Refactor AddGress UserObject build process

gprMax/cmds_geometry/add_grass.py

@@ -64,7 +64,7 @@ class AddGrass(UserObjectGeometry):
         self.kwargs["p1"] = tuple(rot_pts[0, :])
         self.kwargs["p2"] = tuple(rot_pts[1, :])
 
-    def build(self, grid, uip):
+    def build(self, model, uip):
         """Add Grass to fractal box."""
         try:
             p1 = self.kwargs["p1"]
@@ -91,7 +91,7 @@ class AddGrass(UserObjectGeometry):
             self._do_rotate()
 
         # Get the correct fractal volume
-        volumes = [volume for volume in grid.fractalvolumes if volume.ID == fractal_box_id]
+        volumes = [volume for volume in model.fractalvolumes if volume.ID == fractal_box_id]
         try:
             volume = volumes[0]
         except NameError:
@@ -103,7 +103,9 @@ class AddGrass(UserObjectGeometry):
         xf, yf, zf = p2
 
         if frac_dim < 0:
-            logger.exception(f"{self.__str__()} requires a positive value for the fractal dimension")
+            logger.exception(
+                f"{self.__str__()} requires a positive value for the fractal dimension"
+            )
             raise ValueError
         if limits[0] < 0 or limits[1] < 0:
             logger.exception(
@@ -112,12 +114,15 @@ class AddGrass(UserObjectGeometry):
             raise ValueError
 
         # Check for valid orientations
+        grid = uip.grid
         if xs == xf:
             if ys == yf or zs == zf:
                 logger.exception(f"{self.__str__()} dimensions are not specified correctly")
                 raise ValueError
             if xs not in [volume.xs, volume.xf]:
-                logger.exception(f"{self.__str__()} must specify external surfaces on a fractal box")
+                logger.exception(
+                    f"{self.__str__()} must specify external surfaces on a fractal box"
+                )
                 raise ValueError
             fractalrange = (round_value(limits[0] / grid.dx), round_value(limits[1] / grid.dx))
             # xminus surface
@@ -142,7 +147,9 @@ class AddGrass(UserObjectGeometry):
                 logger.exception(f"{self.__str__()} dimensions are not specified correctly")
                 raise ValueError
             if ys not in [volume.ys, volume.yf]:
-                logger.exception(f"{self.__str__()} must specify external surfaces on a fractal box")
+                logger.exception(
+                    f"{self.__str__()} must specify external surfaces on a fractal box"
+                )
                 raise ValueError
             fractalrange = (round_value(limits[0] / grid.dy), round_value(limits[1] / grid.dy))
             # yminus surface
@@ -164,7 +171,9 @@ class AddGrass(UserObjectGeometry):
 
         elif zs == zf:
             if zs not in [volume.zs, volume.zf]:
-                logger.exception(f"{self.__str__()} must specify external surfaces on a fractal box")
+                logger.exception(
+                    f"{self.__str__()} must specify external surfaces on a fractal box"
+                )
                 raise ValueError
             fractalrange = (round_value(limits[0] / grid.dz), round_value(limits[1] / grid.dz))
             # zminus surface
@@ -219,7 +228,8 @@ class AddGrass(UserObjectGeometry):
         # probability values, and convert the 1D index back into a x, y index
         # for the original surface.
         bladesindex = np.unravel_index(
-            np.digitize(A, probability1D), (surface.fractalsurface.shape[0], surface.fractalsurface.shape[1])
+            np.digitize(A, probability1D),
+            (surface.fractalsurface.shape[0], surface.fractalsurface.shape[1]),
         )
 
         # Set the fractal range to minimum and maximum heights of the grass blades
@@ -227,7 +237,9 @@ class AddGrass(UserObjectGeometry):
 
         # Set the fractal surface using the pre-calculated spatial distribution
         # and a random height
-        surface.fractalsurface = np.zeros((surface.fractalsurface.shape[0], surface.fractalsurface.shape[1]))
+        surface.fractalsurface = np.zeros(
+            (surface.fractalsurface.shape[0], surface.fractalsurface.shape[1])
+        )
         for i in range(len(bladesindex[0])):
             surface.fractalsurface[bladesindex[0][i], bladesindex[1][i]] = R.randint(
                 surface.fractalrange[0], surface.fractalrange[1], size=1
@@ -238,11 +250,11 @@ class AddGrass(UserObjectGeometry):
         surface.grass.append(g)
 
         # Check to see if grass has been already defined as a material
-        if not any(x.ID == "grass" for x in grid.materials):
-            create_grass(grid)
+        if not any(x.ID == "grass" for x in model.materials):
+            create_grass(model)
 
         # Check if time step for model is suitable for using grass
-        grass = next((x for x in grid.materials if x.ID == "grass"))
+        grass = next((x for x in model.materials if x.ID == "grass"))
         testgrass = next((x for x in grass.tau if x < grid.dt), None)
         if testgrass:
             logger.exception(

gprMax/fractals.py

@@ -16,6 +16,8 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
+from typing import Optional, Tuple
+
 import numpy as np
 from scipy import fftpack
 
@@ -32,7 +34,17 @@ class FractalSurface:
 
     surfaceIDs = ["xminus", "xplus", "yminus", "yplus", "zminus", "zplus"]
 
-    def __init__(self, xs, xf, ys, yf, zs, zf, dimension, seed):
+    def __init__(
+        self,
+        xs: float,
+        xf: float,
+        ys: float,
+        yf: float,
+        zs: float,
+        zf: float,
+        dimension: float,
+        seed: Optional[int] = None,
+    ):
         """
         Args:
             xs, xf, ys, yf, zs, zf: floats for the extent of the fractal surface
@@ -43,8 +55,9 @@ class FractalSurface:
             seed: int for seed value for random number generator.
         """
 
-        self.ID = None
-        self.surfaceID = None
+        self.ID: str
+        self.surfaceID: str
+        self.operatingonID: str
         self.xs = xs
         self.xf = xf
         self.ys = ys
@@ -56,9 +69,11 @@ class FractalSurface:
         self.nz = zf - zs
         self.dtype = np.dtype(np.complex128)
         self.seed = seed
-        self.dimension = dimension  # Fractal dimension from: http://dx.doi.org/10.1017/CBO9781139174695
+        self.dimension = (
+            dimension  # Fractal dimension from: http://dx.doi.org/10.1017/CBO9781139174695
+        )
         self.weighting = np.array([1, 1], dtype=np.float64)
-        self.fractalrange = (0, 0)
+        self.fractalrange: Tuple[int, int] = (0, 0)
         self.filldepth = 0
         self.grass = []
 
@@ -82,7 +97,9 @@ class FractalSurface:
         self.fractalsurface = np.zeros(surfacedims, dtype=self.dtype)
 
         # Positional vector at centre of array, scaled by weighting
-        v1 = np.array([self.weighting[0] * (surfacedims[0]) / 2, self.weighting[1] * (surfacedims[1]) / 2])
+        v1 = np.array(
+            [self.weighting[0] * (surfacedims[0]) / 2, self.weighting[1] * (surfacedims[1]) / 2]
+        )
 
         # 2D array of random numbers to be convolved with the fractal function
         rng = np.random.default_rng(seed=self.seed)
@@ -137,8 +154,8 @@ class FractalVolume:
             seed: int for seed value for random number generator.
         """
 
-        self.ID = None
-        self.operatingonID = None
+        self.ID: str
+        self.operatingonID: str
         self.xs = xs
         self.xf = xf
         self.ys = ys
@@ -157,7 +174,9 @@ class FractalVolume:
         self.averaging = False
         self.dtype = np.dtype(np.complex128)
         self.seed = seed
-        self.dimension = dimension  # Fractal dimension from: http://dx.doi.org/10.1017/CBO9781139174695
+        self.dimension = (
+            dimension  # Fractal dimension from: http://dx.doi.org/10.1017/CBO9781139174695
+        )
         self.weighting = np.array([1, 1, 1], dtype=np.float64)
         self.nbins = 0
         self.fractalsurfaces = []
@@ -176,7 +195,9 @@ class FractalVolume:
             filterscaling = np.amin(np.array([self.nx, self.ny])) / np.array([self.nx, self.ny])
             filterscaling = np.insert(filterscaling, 2, 1)
         else:
-            filterscaling = np.amin(np.array([self.nx, self.ny, self.nz])) / np.array([self.nx, self.ny, self.nz])
+            filterscaling = np.amin(np.array([self.nx, self.ny, self.nz])) / np.array(
+                [self.nx, self.ny, self.nz]
+            )
 
         # Adjust weighting to account for filter scaling
         self.weighting = np.multiply(self.weighting, filterscaling)
@@ -185,7 +206,11 @@ class FractalVolume:
 
         # Positional vector at centre of array, scaled by weighting
         v1 = np.array(
-            [self.weighting[0] * self.nx / 2, self.weighting[1] * self.ny / 2, self.weighting[2] * self.nz / 2]
+            [
+                self.weighting[0] * self.nx / 2,
+                self.weighting[1] * self.ny / 2,
+                self.weighting[2] * self.nz / 2,
+            ]
         )
 
         # 3D array of random numbers to be convolved with the fractal function
@@ -225,7 +250,9 @@ class FractalVolume:
         bins = np.linspace(np.amin(self.fractalvolume), np.amax(self.fractalvolume), self.nbins)
         for j in range(self.ny):
             for k in range(self.nz):
-                self.fractalvolume[:, j, k] = np.digitize(self.fractalvolume[:, j, k], bins, right=True)
+                self.fractalvolume[:, j, k] = np.digitize(
+                    self.fractalvolume[:, j, k], bins, right=True
+                )
 
     def generate_volume_mask(self):
         """Generate a 3D volume to use as a mask for adding rough surfaces,
@@ -254,7 +281,9 @@ class Grass:
         """
 
         self.numblades = numblades
-        self.geometryparams = np.zeros((self.numblades, 6), dtype=config.sim_config.dtypes["float_or_double"])
+        self.geometryparams = np.zeros(
+            (self.numblades, 6), dtype=config.sim_config.dtypes["float_or_double"]
+        )
         self.seed = seed
         self.set_geometry_parameters()
 

gprMax/grid/fdtd_grid.py

@@ -73,9 +73,7 @@ class FDTDGrid:
         # corrections will be different.
         self.pmls["thickness"] = OrderedDict((key, 10) for key in PML.boundaryIDs)
 
-        # TODO: Add type information.
         self.averagevolumeobjects = True
-        self.fractalvolumes = []
         self.waveforms: List[Waveform] = []
         self.voltagesources: List[VoltageSource] = []
         self.hertziandipoles: List[HertzianDipole] = []

gprMax/model.py

@@ -26,6 +26,7 @@ import numpy as np
 import psutil
 from colorama import Fore, Style, init
 
+from gprMax.fractals import FractalVolume
 from gprMax.grid.cuda_grid import CUDAGrid
 from gprMax.grid.opencl_grid import OpenCLGrid
 from gprMax.materials import ListMaterial, Material, PeplinskiSoil, RangeMaterial
@@ -67,6 +68,7 @@ class Model:
         self.subgrids: List[SubGridBaseGrid] = []
         self.materials: List[Material] = []
         self.mixingmodels: List[Union[PeplinskiSoil, RangeMaterial, ListMaterial]] = []
+        self.fractalvolumes: List[FractalVolume] = []
 
         self.geometryviews: List[GeometryView] = []
         self.geometryobjects: List[GeometryObjects] = []