Index: /issm/trunk/src/m/contrib/musselman/read_netCDF.m =================================================================== --- /issm/trunk/src/m/contrib/musselman/read_netCDF.m (revision 27876) +++ /issm/trunk/src/m/contrib/musselman/read_netCDF.m (revision 27877) @@ -71,8 +71,16 @@ for name = variables class_instance = netcdf.inqVar(resultsGroup, name); - class_instance_name = convertCharsToStrings(netcdf.getVar(resultsGroup, name, 'char')); - model_copy.results = setfield(model_copy.results, class_instance, class_instance_name); - end - disp('Successfully recreated results struct') + class_instance_names_raw = netcdf.getVar(resultsGroup, name, 'char').'; + class_instance_names = cellstr(class_instance_names_raw); + for index = 1:numel(class_instance_names) + class_instance_name = class_instance_names{index}; + model_copy.results = setfield(model_copy.results, class_instance_name, struct()); + end + %model_copy.results = setfield(model_copy.results, class_instance, class_instance_name); + end + disp('Successfully recreated results structs:') + for fieldname = string(fieldnames(model_copy.results)) + disp(fieldname) + end end @@ -100,46 +108,41 @@ function walk_nested_groups(group_location_in_file) global model_copy; - global NCData; - % try to find vars in current level, if it doesn't work it's because there is nothing there - try - % we search the current group level for variables by getting this struct - variables = netcdf.inqVarIDs(group_location_in_file); - - % from the variables struct get the info related to the variables - for variable = variables - [varname, xtype, dimids, numatts] = netcdf.inqVar(group_location_in_file, variable); - - % keep an eye out for nested structs: - if strcmp(varname, 'this_is_a_nested') - is_nested = true; - copy_nested_struct(group_location_in_file) - else - is_nested = false; - copy_variable_data_to_new_model(group_location_in_file,varname, xtype); - end - end - catch ME - rethrow(ME) + global NCData; + % we search the current group level for variables by getting this struct + variables = netcdf.inqVarIDs(group_location_in_file); + + % from the variables struct get the info related to the variables + for variable = variables + [varname, xtype, dimids, numatts] = netcdf.inqVar(group_location_in_file, variable); + + % keep an eye out for nested structs: + if strcmp(varname, 'this_is_a_nested') + is_nested = true; + copy_nested_struct(group_location_in_file) + elseif strcmp(varname, 'solution') + % band-aid pass.. + else + copy_variable_data_to_new_model(group_location_in_file, varname, xtype); + end end % try to find groups in current level, if it doesn't work it's because there is nothing there - try - % if it's not a nested struct, keep searching for subgroups - if isnested - % do nothing - else - % search for nested groups in the current level to feed back to this function - groups = netcdf.inqGrps(group_location_in_file); - if not(isempty(groups)) - for group = groups - %disp('found nested group!!') - group_id = netcdf.inqNcid(group_location_in_file, netcdf.inqGrpName(group)); - %disp(netcdf.inqGrpNameFull(group_id)) - walk_nested_groups(group); - end - end - end - catch % no nested groups here - end + %try + % if it's a nested struct the function copy_nested_struct has already been called + if logical(exist('is_nested', 'var')) + % do nothing + else + % search for nested groups in the current level to feed back to this function + groups = netcdf.inqGrps(group_location_in_file); + if not(isempty(groups)) + for group = groups + group_id = netcdf.inqNcid(group_location_in_file, netcdf.inqGrpName(group)); + %disp(netcdf.inqGrpNameFull(group_id)) + walk_nested_groups(group); + end + end + end + %catch % no nested groups here + %end end @@ -152,5 +155,5 @@ A common multidimensional struct array is the 1xn md.results.TransientSolution struct. The process to recreate is as follows: - 1. Get the name of the struct from group variable name_of_struct + 1. Get the name of the struct from group name 2. Get the fieldnames from the subgroups 3. Recreate the struct with fieldnames @@ -159,6 +162,5 @@ % step 1 - varid = netcdf.inqVarID(group_location_in_file, 'name_of_struct'); - name_of_struct = netcdf.getVar(group_location_in_file, varid)'; + name_of_struct = netcdf.inqGrpName(group_location_in_file); % step 2 @@ -174,12 +176,13 @@ % step 3 - address_in_model = strrep(netcdf.inqGrpNameFull(group_location_in_file), '/', ''); + address_in_model_raw = split(netcdf.inqGrpNameFull(group_location_in_file), '/'); + address_in_model = address_in_model_raw{2}; + % we cannot assign a variable to represent this object as MATLAB treats all variables as copies % and not pointers to the same memory address - % this means that if address_in_model is more than 1 item, we need to modify the code. For now, - % we just hope this will do + % this means that if address_in_model has more than 1 layer, we need to modify the code. For now, + % we just hope this will do. An example of a no-solution would be model().abc.def.ghi.field model_copy.(address_in_model).(name_of_struct) = struct(); - % for every fieldname in the subgroup, create an empty field for fieldname = string(fieldnames) @@ -250,4 +253,6 @@ elseif numel(data) == 1 && xtype == 3 && data == -32767 data = cell(char()); + elseif isempty(all(data)) + data = [] end % band-aid for some cell-char-arrays: @@ -260,10 +265,10 @@ data = data.'; end - + % if we have a list of strings if xtype == 2 try - if strcmp(netcdf.getAtt(group, varid, "type_is"), 'cell_array_of_strings') - data = cellstr(data) + if strcmp(netcdf.getAtt(group_location_in_file, varid, "type_is"), 'cell_array_of_strings') + data = cellstr(data); end catch @@ -280,5 +285,5 @@ %disp('saved int64 as int16') else - arg_to_eval = ['model_copy', address_to_attr, '.', varname, ' = ' , 'data;']; + arg_to_eval = ['model_copy', address_to_attr, '.', varname, ' = data;']; eval(arg_to_eval); end @@ -288,9 +293,16 @@ %class(data) fprintf('Successfully saved %s to %s\n', varname, full_addy); - catch e %e is an MException struct + + catch Me %e is an MException struct + % Some error occurred if you get here. fprintf(1,'There was an error with %s! \n', varname) - fprintf('The message was:\n%s\n',e.message); - fprintf(1,'The identifier was:\n%s\n',e.identifier); - disp() + errorMessage = sprintf('Error in function %s() at line %d.\n\nError Message:\n%s', ME.stack.name, ME.stack.line, ME.message); + fprintf(1, '%s\n', errorMessage); + uiwait(warndlg(errorMessage)); + %line = Me.stack.line + %fprintf(1,'There was an error with %s! \n', varname) + %fprintf('The message was:\n%s\n',Me.message); + %fprintf(1,'The identifier was:\n%s\n',Me.identifier); + % more error handling... end Index: /issm/trunk/src/m/contrib/musselman/write_netCDF.m =================================================================== --- /issm/trunk/src/m/contrib/musselman/write_netCDF.m (revision 27876) +++ /issm/trunk/src/m/contrib/musselman/write_netCDF.m (revision 27877) @@ -95,13 +95,20 @@ % Loop through each class instance in results - class_instance_names = fieldnames(results_var); + class_instance_names = fieldnames(results_var) + + % we save lists of instances to the netcdf + solutions = {} + solutionsteps = {} + resultsdakotas = {} for i = 1:numel(class_instance_names) class_instance_name = class_instance_names{i}; - + % there are often mutliple instances of the same class/struct so we have to number them % Check to see if there is a solutionstep class instance if contains(class_instance_name, 'solutionstep',IgnoreCase=true) quality_control{end+1} = 1; - write_string_to_netcdf('solutionstep', class_instance_name, groupid); + solutionsteps{end+1} = class_instance_name + %varname = ['solutionstep', num2str(i)] + %write_string_to_netcdf(varname, class_instance_name, groupid); disp('Successfully stored class python subclass instance: solutionstep') end @@ -110,5 +117,7 @@ if contains(class_instance_name, 'solution',IgnoreCase=true) quality_control{end+1} = 1; - write_string_to_netcdf('solution', class_instance_name, groupid); + solutions{end+1} = class_instance_name + %varname = ['solution', num2str(i)] + %write_string_to_netcdf(varname, class_instance_name, groupid); disp('Successfully stored class python subclass instance: solution') end @@ -117,9 +126,22 @@ if contains(class_instance_name, 'resultsdakota',IgnoreCase=true) quality_control{end+1} = 1; - write_string_to_netcdf('resultsdakota', class_instance_name, groupid); + resultsdakotas{end+1} = class_instance_name + %varname = ['resultsdakota', num2str(i)] + %write_string_to_netcdf(varname, class_instance_name, groupid); disp('Successfully stored class python subclass instance: resultsdakota') end end - + if ~isempty(solutionsteps) + write_cell_with_strings('solutionstep', solutionsteps, groupid) + end + if ~isempty(solutions) + write_cell_with_strings('solution', solutions, groupid) + end + if ~isempty(resultsdakotas) + write_cell_with_strings('resultsdakota', resultsdakotas, groupid) + end + + + % Check if all class instances were processed correctly if numel(quality_control) ~= numel(class_instance_names) @@ -319,5 +341,7 @@ disp("Beginning transfer of nested MATLAB struct to the NetCDF") - + % make a new subgroup to contain all the others: + group = netcdf.defGrp(group, parent_struct_name); + % make sure other systems can flag the nested struct type dimID = netcdf.defDim(group, 'struct', 6); @@ -327,10 +351,5 @@ netcdf.putVar(group, string_var, method_ID); - % make sure other systems know the name of the parent struct - uint_method=uint8(parent_struct_name).'; - method_ID = char(uint_method); - dimID = netcdf.defDim(group, 'struct_name', [numel(method_ID)]); - string_var = netcdf.defVar(group, 'name_of_struct', "NC_CHAR", dimID); - netcdf.putVar(group, string_var, method_ID); + % other systems know the name of the parent struct because it's covered by the results/qmu functions above % 'a' will always be 1 and is not useful to us @@ -339,5 +358,5 @@ for substruct = 1:no_of_dims % we start by making subgroups with nice names like "TransientSolution_substruct_44" - name_of_subgroup = [parent_struct_name, '_substruct_', num2str(substruct)]; + name_of_subgroup = ['1x', num2str(substruct)]; subgroup = netcdf.defGrp(group, name_of_subgroup);