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Improve noise whitening and coil compression#991

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kdata
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Improve noise whitening and coil compression#991
fzimmermann89 wants to merge 4 commits into
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kdata

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@fzimmermann89 fzimmermann89 commented May 3, 2026

  • fix memory usage in coil whitening. this used >1TB for 3D datasets...
  • add whitening function to KData
  • add varimax option for PCA and coil compression to "rotate" thesubspace such that each of the components has more variance, instead of decreasing information content. makes for example coils a bit more statistically similiar to "real" coils.
  • add option to coil compression to return a compression operator. usefull for "uncompressing" the data or applying same compression to different data
  • improve tests
  • improve exceptino message in PCAOperator: it also failed by mixed devices errors, but always showed a shape missmatch message.

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github-actions Bot commented May 3, 2026

Coverage

Coverage Report
FileStmtsMissCoverMissing
src/mrpro
   _version.py6267%7–8
src/mrpro/algorithms
   varimax.py16194%25
src/mrpro/algorithms/csm
   inati.py25196%43
src/mrpro/algorithms/dcf
   dcf_voronoi.py55493%15, 55–56, 89
src/mrpro/algorithms/optimizers
   adam.py30680%108, 125–129
   cg.py52198%139
   pdhg.py81396%180–181, 187
   pgd.py53492%108, 153–156
src/mrpro/algorithms/reconstruction
   DirectReconstruction.py30293%64, 80
   Reconstruction.py56886%57–59, 123–126, 128, 136
   RegularizedIterativeSENSEReconstruction.py52296%125, 153
   TotalVariationRegularizedReconstruction.py54493%106, 112, 129, 132
src/mrpro/data
   AcqInfo.py165796%49, 56, 134–135, 137, 243, 367
   Dataclass.py3112692%58, 319, 335, 401, 465–467, 480, 575, 595–596, 598, 613–614, 616, 663–664, 669–670, 855–856, 881, 888, 893–894, 896
   DcfData.py33197%62
   EncodingLimits.py97397%37, 127, 130
   IData.py1781293%138, 155–156, 217–225, 258, 304, 322
   IHeader.py174895%49, 98–101, 284, 288, 292, 296
   KData.py2482490%129–130, 145, 152, 163–174, 185, 193, 204, 243, 265–267, 314–315, 387, 615, 617, 689
   KHeader.py1761393%115–121, 148, 196, 203–204, 231–238
   KNoise.py22195%44
   KTrajectory.py95397%163, 165, 185
   Rotation.py7374294%104, 202, 339, 437, 481, 499, 586, 588, 597, 634, 636, 699, 776, 781, 784, 799, 816, 821, 897, 1085, 1090, 1093, 1117, 1121, 1145, 1265, 1267, 1275–1276, 1340, 1422, 1626, 1633–1635, 1694, 1790, 1942, 1977, 1981, 2156, 2177
   SpatialDimension.py1501987%34, 103, 146, 158, 278–280, 293–295, 329, 347, 360, 373, 386, 399, 408–409, 437
src/mrpro/data/traj_calculators
   KTrajectoryCalculator.py26292%84, 95
   KTrajectoryCartesian.py31487%129–132, 136
   KTrajectoryIsmrmrd.py19195%57
   KTrajectorySpiral2D.py571377%63–66, 69, 71, 73, 75, 77, 105, 107, 134–136
src/mrpro/operators
   AveragingOp.py38295%73, 115
   B0InformedFourierOp.py75297%151–154
   CartesianSamplingOp.py112496%152, 191, 266, 387
   ConjugateGradientOp.py89792%62, 64, 100, 106, 228, 230, 233
   ConstraintsOp.py85495%78, 80, 250, 255
   EndomorphOperator.py28293%71, 77
   FiniteDifferenceOp.py29293%40, 126
   FourierOp.py105991%85–87, 192–193, 212, 257, 321, 326
   Functional.py70297%116, 118
   GridSamplingOp.py1651591%72–73, 82–83, 90–91, 94, 96, 98, 282, 290–291, 306, 312–313
   LinearOperator.py202697%217, 255, 296, 305, 313, 330
   LinearOperatorMatrix.py1741989%99, 136, 169, 178, 183, 192–195, 208–211, 219–220, 225–226, 238, 347, 377, 404
   MultiIdentityOp.py16288%58, 63
   NonUniformFastFourierOp.py1981095%72, 99, 221, 223, 261, 263, 340, 397, 471, 476
   Operator.py88397%82, 115, 125
   PatchOp.py49394%93, 129, 144
   ProximableFunctionalSeparableSum.py44393%118, 213, 224
   SliceProjectionOp.py1781094%45, 62, 64, 70, 154, 180, 216, 253, 290, 330
   WaveletOp.py119397%184, 228, 254
   ZeroPadOp.py18194%30
src/mrpro/operators/functionals
   SSIM.py73790%60–80, 82, 86, 114, 147
src/mrpro/operators/models
   EPG.py2561993%31–32, 283, 288, 304–306, 326–327, 332, 356, 361, 386, 391, 545, 599, 738, 755, 782
src/mrpro/phantoms
   EllipsePhantom.py43295%66, 131
   b0map.py262119%37–63
   brainweb.py2974087%276, 290–294, 349–359, 398, 454–457, 479–480, 485–486, 488–489, 493, 501, 508–509, 550, 621, 624–625, 644, 653–656, 667, 669, 700–701, 715, 723
   fastmri.py1061091%50–51, 59, 65, 162, 169–171, 174–175, 189
   m4raw.py74495%58–59, 74, 76
   mdcnn.py71790%58, 62–63, 70, 82, 88, 135
src/mrpro/utils
   RandomGenerator.py1551590%23–24, 36, 38, 188, 212, 428, 446, 528, 799, 829–832, 895, 898
   ema.py42490%49, 74, 78, 82
   filters.py61198%46
   indexing.py177199%321
   pad_or_crop.py39685%40, 43, 46, 49, 66, 73
   reshape.py1531093%176, 370, 482–484, 505, 508–509, 515, 530
   slice_profiles.py49688%21, 37, 119–122, 155
   split_idx.py10280%43, 47
   summarize.py57689%40–41, 70–73, 81
   unit_conversion.py721579%34, 44, 51, 53, 62, 69, 71, 78, 80, 89, 100, 121, 123, 144, 146
TOTAL815350294% 

Tests Skipped Failures Errors Time
3312 0 💤 0 ❌ 0 🔥 2m 27s ⏱️

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github-actions Bot commented May 3, 2026

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@fzimmermann89 fzimmermann89 added the pre-commit.ci autofix run autofix in this PR label May 3, 2026
@pre-commit-ci pre-commit-ci Bot removed the pre-commit.ci autofix run autofix in this PR label May 3, 2026
@fzimmermann89 fzimmermann89 requested review from ckolbPTB and schuenke May 3, 2026 16:58
Comment thread src/mrpro/data/KData.py Outdated
Comment thread tests/data/test_kdata.py Outdated
Comment thread src/mrpro/operators/PCACompressionOp.py Outdated
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2 participants