Index: /issm/trunk/src/m/contrib/musselman/read_netCDF.m =================================================================== --- /issm/trunk/src/m/contrib/musselman/read_netCDF.m (revision 27860) +++ /issm/trunk/src/m/contrib/musselman/read_netCDF.m (revision 27860) @@ -0,0 +1,190 @@ +%{ +Given a NetCDF4 file, this set of functions will perform the following: + 1. Enter each group of the file. + 2. For each variable in each group, update an empty model with the variable's data + 3. Enter nested groups and repeat +%} + + +function model_copy = read_netCDF(filename) + fprintf('NetCDF42C v1.1.12\n'); + + % make a model framework to fill that is in the scope of this file + global model_copy; + model_copy = model(); + + % Check if path exists + if exist(filename, 'file') + fprintf('Opening %s for reading\n', filename); + + % Open the given netCDF4 file + global NCData; + NCData = netcdf.open(filename, 'NOWRITE'); + % Remove masks from netCDF data for easy conversion: NOT WORKING + %netcdf.setMask(NCData, 'NC_NOFILL'); + + % see if results is in there, if it is we have to instantiate some classes + try + results_group_id = netcdf.inqNcid(NCData, "results"); + make_results_subclasses(); + catch + end % 'results' group doesn't exist + + + % see if inversion is in there, if it is we may have to instantiate some classes + try + inversion_group_id = netcdf.inqNcid(NCData, "inversion"); + check_inversion_class(); + catch + end % 'inversion' group doesn't exist + + % loop over first layer of groups in netcdf file + for group = netcdf.inqGrps(NCData) + group_id = netcdf.inqNcid(NCData, netcdf.inqGrpName(group)); + %disp(netcdf.inqGrpNameFull(group_id)) + % hand off first level to recursive search + walk_nested_groups(group_id); + end + + % Close the netCDF file + netcdf.close(NCData); + disp('Model Successfully Copied') + else + fprintf('File %s does not exist.\n', filename); + end +end + + +function make_results_subclasses() + global model_copy; + global NCData; + resultsGroup = netcdf.inqNcid(NCData, "results"); + variables = netcdf.inqVarIDs(resultsGroup); + 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') +end + + +function check_inversion_class() + % get the name of the inversion class: either inversion or m1qn3inversion or taoinversion + global model_copy; + global NCData; + inversionGroup = netcdf.inqNcid(NCData, "inversion"); + varid = netcdf.inqVarID(inversionGroup,'inversion_class_name') + inversion_class = convertCharsToStrings(netcdf.getVar(inversionGroup, varid,'char')); + if inversion_class == 'm1qn3inversion' + model_copy.inversion = m1qn3inversion(); + disp('Successfully created inversion class instance: m1qn3inversion') + elseif inversion_class == 'taoinversion' + model_copy.inversion = taoinversion(); + disp('Successfully created inversion class instance: taoinversion') + else + end +end + + + +%{ +function make_results_subclasses() + global model_copy; + global NCData; + resultsGroup = netcdf.inqNcid(NCData, "results"); + subgroups = netcdf.inqGrps(resultsGroup); + for subgroup = subgroups + groupName = netcdf.inqGrpName(subgroup) + + + + 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') +end +%} + + +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); + %disp(varname) + copy_variable_data_to_new_model(group_location_in_file,varname, xtype); + end + catch + end + + % try to find groups in current level, if it doesn't work it's because there is nothing there + try + % 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 + catch + end +end + +%{ +Since there are two types of objects that MATLAB uses (classes and structs), we have to check +which object we're working with before we can set any fields/attributes of it. After this is completed, +we can write the data to that location in the model. +%} + +function copy_variable_data_to_new_model(group_location_in_file, varname, xtype) + global model_copy; + global NCData; + %disp(varname) + % putting try/catch here so that any errors generated while copying data are logged and not lost by the try/catch in walk_nested_groups + try + %disp(netcdf.inqGrpNameFull(group_location_in_file)) + %disp(class(netcdf.inqGrpNameFull(group_location_in_file))) + adress_to_attr = strrep(netcdf.inqGrpNameFull(group_location_in_file), '/', '.'); + % netcdf uses Row Major Order but MATLAB uses Column Major Order so we need to transpose all arrays w/ more than 1 dim + data = netcdf.getVar(group_location_in_file, netcdf.inqVarID(group_location_in_file, varname)); + + if all(size(data)~=1) + data = data.'; + end + + % the issm c compiler does not work with int64 datatypes, so we need to convert those to int16 + % reference this (very hard to find) link for netcdf4 datatypes: https://docs.unidata.ucar.edu/netcdf-c/current/netcdf_8h_source.html + %xtype + if xtype == 10 + arg_to_eval = ['model_copy', adress_to_attr, '.', varname, ' = ' , 'double(data);']; + eval(arg_to_eval); + %disp('saved int64 as int16') + else + arg_to_eval = ['model_copy', adress_to_attr, '.', varname, ' = ' , 'data;']; + eval(arg_to_eval); + end + + full_addy = netcdf.inqGrpNameFull(group_location_in_file); + %disp(xtype) + %class(data) + fprintf('Successfully saved %s to %s\n', varname, full_addy); + catch e %e is an MException struct + fprintf(1,'The identifier was:\n%s',e.identifier); + fprintf(1,'There was an error! The message was:\n%s',e.message); + % more error handling... + end +end + + +