Merge branch 'master' into ls-v1.6

.github/workflows/release-please.yml

@@ -78,7 +78,7 @@ jobs:
   documentation-deploy:
     runs-on: ubuntu-latest
     needs: release-please
-    # if: ${{ needs.release-please.outputs.release_created }}
+    if: ${{ needs.release-please.outputs.release_created }}
     steps:
       - uses: actions/checkout@v4
       - run: |
@@ -92,7 +92,7 @@ jobs:
           folder: docs/build/html # The folder the action should deploy.
 
   conda-deploy:
-    name: Uploading to Loop3d for python ${{ matrix.os }})
+    name: Building conda package for python ${{ matrix.os }})
     needs: ["documentation-test", "continuous-integration"]
     runs-on: ${{matrix.os}}
     strategy:

LoopStructural/datatypes/_bounding_box.py

@@ -13,7 +13,7 @@ def __init__(
         global_origin: Optional[np.ndarray] = None,
         nsteps: Optional[np.ndarray] = None,
         step_vector: Optional[np.ndarray] = None,
-        dimensions: int = 3,
+        dimensions: Optional[int] = None,
     ):
         """A bounding box for a model, defined by the
         origin, maximum and number of steps in each direction
@@ -40,14 +40,16 @@ def __init__(
             global_origin = origin
         self._origin = np.array(origin)
         self._maximum = np.array(maximum)
-        if global_origin is None:
-            global_origin = np.zeros(3)
 
-        self._global_origin = global_origin
-        self.dimensions = dimensions
-        self.nsteps = np.array([50, 50, 25])
-        if nsteps is not None:
-            self.nsteps = np.array(nsteps)
+        if dimensions is None:
+            if self.origin is None:
+                raise LoopValueError("Origin is not set")
+            self.dimensions = len(self.origin)
+            print(self.dimensions)
+        else:
+            self.dimensions = dimensions
+        if nsteps is None:
+            self.nsteps = np.array([50, 50, 25])
         self.name_map = {
             "xmin": (0, 0),
             "ymin": (0, 1),
@@ -128,7 +130,7 @@ def nelements(self, nelements: Union[int, float]):
         box_vol = self.volume
         ele_vol = box_vol / nelements
         # calculate the step vector of a regular cube
-        step_vector = np.zeros(3)
+        step_vector = np.zeros(self.dimensions)
         step_vector[:] = ele_vol ** (1.0 / 3.0)
         # number of steps is the length of the box / step vector
         nsteps = np.ceil((self.maximum - self.origin) / step_vector).astype(int)
@@ -327,6 +329,7 @@ def regular_grid(
         locs = np.array(
             [xx.flatten(order=order), yy.flatten(order=order), zz.flatten(order=order)]
         ).T
+
         if shuffle:
             # logger.info("Shuffling points")
             rng.shuffle(locs)

LoopStructural/export/exporters.py

@@ -62,9 +62,10 @@ def write_feat_surfs(
         logger.warning("{featurename} is not in the model, skipping")
         return False, []
     has_feats = True
-    x = np.linspace(model.bounding_box[0, 0], model.bounding_box[1, 0], model.nsteps[0])
-    y = np.linspace(model.bounding_box[0, 1], model.bounding_box[1, 1], model.nsteps[1])
-    z = np.linspace(model.bounding_box[1, 2], model.bounding_box[0, 2], model.nsteps[2])
+
+    x = np.linspace(model.bounding_box.bb[0, 0], model.bounding_box.bb[1, 0], model.nsteps[0])
+    y = np.linspace(model.bounding_box.bb[0, 1], model.bounding_box.bb[1, 1], model.nsteps[1])
+    z = np.linspace(model.bounding_box.bb[1, 2], model.bounding_box.bb[0, 2], model.nsteps[2])
     xx, yy, zz = np.meshgrid(x, y, z, indexing="ij")
     points = np.array([xx.flatten(), yy.flatten(), zz.flatten()]).T
     val = model[featurename].evaluate_value(points)
@@ -82,9 +83,9 @@ def write_feat_surfs(
         )
         verts += np.array(
             [
-                model.bounding_box[0, 0],
-                model.bounding_box[0, 1],
-                model.bounding_box[1, 2],
+                model.bounding_box.bb[0, 0],
+                model.bounding_box.bb[0, 1],
+                model.bounding_box.bb[1, 2],
             ]
         )
         model.rescale(verts)
@@ -422,14 +423,7 @@ def _write_vol_evtk(model, file_name, data_label, nsteps, real_coords=True):
 
     """
     # Define grid spacing
-    loop_X = np.linspace(model.bounding_box[0, 0], model.bounding_box[1, 0], nsteps[0])
-    loop_Y = np.linspace(model.bounding_box[0, 1], model.bounding_box[1, 1], nsteps[1])
-    loop_Z = np.linspace(model.bounding_box[0, 2], model.bounding_box[1, 2], nsteps[2])
-
-    # Generate model values in 3d grid
-    xx, yy, zz = np.meshgrid(loop_X, loop_Y, loop_Z, indexing="ij")
-    # xyz is N x 3 vector array
-    xyz = np.array([xx.flatten(), yy.flatten(), zz.flatten()]).T
+    xyz = model.bounding_box.regular_grid(nsteps)
     vals = model.evaluate_model(xyz, scale=False)
     if real_coords:
         model.rescale(xyz)
@@ -471,14 +465,8 @@ def _write_vol_gocad(model, file_name, data_label, nsteps, real_coords=True):
 
     """
     # Define grid spacing in model scale coords
-    loop_X = np.linspace(model.bounding_box[0, 0], model.bounding_box[1, 0], nsteps[0])
-    loop_Y = np.linspace(model.bounding_box[0, 1], model.bounding_box[1, 1], nsteps[1])
-    loop_Z = np.linspace(model.bounding_box[0, 2], model.bounding_box[1, 2], nsteps[2])
-
-    # Generate model values in 3d grid
-    xx, yy, zz = np.meshgrid(loop_X, loop_Y, loop_Z, indexing="ij")
-    # xyz is N x 3 vector array
-    xyz = np.array([xx.flatten(), yy.flatten(), zz.flatten()]).T
+    xyz = model.bounding_box.regular_grid(nsteps)
+
     vals = model.evaluate_model(xyz, scale=False)
     # Use FORTRAN style indexing for GOCAD VOXET
     vol_vals = np.reshape(vals, nsteps, order="F")

LoopStructural/modelling/features/builders/_geological_feature_builder.py

@@ -306,6 +306,7 @@ def install_gradient_constraint(self):
                 vector[norm > 0] /= norm[norm > 0, None]
                 element_idx = np.arange(self.interpolator.support.n_elements)
                 logger.info(f"Adding to least squares matrix: {self.name}")
+
                 self.interpolator.add_gradient_orthogonal_constraints(
                     self.interpolator.support.barycentre[element_idx[::step], :],
                     vector[element_idx[::step], :],

LoopStructural/utils/helper.py

@@ -168,6 +168,11 @@ def gi(i, j):
 
 
 def create_box(bounding_box, nsteps):
+    from LoopStructural.datatypes import BoundingBox
+
+    if isinstance(bounding_box, BoundingBox):
+        bounding_box = bounding_box.bb
+
     tri, xx, yy = create_surface(bounding_box[0:2, :], nsteps[0:2])
 
     zz = np.zeros(xx.shape)

tests/unit/utils/test_bounding_box.py → tests/unit/datatypes/test_bounding_box.py

@@ -10,12 +10,24 @@ def test_create_bounding_box():
     assert bbox.maximum[0] == 1
     assert bbox.maximum[1] == 1
     assert bbox.maximum[2] == 1
+    assert bbox.dimensions == 3
     assert np.all(bbox.bb == np.array([[0, 0, 0], [1, 1, 1]]))
     assert bbox.valid is True
 
 
+def test_create_bounding_box_2d():
+    bbox = BoundingBox(origin=[0, 0], maximum=[1, 1], dimensions=2)
+    assert bbox.origin[0] == 0
+    assert bbox.origin[1] == 0
+    assert bbox.maximum[0] == 1
+    assert bbox.maximum[1] == 1
+    assert bbox.dimensions == 2
+    assert np.all(bbox.bb == np.array([[0, 0], [1, 1]]))
+    assert bbox.valid is True
+
+
 def test_create_bounding_box_from_points():
-    bbox = BoundingBox()
+    bbox = BoundingBox(dimensions=3)
     bbox.fit(np.array([[0, 0, 0], [1, 1, 1]]))
     assert bbox.origin[0] == 0
     assert bbox.origin[1] == 0
@@ -27,6 +39,27 @@ def test_create_bounding_box_from_points():
     assert bbox.valid is True
 
 
+def test_create_bounding_box_from_points_2d():
+    bbox = BoundingBox(dimensions=2)
+    bbox.fit(np.array([[0, 0], [1, 1]]))
+    assert bbox.origin[0] == 0
+    assert bbox.origin[1] == 0
+    assert bbox.maximum[0] == 1
+    assert bbox.maximum[1] == 1
+    assert np.all(bbox.bb == np.array([[0, 0], [1, 1]]))
+    assert bbox.valid is True
+
+
+def test_create_3d_bounding_box_from_2d_points():
+    bbox = BoundingBox(dimensions=3)
+    try:
+        bbox.fit(np.array([[0, 0], [1, 1]]))
+    except Exception as e:
+        assert str(e) == "locations array is 2D but bounding box is 3"
+    else:
+        assert False
+
+
 def test_create_with_buffer():
     bbox = BoundingBox(origin=[0, 0, 0], maximum=[1, 1, 1])
     bbox = bbox.with_buffer(0.2)
@@ -51,8 +84,24 @@ def test_is_inside():
     assert not np.all(bbox.is_inside(np.array([-0.5, 0.5, 0.5])))
 
 
+def test_regular_grid_3d():
+    bbox = BoundingBox(origin=[0, 0, 0], maximum=[1, 1, 1])
+    print(bbox.dimensions)
+    grid = bbox.regular_grid((10, 10, 10))
+    assert grid.shape == (10 * 10 * 10, 3)
+
+
+def test_regular_grid_2d():
+    bbox = BoundingBox(origin=[0, 0], maximum=[1, 1], dimensions=2)
+    print(bbox.dimensions)
+    grid = bbox.regular_grid((10, 10))
+    assert grid.shape == (10 * 10, 2)
+
+
 if __name__ == "__main__":
     test_create_bounding_box()
     test_create_bounding_box_from_points()
     test_create_with_buffer()
     test_is_inside()
+    test_regular_grid_3d()
+    test_regular_grid_2d()