WIP: Add vector geometries by kohr-h · Pull Request #1418 · odlgroup/odl

kohr-h · 2018-08-22T15:46:11Z

I picked up an old WIP branch that I currently need. The code adds support for ASTRA vec geometries in a fairly direct way.

Since the coordinate systems of ODL and ASTRA differ, I've taken the following approach:

The geometries ParallelVecGeometry and ConeVecGeometry take a matrix of shape (N, 6) for 2D or (N, 12) for 3D and determine ndim accordingly.
The vectors are stored as arrays without further modification.
The axes X,Y,Z in the definition of the vectors refer to ODL coordinates, e.g., (rayX, rayY) is defined with respect to the ODL coordinate system.
As a consequence, a conversion step is necessary before handing these vectors over to ASTRA (or, inversely, when we get vectors from ASTRA or from somewhere with ASTRA coordinates).
The reasoning behind this is that ODL should use consistent coordinates internally and translate to other systems when interfacing with other libraries. The "list of vectors" format is just treated as a representation for geometries, without any prescribed coordinate system.

I've added a couple of "check" examples to make sure that the transformations are defined correctly. It's looking good, and the existing geometries are still correct.

TODO:

Move axis swapping in 3D to a separate function so that *3d_geom_to_vecs returns the ASTRA vectors "as expected", and downstream code does the swapping instead.
Add adjointness test for vec geometries
~~Clean up commits~~

Closes #1023

kohr-h · 2018-08-22T15:48:34Z

+    angle_partition, detector_partition, src_radius=1000, det_radius=100,
+    axis=[1, 0, 0])
+
+circle_vecs = odl.tomo.astra_conebeam_3d_geom_to_vec(circle_geometry)


I've renamed this function, TODO change here

kohr-h · 2018-08-22T15:51:37Z

        xi = np.asarray(xi)
        slc = [None] * n
        slc[ax] = slice(None)
+        slc = tuple(slc)


Code like this without conversion from list to tuple raises a DeprecationWarning in NumPy 1.15, we should apply the fix throughout.

kohr-h · 2018-08-22T15:54:14Z

-        'DetectorCount': 10, 'DetectorWidth': 0.2}
-
-    assert is_subdict(correct_subdict, proj_geom)
-    assert 'ProjectionAngles' in proj_geom


This test was kind of pointless since it really tests ASTRA rather than ODL, and some implementation detail of ODL. Not sure if we really need a replacement.

kohr-h · 2018-08-22T15:57:07Z

+            elif geometry.ndim == 3:
+                det_px_area = geometry.det_partition.cell_volume
+                scaling_factor *= (det_px_area ** 2 /
+                                   reco_space.cell_volume ** 2)


Some testing needed here

kohr-h · 2018-08-22T15:59:11Z

+        # ODL x = ASTRA -y, ODL y = ASTRA x
+        # Thus: ODL->ASTRA conversion is a rotation by +90 degrees
+        rot_90 = euler_matrix(np.pi / 2)
+        # Bulk matrix-vector product


with the transposed matrix

kohr-h · 2018-08-22T15:59:42Z

+    if vecs.shape[1] == 6:
+        # 2D geometry
+        # ODL x = ASTRA -y, ODL y = ASTRA x
+        # Thus: ODL->ASTRA conversion is a rotation by +90 degrees


Maybe these comments are redundant

kohr-h · 2018-08-22T16:15:06Z

+        # TODO: shapes are not quite right here. Scalar works, but
+        # vectorized goes wrong
+        ray_dir = np.empty(bcast_shape + (self.ndim,), dtype=float)
+        print('result shape:', ray_dir.shape)


Debug statement, TODO remove

Regarding vectorization, I'd suggest putting it in a separate PR.

adler-j · 2018-08-23T19:05:22Z

Should this be reviewed?

kohr-h · 2018-08-24T07:55:08Z

Should this be reviewed?

Hm, I think some things are still a bit in the flow, so I'll make it a WIP in the title. I'll give a heads-up when it's ready.

pep8speaks · 2019-02-13T13:10:21Z

Checking updated PR...

In the file odl/tomo/backends/astra_cuda.py:

Line 508:5: E303 too many blank lines (2)

In the file odl/tomo/geometry/parallel.py:

Line 1650:9: E303 too many blank lines (2)

Comment last updated at 2020-11-08 00:20:59 UTC

kohr-h · 2020-04-13T10:11:06Z

Deferring until #1540 has landed. Too many overlapping changes.

kohr-h · 2020-09-06T07:23:01Z

Okay, time to pick this one up again.

adriaangraas · 2020-09-06T08:34:11Z

I did a merge with a few minor fixes, may or may not be useful. See your repo.

kohr-h · 2020-09-06T09:17:03Z

I did a merge with a few minor fixes, may or may not be useful. See your repo.

Thanks, I saw it. I'll take it as reference. 👍

kohr-h · 2020-09-08T20:23:43Z

+        elif isinstance(geometry, VecGeometry):
+            scaling_factor = (geometry.det_partition.cell_volume /
+                              vol_space.cell_volume)
+        elif isinstance(geometry, ParallelVecGeometry):
+            if geometry.ndim == 2:
+                # Scales with 1 / cell_volume
+                scaling_factor *= float(vol_space.cell_volume)
+            elif geometry.ndim == 3:
+                # Scales with cell volume
+                scaling_factor /= vol_space.cell_volume


Some part of this logic makes no sense...

kohr-h commented Aug 22, 2018

View reviewed changes

kohr-h changed the title ~~Add vector geometries~~ WIP: Add vector geometries Aug 24, 2018

kohr-h force-pushed the issue-1023__vec_geometry branch from 621e03a to 8d211d6 Compare September 10, 2018 08:56

adler-j mentioned this pull request Sep 11, 2018

Release 1.0.0 #1055

Open

20 tasks

kohr-h force-pushed the issue-1023__vec_geometry branch from f6bf263 to 4052454 Compare March 13, 2019 21:15

kohr-h force-pushed the issue-1023__vec_geometry branch from 4052454 to 521d7cf Compare November 5, 2019 13:19

kohr-h added area: tomo status: postponed type: new feature labels Apr 13, 2020

kohr-h removed the status: postponed label Sep 6, 2020

Holger Kohr and others added 7 commits September 6, 2020 12:41

ENH: add vector geometries, closes odlgroup#1023

d24bad2

WIP: fix weighting for vec backprojection

452a9bf

WIP: vectorize VecGeometry methods

771b38d

MAINT: fix old-style repr of vec geometry

2d99692

ENH: add parallel 2d version of geom->vectors converter

195f2dc

ENH: allow different discr in irrelevant axes in resizing op

6e8b102

WIP: fix adjoint weighting in par2d vec geometry

36f0911

kohr-h added 11 commits September 6, 2020 12:54

ENH: add support for ASTRA parallel_vec

f891d9d

WIP: add axis check examples for vec geometries

567bef6

ENH: fix coord sys handling in vec geometries

87ae3f1

ENH: ditch pkg_resources for pkg_supports function

a05ebd3

WIP: add coords arg to geom->vec converters

bd0a2a5

ENH: add VecGeometry.__getitem__

d487ce3

MAINT: update 3d vec geom example

d3a75a8

Fix imports and names in tomo subpackage

e084e95

Fix astra_setup tests

f21af6b

WIP: simplify index interpolation to rounding

6b8eb8b

WIP: Fix broadcasting in vec geometry methods

252b7d0

kohr-h force-pushed the issue-1023__vec_geometry branch from 1ca6fed to 252b7d0 Compare September 6, 2020 10:59

kohr-h added 2 commits September 6, 2020 13:16

Check dimension in parallel_beam_geometry

047a79d

Minor fixes in docs and comments of astra_setup.py

1445d13

kohr-h commented Sep 8, 2020

View reviewed changes

kohr-h added 4 commits November 8, 2020 01:16

Replace is by == in pspace ops comparison

5562656

Improve formatting in pkg_supports

6ca631d

Temporary weight changes and minor fixes

accaf92

Fix broadcasting in base VecGeometry methods

4bf2d7a

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Comment last updated at 2020-11-08 00:20:59 UTC

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kohr-h commented Aug 22, 2018 •

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