mlarray 0.0.53__tar.gz → 0.0.54__tar.gz

{mlarray-0.0.53 → mlarray-0.0.54}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mlarray
-Version: 0.0.53
+Version: 0.0.54
 Summary: Array format specialized for Machine Learning with Blosc2 backend and standardized metadata.
 Author-email: Karol Gotkowski <karol.gotkowski@dkfz.de>
 License: MIT
@@ -236,10 +236,32 @@ mlarray_header sample.mla
 
 ### mlarray_convert
 
-Convert a NIfTI or NRRD file to MLArray and copy metadata.
+Convert between MLArray and NIfTI/NRRD files.
+
+When converting from NIfTI/NRRD to MLArray, source metadata is copied into
+`meta.source`.
+
+When converting from MLArray to NIfTI/NRRD, only `meta.source` is copied into
+the output header. Spatial metadata (`spacing`, `origin`, `direction`) is set
+explicitly from `meta.spatial`.
+
+`meta.spatial.coord_system` is propagated conservatively. For NRRD input, the
+CLI reads explicit NRRD space metadata when available and maps
+`right-anterior-superior` to `RAS` and `left-posterior-superior` to `LPS`,
+while preserving other explicit NRRD space strings verbatim. For NIfTI input,
+the CLI sets `coord_system` to `LPS` based on the current
+`MedVol -> SimpleITK/ITK` import path, where the imported geometry is
+represented in the ITK physical-space convention. MedVol's reindexing to NumPy
+layout does not change that world-space convention. On NRRD output, `RAS` and
+`LPS` are written back as NRRD `space` metadata when possible; arbitrary custom
+`coord_system` strings are not emitted as NRRD `space` declarations unless they
+already match a supported explicit NRRD space string. NIfTI output preserves
+geometry, but does not export `coord_system` as an explicit NIfTI metadata
+field.
 
 ```bash
 mlarray_convert sample.nii.gz output.mla
+mlarray_convert sample.mla output.nii.gz
 ```
 
 ## Contributing

{mlarray-0.0.53 → mlarray-0.0.54}/README.md

@@ -202,10 +202,32 @@ mlarray_header sample.mla
 
 ### mlarray_convert
 
-Convert a NIfTI or NRRD file to MLArray and copy metadata.
+Convert between MLArray and NIfTI/NRRD files.
+
+When converting from NIfTI/NRRD to MLArray, source metadata is copied into
+`meta.source`.
+
+When converting from MLArray to NIfTI/NRRD, only `meta.source` is copied into
+the output header. Spatial metadata (`spacing`, `origin`, `direction`) is set
+explicitly from `meta.spatial`.
+
+`meta.spatial.coord_system` is propagated conservatively. For NRRD input, the
+CLI reads explicit NRRD space metadata when available and maps
+`right-anterior-superior` to `RAS` and `left-posterior-superior` to `LPS`,
+while preserving other explicit NRRD space strings verbatim. For NIfTI input,
+the CLI sets `coord_system` to `LPS` based on the current
+`MedVol -> SimpleITK/ITK` import path, where the imported geometry is
+represented in the ITK physical-space convention. MedVol's reindexing to NumPy
+layout does not change that world-space convention. On NRRD output, `RAS` and
+`LPS` are written back as NRRD `space` metadata when possible; arbitrary custom
+`coord_system` strings are not emitted as NRRD `space` declarations unless they
+already match a supported explicit NRRD space string. NIfTI output preserves
+geometry, but does not export `coord_system` as an explicit NIfTI metadata
+field.
 
 ```bash
 mlarray_convert sample.nii.gz output.mla
+mlarray_convert sample.mla output.nii.gz
 ```
 
 ## Contributing

mlarray-0.0.54/bench/.gitignore

@@ -0,0 +1,2 @@
+data/
+results/

mlarray-0.0.54/bench/README.md

@@ -0,0 +1,56 @@
+# Benchmark Scripts
+
+This folder contains benchmarking scripts for MLArray IO/layout experiments.
+
+## `bench_io_blosc2_layouts.py`
+
+Benchmarks IO throughput across:
+
+- layout method(s) based on `comp_blosc2_params` (currently baseline copy only)
+- image size tiers (`small`, `medium`, `large`, `very_large`)
+- 2D / 3D / 4D-total array cases with spatial and optional non-spatial axis
+- multiple patch sizes (2D and 3D patch vectors)
+- `MLArray.open(...)` mode/mmap combinations
+- operations:
+  - `read_full`
+  - `read_patch_random`
+  - `write_patch_random`
+- warm and cold cache runs
+
+Outputs are printed to console and written to:
+
+- `bench/results/bench_io_blosc2_layouts.csv`
+- `bench/results/bench_io_blosc2_layouts.json`
+
+### Example
+
+```bash
+python bench/bench_io_blosc2_layouts.py \
+  --tiers small medium \
+  --runs 3 \
+  --cache-mode both \
+  --nthreads 1
+```
+
+If you hit native segfaults in Blosc2 during long runs, isolate each measured run
+in a subprocess (slower, but robust):
+
+```bash
+python bench/bench_io_blosc2_layouts.py \
+  --tiers small medium \
+  --runs 3 \
+  --cache-mode both \
+  --nthreads 1 \
+  --isolate-runs
+```
+
+### Cold cache note (Linux)
+
+For cold-cache read measurements, the script drops Linux page cache **after the dataset has been created on disk and immediately before measured open/read runs**.
+
+This requires root:
+
+- run as root, or
+- run via `sudo`
+
+If cache dropping fails, those runs are recorded with error status in results.