api: Add Hicks (sinc) interpolation api #2342

mloubout · 2024-04-01T16:57:46Z

Add support for kaiser-windowed sinc interpolation

Fixes #595

codecov · 2024-04-01T17:26:24Z

Codecov Report

Attention: Patch coverage is 85.71429% with 28 lines in your changes are missing coverage. Please review.

Project coverage is 79.41%. Comparing base (311cd4e) to head (353af4f).

Files	Patch %	Lines
conftest.py	27.58%	19 Missing and 2 partials ⚠️
devito/operations/interpolators.py	90.74%	4 Missing and 1 partial ⚠️
examples/seismic/acoustic/acoustic_example.py	87.50%	1 Missing ⚠️
examples/seismic/utils.py	93.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2342      +/-   ##
==========================================
- Coverage   86.66%   79.41%   -7.26%     
==========================================
  Files         232      232              
  Lines       43445    43578     +133     
  Branches     8063     8072       +9     
==========================================
- Hits        37653    34606    -3047     
- Misses       5087     8215    +3128     
- Partials      705      757      +52

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EdCaunt · 2024-04-02T15:56:59Z

devito/operations/interpolators.py

+
+    def _arg_defaults(self, coords=None, sfunc=None):
+        args = {}
+        b = self._b_table[self.r]


Does this need a catch for r > 10?

It will just throw a key-error but can add a check (I doubt anyone will run it this high that's a 20x20x20 cube in 3d super expensive)

agree to add a check. Users can be surprising...

FabioLuporini

Can we also add an ABox test in PRO?

FabioLuporini · 2024-04-02T07:06:21Z

.github/workflows/pytest-core-mpi.yml

@@ -48,6 +48,11 @@ jobs:
        python3 scripts/clear_devito_cache.py
        python3 -m pytest --cov --cov-config=.coveragerc --cov-report=xml -m parallel tests/

+    - name: Test examples


for uniformity, "Test examples with MPI" ?

FabioLuporini · 2024-04-02T07:08:54Z

devito/operations/interpolators.py

+    def name(self):
+        return self._name
+
+    def _arg_defaults(self, **args):


if we want this method here it would be cleaner to have this class inhereting from ArgProvider.

Perhaps we move it into a subclass?

No, the interpolator isn't an arg provide, its sparse function is and is calling it only.

FabioLuporini · 2024-04-03T07:21:49Z

devito/operations/interpolators.py

+        # Position only replacement, not radius dependent.
+        # E.g src.inject(vp(x)*src) needs to use vp[posx] at all points
+        # not vp[posx + rx]
+        if pos_only is not None:


if you turn pos_only into pos_only=() (instead of None) you don't need this if I think?

Convention throughout is None for kwargs default (for tuple/dict/...)

no, the convention is to use immutable objects only, and tuple in that sense is fine ; dict/list/set aren't instead obv

for example, I'm using =() in ir/iet/nodes.py

alternatively, you may use as_tuple

FabioLuporini · 2024-04-03T07:22:22Z

devito/operations/interpolators.py

+
+    _name = 'sinc'
+
+    # Table 1


What's Table 2? u mean Table 1 in the paper?

Yes Table 1 in the paper

FabioLuporini · 2024-04-03T07:23:10Z

devito/operations/interpolators.py

+
+    def _arg_defaults(self, coords=None, sfunc=None):
+        args = {}
+        b = self._b_table[self.r]


agree to add a check. Users can be surprising...

FabioLuporini · 2024-04-03T07:23:55Z

devito/operations/interpolators.py

+        coords = coords / np.array(sfunc.grid.spacing)
+        coords = coords - np.floor(coords)
+
+        # Precompute sinc


I think this wants a NOTE: <comment about performance> ? if you measured it's slowish? or is it super quick since the loops are very short?

I haven't seen any drastic slow compute since it's numpified so not sure want to force user to be like "hey here is a warning should I nitpick here"

FabioLuporini · 2024-04-03T07:24:19Z

devito/types/sparse.py

+        if interp == 'sinc' and self._radius < 2:
+            raise ValueError("The 'sinc' interpolator requires a radius of at least 2")
+
+        # Set space ordert to `r` for safety


but not sure why this comment ended up here

FabioLuporini · 2024-04-03T07:25:48Z

examples/seismic/acoustic/acoustic_example.py

@@ -60,21 +60,26 @@ def run(shape=(50, 50, 50), spacing=(20.0, 20.0, 20.0), tn=1000.0,
    solver.jacobian(dm, autotune=autotune)
    info("Applying Gradient")
    solver.jacobian_adjoint(rec, u, autotune=autotune, checkpointing=checkpointing)
-    return summary.gflopss, summary.oi, summary.timings, [rec, u.data]
+    return summary.gflopss, summary.oi, summary.timings, [rec, u.data._local]


this will pick the (dirty) padding as well I think? why not just data or data_with_halo?

for MPI debug the _local is a lot more useful

FabioLuporini · 2024-04-03T07:27:14Z

examples/seismic/acoustic/operators.py

    z = zfs.parent

-    # Functions present in the stencil
-    funcs = retrieve_functions(rhs)
+    # Retrieve vertical derivatives


what's all these new additions?

it does the same, except it only evaluates z derivatives instead of everything since the rest isn't needed which is much cheaper especially for things like tti.

FabioLuporini · 2024-04-03T07:27:21Z

examples/seismic/acoustic/operators.py

-    # Functions present in the stencil
-    funcs = retrieve_functions(rhs)
+    # Retrieve vertical derivatives
+    Dz = {d for d in retrieve_derivatives(rhs) if z in d.dims}


FabioLuporini · 2024-04-03T14:47:04Z

devito/operations/interpolators.py

+        # Position only replacement, not radius dependent.
+        # E.g src.inject(vp(x)*src) needs to use vp[posx] at all points
+        # not vp[posx + rx]
+        if pos_only is not None:


no, the convention is to use immutable objects only, and tuple in that sense is fine ; dict/list/set aren't instead obv

for example, I'm using =() in ir/iet/nodes.py

alternatively, you may use as_tuple

FabioLuporini · 2024-04-03T14:47:17Z

.github/workflows/pytest-core-mpi.yml

+      - name: Test examples with MPI
+        run: |
+          docker run --rm -e DEVITO_SAFE_MATH=1 -e DEVITO_MPI=1 -e OMP_NUM_THREADS=1 --name examplerun devito_img mpiexec -n 2 pytest examples/seismic/acoustic


comment why safe-math needed

FabioLuporini · 2024-04-03T14:48:12Z

devito/operations/interpolators.py

        # List of indirection indices for all adjacent grid points
-        idx_subs, temps = self._interp_idx(variables, implicit_dims=implicit_dims)
+        idx_subs, temps = self._interp_idx(list(fields), implicit_dims=implicit_dims,


why does it need to be casted to a list? it was a tuple already, so it feels pretty odd

mloubout added API api (symbolics, types, ...) feature-request labels Apr 1, 2024

mloubout force-pushed the sinc-interp-final branch 4 times, most recently from 77bd1b2 to 554aece Compare April 1, 2024 17:19

mloubout force-pushed the sinc-interp-final branch 3 times, most recently from f708213 to 0749d57 Compare April 1, 2024 17:57

mloubout marked this pull request as draft April 1, 2024 19:39

mloubout marked this pull request as ready for review April 1, 2024 19:39

mloubout force-pushed the sinc-interp-final branch 4 times, most recently from 2010409 to ef27943 Compare April 2, 2024 16:42

EdCaunt reviewed Apr 2, 2024

View reviewed changes

mloubout force-pushed the sinc-interp-final branch 5 times, most recently from 82cced0 to 8172aab Compare April 3, 2024 03:26

FabioLuporini reviewed Apr 3, 2024

View reviewed changes

mloubout added 7 commits April 3, 2024 08:40

api: support sinc interpolation

cf4b65e

api: numpify sinc precompute and add test

83bbef3

mpi: revamp conftest

4aadbf8

mpi: fix sinc setup with mpi and add back missing mpi example tests

c4ac44e

api: fix sparse position index for negative location

4db1120

examples: improved fs only check z derivs

99448f1

misc: review cleanup

a83fac7

mloubout force-pushed the sinc-interp-final branch 2 times, most recently from 25721fe to 2705f26 Compare April 3, 2024 13:26

FabioLuporini reviewed Apr 3, 2024

View reviewed changes

api: switch to recommended scipy i0 when available

353af4f

mloubout force-pushed the sinc-interp-final branch from 2705f26 to 353af4f Compare April 3, 2024 14:54

mloubout merged commit 364997c into master Apr 3, 2024
31 checks passed

mloubout deleted the sinc-interp-final branch April 3, 2024 17:08

mloubout mentioned this pull request Apr 30, 2024

dsl: Implementation of new interpolation methods #1932

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api: Add Hicks (sinc) interpolation api #2342

api: Add Hicks (sinc) interpolation api #2342

mloubout commented Apr 1, 2024 •

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api: Add Hicks (sinc) interpolation api #2342

api: Add Hicks (sinc) interpolation api #2342

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