Merge branch 'main' into mike/3d_xray

docs/source/_static/scico.css

@@ -1,5 +1,9 @@
 /* furo theme customization */
 
+body[data-theme="dark"] figure img {
+  filter: invert(100%);
+}
+
 .sidebar-drawer {
   width: fit-content !important;
 }

docs/source/pyfigures/cylindgrad.py

@@ -26,21 +26,24 @@
 fig = plot.plt.figure(figsize=(20, 6))
 ax = fig.add_subplot(1, 3, 1, projection="3d")
 ax.quiver(g0, g1, g2, ang[0], ang[1], ang[2], colors=clr, length=0.9)
-ax.set_title("Angular local coordinate axis")
-ax.set_xlabel("$x$")
-ax.set_ylabel("$y$")
-ax.set_zlabel("$z$")
+ax.set_title("Angular local coordinate axis", fontsize=18)
+ax.set_xlabel("$x$", fontsize=15)
+ax.set_ylabel("$y$", fontsize=15)
+ax.set_zlabel("$z$", fontsize=15)
+ax.tick_params(labelsize=15)
 ax = fig.add_subplot(1, 3, 2, projection="3d")
 ax.quiver(g0, g1, g2, rad[0], rad[1], rad[2], colors=clr, length=0.9)
-ax.set_title("Radial local coordinate axis")
-ax.set_xlabel("$x$")
-ax.set_ylabel("$y$")
-ax.set_zlabel("$z$")
+ax.set_title("Radial local coordinate axis", fontsize=18)
+ax.set_xlabel("$x$", fontsize=15)
+ax.set_ylabel("$y$", fontsize=15)
+ax.set_zlabel("$z$", fontsize=15)
+ax.tick_params(labelsize=15)
 ax = fig.add_subplot(1, 3, 3, projection="3d")
 ax.quiver(g0, g1, g2, axi[0], axi[1], axi[2], colors=clr[0], length=0.9)
-ax.set_title("Axial local coordinate axis")
-ax.set_xlabel("$x$")
-ax.set_ylabel("$y$")
-ax.set_zlabel("$z$")
+ax.set_title("Axial local coordinate axis", fontsize=18)
+ax.set_xlabel("$x$", fontsize=15)
+ax.set_ylabel("$y$", fontsize=15)
+ax.set_zlabel("$z$", fontsize=15)
+ax.tick_params(labelsize=15)
 fig.tight_layout()
 fig.show()

docs/source/pyfigures/polargrad.py

@@ -20,15 +20,17 @@
 
 fig, ax = plot.plt.subplots(nrows=1, ncols=2, figsize=(13, 6))
 ax[0].quiver(g0, g1, ang[0], ang[1], clr)
-ax[0].set_title("Angular local coordinate axis")
-ax[0].set_xlabel("$x$")
-ax[0].set_ylabel("$y$")
+ax[0].set_title("Angular local coordinate axis", fontsize=16)
+ax[0].set_xlabel("$x$", fontsize=14)
+ax[0].set_ylabel("$y$", fontsize=14)
+ax[0].tick_params(labelsize=14)
 ax[0].xaxis.set_ticks((-10, -5, 0, 5, 10))
 ax[0].yaxis.set_ticks((-10, -5, 0, 5, 10))
 ax[1].quiver(g0, g1, rad[0], rad[1], clr)
-ax[1].set_title("Radial local coordinate axis")
-ax[1].set_xlabel("$x$")
-ax[1].set_ylabel("$y$")
+ax[1].set_title("Radial local coordinate axis", fontsize=16)
+ax[1].set_xlabel("$x$", fontsize=14)
+ax[1].set_ylabel("$y$", fontsize=14)
+ax[1].tick_params(labelsize=14)
 ax[1].xaxis.set_ticks((-10, -5, 0, 5, 10))
 ax[1].yaxis.set_ticks((-10, -5, 0, 5, 10))
 fig.tight_layout()

docs/source/pyfigures/spheregrad.py

@@ -27,21 +27,24 @@
 fig = plot.plt.figure(figsize=(20, 6))
 ax = fig.add_subplot(1, 3, 1, projection="3d")
 ax.quiver(g0, g1, g2, azi[0], azi[1], azi[2], colors=clr, length=0.9)
-ax.set_title("Azimuthal local coordinate axis")
-ax.set_xlabel("$x$")
-ax.set_ylabel("$y$")
-ax.set_zlabel("$z$")
+ax.set_title("Azimuthal local coordinate axis", fontsize=18)
+ax.set_xlabel("$x$", fontsize=15)
+ax.set_ylabel("$y$", fontsize=15)
+ax.set_zlabel("$z$", fontsize=15)
+ax.tick_params(labelsize=15)
 ax = fig.add_subplot(1, 3, 2, projection="3d")
 ax.quiver(g0, g1, g2, pol[0], pol[1], pol[2], colors=clr, length=0.9)
-ax.set_title("Polar local coordinate axis")
-ax.set_xlabel("$x$")
-ax.set_ylabel("$y$")
-ax.set_zlabel("$z$")
+ax.set_title("Polar local coordinate axis", fontsize=18)
+ax.set_xlabel("$x$", fontsize=15)
+ax.set_ylabel("$y$", fontsize=15)
+ax.set_zlabel("$z$", fontsize=15)
+ax.tick_params(labelsize=15)
 ax = fig.add_subplot(1, 3, 3, projection="3d")
 ax.quiver(g0, g1, g2, rad[0], rad[1], rad[2], colors=clr, length=0.9)
-ax.set_title("Radial local coordinate axis")
-ax.set_xlabel("$x$")
-ax.set_ylabel("$y$")
-ax.set_zlabel("$z$")
+ax.set_title("Radial local coordinate axis", fontsize=18)
+ax.set_xlabel("$x$", fontsize=15)
+ax.set_ylabel("$y$", fontsize=15)
+ax.set_zlabel("$z$", fontsize=15)
+ax.tick_params(labelsize=15)
 fig.tight_layout()
 fig.show()

docs/source/pyfigures/xray_2d_geom.py

@@ -1,24 +1,32 @@
 import numpy as np
 
+import matplotlib as mpl
 import matplotlib.patches as patches
 import matplotlib.pyplot as plt
 
+mpl.rcParams["savefig.transparent"] = True
+
+
 c = 1.0 / np.sqrt(2.0)
 e = 1e-2
 style = "Simple, tail_width=0.5, head_width=4, head_length=8"
 fig, ax = plt.subplots(nrows=1, ncols=3, figsize=(21, 7))
+
+# all plots
 for n in range(3):
     ax[n].set_aspect(1.0)
     ax[n].set_xlim(-1.1, 1.1)
     ax[n].set_ylim(-1.1, 1.1)
     ax[n].set_xticks(np.linspace(-1.0, 1.0, 5))
     ax[n].set_yticks(np.linspace(-1.0, 1.0, 5))
-    ax[n].tick_params(axis="x", labelsize=12)
-    ax[n].tick_params(axis="y", labelsize=12)
-    ax[n].set_xlabel("axis 1", fontsize=14)
-    ax[n].set_ylabel("axis 0", fontsize=14)
+    ax[n].tick_params(axis="x", labelsize=14)
+    ax[n].tick_params(axis="y", labelsize=14)
+    ax[n].set_xlabel("axis 1", fontsize=16)
+    ax[n].set_ylabel("axis 0", fontsize=16)
+
 
 # scico
+ax[0].set_title("scico", fontsize=18)
 plist = [
     patches.FancyArrowPatch((-1.0, 0.0), (-0.5, 0.0), arrowstyle=style, color="r"),
     patches.FancyArrowPatch((-c, -c), (-c / 2.0, -c / 2.0), arrowstyle=style, color="r"),
@@ -31,32 +39,90 @@
         arrowstyle=style,
         color="r",
     ),
-    patches.Arc((0.0, 0.0), 2.0, 2.0, theta1=180, theta2=-45.0, color="b", ls="dotted"),
+    patches.Arc((0.0, 0.0), 2.0, 2.0, theta1=180, theta2=-45.0, color="b", lw=2, ls="dotted"),
     patches.FancyArrowPatch((c - e, -c - e), (c + e, -c + e), arrowstyle=style, color="b"),
 ]
 for p in plist:
     ax[0].add_patch(p)
-ax[0].text(-0.88, 0.02, r"$\theta=0$", color="r", fontsize=14)
-ax[0].text(-3 * c / 4 - 0.01, -3 * c / 4 - 0.1, r"$\theta=\frac{\pi}{4}$", color="r", fontsize=14)
-ax[0].text(0.03, -0.8, r"$\theta=\frac{\pi}{2}$", color="r", fontsize=14)
-ax[0].set_title("scico", fontsize=14)
+
+ax[0].text(-0.88, 0.02, r"$\theta=0$", color="r", fontsize=16)
+ax[0].text(-3 * c / 4 - 0.01, -3 * c / 4 - 0.1, r"$\theta=\frac{\pi}{4}$", color="r", fontsize=16)
+ax[0].text(0.03, -0.8, r"$\theta=\frac{\pi}{2}$", color="r", fontsize=16)
+
+ax[0].plot((1.0, 1.0), (-0.375, 0.375), color="orange", lw=2)
+ax[0].arrow(
+    0.94,
+    0.375,
+    0.0,
+    -0.75,
+    color="orange",
+    lw=1.0,
+    ls="--",
+    head_width=0.03,
+    length_includes_head=True,
+)
+ax[0].text(0.7, 0.0, r"$\theta=0$", color="orange", ha="left", fontsize=16)
+ax[0].plot((-0.375, 0.375), (1.0, 1.0), color="orange", lw=2)
+ax[0].arrow(
+    -0.375,
+    0.94,
+    0.75,
+    0.0,
+    color="orange",
+    lw=1.0,
+    ls="--",
+    head_width=0.03,
+    length_includes_head=True,
+)
+ax[0].text(0.0, 0.82, r"$\theta=\frac{\pi}{2}$", color="orange", ha="center", fontsize=16)
+
 
 # astra
+ax[1].set_title("astra", fontsize=18)
 plist = [
     patches.FancyArrowPatch((0.0, -1.0), (0.0, -0.5), arrowstyle=style, color="r"),
     patches.FancyArrowPatch((c, -c), (c / 2.0, -c / 2.0), arrowstyle=style, color="r"),
     patches.FancyArrowPatch((1.0, 0.0), (0.5, 0.0), arrowstyle=style, color="r"),
-    patches.Arc((0.0, 0.0), 2.0, 2.0, theta1=-90, theta2=45.0, color="b", ls="dotted"),
+    patches.Arc((0.0, 0.0), 2.0, 2.0, theta1=-90, theta2=45.0, color="b", lw=2, ls="dotted"),
     patches.FancyArrowPatch((c + e, c - e), (c - e, c + e), arrowstyle=style, color="b"),
 ]
 for p in plist:
     ax[1].add_patch(p)
-ax[1].text(0.02, -0.75, r"$\theta=0$", color="r", fontsize=14)
-ax[1].text(3 * c / 4 + 0.01, -3 * c / 4 + 0.01, r"$\theta=\frac{\pi}{4}$", color="r", fontsize=14)
-ax[1].text(0.65, 0.05, r"$\theta=\frac{\pi}{2}$", color="r", fontsize=14)
-ax[1].set_title("astra", fontsize=14)
+
+ax[1].text(0.02, -0.75, r"$\theta=0$", color="r", fontsize=16)
+ax[1].text(3 * c / 4 + 0.01, -3 * c / 4 + 0.01, r"$\theta=\frac{\pi}{4}$", color="r", fontsize=16)
+ax[1].text(0.65, 0.05, r"$\theta=\frac{\pi}{2}$", color="r", fontsize=16)
+
+ax[1].plot((-0.375, 0.375), (1.0, 1.0), color="orange", lw=2)
+ax[1].arrow(
+    -0.375,
+    0.94,
+    0.75,
+    0.0,
+    color="orange",
+    lw=1.0,
+    ls="--",
+    head_width=0.03,
+    length_includes_head=True,
+)
+ax[1].text(0.0, 0.82, r"$\theta=0$", color="orange", ha="center", fontsize=16)
+ax[1].plot((-1.0, -1.0), (-0.375, 0.375), color="orange", lw=2)
+ax[1].arrow(
+    -0.94,
+    -0.375,
+    0.0,
+    0.75,
+    color="orange",
+    lw=1.0,
+    ls="--",
+    head_width=0.03,
+    length_includes_head=True,
+)
+ax[1].text(-0.9, 0.0, r"$\theta=\frac{\pi}{2}$", color="orange", ha="left", fontsize=16)
+
 
 # svmbir
+ax[2].set_title("svmbir", fontsize=18)
 plist = [
     patches.FancyArrowPatch((-1.0, 0.0), (-0.5, 0.0), arrowstyle=style, color="r"),
     patches.FancyArrowPatch((-c, c), (-c / 2.0, c / 2.0), arrowstyle=style, color="r"),
@@ -69,15 +135,43 @@
         arrowstyle=style,
         color="r",
     ),
-    patches.Arc((0.0, 0.0), 2.0, 2.0, theta1=45, theta2=180, color="b", ls="dotted"),
+    patches.Arc((0.0, 0.0), 2.0, 2.0, theta1=45, theta2=180, color="b", lw=2, ls="dotted"),
     patches.FancyArrowPatch((c - e, c + e), (c + e, c - e), arrowstyle=style, color="b"),
 ]
 for p in plist:
     ax[2].add_patch(p)
-ax[2].text(-0.88, 0.02, r"$\theta=0$", color="r", fontsize=14)
-ax[2].text(-3 * c / 4 + 0.01, 3 * c / 4 + 0.01, r"$\theta=\frac{\pi}{4}$", color="r", fontsize=14)
-ax[2].text(0.03, 0.75, r"$\theta=\frac{\pi}{2}$", color="r", fontsize=14)
-ax[2].set_title("svmbir", fontsize=14)
+ax[2].text(-0.88, 0.02, r"$\theta=0$", color="r", fontsize=16)
+ax[2].text(-3 * c / 4 + 0.01, 3 * c / 4 + 0.01, r"$\theta=\frac{\pi}{4}$", color="r", fontsize=16)
+ax[2].text(0.03, 0.75, r"$\theta=\frac{\pi}{2}$", color="r", fontsize=16)
+
+ax[2].plot((1.0, 1.0), (-0.375, 0.375), color="orange", lw=2)
+ax[2].arrow(
+    0.94,
+    0.375,
+    0.0,
+    -0.75,
+    color="orange",
+    lw=1.0,
+    ls="--",
+    head_width=0.03,
+    length_includes_head=True,
+)
+ax[2].text(0.7, 0.0, r"$\theta=0$", color="orange", ha="left", fontsize=16)
+
+ax[2].plot((-0.375, 0.375), (-1.0, -1.0), color="orange", lw=2)
+ax[2].arrow(
+    0.375,
+    -0.94,
+    -0.75,
+    0.0,
+    color="orange",
+    lw=1.0,
+    ls="--",
+    head_width=0.03,
+    length_includes_head=True,
+)
+ax[2].text(0.0, -0.82, r"$\theta=\frac{\pi}{2}$", color="orange", ha="center", fontsize=16)
+
 
 fig.tight_layout()
 fig.show()

docs/source/pyfigures/xray_3d_ang.py

@@ -25,7 +25,7 @@
     patches.FancyArrowPatch((0.0, -1.0), (0.0, -0.5), arrowstyle=style, color="r"),
     patches.FancyArrowPatch((c, -c), (c / 2.0, -c / 2.0), arrowstyle=style, color="r"),
     patches.FancyArrowPatch((1.0, 0.0), (0.5, 0.0), arrowstyle=style, color="r"),
-    patches.Arc((0.0, 0.0), 2.0, 2.0, theta1=-90, theta2=45.0, color="b", ls="dotted"),
+    patches.Arc((0.0, 0.0), 2.0, 2.0, theta1=-90, theta2=45.0, color="b", lw=2, ls="dotted"),
     patches.FancyArrowPatch((c + e, c - e), (c - e, c + e), arrowstyle=style, color="b"),
 ]
 for p in plist:

scico/functional/_tvnorm.py

@@ -147,11 +147,15 @@ def _prox_operators(
             # Replicate-pad to the right (resulting in a zero after finite differencing)
             # on all axes subject to finite differencing.
             pad_width = [(0, 1) if i in axes else (0, 0) for i, s in enumerate(input_shape)]  # type: ignore
-            P = Pad(input_shape, pad_width=pad_width, mode="edge", jit=True)
+            P = Pad(
+                input_shape, input_dtype=input_dtype, pad_width=pad_width, mode="edge", jit=True
+            )
             # fused boundary extend and forward transform linop
             WP = W @ P
             # crop operation that is inverse of the padding operation
-            C = Crop(crop_width=pad_width, input_shape=w_input_shape, jit=True)
+            C = Crop(
+                crop_width=pad_width, input_shape=w_input_shape, input_dtype=input_dtype, jit=True
+            )
             # fused adjoint transform and crop linop
             CWT = C @ W.T
         return WP, CWT, ndims, slce

scico/linop/xray/__init__.py

@@ -26,14 +26,10 @@
    :align: center
    :include-source: False
    :show-source-link: False
-   :caption: Comparison of 2D X-ray projector geometries. The red arrows
-      are directed towards the detector, which is oriented with pixel
-      indices ordered in the same direction as clockwise rotation (e.g.
-      in the "scico" geometry, the :math:`\theta=0` projection
-      corresponds to row sums ordered from the top to the bottom of the
-      figure, while the :math:`\theta=\pi` projection
-      corresponds to row sums ordered from the bottom to the top of the
-      figure).
+   :caption: Comparison of 2D X-ray projector geometries. The radial
+      arrows are directed towards the locations of the corresponding
+      detectors, with the direction of increasing pixel indices indicated
+      by the arrows on the dotted lines parallel to the detectors.
 
 |
 

scico/linop/xray/astra.py

@@ -421,9 +421,10 @@ class XRayTransform3D(LinearOperator):  # pragma: no cover
        :align: center
        :include-source: False
        :show-source-link: False
-       :caption: Red arrows indicate the direction of the beam towards
-          the detector (orange) and the arrows parallel to the detector
-          indicate the direction of increasing pixel indices.
+       :caption: Each radial arrow indicates the direction of the beam
+          towards the detector (indicated in orange in the "light"
+          display mode) and the arrow parallel to the detector indicates
+          the direction of increasing pixel indices.
 
     In this case the `z` axis is in the same direction as the
     vertical/row axis of the detector and its projection corresponds to