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Make tests faster #589

Merged
merged 9 commits into from
Jan 4, 2025
Merged

Make tests faster #589

merged 9 commits into from
Jan 4, 2025
+91 −78

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ckolbPTB
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@ckolbPTB ckolbPTB commented Dec 18, 2024 •
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Closes #564

I went through some of the tests and reduced matrix sizes to speed up the tests.

On my MacBook Pro I got similar timing results than @fzimmermann89 reported here: #564 and I got a total run time for most of the tests (not all tests run on my laptop) of 4.5 mins. With these changes this was reduced to 2 mins.

In the github action it seems to reduce the time from ~2min to ~1min.

@koflera Could you please have a look at the tests for the optimizers:

mrpro/tests/algorithms/test_optimizers.py

Line 14 in 9dc1167

def test_optimizers_rosenbrock(optimizer, enforce_bounds_on_x1, optimizer_kwargs):

This currently takes quite some time. Maybe we can speed it up by starting closer to the solution? You can time it yourself by e.g. running pytest tests/algorithms/test_optimizers.py --durations=10

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github-actions bot commented Dec 18, 2024 •
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Coverage

Coverage Report
FileStmtsMissCoverMissing
src/mrpro/algorithms/csm
   inati.py24196%44
   walsh.py16194%34
src/mrpro/algorithms/dcf
   dcf_voronoi.py53492%15, 48–49, 76
src/mrpro/algorithms/optimizers
   adam.py20195%69
src/mrpro/algorithms/reconstruction
   DirectReconstruction.py281643%51–71, 85
   IterativeSENSEReconstruction.py13192%76
   Reconstruction.py502256%42, 54–56, 80–87, 104–113
   RegularizedIterativeSENSEReconstruction.py411759%96–100, 114–139
src/mrpro/data
   AcqInfo.py128398%26, 169, 207
   CsmData.py29390%15, 82–84
   DcfData.py45882%18, 66, 78–83
   IData.py67987%119, 125, 129, 159–167
   IHeader.py75791%75, 109, 127–131
   KHeader.py1531789%25, 119–123, 150, 199, 210, 217–218, 221, 228, 260–271
   KNoise.py311552%39–52, 56–61
   KTrajectory.py811285%108–113, 116–118, 203–207
   MoveDataMixin.py1401887%15, 113, 129, 143–145, 207, 323–325, 338, 417, 437–438, 440, 455–456, 458
   QData.py39782%42, 65–73
   Rotation.py6743595%100, 198, 335, 433, 477, 495, 581, 583, 592, 626, 628, 691, 768, 773, 776, 791, 808, 813, 889, 1077, 1082, 1085, 1109, 1113, 1240, 1242, 1250–1251, 1315, 1397, 1690, 1846, 1881, 1885, 1996
   SpatialDimension.py2322191%34, 104, 141, 148, 154, 274–276, 289–291, 325, 343, 356, 369, 382, 395, 404–405, 420, 429
   acq_filters.py12192%47
src/mrpro/data/_kdata
   KData.py1341887%109–110, 125, 132, 142, 150, 204–205, 243, 248–249, 268–279
   KDataRemoveOsMixin.py29293%44, 46
   KDataSelectMixin.py19289%48, 63
   KDataSplitMixin.py48394%53, 84, 93
src/mrpro/data/traj_calculators
   KTrajectoryCalculator.py25292%23, 45
   KTrajectoryIsmrmrd.py13285%41, 50
   KTrajectoryPulseq.py23196%55
src/mrpro/operators
   CartesianSamplingOp.py89397%118, 157, 280
   ConstraintsOp.py60297%46, 48
   EndomorphOperator.py65297%228, 234
   FiniteDifferenceOp.py27293%40, 105
   FourierOp.py158398%263, 381, 386
   Functional.py71593%20–22, 117, 119
   GridSamplingOp.py136993%72–73, 82–83, 90–91, 94, 96, 98
   LinearOperator.py1681094%55, 91, 190, 220, 261, 270, 278, 287, 295, 320
   LinearOperatorMatrix.py1581690%82, 119, 152, 161, 166, 175–178, 191–194, 203, 215, 304, 331, 359
   MultiIdentityOp.py13285%43, 48
   Operator.py78297%25, 74
   ProximableFunctionalSeparableSum.py39392%50, 103, 110
   SliceProjectionOp.py173895%44, 61, 63, 69, 206, 227, 260, 300
   WaveletOp.py120596%152, 170, 205, 210, 233
   ZeroPadOp.py16194%30
src/mrpro/utils
   filters.py62297%44, 49
   reshape.py60198%191
   slice_profiles.py46687%20, 36, 113–116, 149
   sliding_window.py34197%34
   split_idx.py10280%43, 47
   summarize_tensorvalues.py11918%20–29
   typing.py181139%8–23
   zero_pad_or_crop.py31681%26, 30, 54, 57, 60, 63
TOTAL493336093% 

Tests Skipped Failures Errors Time
2262 0 💤 0 ❌ 0 🔥 1m 10s ⏱️

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github-actions bot commented Dec 18, 2024 •
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📚 Documentation

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I think most low-hanging fruits have been picked now:

4.00s call     tests/operators/test_fourier_op.py::test_fourier_op_gram[radial_phase_encoding_2_coils_non_cartesian_sampling]
3.55s call     tests/operators/test_fourier_op.py::test_fourier_op_gram[3d_nonuniform_3_coils_2_other]
3.04s setup    tests/data/test_kdata.py::test_KData_kspace
1.60s call     tests/algorithms/test_optimizers.py::test_optimizers_rosenbrock[adam-optimizer_kwargs0-True]
1.56s call     tests/data/test_csm_data.py::test_CsmData_smoothing_width[random_kheader0-random_full_ismrmrd_header0-random_acquisition0-from_idata_walsh]
1.55s call     tests/operators/test_fourier_op.py::test_fourier_op_gram[2d_nonuniform_cine_mri_3_cardiac_phases_2_coils]
1.43s call     tests/operators/test_fourier_op.py::test_fourier_op_fwd_adj_property[stack_of_stars_3_other_2_coil_with_oversampling]
1.32s call     tests/operators/test_fourier_op.py::test_fourier_op_fwd_adj_property[3d_nonuniform_3_coils_2_other]
1.28s call     tests/operators/test_fourier_op.py::test_fourier_op_gram[stack_of_stars_3_other_2_coil_with_oversampling]
1.23s call     tests/operators/functionals/test_functional_arithmetic.py::test_functional_scaling_prox_optimality[L1Norm-mean-dim=None-no_target-scalar_weight-float32-shape=[1,2,3]]
1.19s call     tests/algorithms/csm/test_inati.py::test_inati[random_kheader0-random_full_ismrmrd_header0-random_acquisition0]
1.17s call     tests/data/test_kdata.py::test_KData_compress_coils_diff_batch_joint_dims[consistently_shaped_kdata0-random_kheader_shape0-random_acquisition0-random_full_ismrmrd_header0-batching_along_dim-2_and_dim-1]
1.17s call     tests/algorithms/test_optimizers.py::test_optimizers_rosenbrock[adam-optimizer_kwargs0-False]
1.15s call     tests/data/test_rotation.py::test_weighted_mean_dims[shape2-True-dim2-expected_shape2]
1.11s call     tests/data/test_rotation.py::test_align_vectors_near_inf
1.09s call     tests/operators/functionals/test_functional_arithmetic.py::test_functional_scaling_prox_optimality[L1NormViewAsReal-mean-dim=None-random_target-complex_weight-complex64-shape=[1,2,3]]
1.00s call     tests/operators/functionals/test_functionals.py::test_functional_prox_optimality[L1NormViewAsReal-sum-dim=None-random_target-complex_weight-float32-shape=[1,2,3]]

@fzimmermann89 fzimmermann89 self-requested a review January 4, 2025 01:32
@ckolbPTB ckolbPTB merged commit bc2e05a into main Jan 4, 2025
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@ckolbPTB ckolbPTB deleted the speed_up_tests branch January 4, 2025 14:51
@fzimmermann89 fzimmermann89 mentioned this pull request Jan 7, 2025
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Some tests have large runtimes
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@ckolbPTB @fzimmermann89