mlarray 0.0.42__tar.gz → 0.0.44__tar.gz

{mlarray-0.0.42 → mlarray-0.0.44}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mlarray
-Version: 0.0.42
+Version: 0.0.44
 Summary: Array format specialized for Machine Learning with Blosc2 backend and standardized metadata.
 Author-email: Karol Gotkowski <karol.gotkowski@dkfz.de>
 License: MIT

{mlarray-0.0.42 → mlarray-0.0.44}/examples/example_asarray.py

@@ -1,7 +1,7 @@
 import gc
 import os
 import numpy as np
-
+import time
 from mlarray import MLArray
 
 
@@ -68,7 +68,9 @@ if __name__ == "__main__":
     numpy_bytes = array.nbytes
 
     # Convert to in-memory compressed MLArray.
+    start_time = time.time()
     image = MLArray.asarray(array, memory_compressed=True)
+    print("MLArray conversion duration: ", time.time() - start_time)
     rss_after_compressed = get_process_rss_bytes()
 
     # Compressed payload size stored by Blosc2 in RAM.

mlarray-0.0.44/examples/example_bboxes_only.py

@@ -0,0 +1,36 @@
+import json
+import os
+from pathlib import Path
+
+from mlarray import MLArray, Meta, MetaBbox
+
+
+if __name__ == "__main__":
+    filepath = "tmp_metadata_bboxes_only.mla"
+
+    if Path(filepath).is_file():
+        os.remove(filepath)
+
+    # Five example 3D bounding boxes in [z, y, x] order.
+    bboxes = [
+        [[12, 28], [40, 75], [55, 90]],
+        [[48, 70], [18, 36], [10, 24]],
+        [[20, 33], [80, 108], [44, 73]],
+        [[72, 95], [52, 81], [88, 118]],
+        [[5, 16], [12, 30], [100, 126]],
+    ]
+    scores = [0.97, 0.84, 0.76, 0.91, 0.68]
+    labels = ["tumor", "lymph_node", "lesion", "organ_part", "cyst"]
+
+    meta = Meta(
+        source={"case_id": "case-001", "modality": "CT"},
+        bbox=MetaBbox(bboxes=bboxes, scores=scores, labels=labels)
+    )
+
+    # No array data: this MLArray stores metadata only.
+    image = MLArray(meta=meta)
+    image.save(filepath)
+
+    loaded = MLArray(filepath)
+    print("Saved metadata-only MLArray with 3D bboxes:")
+    print(json.dumps(loaded.meta.to_mapping(), indent=2, sort_keys=True))

{mlarray-0.0.42 → mlarray-0.0.44}/mlarray/mlarray.py

@@ -64,9 +64,10 @@ class MLArray:
         else:
             self._store = array
             has_array = array is not None
-            self._validate_and_add_meta(meta, spacing, origin, direction, axis_labels, has_array)        
+            self._validate_and_add_meta(meta, spacing, origin, direction, axis_labels, has_array, validate=False)        
             if copy is not None:
                 self.meta.copy_from(copy.meta)
+            self._validate_and_add_meta(self.meta, validate=True) 
 
     @classmethod
     def open(
@@ -1009,12 +1010,16 @@ class MLArray:
             raise NotImplementedError("Chunk and block size optimization based on patch size is only implemented for 2D and 3D spatial images with at most one further non-spatial axis. Please set the chunk and block size manually or set to None for blosc2 to determine a chunk and block size.")
         if patch_size is not None and patch_size != "default" and (chunk_size is not None or block_size is not None):
             raise RuntimeError("patch_size and chunk_size / block_size cannot both be explicitly set.")
+        if (chunk_size is not None and block_size is None) or (chunk_size is None and block_size is not None):
+            raise RuntimeError("If either chunk/block size is used then both must be set.")
 
         if patch_size == "default": 
             if meta_blosc2 is not None and meta_blosc2.patch_size is not None:  # Use previously loaded patch size, when patch size is not explicitly set and a patch size from a previously loaded image exists
                 patch_size = meta_blosc2.patch_size
             else:  # Use default patch size, when patch size is not explicitly set and no patch size from a previously loaded image exists
                 patch_size = [MLARRAY_DEFAULT_PATCH_SIZE] * num_spatial_axes
+        if chunk_size is not None or block_size is not None:
+            patch_size = None
 
         patch_size = [patch_size] * len(shape) if isinstance(patch_size, int) else patch_size
 
@@ -1056,7 +1061,7 @@ class MLArray:
             raise RuntimeError("Metadata is not serializable.")
         self._store.vlmeta["mlarray"] = metadata
     
-    def _validate_and_add_meta(self, meta, spacing=None, origin=None, direction=None, axis_labels=None, has_array=None):
+    def _validate_and_add_meta(self, meta, spacing=None, origin=None, direction=None, axis_labels=None, has_array=None, validate=True):
         """Validate and attach metadata to the MLArray instance.
 
         Args:
@@ -1097,7 +1102,8 @@ class MLArray:
             self.meta._has_array.has_array = True
         if self.meta._has_array.has_array:
             self.meta.spatial.shape = self.shape
-        self.meta.spatial._validate_and_cast(ndims=self.ndim, spatial_ndims=self._spatial_ndim)
+        if validate:
+            self.meta.spatial._validate_and_cast(ndims=self.ndim, spatial_ndims=self._spatial_ndim)
 
     def _update_blosc2_meta(self):
         """Sync Blosc2 chunk and block sizes into metadata.

{mlarray-0.0.42 → mlarray-0.0.44}/mlarray.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mlarray
-Version: 0.0.42
+Version: 0.0.44
 Summary: Array format specialized for Machine Learning with Blosc2 backend and standardized metadata.
 Author-email: Karol Gotkowski <karol.gotkowski@dkfz.de>
 License: MIT

{mlarray-0.0.42 → mlarray-0.0.44}/mlarray.egg-info/SOURCES.txt

@@ -20,6 +20,7 @@ docs/schema.md
 docs/usage.md
 docs/why.md
 examples/example_asarray.py
+examples/example_bboxes_only.py
 examples/example_channel.py
 examples/example_metadata_only.py
 examples/example_non_spatial.py