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2945 lines (2904 loc) · 127 KB
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classdef csr
%static
properties(Constant)
arc_timeline_file=[getenv('HOME'),'/data/csr/GraceAccCal/arctimeline.GraceAccCal'];
estim_dir_root=[getenv('HOME'),'/data/csr/EstimData/RL05'];
estimdir_file=[csr.estim_dir_root,'/EstimDirs_RL05'];
%calpar_meaning is used to connect with constant, linear, quadratic time functions; therefore, it have the same length as calpar_suffixes
calpar_suffixes={ '', 'D', 'Q'};
calpar_meaning= {'const','linear','quad'}; %these need to be in agreement with what is defined in csr.arc_apply_meaning
%define correspondence between coordinates and columns
calpar_coords= {'X','Y','Z','XY','XZ','YZ','YX','ZX','ZY'};
calpar_col_idx=[ 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 ]; %defines which columns get to have the corresp calpar (biases or scales)
% calpar_mat_idx=[ 1 , 4 , 5 ; 7 , 2 , 6 ; 8 , 9 , 3 ]; %maps a 1x9 vector into a 3x3 matrix, calpar_coords(calpar_mat_idx) should be pretty
calpar_mat_idx=[ 1 , 7 , 8 ; 4 , 2 , 9 ; 5 , 6 , 3 ]; %maps a 1x9 vector into a 3x3 matrix, calpar_coords(calpar_mat_idx) should be pretty
%define the names of the types of calpars and their corresponding codeword prefix
calpar_names = {'bias','scale'};
calpar_prefixes={'AC0' ,'AC1' };
calpar_max_col =[ 3 , 9 ];
%define default grace names
grace_sats={'A','B'};
end
methods(Static)
%% utilities
function timetag=gitversion
%get current git version
[status,timetag]=system(['git -C ',fileparts(which(mfilename)),' log -1 --format=%cd --date=iso-local ',mfilename,'.m']);
%get rid of timezone and leading trash
timetag=timetag(9:27);
%sanity
assert(status==0,[mfilename,': could not determine git time tag'])
end
function log(msg)
logname=fullfile(fileparts(mfilename),'log','import_calpar.log');
if ~exist('msg','var')
if file.exist(logname)
system(['mv -v ',logname,' ',strrep(logname,'.log',''),'.',datestr(datetime('now'),30),'.log']);
end
else
fid = file.open(logname,'a');
fprintf(fid,[strjoin(msg,'\n'),'\n']);
fclose(fid);
end
end
function report(debug,idx,context,id,labels,data,log_flag)
if ~exist('log_flag','var') ||isempty(log_flag)
log_flag=true;
end
if isempty(idx); return; end
[~,ids]=fileparts(id);
if isempty(ids); ids=id; end
msg=cell(1,numel(idx)+2);
msg{1}=str.tablify([36,30,1,5],[context,' for'],ids,':',num2str(numel(idx)));
msg{2}=str.tablify(20,'data','idx',labels{:});
for k=1:numel(idx)
msg_data=cell(1,numel(data));
for l=1:numel(data)
switch numel(data{l})
case 1
msg_data{l}=data{l};
case numel(idx)
msg_data{l}=data{l}(k);
otherwise
msg_data{l}=data{l}(idx(k));
end
end
msg{k+2}=str.tablify(20,ids,idx(k),msg_data{:});
end
if debug;disp(strjoin(msg(1:min([20,numel(msg)])),'\n')); else disp(msg{1}); end;
if log_flag;csr.log(msg);end
end
%% debugging
function out=debug_parameters
%define start/stop pairs and level
i=0;out=struct([]);
% i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
% out(i).start=datetime('2002-04-15 00:00:00'); out(i).stop=out(i).start+days(1)-seconds(1);
% i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
% out(i).start=datetime('2002-04-27 00:00:00'); out(i).stop=out(i).start+days(1)-seconds(1);
% i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
% out(i).start=datetime('2002-05-04 00:00:00'); out(i).stop=out(i).start+days(1)-seconds(1);
% i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
% out(i).start=datetime('2002-05-11 00:00:00'); out(i).stop=out(i).start+days(1)-seconds(1);
% i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
% out(i).start=datetime('2002-05-16 00:00:00'); out(i).stop=out(i).start+days(1)-seconds(1);
% i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
% out(i).start=datetime('2002-08-03 00:00:00'); out(i).stop=out(i).start+days(1)-seconds(1);
% i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
% out(i).start=datetime('2002-08-06 00:00:00'); out(i).stop=out(i).start+days(1)-seconds(1);
% i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
% out(i).start=datetime('2002-08-16 00:00:00'); out(i).stop=out(i).start+days(2)-seconds(1);
% i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
% out(i).start=datetime('2002-08-26 00:00:00'); out(i).stop=out(i).start+days(1)-seconds(1);
% i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
% out(i).start=datetime('2002-09-07 00:00:00'); out(i).stop=out(i).start+days(1)-seconds(1);
% i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
% out(i).start=datetime('2002-09-28 00:00:00'); out(i).stop=out(i).start+days(1)-seconds(1);
% i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
% out(i).start=datetime('2002-09-30 00:00:00'); out(i).stop=out(i).start+days(1)-seconds(1);
% i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
% out(i).start=datetime('2003-01-12 00:00:00'); out(i).stop=datetime('2003-01-15 23:59:59');
% i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
% out(i).start=datetime('2003-11-20 00:00:00'); out(i).stop=out(i).start+days(1)-seconds(1);
% i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
% out(i).start=datetime('2003-11-21 00:00:00'); out(i).stop=out(i).start+days(1)-seconds(1);
% i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
% out(i).start=datetime('2003-11-29 00:00:00'); out(i).stop=datetime('2003-12-02 23:59:59');
i=i+1; out(i).field={'AC0X','AC0Y','AC0Z','AC0XD','AC0YD','AC0ZD','AC0XQ','AC0YQ','AC0ZQ'};
out(i).start=datetime('2006-06-03 00:00:00'); out(i).stop=datetime('2006-06-07 23:59:59');
i=i+1; out(i).field={'AC0X','AC0Y','AC0Z','AC0XD','AC0YD','AC0ZD','AC0XQ','AC0YQ','AC0ZQ'};
out(i).start=datetime('2006-06-12 00:00:00'); out(i).stop=datetime('2006-06-19 23:59:59');
i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
out(i).start=datetime('2008-02-24 00:00:00'); out(i).stop=out(i).start+days(1)-seconds(1);
i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
out(i).start=datetime('2008-02-25 00:00:00'); out(i).stop=out(i).start+days(1)-seconds(1);
i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
out(i).start=datetime('2012-06-30 00:00:00'); out(i).stop=datetime('2012-07-03 23:59:59');
i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
out(i).start=datetime('2013-02-20 00:00:00'); out(i).stop=datetime('2013-02-26 23:59:59');
i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
out(i).start=datetime('2014-08-01 00:00:00'); out(i).stop=out(i).start+days(2)-seconds(1);
i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
out(i).start=datetime('2014-09-13 00:00:00'); out(i).stop=out(i).start+days(2)-seconds(1);
i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
out(i).start=datetime('2015-08-14 00:00:00'); out(i).stop=out(i).start+days(1)-seconds(1);
i=i+1; out(i).field={'AC0X','AC0Y','AC0Z'};
out(i).start=datetime('2017-01-07 00:00:00'); out(i).stop=out(i).start+days(3)-seconds(1);
end
function out=debug_plots(mode,debug,plot_dir)
if ~exist('debug','var') || isempty(debug)
debug=true;
end
if ~exist('mode','var') || isempty(mode)
mode='import_calpar';
end
if ~exist('plot_dir','var') || isempty(plot_dir)
plot_dir=fullfile(plot_dir,['debug_plots_',mode],csr.gitversion);
end
%create dir for plots
if ~exist(plot_dir,'dir'); file.mkdir(plot_dir); end
%get dates of plots
ssl=csr.debug_parameters;
%outputs
out=cell(size(ssl));
%additional arguments
args={};
%branch on mode
switch mode
case 'all'
for i={'import_calpar','compute_calmod','calpar','calpar-gps'}
csr.debug_plots(i{1});
close all
end
%done
return
case 'import_calpar'
name='grace.calpar.csr';
%load calibration parameters
out=datastorage('debug',debug).init(name,'plot_dir',plot_dir);
%retrieve product info
sats=out.product_get(name).mdget('sats');
%loop over the data
for i=1:numel(ssl)
p=out.trim('start',ssl(i).start,'stop',ssl(i).stop);
for f=1:numel(ssl(i).field)
for s=1:numel(sats)
p.plot(...
datanames(name).set_field_path({'*',ssl(i).field{f},sats{s}}),...
'plot_together',{'aak','accatt','estim'}...
);
end
end
end
%done
return
case 'calpar-gps'
start=datetime('2017-01-01');
stop =datetime('2017-01-02');
out=datastorage('start',start,'stop',stop,'debug',debug);
for p={'grace.acc.l1b.csr','grace.acc.calmod.csr','grace.acc.cal.csr','grace.acc.mod.nrtdm','grace.acc.mod.csr'}
out=out.init(p{1});
end
%done
return
case 'calpar'; name='grace.acc.cal.csr.plots';
case 'compute_calmod'; name='grace.acc.calmod.csr'; args={'debug_plot',true};
case 'estimate_poly_calmod'; name='grace.acc.cal.poly0.plots';
case 'psd'; name='grace.acc.psd.plots';
otherwise
error(['unknown mode ''',mode,'''.'])
end
for i=1:numel(ssl)
out{i}=datastorage('start',ssl(i).start,'stop',ssl(i).stop,'debug',debug).init(name,'plot_dir',plot_dir,args{:});
end
end
function out=test(mode,start)
if ~exist('mode','var') || isempty(mode)
mode='poly_calmod';
mode='calpar';
end
if ~exist('start','var') || isempty(start)
% start=datetime('2008-02-26');
start=datetime('2002-04-15');
end
stop =start+days(1)-seconds(1);
%translate modes to metadata names
switch mode
case 'calpar'; name='grace.calpar.csr';
case 'import_l1b'; name='grace.acc.l1b.csr';
case 'calmod'; name='grace.acc.calmod.csr';
case 'mod'; name='grace.acc.mod.csr';
case 'nrtdm'; name='grace.acc.mod.nrtdm';
case 'calacc'; name='grace.acc.cal.csr';
case 'poly_calmod'; name='grace.acc.calmod.poly0';
otherwise
error(['unknown mode ''',mode,'''.'])
end
out=datastorage('debug',true,'start',start,'stop',stop).init(name,'recompute',true);
out.peek
end
%% long-term biases
function out=ltb_data(filename)
%original:
% 52640.00
% -0.54818E-06 -0.24827E-10
% 0.86557E-05 0.17811E-08
% -0.77612E-06 0.49781E-10
%internal:
% MJD AC0X AC0Y* AC0Z
% 0 -0.24827E-10 0.17811E-08 0.49781E-10 %linear term
% 52640.00 -0.54818E-06 0.86557E-05 -0.77612E-06 %contant term
out=flipud(transpose(dlmread(filename)));
end
function out=ltb_args(i)
out=varargs({
'field', 'all', @(i) ischar(i) && ~isempty(i);...
'ltb_scale', 1, @(i) num.isscalar(i) && ~isempty(i);...
'sat', 'A', @(i) ischar(i) && ~isempty(i);...
'bias_files', {...
[getenv('HOME'),'/data/csr/corral-tacc/input/bsA2003'],...
[getenv('HOME'),'/data/csr/corral-tacc/input/bsB2003']...
}, @(i) iscellstr(i) && numel(i)==2; ...
});
if exist('i','var') && ~isempty(i)
out=out.(i);
end
end
function out=ltb(varargin)
v=varargs.wrap('sources',{...
{...
't', datetime('now'),@(i) isdatetime(i) && ~isempty(i);...
},...
csr.ltb_args...
},varargin{:});
%resolve bias files
switch v.sat
case 'A'; bias_file=v.bias_files{1};
case 'B'; bias_file=v.bias_files{2};
otherwise; error(['Unknown sat ''',v.sat,'''.'])
end
%translate field to data index
switch upper(v.field)
case {'X','AC0X'}
lbt_idx=2;
case {'Y','AC0Y1','AC0Y2','AC0Y3','AC0Y4','AC0Y5','AC0Y6','AC0Y7','AC0Y8'}
lbt_idx=3;
case {'Z','AC0Z'}
lbt_idx=4;
case {'ALL','-ALL','RESTORE','REMOVE'}
%if mode is '-all', then "remove" the long-term bias
if any(strcmpi(v.field,{'-ALL','REMOVE'}));v.ltb_scale=-v.ltb_scale;end
x=csr.ltb(v.varargin{:},'field','x');
y=csr.ltb(v.varargin{:},'field','y');
z=csr.ltb(v.varargin{:},'field','z')';
out=x.glue(...
y.glue(....
z));
out.descriptor=['LTB read from ',str.clean(bias_file,'file')];
return
otherwise
out=[];
return
end
%get the data
ltb_data=csr.ltb_data(bias_file);
%number of day since reference epoch (in the ltb file)
d=time.mjd(v.t)-ltb_data(2,1);
%create timeseries object
out=simpletimeseries(...
v.t,...
v.ltb_scale*polyval(ltb_data(:,lbt_idx),d),...
'format','datetime',...
'timesystem','gps',...
'labels',{v.field},...
'units',{'m/s^2'},...
'descriptor',[v.field,' LTB read from ',str.clean(bias_file,'file')]...
);
end
function out=ltb_apply(varargin)
v=varargs.wrap('sources',{...
{...
'ts', [], @(i) isa(i,'simpletimeseries') && ~isempty(i);...
},...
csr.ltb_args...
},varargin{:});
%get long-term biases
ltb=csr.ltb('t',v.ts.t,v.varargin{:});
%add long-term biases (unless ltb is empty, which means this field had no ltb)
if isempty(ltb)
out=v.ts;
else
%NOTICE: this was previously, but it doesn't really make sense and can be confusing
%out=v.ts.scale(v.calpar_scale)+ltb;
assert(~v.isparameter('calpar_scale'),'BUG TRAP: ''calpar_scale'' is no longer supported!')
%add LTB
out=v.ts+ltb;
end
end
%% importers
function obj=import_calpar_slow(obj,product,varargin)
%open log file
csr.log
% add input arguments and metadata to collection of parameters 'v'
v=varargs.wrap('sources',{...
{...
'debugdate', [], @(i) ischar(i) || isempty(i);
},...
csr.ltb_args,...
product.args...
},varargin{:});
%load data
for i=1:numel(v.levels)
for j=1:numel(v.calpars)
tmp=struct('A',[],'B',[]);
for s=1:numel(v.sats)
%read L1B data
f=fullfile(v.import_dir,['gr',v.sats{s},'.',v.calpars{j},'.',v.levels{i},'.GraceAccCal']);
tmp.(v.sats{s})=simpletimeseries.import(f,'cut24hrs',false);
%apply long-term bias
tmp.(v.sats{s})=tmp.(v.sats{s}).set_cols(v.param_col,...
csr.ltb_apply(v.varargin{:},...
'ts',tmp.(v.sats{s}).get_cols(v.param_col),...
'sat',v.sats{s},...
'field',v.calpars{s}...
)...
);
%additional processing: add end of arcs
switch v.levels{i}
case {'aak','accatt'}
error('Needs implementation')
case 'estim'
%get arc stars
arc_starts=tmp.(v.sats{s}).t;
%build arc ends (arc duration given explicitly)
arc_ends=arc_starts+seconds(tmp.(v.sats{s}).y(:,v.arclen_col))-seconds(1);
%patch missing arc durations
idx=find(isnat(arc_ends));
%report edge cases
csr.report(obj.debug,idx,'Arcs without arc length',f,...
{'arc start','arc duraction'},...
{arc_starts, tmp.(v.sats{s}).y(:,v.arclen_col)}...
)
%fix it
if ~isempty(idx);
arc_ends(idx)=dateshift(arc_starts(idx),'end','day')-seconds(1);
end
end
%bug trap
assert(all(~isnat(arc_starts)),...
[mfilename,': found NaT in the arc starts'])
%compute arc day start and end
day_starts=dateshift(arc_starts,'start','day');
day_ends =dateshift(arc_starts,'end', 'day');
%arc ends cannot go over day boundaries
idx=find(arc_ends>=day_ends);
csr.report(obj.debug,idx,'Arc ends over day boundary',f,...
{'curr arc start','curr arc end','day ends'},...
{ arc_starts, arc_ends, day_ends}...
)
%fix it
if ~isempty(idx)
arc_ends(idx)=day_ends(idx)-seconds(1);
end
%bug trap
assert(all(~isnat(arc_ends)),...
[mfilename,': found NaT in the arc starts/ends'])
%surpress over-lapping arcs
idx=find(arc_starts(2:end)-arc_ends(1:end-1)<0);
csr.report(obj.debug,idx,'Over-lapping arcs',f,...
{'curr arc start','curr arc end','next arc start'},...
{ arc_starts, arc_ends, [arc_starts(2:end);arc_starts(1)]}...
)
%fix it
if ~isempty(idx)
arc_ends(idx)=arc_starts(idx+1)-seconds(1);
end
%fancy stuff: handle parameters defined as arc segments
if ~isempty(strfind(v.calpars{j},'AC0Y'))
%there are 8 segments per day
periodicity=days(1)/8;
%get day location for this parameter
day_loc=str2double(v.calpars{j}(end));
%get sub-arc starts/ends
sub_arc_starts=arc_starts+periodicity*(day_loc-1);
sub_arc_ends=arc_starts+periodicity*(day_loc )-seconds(1);
%get sub arc boundaries
sub_arc_bound_starts=max([arc_starts,day_starts],[],2);
sub_arc_bound_ends =min([arc_ends, day_ends ],[],2);
%cap sub-arc start/ends to be within the current day
idx={...
find( sub_arc_starts>sub_arc_bound_ends ),...
find( sub_arc_starts<sub_arc_bound_starts ),...
find( sub_arc_ends >sub_arc_bound_ends ),...
find( sub_arc_ends <sub_arc_bound_starts )...
};
msg={...
'Sub-arc starts after day/arc ends',...
'Sub-arc starts before day/arc starts',...
'Sub-arc ends after day/arc ends',...
'Sub-arc ends before day/arc starts'...
};
for k=1:numel(idx)
csr.report(obj.debug,idx{k},msg{k},f,...
{'sub-arc start','sub-arc end','day start','day end'},...
{ sub_arc_starts, sub_arc_ends, day_starts, day_ends}...
)
%fix it
if ~isempty(idx{k})
switch k
case 1; sub_arc_starts(idx{k})=sub_arc_bound_ends( idx{k});
case 2; sub_arc_starts(idx{k})=sub_arc_bound_starts(idx{k});
case 3; sub_arc_ends( idx{k})=sub_arc_bound_ends( idx{k});
case 4; sub_arc_ends( idx{k})=sub_arc_bound_starts(idx{k});
end
end
end
%propagate the arc extremeties
arc_starts=sub_arc_starts;
arc_ends=sub_arc_ends;
end
%propagate data
arc_start_y=tmp.(v.sats{s}).y;
arc_end_y=tmp.(v.sats{s}).y;
%remove arcs with zero length (only applicable to AC0Y*2-8)
zero_len_idx=find(arc_ends-arc_starts<=0);
csr.report(obj.debug,zero_len_idx,'Non-positive arc length',f,...
{'arc start','arc end','arc_length'},...
{ arc_starts, arc_ends, arc_ends-arc_starts}...
)
if ~isempty(zero_len_idx)
good_idx=(arc_ends-arc_starts>0);
arc_starts =arc_starts( good_idx);
arc_ends =arc_ends( good_idx);
arc_start_y=arc_start_y(good_idx,:);
arc_end_y =arc_end_y( good_idx,:);
end
%debug date report
if ~isempty(v.debugdate)
rep_date=datetime(v.debugdate);
rep_delta=arc_starts-rep_date;
rep_idx=find(abs(rep_delta)==min(abs(rep_delta)));
rep_idx=(rep_idx(1)-8):(rep_idx(end)+8);
csr.report(true,rep_idx,['DEBUG DATE: Arcs around ',datestr(rep_date)],f,...
{'arc start','arc end','arc length','inter-arc gap'},...
{arc_starts(rep_idx ),arc_ends( rep_idx),...
arc_ends( rep_idx )-arc_starts(rep_idx),...
arc_starts(rep_idx+1)-arc_ends( rep_idx)...
},...
false)
end
%build timeseries with arc starts
arc_start_ts=simpletimeseries(arc_starts,arc_start_y,...
'format','datetime',...
'labels',tmp.(v.sats{s}).labels,...
'units',tmp.(v.sats{s}).y_units,...
'timesystem',tmp.(v.sats{s}).timesystem,...
'descriptor',tmp.(v.sats{s}).descriptor...
);
%build timeseries with arc ends
arc_end_ts=simpletimeseries(arc_ends,arc_end_y,...
'format','datetime',...
'labels', tmp.(v.sats{s}).labels,...
'units', tmp.(v.sats{s}).y_units,...
'timesystem',tmp.(v.sats{s}).timesystem,...
'descriptor',['end of arcs for ',tmp.(v.sats{s}).descriptor]...
);
%augment arc starts with arc ends (only new data)
tmp.(v.sats{s})=arc_start_ts.augment(arc_end_ts,'old',true);
end
%propagate data to object
for s=1:numel(v.sats)
obj=obj.data_set(product.dataname.set_field_path([v.levels(i),v.calpars(j),v.sats(s)]),tmp.(v.sats{s}));
end
%user feedback
str.say(str.tablify([15,6,3,6],'loaded data for',v.levels{i},'and',v.calpars{j}))
end
end
%merge cross-track accelerations together
ac0y='AC0Y';
field_part_list={'','D','Q'};
%loop over all levels and sats
for i=1:numel(v.levels)
for s=1:numel(v.sats)
for f=1:numel(field_part_list)
%start with first field
calpar=[ac0y,field_part_list{f},'1'];
ts_now=obj.data_get_scalar(product.dataname.set_field_path([v.levels(i),calpar,v.sats(s)]));
%rename the relevant object fields to remove the '1'
ts_now.labels=strrep(ts_now.labels,calpar,[ac0y,field_part_list{f}]);
ts_now.descriptor=strrep(ts_now.descriptor,calpar,[ac0y,field_part_list{f},'[1-8]']);
%loop over all other calpars
for fpl=2:8
calpar=[ac0y,field_part_list{f},num2str(fpl)];
ts_now=ts_now.augment(...
obj.data_get_scalar(product.dataname.set_field_path([v.levels(i),calpar,v.sats(s)])),...
'quiet',true,...
'old',true,...
'skip_gaps',true...
);
%debug date report
if ~isempty(v.debugdate)
rep_date=datetime(v.debugdate);
str.say('DEBUG DATE: merge AC0Y*:',v.levels{i},':',v.sats{s},':',calpar,' @ ',datestr(rep_date));
idx=ts_now.idx(rep_date);
ts_now.peek((idx-10):(idx+10));
end
end
%save the data
obj=obj.data_set(product.dataname.set_field_path([v.levels(i),{[ac0y,field_part_list{f}]},v.sats(s)]),ts_now);
%user feedback
str.say(str.tablify([29,5,3,6,3,7],'merged cross-track parameter',[ac0y,field_part_list{f}],...
'for',v.levels{i},'and',['GRACE-',v.sats{s}]))
end
end
end
%add gaps
for i=1:numel(v.levels)
for j=1:numel(v.calpars_out)
for s=1:numel(v.sats)
ts_now=obj.data_get_scalar(product.dataname.set_field_path([v.levels(i),v.calpars_out(j),v.sats(s)]));
%debug date report
if ~isempty(v.debugdate)
rep_date=datetime(v.debugdate);
str.say('DEBUG DATE: w/out gaps:',v.levels{i},':',v.sats{s},':',v.calpars_out{j},' @ ',datestr(rep_date));
idx=ts_now.idx(rep_date);
ts_now.peek((idx-10):(idx+10));
end
%get end of arcs and non-consecutive time indexes
end_arc_idx=[false;diff(ts_now.y(:,1))==0];
gap_idx=[diff(ts_now.t)>seconds(1)+ts_now.t_tol;false];
%extend calibration parameters into the gap
gap_start_idx=find(end_arc_idx & gap_idx);
gap_stop_idx=gap_start_idx+1;
% ext_len=minutes(10);
% extension=min( ts_now.t(gap_stop_idx)-ts_now.t(gap_start_idx),ext_len*ones(size(gap_start_idx))*2 )/2;
extension=ts_now.t(gap_stop_idx)-ts_now.t(gap_start_idx);
ts_now.t(gap_start_idx)=ts_now.t(gap_start_idx)+time.round_seconds(extension/2);
ts_now.t(gap_stop_idx )=ts_now.t(gap_start_idx)+seconds(1);
%build timeseries with arc ends
gap_t=ts_now.t(gap_start_idx)+seconds(1);
gaps=simpletimeseries(gap_t,nan(numel(gap_t),ts_now.width),...
'format','datetime',...
'labels',ts_now.labels,...
'units',ts_now.y_units,...
'timesystem',ts_now.timesystem,...
'descriptor',['gaps for ',ts_now.descriptor]...
);
%augment (keep it separate from saving, so that date report works as expected)
ts_now=ts_now.augment(gaps,'old',true,'new',true);
%debug date report
if ~isempty(v.debugdate)
rep_date=datetime(v.debugdate);
str.say('DEBUG DATE: with gaps:',v.levels{i},':',v.sats{s},':',v.calpars_out{j},' @ ',datestr(rep_date));
idx=ts_now.idx(rep_date);
ts_now.peek((idx-10):(idx+10));
end
%save
obj=obj.data_set(product.dataname.set_field_path([v.levels(i),v.calpars_out(j),v.sats(s)]),ts_now);
end
end
end
%loop over all sat and level to check Job IDs agreement across all output calpars
for i=1:numel(v.levels)
for s=1:numel(v.sats)
for j=1:numel(v.calpars_out)-1
dn1=product.dataname.set_field_path([v.levels(i),v.calpars_out(j ),v.sats(s)]);
dn2=product.dataname.set_field_path([v.levels(i),v.calpars_out(j+1),v.sats(s)]);
d1=obj.data_get_scalar(dn1);
d2=obj.data_get_scalar(dn2);
[~,i1,i2]=intersect(d1.t,d2.t);
bad_idx=find(...
d1.y(i1,v.jobid_col) ~= d2.y(i2,v.jobid_col) & ...
d1.mask(i1) & ...
d2.mask(i2) ...
);
if ~isempty(bad_idx)
n=numel(bad_idx);
msg=cell(1,2*n+2);
msg{1}=str.tablify([5,6,24],'found',numel(bad_idx),'Job ID inconsistencies:');
msg{2}=str.tablify([30,6,20,12],'data name','idx','t','Job ID');
for k=1:n
idx=i1(bad_idx(k));
msg{2*k+1}=str.tablify([30,6,20,12],dn1,idx,d1.t(idx),num2str(d1.y(idx,v.jobid_col),'%i'));
idx=i2(bad_idx(k));
msg{2*k+2}=str.tablify([30,6,20,12],dn2,idx,d2.t(idx),num2str(d2.y(idx,v.jobid_col),'%i'));
end
error([mfilename,':',strjoin(msg,'\n')])
end
end
end
end
%loop over all sats, levels and calpars to:
% - in case of estim: ensure that there are no arcs with lenghts longer than consecutive time stamps
% - in case of aak and accatt: ensure that the t0 value is the same as the start of the arc
for s=1:numel(v.sats)
%loop over all required levels
for i=1:numel(v.levels)
switch v.levels{i}
case 'estim'
%this check ensures that there are no arcs with lenghts longer than consecutive time stamps
for j=1:numel(v.calpars_out)
%some calpars do not have t0
if ~any(v.calpars_out{j}(end)=='DQ') || ~isempty(strfind(v.calpars_out{j},'Y'))
str.say(str.tablify([8,32],'Skipping',product.str))
continue
end
str.say(str.tablify([8,32],'Checking',product.str))
%save time series into dedicated var
ts_now=obj.data_get_scalar(product.dataname.set_field_path([v.levels(i),v.calpars_out(j),v.sats(s)]));
%forget about epochs that have been artificially inserted to represent gaps and end of arcs
%the 1e-6 parcel is needed to avoid artificially-inserted gaps that have round-off errors
idx1=find(diff(ts_now.t)>seconds(1)+1e-6);
%get arc lenths
al=ts_now.y(idx1,v.arclen_col);
%get consecutive time difference
dt=[seconds(diff(ts_now.t));0]; dt=dt(idx1);
%find arcs that span over time stamps
bad_idx=find(al-dt>2); %no abs here!
%report if any such epochs have been found
csr.report(obj.debug,bad_idx,'Ilegal arc length in the data',[v.levels{i},'.',v.calpars_out{j},'.',v.sats{s}],...
{'global idx','arc init t','arc length','succ time diff','delta arc len'},...
{idx1,ts_now.t(idx1),al,dt,al-dt}...
) %#ok<FNDSB>
end
case {'aak','accatt'}
%this check ensures that the t0 value is the same as the start of the arc
for j=1:numel(v.calpars_out)
%the Y parameter was constructed from multitple parameters and some calpars do not have t0
if ~any(v.calpars_out{j}(end)=='DQ') || ~isempty(strfind(v.calpars_out{j},'Y'))
str.say(str.tablify([8,32],'Skipping',product.str))
continue
end
str.say(str.tablify([8,32],'Checking',product.str))
%save time series into dedicated var
ts_now=obj.data_get_scalar(product.dataname.set_field_path([v.levels(i),v.calpars_out(j),v.sats(s)]));
%forget about epochs that have been artificially inserted to represent forward steps
idx1=find(diff(ts_now.t)>seconds(1));
%get t0
t0=simpletimeseries.utc2gps(datetime(ts_now.y(idx1,v.t0_col),'convertfrom','modifiedjuliandate'));
%find arcs that have (much) t0 different than their first epoch
bad_idx=find(...
abs(ts_now.t(idx1)-t0)>seconds(1) & ...
ts_now.mask(idx1) & ... %ignore gaps
[true;diff(ts_now.y(idx1,v.jobid_col))~=0] ... %ignore epochs inside the same arc
);
%report if any such epochs have been found
csr.report(obj.debug,bad_idx,'Ilegal t0 in the data',[v.levels{i},'.',v.calpars_out{j},'.',v.sats{s}],...
{'global idx','arc init time','t0','delta time'},...
{idx1,ts_now.t(idx1),t0,ts_now.t(idx1)-t0}...
) %#ok<FNDSB>bo
end
end
end
end
end
function obj=import_calpar(obj,product,varargin)
%open log file
csr.log
% add input arguments and metadata to collection of parameters 'v'
v=varargs.wrap('sources',{...
{...
'debugdate', [], @(i) ischar(i) || isempty(i);
},...
csr.ltb_args,...
product.args...
},varargin{:});
%load data
for i=1:numel(v.levels)
for j=1:numel(v.calpars)
tmp=struct('A',[],'B',[]);
for s=1:numel(v.sats)
%read L1B data
f=fullfile(v.import_dir,['gr',v.sats{s},'.',v.calpars{j},'.',v.levels{i},'.GraceAccCal']);
tmp.(v.sats{s})=simpletimeseries.import(f,'cut24hrs',false);
%apply long-term bias
tmp.(v.sats{s})=tmp.(v.sats{s}).set_cols(v.param_col,...
csr.ltb_apply(v.varargin{:},...
'ts',tmp.(v.sats{s}).get_cols(v.param_col),...
'sat',v.sats{s},...
'field',v.calpars{s}...
)...
);
%additional processing: add end of arcs
switch v.levels{i}
case {'aak','accatt'}
%get arc stars
arc_starts=tmp.(v.sats{s}).t;
%build arc ends
arc_ends=[arc_starts(2:end);dateshift(arc_starts(end),'end','day')]-seconds(1);
% %arc ends are at maximum 24 hours after arc starts (only for those arcs starting at mid-night)
% fix_idx=arc_ends-arc_starts>days(1) & ...
% seconds(arc_starts-dateshift(arc_starts,'start','day'))<tmp.(v.sats{s}).t_tol;
% arc_ends(fix_idx)=arc_starts(fix_idx)+days(1)-seconds(1);
case 'estim'
%get arc stars
arc_starts=tmp.(v.sats{s}).t;
%build arc ends (arc duration given explicitly)
arc_ends=arc_starts+seconds(tmp.(v.sats{s}).y(:,v.arclen_col))-seconds(1);
%patch missing arc durations
idx=find(isnat(arc_ends));
%report edge cases
csr.report(obj.debug,idx,'Arcs without arc length',f,...
{'arc start','arc duraction'},...
{arc_starts, tmp.(v.sats{s}).y(:,v.arclen_col)}...
)
%fix it
if ~isempty(idx);
arc_ends(idx)=dateshift(arc_starts(idx),'end','day')-seconds(1);
end
end
%bug trap
assert(all(~isnat(arc_starts)),...
[mfilename,': found NaT in the arc starts'])
%compute arc day start and end
day_starts=dateshift(arc_starts,'start','day');
day_ends =dateshift(arc_starts,'end', 'day');
%arc ends cannot go over day boundaries
idx=find(arc_ends>=day_ends);
csr.report(obj.debug,idx,'Arc ends over day boundary',f,...
{'curr arc start','curr arc end','day ends'},...
{ arc_starts, arc_ends, day_ends}...
)
%fix it
if ~isempty(idx)
arc_ends(idx)=day_ends(idx)-seconds(1);
end
%bug trap
assert(all(~isnat(arc_ends)),...
[mfilename,': found NaT in the arc starts/ends'])
%surpress over-lapping arcs
idx=find(arc_starts(2:end)-arc_ends(1:end-1)<0);
csr.report(obj.debug,idx,'Over-lapping arcs',f,...
{'curr arc start','curr arc end','next arc start'},...
{ arc_starts, arc_ends, [arc_starts(2:end);arc_starts(1)]}...
)
%fix it
if ~isempty(idx)
arc_ends(idx)=arc_starts(idx+1)-seconds(1);
end
%fancy stuff: handle parameters defined as arc segments
if ~isempty(strfind(v.calpars{j},'AC0Y'))
%there are 8 segments per day
periodicity=days(1)/8;
%get day location for this parameter
day_loc=str2double(v.calpars{j}(end));
%get sub-arc starts/ends
sub_arc_starts=arc_starts+periodicity*(day_loc-1);
sub_arc_ends=arc_starts+periodicity*(day_loc )-seconds(1);
%get sub arc boundaries
sub_arc_bound_starts=max([arc_starts,day_starts],[],2);
sub_arc_bound_ends =min([arc_ends, day_ends ],[],2);
%cap sub-arc start/ends to be within the current day
idx={...
find( sub_arc_starts>sub_arc_bound_ends ),...
find( sub_arc_starts<sub_arc_bound_starts ),...
find( sub_arc_ends >sub_arc_bound_ends ),...
find( sub_arc_ends <sub_arc_bound_starts )...
};
msg={...
'Sub-arc starts after day/arc ends',...
'Sub-arc starts before day/arc starts',...
'Sub-arc ends after day/arc ends',...
'Sub-arc ends before day/arc starts'...
};
for k=1:numel(idx)
csr.report(obj.debug,idx{k},msg{k},f,...
{'sub-arc start','sub-arc end','day start','day end'},...
{ sub_arc_starts, sub_arc_ends, day_starts, day_ends}...
)
%fix it
if ~isempty(idx{k})
switch k
case 1; sub_arc_starts(idx{k})=sub_arc_bound_ends( idx{k});
case 2; sub_arc_starts(idx{k})=sub_arc_bound_starts(idx{k});
case 3; sub_arc_ends( idx{k})=sub_arc_bound_ends( idx{k});
case 4; sub_arc_ends( idx{k})=sub_arc_bound_starts(idx{k});
end
end
end
%propagate the arc extremeties
arc_starts=sub_arc_starts;
arc_ends=sub_arc_ends;
end
%propagate data
arc_start_y=tmp.(v.sats{s}).y;
arc_end_y=tmp.(v.sats{s}).y;
%remove arcs with zero length (only applicable to AC0Y*2-8)
zero_len_idx=find(arc_ends-arc_starts<=0);
csr.report(obj.debug,zero_len_idx,'Non-positive arc length',f,...
{'arc start','arc end','arc_length'},...
{ arc_starts, arc_ends, arc_ends-arc_starts}...
)
if ~isempty(zero_len_idx)
good_idx=(arc_ends-arc_starts>0);
arc_starts =arc_starts( good_idx);
arc_ends =arc_ends( good_idx);
arc_start_y=arc_start_y(good_idx,:);
arc_end_y =arc_end_y( good_idx,:);
end
%debug date report
if ~isempty(v.debugdate)
rep_date=datetime(v.debugdate);
rep_delta=arc_starts-rep_date;
rep_idx=find(abs(rep_delta)==min(abs(rep_delta)));
rep_idx=(rep_idx(1)-8):(rep_idx(end)+8);
csr.report(true,rep_idx,['DEBUG DATE: Arcs around ',datestr(rep_date)],f,...
{'arc start','arc end','arc length','inter-arc gap'},...
{arc_starts(rep_idx ),arc_ends( rep_idx),...
arc_ends( rep_idx )-arc_starts(rep_idx),...
arc_starts(rep_idx+1)-arc_ends( rep_idx)...
},...
false)
end
%build timeseries with arc starts
arc_start_ts=simpletimeseries(arc_starts,arc_start_y,...
'format','datetime',...
'labels',tmp.(v.sats{s}).labels,...
'units',tmp.(v.sats{s}).y_units,...
'timesystem',tmp.(v.sats{s}).timesystem,...
'descriptor',tmp.(v.sats{s}).descriptor...
);
%build timeseries with arc ends
arc_end_ts=simpletimeseries(arc_ends,arc_end_y,...
'format','datetime',...
'labels', tmp.(v.sats{s}).labels,...
'units', tmp.(v.sats{s}).y_units,...
'timesystem',tmp.(v.sats{s}).timesystem,...
'descriptor',['end of arcs for ',tmp.(v.sats{s}).descriptor]...
);
%augment arc starts with arc ends (only new data)
tmp.(v.sats{s})=arc_start_ts.augment(arc_end_ts,'old',true);
end
%propagate data to object
for s=1:numel(v.sats)
obj=obj.data_set(product.dataname.set_field_path([v.levels(i),v.calpars(j),v.sats(s)]),tmp.(v.sats{s}));
end
%user feedback
str.say(str.tablify([15,6,3,6],'loaded data for',v.levels{i},'and',v.calpars{j}))
end
end
%merge cross-track accelerations together
ac0y='AC0Y';
field_part_list={'','D','Q'};
%loop over all levels and sats
for i=1:numel(v.levels)
for s=1:numel(v.sats)
for f=1:numel(field_part_list)
%start with first field
calpar=[ac0y,field_part_list{f},'1'];
ts_now=obj.data_get_scalar(product.dataname.set_field_path([v.levels(i),calpar,v.sats(s)]));
%rename the relevant object fields to remove the '1'
ts_now.labels=strrep(ts_now.labels,calpar,[ac0y,field_part_list{f}]);
ts_now.descriptor=strrep(ts_now.descriptor,calpar,[ac0y,field_part_list{f},'[1-8]']);
%loop over all other calpars
for fpl=2:8
calpar=[ac0y,field_part_list{f},num2str(fpl)];
ts_now=ts_now.augment(...
obj.data_get_scalar(product.dataname.set_field_path([v.levels(i),calpar,v.sats(s)])),...
'quiet',true,...
'old',true,...
'skip_gaps',true...
);
%debug date report
if ~isempty(v.debugdate)
rep_date=datetime(v.debugdate);
str.say('DEBUG DATE: merge AC0Y*:',v.levels{i},':',v.sats{s},':',calpar,' @ ',datestr(rep_date));
idx=ts_now.idx(rep_date);
ts_now.peek((idx-10):(idx+10));
end
end
%save the data
obj=obj.data_set(product.dataname.set_field_path([v.levels(i),{[ac0y,field_part_list{f}]},v.sats(s)]),ts_now);
%user feedback
str.say(str.tablify([29,5,3,6,3,7],'merged cross-track parameter',[ac0y,field_part_list{f}],...
'for',v.levels{i},'and',['GRACE-',v.sats{s}]))
end
end
end
%add gaps
for i=1:numel(v.levels)
for j=1:numel(v.calpars_out)
for s=1:numel(v.sats)
ts_now=obj.data_get_scalar(product.dataname.set_field_path([v.levels(i),v.calpars_out(j),v.sats(s)]));
%debug date report
if ~isempty(v.debugdate)
rep_date=datetime(v.debugdate);
str.say('DEBUG DATE: w/out gaps:',v.levels{i},':',v.sats{s},':',v.calpars_out{j},' @ ',datestr(rep_date));
idx=ts_now.idx(rep_date);
ts_now.peek((idx-10):(idx+10));
end
%get end of arcs and non-consecutive time indexes
end_arc_idx=[false;diff(ts_now.y(:,1))==0];
gap_idx=[diff(ts_now.t)>seconds(1)+ts_now.t_tol;false];
%extend calibration parameters into the gap
gap_start_idx=find(end_arc_idx & gap_idx);
gap_stop_idx=gap_start_idx+1;
% ext_len=minutes(10);
% extension=min( ts_now.t(gap_stop_idx)-ts_now.t(gap_start_idx),ext_len*ones(size(gap_start_idx))*2 )/2;
extension=ts_now.t(gap_stop_idx)-ts_now.t(gap_start_idx);
ts_now.t(gap_start_idx)=ts_now.t(gap_start_idx)+time.round_seconds(extension/2);
ts_now.t(gap_stop_idx )=ts_now.t(gap_start_idx)+seconds(1);
%build timeseries with arc ends
gap_t=ts_now.t(gap_start_idx)+seconds(1);
gaps=simpletimeseries(gap_t,nan(numel(gap_t),ts_now.width),...
'format','datetime',...
'labels',ts_now.labels,...
'units',ts_now.y_units,...
'timesystem',ts_now.timesystem,...
'descriptor',['gaps for ',ts_now.descriptor]...
);
%augment (keep it separate from saving, so that date report works as expected)
ts_now=ts_now.augment(gaps,'old',true,'new',true);
%debug date report
if ~isempty(v.debugdate)
rep_date=datetime(v.debugdate);
str.say('DEBUG DATE: with gaps:',v.levels{i},':',v.sats{s},':',v.calpars_out{j},' @ ',datestr(rep_date));
idx=ts_now.idx(rep_date);
ts_now.peek((idx-10):(idx+10));
end
%save
obj=obj.data_set(product.dataname.set_field_path([v.levels(i),v.calpars_out(j),v.sats(s)]),ts_now);
end
end
end
%loop over all sat and level to check Job IDs agreement across all output calpars
for i=1:numel(v.levels)
for s=1:numel(v.sats)
for j=1:numel(v.calpars_out)-1
dn1=product.dataname.set_field_path([v.levels(i),v.calpars_out(j ),v.sats(s)]);
dn2=product.dataname.set_field_path([v.levels(i),v.calpars_out(j+1),v.sats(s)]);
d1=obj.data_get_scalar(dn1);
d2=obj.data_get_scalar(dn2);
[~,i1,i2]=intersect(d1.t,d2.t);
bad_idx=find(...
d1.y(i1,v.jobid_col) ~= d2.y(i2,v.jobid_col) & ...
d1.mask(i1) & ...
d2.mask(i2) ...
);
if ~isempty(bad_idx)
n=numel(bad_idx);
msg=cell(1,2*n+2);
msg{1}=str.tablify([5,6,24],'found',numel(bad_idx),'Job ID inconsistencies:');
msg{2}=str.tablify([30,6,20,12],'data name','idx','t','Job ID');
for k=1:n
idx=i1(bad_idx(k));
msg{2*k+1}=str.tablify([30,6,20,12],dn1,idx,d1.t(idx),num2str(d1.y(idx,v.jobid_col),'%i'));
idx=i2(bad_idx(k));
msg{2*k+2}=str.tablify([30,6,20,12],dn2,idx,d2.t(idx),num2str(d2.y(idx,v.jobid_col),'%i'));
end
error([mfilename,':',strjoin(msg,'\n')])
end
end
end