cornucopia 0.0.0__py3-none-any.whl

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Files changed (65) hide show
  1. cornucopia/__init__.py +73 -0
  2. cornucopia/base.py +1915 -0
  3. cornucopia/baseutils.py +575 -0
  4. cornucopia/contrast.py +260 -0
  5. cornucopia/ctx.py +25 -0
  6. cornucopia/fov.py +707 -0
  7. cornucopia/geometric.py +2068 -0
  8. cornucopia/intensity.py +1358 -0
  9. cornucopia/io.py +161 -0
  10. cornucopia/kspace.py +505 -0
  11. cornucopia/labels.py +1872 -0
  12. cornucopia/noise.py +508 -0
  13. cornucopia/psf.py +463 -0
  14. cornucopia/qmri.py +1288 -0
  15. cornucopia/random.py +1480 -0
  16. cornucopia/special.py +159 -0
  17. cornucopia/synth.py +708 -0
  18. cornucopia/tests/__init__.py +0 -0
  19. cornucopia/tests/test_backward_geometric.py +173 -0
  20. cornucopia/tests/test_backward_intensity.py +243 -0
  21. cornucopia/tests/test_backward_kspace.py +115 -0
  22. cornucopia/tests/test_backward_noise.py +169 -0
  23. cornucopia/tests/test_backward_psf.py +142 -0
  24. cornucopia/tests/test_backward_qmri.py +249 -0
  25. cornucopia/tests/test_backward_random.py +44 -0
  26. cornucopia/tests/test_backward_synth.py +72 -0
  27. cornucopia/tests/test_base.py +401 -0
  28. cornucopia/tests/test_geometric.py +26 -0
  29. cornucopia/tests/test_intensity.py +9 -0
  30. cornucopia/tests/test_random.py +722 -0
  31. cornucopia/tests/test_run_contrast.py +28 -0
  32. cornucopia/tests/test_run_fov.py +132 -0
  33. cornucopia/tests/test_run_geometric.py +157 -0
  34. cornucopia/tests/test_run_intensity.py +192 -0
  35. cornucopia/tests/test_run_kspace.py +70 -0
  36. cornucopia/tests/test_run_labels.py +224 -0
  37. cornucopia/tests/test_run_noise.py +127 -0
  38. cornucopia/tests/test_run_psf.py +115 -0
  39. cornucopia/tests/test_run_qmri.py +114 -0
  40. cornucopia/tests/test_run_synth.py +67 -0
  41. cornucopia/typing.py +97 -0
  42. cornucopia/utils/__init__.py +0 -0
  43. cornucopia/utils/b0.py +745 -0
  44. cornucopia/utils/bounds.py +412 -0
  45. cornucopia/utils/compat.py +47 -0
  46. cornucopia/utils/conv.py +305 -0
  47. cornucopia/utils/gmm.py +169 -0
  48. cornucopia/utils/indexing.py +911 -0
  49. cornucopia/utils/io.py +258 -0
  50. cornucopia/utils/jit.py +128 -0
  51. cornucopia/utils/kernels.py +288 -0
  52. cornucopia/utils/morpho.py +234 -0
  53. cornucopia/utils/mrf.py +574 -0
  54. cornucopia/utils/padding.py +173 -0
  55. cornucopia/utils/patch.py +302 -0
  56. cornucopia/utils/pool.py +282 -0
  57. cornucopia/utils/py.py +348 -0
  58. cornucopia/utils/smart_inplace.py +163 -0
  59. cornucopia/utils/version.py +57 -0
  60. cornucopia/utils/warps.py +606 -0
  61. cornucopia-0.0.0.dist-info/METADATA +92 -0
  62. cornucopia-0.0.0.dist-info/RECORD +65 -0
  63. cornucopia-0.0.0.dist-info/WHEEL +5 -0
  64. cornucopia-0.0.0.dist-info/licenses/LICENSE +21 -0
  65. cornucopia-0.0.0.dist-info/top_level.txt +1 -0
cornucopia/__init__.py ADDED
@@ -0,0 +1,73 @@
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+ """
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+ Flexible transforms for pre-processing and augmentation
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+
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+ Example on how to use this machinery to generate within-subject
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+ image pairs with a random affine deformation between them::
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+
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+ # It's easy to randomize deterministic parameters of a transform
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+ rand_chi = trf.RandomizedTransform(
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+ trf.ChiNoiseTransform, dict(sigma=trf.Uniform(0.01, 0.3)))
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+
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+ # SequentialTransform is equivalent to monai's Compose
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+ # MappedTransform make sit possible to process only some inputs (the
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+ # others are kept untouched)
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+ demo_transformer = trf.SequentialTransform([
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+ trf.MappedTransform(img=trf.ToTensorTransform(3, dtype=torch.float32),
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+ seg=trf.ToTensorTransform(3, dtype=torch.int64)),
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+ trf.MappedTransform(seg=trf.OneHotTransform([1])),
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+ trf.MappedTransform(img=trf.QuantileTransform()),
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+ trf.MakeAffinePair(trf.RandomAffineTransform()),
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+ trf.MappedTransform(img=trf.MultFieldTransform()),
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+ trf.MappedTransform(img=rand_chi),
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+ ])
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+
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+ # Apply the workflow
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+ img_and_seg, flow_and_mat = demo_transformer(dict(img=dat, seg=lab))
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+
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+ # Unpile everything
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+ img1, img2 = img_and_seg['img']
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+ seg1, seg2 = img_and_seg['seg']
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+ flow = flow_and_mat['flow']
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+
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+ """
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+
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+ from . import random # noqa: F401
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+ from . import ctx # noqa: F401
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+ from . import base # noqa: F401
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+ from . import baseutils # noqa: F401
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+ from . import special # noqa: F401
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+ from . import contrast # noqa: F401
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+ from . import geometric # noqa: F401
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+ from . import intensity # noqa: F401
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+ from . import io # noqa: F401
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+ from . import fov # noqa: F401
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+ from . import kspace # noqa: F401
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+ from . import labels # noqa: F401
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+ from . import noise # noqa: F401
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+ from . import psf # noqa: F401
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+ from . import qmri # noqa: F401
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+ from . import synth # noqa: F401
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+ from . import typing # noqa: F401
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+ from . import utils # noqa: F401
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+
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+ from .random import * # noqa: F401,F403
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+ from .ctx import * # noqa: F401,F403
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+ from .base import * # noqa: F401,F403
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+ from .special import * # noqa: F401,F403
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+ from .contrast import * # noqa: F401,F403
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+ from .geometric import * # noqa: F401,F403
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+ from .intensity import * # noqa: F401,F403
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+ from .io import * # noqa: F401,F403
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+ from .fov import * # noqa: F401,F403
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+ from .kspace import * # noqa: F401,F403
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+ from .labels import * # noqa: F401,F403
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+ from .noise import * # noqa: F401,F403
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+ from .psf import * # noqa: F401,F403
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+ from .qmri import * # noqa: F401,F403
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+ from .synth import * # noqa: F401,F403
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+ from .utils.patch import patch_apply # noqa: F401,F403
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+
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+ try:
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+ from ._version import __version__
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+ except ImportError:
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+ __version__ = None