m
+++ b/matlab/TCV_IMAS/tcv_ids_bpol_probe.m
@@ -53,7 +53,7 @@ for ii=1:Nprobes
sub_ids_struct_out{ii}.toroidal_angle = 0.; % to see if should match sector 3 (bpol003)
aa = gdat_tcv( shot, ['static("ANG_M")[$1]'',''' sub_ids_struct_out{ii}.name '']);
- sub_ids_struct_out{ii}.poloidal_angle = aa.data;
+ sub_ids_struct_out{ii}.poloidal_angle = -aa.data;
ij=strmatch(names{ii},probes_name);
sub_ids_struct_out{ii}.area = probes_area(ij);
sub_ids_struct_out{ii}.length = probes_length(ij);
diff --git a/matlab/TCV_IMAS/tcv_ids_headpart.m b/matlab/TCV_IMAS/tcv_ids_headpart.m
index 90914a7a..911f2baf 100644
--- a/matlab/TCV_IMAS/tcv_ids_headpart.m
+++ b/matlab/TCV_IMAS/tcv_ids_headpart.m
@@ -7,8 +7,9 @@ function [ids_generic, params_ids_generic] = tcv_ids_headpart(shot,ids_in,ids_na
%
% varargin options:
%
-% 'comment': comment to include in ids_properties
+% 'comment': comment to include in ids_properties, using gdat_params for example cocos_in and cocos_out
% 'homogeneous_time': homogeneous_time in ids_properties: 1 (default) if the whole ids has same time, 0 otherwise
+% 'gdat_params': gdat params structure
%
%
% example:
@@ -23,7 +24,8 @@ p = inputParser;
p.addOptional('shot', [], @(x) (isnumeric(x) && isscalar(x) && (x == round(x)))); % integer
p.addOptional('ids_in', struct([]), @(x) (isstruct(x)));
p.addOptional('ids_name', '', @(x) (ischar(x))); % char
-p.addOptional('comment', 'default comment', @(x) isempty(x) || ischar(x)); % char
+p.addOptional('gdat_params', [], @(x) (isempty(x) || isstruct(x))); % char
+p.addOptional('comment', '', @(x) isempty(x) || ischar(x)); % char
p.addOptional('homogeneous_time', 1, @(x) (isnumeric(x) && isscalar(x) && (x == round(x))));
p.parse(shot,ids_in,ids_name);
@@ -39,6 +41,8 @@ names = fieldnames(params);
mask = structfun(@isempty,params);
if any(mask),
params = rmfield(params,unique([names(mask); p.UsingDefaults.']));
+ p.parse(params);
+ params = p.Results;
end
params_ids_generic = params;
@@ -48,8 +52,55 @@ ids_generic = ids_in;
%
% ids_properties
%
+subcall='';
+% $$$ if nargin>=5 && ~isempty(varargin)
+% $$$ for i=1:length(varargin)
+% $$$ if ~isempty(varargin{i})
+% $$$ if ischar(varargin{i})
+% $$$ subcall_add = [',' varargin{i}];
+% $$$ elseif isnumeric(varargin{i})
+% $$$ subcall_add = [',' num2str(varargin{i})];
+% $$$ elseif isstruct(varargin{i})
+% $$$ subcall_add = [',' 'struct_in'];
+% $$$ elseif iscell(varargin{i})
+% $$$ subcall_add = [',' 'cell_in'];
+% $$$ end
+% $$$ else
+% $$$ subcall_add = [',[]'];
+% $$$ end
+% $$$ subcall(end+1:end+length(subcall_add)) = subcall_add;
+% $$$ end
+% $$$ subcall(end+1:end+2) = '; ';
+% $$$ end
ids_generic.ids_properties.comment = params_ids_generic.comment;
+if ~isempty(subcall)
+ add_to_comment = ['varargin: ' subcall];
+ if isempty(ids_generic.ids_properties.comment)
+ ids_generic.ids_properties.comment = add_to_comment;
+ else
+ ids_generic.ids_properties.comment(end+1:end+length(add_to_comment)+2) = ['; ' add_to_comment];
+ end
+end
+
+ids_generic.ids_properties.provider = ['tcv_get_ids_' ids_name];
+if ~isempty(params_ids_generic.gdat_params)
+ if isfield(params_ids_generic.gdat_params,'cocos_in') && isfield(params_ids_generic.gdat_params,'cocos_out')
+ comment_add = ['from TCV cocos_in=' num2str(params_ids_generic.gdat_params.cocos_in) ' transformed to cocos_out=' num2str(params_ids_generic.gdat_params.cocos_out)];
+ if isempty(ids_generic.ids_properties.comment)
+ ids_generic.ids_properties.comment = comment_add;
+ else
+ ids_generic.ids_properties.comment(end+1:end+length(comment_add)+2) = ['; ' comment_add];
+ end
+ else
+ warning('cocos_in and cocos_out expected to be fields of gdat_params')
+ end
+ if isfield(params_ids_generic.gdat_params,'error_bar')
+ provider_add = ['; error_bar option: ' params_ids_generic.gdat_params.error_bar];
+ ids_generic.ids_properties.provider(end+1:end+length(provider_add)) = provider_add;
+ else
+ warning('cocos_in and cocos_out expected to be fields of gdat_params')
+ end
+end
ids_generic.ids_properties.homogeneous_time = params_ids_generic.homogeneous_time;
ids_generic.ids_properties.source = ['TCV shot #' num2str(params_ids_generic.shot)];
-ids_generic.ids_properties.provider = ['tcv_get_ids_' ids_name];
ids_generic.ids_properties.creation_date = date;
--
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