Adapting compare.py to allow for non tipsy files

genetIC/src/simulation/field/maskfield.hpp

@@ -75,19 +75,15 @@ namespace fields {
 
           // Loop over all cells and see if it is contained in the next level grid
           // grid.containsPoint might be the useful method
-          // This loop should be easily pragma openmped
 
           auto current_grid = this->multiLevelContext->getGridForLevel(level);
           auto next_level_grid = this->multiLevelContext->getGridForLevel(level + 1);
 
 #pragma omp parallel for
           for (size_t i = 0; i < current_grid.size3; i++) {
-            Coordinate<int> cell_coord = current_grid.getCellCoordinate(i);
-
-            if (next_level_grid.containsCellWithCoordinate(cell_coord)) {
+            Coordinate<T> cell_coord(current_grid.getCellCentroid(i));
+            if (next_level_grid.containsPoint(cell_coord)) {
               this->getFieldForLevel(level).getDataVector()[i] = 1;
-            } else {
-              this->getFieldForLevel(level).getDataVector()[i] = 0;
             }
           }
 

genetIC/src/simulation/grid/grid.hpp

@@ -169,6 +169,7 @@ namespace grids {
       return false;
     }
 
+    //! True if point in physical coordinates is on this grid
     virtual bool containsPoint(const Coordinate<T> &coord) const {
       return Window<T>(periodicDomainSize, offsetLower, offsetLower + thisGridSize).contains(coord);
     }
@@ -183,11 +184,15 @@ namespace grids {
       return pos;
     }
 
+    //! True if cell with pixel coordinates is on this grid
+    /*! Does not take into account offset or physical coordinates
+     */
     virtual bool containsCellWithCoordinate(Coordinate<int> coord) const {
       return coord.x >= 0 && coord.y >= 0 && coord.z >= 0 &&
              (unsigned) coord.x < size && (unsigned) coord.y < size && (unsigned) coord.z < size;
     }
 
+    //! True if cell number is less than Ncell cubed
     virtual bool containsCell(size_t i) const {
       return i < size3;
     }
@@ -241,7 +246,7 @@ namespace grids {
       return getCellIndexNoWrap(coordinate.x, coordinate.y, coordinate.z);
     }
 
-
+    //! Returns cell id in pixel coordinates
     Coordinate<int> getCellCoordinate(int id) const {
       size_t x, y;
 
@@ -263,7 +268,9 @@ namespace grids {
       return kMin;
     }
 
-
+    //! Returns coordinate of centre of cell id, in physical box coordinates
+    /*! Takes into account grid offsets wrt base grid, pixel size etc
+     */
     Coordinate<T> getCellCentroid(size_t id) const {
       Coordinate<int> coord = getCellCoordinate(id);
       return getCellCentroid(coord);

genetIC/tests/compare.py

@@ -45,9 +45,10 @@ def default_comparisons():
     for ps, ps_test in zip(powspecs, powspecs_test):
         compare_ps(ps,ps_test)
 
-    output_file = glob.glob(sys.argv[1]+"/*.tipsy")
-    assert len(output_file)==1, "Could not find a unique output file to test against"
-    compare(pynbody.load(output_file[0]),pynbody.load(sys.argv[1]+"/reference_output"))
+    if os.path.exists(sys.argv[1]+"/*.tipsy"):
+        output_file = glob.glob(sys.argv[1]+"/*.tipsy")
+        assert len(output_file)==1, "Could not find a unique output file to test against"
+        compare(pynbody.load(output_file[0]),pynbody.load(sys.argv[1]+"/reference_output"))
 
 if __name__=="__main__":
     warnings.simplefilter("ignore")

genetIC/tests/test_08a_output_grafic/paramfile.txt

@@ -1,4 +1,5 @@
 # Test grafic output, especially if refinement masks are generated correctly
+# Test is done on numpy arrays rather than tipsy files as usually done
 
 
 # output parameters
@@ -14,26 +15,31 @@ s8  0.817
 zin	99
 camb    ../camb_transfer_kmax40_z0_post2015.dat
 
+# fourier seeding
+seed	8896131
+
 # basegrid 50 Mpc/h, 64^3
 basegrid 50.0 64
 
-centre 32.5 32.5 32.5
+centre 49 25 25
 select_nearest
 zoomgrid 2 64
 
-centre 32.5 32.5 32.5
+centre 49 25 25
 select_nearest
 zoomgrid 2 64
 
-# fourier seeding
-seed	8896131
+centre 49 25 25
+select_nearest
+zoomgrid 2 64
 
+centre 49 25 25
+select_sphere 2
 
 done
 
 dump_mask 0
 dump_mask 1
 dump_mask 2
 dump_mask 3
-dump_mask 4