mlarray 0.0.35__tar.gz → 0.0.37__tar.gz

{mlarray-0.0.35 → mlarray-0.0.37}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mlarray
-Version: 0.0.35
+Version: 0.0.37
 Summary: Array format specialized for Machine Learning with Blosc2 backend and standardized metadata.
 Author-email: Karol Gotkowski <karol.gotkowski@dkfz.de>
 License: MIT

{mlarray-0.0.35 → mlarray-0.0.37}/docs/usage.md

@@ -128,6 +128,43 @@ image.save("with-metadata.mla")
 
 ---
 
+## Non-spatial data usage
+
+Use `axis_labels` to mark which axes are spatial and which are non-spatial
+(channels, temporal, components, etc.). Spatial metadata (`spacing`, `origin`,
+`direction`) is specified only for the spatial axes, while the full array shape
+includes both spatial and non-spatial axes.
+
+```python
+import numpy as np
+from mlarray import MLArray, MetaSpatial
+
+# Example shape: (time, z, y, x, channels)
+array = np.random.random((2, 6, 4, 4, 3, 2))
+
+axis_labels = [
+    MetaSpatial.AxisLabel.temporal,
+    MetaSpatial.AxisLabel.spatial_z,
+    MetaSpatial.AxisLabel.spatial_y,
+    "spatial_x",  # Possible to pass predefined labels as string as well
+    MetaSpatial.AxisLabel.channel,
+    "some-other-type"  # Possible to pass arbitrary strings as well
+]
+
+image = MLArray(
+    array,
+    spacing=(2.5, 0.7, 0.7),  # spatial axes only (z, y, x)
+    origin=(0.0, 0.0, 0.0),
+    axis_labels=axis_labels,
+)
+
+# 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)
+```
+
+
+
 ## Patch size variants
 
 MLArray stores arrays in a chunked layout to enable efficient partial reads. You can control how data is chunked using `patch_size` (recommended in most cases), or manually specify chunk and block sizes when you need full control.

mlarray-0.0.37/examples/example_non_spatial.py

@@ -0,0 +1,42 @@
+import numpy as np
+import os
+from pathlib import Path
+from mlarray import MLArray, Meta, MetaBbox, MetaSpatial
+import json
+
+
+if __name__ == '__main__':
+    print("Creating array...")
+    array = np.random.random((2, 6, 4, 4, 3, 2))
+    axis_labels = [
+        MetaSpatial.AxisLabel.temporal,
+        MetaSpatial.AxisLabel.spatial_z,
+        MetaSpatial.AxisLabel.spatial_y,
+        "spatial_x",  # Possible to pass predefined labels as string as well
+        MetaSpatial.AxisLabel.channel,
+        "some-other-type"  # Possible to pass arbitrary strings as well
+    ]
+    spacing = np.array((2, 2.5, 4))
+    origin = (1, 1, 1)
+    direction = [[1, 2, 3], [4, 5, 6], [7, 8, 9]]
+    source_meta = {"tmp1": "This is an image", "tmp2": 5, "tmp3": {"test1": 16.4587, "test2": [1, 2, 3, 4, 5, 6]}}
+    bboxes = [[[0, 1], [0, 1], [0, 1]]]
+    filepath = "tmp.mla"
+
+    if Path(filepath).is_file():
+        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.meta.spatial.axis_units = ["s", "mm", "mm", "mm", ""]
+    print("Saving image...")
+    image.save(filepath, patch_size=None)
+
+    print("Loading image...")
+    image = MLArray(filepath)
+    print(json.dumps(image.meta.to_mapping(), indent=2, sort_keys=True))
+    print("Image mean value: ", np.mean(image.to_numpy()))
+    print("Some array data: \n", image[:2, :2, 0])
+
+    if Path(filepath).is_file():
+        os.remove(filepath)

{mlarray-0.0.35 → mlarray-0.0.37}/mlarray.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mlarray
-Version: 0.0.35
+Version: 0.0.37
 Summary: Array format specialized for Machine Learning with Blosc2 backend and standardized metadata.
 Author-email: Karol Gotkowski <karol.gotkowski@dkfz.de>
 License: MIT

{mlarray-0.0.35 → mlarray-0.0.37}/mlarray.egg-info/SOURCES.txt

@@ -21,6 +21,7 @@ docs/usage.md
 docs/why.md
 examples/example_channel.py
 examples/example_metadata_only.py
+examples/example_non_spatial.py
 examples/example_open.py
 examples/example_save_load.py
 mlarray/__init__.py