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Commit c717a791 authored by Pierre Cazenave's avatar Pierre Cazenave

Code taken from replace_FVCOM_restart_vars.m which did the cloning of the...

Code taken from replace_FVCOM_restart_vars.m which did the cloning of the restart NetCDF file and replaced the requested variables with interpolated versions. This makes it easier to generate restart files using a range of sources
parent eaf013a6
function write_FVCOM_restart(fv_restart, out_restart, data)
% Duplicate an FVCOM restart file, replacing variable values with those
% specified in the struct data.
% function write_FVCOM_restart(fv_restart, out_restart, data)
% Use an existing FVCOM restart file as a template, export all existing
% data except for variables whose names match the data in the struct
% 'data'.
% fv_restart = full path to an existing FVCOM restart file.
% out_restart = full path to the restart file to be created.
% data = struct whose field names are the variable names to be
% replaced.
% FVCOM restart file.
% data.temp = interpolated_temp;
% data.salinity = interpolated_salinity;
% write_FVCOM_restart('/tmp/fvcom_restart.nc', data)
% Author(s):
% Pierre Cazenave (Plymouth Marine Laboratory)
% Revision history:
% 2013-02-08 First version.
subname = 'write_FVCOM_tsobc';
global ftbverbose
if ftbverbose
fprintf(['begin : ' subname '\n'])
% Get the fieldnames which must match the variable names to be replaced
% (case sensitive).
fnames = fieldnames(data);
nf = length(fnames);
nc = netcdf.open(fv_restart, 'NOWRITE');
ncout = netcdf.create(out_restart, 'clobber');
[numdims, numvars, numglobatts, unlimdimID] = netcdf.inq(nc);
% Define the dimensions for all variables.
dimid = nan(numdims, 1);
dimnames = cell(numdims, 1);
dimlengths = nan(numdims, 1);
for ii = 1:numdims
[dimname, dimlen] = netcdf.inqDim(nc, ii - 1);
if ii ~= unlimdimID + 1 % NetCDF indices start at zero
dimid(ii) = netcdf.defDim(ncout, dimname, dimlen);
dimid(ii) = netcdf.defDim(ncout, dimname, netcdf.getConstant('NC_UNLIMITED'));
dimnames{ii} = dimname;
dimlengths(ii) = dimlen;
% Now define the variables and attributes.
for ii = 1:numvars
% Find name of the current variable.
[varname, xtype, varDimIDs, varAtts] = netcdf.inqVar(nc, ii - 1);
% Create the variables.
varid = netcdf.defVar(ncout, varname, xtype, varDimIDs);
% Get each attribute and add it to the current variable.
for j = 1:varAtts
attname = netcdf.inqAttName(nc, varid, j - 1);
attval = netcdf.getAtt(nc, varid, attname);
netcdf.putAtt(ncout, varid, attname, attval);
% Do the global attributes
for ii = 1:numglobatts
% Find the current global attribute's name and value.
gattname = netcdf.inqAttName(nc, netcdf.getConstant('NC_GLOBAL'), ii - 1);
gattval = netcdf.getAtt(nc, netcdf.getConstant('NC_GLOBAL'), gattname);
% Put that back into the output NetCDF file.
netcdf.putAtt(ncout, netcdf.getConstant('NC_GLOBAL'), gattname, gattval);
% Get the existing data and output to the new NetCDF file, except for
% variables which match the fieldnames in the data struct.
for ii = 1:numvars
[varname, ~, varDimIDs, ~] = netcdf.inqVar(nc, ii - 1);
varid = netcdf.inqVarID(nc, varname);
if ftbverbose
fprintf('\tvariable %s... ', varname)
% We need the data irrespective of whether we're replacing it or not,
% so grab it outside the if statement below.
data = netcdf.getVar(nc, varid);
% Get the size of the data and the dimension names.
currDimsNames = dimnames(varDimIDs + 1);
currDimsLengths = dimlengths(varDimIDs + 1);
% Find whether we've got an unlimited dimension in this data.
wasUnlimited = -1;
for jj = varDimIDs
if numel(unlimdimID) > 1
error('Do not currently support multiple unlimited dimensions.')
if strcmpi(dimnames(jj + 1), dimnames(unlimdimID + 1))
wasUnlimited = jj;
% Since the restart file has a number of time values, we'll ramp up the
% replacement data from the existing start condition to the actual
% value over the time steps. So, we need to know how many time steps we
% actually have.
% Get the dimension data ready for the replacement arrays.
tIdx = strncmp(dimnames(unlimdimID + 1), currDimsNames, length(dimnames{unlimdimID + 1}));
% Not sure about the hardcoded strings below...
sIdx = strncmp('siglay', currDimsNames, length(dimnames{unlimdimID + 1}));
nIdx = strncmp('node', currDimsNames, length(dimnames{unlimdimID + 1}));
nt = currDimsLengths(tIdx);
ns = currDimsLengths(sIdx);
nd = currDimsLengths(nIdx);
% Iterate through the field names to see if we're on one of the
% variables to be replaced.
for vv = 1:nf
if strcmp(varname, fnames{vv})
% To make the scaling go from the initial value to the POLCOMS
% value, we need to take the scale the difference between the end
% members by the scaling factor at each time and add to the current
% time's value.
sfvdata = nan(nd, ns, nt);
ss = 0:1 / (nt - 1):1; % scale from 0 to 1.
startdata = squeeze(data(:, :, 1)); % use the first modelled time step
for tt = 1:nt;
if tt == 1
sfvdata(:, :, 1) = startdata;
td = data.(fnames{vv}) - startdata;
sfvdata(:, :, tt) = startdata + (ss(tt) .* td);
% Replace the values with the scaled interpolated values.
netcdf.putVar(ncout, varid, sfvdata)
% We need to check if the dimension is unlimited, and use a start
% and end with netcdf.putVar if it is. This is largely because
% MATLAB can't handle unlimited dimensions in the same way as it
% does finite dimensions.
if wasUnlimited < 0
% We can just dump the entire data without specifying over what
% indices.
netcdf.putVar(ncout, varid, data);
% Use the dimension length we extracted above to output the
% data with the valid unlimited dimension format.
netcdf.putVar(ncout, varid, zeros(length(currDimsLengths), 1), currDimsLengths, data);
if ftbverbose
if ftbverbose
fprintf(['end : ' subname '\n'])
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