radiobject 0.1.0__py3-none-any.whl

radiobject-0.1.0.dist-info/METADATA

@@ -0,0 +1,139 @@
+Metadata-Version: 2.4
+Name: radiobject
+Version: 0.1.0
+Summary: TileDB-backed data structure for radiology data at scale
+Project-URL: Repository, https://github.com/samueldsouza/radiobject
+Author: Samuel D'Souza
+License-Expression: MIT
+License-File: LICENSE
+Keywords: dicom,machine-learning,medical-imaging,nifti,radiology,tiledb
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.11
+Requires-Dist: boto3>=1.34.0
+Requires-Dist: botocore[crt]>=1.42.36
+Requires-Dist: matplotlib>=3.8.0
+Requires-Dist: nibabel>=5.2.0
+Requires-Dist: numpy>=1.26.0
+Requires-Dist: psutil>=5.9.0
+Requires-Dist: pydantic>=2.0.0
+Requires-Dist: pydicom>=2.4.0
+Requires-Dist: tiledb>=0.36.0
+Requires-Dist: tqdm>=4.66.0
+Provides-Extra: dev
+Requires-Dist: jupyter>=1.1.1; extra == 'dev'
+Requires-Dist: nbconvert>=7.16.6; extra == 'dev'
+Requires-Dist: pandas>=2.0.0; extra == 'dev'
+Requires-Dist: pre-commit>=3.0.0; extra == 'dev'
+Requires-Dist: pytest>=8.0.0; extra == 'dev'
+Requires-Dist: ruff>=0.1.0; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: mkdocs-material>=9.5.0; extra == 'docs'
+Requires-Dist: mkdocs>=1.5.0; extra == 'docs'
+Requires-Dist: mkdocstrings[python]>=0.24.0; extra == 'docs'
+Requires-Dist: pandas>=2.0.0; extra == 'docs'
+Provides-Extra: download
+Requires-Dist: requests>=2.31.0; extra == 'download'
+Requires-Dist: tcia-utils>=0.5.0; extra == 'download'
+Provides-Extra: ml
+Requires-Dist: monai>=1.3.0; extra == 'ml'
+Requires-Dist: pandas>=2.0.0; extra == 'ml'
+Requires-Dist: scikit-learn>=1.3.0; extra == 'ml'
+Requires-Dist: simpleitk>=2.3.0; extra == 'ml'
+Requires-Dist: tcia-utils>=0.5.0; extra == 'ml'
+Requires-Dist: torch>=2.0.0; extra == 'ml'
+Requires-Dist: torchio>=0.19.0; extra == 'ml'
+Provides-Extra: monai
+Requires-Dist: monai>=1.3.0; extra == 'monai'
+Requires-Dist: torch>=2.0.0; extra == 'monai'
+Provides-Extra: torchio
+Requires-Dist: torch>=2.0.0; extra == 'torchio'
+Requires-Dist: torchio>=0.19.0; extra == 'torchio'
+Provides-Extra: tutorials
+Requires-Dist: jupyter>=1.1.1; extra == 'tutorials'
+Requires-Dist: requests>=2.31.0; extra == 'tutorials'
+Requires-Dist: tcia-utils>=0.5.0; extra == 'tutorials'
+Description-Content-Type: text/markdown
+
+# RadiObject
+
+**What?** A TileDB-backed data structure for radiology data at scale.
+
+**Why?** NIfTI/DICOM must be read from local disk and don't support partial reads.
+TileDB enables cloud-native storage (S3), efficient partial reads, and
+hierarchical organization of multi-volume datasets.
+
+*[Thoughts](https://souzy.up.railway.app/thoughts/radiology-object)*
+
+## Installation
+
+```bash
+pip install radiobject
+```
+
+## Quick Start
+
+```python
+from radiobject import RadiObject
+
+# Create from NIfTI files using images dict (recommended)
+radi = RadiObject.from_niftis(
+    uri="./my-dataset",
+    images={
+        "CT": "./imagesTr/*.nii.gz",      # Glob pattern
+        "seg": "./labelsTr",               # Directory path
+    },
+    validate_alignment=True,               # Ensure matching subjects across collections
+    obs_meta=metadata_df,                  # Optional subject-level metadata
+)
+
+# Access data (pandas-like)
+vol = radi.CT.iloc[0]            # First CT volume
+data = vol[100:200, :, :]        # Partial read (only loads needed tiles)
+
+# Filtering (returns views)
+subset = radi.filter("age > 40")       # Query expression
+subset = radi.head(10)                 # First 10 subjects
+subset.materialize("./subset")         # Write to storage
+```
+
+Works with local paths or S3 URIs (`s3://bucket/dataset`).
+
+## How It Works
+
+NIfTI requires decompressing entire volumes; TileDB reads only the tiles needed.
+This enables **200-660x faster** partial reads. [See benchmarks →](docs/BENCHMARKS.md)
+
+## Sample Data
+
+Download sample datasets for tutorials and testing:
+
+```bash
+# Install download dependencies
+pip install radiobject[download]
+
+# Download BraTS brain tumor data (for tutorials 00-04)
+python scripts/download_dataset.py msd-brain-tumour
+
+# List all available datasets
+python scripts/download_dataset.py --list
+```
+
+## Documentation
+
+- **[Tutorials](notebooks/README.md)** - Interactive notebooks
+- **[Data Access](docs/DATA_ACCESS.md)** - Ingestion, queries, filtering
+- **[ML Integration](docs/ML_INTEGRATION.md)** - MONAI/TorchIO setup
+- **[Design](docs/DESIGN.md)** - Architecture decisions
+- **[Benchmarks](docs/BENCHMARKS.md)** - Performance analysis
+- **[Datasets](docs/DATASETS.md)** - Available datasets and download instructions
+
+## License
+
+MIT

radiobject-0.1.0.dist-info/RECORD

@@ -0,0 +1,37 @@
+radiobject/__init__.py,sha256=lT5WwY92jM6Z3CCSrH92Eb6utAto1hS2sS4gtlfhcvg,655
+radiobject/_types.py,sha256=EZVH-dHZOe98biqdyWcJYkIN7TxpeoI3VEa_vnGgrPU,567
+radiobject/ctx.py,sha256=3vPNCQsWPyKZbJSQ3UqNlpsYq1o_1W9y1GNj3-Uft1M,12198
+radiobject/dataframe.py,sha256=QnScrKApnXvJClZzHN7iZTyAn0jKxaqDE0tw-Tf8eq0,6897
+radiobject/imaging_metadata.py,sha256=t4FdD3p8oJrvcCALz-BQvN7ZJNZ2BmdeRmvvbbjr0Nk,11909
+radiobject/indexing.py,sha256=5RF0b5j_zQE6NdQczfx9wVGNZdpUMG7XdiCLmk43aIQ,1451
+radiobject/ingest.py,sha256=JgeGU-by5_qAiGgeP_JilWzgwLMn0eyHtISkdqOpRJM,4126
+radiobject/orientation.py,sha256=SFLoindOBBU65hIG2hel7Dba0X3Foq6OaMg_OoA-GkM,9308
+radiobject/parallel.py,sha256=q8RsU_LEr28djSMY4QD-ZXComCoO62nO0hlExgbyc1Y,1797
+radiobject/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+radiobject/query.py,sha256=s1tYYvu-geRlgcOL3VnTKLPnsjq3DUnMoxztTVHKx4M,31312
+radiobject/radi_object.py,sha256=ilgeAbv8gPkYBmaJi5YXoDiOz6Q78TTOg-_TN4alN4A,65017
+radiobject/streaming.py,sha256=0lZgm3r_h8xj8s9w7myHUnO0CFSUrGQ1YQgRT0o6HvI,13623
+radiobject/utils.py,sha256=0KgPOYLQgnUqM8Ac8j8Qw8n68E5jQY1LQma5OHXmUjE,452
+radiobject/volume.py,sha256=xVE0arLPi3UQTdpbYxTo9ofvIvkBSacX-mHBcRAfYwY,15970
+radiobject/volume_collection.py,sha256=apZ39z3UWqiL8EwUPJziZM3U9rLQuaJfhP1GWMXi_wo,46321
+radiobject/ml/__init__.py,sha256=fB_yobxqBslIbtxSrKNosY_MQx8Np-6AW-cLESatwzM,807
+radiobject/ml/cache.py,sha256=G6SFlCuYp3fEWtwxgg4lwo7QYLktK6o92mi6qhvtrwo,1135
+radiobject/ml/config.py,sha256=2JPLTR4COzwnDpiKf99ywCh2FA1Vg6aLRY4V51ohyWQ,1267
+radiobject/ml/distributed.py,sha256=9q9hNMP1k0oy6_XaQa2HJ8mdIfFrruvwebygHdHbswI,2699
+radiobject/ml/factory.py,sha256=yr9-2KRi3K-4bErda9yWL8-xQ5ALus3VsUUT9wae_RI,9249
+radiobject/ml/compat/__init__.py,sha256=3INe8wl2dTUWyFryjbeOeehREF_dyVhdcwVe5tTsDPo,956
+radiobject/ml/compat/torchio.py,sha256=YVjJJoK-UVfdzdKNIo_UCQmOGieU3gUTcuwXH-E1ygg,3343
+radiobject/ml/datasets/__init__.py,sha256=MkcGSVYdXiPy5P5zDvP1b4E6Hh3kXQIVBkh9eGhVbwA,418
+radiobject/ml/datasets/collection_dataset.py,sha256=Xn69zCvpQVW2wElEshG6kJy3jRso7DGn9ualOxhCPZw,7302
+radiobject/ml/datasets/multimodal.py,sha256=upKZZn3lphTCffaCuzoNcrRPXoMWOih4dGPwLzrNJZA,4293
+radiobject/ml/datasets/patch_dataset.py,sha256=3L4zH9VSS4HLkD0Sbv_uIdHGa_e3amovFKGrPr415f0,5404
+radiobject/ml/datasets/segmentation_dataset.py,sha256=mXIukHNaHCoQg-Scvy65gqbq8Ams6GPXnaVQJuq1Vyk,8546
+radiobject/ml/datasets/volume_dataset.py,sha256=FriJbcPlYSYK1exH60D-U8gBhk98MIbHuScXtV-Z_Ds,8503
+radiobject/ml/utils/__init__.py,sha256=eh8NXj00jBVrCIXjCSvM7TeaWpcStAXk-AspcB_HoOQ,385
+radiobject/ml/utils/labels.py,sha256=NOprMYexICdLu5yiOiYMfUawq53s8wpBPOx93WaKcuY,3591
+radiobject/ml/utils/validation.py,sha256=KtwHY8hsYaLWkS-_84mXA0eS4x9b01ykpKCspLuh5pk,2760
+radiobject/ml/utils/worker_init.py,sha256=ZZNd68m_Z3yIUxkNWsJYPEbNPNTaoFgH6xxdHuqelfA,285
+radiobject-0.1.0.dist-info/METADATA,sha256=D6mmYYORr7_nin3bHI1IgDsHh4Gkmy6HGAKBvSmjdAI,4808
+radiobject-0.1.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+radiobject-0.1.0.dist-info/licenses/LICENSE,sha256=4M92OGqVJ7ben6C2MQ2NEhy7TRsPrN0hGbE75-g8YwQ,1071
+radiobject-0.1.0.dist-info/RECORD,,

radiobject-0.1.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.28.0
+Root-Is-Purelib: true
+Tag: py3-none-any

radiobject-0.1.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Samuel D'Souza
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.