v0.241015

What's Changed

• description added by @ckolbPTB in #18
• Initial work on KData and ISMRMRD loading by @fzimmermann89 in #29
• fix names in from_ismrmrd_encodingLimitsType() by @schuenke in #31
• Make KData a frozen dataclass by @fzimmermann89 in #36
• Fix mypy ignore missing imports by @fzimmermann89 in #45
• Fix mypy #2 by @fzimmermann89 in #48
• Remove _get_shape from Trajectory base by @fzimmermann89 in #43
• Add torch, numpy to pre-commit/mypy venv by @fzimmermann89 in #49
• switch from autopep8 to black pre-commit hook by @schuenke in #55
• Add codespell to pre-commit by @fzimmermann89 in #56
• Remove 'clear' dictionary from codespell check by @fzimmermann89 in #57
• Ismrmrd test data by @ckolbPTB in #51
• switch CI pipeline from unittest to pytest by @schuenke in #59
• Initial IData and IHeader implementations by @fzimmermann89 in #30
• Update VSCode settings & recommended extensions by @schuenke in #60
• Pytest warnings by @schuenke in #66
• RPE trajectory by @ckolbPTB in #62
• Fix #38: Set trajectory_dimensions always to 3 by @fzimmermann89 in #75
• Refactor ktraj to a dataclass with kz,ky,kx & add DCF calculation by @fzimmermann89 in #76
• Change phantom to torch by @ckolbPTB in #77
• Sim coil sensitivities by @ckolbPTB in #79
• Fix #73: Let test pipeline fail if tests fail by @fzimmermann89 in #74
• Run tests in parallel by @schuenke in #89
• QData and QHeader implementation by @schote in #40
• CsmData with Walsh-Method implementation by @ckolbPTB in #83
• Fixing DCF logic bugs by @fzimmermann89 in #86
• hotfix vscode pytest-xdist issues (#87) by @fzimmermann89 in #101
• Documentation by @schote in #99
• Hotfix: Docu pipeline by @schote in #103
• Implementation of ktraj shaped like original raw data by @ckolbPTB in #107
• Implementation of KTrajectoryRadial2D by @schote in #105
• Implementation of Sensitivityop by @guastinimara in #110
• Testing by @schuenke in #108
• Ismrmrd traj by @ckolbPTB in #113
• Noise measurement data class and prewhitening algo added by @ckolbPTB in #114
• Remove oversampling and fft added by @ckolbPTB in #116
• KTrajectoryPulseq by @JoHa0811 in #111
• docu for users and devs extended by @ckolbPTB in #121
• Operator Template and Nufft by @fzimmermann89 in #104
• reading in of all dcm files from folder by @ckolbPTB in #124
• Reshape instead of view by @ckolbPTB in #127
• update supported python version to 3.10 & 3.11 by @schuenke in #133
• clean up by @ckolbPTB in #137
• Define trajectories to fit encoding_matrix and encoding_limits by @ckolbPTB in #140
• Cartesian trajectory by @ckolbPTB in #142
• fixed issue #141 by @SimoneHufnagel in #145
• Signal models added: Inversion and saturation recovery, MOLLI by @Stef-Martin in #129
• WASABI(TI) signal models by @schuenke in #130
• Fftshift for FourierOp by @ckolbPTB in #143
• Hotfix #143: zero_pad_or_crop broken for dim=None by @fzimmermann89 in #149
• Gpu support by @ckolbPTB in #136
• Hotfix for PyTorch 2.2 by @ckolbPTB in #152
• Disable cuda tests in VScode Test Explorer by @schuenke in #155
• Enable data which does not allow for a reshape into k2 and k1 by @ckolbPTB in #153
• Allow more than one other dim in KTrajectory by @fzimmermann89 in #160
• Bump maximum allowed python to 3.12 by @fzimmermann89 in #163
• Synthetic Sugar for Operators (needs python 3.11) by @fzimmermann89 in #128
• Fix ignore flags by @fzimmermann89 in #159
• Clean up code by @schuenke in #157
• Switch to Processes for voronoi cell volume calculation by @fzimmermann89 in #170
• Framework py -> ipynb -> docu by @ckolbPTB in #118
• Cartesian sampling operator by @ckolbPTB in #146
• Update README.md by @fzimmermann89 in #167
• HOTIFX: Binder to use main branch by @ckolbPTB in #176
• Limit xsd version by @fzimmermann89 in #177
• Cart sampling index int64 by @ckolbPTB in #182
• Lbfgs box by @schuenke in #131
• Same ndim for all AcqInfo fields by @ckolbPTB in #191
• Fix operator chaining by @fzimmermann89 in #189
• Return copy in remove readout os by @fzimmermann89 in #204
• Split data and select subset by @ckolbPTB in #117
• Switch to Ruff for linting and formatting by @schuenke in #193
• docu update by @ckolbPTB in #214
• Docker tests by @ckolbPTB in #175
• fix link by @ckolbPTB in #219
• move sensitivity operator tests to using dotproduct_adjointness_test by @fzimmermann89 in #220
• Generalized matrix operator by @fzimmermann89 in #212
• Conjugate Gradient by @koflera in #195
• Fix 221: Cartesian sampling op for random undersampling with varying pattern along other by @fzimmermann89 in #223
• Add separable nd-filters and sliding window by @fzimmermann89 in #161
• Clean up by @ckolbPTB in #218
• Support bipolar readout by @ckolbPTB in #222
• Fix #216 by @fzimmermann89 in #225
• Add from_array_zxy, zyx read-only property and tests to SpatialDimension by @fzimmermann89 in #238
• Move kernel in filters to input device. Fixes #239 by @fzimmermann89 in #240
• Rotation class by @fzimmermann89 in #209
• allow batch dimension in signal models by @fzimmermann89 in #226
• Detection tolerance for KTrajectoryPulseq by @schuenke in #232
• Restructure algorithms & Move to direct imports in src by @schuenke in #215
• Example script for pulseq radial 2D golden angle acquisition by @schuenke in #235
• Switch to direct import in einsumop by @fzimmermann89 in #246
• Read in multiple dicom files by @ckolbPTB in #248
• mono-exponential decay model added by @ckolbPTB in #245
• Add operator-tensor multiplication and type hints by @fzimmermann89 in #262
• Add .to/.cuda/cpu to KNoise by @fzimmermann89 in #263
• add rss to idata by @fzimmermann89 in #264
• switch in einsumop to einops notation by @fzimmermann89 in #265
• add as_operator to DcfData and CsmData by @fzimmermann89 in #266
• fix imports and add py.typed marker by @fzimmermann89 in #267
• Improve docstrings and variable names by @fzimmermann89 in #268
• Do not check notebooks for spelling mistakes by @ckolbPTB in #277
• Magnitude and Phase operator by @ckolbPTB in #273
• add fourierop.from_kdata by @fzimmermann89 in #269
• Allow multiple other dimensions in prewhiten data by @fzimmermann89 in #272
• add direct reconstruction by @fzimmermann89 in #270
• Bump pytorch and ismrmrd version by @fzimmermann89 in #281
• Allow different total number of phase encode steps in KData by @fzimmermann89 in #207
• Projection operator by @fzimmermann89 in #237
• Motion / Gridsample operator by @fzimmermann89 in #241
• Make trajectory always float by @fzimmermann89 in #286
• Unify .to / .cpu / .cuda for data classes by @fzimmermann89 in #279
• Add EndomorphOperator by @fzimmermann89 in #280
• Fix types by @fzimmermann89 in #282
• Precommit: run mypy on all files, including tests. by @fzimmermann89 in #283
• Fix reshaping of SpatialDimension in acq_info by @ckolbPTB in #301
• Rename all files to categorize them as 'public' for linters by @schuenke in #302
• Make TE, TR... to tensors in the header by @ckolbPTB in #271
• Different modes and values for padding in separable filter by @ckolbPTB in #299
• Finite difference operator by @ckolbPTB in #297
• T1 and T2star mapping by @ckolbPTB in #278
• Notebook typo by @ckolbPTB in #310
• Tests for signal models separated by @ckolbPTB in #312
• Docker build for main by @ckolbPTB in #318
• Remove pytest filter warning for optimizers by @ckolbPTB in #324
• Select ISMRMRD acquisitions with a function instead of ignore flags by @ckolbPTB in #315
• Remove optional and default in doc string by @ckolbPTB in #337
• Update documentation by @schuenke in #332
• power iteration and operator-norm by @koflera in #224
• HotFix: Ensure correct return type of matplotlib by @ckolbPTB in #344
• Transient steady state model by @ckolbPTB in #319
• Fix #316 by @koflera in #357
• Cleanup imports by @JoHa0811 in #355
• Remove duplicate KDataProtocol by @Pierrickkk in #356
• Manage dependencies by @schuenke in #348
• Consider user indices when sorting kdata by @Pierrickkk in #354
• Bump the all-actions group with 3 updates by @dependabot in #358
• Separate test for iterative_walsh algo by @ckolbPTB in #350
• Change references to numpydoc-style by @JoHa0811 in #352
• Separate conftest into subdirectories by @ckolbPTB in #360
• Remove unused parameters in adam by @JoHa0811 in #363
• Moved 1D,2D,3D dcf with voronoi calculations to algorithms by @Stef-Martin in #349
• Add parameter/attribute doc strings for data classes by @ckolbPTB in #365
• Run pytest also for changes to .md by @ckolbPTB in #366
• Update readme by @ckolbPTB in #362
• Add dtype promotion of result in separable filter by @fzimmermann89 in #342
• Fix warning in pickle test by @ckolbPTB in #372
• Remove copyright statement from files by @ckolbPTB in #375
• file.flush() after file.write() in examples by @ckolbPTB in #374
• Add callback to lbfgs and adam by @koflera in #353
• Fix doc string format by @ckolbPTB in #376
• Allow tensor input for transient steady state model by @ckolbPTB in #378
• Select number of cores for pytest in VSCode automatically by @ckolbPTB in #322
• Add Iterative SENSE Reconstruction by @ckolbPTB in #287
• SI unit conversion in dicom and unit info in docstring by @ckolbPTB in #367
• Improve readability of dimension operations by @ckolbPTB in #380
• Remove copyright from OptimizerStatus by @ckolbPTB in #383
• Csm Inati 2D and 3D by @ckolbPTB in #345
• Adapt it sense functions by @ckolbPTB in #379
• Add repr method to dataclasses and header by @Stef-Martin in #364
• Golden Radial T1 mapping example by @ckolbPTB in #377
• Fix errors due to pydicom 3.0 by @ckolbPTB in #391
• Add Wavelet Operator by @schuenke in #294
• Add Identity LinearOperator by @fzimmermann89 in #390
• Change MOLLI from (a,b,T1) to (a,c=b/a,T1) by @ckolbPTB in #406
• Move SliceProjectionOp to new autograd.Function syntax by @fzimmermann89 in #409
• Move Rotation to data and create utils.typing by @fzimmermann89 in #418
• Move GridSampleOp to new autograd.Function syntax by @fzimmermann89 in #408
• Add link to summary as PR comment by @ckolbPTB in #423
• Fix434 - no link to docu for merge with main by @ckolbPTB in #437
• Gitignore common data file types by @ckolbPTB in #424
• Removed iterative from walsh by @bernharb in #427
• Update ruff, typos, mypy by @fzimmermann89 in #429
• Add RearrangeOp by @fzimmermann89 in #412
• Add Functional base class by @fzimmermann89 in #396
• Bump MishaKav/pytest-coverage-comment from 1.1.52 to 1.1.53 in the all-actions group by @dependabot in #442
• Add L2NormSquared Functional by @fzimmermann89 in #398
• Add L1NormViewAsReal Functional by @fzimmermann89 in #399
• Zero functional by @fzimmermann89 in #433
• Add gram to LinearOperator by @fzimmermann89 in #443
• Allow adjoint to be used as autograd backward by @fzimmermann89 in #404
• Add ZeroOp as neutral elements of addition, make IdentityOp neutral element of composition by @fzimmermann89 in #431
• Add check-added-large-files to precommit by @fzimmermann89 in #446
• Add continuous deployment (CD) pipeline by @schuenke in #439

New Contributors

• @schote made their first contribution in #40
• @guastinimara made their first contribution in #110
• @JoHa0811 made their first contribution in #111
• @SimoneHufnagel made their first contribution in #145
• @Stef-Martin made their first contribution in #129
• @koflera made their first contribution in #195
• @Pierrickkk made their first contribution in #356
• @dependabot made their first contribution in #358
• @bernharb made their first contribution in #427

Full Changelog: https://github.com/PTB-MR/mrpro/commits/v0.241015