Merge branch 'develop'

socib · Jun 6, 2016 · 41cf8e4 · 41cf8e4
2 parents 1cc81fc + 31e3f35
commit 41cf8e4
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diff --git a/README.md b/README.md
@@ -22,10 +22,12 @@ The following features are already implemented in the glider toolbox:
  - Support for different glider models:
  - Slocum G1 and G2
  - Seaglider
+ - SeaExplorer
  - Deployment metadata gathering from virtually any database.
  - File retrieval from multiple dockservers/basestations for real time processing.
  - Improved Slocum raw data loading from ascii files (`.dba`).
  - Improved Seaglider raw data loading from ascii files (`.log` and `.eng`).
+ - SeaExplorer raw data loading from ascii files (`.gli` and `.pld`).
  - Data processing, including:
  - unit conversions
  - factory calibrations
@@ -41,7 +43,7 @@ The following features are already implemented in the glider toolbox:
  - parameters for data gridding
  - customizable standard NetCDF product and figure outputs
 
-The following features are planned:
+The following features are planned or in development:
 
  - automatic quality control of processed data.
 
@@ -87,10 +89,12 @@ developed to automatically process the data from a glider fleet is not needed:
 
  - Slocum data file API:
  [`dba2mat`][dba2mat], [`dbacat`][dbacat], and [`dbamerge`][dbamerge]
- - Seaglider data file API: 
- [`sglog2mat`][sglog2mat], [`sglogcat`][sglogcat], 
- [`sgeng2mat`][sgeng2mat], [`sgengcat`][sgengcat], 
+ - Seaglider data file API:
+ [`sglog2mat`][sglog2mat], [`sglogcat`][sglogcat],
+ [`sgeng2mat`][sgeng2mat], [`sgengcat`][sgengcat],
  and [`sglogenmerge`][sglogengmerge]
+ - SeaExplorer data file API:
+ [`sx2mat`][sx2mat], [`sxcat`][sxcat], and [`sxmerge`][sxmerge]
  - More convenient [NetCDF interface][netcdf_dsl]:
  [`loadnc`][loadnc] and [`savenc`][savenc]
  - RFC-compliant [JSON interface][json_rfc]:
@@ -111,6 +115,9 @@ developed to automatically process the data from a glider fleet is not needed:
  [sgeng2mat]: http://www.socib.es/users/glider/glider_toolbox/doc/m/reading_tools/sgeng2mat
  [sgengcat]: http://www.socib.es/users/glider/glider_toolbox/doc/m/reading_tools/sgengcat
  [sglogengmerge]: http://www.socib.es/users/glider/glider_toolbox/doc/m/reading_tools/sglogengmerge
+ [sx2mat]: http://www.socib.es/users/glider/glider_toolbox/doc/m/reading_tools/sx2mat
+ [sxcat]: http://www.socib.es/users/glider/glider_toolbox/doc/m/reading_tools/sxcat
+ [sxmerge]: http://www.socib.es/users/glider/glider_toolbox/doc/m/reading_tools/sxmerge
  [netcdf_dsl]: http://repository.socib.es/repository/entry/show/Top/Public+Staff/jbeltran/Octave+and+MATLAB/Octave+and+MATLAB+notes#Load%20and%20save%20data%20in%20NetCDF%20format
  [loadnc]: http://www.socib.es/users/glider/glider_toolbox/doc/m/common_tools/loadnc
  [savenc]: http://www.socib.es/users/glider/glider_toolbox/doc/m/common_tools/savenc
@@ -154,7 +161,7 @@ and [SOCIB][socib] by Tomeu Garau. He is the true glider man.
 Copyright
 ---------
 
-Copyright (C) 2013-2015
+Copyright (C) 2013-2016
 ICTS SOCIB - Servei d'observació i predicció costaner de les Illes Balears
 <http://www.socib.es>
 

diff --git a/m/common_tools/@sftp/cd.m b/m/common_tools/@sftp/cd.m
@@ -27,7 +27,7 @@
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2014-2015
+% Copyright (C) 2014-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/@sftp/close.m b/m/common_tools/@sftp/close.m
@@ -16,7 +16,7 @@ function close(h)
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2014-2015
+% Copyright (C) 2014-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/@sftp/delete.m b/m/common_tools/@sftp/delete.m
@@ -16,7 +16,7 @@ function delete(h, filename)
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2014-2015
+% Copyright (C) 2014-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/@sftp/dir.m b/m/common_tools/@sftp/dir.m
@@ -36,7 +36,7 @@
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2014-2015
+% Copyright (C) 2014-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/@sftp/mget.m b/m/common_tools/@sftp/mget.m
@@ -35,7 +35,7 @@
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2014-2015
+% Copyright (C) 2014-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/@sftp/mkdir.m b/m/common_tools/@sftp/mkdir.m
@@ -16,7 +16,7 @@ function mkdir(h, dirname)
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2014-2015
+% Copyright (C) 2014-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/@sftp/mput.m b/m/common_tools/@sftp/mput.m
@@ -28,7 +28,7 @@
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2014-2015
+% Copyright (C) 2014-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/@sftp/private/mexsftp.c b/m/common_tools/@sftp/private/mexsftp.c
@@ -3,7 +3,7 @@
  * @brief Mex interface to libssh for sftp connection.
  * @author Joan Pau Beltran <joanpau.beltran@socib.cat>
  *
- * Copyright (C) 2014-2015
+ * Copyright (C) 2014-2016
  * ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears.
  * <http://www.socib.es>
  *

diff --git a/m/common_tools/@sftp/private/mexsftp.m b/m/common_tools/@sftp/private/mexsftp.m
@@ -94,7 +94,7 @@
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2014-2015
+% Copyright (C) 2014-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/@sftp/rename.m b/m/common_tools/@sftp/rename.m
@@ -16,7 +16,7 @@ function rename(h, oldname, newname)
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2014-2015
+% Copyright (C) 2014-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/@sftp/rmdir.m b/m/common_tools/@sftp/rmdir.m
@@ -16,7 +16,7 @@ function rmdir(h, dirname)
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2014-2015
+% Copyright (C) 2014-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/@sftp/sftp.m b/m/common_tools/@sftp/sftp.m
@@ -30,7 +30,7 @@
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2014-2015
+% Copyright (C) 2014-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/getfiles.m b/m/common_tools/getfiles.m
@@ -67,7 +67,7 @@
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2014-2015
+% Copyright (C) 2014-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/loadjson.m b/m/common_tools/loadjson.m
@@ -63,7 +63,7 @@
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2013-2015
+% Copyright (C) 2013-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/loadnc.m b/m/common_tools/loadnc.m
@@ -77,7 +77,7 @@
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2013-2015
+% Copyright (C) 2013-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/posixtime2utc.m b/m/common_tools/posixtime2utc.m
@@ -30,7 +30,7 @@
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2013-2015
+% Copyright (C) 2013-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/printfigure.m b/m/common_tools/printfigure.m
@@ -150,7 +150,7 @@
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2013-2015
+% Copyright (C) 2013-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/savejson.m b/m/common_tools/savejson.m
@@ -68,7 +68,7 @@
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2013-2015
+% Copyright (C) 2013-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/savenc.m b/m/common_tools/savenc.m
@@ -86,7 +86,7 @@ function savenc(var_data, var_meta, global_meta, filename)
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2013-2015
+% Copyright (C) 2013-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %
@@ -127,7 +127,11 @@ function savenc(var_data, var_meta, global_meta, filename)
  % Set dimensions.
  if isfield(global_meta, 'dimensions')
  for global_dim = global_meta.dimensions(:)'
- nc(global_dim.name) = global_dim.length; 
+ if isfield(global_dim, 'unlimited') && (global_dim.unlimited)
+ nc(global_dim.name) = 0;
+ else
+ nc(global_dim.name) = global_dim.length;
+ end
  end
  end
  % Set variable dimensions and attributes, and variable data.
@@ -157,6 +161,14 @@ function savenc(var_data, var_meta, global_meta, filename)
  nc{var_name}.(var_att.name) = var_att.value;
  end
  end
+ end
+ for var_idx = 1:numel(field_name_list)
+ field_name = field_name_list{var_idx};
+ if isfield(var_meta.(field_name), 'name')
+ var_name = var_meta.(field_name).name;
+ else
+ var_name = field_name;
+ end
  % Set the variable data with fill value and scale handling enabled.
  % Give the range for record dimensions.
  nc_var = nc{var_name};
@@ -179,13 +191,19 @@ function savenc(var_data, var_meta, global_meta, filename)
  try
  % Set global attributes.
  if isfield(global_meta, 'attributes')
- arrayfun(@(a) nc_attput(filename, nc_global, a.name, a.value), ...
- global_meta.attributes);
+ for global_att = global_meta.attributes(:)'
+ nc_attput(filename, nc_global, global_att.name, global_att.value);
+ end
  end
  % Set dimensions.
  if isfield(global_meta, 'dimensions')
- arrayfun(@(d) nc_adddim(filename, d.name, d.length), ...
- global_meta.dimensions);
+ for global_dim = global_meta.dimensions(:)'
+ if isfield(global_dim, 'unlimited') && (global_dim.unlimited)
+ nc_adddim(filename, global_dim.name, 0);
+ else
+ nc_adddim(filename, global_dim.name, global_dim.length);
+ end
+ end
  end
  % Set variable dimensions and attributes, and variable data.
  field_name_list = intersect(fieldnames(var_data), fieldnames(var_meta));
@@ -217,6 +235,14 @@ function savenc(var_data, var_meta, global_meta, filename)
  'Value', {var_meta.(field_name).attributes.value});
  end
  nc_addvar(filename, nc_var);
+ end
+ for var_idx = 1:numel(field_name_list)
+ field_name = field_name_list{var_idx};
+ if isfield(var_meta.(field_name), 'name')
+ var_name = var_meta.(field_name).name;
+ else
+ var_name = field_name;
+ end
  nc_varput(filename, var_name, var_data.(field_name))
  end
  catch exception

diff --git a/m/common_tools/strc.m b/m/common_tools/strc.m
@@ -30,7 +30,7 @@
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2014-2015
+% Copyright (C) 2014-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/strfstruct.m b/m/common_tools/strfstruct.m
@@ -104,7 +104,7 @@
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2013-2015
+% Copyright (C) 2013-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/common_tools/utc2posixtime.m b/m/common_tools/utc2posixtime.m
@@ -30,7 +30,7 @@
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2013-2015
+% Copyright (C) 2013-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/configBasestations.m b/m/configBasestations.m
@@ -23,7 +23,7 @@
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2014-2015
+% Copyright (C) 2014-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %

diff --git a/m/configDBAccess.m b/m/configDBAccess.m
@@ -23,7 +23,7 @@
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2013-2015
+% Copyright (C) 2013-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %
@@ -42,7 +42,7 @@
 
  error(nargchk(0, 0, nargin, 'struct'));
 
- db_access.url  = 'jdbc:postgresql://mydb.myportal.mydomain:5433/my_data_base';
+ db_access.server = 'jdbc:postgresql://mydb.myportal.mydomain:5433/my_data_base';
  db_access.name = 'my_data_base';
  db_access.user = 'myself';
  db_access.pass = 'top_secret';

diff --git a/m/configDTDeploymentInfoQueryDB.m b/m/configDTDeploymentInfoQueryDB.m
@@ -25,7 +25,7 @@
 % Authors:
 % Joan Pau Beltran <joanpau.beltran@socib.cat>
 
-% Copyright (C) 2013-2015
+% Copyright (C) 2013-2016
 % ICTS SOCIB - Servei d'observacio i prediccio costaner de les Illes Balears
 % <http://www.socib.es>
 %
@@ -61,12 +61,14 @@
  };
 
  deployment_fields = fields_map(:,1)';
- db_fields = fields_map(:,2)';
+ database_fields = fields_map(:,2)';
 
  % Build the query.
- db_fields_str = [sprintf('%s, ', db_fields{1:end-1}) db_fields{end}];
-
- sql_query = ['select ' db_fields_str ...
+ deployment_ids_str = ...
+ [sprintf('%s, ', deployment_ids{1:end-1}) deployment_ids{end}];
+ database_fields_str = ...
+ [sprintf('%s, ', database_fields{1:end-1}) database_fields{end}];
+ sql_query = ['select ' database_fields_str ...
  ' from instrumentation.deployment' ...
  ' inner join instrumentation.instrument' ...
  ' on (deployment_instrument_id=instrument_id)' ...
@@ -78,6 +80,6 @@
  ' on (instrument_platform_platform_id = platform_id)' ...
  ' inner join instrumentation.institution' ...
  ' on (deployment_institution_id=institution_id)' ...
- ' where (deployment_id in (' deployment_ids '));'];
+ ' where (deployment_id in (' deployment_ids_str '));'];
 
 end