added new parameter file options to specify the bounding ellipsoid directly,

the new options are region_ellipsoid_matrix[0-2] for the matrix and
region_ellipsoid_center for the ellipsoid center.

fixed a bug that caused velocity data to be used from region_point file
(need to check the units in all tools, so better to disable it atm)

plugins/point_file_reader.hh

@@ -9,6 +9,12 @@
 
 struct point_reader{
     
+    int num_columns;
+    
+    point_reader( void )
+    : num_columns( 0 )
+    { }
+    
     bool isFloat( std::string myString )
     {
         std::istringstream iss(myString);
@@ -118,6 +124,8 @@ struct point_reader{
         }
         else
             LOGERR("Problem interpreting the region point file \'%s\'", fname.c_str() );
+        
+        num_columns = colcount;
     }
     
     

plugins/region_ellipsoid.cc

@@ -508,6 +508,21 @@ public:
             point_reader pfr;
             pfr.read_points_from_file( point_file, vfac_, pp );
             
+            // if file has more than three columns, just take first three
+            // at the moment...
+            if( pfr.num_columns > 3 )
+            {
+                std::vector<double> xx;
+                xx.reserve( 3 * pp.size()/pfr.num_columns );
+                
+                for( size_t i=0; i<pp.size()/pfr.num_columns; ++i )
+                    for( size_t j=0; j<3; ++j )
+                        xx.push_back( pp[ pfr.num_columns * i + j ] );
+                
+                pp.swap( xx );
+            }
+            
+            
             if( cf.containsKey("setup","region_point_shift") )
             {
                 std::string point_shift = cf.getValue<std::string>("setup","region_point_shift");

random.cc

@@ -162,10 +162,10 @@ void rapid_proto_ngenic_rng( size_t res, long baseseed, random_numbers<T>& R )
   // copy to array that holds the random numbers
 
   #pragma omp parallel for
-  for( size_t i=0; i<res; ++i )
+  for( int i=0; i<(int)res; ++i )
     for( size_t j=0; j<res; ++j )
       for( size_t k=0; k<res; ++k )
-	R(i,j,k) = rnoise[ (i*res+j)*res+k ];
+	R(i,j,k) = rnoise[ ((size_t)i*res+j)*res+k ];
 
   delete[] rnoise;
 
@@ -194,6 +194,9 @@ random_numbers<T>::random_numbers( unsigned res, unsigned cubesize, long basesee
 	bool musicnoise = true;
 	if( !musicnoise )
 	  cubesize_ = res_;
+    
+    if( !musicnoise )
+        LOGERR("This currently breaks compatibility. Need to disable by hand! Make sure to not check into repo");
 
 	initialize();