mlarray 0.0.45__tar.gz → 0.0.47__tar.gz

{mlarray-0.0.45 → mlarray-0.0.47}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mlarray
-Version: 0.0.45
+Version: 0.0.47
 Summary: Array format specialized for Machine Learning with Blosc2 backend and standardized metadata.
 Author-email: Karol Gotkowski <karol.gotkowski@dkfz.de>
 License: MIT
@@ -174,42 +174,54 @@ Default patch size (192):
 ```python
 from mlarray import MLArray
 
-image = MLArray("sample.mla")
-image.save("default-patch.mla")  # Default patch_size is 'default' -> Isotropic patch size of 192 pixels
-image.save("default-patch.mla", patch_size='default')
+image = MLArray("sample.mla")  # Existing file
+image.save("default-patch.mla")  # Keeps existing layout metadata
+
+loaded = MLArray("sample.mla")
+image = MLArray(loaded.to_numpy(), patch_size='default')
+image.save("default-patch-relayout.mla")  # Uses constructor patch_size='default' (192)
 ```
 
 Custom isotropic patch size (512):
 ```python
 from mlarray import MLArray
 
-image = MLArray("sample.mla")
-image.save("patch-512.mla", patch_size=512)
+loaded = MLArray("sample.mla")
+image = MLArray(loaded.to_numpy(), patch_size=512)
+image.save("patch-512.mla")
 ```
 
 Custom non-isotropic patch size:
 ```python
 from mlarray import MLArray
 
-image = MLArray("sample.mla")
-image.save("patch-non-iso.mla", patch_size=(128, 192, 256))
+loaded = MLArray("sample.mla")
+image = MLArray(loaded.to_numpy(), patch_size=(128, 192, 256))
+image.save("patch-non-iso.mla")
 ```
 
 Manual chunk/block size:
 ```python
 from mlarray import MLArray
 
-image = MLArray("sample.mla")
-image.save("manual-chunk-block.mla", chunk_size=(1, 128, 128), block_size=(1, 32, 32))
+loaded = MLArray("sample.mla")
+image = MLArray(
+    loaded.to_numpy(),
+    patch_size=None,
+    chunk_size=(1, 128, 128),
+    block_size=(1, 32, 32),
+)
+image.save("manual-chunk-block.mla")
 ```
 
 Let Blosc2 itself configure chunk/block size:
 ```python
 from mlarray import MLArray
 
-image = MLArray("sample.mla")
+loaded = MLArray("sample.mla")
+image = MLArray(loaded.to_numpy(), patch_size=None)
 # If patch_size, chunk_size and block_size are all None, Blosc2 will auto-configure chunk and block size
-image.save("manual-chunk-block.mla", patch_size=None)
+image.save("blosc2-auto.mla")
 ```
 
 ## CLI

{mlarray-0.0.45 → mlarray-0.0.47}/README.md

@@ -140,42 +140,54 @@ Default patch size (192):
 ```python
 from mlarray import MLArray
 
-image = MLArray("sample.mla")
-image.save("default-patch.mla")  # Default patch_size is 'default' -> Isotropic patch size of 192 pixels
-image.save("default-patch.mla", patch_size='default')
+image = MLArray("sample.mla")  # Existing file
+image.save("default-patch.mla")  # Keeps existing layout metadata
+
+loaded = MLArray("sample.mla")
+image = MLArray(loaded.to_numpy(), patch_size='default')
+image.save("default-patch-relayout.mla")  # Uses constructor patch_size='default' (192)
 ```
 
 Custom isotropic patch size (512):
 ```python
 from mlarray import MLArray
 
-image = MLArray("sample.mla")
-image.save("patch-512.mla", patch_size=512)
+loaded = MLArray("sample.mla")
+image = MLArray(loaded.to_numpy(), patch_size=512)
+image.save("patch-512.mla")
 ```
 
 Custom non-isotropic patch size:
 ```python
 from mlarray import MLArray
 
-image = MLArray("sample.mla")
-image.save("patch-non-iso.mla", patch_size=(128, 192, 256))
+loaded = MLArray("sample.mla")
+image = MLArray(loaded.to_numpy(), patch_size=(128, 192, 256))
+image.save("patch-non-iso.mla")
 ```
 
 Manual chunk/block size:
 ```python
 from mlarray import MLArray
 
-image = MLArray("sample.mla")
-image.save("manual-chunk-block.mla", chunk_size=(1, 128, 128), block_size=(1, 32, 32))
+loaded = MLArray("sample.mla")
+image = MLArray(
+    loaded.to_numpy(),
+    patch_size=None,
+    chunk_size=(1, 128, 128),
+    block_size=(1, 32, 32),
+)
+image.save("manual-chunk-block.mla")
 ```
 
 Let Blosc2 itself configure chunk/block size:
 ```python
 from mlarray import MLArray
 
-image = MLArray("sample.mla")
+loaded = MLArray("sample.mla")
+image = MLArray(loaded.to_numpy(), patch_size=None)
 # If patch_size, chunk_size and block_size are all None, Blosc2 will auto-configure chunk and block size
-image.save("manual-chunk-block.mla", patch_size=None)
+image.save("blosc2-auto.mla")
 ```
 
 ## CLI

{mlarray-0.0.45 → mlarray-0.0.47}/docs/optimization.md

@@ -75,10 +75,10 @@ import numpy as np
 from mlarray import MLArray
 
 array = np.random.random((128, 256, 256))
-image = MLArray(array)
+image = MLArray(array, patch_size=(128, 192, 256))
 
 # Optimize storage layout for 3D patches of 128×192×256 (spatial axes)
-image.save("patch-non-iso.mla", patch_size=(128, 192, 256))
+image.save("patch-non-iso.mla")
 ```
 
 When to use:
@@ -164,12 +164,14 @@ If you already know what you’re doing (or want to reproduce a very specific la
 ```python
 from mlarray import MLArray
 
-image = MLArray("sample.mla")
-image.save(
-    "manual-layout.mla",
+loaded = MLArray("sample.mla")
+image = MLArray(
+    loaded.to_numpy(),
+    patch_size=None,
     chunk_size=(1, 128, 128),
     block_size=(1, 32, 32),
 )
+image.save("manual-layout.mla")
 ```
 
 When to use:
@@ -186,10 +188,11 @@ If you set `patch_size=None` (and don’t provide chunk/block sizes), Blosc2 wil
 ```python
 from mlarray import MLArray
 
-image = MLArray("sample.mla")
+loaded = MLArray("sample.mla")
+image = MLArray(loaded.to_numpy(), patch_size=None)
 
 # If patch_size, chunk_size and block_size are all None, Blosc2 auto-configures
-image.save("blosc2-auto.mla", patch_size=None)
+image.save("blosc2-auto.mla")
 ```
 
 When to use:

{mlarray-0.0.45 → mlarray-0.0.47}/docs/usage.md

@@ -156,11 +156,12 @@ image = MLArray(
     spacing=(2.5, 0.7, 0.7),  # spatial axes only (z, y, x)
     origin=(0.0, 0.0, 0.0),
     axis_labels=axis_labels,
+    patch_size=None,
 )
 
 # Optional per-axis units (length = full array ndims)
 image.meta.spatial.axis_units = ["s", "mm", "mm", "mm", ""]
-image.save("time-series.mla", patch_size=None)
+image.save("time-series.mla")
 ```
 
 
@@ -177,8 +178,11 @@ Uses the default patch configuration, optimized for typical ML patch-based acces
 from mlarray import MLArray
 
 image = MLArray("sample.mla")
-image.save("default-patch.mla")  # Default patch_size is 'default' -> Isotropic patch size of 192 pixels
-image.save("default-patch.mla", patch_size='default')
+image.save("default-patch.mla")  # Keeps existing layout metadata
+
+loaded = MLArray("sample.mla")
+image = MLArray(loaded.to_numpy(), patch_size='default')
+image.save("default-patch-relayout.mla")  # Uses constructor patch_size='default' (192)
 ```
 
 ### Custom isotropic patch size (512)
@@ -188,8 +192,9 @@ A larger patch size can improve throughput when you typically load large regions
 ```python
 from mlarray import MLArray
 
-image = MLArray("sample.mla")
-image.save("patch-512.mla", patch_size=512)
+loaded = MLArray("sample.mla")
+image = MLArray(loaded.to_numpy(), patch_size=512)
+image.save("patch-512.mla")
 ```
 
 ### Custom non-isotropic patch size
@@ -199,8 +204,9 @@ Non-isotropic patches are useful when one axis behaves differently (e.g., fewer
 ```python
 from mlarray import MLArray
 
-image = MLArray("sample.mla")
-image.save("patch-non-iso.mla", patch_size=(128, 192, 256))
+loaded = MLArray("sample.mla")
+image = MLArray(loaded.to_numpy(), patch_size=(128, 192, 256))
+image.save("patch-non-iso.mla")
 ```
 
 ### Manual chunk/block size
@@ -210,8 +216,14 @@ For advanced use cases, you can explicitly define the chunk and block size used
 ```python
 from mlarray import MLArray
 
-image = MLArray("sample.mla")
-image.save("manual-chunk-block.mla", chunk_size=(1, 128, 128), block_size=(1, 32, 32))
+loaded = MLArray("sample.mla")
+image = MLArray(
+    loaded.to_numpy(),
+    patch_size=None,
+    chunk_size=(1, 128, 128),
+    block_size=(1, 32, 32),
+)
+image.save("manual-chunk-block.mla")
 ```
 
 ### Let Blosc2 itself configure chunk/block size
@@ -221,7 +233,8 @@ If you disable MLArray patch sizing, Blosc2 can choose chunk and block sizes aut
 ```python
 from mlarray import MLArray
 
-image = MLArray("sample.mla")
+loaded = MLArray("sample.mla")
+image = MLArray(loaded.to_numpy(), patch_size=None)
 # If patch_size, chunk_size and block_size are all None, Blosc2 will auto-configure chunk and block size
-image.save("manual-chunk-block.mla", patch_size=None)
+image.save("blosc2-auto.mla")
 ```

{mlarray-0.0.45 → mlarray-0.0.47}/examples/example_asarray.py

@@ -69,7 +69,7 @@ if __name__ == "__main__":
 
     # Convert to in-memory compressed MLArray.
     start_time = time.time()
-    image = MLArray.asarray(array, memory_compressed=True)
+    image = MLArray.asarray(array)
     print("MLArray conversion duration: ", time.time() - start_time)
     rss_after_compressed = get_process_rss_bytes()
 

{mlarray-0.0.45 → mlarray-0.0.47}/examples/example_non_spatial.py

@@ -27,10 +27,10 @@ if __name__ == '__main__':
         os.remove(filepath)
 
     print("Initializing image...")
-    image = MLArray(array, spacing=spacing, origin=origin, direction=direction, axis_labels=axis_labels, meta=Meta(source=source_meta, bbox=MetaBbox(bboxes)))
+    image = MLArray(array, spacing=spacing, origin=origin, direction=direction, axis_labels=axis_labels, meta=Meta(source=source_meta, bbox=MetaBbox(bboxes)), patch_size=None)
     image.meta.spatial.axis_units = ["s", "mm", "mm", "mm", ""]
     print("Saving image...")
-    image.save(filepath, patch_size=None)
+    image.save(filepath)
 
     print("Loading image...")
     image = MLArray(filepath)