Add VAE network

[fzimmermann89]

No description provided.

[fzimmermann89]

Stack from ghstack (oldest at bottom):

• Add DiT network #964
• -> Add VAE network #961
• add hourglass transformer architecture and tests #960
• add uformer architecture and tests #959
• add swinir architecture and tests #958
• add restormer architecture and tests #957
• Add MLP network and tests #963
• add unet, basic cnn, and residual blocks #956
• add positional encodings and attention modules #955
• add data consistency modules and tests #954
• add core nn foundations and layers #953
• Add fast path to PatchOp adjoint #962

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
src/mrpro
_version.py	6	2	67%	7–8
src/mrpro/algorithms/csm
inati.py	25	1	96%	43
src/mrpro/algorithms/dcf
dcf_voronoi.py	55	4	93%	15, 55–56, 89
src/mrpro/algorithms/optimizers
adam.py	30	6	80%	108, 125–129
cg.py	52	1	98%	139
pdhg.py	81	3	96%	180–181, 187
pgd.py	53	4	92%	108, 153–156
src/mrpro/algorithms/reconstruction
DirectReconstruction.py	30	2	93%	64, 80
Reconstruction.py	56	8	86%	57–59, 123–126, 128, 136
RegularizedIterativeSENSEReconstruction.py	52	2	96%	125, 153
TotalVariationRegularizedReconstruction.py	54	4	93%	106, 112, 129, 132
src/mrpro/data
AcqInfo.py	165	7	96%	49, 56, 134–135, 137, 243, 367
Dataclass.py	311	26	92%	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.py	33	1	97%	62
EncodingLimits.py	97	3	97%	37, 127, 130
IData.py	178	12	93%	138, 155–156, 217–225, 258, 304, 322
IHeader.py	174	8	95%	49, 98–101, 284, 288, 292, 296
KData.py	230	24	90%	122–123, 138, 145, 156–167, 178, 186, 197, 236, 258–260, 307–308, 380, 546, 548, 620
KHeader.py	176	13	93%	115–121, 148, 196, 203–204, 231–238
KNoise.py	22	1	95%	44
KTrajectory.py	95	3	97%	163, 165, 185
Rotation.py	737	42	94%	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.py	150	19	87%	34, 103, 146, 158, 278–280, 293–295, 329, 347, 360, 373, 386, 399, 408–409, 437
src/mrpro/data/traj_calculators
KTrajectoryCalculator.py	26	2	92%	84, 95
KTrajectoryCartesian.py	31	4	87%	129–132, 136
KTrajectoryIsmrmrd.py	19	1	95%	57
KTrajectorySpiral2D.py	57	13	77%	63–66, 69, 71, 73, 75, 77, 105, 107, 134–136
src/mrpro/nn
AbsolutePositionEncoding.py	31	1	97%	70
AxialRoPE.py	33	4	88%	62, 78, 81, 101
DropPath.py	17	1	94%	54
FourierFeatures.py	14	1	93%	29
LayerNorm.py	43	1	98%	42
PermutedBlock.py	36	3	92%	56, 59, 64
PixelShuffle.py	95	5	95%	60, 117, 148–149, 224
Residual.py	12	5	58%	22–24, 41, 45
Sequential.py	23	2	91%	47, 58
Upsample.py	25	7	72%	32–33, 37–41
join.py	56	1	98%	155
src/mrpro/nn/attention
LinearSelfAttention.py	39	1	97%	72
MultiHeadAttention.py	39	6	85%	76–78, 85–86, 104
NeighborhoodSelfAttention.py	53	3	94%	21, 182, 229
SpatialTransformerBlock.py	74	5	93%	79, 113, 117, 169–170
src/mrpro/nn/data_consistency
AnalyticCartesianDC.py	33	4	88%	48, 50, 88, 91
ConjugateGradientDC.py	42	7	83%	31, 33, 95, 101–102, 107–108
GradientDescentDC.py	30	3	90%	46, 48, 91
src/mrpro/nn/nets
BasicCNN.py	37	7	81%	66, 68, 73–74, 83–86
HourglassTransformer.py	40	1	98%	71
MLP.py	47	7	85%	66–67, 75, 86–89, 112
Restormer.py	60	2	97%	102, 175
SwinIR.py	42	1	98%	53
UNet.py	150	7	95%	155, 162–168, 252, 257, 268
VAE.py	47	3	94%	61–63
src/mrpro/operators
AveragingOp.py	38	2	95%	73, 115
B0InformedFourierOp.py	75	2	97%	151–154
CartesianSamplingOp.py	112	4	96%	152, 191, 266, 387
ConjugateGradientOp.py	89	7	92%	62, 64, 100, 106, 228, 230, 233
ConstraintsOp.py	85	4	95%	78, 80, 250, 255
EndomorphOperator.py	28	2	93%	71, 77
FiniteDifferenceOp.py	29	2	93%	40, 126
FourierOp.py	105	8	92%	85–87, 192–193, 212, 257, 326
Functional.py	70	2	97%	116, 118
GridSamplingOp.py	165	15	91%	72–73, 82–83, 90–91, 94, 96, 98, 282, 290–291, 306, 312–313
LinearOperator.py	202	6	97%	217, 255, 296, 305, 313, 330
LinearOperatorMatrix.py	174	19	89%	99, 136, 169, 178, 183, 192–195, 208–211, 219–220, 225–226, 238, 347, 377, 404
MultiIdentityOp.py	16	2	88%	58, 63
NonUniformFastFourierOp.py	198	10	95%	72, 99, 221, 223, 261, 263, 340, 397, 471, 476
Operator.py	88	3	97%	82, 115, 125
PatchOp.py	76	6	92%	98, 128–129, 137, 151, 184
ProximableFunctionalSeparableSum.py	44	3	93%	118, 213, 224
SliceProjectionOp.py	178	10	94%	45, 62, 64, 70, 154, 180, 216, 253, 290, 330
WaveletOp.py	119	3	97%	184, 228, 254
ZeroPadOp.py	18	1	94%	30
src/mrpro/operators/functionals
SSIM.py	73	7	90%	60–80, 82, 86, 114, 147
src/mrpro/operators/models
EPG.py	256	19	93%	31–32, 283, 288, 304–306, 326–327, 332, 356, 361, 386, 391, 545, 599, 738, 755, 782
src/mrpro/phantoms
EllipsePhantom.py	43	2	95%	66, 131
b0map.py	26	21	19%	37–63
brainweb.py	297	40	87%	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.py	106	10	91%	50–51, 59, 65, 162, 169–171, 174–175, 189
m4raw.py	74	4	95%	58–59, 74, 76
mdcnn.py	71	7	90%	58, 62–63, 70, 82, 88, 135
src/mrpro/utils
RandomGenerator.py	155	14	91%	23–24, 36, 38, 188, 212, 428, 446, 528, 829–832, 895, 898
ema.py	42	4	90%	49, 74, 78, 82
filters.py	61	1	98%	46
indexing.py	177	1	99%	321
pad_or_crop.py	39	5	87%	40, 43, 46, 49, 73
reshape.py	153	10	93%	176, 370, 482–484, 505, 508–509, 515, 530
slice_profiles.py	49	6	88%	21, 37, 119–122, 155
split_idx.py	10	2	80%	43, 47
summarize.py	57	6	89%	40–41, 70–73, 81
to_tuple.py	9	1	89%	34
unit_conversion.py	72	15	79%	34, 44, 51, 53, 62, 69, 71, 78, 80, 89, 100, 121, 123, 144, 146
TOTAL	9740	590	94%

Tests	Skipped	Failures	Errors	Time
3462	8 💤	0 ❌	0 🔥	5m 10s ⏱️

[github-actions]

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