From f58be82f678c68f539ddfb88b9643e6d7aabb50f Mon Sep 17 00:00:00 2001
From: Olivier Sauter <Olivier.Sauter@epfl.ch>
Date: Thu, 14 Nov 2019 21:31:25 +0100
Subject: [PATCH] add netcdf hdf5 related get files
---
matlab/CHDF/cdf2mat.m | 105 ++++++++++++++++++++
matlab/CHDF/transp_netcdf2mat.m | 160 ++++++++++++++++++++++++++++++
matlab/TCV/gdat_tcv.m | 32 +++++-
matlab/TCV/tcv_help_parameters.m | 1 +
matlab/TCV/tcv_requests_mapping.m | 2 +-
matlab/gdatpaths.m | 2 +-
6 files changed, 299 insertions(+), 3 deletions(-)
create mode 100644 matlab/CHDF/cdf2mat.m
create mode 100644 matlab/CHDF/transp_netcdf2mat.m
diff --git a/matlab/CHDF/cdf2mat.m b/matlab/CHDF/cdf2mat.m
new file mode 100644
index 00000000..22eaf3b7
--- /dev/null
+++ b/matlab/CHDF/cdf2mat.m
@@ -0,0 +1,105 @@
+function cdf2mat_out = cdf2mat(pfname)
+%
+% reads all variables and coordinates from netcdf
+% some trials with netcdf, using 50725c01.cdf as test
+%
+% Based on TANSP netcdf file, but should work with other if simple group structure probably
+%
+% Uses matlab netcdf.open, ncinfo, netcdf.inqVarIDs, netcd.getVar, etc
+%
+
+%
+if ~exist(pfname,'file')
+ error([pfname ' is not a valid filename for a netcdf file']);
+end
+
+try
+ funnetcdf=netcdf.open(pfname,'nowrite');
+catch ME
+ warning(['problems with netcdf.open(' pfname ',''nowrite''); May be not a netcdf file?']);
+ rethrow(ME)
+end
+
+% all data of all vars
+
+allinfo=ncinfo(pfname);
+
+allvarids=netcdf.inqVarIDs(funnetcdf);
+allvarnames={allinfo.Variables(:).Name};
+if length(allvarnames) ~= length(allvarids)
+ allinfo;
+ error('problem with Variables, may be several groups')
+ return
+end
+
+[varnames_sorted,~]=sort(allvarnames);
+
+% to find a variable:
+% strmatch('GFUN',allvarnames,'exact')
+
+% construct relevant data strtucture
+
+coordnames=strtrim({allinfo.Dimensions(:).Name});
+[coordnames_sorted,~]=sort(coordnames);
+fields_variables_to_copy = {'Name', 'Dimensions', 'Size', 'Datatype'};
+for i=1:length(coordnames_sorted)
+ matcdf.coords(i).name = coordnames_sorted{i};
+ matcdf.coords(i).index_allvarnames = strmatch(matcdf.coords(i).name,allvarnames,'exact');
+ matcdf.coords(i).index_varnames_sorted = strmatch(matcdf.coords(i).name,varnames_sorted,'exact');
+ matcdf.coords(i).varid = allvarids(matcdf.coords(i).index_allvarnames);
+ if strcmp(allinfo.Variables(matcdf.coords(i).index_allvarnames).Datatype,'single')
+ matcdf.coords(i).data = netcdf.getVar(funnetcdf,matcdf.coords(i).varid,'double');
+ else
+ matcdf.coords(i).data = netcdf.getVar(funnetcdf,matcdf.coords(i).varid);
+ end
+ for ij=1:length(fields_variables_to_copy)
+ matcdf.coords(i).(fields_variables_to_copy{ij}) = allinfo.Variables(matcdf.coords(i).index_allvarnames).(fields_variables_to_copy{ij});
+ end
+ matcdf.coords(i).units = strtrim(allinfo.Variables(matcdf.coords(i).index_allvarnames).Attributes(1).Value);
+ matcdf.coords(i).long_name = strtrim(allinfo.Variables(matcdf.coords(i).index_allvarnames).Attributes(2).Value);
+ matcdf.coords(i).label = [matcdf.coords(i).name ' ' num2str(matcdf.coords(i).Size) ': ' matcdf.coords(i).long_name];
+ cdf2mat_out.coords.(matcdf.coords(i).name) = matcdf.coords(i);
+end
+
+for i=1:length(varnames_sorted)
+ matcdf.vars(i).name = varnames_sorted{i};
+ matcdf.vars(i).index_allvarnames = strmatch(matcdf.vars(i).name,allvarnames,'exact');
+ matcdf.vars(i).varid = allvarids(matcdf.vars(i).index_allvarnames);
+ if strcmp(allinfo.Variables(matcdf.vars(i).index_allvarnames).Datatype,'single')
+ matcdf.vars(i).data = netcdf.getVar(funnetcdf,matcdf.vars(i).varid,'double');
+ else
+ matcdf.vars(i).data = netcdf.getVar(funnetcdf,matcdf.vars(i).varid);
+ end
+ for ij=1:length(fields_variables_to_copy)
+ matcdf.vars(i).(fields_variables_to_copy{ij}) = allinfo.Variables(matcdf.vars(i).index_allvarnames).(fields_variables_to_copy{ij});
+ end
+ matcdf.vars(i).units = strtrim(allinfo.Variables(matcdf.vars(i).index_allvarnames).Attributes(1).Value);
+ matcdf.vars(i).long_name = strtrim(allinfo.Variables(matcdf.vars(i).index_allvarnames).Attributes(2).Value);
+ matcdf.vars(i).label = matcdf.vars(i).name;
+ for j=1:length(matcdf.vars(i).Dimensions)
+ ij = strmatch(matcdf.vars(i).Dimensions(j).Name,coordnames_sorted,'exact');
+ matcdf.vars(i).dim{j} = matcdf.coords(ij).data;
+ matcdf.vars(i).dimunits{j} = matcdf.coords(ij).units;
+ matcdf.vars(i).dimname{j} = matcdf.coords(ij).name;
+ if j==1
+ matcdf.vars(i).label = [matcdf.vars(i).label '(' matcdf.coords(ij).name];
+ else
+ matcdf.vars(i).label = [matcdf.vars(i).label ',' matcdf.coords(ij).name];
+ end
+ if j==length(matcdf.vars(i).Dimensions)
+ matcdf.vars(i).label = [matcdf.vars(i).label ')'];
+ end
+ end
+ matcdf.vars(i).label = [matcdf.vars(i).label ': ' matcdf.vars(i).long_name ' [' matcdf.vars(i).units ']'];
+ cdf2mat_out.allvars.(matcdf.vars(i).name) = matcdf.vars(i);
+end
+top_attr_names = {allinfo.Attributes(:).Name};
+ij = strmatch('shot',top_attr_names,'exact');
+cdf2mat_out.shot = allinfo.Attributes(ij).Value;
+cdf2mat_out.fname = pfname;
+cdf2mat_out.id = pfname(length(pfname)-11:length(pfname)-4);
+
+netcdf.close(funnetcdf);
+
+clear matcdf
+return
diff --git a/matlab/CHDF/transp_netcdf2mat.m b/matlab/CHDF/transp_netcdf2mat.m
new file mode 100644
index 00000000..575bd91c
--- /dev/null
+++ b/matlab/CHDF/transp_netcdf2mat.m
@@ -0,0 +1,160 @@
+%
+% some trials with netcdf, using 50725c01.cdf as test
+%
+% Installed matlab netcdf toolbox from web (http://crusty.er.usgs.gov/~cdenham/MexCDF/nc4ml5.html#GUIDE)
+%
+% then
+
+[fname,pname]=uigetfile('*.cdf','Open NetCDF File');
+funnetcdf=netcdf.open([pname fname],'nowrite');
+
+% all data of all vars
+allinfo=ncinfo([pname fname]);
+allvarids=netcdf.inqVarIDs(funnetcdf);
+allvarnames={allinfo.Variables(:).Name};
+if length(allvarnames) ~= length(allvarids)
+ allinfo
+ error('problem with Variables, may be several groups')
+ return
+end
+
+[varnames_sorted,ind_sort_varnames]=sort(allvarnames);
+
+% to find a variable:
+% strmatch('GFUN',allvarnames,'exact')
+
+% then data of var{1} of name allvarnames{1} (='TIME') can be obtained from:
+% time_data=funnetcdf{'TIME'}(:);
+% or
+% time_data=funnetcdf{allvarnames{1}}(:);
+
+% coordinates variables:
+% >>coord(funnetcdf)
+% TIME
+% TIME3
+% X
+% XB
+% THETA
+% EION
+% KSID
+% RMJSYM
+% RMAJM
+% ILDEN
+% IVISB
+% INTNC
+
+% construct relevant data strtucture
+
+coordnames=strtrim({allinfo.Dimensions(:).Name});
+[coordnames_sorted,ind_sort_coordnames]=sort(coordnames);
+fields_variables_to_copy = {'Name', 'Dimensions', 'Size', 'Datatype'};
+for i=1:length(coordnames_sorted)
+ matcdf.coords(i).name = coordnames_sorted{i};
+ matcdf.coords(i).index_allvarnames = strmatch(matcdf.coords(i).name,allvarnames,'exact');
+ matcdf.coords(i).index_varnames_sorted = strmatch(matcdf.coords(i).name,varnames_sorted,'exact');
+ matcdf.coords(i).varid = allvarids(matcdf.coords(i).index_allvarnames);
+ if strcmp(allinfo.Variables(matcdf.coords(i).index_allvarnames).Datatype,'single')
+ matcdf.coords(i).data = netcdf.getVar(funnetcdf,matcdf.coords(i).varid,'double');
+ else
+ matcdf.coords(i).data = netcdf.getVar(funnetcdf,matcdf.coords(i).varid);
+ end
+ for ij=1:length(fields_variables_to_copy)
+ matcdf.coords(i).(fields_variables_to_copy{ij}) = allinfo.Variables(matcdf.coords(i).index_allvarnames).(fields_variables_to_copy{ij});
+ end
+ matcdf.coords(i).units = strtrim(allinfo.Variables(matcdf.coords(i).index_allvarnames).Attributes(1).Value);
+ matcdf.coords(i).long_name = strtrim(allinfo.Variables(matcdf.coords(i).index_allvarnames).Attributes(2).Value);
+ matcdf.coords(i).label = [matcdf.coords(i).name ' ' num2str(matcdf.coords(i).Size) ': ' matcdf.coords(i).long_name];
+ matcdf_per_name.coords.(matcdf.coords(i).name) = matcdf.coords(i);
+end
+
+for i=1:length(varnames_sorted)
+ matcdf.vars(i).name = varnames_sorted{i};
+ matcdf.vars(i).index_allvarnames = strmatch(matcdf.vars(i).name,allvarnames,'exact');
+ matcdf.vars(i).varid = allvarids(matcdf.vars(i).index_allvarnames);
+ if strcmp(allinfo.Variables(matcdf.vars(i).index_allvarnames).Datatype,'single')
+ matcdf.vars(i).data = netcdf.getVar(funnetcdf,matcdf.vars(i).varid,'double');
+ else
+ matcdf.vars(i).data = netcdf.getVar(funnetcdf,matcdf.vars(i).varid);
+ end
+ for ij=1:length(fields_variables_to_copy)
+ matcdf.vars(i).(fields_variables_to_copy{ij}) = allinfo.Variables(matcdf.vars(i).index_allvarnames).(fields_variables_to_copy{ij});
+ end
+ matcdf.vars(i).units = strtrim(allinfo.Variables(matcdf.vars(i).index_allvarnames).Attributes(1).Value);
+ matcdf.vars(i).long_name = strtrim(allinfo.Variables(matcdf.vars(i).index_allvarnames).Attributes(2).Value);
+ matcdf.vars(i).label = matcdf.vars(i).name;
+ for j=1:length(matcdf.vars(i).Dimensions)
+ ij = strmatch(matcdf.vars(i).Dimensions(j).Name,coordnames_sorted,'exact');
+ matcdf.vars(i).dim{j} = matcdf.coords(ij).data;
+ matcdf.vars(i).dimunits{j} = matcdf.coords(ij).units;
+ matcdf.vars(i).dimname{j} = matcdf.coords(ij).name;
+ if j==1
+ matcdf.vars(i).label = [matcdf.vars(i).label '(' matcdf.coords(ij).name];
+ else
+ matcdf.vars(i).label = [matcdf.vars(i).label ',' matcdf.coords(ij).name];
+ end
+ if j==length(matcdf.vars(i).Dimensions)
+ matcdf.vars(i).label = [matcdf.vars(i).label ')'];
+ end
+ end
+ matcdf.vars(i).label = [matcdf.vars(i).label ': ' matcdf.vars(i).long_name ' [' matcdf.vars(i).units ']'];
+ matcdf_per_name.allvars.(matcdf.vars(i).name) = matcdf.vars(i);
+end
+top_attr_names = {allinfo.Attributes(:).Name};
+ij = strmatch('shot',top_attr_names,'exact');
+matcdf_per_name.shot = allinfo.Attributes(ij).Value;
+
+%
+% save 63704V32_matcdf.mat matcdf_per_name
+clear matcdf
+netcdf.close(funnetcdf);
+
+% break
+% to see the list:
+%%
+
+% load 63704V32_matcdf.mat
+%%
+
+varnames = fieldnames(matcdf_per_name.allvars);
+for i=1:length(varnames)
+ varnames_labels{i} = matcdf_per_name.allvars.(varnames{i}).label;
+end
+coordnames = fieldnames(matcdf_per_name.coords);
+for i=1:length(coordnames)
+ coordnames_labels{i} = matcdf_per_name.coords.(coordnames{i}).label;
+end
+%%
+matcdf.hfig_main=figure;
+set(matcdf.hfig_main,'position',[50 80 900 750])
+matcdf.hvarnames=uicontrol('style','listbox','string',varnames_labels,'position',[20 205 800 510]);
+matcdf.hvarnames_text=uicontrol('style','text','string','variables (dims): long name [units]','position',[20 720 300 15]);
+
+matcdf.hcoord=uicontrol('style','listbox','string',coordnames_labels,'position',[20 20 600 160]);
+matcdf.hcoord_text=uicontrol('style','text','string','coordinates (size)','position',[20 185 100 15]);
+
+matcdf.h(1)=uicontrol('style','pushbutton','String','Display variable','position',[650 20 200 20], ...
+ 'Callback','aa=matcdf_per_name.allvars.(varnames{get(matcdf.hvarnames,''Value'')})');
+matcdf.h(2)=uicontrol('style','pushbutton','String','Plot variable','position',[650 50 200 20], ...
+ 'Callback','figure(matcdf.hfig_plot);plot(matcdf_per_name.allvars.(varnames{get(matcdf.hvarnames,''Value'')}).data)');
+
+matcdf.h(3)=uicontrol('style','pushbutton','String','Plot transposed var.','position',[650 80 200 20], ...
+ 'Callback','figure(matcdf.hfig_plot);plot(matcdf_per_name.allvars.(varnames{get(matcdf.hvarnames,''Value'')}).data'')');
+cback = ['figure(matcdf.hfig_plot);plot(matcdf_per_name.allvars.(varnames{get(matcdf.hvarnames,''Value'')}).dim{1},' ...
+ 'matcdf_per_name.allvars.(varnames{get(matcdf.hvarnames,''Value'')}).data); ', ...
+ 'xlabel([matcdf_per_name.allvars.(varnames{get(matcdf.hvarnames,''Value'')}).dimname{1} '' '' ', ...
+ 'matcdf_per_name.allvars.(varnames{get(matcdf.hvarnames,''Value'')}).dimunits{1}]);', ...
+ 'ylabel([matcdf_per_name.allvars.(varnames{get(matcdf.hvarnames,''Value'')}).name '' '' ', ...
+ 'matcdf_per_name.allvars.(varnames{get(matcdf.hvarnames,''Value'')}).units]);'];
+matcdf.h(4)=uicontrol('style','pushbutton','String','Plot vs dim 1','position',[650 110 200 20], ...
+ 'Callback',cback);
+cback = ['figure(matcdf.hfig_plot);plot(matcdf_per_name.allvars.(varnames{get(matcdf.hvarnames,''Value'')}).dim{2},' ...
+ 'matcdf_per_name.allvars.(varnames{get(matcdf.hvarnames,''Value'')}).data); ', ...
+ 'xlabel([matcdf_per_name.allvars.(varnames{get(matcdf.hvarnames,''Value'')}).dimname{2} '' '' ', ...
+ 'matcdf_per_name.allvars.(varnames{get(matcdf.hvarnames,''Value'')}).dimunits{2}]);', ...
+ 'ylabel([matcdf_per_name.allvars.(varnames{get(matcdf.hvarnames,''Value'')}).name '' '' ', ...
+ 'matcdf_per_name.allvars.(varnames{get(matcdf.hvarnames,''Value'')}).units]);'];
+matcdf.h(5)=uicontrol('style','pushbutton','String','Plot vs dim 2','position',[650 140 200 20], ...
+ 'Callback',cback);
+
+matcdf.hfig_plot=figure;
+%%
diff --git a/matlab/TCV/gdat_tcv.m b/matlab/TCV/gdat_tcv.m
index 65c4e01c..6d6c6986 100644
--- a/matlab/TCV/gdat_tcv.m
+++ b/matlab/TCV/gdat_tcv.m
@@ -222,7 +222,7 @@ if (nargin>=ivarargin_first_char)
end
% enforce lower case for any character driven input
if ischar(varargin_eff{i+1}) && ~strcmp('path',varargin_eff{i})
- gdat_params.(lower(varargin_eff{i})) = lower(varargin_eff{i+1});
+ gdat_params.(lower(varargin_eff{i})) = varargin_eff{i+1}; % cannot enforce lower(params value) if filename or else are case sensitive
else
gdat_params.(lower(varargin_eff{i})) = varargin_eff{i+1};
end
@@ -3142,6 +3142,36 @@ keyboard
end
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ case {'transp'}
+ % read transp netcdf output file provided in source parameter and generate substructure with all variables
+ if ~isfield(gdat_data.gdat_params,'source') || isempty(gdat_data.gdat_params.source) || ~exist(gdat_data.gdat_params.source,'file')
+ warning([char(10) 'requires a netcdf file in ''source'' parameter' char(10)])
+ return
+ end
+
+ gdat_data.transp = cdf2mat(gdat_data.gdat_params.source);
+
+ % deal with errors and exceptions
+ % XB and X are rhotor_norm and not r/a radii
+ vars2change = {'X', 'XB'};
+ main_substruct = {'coords','allvars'};
+ subfields = {'long_name', 'label'};
+ for i=1:length(vars2change)
+ for j=1:length(main_substruct)
+ for k=1:length(subfields)
+ try
+ gdat_data.transp.(main_substruct{j}).(vars2change{i}).(subfields{k}) = strrep(gdat_data.transp.coords.(vars2change{i}).(subfields{k}),'x"r/a" bdy','sqrt(Phi/Philim)');
+ gdat_data.transp.(main_substruct{j}).(vars2change{i}).(subfields{k}) = strrep(gdat_data.transp.coords.(vars2change{i}).(subfields{k}),'x"r/a" ctr', ...
+ 'sqrt(Phi/Philim)');
+ catch
+ end
+ end
+ end
+ end
+ gdat_data.data_fullpath = ['.transp structure obtained from cdf2mat(gdat_data.gdat_params.source)'];
+ gdat_data.help='Can use transp_gui(gdat_data.transp) to browse and plot';
+
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case {'ttprime', 'ttprime_rho'}
if liuqe_matlab==0
diff --git a/matlab/TCV/tcv_help_parameters.m b/matlab/TCV/tcv_help_parameters.m
index 289e15be..2d232d30 100644
--- a/matlab/TCV/tcv_help_parameters.m
+++ b/matlab/TCV/tcv_help_parameters.m
@@ -45,6 +45,7 @@ help_struct_all.source = sprintf('%s\n','cxrs: [1 2 3] (default systems);', ...
'mhd request: ''23'':23 LFS/HFS (default), ''23full'': 23cm sector 3 and 11, ''0'':z=0 LFS/HFS, ''0full'': 0cm sector 3 and 11', ...
'powers: ohmic in any case + ''ec'', ''nbi'', ''rad'' ', ...
'rtc: defined, all, adcs', ...
+ 'transp: source provides the netcdf file', ...
'icds: ''ec'', ''nbi'' ', ...
'ids_names for request ''ids'' like magnetics, equilibrium, etc');
help_struct_all.source_ec = sprintf('%s\n','toray (for toray nodes), no other source for eccd yet implemented');
diff --git a/matlab/TCV/tcv_requests_mapping.m b/matlab/TCV/tcv_requests_mapping.m
index b503f245..499bbd90 100644
--- a/matlab/TCV/tcv_requests_mapping.m
+++ b/matlab/TCV/tcv_requests_mapping.m
@@ -423,7 +423,7 @@ switch lower(data_request)
mapping.label = 'Ti';
mapping.method = 'switchcase';
case 'transp'
- mapping.label = 'transp output';
+ mapping.label = 'transp output from netcdf file';
mapping.method = 'switchcase';
case {'ttprime', 'ttprime_rho'}
mapping.timedim = 2;
diff --git a/matlab/gdatpaths.m b/matlab/gdatpaths.m
index d7dcdd43..108aff2e 100644
--- a/matlab/gdatpaths.m
+++ b/matlab/gdatpaths.m
@@ -19,7 +19,7 @@ a = fileparts(a);
% machines=[{'JET'} {'TCV'} {'AUG'} {'D3D'}];
% machines=[{'JET'} {'TCV'} {'AUG'} {'KSTAR'}];
-machines=[{'JET'} {'TCV'} {'AUG'} {'D3D'} {'KSTAR'} {'TCV_IMAS'} {'AUG_IMAS'}];
+machines=[{'JET'} {'TCV'} {'AUG'} {'D3D'} {'KSTAR'} {'TCV_IMAS'} {'AUG_IMAS'} {'CHDF'}];
add_paths = cell(1,length(machines));
for i=1:length(machines)
--
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