Path included in ppmsec2cdf, station format update

calculate_baselines_environment.m

@@ -97,27 +97,6 @@ end
 % specified in parameter file, it is required at command-line.
 % =========================================================================
 
-% -------------------------------------------------------------------------
-% Specify required arguments
-% -------------------------------------------------------------------------
-
-% Station name
-arg_specs.station.required=1;
-arg_specs.station.type='char';
-arg_specs.station.dim1=1;
-arg_specs.station.dim2=5;
-
-% Number of DI measurements to be read for given year
-arg_specs.number_DI.required=1;
-arg_specs.number_DI.type = 'numeric';
-arg_specs.number_DI.dim1 = 1;
-arg_specs.number_DI.dim2 = 1;
-
-arg_specs.startdate.required=1;
-arg_specs.startdate.type='char';
-arg_specs.startdate.dim1=1;
-arg_specs.startdate.dim2=10;
-
 % -------------------------------------------------------------------------
 % Try to read default values from parameter file
 % -------------------------------------------------------------------------
@@ -131,26 +110,56 @@ arg_specs.parfile.dim1=1;
 [arg_parsed state]=parse_arg(arg_specs,varargin);
 
 % Check if parameter file exists
-if ~exist(arg_parsed.parfile,'file')
-    
+if ~exist(arg_parsed.parfile,'file') 
     warning(['Specified parameter file ' arg_parsed.parfile ...
         'does not exist. I will try to get all parameters from command-line.']);
+end
     
 % Set default values from parameter file
-else
+
    
-    [arg_specs.path.default, ...
-     arg_specs.station.default, ...
-     arg_specs.startdate.default]=...
-     read_parameters(arg_parsed.parfile,'PATH','STATION','DATE',...
-                                        {0,0,0});
+[arg_specs.path.default, ...
+ arg_specs.station.default, ...
+ arg_specs.startdate.default]=...
+ read_parameters(arg_parsed.parfile,'PATH','STATION','DATE',...
+                                    {0,0,0});
     
+% Remove NaNs (no value specified in parfile) and set to required if no
+% default was specified
+for field=fields(arg_specs)'
+   if isnan(arg_specs.(field{1}).default)
+       arg_specs.(field{1})=rmfield(arg_specs.(field{1}),'default');
+       arg_specs.(field{1}).required=1;
+   end
 end
 
 % -------------------------------------------------------------------------
-% Specify optional arguments
+% Build struct of command-line specifications
 % -------------------------------------------------------------------------
 
+%
+% Specify required arguments
+
+% Station name
+arg_specs.station.required=1;
+arg_specs.station.type='char';
+arg_specs.station.dim1=1;
+arg_specs.station.dim2=5;
+
+% Number of DI measurements to be read for given year
+arg_specs.number_DI.required=1;
+arg_specs.number_DI.type = 'numeric';
+arg_specs.number_DI.dim1 = 1;
+arg_specs.number_DI.dim2 = 1;
+
+arg_specs.startdate.required=1;
+arg_specs.startdate.type='char';
+arg_specs.startdate.dim1=1;
+arg_specs.startdate.dim2=10;
+
+%
+% Specify optional arguments
+
 % Source for temperature readings
 % 'c' for cdf
 arg_specs.tempsource.default='c';
@@ -176,14 +185,13 @@ arg_specs.stopdate.dim1=1;
 arg_specs.stopdate.dim2=10;
 
 % -------------------------------------------------------------------------
-% Parse arguments
+% Parse arguments from command-line
 % -------------------------------------------------------------------------
 
 [arg_parsed, state]=parse_arg(arg_specs,varargin);
 
-% -------------------------------------------------------------------------
+%
 % Error treatment
-% -------------------------------------------------------------------------
 
 % if ~isempty(arg_parsed.number_DI) && isempty(arg_parsed.year)
 %     error('Year must be specified if number_DI is given');
@@ -203,8 +211,12 @@ elseif (state.err == 2) % error occured, stop execution
     error(state.errmsg);
 end
 
+% =========================================================================
+% Assign all the parameters
+% =========================================================================
+
 % -------------------------------------------------------------------------
-% Assign input arguments
+% General parameters
 % -------------------------------------------------------------------------
 
 % This was removed as option here !
@@ -233,9 +245,9 @@ if ~strcmp(arg_parsed.stopdate(1:4),arg_parsed.startdate(1:4))
         'allowed! \n Startyear is used: ' num2str(year)]);
 end
 
-% =========================================================================
-% GENERATE PATHS
-% =========================================================================
+% -------------------------------------------------------------------------
+% Generate paths
+% -------------------------------------------------------------------------
 
 return_array = [];  %returnes baseliens etc from function
 

ppmsec2cdf.m

@@ -235,8 +235,51 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 function ppmsec2cdf(varargin)
 
+% =========================================================================
+% Get parameters from input file and command-line arguments:
+%
+% First, read from parameter file. The default parameter file is
+% 'parameters_win.txt', and is overwritten by command-line passed
+% parameter file.
+% Then overwrite with command-line arguments. If a parameter is not 
+% specified in parameter file, it is required at command-line.
+% =========================================================================
+
 % -------------------------------------------------------------------------
-% Parse input arguments
+% Try to read default values from parameter file
+% -------------------------------------------------------------------------
+
+% First try to get parameter file
+arg_specs.parfile.default='parameters_win.txt';
+arg_specs.parfile.type='char';
+arg_specs.parfile.dim1=1;
+
+% Parse arguments for parameter file
+[arg_parsed state]=parse_arg(arg_specs,varargin);
+
+% Check if parameter file exists
+if ~exist(arg_parsed.parfile,'file')
+    warning(['Specified parameter file ' arg_parsed.parfile ...
+        'does not exist. I will try to get all parameters from command-line.']);
+end
+
+[arg_specs.path.default, ...
+ arg_specs.station.default, ...
+ arg_specs.starttime.default]=...
+ read_parameters(arg_parsed.parfile,'PATH','STATION','DATE',...
+                                    {0,0,0});
+
+% Remove NaNs (no value specified in parfile) and set to required if no
+% default was specified
+for field=fields(arg_specs)'
+   if isnan(arg_specs.(field{1}).default)
+       arg_specs.(field{1})=rmfield(arg_specs.(field{1}),'default');
+       arg_specs.(field{1}).required=1;
+   end
+end
+
+% -------------------------------------------------------------------------
+% Build struct of command-line specifications
 % -------------------------------------------------------------------------
 
 %
@@ -256,20 +299,6 @@ arg_specs.station.required=1;
 arg_specs.station.dim2=5;
 arg_specs.station.type='char';
 %arg_specs.valid =  {'BFO1s';'MSN0g';'NGK0g';'NGK1g';'NGK2g'; 'NGK3g';'NGK6g';'NGK7g';'NGK8g';'WNG0g';'WNG1g';'WNG2g';'WNG3g';'VNA1s';'SHE0g';'VSS0g';'TTB0g';'TTB1l';'PUL0g';'TEL0g';'VNA1s';'VSS0g'};
-% station_array = ['SMA0g'];             
-%station_array = ['MSN0g'];
-%station_array = ['WNG1g'];
-%station_array = ['LRV1a'];
-%station_array = ['SMA0g'];
-%station_array = ['PUL0g'; 'TEL0g'];
-%station_array = ['TDC1d'];
-%station_array = ['NGK0g'];
-% station_array = ['BFO1s'];
-%station_array = ['VSS0g'];
-%station_array = ['TDC1d'];
-%station_array = ['VSS1g'];
-%station_array = ['VNA1s'];
-% station_array = ['MAR1l'];
 
 %
 % Specify optional arguments
@@ -283,8 +312,9 @@ arg_specs.DontWriteFTPDownload.valid={0,1};
 arg_specs.MakeTromsoFile.default=0;
 arg_specs.MakeTromsoFile.valid={0,1};
 
-%
-% Parse arguments
+% -------------------------------------------------------------------------
+% Parse arguments from command-line
+% -------------------------------------------------------------------------
 
 [arg_parsed state]=parse_arg(arg_specs,varargin);
 
@@ -297,9 +327,9 @@ elseif (state.err == 2) % error occured, stop execution
 end
     
 
-% -------------------------------------------------------------------------
-% Assign input arguments
-% -------------------------------------------------------------------------
+% =========================================================================
+% Assign all the parameters
+% =========================================================================
 
 DontWriteFTPDownload = arg_parsed.DontWriteFTPDownload;
 
@@ -323,27 +353,14 @@ station_array=arg_parsed.station;
 % PATHS, depending on OS
 %   
 
-opsys = computer;
-if strcmp(opsys(1:2), 'GL')  == 1
-  % root path  
-  path1 = '/nfs/magobs/magdata/data';
-  path1 = '/home/variomet/jmat'
-  bs = '/'; % slash
-elseif strcmp(opsys(1:2), 'PC')  == 1
-  path1 = 'Y:\laptop_data';
-  if strcmp(pwd, 'O:\jmat\0programme_win') % ERKENNT KATRINS RECHNER
-    path1 = 'O:\jmat';
-  end
-
-  bs = '\'; % backslash
-else
-  diplay('operating system not recognised');
-end
+path1 = arg_parsed.path;
 
-% -------------------------------------------------------------------------
-% START WITH PROCESSING
-% -------------------------------------------------------------------------
+% =========================================================================
+% Start with processing
+% =========================================================================
 
+bs=backslash;
+opsys=computer;
 array_size = 86400;
 
 timestamp_check_vs_GPS_list = []; %introduced 2014-01-26

varlab_01.m

@@ -218,6 +218,8 @@ end
                                     1, 1, 1,...
                                     1, 1, 1,...
                                     1});
+                                
+                                
                                           
 % Remove NaNs (no value specified in parfile) and set to required if no
 % default was specified
@@ -250,7 +252,7 @@ arg_specs.time.dim2=4;
 % Neighbour station 1
 arg_specs.neighbour1.type='char';
 arg_specs.neighbour1.dim1=1;
-arg_specs.neighbour1.dim2=4;
+arg_specs.neighbour1.dim2=5;
 % NOT YET USED
 arg_specs.first_diff_active.valid={0, 1};
 % NOT YET USED
@@ -312,7 +314,7 @@ end
 % Assign general parameters
 showdate        = strrep(arg_parsed.date,'-','');
 hhmm            = arg_parsed.time;
-STATION         = arg_parsed.station;       % Station name
+STATION         = arg_parsed.station(1:4);  % Station name
 NEIGHBOUR1      = arg_parsed.neighbour1;    % Neighbour 1 station name
 NEIGHBOUR2      = arg_parsed.neighbour2;    % Neighbour 2 station name
 LENGTH          = arg_parsed.length;        % Length of observation interval in minutes