MAINT: update doctests and fix some minor things

examples/tomo/checks/check_axes_cone2d_bp.py

@@ -39,7 +39,6 @@
 grid = odl.RectGrid(np.linspace(0, 2 * np.pi, 360, endpoint=False))
 angle_partition = odl.uniform_partition_fromgrid(grid)
 
-# Make detector large enough to cover the object
 # Make detector large enough to cover the object
 src_radius = 500
 det_radius = 1000

examples/tomo/checks/check_axes_cone2d_fp.py

@@ -6,8 +6,8 @@
 
 Both pairs of plots of ODL projections and NumPy axis sums should look
 similar in the sense that they should show the same features in the
-right arrangement (not flipped, rotated, etc.), but differing in
-magnification.
+right arrangement (not flipped, rotated, etc.), up to differences in
+magnification and other cone effects.
 """
 
 import matplotlib.pyplot as plt
@@ -42,7 +42,6 @@
 grid = odl.RectGrid([0, np.pi / 2, np.pi, 3 * np.pi / 2])
 angle_partition = odl.uniform_partition_fromgrid(grid)
 
-# Make detector large enough to cover the object
 # Make detector large enough to cover the object
 src_radius = 500
 det_radius = 1000

examples/tomo/checks/check_axes_cone3d_bp.py

@@ -48,7 +48,7 @@
     axis=[0, 0, 1])
 
 # Create projections and back-projection
-ray_trafo = odl.tomo.RayTransform(reco_space, geometry)
+ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cuda')
 proj_data = ray_trafo(phantom)
 backproj = ray_trafo.adjoint(proj_data)
 backproj.show('Backprojection, axis = [0, 0, 1], middle z slice',
@@ -65,7 +65,7 @@
     axis=[0, 1, 0])
 
 # Create projections and back-projection
-ray_trafo = odl.tomo.RayTransform(reco_space, geometry)
+ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cuda')
 proj_data = ray_trafo(phantom)
 backproj = ray_trafo.adjoint(proj_data)
 backproj.show('Backprojection, axis = [0, 1, 0], middle y slice',
@@ -82,7 +82,7 @@
     axis=[1, 0, 0])
 
 # Create projections and back-projection
-ray_trafo = odl.tomo.RayTransform(reco_space, geometry)
+ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cuda')
 proj_data = ray_trafo(phantom)
 backproj = ray_trafo.adjoint(proj_data)
 backproj.show('Backprojection, axis = [1, 0, 0], almost max x slice',

examples/tomo/checks/check_axes_cone3d_fp.py

@@ -4,10 +4,10 @@
 back-ends, a check is needed to confirm that the translation steps are
 done correctly.
 
-All pairs of plots of ODL projections and NumPy axis sums should look
+Both pairs of plots of ODL projections and NumPy axis sums should look
 similar in the sense that they should show the same features in the
-right arrangement (not flipped, rotated, etc.), but differing in
-magnification.
+right arrangement (not flipped, rotated, etc.), up to differences in
+magnification and other cone effects.
 """
 
 import matplotlib.pyplot as plt
@@ -61,7 +61,7 @@
 assert np.allclose(geometry.src_to_det_init, [0, 1, 0])
 
 # Create projections
-ray_trafo = odl.tomo.RayTransform(reco_space, geometry)
+ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cuda')
 proj_data = ray_trafo(phantom)
 
 # Axes in this image are (x, z). This corresponds to
@@ -107,7 +107,7 @@
 assert np.allclose(geometry.src_to_det_init, [0, 0, -1])
 
 # Create projections
-ray_trafo = odl.tomo.RayTransform(reco_space, geometry)
+ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cuda')
 proj_data = ray_trafo(phantom)
 
 # Axes in this image are (x, y). This corresponds to:
@@ -153,7 +153,7 @@
 assert np.allclose(geometry.src_to_det_init, [0, 1, 0])
 
 # Create projections
-ray_trafo = odl.tomo.RayTransform(reco_space, geometry)
+ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cuda')
 proj_data = ray_trafo(phantom)
 
 # Axes in this image are (y, x). This corresponds to

examples/tomo/checks/check_axes_parallel2d_fp.py

@@ -64,7 +64,7 @@
 assert np.allclose(geometry.det_pos_init, [0, 1])
 
 # Create projections
-ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cuda')
+ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cpu')
 proj_data = ray_trafo(phantom)
 
 # Axis in this image is x. This corresponds to 0 degrees.

examples/tomo/checks/check_axes_parallel3d_bp.py

@@ -41,7 +41,7 @@
                                            axis=[0, 0, 1])
 
 # Create projections and back-projection
-ray_trafo = odl.tomo.RayTransform(reco_space, geometry)
+ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cuda')
 proj_data = ray_trafo(phantom)
 backproj = ray_trafo.adjoint(proj_data)
 backproj.show('Backprojection, axis = [0, 0, 1], middle z slice',
@@ -57,7 +57,7 @@
                                            axis=[0, 1, 0])
 
 # Create projections and back-projection
-ray_trafo = odl.tomo.RayTransform(reco_space, geometry)
+ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cuda')
 proj_data = ray_trafo(phantom)
 backproj = ray_trafo.adjoint(proj_data)
 backproj.show('Backprojection, axis = [0, 1, 0], middle y slice',
@@ -73,7 +73,7 @@
                                            axis=[1, 0, 0])
 
 # Create projections and back-projection
-ray_trafo = odl.tomo.RayTransform(reco_space, geometry)
+ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cuda')
 proj_data = ray_trafo(phantom)
 backproj = ray_trafo.adjoint(proj_data)
 backproj.show('Backprojection, axis = [1, 0, 0], almost max x slice',

examples/tomo/checks/check_axes_parallel3d_fp.py

@@ -56,7 +56,7 @@
 assert np.allclose(geometry.det_pos_init, [0, 1, 0])
 
 # Create projections
-ray_trafo = odl.tomo.RayTransform(reco_space, geometry)
+ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cuda')
 proj_data = ray_trafo(phantom)
 
 # Axes in this image are (x, z). This corresponds to
@@ -101,7 +101,7 @@
 assert np.allclose(geometry.det_pos_init, [0, 0, -1])
 
 # Create projections
-ray_trafo = odl.tomo.RayTransform(reco_space, geometry)
+ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cuda')
 proj_data = ray_trafo(phantom)
 
 # Axes in this image are (x, y). This corresponds to:
@@ -146,7 +146,7 @@
 assert np.allclose(geometry.det_pos_init, [0, 1, 0])
 
 # Create projections
-ray_trafo = odl.tomo.RayTransform(reco_space, geometry)
+ray_trafo = odl.tomo.RayTransform(reco_space, geometry, impl='astra_cuda')
 proj_data = ray_trafo(phantom)
 
 # Axes in this image are (y, x). This corresponds to

odl/tomo/backends/astra_cuda.py

@@ -275,7 +275,7 @@ def call_backward(self, proj_data, out=None):
 
         # Copy result to CPU memory
         if self.geometry.ndim == 2:
-            # Rotate 90 degrees counter-clockwise from coordinate system
+            # Rotate 90 degrees clockwise from coordinate system
             # (rows, cols) to (x, y)
             out[:] = np.rot90(self.out_array, -1)
         elif self.geometry.ndim == 3:

odl/tomo/backends/astra_setup.py

@@ -237,7 +237,7 @@ def astra_conebeam_3d_geom_to_vec(geometry):
 
     References
     ----------
-    .. _astra projection geometry documentation:
+    .. _ASTRA projection geometry documentation:
        http://www.astra-toolbox.com/docs/geom3d.html#projection-geometries
     """
     angles = geometry.angles
@@ -297,7 +297,7 @@ def astra_conebeam_2d_geom_to_vec(geometry):
 
     References
     ----------
-    .. _astra projection geometry documentation:
+    .. _ASTRA projection geometry documentation:
        http://www.astra-toolbox.com/docs/geom3d.html#projection-geometries
     """
     angles = geometry.angles
@@ -350,7 +350,7 @@ def astra_parallel_3d_geom_to_vec(geometry):
 
     References
     ----------
-    .. _astra projection geometry documentation:
+    .. _ASTRA projection geometry documentation:
        http://www.astra-toolbox.com/docs/geom3d.html#projection-geometries
     """
     angles = geometry.angles

odl/tomo/geometry/conebeam.py

@@ -43,6 +43,9 @@ class HelicalConeFlatGeometry(DivergentBeamGeometry, AxisOrientedGeometry):
     the initial source-to-detector vector is ``(0, 1, 0)``, and the
     initial detector axes are ``[(1, 0, 0), (0, 0, 1)]``.
 
+    For details, check `the online docs
+    <https://odlgroup.github.io/odl/guide/geometry_guide.html>`_.
+
     See Also
     --------
     CircularConeFlatGeometry : Case with zero pitch
@@ -118,7 +121,6 @@ def __init__(self, apart, dpart, src_radius, det_radius, pitch,
         Initialization with default parameters and some (arbitrary)
         choices for pitch and radii:
 
-        >>> e_x, e_y, e_z = np.eye(3)  # standard unit vectors
         >>> apart = odl.uniform_partition(0, 4 * np.pi, 10)
         >>> dpart = odl.uniform_partition([-1, -1], [1, 1], (20, 20))
         >>> geom = HelicalConeFlatGeometry(
@@ -128,8 +130,12 @@ def __init__(self, apart, dpart, src_radius, det_radius, pitch,
         >>> geom.det_refpoint(0)
         array([ 0., 10.,  0.])
         >>> np.allclose(geom.src_position(2 * np.pi),
-        ...     geom.src_position(0) + (0, 0, 2))  # z shift due to pitch
+        ...             geom.src_position(0) + (0, 0, 2))  # z shift by pitch
         True
+
+        Checking the default orientation:
+
+        >>> e_x, e_y, e_z = np.eye(3)  # standard unit vectors
         >>> np.allclose(geom.axis, e_z)
         True
         >>> np.allclose(geom.src_to_det_init, e_y)
@@ -235,10 +241,8 @@ def __init__(self, apart, dpart, src_radius, det_radius, pitch,
         if det_axes_init is None:
             vecs_to_transform.extend(default_det_axes_init)
 
-        transformed_vecs, matrix = transform_system(
+        transformed_vecs = transform_system(
             axis, default_axis, vecs_to_transform, matrix=init_matrix)
-        # Store matrix computed from the vectors for reference
-        self._rot_matrix_from_vecs = matrix if init_matrix is None else None
 
         axis = transformed_vecs[0]
         if src_to_det_init is None:
@@ -341,8 +345,9 @@ def det_refpoint(self, angle):
 
         For an angle ``phi``, the detector position is given by::
 
-            ref(phi) = det_rad * rot_matrix(phi) * src_to_det_init +
-                       (pitch_offset + pitch * phi) * axis
+            det_ref(phi) = translation +
+                           rot_matrix(phi) * (det_rad * src_to_det_init) +
+                           (pitch_offset + pitch * phi) * axis
 
         where ``src_to_det_init`` is the initial unit vector pointing
         from source to detector.
@@ -361,6 +366,21 @@ def det_refpoint(self, angle):
         See Also
         --------
         rotation_matrix
+
+        Examples
+        --------
+        With default arguments, the detector starts at ``det_rad * e_y``
+        and rotates to ``det_rad * (-e_x) + pitch/4 * e_z`` at
+        90 degrees:
+
+        >>> apart = odl.uniform_partition(0, 4 * np.pi, 10)
+        >>> dpart = odl.uniform_partition([-1, -1], [1, 1], (20, 20))
+        >>> geom = HelicalConeFlatGeometry(
+        ...     apart, dpart, src_radius=5, det_radius=10, pitch=2)
+        >>> np.allclose(geom.det_refpoint(0), [0, 10, 0])
+        True
+        >>> np.allclose(geom.det_refpoint(np.pi / 2), [-10, 0, 0.5])
+        True
         """
         angle = float(angle)
         if angle not in self.motion_params:
@@ -405,6 +425,21 @@ def src_position(self, angle):
         See Also
         --------
         rotation_matrix
+
+        Examples
+        --------
+        With default arguments, the source starts at ``src_rad * (-e_y)``
+        and rotates to ``src_rad * e_x + pitch/4 * e_z`` at
+        90 degrees:
+
+        >>> apart = odl.uniform_partition(0, 4 * np.pi, 10)
+        >>> dpart = odl.uniform_partition([-1, -1], [1, 1], (20, 20))
+        >>> geom = HelicalConeFlatGeometry(
+        ...     apart, dpart, src_radius=5, det_radius=10, pitch=2)
+        >>> np.allclose(geom.src_position(0), [0, -5, 0])
+        True
+        >>> np.allclose(geom.src_position(np.pi / 2), [5, 0, 0.5])
+        True
         """
         angle = float(angle)
         if angle not in self.motion_params:
@@ -486,6 +521,9 @@ class CircularConeFlatGeometry(HelicalConeFlatGeometry):
     the initial source-to-detector vector is ``(0, 1, 0)``, and the
     initial detector axes are ``[(1, 0, 0), (0, 0, 1)]``.
 
+    For details, check `the online docs
+    <https://odlgroup.github.io/odl/guide/geometry_guide.html>`_.
+
     See Also
     --------
     HelicalConeFlatGeometry : General case with motion in z direction
@@ -552,7 +590,6 @@ def __init__(self, apart, dpart, src_radius, det_radius, axis=(0, 0, 1),
         Initialization with default parameters and some (arbitrary)
         choices for the radii:
 
-        >>> e_x, e_y, e_z = np.eye(3)  # standard unit vectors
         >>> apart = odl.uniform_partition(0, 4 * np.pi, 10)
         >>> dpart = odl.uniform_partition([-1, -1], [1, 1], (20, 20))
         >>> geom = CircularConeFlatGeometry(
@@ -563,6 +600,10 @@ def __init__(self, apart, dpart, src_radius, det_radius, axis=(0, 0, 1),
         array([ 0., 10.,  0.])
         >>> np.allclose(geom.src_position(2 * np.pi), geom.src_position(0))
         True
+
+        Checking the default orientation:
+
+        >>> e_x, e_y, e_z = np.eye(3)  # standard unit vectors
         >>> np.allclose(geom.axis, e_z)
         True
         >>> np.allclose(geom.src_to_det_init, e_y)