dbdicom 0.2.0__py3-none-any.whl → 0.2.3__py3-none-any.whl

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Files changed (52) hide show
  1. dbdicom/__init__.py +5 -3
  2. dbdicom/create.py +77 -70
  3. dbdicom/dro.py +174 -0
  4. dbdicom/ds/dataset.py +30 -3
  5. dbdicom/ds/types/mr_image.py +18 -7
  6. dbdicom/extensions/__init__.py +10 -0
  7. dbdicom/{wrappers → extensions}/dipy.py +191 -205
  8. dbdicom/extensions/elastix.py +503 -0
  9. dbdicom/extensions/matplotlib.py +107 -0
  10. dbdicom/extensions/numpy.py +271 -0
  11. dbdicom/{wrappers → extensions}/scipy.py +131 -32
  12. dbdicom/{wrappers → extensions}/skimage.py +1 -1
  13. dbdicom/extensions/sklearn.py +243 -0
  14. dbdicom/extensions/vreg.py +1390 -0
  15. dbdicom/external/dcm4che/bin/emf2sf +57 -57
  16. dbdicom/manager.py +91 -36
  17. dbdicom/pipelines.py +66 -0
  18. dbdicom/record.py +447 -80
  19. dbdicom/types/instance.py +46 -20
  20. dbdicom/types/series.py +2182 -399
  21. dbdicom/utils/image.py +152 -21
  22. dbdicom/utils/variables.py +8 -2
  23. dbdicom/utils/vreg.py +327 -135
  24. dbdicom-0.2.3.dist-info/METADATA +88 -0
  25. dbdicom-0.2.3.dist-info/RECORD +67 -0
  26. {dbdicom-0.2.0.dist-info → dbdicom-0.2.3.dist-info}/WHEEL +1 -1
  27. dbdicom/external/__pycache__/__init__.cpython-310.pyc +0 -0
  28. dbdicom/external/__pycache__/__init__.cpython-37.pyc +0 -0
  29. dbdicom/external/dcm4che/__pycache__/__init__.cpython-310.pyc +0 -0
  30. dbdicom/external/dcm4che/__pycache__/__init__.cpython-37.pyc +0 -0
  31. dbdicom/external/dcm4che/bin/__pycache__/__init__.cpython-310.pyc +0 -0
  32. dbdicom/external/dcm4che/bin/__pycache__/__init__.cpython-37.pyc +0 -0
  33. dbdicom/external/dcm4che/lib/linux-x86/libclib_jiio.so +0 -0
  34. dbdicom/external/dcm4che/lib/linux-x86-64/libclib_jiio.so +0 -0
  35. dbdicom/external/dcm4che/lib/linux-x86-64/libopencv_java.so +0 -0
  36. dbdicom/external/dcm4che/lib/solaris-sparc/libclib_jiio.so +0 -0
  37. dbdicom/external/dcm4che/lib/solaris-sparc/libclib_jiio_vis.so +0 -0
  38. dbdicom/external/dcm4che/lib/solaris-sparc/libclib_jiio_vis2.so +0 -0
  39. dbdicom/external/dcm4che/lib/solaris-sparcv9/libclib_jiio.so +0 -0
  40. dbdicom/external/dcm4che/lib/solaris-sparcv9/libclib_jiio_vis.so +0 -0
  41. dbdicom/external/dcm4che/lib/solaris-sparcv9/libclib_jiio_vis2.so +0 -0
  42. dbdicom/external/dcm4che/lib/solaris-x86/libclib_jiio.so +0 -0
  43. dbdicom/external/dcm4che/lib/solaris-x86-64/libclib_jiio.so +0 -0
  44. dbdicom/wrappers/__init__.py +0 -7
  45. dbdicom/wrappers/elastix.py +0 -855
  46. dbdicom/wrappers/numpy.py +0 -119
  47. dbdicom/wrappers/sklearn.py +0 -151
  48. dbdicom/wrappers/vreg.py +0 -273
  49. dbdicom-0.2.0.dist-info/METADATA +0 -276
  50. dbdicom-0.2.0.dist-info/RECORD +0 -81
  51. {dbdicom-0.2.0.dist-info → dbdicom-0.2.3.dist-info}/LICENSE +0 -0
  52. {dbdicom-0.2.0.dist-info → dbdicom-0.2.3.dist-info}/top_level.txt +0 -0
@@ -0,0 +1,88 @@
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+ Metadata-Version: 2.1
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+ Name: dbdicom
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+ Version: 0.2.3
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+ Summary: A pythonic interface for reading and writing DICOM databases
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+ Author-email: Steven Sourbron <s.sourbron@sheffield.ac.uk>, Ebony Gunwhy <e.gunwhy@sheffield.ac.uk>
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+ Project-URL: Homepage, https://qib-sheffield.github.io/dbdicom/
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+ Keywords: python,medical imaging,DICOM
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+ Classifier: Development Status :: 3 - Alpha
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+ Classifier: Intended Audience :: Developers
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: Topic :: Scientific/Engineering
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+ Classifier: Environment :: Console
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+ Classifier: Operating System :: OS Independent
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+ Classifier: License :: OSI Approved :: Apache Software License
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+ Classifier: Programming Language :: Python
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+ Classifier: Programming Language :: Python :: 3
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+ Requires-Python: >=3.6
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+ Description-Content-Type: text/markdown
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+ License-File: LICENSE
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+ Requires-Dist: matplotlib
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+ Requires-Dist: nibabel
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+ Requires-Dist: numpy<=1.26.4
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+ Requires-Dist: pandas
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+ Requires-Dist: pydicom
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+ Requires-Dist: python-gdcm
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+ Requires-Dist: pylibjpeg-libjpeg
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+ Requires-Dist: importlib-resources
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+ Requires-Dist: scipy
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+ Requires-Dist: imageio
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+ Provides-Extra: docs
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+ Requires-Dist: sphinx; extra == "docs"
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+ Requires-Dist: pydata-sphinx-theme; extra == "docs"
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+ Requires-Dist: myst-parser; extra == "docs"
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+ Requires-Dist: sphinx-copybutton; extra == "docs"
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+ Requires-Dist: sphinx-design; extra == "docs"
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+ Requires-Dist: sphinx-remove-toctrees; extra == "docs"
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+ Requires-Dist: autodocsumm; extra == "docs"
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+ Requires-Dist: docutils; extra == "docs"
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+ Requires-Dist: sphinxcontrib-applehelp; extra == "docs"
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+ Requires-Dist: sphinxcontrib-devhelp; extra == "docs"
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+ Requires-Dist: sphinxcontrib-htmlhelp; extra == "docs"
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+ Requires-Dist: sphinxcontrib-jsmath; extra == "docs"
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+ Requires-Dist: sphinxcontrib-qthelp; extra == "docs"
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+ Requires-Dist: sphinxcontrib-serializinghtml; extra == "docs"
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+ Requires-Dist: sphinx-gallery; extra == "docs"
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+ Provides-Extra: extensions
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+ Requires-Dist: scipy; extra == "extensions"
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+ Requires-Dist: scikit-image<=0.19.0; extra == "extensions"
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+ Requires-Dist: SimpleITK-SimpleElastix; extra == "extensions"
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+ Requires-Dist: itk-elastix; extra == "extensions"
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+ Requires-Dist: dipy; extra == "extensions"
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+ Requires-Dist: scikit-learn; extra == "extensions"
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+
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+ `dbdicom` is a Pythonic interface for reading and writing DICOM databases.
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+
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+ # Installation
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+
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+ `pip install dbdicom`
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+
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+ # Documentation
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+
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+ For more detail, see the current [dbdicom documentation](https://qib-sheffield.github.io/dbdicom/).
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+
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+ # Ambition
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+
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+ The DICOM format is the universally recognised standard for medical imaging,
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+ but working with DICOM data remains a challenging task for data scientists.
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+
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+ ``dbdicom`` aims to provide an intuitive programming interface for reading and
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+ writing DICOM databases - replacing unfamiliar DICOM-native concepts by
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+ pythonic language and syntax.
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+
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+ # Disclaimer
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+
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+ `dbdicom` is developed in public and currently trialled in ongoing
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+ multi-centre clinical studies
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+ [iBEAt](https://bmcnephrol.biomedcentral.com/articles/10.1186/s12882-020-01901-x>)
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+ and [AFiRM](https://www.uhdb.nhs.uk/afirm-study/). However, ``dbdicom`` is
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+ work in progress and **not yet sufficiently stable for wider use**. Current
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+ dissemination activities, such as on the
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+ [ISMRM (Toronto 2023)](https://www.ismrm.org/23m/), are limited in scope and
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+ intended to get early feedback from the community.
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+
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+
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+
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+
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+
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+
@@ -0,0 +1,67 @@
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+ dbdicom/__init__.py,sha256=rXC7OyQufyuAHqkUxxnw-LaQSw_Z1pZu86QNvj5wtrI,503
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+ dbdicom/create.py,sha256=v_hLU-5OtJn38FSUDw7d6B0bCIg1LQB49449aG6Jrhs,16518
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+ dbdicom/dro.py,sha256=onVacXzCqFj6MdKOAAIB8jE-AVcrdbrJHE60sihAuzY,8138
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+ dbdicom/manager.py,sha256=dn09ieznzTThhvcSBsLLwW5kAS6iWRTau-fhSlXyWhQ,83685
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+ dbdicom/message.py,sha256=kHcb-WuK_SzIqX76X55YIqSbTn3OdFC052qDkaKfIC8,3581
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+ dbdicom/pipelines.py,sha256=keBsBEjEipfu9reh3ExhHT2sgRksbL5MuRDHF4OywEI,2280
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+ dbdicom/record.py,sha256=p5WH1f5Bearn5ZHdCT9h11BUfo5O9GuSz1Dk8gH4BLM,66387
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+ dbdicom/ds/__init__.py,sha256=gX_ui37gPc_A9h0ZsBYj1-Uh7QdlmtBGrbcbXuOM8Bk,459
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+ dbdicom/ds/create.py,sha256=_np1bXXH6lfls6JSrPPbgy8X8q6QOj5s83tYUIAaEUk,2132
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+ dbdicom/ds/dataset.py,sha256=JL2xPQr-xI-cbirwzlG6ROH3cTj9Ruyd8L3roYfiXNA,29257
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+ dbdicom/ds/dictionaries.py,sha256=g_9EB5jXBmzxp0GFhYC6lQ-tKwxje03ukV5EAH3E_l0,23717
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+ dbdicom/ds/types/ct_image.py,sha256=2TvEl267TnIkkuJQzPLh9STeSJxKt_ZQi4SEBYmQuiI,3189
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+ dbdicom/ds/types/enhanced_mr_image.py,sha256=lTvLhMpCiDauAov_IW5epCFKKRhgLfy2d0oC2uab0wc,31336
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+ dbdicom/ds/types/mr_image.py,sha256=Eaz_jma1VQ2sh0RBWUnQX-8AgPst859e9LFhvv9Rnzw,9769
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+ dbdicom/ds/types/parametric_map.py,sha256=hc5ms5SarLu3ocitK4aM4dW38rbUxDWVRExFeFmZsVY,11699
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+ dbdicom/ds/types/ultrasound_multiframe_image.py,sha256=9x2G4pRFYXSoxnaAMLF8okusSkWsSzCdGr5jltxD0Wc,3213
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+ dbdicom/ds/types/xray_angiographic_image.py,sha256=KhDDVVsZ3himE1P6qFdi401rYcbWCyGZx7inqg-v8oc,3676
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+ dbdicom/extensions/__init__.py,sha256=YOzQYid1QHRQYSYBLYTmeRK6_LrucV6xPaumoiO_K8Q,126
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+ dbdicom/extensions/dipy.py,sha256=CrSjU14JwNpMP7AIH-CR3wkoQB19MYbS4efOEVczurQ,16806
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+ dbdicom/extensions/elastix.py,sha256=0gNgiC0RAEjLBhovgRtaLy31xxUy6rJWoapm_3tMCQ8,22522
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+ dbdicom/extensions/matplotlib.py,sha256=k9KK-mZW8TpW37PgoFre3yb4ffRCRrPVeQKEGZnQoXw,4218
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+ dbdicom/extensions/numpy.py,sha256=13PPKj-GCAstSb7uQ8_XAZ2borYkDVKhqcAs7KVA6pc,10542
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+ dbdicom/extensions/scipy.py,sha256=xQ3H3puoE9kF1qG5Pvl6gaQD4TdL6-f3V8Cz7z1_L0A,52884
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+ dbdicom/extensions/skimage.py,sha256=hP2get4UTpu0ZSlbAvQmwaKRvGupHLn39L0BctgzZ-0,38563
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+ dbdicom/extensions/sklearn.py,sha256=KxxAlzh8ZI7YBkLS529k9VaAObCCVZT8exvEQThcYCY,9351
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+ dbdicom/extensions/vreg.py,sha256=6U9l9p18Cfs67pAn3ROhalcPVioNVdB0Hi9Co-eAegU,67541
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+ dbdicom/external/__init__.py,sha256=XNQqfspyf6vFGedXlRKZsUB8k8E-0W19Uamwn8Aioxo,316
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+ dbdicom/external/dcm4che/README.md,sha256=0aAGRs36W3_0s5LzWHRGf_tqariS_JP4iJggaxnD4Xw,8987
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+ dbdicom/external/dcm4che/__init__.py,sha256=YwpeMCLrxffGOkchsGjgAuB6ia3VX_tx9Y7ru9EWtoY,35
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+ dbdicom/external/dcm4che/bin/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ dbdicom/external/dcm4che/bin/deidentify,sha256=64MNIEpp-CWzFSb6TV0KtyCBvD7XyEsovRjBeyxDqSc,1698
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+ dbdicom/external/dcm4che/bin/deidentify.bat,sha256=kVXUkcy1C4Y3KjC2NJwmmR0pufSJWmaof_LR5CTAxMg,1455
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+ dbdicom/external/dcm4che/bin/emf2sf,sha256=svCzkZ-QhdVTV0NNHOpBiwNBMODVWZHJIFA7cWaN2bM,1622
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+ dbdicom/external/dcm4che/bin/emf2sf.bat,sha256=Vh0ry9KNJX_WXcyCrLSxbJ_6Crot9rjmwi__u2GZqLY,1375
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+ dbdicom/external/dcm4che/etc/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ dbdicom/external/dcm4che/etc/emf2sf/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ dbdicom/external/dcm4che/etc/emf2sf/log4j.properties,sha256=3hHcBFt2oNRjvHtix5bfuEsnKfdv5IYOkbsyoY9g7cM,223
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+ dbdicom/external/dcm4che/lib/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ dbdicom/external/dcm4che/lib/commons-cli-1.4.jar,sha256=_Tx8lUWpzbIFHR-RVcT3ax5KxaVzBEBKbu21eP-6cyg,53820
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+ dbdicom/external/dcm4che/lib/dcm4che-core-5.23.1.jar,sha256=UEnSQwDE1IHv5kGtK8vkdaQ9OF_cNwOsxB5NSIMkS2s,506505
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+ dbdicom/external/dcm4che/lib/dcm4che-emf-5.23.1.jar,sha256=fcspodANPlRz-3EIx3TEZWU45JDP4RXzLuWbFoQEPMY,13418
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+ dbdicom/external/dcm4che/lib/dcm4che-tool-common-5.23.1.jar,sha256=3SN3NSTf4AIHuUCsk_5E2wXd3MuFvQZIYSSq1PHcgNM,21301
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+ dbdicom/external/dcm4che/lib/dcm4che-tool-emf2sf-5.23.1.jar,sha256=pkpJRD00HQ4sEjaL7_iQ_8lBeQPttHelNAxcT-rMIVQ,7332
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+ dbdicom/external/dcm4che/lib/log4j-1.2.17.jar,sha256=HTFpZEVpdyBScJF1Q2kIKmZRvUl4G2AF3rlOVnU0Bvk,489884
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+ dbdicom/external/dcm4che/lib/slf4j-api-1.7.30.jar,sha256=zboHlk0btAoHYUhcax6ML4_Z6x0ZxTkorA1_lRAQXFc,41472
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+ dbdicom/external/dcm4che/lib/slf4j-log4j12-1.7.30.jar,sha256=TUHgHEDK-KbHSt0rBzBV2KTOHDDlgVQXexPxLXirvns,12211
47
+ dbdicom/external/dcm4che/lib/macosx-x86-64/libopencv_java.jnilib,sha256=A2uOWIUQX3KcG850ElpW4lVtn2uyPpJHZq9cPlpJjMY,15137664
48
+ dbdicom/external/dcm4che/lib/windows-x86/clib_jiio.dll,sha256=C2dAjNyefOm3POrUxorEF6T-FTztpo0nfGAsUrDyQyg,720896
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+ dbdicom/external/dcm4che/lib/windows-x86/clib_jiio_sse2.dll,sha256=uD9GLN_hPf9mM9APzlp9j6770awKP6xnlaooMrxHpkg,1089536
50
+ dbdicom/external/dcm4che/lib/windows-x86/clib_jiio_util.dll,sha256=wi4yyrI1gTRo_bBpj0E097BQBiHZd8IqVifKr6kfkRE,40960
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+ dbdicom/external/dcm4che/lib/windows-x86/opencv_java.dll,sha256=QanyzLy0Cd79-aOVPwOcXwikUYeutne0Au-Um91_B4M,8505856
52
+ dbdicom/external/dcm4che/lib/windows-x86-64/opencv_java.dll,sha256=TmjW2SbG4MR3GQ95T8xCVVDLgsdKukgaHBPUvWkfXp8,11039232
53
+ dbdicom/types/database.py,sha256=Ur-VE6Uixw4nV6QUY8fnMSUgDvvk54KhiUvbmS3bGuE,3066
54
+ dbdicom/types/instance.py,sha256=DsQOiHmX9W2cffvJUqE25gBAIlMGSm8Z33F-HKk3fcI,6881
55
+ dbdicom/types/patient.py,sha256=YtBTwJDo8EiquJ2vLcyBW7Pzz7EISKhzvxq2506QSNo,1312
56
+ dbdicom/types/series.py,sha256=OlDHfJs2NX5kpioNvbQv2QVCTITyWr_1CTNyipAe8Zs,100936
57
+ dbdicom/types/study.py,sha256=iX6gjA905DBvmTEwxSuppp_E7XXkTHvN3ezAnu362Es,2031
58
+ dbdicom/utils/dcm4che.py,sha256=Vxq8NYWWK3BuqJkzhBQ89oMqzJlnxqTxgsgTo_Frznc,2317
59
+ dbdicom/utils/files.py,sha256=HkAr03EmpcLkfcr6cS13_g-vqbE1acRYmTJP3e5zNas,2844
60
+ dbdicom/utils/image.py,sha256=qDEAILBuEToFQpbfAkqVNw3xX-rUX6gOVHUDqNbrSHM,24159
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+ dbdicom/utils/variables.py,sha256=vUh5cDnmCft5hoXDYXUvfkg5Cy5WlgMAogU38Y_BKRo,5753
62
+ dbdicom/utils/vreg.py,sha256=KPnc930-K0Uz7M9YJ2jDhwqnpjkaPfHYENsDcnKVqIo,112730
63
+ dbdicom-0.2.3.dist-info/LICENSE,sha256=HrhfyXIkWY2tGFK11kg7vPCqhgh5DcxleloqdhrpyMY,11558
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+ dbdicom-0.2.3.dist-info/METADATA,sha256=Q1Bx8vLj-c8cGjAkh77rLNUgK8LRb-I2z3ZSB23DAMw,3400
65
+ dbdicom-0.2.3.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
66
+ dbdicom-0.2.3.dist-info/top_level.txt,sha256=nJWxXg4YjD6QblfmhrzTMXcr8FSKNc0Yk-CAIDUsYkQ,8
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+ dbdicom-0.2.3.dist-info/RECORD,,
@@ -1,5 +1,5 @@
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  Wheel-Version: 1.0
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- Generator: bdist_wheel (0.40.0)
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+ Generator: setuptools (75.6.0)
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  Root-Is-Purelib: true
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  Tag: py3-none-any
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@@ -1,7 +0,0 @@
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- # from . import (
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- # numpy,
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- # dipy,
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- # scipy,
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- # elastix,
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- # skimage,
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- # )