dbdicom 0.2.6__py3-none-any.whl → 0.3.0__py3-none-any.whl

dbdicom/types/study.py

@@ -1,58 +0,0 @@
-# Importing annotations to handle or sign in import type hints
-from __future__ import annotations
-
-import os
-import numpy as np
-from dbdicom.record import Record
-
-class Study(Record):
-
-    name = 'StudyInstanceUID'
-
-    def remove(self):
-        self.manager.delete_studies([self.uid])
-
-    def new_series(self, **kwargs):
-        attr = {**kwargs, **self.attributes}
-        uid, key = self.manager.new_series(parent=self.uid, key=self.key(), **attr)
-        return self.record('Series', uid, key, **attr)
-
-    def parent(self):
-        #uid = self.manager.register.at[self.key(), 'PatientID']
-        key = self.key()
-        uid = self.manager._at(key, 'PatientID')
-        return self.record('Patient', uid, key=key)
-
-    def children(self, **kwargs):
-        return self.series(**kwargs)
-
-    def new_child(self, dataset=None, **kwargs): 
-        attr = {**kwargs, **self.attributes}
-        return self.new_series(**attr)
-    
-    def new_sibling(self, suffix=None, **kwargs):
-        if suffix is not None:
-            desc = self.manager._at(self.key(), 'StudyDescription')
-            kwargs['StudyDescription'] = desc + ' [' + suffix + ']'
-        return self.parent().new_child(**kwargs)
-
-    def _copy_from(self, record, **kwargs):
-        attr = {**kwargs, **self.attributes}
-        uids = self.manager.copy_to_study(record.uid, self.uid, **attr)
-        if isinstance(uids, list):
-            return [self.record('Series', uid, **attr) for uid in uids]
-        else:
-            return self.record('Series', uids, **attr)
-
-    def zeros(*args, **kwargs): # OBSOLETE - remove
-        return zeros(*args, **kwargs)
-
-
-def zeros(study, shape, dtype='mri'): # OBSOLETE - remove
-    series = study.new_series()
-    array = np.zeros(shape, dtype=np.float32)
-    if dtype not in ['mri', 'MRImage']:
-        message = 'dbdicom can only create images of type MRImage at this stage'
-        raise ValueError(message)
-    series.set_pixel_array(array)
-    return series

dbdicom-0.2.6.dist-info/METADATA

@@ -1,72 +0,0 @@
-Metadata-Version: 2.4
-Name: dbdicom
-Version: 0.2.6
-Summary: A pythonic interface for reading and writing DICOM databases
-Author-email: Steven Sourbron <s.sourbron@sheffield.ac.uk>, Ebony Gunwhy <e.gunwhy@sheffield.ac.uk>
-Project-URL: Homepage, https://qib-sheffield.github.io/dbdicom/
-Keywords: python,medical imaging,DICOM
-Classifier: Development Status :: 3 - Alpha
-Classifier: Intended Audience :: Developers
-Classifier: Intended Audience :: Science/Research
-Classifier: Topic :: Scientific/Engineering
-Classifier: Environment :: Console
-Classifier: Operating System :: OS Independent
-Classifier: License :: OSI Approved :: Apache Software License
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: matplotlib
-Requires-Dist: nibabel
-Requires-Dist: numpy
-Requires-Dist: pandas
-Requires-Dist: pydicom
-Requires-Dist: python-gdcm
-Requires-Dist: pylibjpeg-libjpeg
-Requires-Dist: importlib-resources
-Requires-Dist: scipy
-Requires-Dist: imageio
-Requires-Dist: vreg
-Provides-Extra: extensions
-Requires-Dist: scikit-image; extra == "extensions"
-Requires-Dist: itk-elastix; extra == "extensions"
-Requires-Dist: dipy; extra == "extensions"
-Requires-Dist: scikit-learn; extra == "extensions"
-Dynamic: license-file
-
-`dbdicom` is a Pythonic interface for reading and writing DICOM databases.
-
-# Installation
-
-`pip install dbdicom`
-
-# Documentation
-
-For more detail, see the current [dbdicom documentation](https://qib-sheffield.github.io/dbdicom/).
-
-# Ambition
-
-The DICOM format is the universally recognised standard for medical imaging, 
-but working with DICOM data remains a challenging task for data scientists. 
-
-``dbdicom`` aims to provide an intuitive programming interface for reading and 
-writing DICOM databases - replacing unfamiliar DICOM-native concepts by 
-pythonic language and syntax. 
-
-# Disclaimer
-
-`dbdicom` is developed in public and currently trialled in ongoing 
-multi-centre clinical studies 
-[iBEAt](https://bmcnephrol.biomedcentral.com/articles/10.1186/s12882-020-01901-x>) 
-and [AFiRM](https://www.uhdb.nhs.uk/afirm-study/). However, ``dbdicom`` is 
-work in progress and **not yet sufficiently stable for wider use**. Current 
-dissemination activities, such as on the 
-[ISMRM (Toronto 2023)](https://www.ismrm.org/23m/), are limited in scope and 
-intended to get early feedback from the community. 
-
-
-
-
-
-

dbdicom-0.2.6.dist-info/RECORD

@@ -1,66 +0,0 @@
-dbdicom/__init__.py,sha256=rXC7OyQufyuAHqkUxxnw-LaQSw_Z1pZu86QNvj5wtrI,503
-dbdicom/create.py,sha256=v_hLU-5OtJn38FSUDw7d6B0bCIg1LQB49449aG6Jrhs,16518
-dbdicom/dro.py,sha256=onVacXzCqFj6MdKOAAIB8jE-AVcrdbrJHE60sihAuzY,8138
-dbdicom/manager.py,sha256=dn09ieznzTThhvcSBsLLwW5kAS6iWRTau-fhSlXyWhQ,83685
-dbdicom/message.py,sha256=kHcb-WuK_SzIqX76X55YIqSbTn3OdFC052qDkaKfIC8,3581
-dbdicom/pipelines.py,sha256=keBsBEjEipfu9reh3ExhHT2sgRksbL5MuRDHF4OywEI,2280
-dbdicom/record.py,sha256=p5WH1f5Bearn5ZHdCT9h11BUfo5O9GuSz1Dk8gH4BLM,66387
-dbdicom/ds/__init__.py,sha256=gX_ui37gPc_A9h0ZsBYj1-Uh7QdlmtBGrbcbXuOM8Bk,459
-dbdicom/ds/create.py,sha256=_np1bXXH6lfls6JSrPPbgy8X8q6QOj5s83tYUIAaEUk,2132
-dbdicom/ds/dataset.py,sha256=T4SeXSz6aPgK9T7kmk8IN1hvuKfSQ-E-_CrhcXKaQ4E,29347
-dbdicom/ds/dictionaries.py,sha256=g_9EB5jXBmzxp0GFhYC6lQ-tKwxje03ukV5EAH3E_l0,23717
-dbdicom/ds/types/ct_image.py,sha256=2TvEl267TnIkkuJQzPLh9STeSJxKt_ZQi4SEBYmQuiI,3189
-dbdicom/ds/types/enhanced_mr_image.py,sha256=lTvLhMpCiDauAov_IW5epCFKKRhgLfy2d0oC2uab0wc,31336
-dbdicom/ds/types/mr_image.py,sha256=Eaz_jma1VQ2sh0RBWUnQX-8AgPst859e9LFhvv9Rnzw,9769
-dbdicom/ds/types/parametric_map.py,sha256=hc5ms5SarLu3ocitK4aM4dW38rbUxDWVRExFeFmZsVY,11699
-dbdicom/ds/types/ultrasound_multiframe_image.py,sha256=9x2G4pRFYXSoxnaAMLF8okusSkWsSzCdGr5jltxD0Wc,3213
-dbdicom/ds/types/xray_angiographic_image.py,sha256=KhDDVVsZ3himE1P6qFdi401rYcbWCyGZx7inqg-v8oc,3676
-dbdicom/extensions/__init__.py,sha256=ag6Qs2g3g9VHYF1WKsGxMpv_HgbqjfPn_UzjoEaKG-0,115
-dbdicom/extensions/dipy.py,sha256=CrSjU14JwNpMP7AIH-CR3wkoQB19MYbS4efOEVczurQ,16806
-dbdicom/extensions/elastix.py,sha256=0gNgiC0RAEjLBhovgRtaLy31xxUy6rJWoapm_3tMCQ8,22522
-dbdicom/extensions/matplotlib.py,sha256=k9KK-mZW8TpW37PgoFre3yb4ffRCRrPVeQKEGZnQoXw,4218
-dbdicom/extensions/numpy.py,sha256=13PPKj-GCAstSb7uQ8_XAZ2borYkDVKhqcAs7KVA6pc,10542
-dbdicom/extensions/scipy.py,sha256=xQ3H3puoE9kF1qG5Pvl6gaQD4TdL6-f3V8Cz7z1_L0A,52884
-dbdicom/extensions/skimage.py,sha256=b2UhSn96KXonq9cwgDg7hMm_ySA1NsnWxYHSY9oQI6o,38569
-dbdicom/extensions/sklearn.py,sha256=KxxAlzh8ZI7YBkLS529k9VaAObCCVZT8exvEQThcYCY,9351
-dbdicom/extensions/vreg.py,sha256=PbCqTRsLKmbksRYsM_piBrcJL2XV89_jenw85Ozjzwk,67522
-dbdicom/external/__init__.py,sha256=XNQqfspyf6vFGedXlRKZsUB8k8E-0W19Uamwn8Aioxo,316
-dbdicom/external/dcm4che/README.md,sha256=0aAGRs36W3_0s5LzWHRGf_tqariS_JP4iJggaxnD4Xw,8987
-dbdicom/external/dcm4che/__init__.py,sha256=YwpeMCLrxffGOkchsGjgAuB6ia3VX_tx9Y7ru9EWtoY,35
-dbdicom/external/dcm4che/bin/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-dbdicom/external/dcm4che/bin/deidentify,sha256=64MNIEpp-CWzFSb6TV0KtyCBvD7XyEsovRjBeyxDqSc,1698
-dbdicom/external/dcm4che/bin/deidentify.bat,sha256=kVXUkcy1C4Y3KjC2NJwmmR0pufSJWmaof_LR5CTAxMg,1455
-dbdicom/external/dcm4che/bin/emf2sf,sha256=svCzkZ-QhdVTV0NNHOpBiwNBMODVWZHJIFA7cWaN2bM,1622
-dbdicom/external/dcm4che/bin/emf2sf.bat,sha256=Vh0ry9KNJX_WXcyCrLSxbJ_6Crot9rjmwi__u2GZqLY,1375
-dbdicom/external/dcm4che/etc/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-dbdicom/external/dcm4che/etc/emf2sf/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-dbdicom/external/dcm4che/etc/emf2sf/log4j.properties,sha256=3hHcBFt2oNRjvHtix5bfuEsnKfdv5IYOkbsyoY9g7cM,223
-dbdicom/external/dcm4che/lib/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-dbdicom/external/dcm4che/lib/commons-cli-1.4.jar,sha256=_Tx8lUWpzbIFHR-RVcT3ax5KxaVzBEBKbu21eP-6cyg,53820
-dbdicom/external/dcm4che/lib/dcm4che-core-5.23.1.jar,sha256=UEnSQwDE1IHv5kGtK8vkdaQ9OF_cNwOsxB5NSIMkS2s,506505
-dbdicom/external/dcm4che/lib/dcm4che-emf-5.23.1.jar,sha256=fcspodANPlRz-3EIx3TEZWU45JDP4RXzLuWbFoQEPMY,13418
-dbdicom/external/dcm4che/lib/dcm4che-tool-common-5.23.1.jar,sha256=3SN3NSTf4AIHuUCsk_5E2wXd3MuFvQZIYSSq1PHcgNM,21301
-dbdicom/external/dcm4che/lib/dcm4che-tool-emf2sf-5.23.1.jar,sha256=pkpJRD00HQ4sEjaL7_iQ_8lBeQPttHelNAxcT-rMIVQ,7332
-dbdicom/external/dcm4che/lib/log4j-1.2.17.jar,sha256=HTFpZEVpdyBScJF1Q2kIKmZRvUl4G2AF3rlOVnU0Bvk,489884
-dbdicom/external/dcm4che/lib/slf4j-api-1.7.30.jar,sha256=zboHlk0btAoHYUhcax6ML4_Z6x0ZxTkorA1_lRAQXFc,41472
-dbdicom/external/dcm4che/lib/slf4j-log4j12-1.7.30.jar,sha256=TUHgHEDK-KbHSt0rBzBV2KTOHDDlgVQXexPxLXirvns,12211
-dbdicom/external/dcm4che/lib/macosx-x86-64/libopencv_java.jnilib,sha256=A2uOWIUQX3KcG850ElpW4lVtn2uyPpJHZq9cPlpJjMY,15137664
-dbdicom/external/dcm4che/lib/windows-x86/clib_jiio.dll,sha256=C2dAjNyefOm3POrUxorEF6T-FTztpo0nfGAsUrDyQyg,720896
-dbdicom/external/dcm4che/lib/windows-x86/clib_jiio_sse2.dll,sha256=uD9GLN_hPf9mM9APzlp9j6770awKP6xnlaooMrxHpkg,1089536
-dbdicom/external/dcm4che/lib/windows-x86/clib_jiio_util.dll,sha256=wi4yyrI1gTRo_bBpj0E097BQBiHZd8IqVifKr6kfkRE,40960
-dbdicom/external/dcm4che/lib/windows-x86/opencv_java.dll,sha256=QanyzLy0Cd79-aOVPwOcXwikUYeutne0Au-Um91_B4M,8505856
-dbdicom/external/dcm4che/lib/windows-x86-64/opencv_java.dll,sha256=TmjW2SbG4MR3GQ95T8xCVVDLgsdKukgaHBPUvWkfXp8,11039232
-dbdicom/types/database.py,sha256=Ur-VE6Uixw4nV6QUY8fnMSUgDvvk54KhiUvbmS3bGuE,3066
-dbdicom/types/instance.py,sha256=_j38VQqjaJITQX98WyqBqGXvYcpzRP8TRmpZ7wwu5-E,7655
-dbdicom/types/patient.py,sha256=YtBTwJDo8EiquJ2vLcyBW7Pzz7EISKhzvxq2506QSNo,1312
-dbdicom/types/series.py,sha256=-GIMoGzgW-SWLZ9VexcB2TjB9pzi953YuzZCBwF1-KI,111898
-dbdicom/types/study.py,sha256=iX6gjA905DBvmTEwxSuppp_E7XXkTHvN3ezAnu362Es,2031
-dbdicom/utils/dcm4che.py,sha256=Vxq8NYWWK3BuqJkzhBQ89oMqzJlnxqTxgsgTo_Frznc,2317
-dbdicom/utils/files.py,sha256=HkAr03EmpcLkfcr6cS13_g-vqbE1acRYmTJP3e5zNas,2844
-dbdicom/utils/image.py,sha256=IPTD-4adMy5rf5rgSwfR6ImuBZojMfnp4-zKeuG9zik,26385
-dbdicom/utils/variables.py,sha256=vUh5cDnmCft5hoXDYXUvfkg5Cy5WlgMAogU38Y_BKRo,5753
-dbdicom-0.2.6.dist-info/licenses/LICENSE,sha256=HrhfyXIkWY2tGFK11kg7vPCqhgh5DcxleloqdhrpyMY,11558
-dbdicom-0.2.6.dist-info/METADATA,sha256=PwaXplDjZ7num1iqyWF9sS8IALHwW85zEm-LksCP24g,2532
-dbdicom-0.2.6.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
-dbdicom-0.2.6.dist-info/top_level.txt,sha256=nJWxXg4YjD6QblfmhrzTMXcr8FSKNc0Yk-CAIDUsYkQ,8
-dbdicom-0.2.6.dist-info/RECORD,,