Merge branch 'master' of https://github.com/IPGP/webobs

CODE/matlab/mktides.m

@@ -19,13 +19,13 @@
 %
 %	Author: F. Beauducel, WEBOBS/IPGP
 %	Created: 2015
-%	Updated: 2022-07-26
+%	Updated: 2024-08-26
 
 
 g = 9.81;
 
 
-if numel(opt) == 1
+if isscalar(opt)
 	tidemode = opt;
 	wavemode = 'ALL';
 	kindmode = 'TL';
@@ -72,7 +72,12 @@
 	wosystem(sprintf('sed "s/[:\\/]/ /g" %s > %s',fdat,ftmp));
 	dd = load(ftmp);
 	T.t = datenum(dd(:,1),dd(:,2),dd(:,3),dd(:,4),dd(:,5),0);
-	T.d = g*dd(:,[7,6]);
+	switch kindmode
+		case 'TL'
+			T.d = g*dd(:,[7,6]);
+		otherwise
+			T.d = dd(:,6);
+	end
 	fprintf('done.\n');
 else
 	fprintf('** WARNING ** tides file does not exist!\n');

CODE/matlab/readfmtdata.m

@@ -24,7 +24,7 @@
 %
 %	Authors: François Beauducel, Jean-Marie Saurel, WEBOBS/IPGP
 %	Created: 2013-12-29, in Guadeloupe, French West Indies
-%	Updated: 2022-10-26
+%	Updated: 2024-07-02
 
 wofun = sprintf('WEBOBS{%s}',mfilename);
 
@@ -33,9 +33,13 @@
 wosystem(sprintf('mkdir -p %s',F.ptmp));
 
 if isfield(P,'FORM')
-
-	D = readfmtdata_woform(WO,P,N);
-
+	% legacy forms (datafile)
+	f = sprintf('%s/%s',WO.PATH_DATA_DB,P.FORM.FILE_NAME);
+	if exist(f,'file')
+		D = readfmtdata_woform(WO,P,N);
+	else
+		D = readfmtdata_genform(WO,P,N);
+	end
 else
 
 	for n = 1:length(N)

CODE/matlab/readfmtdata_quake.m

@@ -39,7 +39,7 @@
 %
 %	Authors: François Beauducel and Jean-Marie Saurel, WEBOBS/IPGP
 %	Created: 2016-07-10, in Yogyakarta (Indonesia)
-%	Updated: 2023-08-25
+%	Updated: 2024-07-12
 
 wofun = sprintf('WEBOBS{%s}',mfilename);
 
@@ -57,12 +57,12 @@
 		P.(fd) = [-Inf,Inf];
 	end
 end
-if isfield(P,'EVENTTYPE_EXCLUDED_LIST')
+if isfield(P,'EVENTTYPE_EXCLUDED_LIST') && ~isempty(P.EVENTTYPE_EXCLUDED_LIST)
 	extypes = split(P.EVENTTYPE_EXCLUDED_LIST,',');
 else
 	extypes = {''};
 end
-if isfield(P,'EVENTSTATUS_EXCLUDED_LIST')
+if isfield(P,'EVENTSTATUS_EXCLUDED_LIST') && ~isempty(P.EVENTSTATUS_EXCLUDED_LIST)
 	exstatus = split(P.EVENTSTATUS_EXCLUDED_LIST,',');
 else
 	exstatus = {''};

CODE/matlab/readfmtdata_woform.m

@@ -25,6 +25,10 @@
 %		D.d (Distance Temp Wind)
 %		D.e (Distance Temp Wind)
 %
+%	form 'RIVERS'
+%		D.t (datenum)
+%		D.d (18 columns)
+%
 %	form 'RAINWATER'
 %		D.t (datenum)
 %		D.d (18 columns)
@@ -35,21 +39,21 @@
 %
 %	**WARNING** this file must be iso-8859 (unicode) encoded and NOT utf-8
 %
-%	Author: Fran�ois Beauducel, WEBOBS/IPGP
+%	Author: François Beauducel, WEBOBS/IPGP
 %	Created: 2016-07-10, in Yogyakarta (Indonesia)
-%	Updated: 2023-08-30
+%	Updated: 2024-10-03
 
 wofun = sprintf('WEBOBS{%s}',mfilename);
 
 GMOL = readcfg(WO,sprintf('%s/etc/gmol.conf',WO.ROOT_CODE));
 
-f = sprintf('%s/%s',WO.PATH_DATA_DB,P.FORM.FILE_NAME);
-if ~exist(f,'file')
-	error('%s: %s not found [%s].',wofun,f,P.FORM.SELFREF);
+if ~ismember(P.FORM.SELFREF,{'EAUX','GAZ','EXTENSO','RAINWATER','SOILSOLUTION','RIVERS'})
+	error('%s: unknown woform [%s].',wofun,P.FORM.SELFREF);
 end
 
 fprintf('%s: importing FORM data [%s] ...\n',wofun,P.FORM.SELFREF);
 
+f = sprintf('%s/%s',WO.PATH_DATA_DB,P.FORM.FILE_NAME);
 data = readdatafile(f,[],'HeaderLines',1);
 
 % replaces missing hours by default time, converts to datenum
@@ -86,8 +90,8 @@
 	e = zeros(size(d));
 	nm = {'type','TA','TS','pH','Flux','Cond','Level','Li+','Na+','K+','Mg++','Ca++','F-','Cl-','Br-','NO3-','SO4--','HCO3-','I-', ...
 		'\delta^{13}C','\delta^{18}O','{\delta}D','Cl-/SO4-- ','HCO3-/SO4--','Mg++/Cl-','Cond_{25}','NICB'};
-	un = {    '','�C','�C',  '','l/mn',  '�S',    'm','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l', ...
-		    '',    '',  '',          '',           '',        '',    '�S',   '%'};
+	un = {    '','°C','°C',  '','l/mn',  'µS',    'm','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l', ...
+		    '',    '',  '',          '',           '',        '',    'µS',   '%'};
 
 	D = share2nodes(t,d,e,data(:,4),P,N,nm,un);
 
@@ -107,7 +111,7 @@
 
 	e = zeros(size(d));
 	nm = {'Temperature','pH','Flux',  'Rn','type','H_2','He','CO','CH_4','N_2','H_2S','Ar','CO_2','SO_2','O_2','\delta^{13}C','\delta^{18}O','S/C'};
-	un = {  '�C',  '',   '-','#/mn',    '', '%', '%', '%',  '%', '%',  '%', '%',  '%',  '%', '%',    '',    '',   ''};
+	un = {  '°C',  '',   '-','#/mn',    '', '%', '%', '%',  '%', '%',  '%', '%',  '%',  '%', '%',    '',    '',   ''};
 
 	D = share2nodes(t,d,e,data(:,4),P,N,nm,un);
 
@@ -125,7 +129,7 @@
 	e(e==0) = 1;	% forces error = 1
 
 	nm = {'Distance','TempAir','Wind'};
-	un = {      'mm',     '�C',   '-'};
+	un = {      'mm',     '°C',   '-'};
 
 	D = share2nodes(t,d,e,data(:,4),P,N,nm,un);
 
@@ -141,7 +145,7 @@
 	e(e==0) = 1;	% forces error = 1
 
 	nm = {'Perp.','Para.','Vert.','TempAir'};
-	un = {   'mm',   'mm',   'mm',  '�C'};
+	un = {   'mm',   'mm',   'mm',  '°C'};
 
 	D = share2nodes(t,d,e,data(:,4),P,N,nm,un);
 
@@ -170,7 +174,7 @@
 	e = zeros(size(d));
 	nm = {'Rainmeter','pH','Cond','Na+','K+','Mg++','Ca++','HCO3-','Cl-','SO4--', ...
 		'{\delta}D','\delta^{18}O','Cl-/Na+ ','SO4--/Na+','Mg++/Na+','NICB'};
-	un = {    'mm/day',  '',  '�S', 'mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l', ...
+	un = {    'mm/day',  '',  'µS', 'mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l', ...
 		    '%{\fontsize{5}o}',    '%{\fontsize{5}o}',    '',      '',      '',  '%'};
 
 	D = share2nodes(t,d,e,data(:,4),P,N,nm,un);
@@ -198,11 +202,51 @@
 	e = zeros(size(d));
 	nm = {'Duration','Depth','Level','pH','Cond','Na+',  'K+',    'Mg++',  'Ca++',  'HCO3-', 'Cl-',   'NO3-',  'SO4--', ...
 		'SiO2','DOC','Cl-/Na+ ','SO4--/Na+','Mg++/Na+','NICB'};
-	un = {    'day', 'cm'   , ''    ,'',  '�S', 'mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l', ...
+	un = {    'day', 'cm'   , ''    ,'',  'µS', 'mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l', ...
 		'ppm', 'ppm','',        '',         '',        '%'};
 
 	D = share2nodes(t,d,e,data(:,4),P,N,nm,un);
 
+case 'RIVERS'
+	% type of sampling
+	FT = readcfg(WO,sprintf('%s/%s',P.FORM.ROOT,P.FORM.FILE_TYPE));
+	tcod = fieldnames(FT);
+	% replaces type of sampling by a number
+	for i = 1:length(tcod)
+		data(strcmp(data(:,6),tcod(i)),6) = {num2str(i)};
+	end
+	% type of flacon (bottle)
+	FB = readcfg(WO,sprintf('%s/%s',P.FORM.ROOT,P.FORM.FILE_FLACONS));
+	tcod = fieldnames(FB);
+	% replaces type of bottle by a number
+	for i = 1:length(tcod)
+		data(strcmp(data(:,7),tcod(i)),7) = {num2str(i)};
+	end
+	% converts all fields to numbers (after replacing french decimal points)
+	d = str2double(regexprep(data(:,5:end),',','.'));
+	% converts concentrations to mmol/l
+	elm = {'Na','K','Mg','Ca','HCO3','Cl','SO4'};
+	for i = 1:length(elm)
+		d(:,i+7) = d(:,i+7)/str2double(GMOL.(elm{i}));
+	end
+	% adds 5 new columns with chemical ratios an NICB
+	d(:,19) = d(:,14)./d(:,8); % SO4/Na
+	d(:,20) = d(:,13)./d(:,8); % Cl/Na
+	d(:,21) = d(:,11)./d(:,8); % Ca/Na
+	d(:,22) = d(:,10)./d(:,8); % Mg/Na
+	% computes NICB (Mg++, Ca++ and SO4-- are double counted)
+	cations = rsum(d(:,[8,9,10,10,11,11])');
+	anions = rsum(d(:,[12,13,14,14])');
+	d(:,23) = 100*((cations - anions)./(cations + anions))';
+
+	e = zeros(size(d));
+	nm = {'level','type','flacon','TR','Sload','pH','Cond25','Cond','Na+','K+','Mg++','Ca++','HCO3-','Cl-','SO4--','SiO2','DOC','POC', ...
+		'SO4/Na','Cl/Na','Ca/Na','Mg/Na','NICB'};
+	un = { 'm','','','°C','mg/L',  '','µS',  'µS','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','mmol/l','ppm','ppm','ppm', ...
+		    '',    '',  '',      '',   '%'};
+
+	D = share2nodes(t,d,e,data(:,4),P,N,nm,un);
+
 end
 
 

CODE/matlab/readproc.m

@@ -23,7 +23,7 @@
 %
 %	Authors: F. Beauducel, D. Lafon, WEBOBS/IPGP
 %	Created: 2013-04-05
-%	Updated: 2022-10-26
+%	Updated: 2024-08-06
 
 
 proc = varargin{1};
@@ -32,7 +32,7 @@
 if strncmp(proc,'/',1)	% if argument contains a path filename, will read it as is...
 	f = proc;
 else
-	proc = regexprep(proc,'PROC.','');
+	proc = regexprep(proc,'PROC\.','');
 	f = sprintf('%s/%s/%s.conf',WO.PATH_PROCS,proc,proc);
 end
 

CODE/matlab/superprocs/gnss.m

@@ -197,9 +197,7 @@
 modelling_cmap = field2num(P,'MODELLING_COLORMAP',ryb(256));
 modelling_colorshading = field2num(P,'MODELLING_COLOR_SHADING',0.3);
 modelling_topo_rgb = field2num(P,'MODELLING_TOPO_RGB',.5*[1,1,1]);
-% color reference for model space: 'pdf' or 'volpdf' (source volume sign x pdf, new default)
 modelling_coloref = lower(field2str(P,'MODELLING_COLORREF','volpdf'));
-% colors for displacement arrows
 datarrcol = field2num(P,'MODELLING_DATA_COLOR',[0,0,0]); % color of model arrows
 modarrcol = field2num(P,'MODELLING_MODEL_COLOR',[.7,0,0]); % color of model arrows
 resarrcol = field2num(P,'MODELLING_RESIDUAL_COLOR',[0,.5,0]); % color of residual arrows
@@ -220,6 +218,8 @@
 
 modelling_source_type = field2str(P,'MODELLING_SOURCE_TYPE','isotropic','notempty');
 
+tickfactorlim = 5e3; % above 5 km width/depth axis will be in km
+
 % some modelling parameters are structure fields to pass them to other functions
 modelopt.horizonly = isok(P,'MODELLING_HORIZONTAL_ONLY');
 modelopt.minerror = field2num(P,'MODELLING_MINERROR_MM',5); % minimum error on data (in mm)
@@ -228,58 +228,30 @@
 if numel(modelopt.enuerror) < 3
 	modelopt.enuerror = ones(1,3);
 end
-% a priori source depth (value, gaussian STD in m)
 modelopt.apriori_depth = field2num(P,'MODELLING_APRIORI_DEPTH_M');
-% a priori horizontal error around the target (in STD, km), 0 or NaN = no a priori
 modelopt.apriori_horizontal = field2num(P,'MODELLING_APRIORI_HSTD_KM');
 modelopt.msig = field2num(P,'MODELLING_SIGMAS',1);
 modelopt.misfitnorm = field2str(P,'MODELLING_MISFITNORM','L1');
 modelopt.multi = field2num(P,'MODELLING_MULTIPLE_SOURCES',1,'notempty');
 
-% MODELLING pCDM parameters (see invpcdm.m)
-% number of iterations (adjusting the parameter's limits)
+% MODELLING pCDM parameters (see invpcdm.m and PROC.GNSS template)
 PCDM.iterations = field2num(P,'MODELLING_PCDM_ITERATIONS',5);
-% number of random samples: scalar or list for each iteration
 PCDM.random_sampling = field2num(P,'MODELLING_PCDM_RANDOM_SAMPLING',200000);
-% elastic parameter (Poisson's ratio) nu
 PCDM.nu = field2num(P,'MODELLING_PCDM_NU',0.25);
-% dV parameter limits: total volume variation (in m3)
 PCDM.dvlim = field2num(P,'MODELLING_PCDM_DVLIM',[-1e7,1e7]);
-% A parameter limits: horizontal over total volume variation ratio
-% A = dVZ/(dVX+dVY+dVZ)
-% 	0 = vertical (dyke or pipe following B value)
-% 	1 = horizontal (sill)
-% 	1/3 = isotrop if B = 0.5
 PCDM.alim = field2num(P,'MODELLING_PCDM_ALIM',[0,1]);
-% B parameter limits: vertical volume variation ratio
-% B = dVY/(dVX+dVY)
-% 	0 = dyke if A = 0, dyke+sill otherwise
-% 	1 = dyke if A = 0, dyke+sill otherwise
-% 	0.5 = isotrop if A = 1/3, pipe if A = 0
 PCDM.blim = field2num(P,'MODELLING_PCDM_BLIM',[0,1]);
-% OmegaX parameter limits: rotation angle around X axis (West-East)
 PCDM.oxlim = field2num(P,'MODELLING_PCDM_OXLIM',[-45,45]);
-% OmegaY parameter limits: rotation angle around Y axis (South-North)
 PCDM.oylim = field2num(P,'MODELLING_PCDM_OYLIM',[-45,45]);
-% OmegaZ parameter limits: rotation angle around Z axis (Bottom-Up)
 PCDM.ozlim = field2num(P,'MODELLING_PCDM_OZLIM',[-45,45]);
-% number of bins for probability vs parameter map (heatmap)
 PCDM.heatmap_grid = field2num(P,'MODELLING_PCDM_HEATMAP_GRID',50);
-% graphical parameter for heatmaps
 PCDM.heatmap_saturation = field2num(P,'MODELLING_PCDM_HEATMAP_SATURATION',0.4);
-% number of bins used to smooth the maximum probability curve
 PCDM.heatmap_smooth_span = field2num(P,'MODELLING_PCDM_HEATMAP_SMOOTH_SPAN',5);
-% polynomial degree to smooth the maximum probability curve
 PCDM.heatmap_smooth_degree = field2num(P,'MODELLING_PCDM_HEATMAP_SMOOTH_DEGREE',1);
-% minimum number of models to compute maximum probability curve
 PCDM.newlimit_threshold = field2num(P,'MODELLING_PCDM_NEW_THRESHOLD',2);
-% tolerance ratio to extend the edge limits
 PCDM.newlimit_edge_ratio = field2num(P,'MODELLING_PCDM_NEW_LIMIT_EDGE_RATIO',20);
-% factor of extension (from the previous interval) when reaching an edge
 PCDM.newlimit_extend = field2num(P,'MODELLING_PCDM_NEW_LIMIT_EXTEND',1);
-% option to export supplementary graphs (intermediate results per iteration)
 PCDM.supplementary_graphs = isok(P,'MODELLING_PCDM_SUPPLEMENTARY_GRAPHS');
-tickfactorlim = 5e3; % above 5 km width/depth axis will be in km
 
 % MODELTIME parameters
 modeltime_source_type = field2str(P,'MODELTIME_SOURCE_TYPE','isotropic','notempty');

CODE/python/AAA/requirements.txt

@@ -3,6 +3,6 @@ obspy==1.2.2
 pandas==0.25.3
 pathlib2==2.3.5
 python-speech-features==0.4
-scikit-learn==0.22.2.post1
-scipy==1.4.1
+scikit-learn==1.5.0
+scipy==1.10.0
 sympy==1.0

CODE/shells/download_orbit → CODE/shells/gnss/download_orbit

@@ -12,14 +12,14 @@
 #
 if [ $# -lt 2 ]; then
 	echo "     Syntax: download_orbit DAYS DEST [options]"
-	echo "Description: downloads best avalaible orbit for chosen dates from the"
+	echo "Description: downloads best available orbit for chosen dates from the"
 	echo "             JPL secured web server (see "
 	echo "             https://sideshow.jpl.nasa.gov/pub/JPL_GNSS_Products)"
 	echo "  Arguments:"
 	echo "        DAYS = number of days to process (from start day)"
 	echo "        DEST = root directory where orbits shall be saved"
 	echo "    Options:"
-	echo "        -o ORBIT = type of orbit (Ultra, Rapid or Final)"
+	echo "        -o ORBIT = type of orbit (Ultra, Rapid, Final, or Rapid_GE)"
 	echo "        -d STARTDAY = days to start retrieving (YYYY/mm/dd)"
    	echo "        -r DAYS = remove orbit files older than DAYS days"
 	echo "        -v = verbose mode"
@@ -64,7 +64,7 @@ for (( i=1; i<=$#; i++)); do
 			if [ "$ORBIT" != "Rapid" ]; then
 				if [ "$ORBIT" != "Final" ]; then
 					if [ "$ORBIT" != "Rapid_GE" ]; then
-						echo "Error : Please enter orbit as Ultra, Rapid or Final"
+						echo "Error : Please enter orbit as Ultra, Rapid, Final, or Rapid_GE"
 						exit 0
 					fi
 				fi
@@ -126,7 +126,7 @@ for day in $DAYLIST; do
 				echo " OK."
 				break
 			else
-				echo " not yet avalaible!"
+				echo " not yet available!"
 			fi
 
 		else

CODE/shells/gnss_run_gipsyx → CODE/shells/gnss/gnss_run_gipsyx

@@ -343,6 +343,7 @@ for station in $NODES; do
 						echo "   file $gipsyres [$orbit] already exists..."
 						break
 					else
+						NFORBLOOP=0 ### we force the standard case here (fiducial orbits)
 						if [ "$ORBITSDIR" != "" ]; then #running Gipsy from local orbit
 							case $orbit in
 							flinn)
@@ -369,7 +370,6 @@ for station in $NODES; do
 
 						else #running Gipsy from direct download
 							ORBITOPT=$orbit
-							NFORBLOOP=0 ### we force the standard case here (fiducial orbits)
 						fi
 
 						# if we use NF orbits, add the necessary options -prodTypeGNSS nf -gdCov
@@ -437,7 +437,7 @@ for station in $NODES; do
 						fi
 					fi
 				done
-				if [ -z $ERROR ]; then
+				if [[ -z $ERROR && -e $LOG ]]; then
 					mv -f $LOG $gipsylog
 					gzip -f $gipsylog
 				fi

CODE/shells/gnss_run_gipsyx.rc → CODE/shells/gnss/gnss_run_gipsyx_template.rc

@@ -8,7 +8,7 @@
 # main temporary directory (/tmp per default, change is recommended)
 TMPDIRMAIN=/tmp
 
-# prepares GIPSYX processing
+# prepares GIPSYX processing (this is GipsyX's rc file, in the GipsyX folder)
 source /home/wo/GipsyX-1.2/rc_GipsyX.sh
 
 # grid of a local WebObs that contains the station list (nodes)