Finalization of the new filtering infrastructure: speed optimizations (IOManager, MeteoProcessor), clean up

The definition of the "<<" operator has been written for IOManager and made more consistent for others

Added functionality to the Meteo2DInterpolator: it is now possible to access the iomanager and hence to access historical data points from within any spatial interpolation.

The IOManager has been expanded to:
1) cache already filtered data points and
2) provide a getAvgSamplingRate() function that returns the average data points seen per day.

Introducing the new IOManager - the user interface to meteoio. This version is fully backwards compatible, but does not incorporate all features of the BufferedIOHandler: the grid reading and writing are currently not supported by this IOManager.

MeteoData now has an extra public member variable: StationData meta. It will hold the meta information of the measurment instead of dragging along a second vector<StationData> alongside the vector<MeteoData> everywhere.

This has huge implications: the IOInterface has been rewritten, subsequently changes need to be propagated into all plugins and all modules dealing with meta data.

Small bugfix for BufferedIOHandler, in some cases the rebuffering did not occur, even though buffer was at its end.

Small adjustments to accumulate resampling filter: return IOUtils::nodata in all cases where accumulation is not possible

The comparison operator of Coords has been reviewed and improved. The << operator that is not available for a parclass (for popc) can be replaced with IOHandler.toString() for POPC

Temporary fix for the << operator and POPC: a par class can not have a "friend" method... (so IOHandler can not redefine "<<" the way we used to do). Therefore, it has been disabled for popc

More debugging help: the "<<" operator has been redefined for MeteoFilter, MeteoProcessor and BufferedIOHandler. Since the Config object is copied all over the place, it is not always printed.

The bufferAlways method of BufferedIOHandler has been renamed as setBufferProperties. The A3DIO, IMISIO, SMETIO and SNIO plugins now correctly support time zones. The plugin howto documentation now warns the developer to take care of time zones issues.

The DEMObject was not properly buffered (the update flag was not honored), this has been fixed. The A3DIO plugin now implements readStationData. A few speed improvements have been brought to A3DIO and SMETIO by using the "reserve" method of the vectors (so that the vectors don't have to reallocate memory constantly).

MeteoData is now able to hold any meteo parameters, however the ones in MeteoData::Parameters are the only ones that go through the filtering and resampling for now. To add a new parameter to a MeteoData object do the following:

md.addParameter("VVT");
md.param("VVT") = 222.0;

Added feature to BufferedIOHandler: By calling readStationData(date, vecStations) an extra attempt will be made to fill the StationData object with other values than nodata in readMeteoData(date, vecMeteo, vecStation), if the object is not already different from nodata.

Implementation of binary search in IOUtils::seek(date, vecMeteo) - therefore the implementation of seek in BufferedIOHandler became obsolete. BufferedIOHandler now fully relies on IOUtils::seek and IOUtils::npos.

The new filtering and resampling framework. Filtering/Processing and Resampling have been separated from each other, the Resampling is now done with the class Meteo1DInterpolator which utilizes the static algorithms within ResamplingAlgorithms. The filtering remains a task of class MeteoFilter. The calling of the resampling and filtering as well as the data selection is now based in the facade class MeteoProcessor. MeteoProcessor::processData function calls the filtering algorithms, then passes the filtered data to the resampling algorithms and finally runs a "check only" filtering pass.

The filtering system underwent some changes in order to simplify the tasks at hand, the interface has changed.

The RateFilter is currently disfunctional, needs to be reimplemented.

Changes to StationData: new string stationID (shortname)  to describe a station in short, stationName shall be used for long description of a station. changes required an adaptation within the plugins

Changes to ConfigReader: comments may appear anywhere (also after key value pairs or section names), everything after a '#' or ';' is disregarded.

PGMIO: small fix: xllcorner mixed up with yllcorner

FilterAlgorithms: extrapolate algorithm refined

Overall all include statements within in the library have been replaced by angle brackets, the default install path for the include file is $CMAKE_INSTALL_DIR/include/meteoio, the meteoio libraries (static and shared) will be installed in $CMAKE_INSTALL_DIR/lib per default.

The plugins will be installed in the subdirectory $CMAKE_INSTALL_DIR/lib/meteoio/plugins

Then, the remaining namespace issues with doxygen have been fixed, by enclosing the full class implementation in the namespace (as seen for the libstdc++). This removes all these irritating issues. But the popc version has been broken by the change (as seen in LegacyIO).

Changed the name of the Date_IO class to Date. In case of namespace conflicts, just use mio::Date to reference the MeteoIO Date class.

The Date_IO class has been deeply rewriten. The conversion methods have been checked (with references added), the class now uses real julian date (internally as a reference) and can generate a variety of outputs (julian, modified julian, truncated julian, unix, excel). It also works properly with time zones and a simplified version of dayligh saving time (it assumes that DST always introduces a +1 hour shift, which should always be true but on one AUstralian Island: Lord Howe Island). Some now invalid calls have been fixed in plugins (the short setDate(yy,mm,dd) call is now longer supported but migth be misinterpreted by the compiler for another call, despite types mismatch).

A new example code has been added: time.cc

changed the way we deal with the projection parameters within the io.ini. COORDSYS must be declared in the [Input] section and is optional for the [Output] section (it becomes mandatory if a function is to be used, that creates output)

The parsing of the ConfigReader object is done in IOUtils, this is not the final solution on that.

Corrected a few bugs within ImisIO.cc and made the cmake compilation of the ImisIO plugin more convenient. Two paths need to be configured: One where the instantclient include files are located and one to specify where the libs occi and clntsh are to be found

The << operator has been overloaded for a few types (Arrays, Grids, Coords, Dates, Meteo and Station data) and the to_String() methods removed (except for Dates because it might make sense there to get a string) as a way to provide easy debugging output. This makes the meteo_reading example even simpler! 

The minimum required CMake has been changed to an earlier version (it seems to work fine). 

a new function called: readStationData has been added. It expects a date and a vector<StationData> as parameters and returns the meta data for the required date (often this date is irrelevant, because stations are fixed, then just pass any date).

replaced the io.ini parameters BUFFERSTRATEGY and BUFFERBEFORE BUFFERAFTER with two functions to be excplicitly called for the same effect: bufferAlways(bool) and setBufferDuration(Date_IO bufferbefore, Date_IO bufferafter)

The buffering system shows itself improved - a fine tuning of the performance is possible through the following tags:
BUFFERSTRATEGY = [always | newinterval] # default: always
BUFFERPERIOD = 1 2 

The BUFFERPERIOD tag configures the amount of days before and after a requested date the BufferedIOHandler will try to buffer. The BUFFERSTRATEGY determines how the buffer reacts if it already tried to buffer a certain interval and another date out of that interval is requested: "always" means a rebuffering is always attempted, newinterval means that rebuffering is not attempted if a requested date falls into a previously extracted interval.

The plugin's interface (IOInterface) has been slightly modified: readSpecialPoints now returns a vector of Coords. This means that a plugin can provide coordinates as (lat,long) or (easting, northing) or (grid_i, grid_j). All the plugins have been modified accordingly and POINTS and POINTSArray have been removed from Array.h

The Special_PTS and CSpecialPointsArray structures have been renamed in "POINT" and "POINTSArray" (there was no reason to call them "special points"). 

A few new methods have been added to DEMObject: getPointsBetween that returns a vector containing the indices of all points located on the line between two points (given by their real world (x,y) coordinates), horizontalDistance that returns the horizontal distance between two points and terrainDistance that returns the distance between two point accros the terrain as described by the DEM (ie: going up and down the terrain).

A new slope computation algorithm has bee added: CARD It computes the slope using Corripio and then discretizes the azimuth along 8 cardinal directions and the slope by degrees. This should be all that GEOtop needs for its drainage direction (then simply calling a dem.update("CARDINAL")).

The copyright notices have been put in place in all files (headers and cc) with proper attribution of copyright.

The documentation has been improved, specially fixing issue 22. Warning messages of doxygen have been fixed. An example subdirectory has been created in /doc and contains (currently) 2 examples of code using MeteoIO.

The MeteoFilter class instance is a private member of BufferedIOHandler - that way it only needs to be created once - the ConfigReader object is only parsed once ...

MeteoFilter operates on static filter algorithms which are defined in FilterAlgorithms.*
FilterProperties is a small helper class to declare properties of an Algorithm (e.g. how many data points it requires, ...)
The new MeteoFilter system is utilized by class BufferedIOHandler.

The old filter system is removed from Makefiles/CMake and the SVN directory.
Legacy MeteoIO classes Meteo1DResampler and MeteoBuffer, which were solely required by the old filter system are also removed.