Speed up tests (swc, plotting)

jaxley/utils/plot_utils.py

@@ -103,6 +103,7 @@ def create_cone_frustum_mesh(
     radius_top: float,
     bottom_dome: bool = False,
     top_dome: bool = False,
+    resolution: int = 100,
 ) -> ndarray:
     """Generates mesh points for a cone frustum, with optional domes at either end.
 
@@ -120,12 +121,14 @@ def create_cone_frustum_mesh(
             The dome is a hemisphere with radius `radius_bottom`.
         top_dome: If True, a dome is added to the top of the frustum.
             The dome is a hemisphere with radius `radius_top`.
+        resolution: defines the resolution of the mesh.
+            If too low (typically <10), can result in errors.
+            Useful too have a simpler mesh for plotting.
 
     Returns:
         An array of mesh points.
     """
 
-    resolution = 100
     t = np.linspace(0, 2 * np.pi, resolution)
 
     # Determine the total height including domes
@@ -175,7 +178,9 @@ def create_cone_frustum_mesh(
     return np.stack([x_coords, y_coords, z_coords])
 
 
-def create_cylinder_mesh(length: float, radius: float) -> ndarray:
+def create_cylinder_mesh(
+    length: float, radius: float, resolution: int = 100
+) -> ndarray:
     """Generates mesh points for a cylinder.
 
     This is used to render cylindrical compartments in 3D (and to project it to 2D)
@@ -184,12 +189,14 @@ def create_cylinder_mesh(length: float, radius: float) -> ndarray:
     Args:
         length: The length of the cylinder.
         radius: The radius of the cylinder.
+        resolution: defines the resolution of the mesh.
+            If too low (typically <10), can result in errors.
+            Useful too have a simpler mesh for plotting.
 
     Returns:
         An array of mesh points.
     """
     # Define cylinder
-    resolution = 100
     t = np.linspace(0, 2 * np.pi, resolution)
     z_coords = np.linspace(-length / 2, length / 2, resolution)
     t_grid, z_coords = np.meshgrid(t, z_coords)
@@ -199,19 +206,21 @@ def create_cylinder_mesh(length: float, radius: float) -> ndarray:
     return np.stack([x_coords, y_coords, z_coords])
 
 
-def create_sphere_mesh(radius: float) -> np.ndarray:
+def create_sphere_mesh(radius: float, resolution: int = 100) -> np.ndarray:
     """Generates mesh points for a sphere.
 
     This is used to render spherical compartments in 3D (and to project it to 2D)
     as part of `plot_comps`.
 
     Args:
         radius: The radius of the sphere.
+        resolution: defines the resolution of the mesh.
+            If too low (typically <10), can result in errors.
+            Useful too have a simpler mesh for plotting.
 
     Returns:
         An array of mesh points.
     """
-    resolution = 100
     phi = np.linspace(0, np.pi, resolution)
     theta = np.linspace(0, 2 * np.pi, resolution)
 
@@ -302,8 +311,9 @@ def plot_comps(
     ax: Optional[Axes] = None,
     comp_plot_kwargs: Dict = {},
     true_comp_length: bool = True,
+    resolution: int = 100,
 ) -> Axes:
-    """Plot compartmentalized neural mrophology.
+    """Plot compartmentalized neural morphology.
 
     Plots the projection of the cylindrical compartments.
 
@@ -320,6 +330,9 @@ def plot_comps(
             start and end point of the neurite. This can lead to overlapping and
             miss-aligned cylinders. Setting this False will use the straight-line
             distance instead for nicer plots.
+        resolution: defines the resolution of the mesh.
+            If too low (typically <10), can result in errors.
+            Useful too have a simpler mesh for plotting.
 
     Returns:
         Plot of the compartmentalized morphology.
@@ -340,7 +353,7 @@ def plot_comps(
             radius = xyzr[:, -1]
             center = xyzr[0, :3]
             if len(dims) == 3:
-                xyz = create_sphere_mesh(radius)
+                xyz = create_sphere_mesh(radius, resolution)
                 ax = plot_mesh(
                     xyz,
                     np.array([0, 0, 1]),
@@ -368,7 +381,7 @@ def plot_comps(
                 center = comp[["x", "y", "z"]]
                 radius = comp["radius"]
                 length = comp["length"] if true_comp_length else l
-                xyz = create_cylinder_mesh(length, radius)
+                xyz = create_cylinder_mesh(length, radius, resolution)
                 ax = plot_mesh(
                     xyz,
                     axis,
@@ -386,6 +399,7 @@ def plot_morph(
     dims: Tuple[int] = (0, 1),
     col: str = "k",
     ax: Optional[Axes] = None,
+    resolution: int = 100,
     morph_plot_kwargs: Dict = {},
 ) -> Axes:
     """Plot the detailed morphology.
@@ -404,6 +418,10 @@ def plot_morph(
         ax: The matplotlib axis to plot on.
         morph_plot_kwargs: The plot kwargs for plt.fill.
 
+        resolution: defines the resolution of the mesh.
+            If too low (typically <10), can result in errors.
+            Useful too have a simpler mesh for plotting.
+
     Returns:
         Plot of the detailed morphology."""
     if ax is None:
@@ -424,7 +442,12 @@ def plot_morph(
                 dxyz = xyzr2[:3] - xyzr1[:3]
                 length = np.sqrt(np.sum(dxyz**2))
                 points = create_cone_frustum_mesh(
-                    length, xyzr1[-1], xyzr2[-1], bottom_dome=True, top_dome=True
+                    length,
+                    xyzr1[-1],
+                    xyzr2[-1],
+                    bottom_dome=True,
+                    top_dome=True,
+                    resolution=resolution,
                 )
                 plot_mesh(
                     points,
@@ -437,7 +460,12 @@ def plot_morph(
                 )
         else:
             points = create_cone_frustum_mesh(
-                0, xyzr[:, -1], xyzr[:, -1], bottom_dome=True, top_dome=True
+                0,
+                xyzr[:, -1],
+                xyzr[:, -1],
+                bottom_dome=True,
+                top_dome=True,
+                resolution=resolution,
             )
             plot_mesh(
                 points,

tests/test_plotting_api.py

@@ -19,31 +19,58 @@
 from jaxley.synapses import IonotropicSynapse
 
 
-def test_cell():
-    dirname = os.path.dirname(__file__)
-    fname = os.path.join(dirname, "swc_files", "morph.swc")
-    cell = jx.read_swc(fname, nseg=4)
+@pytest.fixture(scope="module")
+def comp() -> jx.Compartment:
+    comp = jx.Compartment()
+    comp.compute_xyz()
+    return comp
+
+
+@pytest.fixture(scope="module")
+def branch(comp) -> jx.Branch:
+    branch = jx.Branch(comp, 4)
+    branch.compute_xyz()
+    return branch
 
+
+@pytest.fixture(scope="module")
+def cell(branch) -> jx.Cell:
+    cell = jx.Cell(branch, [-1, 0, 0, 1, 1])
+    cell.compute_xyz()
+    return cell
+
+
+@pytest.fixture(scope="module")
+def simple_net(cell) -> jx.Network:
+    net = jx.Network([cell] * 4)
+    net.compute_xyz()
+    return net
+
+
+@pytest.fixture(scope="module")
+def morph_cell() -> jx.Cell:
+    morph_cell = jx.read_swc(
+        os.path.join(os.path.dirname(__file__), "swc_files", "morph.swc"),
+        nseg=1,
+    )
+    return morph_cell
+
+
+def test_cell(morph_cell):
     # Plot 1.
     _, ax = plt.subplots(1, 1, figsize=(3, 3))
-    ax = cell.vis(ax=ax)
-    ax = cell.branch([0, 1, 2]).vis(ax=ax, col="r")
-    ax = cell.branch(1).loc(0.9).vis(ax=ax, col="b")
+    ax = morph_cell.vis(ax=ax)
+    ax = morph_cell.branch([0, 1, 2]).vis(ax=ax, col="r")
+    ax = morph_cell.branch(1).loc(0.9).vis(ax=ax, col="b")
 
     # Plot 2.
-    cell.branch(0).add_to_group("soma")
-    cell.branch(1).add_to_group("soma")
-    ax = cell.soma.vis()
-
+    morph_cell.branch(0).add_to_group("soma")
+    morph_cell.branch(1).add_to_group("soma")
+    ax = morph_cell.soma.vis()
 
-def test_network():
-    dirname = os.path.dirname(__file__)
-    fname = os.path.join(dirname, "swc_files", "morph.swc")
-    cell1 = jx.read_swc(fname, nseg=4)
-    cell2 = jx.read_swc(fname, nseg=4)
-    cell3 = jx.read_swc(fname, nseg=4)
 
-    net = jx.Network([cell1, cell2, cell3])
+def test_network(morph_cell):
+    net = jx.Network([morph_cell, morph_cell, morph_cell])
     connect(
         net.cell(0).branch(0).loc(0.0),
         net.cell(1).branch(0).loc(0.0),
@@ -81,11 +108,7 @@ def test_network():
     ax = net.excitatory.vis()
 
 
-def test_vis_networks_built_from_scartch():
-    comp = jx.Compartment()
-    branch = jx.Branch(comp, 4)
-    cell = jx.Cell(branch, parents=[-1, 0, 0, 1, 1])
-
+def test_vis_networks_built_from_scratch(comp, branch, cell):
     net = jx.Network([cell, cell])
     connect(
         net.cell(0).branch(0).loc(0.0),
@@ -110,25 +133,15 @@ def test_vis_networks_built_from_scartch():
 
     # Plot 3.
     _, ax = plt.subplots(1, 1, figsize=(3, 3))
-    comp.compute_xyz()
     ax = comp.vis(ax=ax)
 
     # Plot 4.
     _, ax = plt.subplots(1, 1, figsize=(3, 3))
-    branch.compute_xyz()
     ax = branch.vis(ax=ax)
 
 
-def test_mixed_network():
-    dirname = os.path.dirname(__file__)
-    fname = os.path.join(dirname, "swc_files", "morph.swc")
-    cell1 = jx.read_swc(fname, nseg=4)
-
-    comp = jx.Compartment()
-    branch = jx.Branch(comp, 4)
-    cell2 = jx.Cell(branch, parents=[-1, 0, 0, 1, 1])
-
-    net = jx.Network([cell1, cell2])
+def test_mixed_network(morph_cell, cell):
+    net = jx.Network([morph_cell, cell])
     connect(
         net.cell(0).branch(0).loc(0.0),
         net.cell(1).branch(0).loc(0.0),
@@ -145,9 +158,9 @@ def test_mixed_network():
     net.cell(1).move(0, -800)
     net.rotate(180)
 
-    before_xyzrs = deepcopy(net.xyzr[len(cell1.xyzr) :])
+    before_xyzrs = deepcopy(net.xyzr[len(morph_cell.xyzr) :])
     net.cell(1).rotate(90)
-    after_xyzrs = net.xyzr[len(cell1.xyzr) :]
+    after_xyzrs = net.xyzr[len(morph_cell.xyzr) :]
     # Test that rotation worked as expected.
     for b, a in zip(before_xyzrs, after_xyzrs):
         assert np.allclose(b[:, 0], -a[:, 1], atol=1e-6)
@@ -156,34 +169,24 @@ def test_mixed_network():
     _ = net.vis(detail="full")
 
 
-def test_volume_plotting():
-    comp = jx.Compartment()
-    comp.compute_xyz()
-    branch = jx.Branch(comp, 4)
-    branch.compute_xyz()
-    cell = jx.Cell([branch] * 3, [-1, 0, 0])
-    cell.compute_xyz()
-    net = jx.Network([cell] * 4)
-    net.compute_xyz()
-
-    morph_cell = jx.read_swc(
-        os.path.join(os.path.dirname(__file__), "swc_files", "morph.swc"),
-        nseg=1,
-    )
-
+def test_volume_plotting_2d(comp, branch, cell, simple_net, morph_cell):
     fig, ax = plt.subplots()
-    for module in [comp, branch, cell, net, morph_cell]:
-        module.vis(type="comp", ax=ax)
+    for module in [comp, branch, cell, simple_net, morph_cell]:
+        module.vis(type="comp", ax=ax, morph_plot_kwargs={"resolution": 6})
     plt.close(fig)
 
+
+def test_volume_plotting_3d(comp, branch, cell, simple_net, morph_cell):
     # test 3D plotting
-    for module in [comp, branch, cell, net, morph_cell]:
-        module.vis(type="comp", dims=[0, 1, 2])
+    for module in [comp, branch, cell, simple_net, morph_cell]:
+        module.vis(type="comp", dims=[0, 1, 2], morph_plot_kwargs={"resolution": 6})
     plt.close()
 
+
+def test_morph_plotting(morph_cell):
     # test morph plotting (does not work if no radii in xyzr)
-    morph_cell.vis(type="morph")
+    morph_cell.vis(type="morph", morph_plot_kwargs={"resolution": 6})
     morph_cell.branch(1).vis(
-        type="morph", dims=[0, 1, 2]
+        type="morph", dims=[0, 1, 2], morph_plot_kwargs={"resolution": 6}
     )  # plotting whole thing takes too long
     plt.close()

tests/test_swc.py

@@ -180,7 +180,7 @@ def test_swc_voltages(file):
     for i in trunk_inds + tuft_inds + basal_inds:
         cell.branch(i).loc(0.05).record()
 
-    voltages_jaxley = jx.integrate(cell, delta_t=dt)
+    voltages_jaxley = jx.integrate(cell, delta_t=dt, voltage_solver="jax.sparse")
 
     ################### NEURON #################
     stim = h.IClamp(h.soma[0](0.1))