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UNM_assign_soil_data_labels.m
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UNM_assign_soil_data_labels.m
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function fluxall = UNM_assign_soil_data_labels( sitecode, year, fluxall )
% UNM_ASSIGN_SOIL_DATA_LABELS - assign labels to soil measurements.
%
% Labels are of the format soilT_cover_index_depth_*, where cover, index, and
% depth are character strings. e.g. "soilT_O_2_12.5_avg" denotes cover type
% open, index (pit) 2, and depth of 12.5 cm. Depth is followed by an
% underscore, and then optional arbitrary text.
%
% USAGE:
% fluxall = UNM_assign_soil_data_labels( sitecode, year, fluxall )
%
% INPUTS
% sitecode: integer or UNM_sites object; site to consider
% year: integer; year to consider
% fluxall: matlab dataset object; parsed fluxall.xls or fluxall.txt data
%
% OUTPUTS
% fluxall: matlab dataset object; fluxall.xls data with relabeled soil data
% columns
%
% SEE ALSO
% dataset, UNM_parse_fluxall_txt_file, UNM_parse_fluxall_xls_file
%
% author: Timothy W. Hilton, UNM, May-July 2012
if ~isa( sitecode, 'UNM_sites' )
sitecode = UNM_sites( sitecode );
end
% The actual work is performed by two helper functions:
fluxall = format_soilT_and_SWC_labels( sitecode, year, fluxall );
fluxall = format_SHF_labels( sitecode, year, fluxall );
%============================================================
% helper functions for UNM_assign_soil_data_labels
%============================================================
function fluxall = format_SHF_labels( sitecode, year, fluxall )
% SHF_COLUMNS - identifies soil heat flux (SHF) columns and assigns descriptive
% labels.
% regular expression to identify strings containing 'shf' or 'hfp',
% case-insensitive
re_SHF = '.*([Ss][Hh][Ff]).*|.*([Hh][Ff][Pp]).*';
[ ~, idx_SHF ] = regexp_header_vars( fluxall, re_SHF );
SHF_vars = fluxall.Properties.VarNames( idx_SHF );
switch sitecode
case UNM_sites.GLand
if year < 2012
% 2007-2011 GLand should have two SHF observations (grass and open)
if numel( idx_SHF ) < 2
error( sprintf( [ 'unable to locate 2 SHF measurements for ', ...
'GLand %d' ], year ) );
end
switch year
case 2007
fluxall.Properties.VarNames( idx_SHF ) = ...
{ 'SHF_grass_1', 'SHF_open_1' }';
case 2008
fluxall.Properties.VarNames( idx_SHF ) = ...
{ 'SHF_open_1', 'SHF_grass_1' }';
case { 2009, 2010, 2011 }
% these SHF variables are labeled "hfp01_COVER_Avg" -- reformat these to
% SHF_COVER_1
SHF_vars = regexprep( SHF_vars, 'hfp(01)?', 'SHF' );
SHF_vars = regexprep( SHF_vars, '([0-9])_Avg', '$1' );
SHF_vars = regexprep( SHF_vars, '_Avg', '_1' );
fluxall.Properties.VarNames( idx_SHF ) = SHF_vars;
end
else
SHF_vars = regexprep( SHF_vars, 'hfp', 'SHF' );
SHF_vars = regexprep( SHF_vars, '_Avg', '' );
fluxall.Properties.VarNames( idx_SHF ) = SHF_vars;
end
case UNM_sites.SLand
if ismember( year, [ 2007, 2008 ] )
SHF_vars = replace_hex_chars( SHF_vars );
SHF_vars = regexprep( SHF_vars, ...
{ 'shf_Avg\(1\)', 'shf_Avg\(2\)' }, ...
{ 'SHF_shrub_1', 'SHF_open_1' }, ...
'once' );
elseif ismember( year, [ 2009, 2010 ] )
old_vars = { 'hfp01_1_Avg', 'hfp01_2_Avg', 'hfp01_3_Avg', ...
'hfp01_4_Avg', 'hfp01_5_Avg', 'hfp01_6_Avg' };
new_vars = { 'SHF_shrub_1', 'SHF_shrub_2', 'SHF_grass_1', ...
'SHF_grass_2', 'SHF_open_1', 'SHF_open_2' };
SHF_vars = regexprep( SHF_vars, old_vars, new_vars, 'once' );
elseif year >= 2011
old_vars = { 'shf_sh_1_Avg', 'shf_sh_2_Avg', 'shf_gr_1_Avg', ...
'shf_gr_2_Avg', 'shf_op_1_Avg', 'shf_op_2_Avg' };
new_vars = { 'SHF_shrub_1', 'SHF_shrub_2', 'SHF_grass_1', ...
'SHF_grass_2', 'SHF_open_1', 'SHF_open_2' };
SHF_vars = regexprep( SHF_vars, old_vars, new_vars, 'once' );
end
fluxall.Properties.VarNames( idx_SHF ) = SHF_vars;
case UNM_sites.JSav
SHF_vars = replace_hex_chars( SHF_vars );
SHF_vars = regexprep( SHF_vars, ...
{ 'shf_Avg.*1.*', 'shf_Avg.*2.*', ...
'shf_Avg.*3.*', 'shf_Avg.*4.*' }, ...
{ 'SHF_open_1', 'SHF_open_2', ...
'SHF_edge_1', 'SHF_juniper_1' }, ...
'once' );
fluxall.Properties.VarNames( idx_SHF ) = SHF_vars;
case UNM_sites.PJ | UNM_sites.TestSite
% capitalize "shf" and remove trailing "_Avg"
SHF_vars = regexprep( SHF_vars, { 'shf', '_Avg' }, { 'SHF', '' } );
case UNM_sites.PPine
SHF_vars = replace_hex_chars( SHF_vars );
SHF_vars = regexprep( SHF_vars, ...
{ 'shf_Avg.*1.*', 'shf_Avg.*2.*', ...
'shf_Avg.*3.*' }, ...
{ 'SHF_ponderosa_1', 'SHF_ponderosa_2', ...
'SHF_ponderosa_3' }, ...
'once' );
fluxall.Properties.VarNames( idx_SHF ) = SHF_vars;
case UNM_sites.MCon
SHF_vars = replace_hex_chars( SHF_vars );
SHF_vars = regexprep( SHF_vars, ...
{ 'shf_Avg.*1.*', 'shf_Avg.*2.*', ...
'shf_Avg.*3.*' }, ...
{ 'SHF_mcon_1', 'SHF_mcon_2', ...
'SHF_mcon_3' }, ...
'once' );
fluxall.Properties.VarNames( idx_SHF ) = SHF_vars;
case UNM_sites.New_GLand
vars = fluxall.Properties.VarNames;
vars = regexprep( vars, ...
{ 'grass_1_Avg', 'grass_2_Avg', ...
'open_1_Avg', 'open_2_Avg' }, ...
{ 'SHF_open_1', 'SHF_open_2', ...
'SHF_grass_1', 'SHF_grass_2' }, ...
'once' );
fluxall.Properties.VarNames = vars;
end
%============================================================
function fluxall = format_soilT_and_SWC_labels( sitecode, year, fluxall )
% SOILT_AND_SWC_COLUMNS - identifies soil temperature (soilT) and soil water
% content (SWC) columns and assigns descriptive labels.
placeholder = 0;
labels_template = struct( 'labels', { 'placeholder' }, ...
'columns', [ placeholder ] );
echo_SWC_labels = labels_template;
cs616_SWC_labels = labels_template;
soilT_labels = labels_template;
TCAV_labels = labels_template;
%place holders
% cs616_SWC_labels.columns = [];
% cs616_SWC_labels.labels = {};
% echo_SWC_labels.columns = [];
% echo_SWC_labels.labels = {};
% soilT_labels.columns = [];
% soilT_labels.labels = {};
switch sitecode
% --------------------------------------------------
case UNM_sites.GLand
descriptive_soilT_labels = { 'soilT_open_1_2p5', ...
'soilT_open_1_12p5', ...
'soilT_open_1_22p5', ...
'soilT_grass_1_2p5', ...
'soilT_grass_1_12p5', ...
'soilT_grass_1_22p5', ...
'soilT_open_2_2p5', ...
'soilT_open_2_12p5', ...
'soilT_open_2_22p5', ...
'soilT_grass_2_2p5', ...
'soilT_grass_2_12p5', ...
'soilT_grass_2_22p5', ...
'soilT_open_3_2p5', ...
'soilT_open_3_12p5', ...
'soilT_open_3_22p5', ...
'soilT_open_3_37p5', ...
'soilT_grass_3_2p5', ...
'soilT_grass_3_12p5', ...
'soilT_grass_3_22p5', ...
'soilT_grass_3_37p5' };
descriptive_cs616_labels = { 'cs616SWC_open_1_2p5', ...
'cs616SWC_open_1_12p5', ...
'cs616SWC_open_1_22p5', ...
'cs616SWC_grass_1_2p5', ...
'cs616SWC_grass_1_12p5', ...
'cs616SWC_grass_1_22p5', ...
'cs616SWC_open_2_2p5', ...
'cs616SWC_open_2_12p5', ...
'cs616SWC_open_2_22p5', ...
'cs616SWC_grass_2_2p5', ...
'cs616SWC_grass_2_12p5', ...
'cs616SWC_grass_2_22p5', ...
'cs616SWC_open_3_2p5', ...
'cs616SWC_open_3_12p5', ...
'cs616SWC_open_3_22p5', ...
'cs616SWC_open_3_37p5', ...
'cs616SWC_grass_3_2p5', ...
'cs616SWC_grass_3_12p5', ...
'cs616SWC_grass_3_22p5', ...
'cs616SWC_grass_3_37p5' };
switch year
case { 2007, 2008 }
[ ~, idx_cs616 ] = regexp_header_vars( fluxall, 'cs616' );
% the two 52.5 cm observations to not actually exist (conversation
% with Marcy, 26 Apr 2012) --TWH
idx_to_remove = idx_cs616( [ 17, 22, 23 ] );
idx_cs616 = idx_cs616( [ 1:16, 18:21 ] );
fluxall.Properties.VarNames( idx_cs616 ) = descriptive_cs616_labels;
fluxall( :, idx_to_remove ) = [];
case { 2009, 2010 }
[ ~, idx_cs616 ] = regexp_header_vars( fluxall, 'cs616' );
% the two 52.5 cm observations to not actually exist (conversation
% with Marcy, 26 Apr 2012) --TWH
idx_to_remove = idx_cs616( [ 17, 22 ] );
idx_cs616 = idx_cs616( [ 1:16, 18:21 ] );
fluxall.Properties.VarNames( idx_cs616 ) = descriptive_cs616_labels;
fluxall( :, idx_to_remove ) = [];
% change mux25t... labels to descriptive soilT labels
[ ~, idx_Tsoil ] = regexp_header_vars( fluxall, 'mux25t' );
fluxall.Properties.VarNames( idx_Tsoil ) = descriptive_soilT_labels;
[ ~, idx_TCAV ] = regexp_header_vars( fluxall, 'TCAV|tcav' );
fluxall.Properties.VarNames( idx_TCAV ) = ...
{ 'TCAV_open_Avg', 'TCAV_cover_Avg' };
case { 2011, 2012 }
% this year cs616 SWC are labeled open1_12.5, grass2_2.5, etc. They
% are in columns 203 to 222
re = '(^(open|grass)[12]_[0-9]{1,2}p5cm|swc.*)'; % regular expression to
% identify cs616 labels
[ ~, idx_cs616 ] = regexp_header_vars( fluxall, re );
% prepend 'cs616SWC_' to labels and separate cover type from pit number
% (e.g. grass1... -> cs616_grass_1...
fluxall.Properties.VarNames( idx_cs616 ) = ...
strcat( 'cs616SWC_', fluxall.Properties.VarNames( idx_cs616 ) );
fluxall.Properties.VarNames( idx_cs616 ) = ...
regexprep( fluxall.Properties.VarNames( idx_cs616 ), ...
'(grass|open)', '$1_');
% % the two 52.5 cm observations to not actually exist (conversation
% % with Marcy, 26 Apr 2012) --TWH
% idx_to_remove = idx_cs616( [ 17, 22 ] );
% idx_cs616 = idx_cs616( [ 1:16, 18:21 ] );
% change mux25t... labels to descriptive soilT labels
[ ~, idx_Tsoil ] = regexp_header_vars( fluxall, '(mux25t|soilT)' );
fluxall.Properties.VarNames( idx_Tsoil ) = descriptive_soilT_labels;
% some files in late 2012 are labeled "soilt..." not "soilT..."
[ ~, idx_Tsoil ] = regexp_header_vars( fluxall, 'soilt' );
fluxall.Properties.VarNames( idx_Tsoil ) = ...
regexprep( fluxall.Properties.VarNames( idx_Tsoil ), ...
'soilt', ...
'soilT' );
fluxall.Properties.VarNames( idx_Tsoil ) = ...
regexprep( fluxall.Properties.VarNames( idx_Tsoil ), ...
'_Avg', ...
'' );
fluxall.Properties.VarNames( idx_Tsoil ) = ...
format_probe_strings( fluxall.Properties.VarNames( idx_Tsoil ) );
end %switch GLand year
% --------------------------------------------------
case UNM_sites.SLand
descriptive_cs616_labels = { 'cs616SWC_open_1_2p5', ...
'cs616SWC_open_1_12p5', ...
'cs616SWC_open_1_22p5', ...
'cs616SWC_open_1_37p5', ...
'cs616SWC_open_1_52p5', ...
'cs616SWC_cover_1_2p5', ...
'cs616SWC_cover_1_12p5', ...
'cs616SWC_cover_1_22p5', ...
'cs616SWC_cover_1_37p5', ...
'cs616SWC_cover_1_52p5', ...
'cs616SWC_open_2_2p5', ...
'cs616SWC_open_2_12p5', ...
'cs616SWC_open_2_22p5', ...
'cs616SWC_open_2_37p5', ...
'cs616SWC_open_2_52p5', ...
'cs616SWC_cover_2_2p5', ...
'cs616SWC_cover_2_12p5', ...
'cs616SWC_cover_2_22p5', ...
'cs616SWC_cover_2_37p5', ...
'cs616SWC_cover_2_52p5' };
descriptive_soilT_labels = { 'soilT_open_1_2p5', 'soilT_open_1_12p5', ...
'soilT_open_1_22p5', 'soilT_open_1_37p5', ...
'soilT_open_1_52p5', 'soilT_cover_1_2p5', ...
'soilT_cover_1_12p5', 'soilT_cover_1_22p5', ...
'soilT_cover_1_37p5', 'soilT_cover_1_52p5', ...
'soilT_open_2_2p5', 'soilT_open_2_12p5', ...
'soilT_open_2_22p5', 'soilT_open_2_37p5', ...
'soilT_open_2_52p5', 'soilT_cover_2_2p5', ...
'soilT_cover_2_12p5', 'soilT_cover_2_22p5', ...
'soilT_cover_2_37p5', 'soilT_cover_2_52p5' };
switch year
case { 2007, 2008, 2009, 2010 }
[ ~, idx_cs616 ] = regexp_header_vars( fluxall, 'cs616_wcr.*' );
fluxall.Properties.VarNames( idx_cs616( 1:20 ) ) = ...
descriptive_cs616_labels;
fluxall( :, idx_cs616( 21:end ) ) = [];
% change mux25t... labels to descriptive soilT labels
[ ~, idx_Tsoil ] = regexp_header_vars( fluxall, 'mux25t' );
if ~isempty( idx_Tsoil )
fluxall.Properties.VarNames( idx_Tsoil ) = descriptive_soilT_labels;
end
case { 2011, 2012 }
% change soil_h2o... labels to descriptive SWC labels
[ ~, idx_cs616 ] = regexp_header_vars( fluxall, '(soil_h2o_.*_Avg|cs616SWC)' );
fluxall.Properties.VarNames( idx_cs616 ) = descriptive_cs616_labels;
% change mux25t... labels to descriptive soilT labels
[ ~, idx_Tsoil ] = regexp_header_vars( fluxall, 'mux25t' );
if ~isempty( idx_Tsoil )
fluxall.Properties.VarNames( idx_Tsoil ) = descriptive_soilT_labels;
end
% some files in late 2012 are labeled "soilt..._Avg" not "soilT..."
[ ~, idx_Tsoil ] = regexp_header_vars( fluxall, 'soilt' );
fluxall.Properties.VarNames( idx_Tsoil ) = ...
regexprep( fluxall.Properties.VarNames( idx_Tsoil ), ...
'soilt', ...
'soilT' );
fluxall.Properties.VarNames( idx_Tsoil ) = ...
regexprep( fluxall.Properties.VarNames( idx_Tsoil ), ...
'_Avg', ...
'' );
fluxall.Properties.VarNames( idx_Tsoil ) = ...
format_probe_strings( fluxall.Properties.VarNames( idx_Tsoil ) );
end % switch SLand year
% --------------------------------------------------
case UNM_sites.JSav
soilT_descriptive_labels_2008 = { 'soilT_open_1_5', 'soilT_open_1_10', ...
'soilT_open_1_20', 'soilT_open_1_40', ...
'soilT_open_1_62', 'soilT_open_2_5', ...
'soilT_open_2_10', 'soilT_open_2_20', ...
'soilT_open_2_40', 'soilT_open_2_62', ...
'soilT_edge_1_5', 'soilT_edge_1_10', ...
'soilT_edge_1_20', 'soilT_edge_1_40', ...
'soilT_edge_1_62', 'soilT_canopy_1_5', ...
'soilT_canopy_1_10', 'soilT_canopy_1_20', ...
'soilT_canopy_1_40', 'soilT_canopy_1_62' };
cs616_descriptive_labels_preJul09 = { 'cs616SWC_open_1_5', ...
'cs616SWC_open_1_10', 'cs616SWC_open_1_20', ...
'cs616SWC_open_1_40', 'cs616SWC_open_2_5', ...
'cs616SWC_open_2_10', 'cs616SWC_open_2_20', ...
'cs616SWC_open_2_40', 'cs616SWC_edge_1_5', ...
'cs616SWC_edge_1_10', 'cs616SWC_edge_1_20', ...
'cs616SWC_edge_1_40', 'cs616SWC_canopy_1_5', ...
'cs616SWC_canopy_1_10', 'cs616SWC_canopy_1_20', ...
'cs616SWC_canopy_1_40' };
cs616_descriptive_labels_postJul09 = { 'cs616SWC_juniper_1_2p5', ...
'cs616SWC_juniper_1_12p5', ...
'cs616SWC_juniper_1_32p5', 'cs616SWC_juniper_2_2p5', ...
'cs616SWC_juniper_2_12p5', ...
'cs616SWC_juniper_2_32p5', 'cs616SWC_juniper_3_2p5', ...
'cs616SWC_juniper_3_12p5', ...
'cs616SWC_juniper_3_32p5', 'cs616SWC_open_1_2p5', ...
'cs616SWC_open_1_12p5', 'cs616SWC_open_1_32p5', ...
'cs616SWC_open_2_2p5', 'cs616SWC_open_2_12p5', ...
'cs616SWC_open_2_32p5', 'cs616SWC_open_3_2p5', ...
'cs616SWC_open_3_12p5', 'cs616SWC_open_3_32p5' };
switch year
case 2007
% It doesn't appear from the TOA5 files that there were any
% soil measurements at the site prior to 8/31/2007. Between this
% date and 2/25/2008 there were 28 Tsoil sensors, which was then
% reduced to 20 Tsoil sensors. 16 VWC sensors were installed on
% 8/31/2007, and these were renamed (but not changed)
% on 2/25/2008. -- GEM
vars = fluxall.Properties.VarNames;
[ ~, idx_cs616 ] = regexp_header_vars( fluxall, 'VWC.*' );
if ~isempty(idx_cs616)
vars( idx_cs616 ) = cs616_descriptive_labels_preJul09;
end
%soil T
[ ~, idx_Tsoil ] = regexp_header_vars( fluxall, '[sS]oilT_' );
% Ensure that the mid-2007 change is ok, but these may be
% the wrong labels for pre-2/25/2007 sensors entirely. --GEM
if length(idx_Tsoil) > length(soilT_descriptive_labels_2008)
idx_Tsoil = idx_Tsoil(1:length(soilT_descriptive_labels_2008));
end
if ~isempty( idx_Tsoil )
vars( idx_Tsoil ) = soilT_descriptive_labels_2008;
end
warning( 'temperature data not yet labeled for JSav 2007' );
case 2008
vars = fluxall.Properties.VarNames;
[ ~, idx_cs616 ] = regexp_header_vars( fluxall, 'cs616.*' );
vars( idx_cs616 ) = cs616_descriptive_labels_preJul09;
%soil T
[ ~, idx_Tsoil ] = regexp_header_vars( fluxall, '[sS]oilT_' );
if ~isempty( idx_Tsoil )
vars( idx_Tsoil ) = soilT_descriptive_labels_2008;
end
%TCAV
[ ~, idx_TCAV ] = regexp_header_vars( fluxall, 'TCAV' );
if ~isempty( idx_TCAV )
vars( idx_TCAV ) = replace_hex_chars( vars( idx_TCAV ) );
vars( idx_TCAV ) = format_probe_strings( vars( idx_TCAV ) );
end
fluxall.Properties.VarNames = vars;
case 2009
% there was a major SWC instrument changeover on 9 Jul 2009. In the
% 2009 Fluxall file, some columns appear to have data from one
% instrument prior to 9 July, and from another after 9 July. These
% columns appear to have two headers at the top, one for each
% instrument. --TWH
vars = fluxall.Properties.VarNames;
%CS616 SWC probes
[ ~, idx_cs616 ] = regexp_header_vars( fluxall, 'cs616.*' );
if not( isempty( idx_cs616 ) )
vars( idx_cs616 ) = regexprep( vars( idx_cs616 ), ...
'cs616_', 'cs616SWC_' );
vars( idx_cs616 ) = replace_hex_chars( vars( idx_cs616 ) );
vars( idx_cs616 ) = format_probe_strings( vars( idx_cs616 ) );
end
%soil T
[ ~, idx_Tsoil ] = regexp_header_vars( fluxall, '[sS]oilT_' );
if ~isempty( idx_Tsoil )
vars( idx_Tsoil ) = regexprep( vars( idx_Tsoil ), ...
'[sS]oilT', 'soilT' );
vars( idx_Tsoil ) = regexprep( vars( idx_Tsoil ), '_Avg$', '' );
vars( idx_Tsoil ) = replace_hex_chars( vars( idx_Tsoil ) );
vars( idx_Tsoil ) = format_probe_strings( vars( idx_Tsoil ) );
end
%TCAV
[ ~, idx_TCAV ] = regexp_header_vars( fluxall, 'TCAV' );
if ~isempty( idx_TCAV )
vars( idx_TCAV ) = replace_hex_chars( vars( idx_TCAV ) );
vars( idx_TCAV ) = format_probe_strings( vars( idx_TCAV ) );
end
fluxall.Properties.VarNames = genvarname( vars );
case { 2010, 2011, 2012, 2013 } %RJL added 2013 02/04/2014
% echo SWC probes
vars = fluxall.Properties.VarNames;
[ ~, idx_echo ] = regexp_header_vars( fluxall, 'SWC.*' );
vars( idx_echo ) = strrep( vars( idx_echo ), 'SWC', 'echoSWC' );
vars( idx_echo ) = replace_hex_chars( vars( idx_echo ) );
vars( idx_echo ) = format_probe_strings( vars( idx_echo ) );
%CS616 SWC probes
[ ~, idx_cs616 ] = regexp_header_vars( fluxall, 'cs616.*' );
if not( isempty( idx_cs616 ) )
vars( idx_cs616 ) = cs616_descriptive_labels_postJul09;
vars( idx_cs616 ) = replace_hex_chars( vars( idx_cs616 ) );
vars( idx_cs616 ) = format_probe_strings( vars( idx_cs616 ) );
end
%soil T
[ ~, idx_Tsoil ] = regexp_header_vars( fluxall, 'SoilT_' );
if ~isempty( idx_Tsoil )
vars( idx_Tsoil ) = regexprep( vars( idx_Tsoil ), ...
'SoilT', 'soilT' );
vars( idx_Tsoil ) = regexprep( vars( idx_Tsoil ), '_Avg', '' );
vars( idx_Tsoil ) = replace_hex_chars( vars( idx_Tsoil ) );
vars( idx_Tsoil ) = format_probe_strings( vars( idx_Tsoil ) );
end
%TCAV
[ ~, idx_TCAV ] = regexp_header_vars( fluxall, 'TCAV' );
if ~isempty( idx_TCAV )
vars( idx_TCAV ) = replace_hex_chars( vars( idx_TCAV ) );
vars( idx_TCAV ) = format_probe_strings( vars( idx_TCAV ) );
end
% soil heat flux
[ ~, idx_shf ] = regexp_header_vars( fluxall, 'shf' );
if ~isempty( idx_shf )
vars( idx_shf ) = replace_hex_chars( vars( idx_shf ) );
vars( idx_shf ) = format_probe_strings( vars( idx_shf ) );
end
fluxall.Properties.VarNames = vars;
end % switch JSav year
% --------------------------------------------------
case UNM_sites.PJ
% note that PJ and PJ girdle do not report soil moisture or soil T in
% their FluxAll files (except for 2008 ), so their soil data are parsed separately.
switch year
case 2008
[ ~, idx_echo ] = regexp_header_vars( fluxall, 'echo.*' );
swc_vars = arrayfun( @(x) { sprintf( 'echoSWC_%d', x ) }, ...
1:numel( idx_echo ) );
fluxall.Properties.VarNames( idx_echo ) = swc_vars;
fluxall.Properties.VarNames( idx_echo ) = ...
strrep( fluxall.Properties.VarNames( idx_echo ), ...
'SWC', 'echoSWC' );
end
TCAV_labels.labels = { 'TCAV_pinon_1_Avg', 'TCAV_juniper_1_Avg' };
% --------------------------------------------------
case UNM_sites.PPine
% PPine soil water content is in another file, parsed separately from
% UNM_Ameriflux_prepare_soil_met.m
switch year
case { 2009, 2010, 2011 }
[ ~, idx_soilT ] = regexp_header_vars( fluxall, 'T107.*' );
if isempty( idx_soilT )
[ ~, idx_soilT ] = regexp_header_vars( fluxall, 'soilT.*' );
if isempty( idx_soilT )
error( ['no soil temperature found (expecting ' ...
'soilT_ponderosa_X_Y'] );
end
else
fluxall.Properties.VarNames( idx_soilT ) = ...
{ 'soilT_ponderosa_1_5', ...
'soilT_ponderosa_2_5', ...
'soilT_ponderosa_3_5', ...
'soilT_ponderosa_4_5', ...
'soilT_ponderosa_5_5', ...
'soilT_ponderosa_6_5', ...
'soilT_ponderosa_7_5', ...
'soilT_ponderosa_8_5', ...
'soilT_ponderosa_9_5', ...
'soilT_ponderosa_10_5', ...
'soilT_ponderosa_11_5', ...
'soilT_ponderosa_12_5' };
end
[ ~, idx_TCAV ] = regexp_header_vars( fluxall, 'TCAV.*' );
if ~isempty( idx_TCAV )
fluxall.Properties.VarNames{ idx_TCAV } = 'TCAV_ponderosa_1';
end
end
case UNM_sites.MCon
% MCon soil water content is in another file, parsed separately from
% UNM_Ameriflux_prepare_soil_met.m
[ ~, idx_soilT ] = regexp_header_vars( fluxall, 'T107.*' );
if not( isempty( idx_soilT ) )
fluxall.Properties.VarNames( idx_soilT ) = ...
{ 'soilT_mcon_1_5', ...
'soilT_mcon_2_5', ...
'soilT_mcon_3_5', ...
'soilT_mcon_4_5' };
end
[ ~, idx_TCAV ] = regexp_header_vars( fluxall, 'TCAV.*' );
if ~isempty( idx_TCAV )
fluxall.Properties.VarNames{ idx_TCAV } = 'TCAV_mcon_1';
end
case UNM_sites.New_GLand % unburned grass
[ ~, idx_cs616 ] = regexp_header_vars( fluxall, '(Soilwcr.*|cs616.*)' );
swc_vars = fluxall.Properties.VarNames( idx_cs616 );
swc_vars = strrep( swc_vars, 'Soilwcr', 'cs616SWC' );
swc_vars = replace_hex_chars( swc_vars );
swc_vars = format_probe_strings( swc_vars );
fluxall.Properties.VarNames( idx_cs616 ) = swc_vars;
[ ~, idx_soilT ] = regexp_header_vars( fluxall, 'SoilT.*' );
T_vars = fluxall.Properties.VarNames( idx_soilT );
T_vars = regexprep( T_vars, 'SoilT', 'soilT' );
T_vars = regexprep( T_vars, '_Avg$', '' );
T_vars = replace_hex_chars( T_vars );
T_vars = format_probe_strings( T_vars );
fluxall.Properties.VarNames( idx_soilT ) = T_vars;
vars = fluxall.Properties.VarNames;
[ ~, idx_TCAV ] = regexp_header_vars( fluxall, 'TCAV' );
vars( idx_TCAV ) = regexprep( vars( idx_TCAV ), '_Avg', '_1' );
fluxall.Properties.VarNames = vars;
end
%==================================================