Merge branch 'waltsims:master' into auto-chunking

Dockerfile

@@ -4,7 +4,8 @@ RUN apt-get update
 RUN apt-get install -y gfortran libopenblas-dev liblapack-dev libgl1-mesa-glx libglib2.0-0 libgl1-mesa-glx libglib2.0-0 git
 RUN pip install --upgrade pip
 COPY pyproject.toml .
-COPY README.md .
+#COPY README.md .
+COPY docs/ docs
 COPY LICENSE .
 COPY kwave/ kwave
 RUN pip install '.[test]'

kwave/utils/kwave_array.py

@@ -26,6 +26,7 @@ class Element:
     active: bool
     measure: float
 
+    label: Optional[str] = None
     group_type: Optional[str] = None
     element_number: Optional[int] = None
 
@@ -36,10 +37,13 @@ class Element:
     radius_of_curvature: Optional[float] = None
     position: Optional[np.ndarray] = None
     focus_position: Optional[np.ndarray] = None
+
+    # custom element
+    integration_points: Optional[np.ndarray] = None
 
     length: Optional[float] = None
     width: Optional[float] = None
-    orientation: Optional = None
+    orientation: Optional[np.ndarray] = None
 
     start_point: Optional[np.ndarray] = None
     end_point: Optional[np.ndarray] = None
@@ -220,7 +224,43 @@ def add_bowl_element(self, position, radius, diameter, focus_pos):
             active=True,
             measure=area
         ))
+
+    def add_custom_element(self, integration_points, measure, element_dim, label):
+
+        assert isinstance(integration_points, (np.ndarray)), "'integration_points' must be a numpy array"
+        assert isinstance(measure, (int, float)), "'measure' must be an integer or float"
+        assert isinstance(element_dim, (int)) and element_dim in [1, 2, 3], "'element_dim' must be an integer and either 1, 2 or 3"
+        assert isinstance(label, (str)), "'label' must be a string"
+
+        # check the dimensionality of the integration points
+        input_dim = integration_points.shape[0]
+        if (input_dim < 1) or (input_dim > 3):
+            raise ValueError("Input integration_points must be a 1 x N (in 1D), 2 x N (in 2D), or 3 x N (in 3D) array.")
+
+        # check if this is the first element, and set the dimension
+        if self.number_elements == 0:
+            self.dim = input_dim
+
+        # check that the element is being added to an array with the
+        # correct dimensions
+        if self.dim != input_dim:
+            raise ValueError(f"{input_dim}D custom element cannot be added to an array with {self.dim}D elements.")
 
+        self.number_elements += 1
+
+        self.elements.append(
+            Element(
+                group_id=0,
+                type='custom',
+                dim=element_dim,
+                label=label,
+                integration_points=integration_points,
+                active=True,
+                measure=measure
+            )
+        )
+
+
     def add_rect_element(self, position, Lx, Ly, theta):
 
         assert isinstance(position, (list, tuple)), "'position' must be a list or tuple"

tests/matlab_test_data_collectors/matlab_collectors/collect_kWaveArray.m

@@ -38,6 +38,11 @@
 recorder.recordObject('kwave_array', kwave_array);
 recorder.increment();
 
+% Useful for testing addCustomElement in 3D
+kwave_array.addCustomElement(single([[1, 1, 1, 2, 2, 2, 3, 3, 3]; [1, 2, 3, 1, 2, 3, 1, 2, 3]; [0, 0, 0, 0, 0, 0, 0, 0, 0]]), 9, 2, 'custom_3d');
+recorder.recordObject('kwave_array', kwave_array);
+recorder.increment();
+
 % Useful for testing addRectElement in 3D
 kwave_array.addRectElement([12, -8, 0.3], 3, 4, [2, 4, 5]);
 recorder.recordObject('kwave_array', kwave_array);
@@ -61,6 +66,11 @@
 recorder.recordObject('kwave_array', kwave_array);
 recorder.increment();
 
+% Useful for testing addCustomElement in 2D
+kwave_array.addCustomElement(single([[1, 1, 1, 2, 2, 2, 3, 3, 3]; [1, 2, 3, 1, 2, 3, 1, 2, 3]]), 9, 1, 'custom_2d');
+recorder.recordObject('kwave_array', kwave_array);
+recorder.increment();
+
 % Useful for testing addRectElement in 2D
 kwave_array.addRectElement([12, -8], 3, 4, 2);
 recorder.recordObject('kwave_array', kwave_array);

tests/matlab_test_data_collectors/matlab_collectors/collect_resize.m

@@ -3,9 +3,7 @@
 output_file = 'collectedValues/resize.mat';
 recorder = utils.TestRecorder(output_file);
 
-% TODO: test also for nearest
-% interp_methods = {'nearest', 'linear'};
-interp_methods = {'linear'};
+interp_methods = {'nearest', 'linear'};
 
 % Generate a random 3D volume with dimensions Nx x Ny x Nz
 Nx = randi([10,20]);
@@ -30,4 +28,3 @@
 
 end
 recorder.saveRecordsToDisk(); 
-

tests/matlab_test_data_collectors/python_testers/kWaveArray_test.py

@@ -2,6 +2,7 @@
 from pathlib import Path
 
 import numpy as np
+import pytest
 from kwave.kgrid import kWaveGrid
 
 from kwave.utils.kwave_array import kWaveArray
@@ -44,6 +45,22 @@ def test_kwave_array():
     check_kwave_array_equality(kwave_array, reader.expected_value_of('kwave_array'))
     reader.increment()
 
+    kwave_array.add_custom_element(
+        integration_points=np.array([[1, 1, 1, 2, 2, 2, 3, 3, 3], [1, 2, 3, 1, 2, 3, 1, 2, 3], [0, 0, 0, 0, 0, 0, 0, 0, 0]], dtype=np.float32),
+        measure=9,
+        element_dim=2, label='custom_3d'
+    )
+    check_kwave_array_equality(kwave_array, reader.expected_value_of('kwave_array'))
+
+    with pytest.raises(ValueError):
+        kwave_array.add_custom_element(
+            integration_points=np.array([[1, 1, 1, 2, 2, 2, 3, 3, 3], [1, 2, 3, 1, 2, 3, 1, 2, 3]], dtype=np.float32),
+            measure=9,
+            element_dim=2, label='custom_3d'
+        )
+
+    reader.increment()
+
     kwave_array.add_rect_element([12, -8, 0.3], 3, 4, [2, 4, 5])
     check_kwave_array_equality(kwave_array, reader.expected_value_of('kwave_array'))
     reader.increment()
@@ -61,6 +78,13 @@ def test_kwave_array():
     check_kwave_array_equality(kwave_array, reader.expected_value_of('kwave_array'))
     reader.increment()
 
+    kwave_array.add_custom_element(
+        np.array([[1, 1, 1, 2, 2, 2, 3, 3, 3], [1, 2, 3, 1, 2, 3, 1, 2, 3]], dtype=np.float32),
+        9, 1, label='custom_2d'
+    )
+    check_kwave_array_equality(kwave_array, reader.expected_value_of('kwave_array'))
+    reader.increment()
+
     # Useful for testing addRectElement in 2D
     kwave_array.add_rect_element([12, -8], 3, 4, 2)
     check_kwave_array_equality(kwave_array, reader.expected_value_of('kwave_array'))

tests/matlab_test_data_collectors/python_testers/test_resize.py

@@ -22,5 +22,6 @@ def test_resize():
 
         assert np.allclose(expected_resized_volume,
                            resized_volume), f"Results do not match for {i + 1} dimensional case."
+        reader.increment()
 
-    logging.log(logging.INFO, 'revolve2d(..) works as expected!')
+    logging.log(logging.INFO, 'resize(..) works as expected!')