Fix errors due to pydicom 3.0

[ckolbPTB]

Pydicom 3.0 was released which led to several errors due to deprecation, see e.g. https://github.com/pydicom/pydicom/pull/1567/files#diff-9b5a2e48457143cde31b1bbe1c7546a6733e577c306cfe582d56099851e12468

[github-actions[bot]]

Coverage Report

File	Stmts	Miss	Cover	Missing
src/mrpro/algorithms/csm
inati.py	24	1	96%	44
iterative_walsh.py	15	1	93%	37
src/mrpro/algorithms/dcf
dcf_voronoi.py	53	4	92%	15, 48–49, 76
src/mrpro/algorithms/optimizers
adam.py	20	1	95%	69
src/mrpro/algorithms/reconstruction
DirectReconstruction.py	28	16	43%	51–71, 85
IterativeSENSEReconstruction.py	42	23	45%	77–78, 88–98, 113–124, 138–149
Reconstruction.py	51	24	53%	41, 53–55, 79–86, 103–114
src/mrpro/data
AcqInfo.py	128	2	98%	174, 214
CsmData.py	28	3	89%	14, 84–86
DcfData.py	44	8	82%	17, 65, 77–82
IData.py	67	9	87%	119, 125, 129, 159–167
IHeader.py	75	7	91%	75, 109, 127–131
KHeader.py	164	17	90%	24, 126–130, 157, 207, 218, 225–226, 229, 236, 275–286
KNoise.py	31	15	52%	39–52, 56–61
KTrajectory.py	69	5	93%	178–182
MoveDataMixin.py	126	14	89%	14, 109, 125, 139–141, 202, 265, 279, 358, 378–379, 396–397
QData.py	39	7	82%	42, 65–73
SpatialDimension.py	46	2	96%	64, 103
TrajectoryDescription.py	14	1	93%	23
acq_filters.py	10	1	90%	47
src/mrpro/data/_kdata
KData.py	105	16	85%	107–108, 117, 125, 179–180, 215, 220–221, 240–251
KDataRemoveOsMixin.py	29	2	93%	43, 45
KDataSelectMixin.py	20	2	90%	46, 62
KDataSplitMixin.py	48	3	94%	49, 79, 88
src/mrpro/data/traj_calculators
KTrajectoryCalculator.py	25	2	92%	23, 45
KTrajectoryIsmrmrd.py	13	2	85%	41, 50
KTrajectoryPulseq.py	29	1	97%	54
src/mrpro/operators
CartesianSamplingOp.py	50	9	82%	49–50, 55–56, 61–62, 88, 91, 114
ConstraintsOp.py	60	2	97%	46, 48
EndomorphOperator.py	51	2	96%	209, 213
FiniteDifferenceOp.py	27	2	93%	48, 113
FourierOp.py	77	1	99%	131
GridSamplingOp.py	123	9	93%	60–61, 70–71, 78–79, 82, 84, 86
LinearOperator.py	80	4	95%	32, 131, 251, 256
Operator.py	52	1	98%	21
SliceProjectionOp.py	166	8	95%	39, 46, 48, 54, 191, 212, 245, 285
ZeroPadOp.py	16	1	94%	30
src/mrpro/utils
Rotation.py	453	28	94%	58–66, 106, 283, 368, 370, 397, 452, 457, 460, 475, 492, 497, 640, 645, 648, 664, 668, 742, 744, 752–753, 993, 1075
filters.py	62	2	97%	44, 49
slice_profiles.py	45	6	87%	18, 34, 111–114, 147
sliding_window.py	34	1	97%	34
split_idx.py	10	2	80%	43, 47
summarize_tensorvalues.py	11	9	18%	20–29
zero_pad_or_crop.py	31	6	81%	26, 30, 54, 57, 60, 63
TOTAL	3487	282	92%

Tests	Skipped	Failures	Errors	Time
762	0 :zzz:	0 :x:	0 :fire:	1m 9s :stopwatch:

[ckolbPTB]

Currently all warnings are raised as errors in pytest (see https://github.com/PTB-MR/mrpro/blob/ca2f07b7030fe8ce3674f23207f974efcbc09fd3/pyproject.toml#L66)

This means that e.g DeprecationWarnings in other packages lead to errors. @fzimmermann89 @schuenke : Is this the behaviour we want, or should it only lead to errors for warning raised directly by our mrpro code?

[fzimmermann89]

DeprecationWarnings as errors makes sense IMHO.

It would be better if we could somehow set a depth for this, i.e. only if we call deprecated code it should error, not if one of our dependencies calls a deprecated function. But I think that might not be possible to detect..

[fzimmermann89]

(If third party code throws a DeprecationWarning that we cannot fix, we could add an ignore to the toml filter warning setting for this deprecating warning)

[fzimmermann89]

@CodiumAI-Agent /review

[CodiumAI-Agent]

PR Reviewer Guide 🔍

(Review updated until commit https://github.com/PTB-MR/mrpro/commit/6bbf37f3170b789183db2e41d140232d9a46afac)

⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Key issues to review Type Consistency The function `get_item` and `get_items_from_all_dicoms` have changed the type of the `name` parameter from `str | TagType` to `TagType` only. Ensure that this change does not break existing functionality where a string might be passed.

[fzimmermann89]

Got it, TagType includes str

...and you already answered the question :D sorry

[CodiumAI-Agent]

Persistent review updated to latest commit https://github.com/PTB-MR/mrpro/commit/c51e21ff4796e14f19aa072ab56022a166fe9775

[CodiumAI-Agent]

Persistent review updated to latest commit https://github.com/PTB-MR/mrpro/commit/6bbf37f3170b789183db2e41d140232d9a46afac