Merge main into workflow dev branch

.gitattributes

@@ -0,0 +1 @@
+*.ipynb -linguist-detectable

.gitignore

@@ -1,3 +1,4 @@
+.benchmarks
 niivue-images/
 pydicom-data/
 downloaded_testfiles/

Cargo.toml

@@ -18,4 +18,5 @@ rmpv = "1.0.0"
 safetensors = "0.3.0"
 serde = { version = "1.0.156", features = ["derive"] }
 serde_json = "1.0.94"
+snafu = { version = "0.7.4", features = ["rust_1_61", "backtraces-impl-std"] }
 

Makefile

@@ -14,7 +14,16 @@ prep_test:
 
 test: prep_test
 	cargo test
-	pytest
+	pytest --benchmark-disable
+
+bench: prep_test
+	pytest --benchmark-enable --benchmark-group-by=fullfunc
+
+bench-dicom-baselines:
+	pytest test/dicom_baseline_comparisons.py --benchmark-group-by=param -s --benchmark-save=dicom_baselines_comparisons
+
+bench-nifti-baselines:
+	pytest test/nifti_baseline_comparisons.py --benchmark-group-by=param -s --benchmark-save=nifti_baselines_comparisons
 
 fmt:
 	cargo fmt

README.md

@@ -2,27 +2,23 @@
 
 Nimble Digital Imaging for Medicine
 
-Near lossless and easy conversion from DICOM and back
-- Done
+## Pipeline
 
-Support for fast and random access of metadata
-- Done
+### Completed
 
-Extremely fast and zero-copy loading to CPU/GPU
-- Done
+- [x] Near lossless and easy conversion from DICOM and back
+- [x] Support for fast and random access of metadata
+- [x] Extremely fast and zero-copy loading to CPU/GPU
+- [x] Safe: no codegen/exec based on the metadata
+- [x] Support for ITK file formats [[ref](https://simpleitk.readthedocs.io/en/v1.2.4/Documentation/docs/source/IO.html#images)], including NIfTI
 
+### WIP
 All relevant data types including uint16, f16, bf16, complex64 and complex128
 - Currently supports f32, trivial to support other datatypes
 
 Bindings for Python and conversion to NumPy/CuPy/JAX/Torch tensors
 - Currently supports loading to Torch tensors (easily extensible)
 
-Safe: no codegen/exec based on the metadata
-- Done
-
-Support for ITK file formats [[ref](https://simpleitk.readthedocs.io/en/v1.2.4/Documentation/docs/source/IO.html#images)], including NIfTI
-- Done
-
 
 ## Installation
 
@@ -51,7 +47,7 @@ dimble.dicom_to_dimble('xray.dicom', 'xray.dimble')
 dataset = dimble.load_dimble('xray.dimble', fields=["7FE00010"], device="cpu")
 
 # load a dimble file's pixel data sliced to a 224x224 chunk offset by 100 in each dimension
-dataset = dimble.load_dimble('xray.dimble', fields=["7FE00010"], device="cpu", slices=[slice(100:100+224), slice(100:100+224)])
+dataset = dimble.load_dimble('xray.dimble', fields=["7FE00010"], device="cpu", slices=[slice(100,100+224), slice(100,100+224)])
 
 # convert back to dicom
 dimble.dimble_to_dicom("xray.dimble", "xray.dicom")

dimble/__init__.py

@@ -5,13 +5,17 @@
     dimble_to_nifti,
     load_dimble,
     nifti_to_dimble,
+    rglob_dicom,
 )
 
+rglob_dicom
+
 __all__ = [
     "dicom_to_dimble",
     "dimble_to_dicom",
     "load_dimble",
     "nifti_to_dimble",
     "dimble_to_nifti",
     "_create_temp_dir",
+    "rglob_dicom",
 ]

dimble/dimble.py

@@ -133,3 +133,7 @@ def dimble_to_nifti(dimble_path: Path, output_path: Path) -> None:
         sitk.WriteImage(itk_image, output_path)
     finally:
         ir_path.unlink(missing_ok=True)
+
+def rglob_dicom(path: Path) -> list[Path]:
+    dicom_extensions = [".dcm", ".dicom", ".DCM", ".DICOM"]
+    return [p for p in path.rglob("*") if p.suffix in dicom_extensions]