Some uncommitted fixes to the documentation are now committed. Hopefully all...

Some uncommitted fixes to the documentation are now committed. Hopefully all the namespace issues (ie: broken links) are now fixed!

src/A3DIO.cc

@@ -17,17 +17,21 @@
 */
 #include "A3DIO.h"
 
+using namespace std;
+using namespace mio;
+
+namespace mio {
 /**
  * @page a3d A3D
  * @section a3d_format Format
- * This plugin reads legacy Alpine3D meteorological input files. It reads the meteo1d.txt file that contains, as measured at one unique location, the following fields: 
+ * This plugin reads legacy Alpine3D meteorological input files. It reads the meteo1d.txt file that contains, as measured at one unique location, the following fields:
  * - air temperature in field ta
  * - incoming short wave radiation in field iswr
  * - wind velocity in field vw
  * - relative humidity in field rh
  * - incoming long wave radiation in field ea
  * - precipitations in field nswc
- * 
+ *
  * and optionally a list of stations with their measurements (meteo2d files) for the following parameters (with YYYY being the 4-digits year):
  * - precipitations (file named precYYYY.txt)
  * - relative humidity (file named rhumYYYY.txt)
@@ -46,15 +50,13 @@
  * @section a3d_keywords Keywords
  * This plugin uses the following keywords:
  * - METEOPATH: string containing the path to the meteorological files (ie: where to find meteo1d.txt and meteo2d files)
- * - COORDSYS: input coordinate system (see Coordinate) specified in the [Input] section
- * - COORDPARAM: extra input coordinates parameters (see Coordinate) specified in the [Input] section
- * - COORDSYS: output coordinate system (see Coordinate) specified in the [Output] section
- * - COORDPARAM: extra output coordinates parameters (see Coordinate) specified in the [Output] section
+ * - COORDSYS: input coordinate system (see Coords) specified in the [Input] section
+ * - COORDPARAM: extra input coordinates parameters (see Coords) specified in the [Input] section
+ * - COORDSYS: output coordinate system (see Coords) specified in the [Output] section
+ * - COORDPARAM: extra output coordinates parameters (see Coords) specified in the [Output] section
  * - SPECIALPTSFILE: a path+file name to the a file containing grid coordinates of special points of interest (for special outputs)
  */
-
-using namespace std;
-using namespace mio;
+}
 
 const double A3DIO::plugin_nodata = -9999.0; //plugin specific nodata value
 
@@ -123,7 +125,7 @@ void A3DIO::readAssimilationData(const Date& date_in, Grid2DObject& da_out)
 	throw IOException("Nothing implemented here", AT);
 }
 
-void A3DIO::writeMeteoData(const std::vector< std::vector<MeteoData> >&, 
+void A3DIO::writeMeteoData(const std::vector< std::vector<MeteoData> >&,
 					  const std::vector< std::vector<StationData> >&,
 					  const std::string&)
 {
@@ -143,8 +145,8 @@ void A3DIO::readMeteoData(const Date& dateStart, const Date& dateEnd, std::vecto
 	readMeteoData(dateStart, dateEnd, vecMeteo, vecStation);
 }
 
-void A3DIO::readMeteoData(const Date& dateStart, const Date& dateEnd, 
-					 std::vector< std::vector<MeteoData> >& vecMeteo, 
+void A3DIO::readMeteoData(const Date& dateStart, const Date& dateEnd,
+					 std::vector< std::vector<MeteoData> >& vecMeteo,
 					 std::vector< std::vector<StationData> >& vecStation,
 					 const unsigned int& stationindex)
 {
@@ -164,7 +166,7 @@ void A3DIO::readMeteoData(const Date& dateStart, const Date& dateEnd,
 	try {
 		read2DMeteo(vecMeteo, vecStation);
 	} catch(std::exception& e){
-		std::cerr << "[E] No meteo2d data found or error while reading it, using only Meteo1D data: " 
+		std::cerr << "[E] No meteo2d data found or error while reading it, using only Meteo1D data: "
 			<< std::endl << "\t" << e.what() << std::endl;
 	}
 }
@@ -185,11 +187,11 @@ void A3DIO::convertUnits(MeteoData& meteo)
 	}
 }
 
-void A3DIO::read1DMeteo(const Date& dateStart, const Date& dateEnd, 
-				std::vector< std::vector<MeteoData> >& vecMeteo, 
+void A3DIO::read1DMeteo(const Date& dateStart, const Date& dateEnd,
+				std::vector< std::vector<MeteoData> >& vecMeteo,
 				std::vector< std::vector<StationData> >& vecStation)
 {
-	double latitude=IOUtils::nodata, longitude=IOUtils::nodata, 
+	double latitude=IOUtils::nodata, longitude=IOUtils::nodata,
 		xcoord=IOUtils::nodata, ycoord=IOUtils::nodata, altitude=IOUtils::nodata;
 	std::string tmp="", line="";
 	Date tmp_date;
@@ -213,7 +215,7 @@ void A3DIO::read1DMeteo(const Date& dateStart, const Date& dateEnd,
 	}
 
 	char eoln = IOUtils::getEoln(fin); //get the end of line character for the file
-   
+
 	//Go through file, save key value pairs
 	try {
 		//Read in station meta data
@@ -246,7 +248,7 @@ void A3DIO::read1DMeteo(const Date& dateStart, const Date& dateEnd,
 
 		//Read one line, construct Date object and see whether date is greater or equal than the date_in object
 		IOUtils::skipLines(fin, 1, eoln); //skip rest of line
-		
+
 		//Loop going through the data sequentially until dateStart is found
 		do {
 			getline(fin, line, eoln); //read complete line
@@ -297,7 +299,7 @@ bool A3DIO::readMeteoDataLine(std::string& line, MeteoData& tmpdata, std::string
 		return true;
 		//throw InvalidFormatException("Premature End of Line or no data for date " + date_in + " found in File " + filename, AT);
 	}
-      
+
 	for (int ii=0; ii<4; ii++) {
 		if (!IOUtils::convertString(tmp_ymdh[ii], tmpvec.at(ii), std::dec))
 			throw InvalidFormatException(filename + ": " + line, AT);
@@ -306,13 +308,13 @@ bool A3DIO::readMeteoDataLine(std::string& line, MeteoData& tmpdata, std::string
 	tmp_date.setDate(tmp_ymdh[0],tmp_ymdh[1],tmp_ymdh[2],tmp_ymdh[3], 0);
 
 	//Read rest of line with values ta, iswr, vw, rh, ea, hnw
-  
+
 	for (int ii=0; ii<6; ii++) { //go through the columns
 		if (!IOUtils::convertString(tmp_values[ii], tmpvec.at(ii+4), std::dec)) {
 			throw InvalidFormatException(filename + ": " + line, AT);
 		}
 	}
-     
+
 	tmpdata.setDate(tmp_date);
 	tmpdata.setData(MeteoData::TA, tmp_values[0]);
 	tmpdata.setData(MeteoData::ISWR, tmp_values[1]);
@@ -320,24 +322,24 @@ bool A3DIO::readMeteoDataLine(std::string& line, MeteoData& tmpdata, std::string
 	tmpdata.setData(MeteoData::RH, tmp_values[3]);
 	tmpdata.setData(MeteoData::ILWR, tmp_values[4]);
 	tmpdata.setData(MeteoData::HNW, tmp_values[5]);
- 	
+
 	return false;
 }
 
 
 /*
-  Preamble: Files are in METEOFILE directory. 4 types of files: 
+  Preamble: Files are in METEOFILE directory. 4 types of files:
   prec????.txt == hnw
   rh????.txt == rh
   ta????.txt == ta
   wspd????.txt == vw
-  
-  Remarks: The headers of the files may defer - for each unique 
+
+  Remarks: The headers of the files may defer - for each unique
   StationData one MeteoData and one StationData object will be created
 */
  void A3DIO::read2DMeteo(std::vector< std::vector<MeteoData> >& vecMeteo, std::vector< std::vector<StationData> >& vecStation)
 {
-	
+
 	unsigned int stations=0, bufferindex=0;
 	std::map<std::string, unsigned int> hashStations = std::map<std::string, unsigned int>();
 	std::vector<std::string> filenames = std::vector<std::string>();
@@ -345,9 +347,9 @@ bool A3DIO::readMeteoDataLine(std::string& line, MeteoData& tmpdata, std::string
 	//Requirement: meteo1D data must exist:
 	if ((vecMeteo.size() == 0) || (vecMeteo[0].size() == 0))
 		return;
-	
+
 	//1D and 2D data must correspond, that means that if there is 1D data
-	//for a certain date (e.g. 1.1.2006) then 2D data must exist (prec2006.txt etc), 
+	//for a certain date (e.g. 1.1.2006) then 2D data must exist (prec2006.txt etc),
 	//otherwise throw FileNotFoundException
 	Date startDate(vecMeteo[0][0].date);
 	Date endDate(vecMeteo[0][vecMeteo[0].size()-1].date);
@@ -359,8 +361,8 @@ bool A3DIO::readMeteoDataLine(std::string& line, MeteoData& tmpdata, std::string
 	std::cerr << "[I] Number of 2D meteo stations: " << stations << std::endl;
 
 	if (stations < 1) {
-		throw InvalidFormatException("No StationData found in 2D Meteo Files", AT); 
-	} 
+		throw InvalidFormatException("No StationData found in 2D Meteo Files", AT);
+	}
 
 	std::vector<StationData> tmpvecS = std::vector<StationData>(stations); //stores unique stations
 
@@ -389,7 +391,7 @@ bool A3DIO::readMeteoDataLine(std::string& line, MeteoData& tmpdata, std::string
 			read2DMeteoData(filenames[2], "ta", hashStations, vecMeteo, bufferindex);
 			bufferindex = currentindex;
 			read2DMeteoData(filenames[3], "vw", hashStations, vecMeteo, bufferindex);
-			
+
 			if(filenames.size() == 5) { //for keeping dw optional
 				bufferindex = currentindex;
 				read2DMeteoData(filenames.at(4), "dw", hashStations, vecMeteo, bufferindex);
@@ -405,14 +407,14 @@ bool A3DIO::readMeteoDataLine(std::string& line, MeteoData& tmpdata, std::string
 		//clear all 2D meteo data if error occurs
 		if (vecMeteo.size() > 1)
 			vecMeteo.erase(vecMeteo.begin()+1, vecMeteo.end());
-		
+
 		if (vecStation.size() > 1)
 			vecStation.erase(vecStation.begin()+1, vecStation.end());
 
 		cleanup();
 		throw;
 	}
-  
+
 	//clean data and convert the units
 	for (unsigned int ii=1; ii<vecMeteo.size(); ii++) { //loop over all stations except 1D Meteo
 		for (unsigned int jj=0; jj<vecMeteo[ii].size(); jj++){ //Meteo1D data already cleaned
@@ -428,7 +430,7 @@ void A3DIO::constructMeteo2DFilenames(const Date& startDate, const Date& endDate
 	std::string tmp;
 
 	filenames.clear();
- 
+
 	startDate.getDate(startyear, dummy, dummy, dummy, dummy);
 	endDate.getDate(endyear, dummy, dummy, dummy, dummy);
 	cfg.getValue("METEOPATH", "Input", tmp);
@@ -447,7 +449,7 @@ void A3DIO::constructMeteo2DFilenames(const Date& startDate, const Date& endDate
 		filenames.push_back(rhFilename);
 		filenames.push_back(taFilename);
 		filenames.push_back(wspdFilename);
-		
+
 		if (IOUtils::fileExists(wdirFilename)) //keeping wdir optional
 			filenames.push_back(wdirFilename);
 	}
@@ -464,7 +466,7 @@ unsigned int A3DIO::getNrOfStations(std::vector<std::string>& filenames, std::ma
 {
 	std::vector<std::string> tmpvec;
 	std::string line_in="";
-  
+
 	for (unsigned int ii=0; ii<filenames.size(); ii++) {
 		//cout << *it << endl;
 		std::string filename = filenames[ii];
@@ -472,10 +474,10 @@ unsigned int A3DIO::getNrOfStations(std::vector<std::string>& filenames, std::ma
 		fin.clear();
 		fin.open (filename.c_str(), std::ifstream::in);
 		if (fin.fail()) throw FileAccessException(filename, AT);
-  
+
 		char eoln = IOUtils::getEoln(fin); //get the end of line character for the file
 
-		IOUtils::skipLines(fin, 4, eoln); 
+		IOUtils::skipLines(fin, 4, eoln);
 		getline(fin, line_in, eoln); //5th line holds the names of the stations
 		unsigned int cols = IOUtils::readLineToVec(line_in, tmpvec);
 		if ( cols > 4) { // if there are any stations
@@ -489,16 +491,16 @@ unsigned int A3DIO::getNrOfStations(std::vector<std::string>& filenames, std::ma
 			}
 		}
 		cleanup();
-	}  
-  
+	}
+
 	return (hashStations.size());
 }
 
-void A3DIO::read2DMeteoData(const std::string& filename, const std::string& parameter, 
-					std::map<std::string,unsigned int>& hashStations, 
+void A3DIO::read2DMeteoData(const std::string& filename, const std::string& parameter,
+					std::map<std::string,unsigned int>& hashStations,
 					std::vector< std::vector<MeteoData> >& vecM, unsigned int& bufferindex)
 {
-	
+
 	std::string line_in = "";
 	unsigned int columns;
 	std::vector<std::string> tmpvec, vec_names;
@@ -512,7 +514,7 @@ void A3DIO::read2DMeteoData(const std::string& filename, const std::string& para
 	}
 
 	char eoln = IOUtils::getEoln(fin); //get the end of line character for the file
-	
+
 	IOUtils::skipLines(fin, 4, eoln); //skip first 4 lines
 	getline(fin, line_in, eoln); //line containing UNIQUE station names
 	columns = IOUtils::readLineToVec(line_in, vec_names);
@@ -523,7 +525,7 @@ void A3DIO::read2DMeteoData(const std::string& filename, const std::string& para
 	MeteoData& lastMeteoData = vecM[0][vecM[0].size()-1]; //last time stamp in buffer of 1D meteo
 
 	do {
-		getline(fin, line_in, eoln); 
+		getline(fin, line_in, eoln);
 		std::string tmpline = line_in;
 		IOUtils::trim(tmpline);
 
@@ -532,11 +534,11 @@ void A3DIO::read2DMeteoData(const std::string& filename, const std::string& para
 		}
 
 		if (IOUtils::readLineToVec(line_in, tmpvec)!=columns) { //Every station has to have its own column
-			throw InvalidFormatException("Premature End of Line or no data for date " 
-			                             + vecM[0][bufferindex].date.toString(Date::FULL) + " found in File " 
+			throw InvalidFormatException("Premature End of Line or no data for date "
+			                             + vecM[0][bufferindex].date.toString(Date::FULL) + " found in File "
 			                             + filename, AT);
 		}
-    
+
 		for (int ii=0; ii<4; ii++) {
 			if (!IOUtils::convertString(tmp_ymdh[ii], tmpvec[ii], std::dec)) {
 				throw InvalidFormatException("Check date columns in " + filename, AT);
@@ -548,7 +550,7 @@ void A3DIO::read2DMeteoData(const std::string& filename, const std::string& para
 		if (tmp_date == currentMeteoData.date) {
 			//Read in data
 			for (unsigned int ii=4; ii<columns; ii++) {
-				unsigned int stationnr = hashStations[vec_names.at(ii)]; 
+				unsigned int stationnr = hashStations[vec_names.at(ii)];
 				MeteoData& tmpmd = vecM[stationnr][bufferindex];
 				tmpmd.date = tmp_date;
 
@@ -556,31 +558,31 @@ void A3DIO::read2DMeteoData(const std::string& filename, const std::string& para
 					if (!IOUtils::convertString(tmpmd.hnw, tmpvec[ii], std::dec)) {
 						throw ConversionFailedException("For hnw value in " + filename + "  for date " + tmpmd.date.toString(Date::FULL), AT);
 					}
-	  
+
 				} else if (parameter == "rh") {
 					if (!IOUtils::convertString(tmpmd.rh, tmpvec[ii], std::dec)) {
 						throw ConversionFailedException("For rh value in " + filename + "  for date " + tmpmd.date.toString(Date::FULL), AT);
 					}
-	  
+
 				} else if (parameter == "ta") {
-					if (!IOUtils::convertString(tmpmd.ta, tmpvec[ii], std::dec)) 
+					if (!IOUtils::convertString(tmpmd.ta, tmpvec[ii], std::dec))
 						throw ConversionFailedException("For ta value in " + filename + "  for date " + tmpmd.date.toString(Date::FULL), AT);
-    
+
 				} else if (parameter == "vw") {
-					if (!IOUtils::convertString(tmpmd.vw, tmpvec[ii], std::dec)) { 
+					if (!IOUtils::convertString(tmpmd.vw, tmpvec[ii], std::dec)) {
 						throw ConversionFailedException("For vw value in " + filename + "  for date " + tmpmd.date.toString(Date::FULL), AT);
 					}
 				} else if (parameter == "dw") {
-					if (!IOUtils::convertString(tmpmd.dw, tmpvec[ii], std::dec)) { 
+					if (!IOUtils::convertString(tmpmd.dw, tmpvec[ii], std::dec)) {
 						throw ConversionFailedException("For dw value in " + filename + "  for date " + tmpmd.date.toString(Date::FULL), AT);
 					}
 				}
 			}
-			
+
 			bufferindex++;
 		}
 	} while((tmp_date<lastMeteoData.date) && (!fin.eof()));
-	
+
 	cleanup();
 }
 
@@ -596,7 +598,7 @@ void A3DIO::read2DMeteoHeader(const std::string& filename, std::map<std::string,
 	if (fin.fail()) {
 		throw FileAccessException(filename, AT);
 	}
-  
+
 	char eoln = IOUtils::getEoln(fin); //get the end of line character for the file
 
 	IOUtils::skipLines(fin, 1, eoln);
@@ -645,7 +647,7 @@ void A3DIO::read2DMeteoHeader(const std::string& filename, std::map<std::string,
 		    || (!IOUtils::convertString(easting, vec_xcoord.at(ii), std::dec))
 		    || (!IOUtils::convertString(northing, vec_ycoord.at(ii), std::dec))
 		    || (!IOUtils::convertString(stationName, vec_names.at(ii), std::dec))) {
-			throw ConversionFailedException("Conversion of station description failed in " + filename, AT);  
+			throw ConversionFailedException("Conversion of station description failed in " + filename, AT);
 		}
 		coordinate.setXY(easting, northing, altitude);
 		vecS[stationnr-1].stationName = stationName;
@@ -673,7 +675,7 @@ void A3DIO::readSpecialPoints(std::vector<Coords>& pts)
 	char eoln = IOUtils::getEoln(fin); //get the end of line character for the file
 
 	while (!fin.eof()) {
-		getline(fin, line_in, eoln); 
+		getline(fin, line_in, eoln);
 
 		if (IOUtils::readLineToVec(line_in, tmpvec)==2) { //Try to convert
 			int x, y;
@@ -702,7 +704,7 @@ void A3DIO::readSpecialPoints(std::vector<Coords>& pts)
 void A3DIO::write2DGrid(const Grid2DObject&, const std::string&)
 {
 	//Nothing so far
-	throw IOException("Nothing implemented here", AT);	
+	throw IOException("Nothing implemented here", AT);
 }
 
 

src/ConfigReader.h

@@ -31,14 +31,14 @@ namespace mio {
 
 /**
  * @class ConfigReader
- * @brief A class that reads a key/value file. These files (typically named *.ini) have the following structure:
+ * @brief A class that reads a key/value file. These files (typically named *.ini) follow the INI file format standard (see http://en.wikipedia.org/wiki/INI_file) and have the following structure:
  * - they consist of 0 or more explicitly indicated sections, which start with a sectionname enclosed in square brackets
  *   e.g. [General] or [Filter]
- * - within each section there are 0 or more key value pairs defined: KEY = VALUE 
+ * - within each section there are 0 or more key value pairs defined: KEY = VALUE
  * - in this implementation each key is unique within its section
  * - lines that start with a semicolon ';' or a hash sign '#' are ignored (regarded as comments)
  * - empty lines are ignored
- * - if there is no section name given in a file, the default section called "GENERAL" is assumed 
+ * - if there is no section name given in a file, the default section called "GENERAL" is assumed
  * - a VALUE for a KEY can consist of multiple whitespace separated values (e.g. MYNUMBERS = 17.77 -18.55 8888 99.99)
  *
  * @author Thomas Egger
@@ -49,7 +49,7 @@ namespace IOUtils {
 	void toUpper(std::string& str);
 	template <class T> void getValueForKey(const std::map<std::string,std::string>& properties,
 								    const std::string& key, T& t);
-	template <class T> void getValueForKey(const std::map<std::string,std::string>& properties, 
+	template <class T> void getValueForKey(const std::map<std::string,std::string>& properties,
 								    const std::string& key, std::vector<T>& vecT);
 }
 
@@ -115,12 +115,12 @@ class ConfigReader {
 		 * @param[out] vecT a variable of class vector<T> into which the values for the corresponding key are saved
 		 * @param[in] options indicating whether an exception should be raised, when key is not present
 		 */
-		template <class T> void getValue(const std::string& key, 
-								   std::vector<T>& vecT, 
+		template <class T> void getValue(const std::string& key,
+								   std::vector<T>& vecT,
 								   const unsigned int& options=0) const {
 			getValue(key, "GENERAL", vecT, options);
 		}
-		
+
 		/**
 		 * @brief Template function to retrieve a vector of values of class T for a certain key
 		 * @code
@@ -129,12 +129,12 @@ class ConfigReader {
 		 * @endcode
 		 * @param[in] key std::string representing a KEY in the key/value file
 		 * @param[in] section std::string representing a section name; the key has to be part of this section
-		 * @param[out] vecT a variable of class vector<T> into which the values for the corresponding key are saved 
+		 * @param[out] vecT a variable of class vector<T> into which the values for the corresponding key are saved
 		 * @param[in] options indicating whether an exception should be raised, when key is not present
 		 */
-		template <class T> void getValue(const std::string& key, 
-								   const std::string& section, 
-								   std::vector<T>& vecT, 
+		template <class T> void getValue(const std::string& key,
+								   const std::string& section,
+								   std::vector<T>& vecT,
 								   const unsigned int& options=0) const {
 			try {
 				vecT.clear();
@@ -166,8 +166,8 @@ class ConfigReader {
 		 * @param[out] t a variable of class T into which the value for the corresponding key is saved (e.g. double, int, std::string)
 		 * @param[in] options indicating whether an exception should be raised, when key is not present
 		 */
-		template <class T> void getValue(const std::string& key, const std::string& section, 
-								   T& t, 
+		template <class T> void getValue(const std::string& key, const std::string& section,
+								   T& t,
 								   const unsigned int& options=0) const {
 			try {
 				std::string _section = section;
@@ -180,7 +180,7 @@ class ConfigReader {
 				}
 			}
 		}
-		
+
 
 		/**
 		 * @brief Function that searches for a given string within the keys of section (default: GENERAL)
@@ -194,7 +194,7 @@ class ConfigReader {
 		 *  unsigned int nrOfMatches = getKeys(myVec, "TA::", "Filters");
 		 * @endcode
 		 */
-		unsigned int findKeys(std::vector<std::string>& vecResult, 
+		unsigned int findKeys(std::vector<std::string>& vecResult,
 						  const std::string keystart, const std::string section="GENERAL") const;
 
 		static const unsigned int nothrow;

src/Coords.cc

@@ -24,6 +24,7 @@
 using namespace std;
 using namespace mio;
 
+namespace mio {
  /**
  * @page coords Available coordinate systems
  * Geographic coordinates will be transparently and automatically converted to lat/lon and any other coordinate system that
@@ -58,6 +59,7 @@ using namespace mio;
  * @endcode
  *
  */
+}
 
 const struct mio::Coords::ELLIPSOID mio::Coords::ellipsoids[] = {
 	{ 6378137.,	6356752.3142 }, ///< E_WGS84
@@ -356,12 +358,12 @@ void Coords::setGridIndex(const int _grid_i, const int _grid_j, const int _grid_
 }
 
 /**
-* \anchor Coordinate_types
 * @brief Set projection to use
 * This projection will be used for converting between lat/lon and East/North
 * @param[in] _coordinatesystem string identifying the coordinate system to use
 * @param[in] _parameters string giving some additional parameters for the projection (optional)
 *
+*  \anchor Coordinate_types
 * The coordinate system can be any of the following:
 * - CH1903 for coordinates in the Swiss Grid [ref: http://geomatics.ladetto.ch/ch1903_wgs84_de.pdf]
 * - UTM for UTM coordinates (the zone must be specified in the parameters, for example 31T) [ref: http://www.oc.nps.edu/oc2902w/maps/utmups.pdf]

src/FilterAlgorithms.cc

@@ -17,32 +17,33 @@
 */
 #include "FilterAlgorithms.h"
 
+using namespace std;
+using namespace mio;
+
+namespace mio {
  /**
  * @page filters Filters overview
  * The filtering infrastructure is described in FilterAlgorithms (for its API). The goal of this page is to give an overview of the available filters and their usage.
- * 
+ *
  * @section filters_modes Modes of operation
  * It should be noted that filters often have two modes of operations: soft or hard. In soft mode, all value that is rejected is replaced by the filter parameter's value. This means that for a soft min filter set at 0.0, all values less than 0.0 will be replaced by 0.0. In hard mode, all rejected values are replaced by nodata.
  *
  * @section filters_available Available filters
  * The filters that are currently available are the following:
- * - rate: rate of change filter, see mio::FilterAlgorithms::RateFilter
- * - min_max: range check filter, see mio::FilterAlgorithms::MinMaxFilter
- * - min: minimum check filter, see mio::FilterAlgorithms::MinValueFilter
- * - max: maximum check filter, see mio::FilterAlgorithms::MaxValueFilter
- * - mad: median absolute deviation, see mio::FilterAlgorithms::MedianAbsoluteDeviationFilter
- * 
+ * - rate: rate of change filter, see FilterAlgorithms::RateFilter
+ * - min_max: range check filter, see FilterAlgorithms::MinMaxFilter
+ * - min: minimum check filter, see FilterAlgorithms::MinValueFilter
+ * - max: maximum check filter, see FilterAlgorithms::MaxValueFilter
+ * - mad: median absolute deviation, see FilterAlgorithms::MedianAbsoluteDeviationFilter
+ *
  * A few data transformations are also supported besides filtering:
- * - accumulate: data accumulates over a given period, see mio::FilterAlgorithms::AccumulateProcess
- * - resample: linear data resampling, mio::FilterAlgorithms::LinResamplingProcess
- * - median_avg: running median average over a given window, see mio::FilterAlgorithms::MedianAvgProcess
- * - mean_avg: running mean average over a given window, see mio::FilterAlgorithms::MeanAvgProcess
- * - wind_avg: vector average over a given window, see mio::FilterAlgorithms::WindAvgProcess
+ * - accumulate: data accumulates over a given period, see FilterAlgorithms::AccumulateProcess
+ * - resample: linear data resampling, FilterAlgorithms::LinResamplingProcess
+ * - median_avg: running median average over a given window, see FilterAlgorithms::MedianAvgProcess
+ * - mean_avg: running mean average over a given window, see FilterAlgorithms::MeanAvgProcess
+ * - wind_avg: vector average over a given window, see FilterAlgorithms::WindAvgProcess
  */
-
-using namespace std;
-using namespace mio;
-
+}
 #define PI 3.141592653589
 
 std::map<std::string, FilterProperties> FilterAlgorithms::filterMap;
@@ -81,7 +82,7 @@ void FilterAlgorithms::parseFilterArguments(const std::string& filtername, const
 {
 	isSoft = false;
 	unsigned int argindex = 0;
-	vecArgs_out.clear(); 
+	vecArgs_out.clear();
 	double tmp;
 
 	//Test for softness
@@ -102,7 +103,7 @@ void FilterAlgorithms::parseFilterArguments(const std::string& filtername, const
 	}
 }
 
-void FilterAlgorithms::parseWindowFilterArguments(const std::string& filtername, 
+void FilterAlgorithms::parseWindowFilterArguments(const std::string& filtername,
                                                   const std::vector<std::string>& vecArgs_in,
                                                   const unsigned int& minArgs, const unsigned int& maxArgs,
                                                   bool& isSoft, std::string& windowposition, std::vector<double>& vecArgs_out)
@@ -113,7 +114,7 @@ void FilterAlgorithms::parseWindowFilterArguments(const std::string& filtername,
 	for (unsigned int ii=0; ii<vecArgs_in.size(); ii++){
 		//Check for "left", "right" or "center" keywords
 		if ((vecArgs_in[ii] == "center") || (vecArgs_in[ii] == "left") || (vecArgs_in[ii] == "right")){
-			if (alreadyDefined) 
+			if (alreadyDefined)
 				throw InvalidArgumentException("Invalid or redefined arguments for filter " + filtername, AT);
 			windowposition = vecArgs_in[ii];
 			alreadyDefined = true;
@@ -125,7 +126,7 @@ void FilterAlgorithms::parseWindowFilterArguments(const std::string& filtername,
 	parseFilterArguments(filtername, vecArgs_new, minArgs, maxArgs, isSoft, vecArgs_out);
 }
 
-bool FilterAlgorithms::getWindowData(const std::string& filtername, const std::vector<MeteoData>& vecM, 
+bool FilterAlgorithms::getWindowData(const std::string& filtername, const std::vector<MeteoData>& vecM,
                                      const unsigned int& pos,
                                      const Date& date, const std::vector<std::string>& _vecArgs,
                                      const unsigned int& paramindex, std::vector<double>& vecWindow,
@@ -134,7 +135,7 @@ bool FilterAlgorithms::getWindowData(const std::string& filtername, const std::v
 	vecWindow.clear();
 	bool isSoft = false;
 	std::string windowposition = "center"; //the default is a centered window
-	std::vector<double> vecArgs; 
+	std::vector<double> vecArgs;
 	parseWindowFilterArguments(filtername, _vecArgs, 2, 2, isSoft, windowposition, vecArgs);
 
 	if (vecArgs[0] < 1) //the window size has to be at least 1
@@ -145,7 +146,7 @@ bool FilterAlgorithms::getWindowData(const std::string& filtername, const std::v
 	//Deal with first parameter: minimal number of data points
 	unsigned int windowSize = (unsigned int)vecArgs[0];
 	unsigned int increment = 0;
-	if (windowposition=="right"){ 
+	if (windowposition=="right"){
 		increment = (unsigned int)windowSize - 1; //window reaches to the right
 		if ((date != vecM[pos].date) && (increment>0)) increment--;
 	} else if (windowposition=="left") {
@@ -194,7 +195,7 @@ bool FilterAlgorithms::getWindowData(const std::string& filtername, const std::v
 			} else {
 				if (startposition<(vecM.size()-1)) startposition++;
 				else return false; //time window not big enough
-			}			
+			}
 		} else if ((windowposition == "center") && (isSoft)){ //expand to left and right (whereever possible)
 			if ((endposition+startposition)%2 == 0) { //try to alternate when broadening window
 				if (endposition > 0) endposition--;
@@ -204,16 +205,16 @@ bool FilterAlgorithms::getWindowData(const std::string& filtername, const std::v
 				if (startposition<(vecM.size()-1)) startposition++;
 				else if (endposition > 0) endposition--;
 				else return false; //time window not big enough
-			}	
+			}
 		}
 	}
-	
+
 	//Date gap(vecM[startposition].date - vecM[endposition].date);
 	//cout << "The final gap is " << gap << "  windowposition: " << windowposition << endl;
 
 	//Push all relevant data elements into the vector vecWindow
 	//cout << "Start: " << startposition << "  End: " << endposition << endl;
-	for (unsigned int ii=startposition+1; (ii--) > endposition; ){		
+	for (unsigned int ii=startposition+1; (ii--) > endposition; ){
 		const double& tmp = vecM[ii].param(paramindex);
 		if (tmp != IOUtils::nodata) {