mlarray 0.0.32__tar.gz → 0.0.39__tar.gz

{mlarray-0.0.32 → mlarray-0.0.39}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mlarray
-Version: 0.0.32
+Version: 0.0.39
 Summary: Array format specialized for Machine Learning with Blosc2 backend and standardized metadata.
 Author-email: Karol Gotkowski <karol.gotkowski@dkfz.de>
 License: MIT
@@ -118,15 +118,15 @@ image = MLArray(
 
 print(image.spacing)  # [1.0, 1.0, 1.5]
 print(image.origin)  # [10.0, 10.0, 30.0]
-print(image.meta.original)  # {"patient_id": "123", "modality": "CT"}
+print(image.meta.source)  # {"patient_id": "123", "modality": "CT"}
 
 image.spacing[1] = 5.3
-image.meta.original["study_id"] = "study-001"
+image.meta.source["study_id"] = "study-001"
 image.save("with-metadata.mla")
 
 # Open memory-mapped
 image = MLArray.open("with-metadata.mla", mmap='r+')  
-image.meta.original["study_id"] = "new-study"  # Modify metadata
+image.meta.source["study_id"] = "new-study"  # Modify metadata
 image.close()  # Close and save metadata, only necessary to save modified metadata
 ```
 
@@ -157,13 +157,13 @@ from mlarray import MLArray, Meta
 array = np.random.random((64, 128, 128))
 image = MLArray(
     array,
-    meta=Meta(original={"patient_id": "123", "modality": "CT"}, is_seg=True),  # Add metadata in a pre-defined format
+    meta=Meta(source={"patient_id": "123", "modality": "CT"}, is_seg=True),  # Add metadata in a pre-defined format
 )
 
-print(image.meta.original)  # {"patient_id": "123", "modality": "CT"}
+print(image.meta.source)  # {"patient_id": "123", "modality": "CT"}
 print(image.meta.is_seg)  # True
 
-image.meta.original["study_id"] = "study-001"
+image.meta.source["study_id"] = "study-001"
 image.meta.is_seg = False
 image.save("with-metadata.mla")
 ```

{mlarray-0.0.32 → mlarray-0.0.39}/README.md

@@ -84,15 +84,15 @@ image = MLArray(
 
 print(image.spacing)  # [1.0, 1.0, 1.5]
 print(image.origin)  # [10.0, 10.0, 30.0]
-print(image.meta.original)  # {"patient_id": "123", "modality": "CT"}
+print(image.meta.source)  # {"patient_id": "123", "modality": "CT"}
 
 image.spacing[1] = 5.3
-image.meta.original["study_id"] = "study-001"
+image.meta.source["study_id"] = "study-001"
 image.save("with-metadata.mla")
 
 # Open memory-mapped
 image = MLArray.open("with-metadata.mla", mmap='r+')  
-image.meta.original["study_id"] = "new-study"  # Modify metadata
+image.meta.source["study_id"] = "new-study"  # Modify metadata
 image.close()  # Close and save metadata, only necessary to save modified metadata
 ```
 
@@ -123,13 +123,13 @@ from mlarray import MLArray, Meta
 array = np.random.random((64, 128, 128))
 image = MLArray(
     array,
-    meta=Meta(original={"patient_id": "123", "modality": "CT"}, is_seg=True),  # Add metadata in a pre-defined format
+    meta=Meta(source={"patient_id": "123", "modality": "CT"}, is_seg=True),  # Add metadata in a pre-defined format
 )
 
-print(image.meta.original)  # {"patient_id": "123", "modality": "CT"}
+print(image.meta.source)  # {"patient_id": "123", "modality": "CT"}
 print(image.meta.is_seg)  # True
 
-image.meta.original["study_id"] = "study-001"
+image.meta.source["study_id"] = "study-001"
 image.meta.is_seg = False
 image.save("with-metadata.mla")
 ```

{mlarray-0.0.32 → mlarray-0.0.39}/docs/api.md

@@ -12,12 +12,14 @@
 
 ::: mlarray.meta.Meta
 
-::: mlarray.meta.MetaOriginal
+::: mlarray.meta.MetaSource
 
 ::: mlarray.meta.MetaExtra
 
 ::: mlarray.meta.MetaSpatial
 
+::: mlarray.meta.AxisLabelEnum
+
 ::: mlarray.meta.MetaStatistics
 
 ::: mlarray.meta.MetaBbox

{mlarray-0.0.32 → mlarray-0.0.39}/docs/optimization.md

@@ -25,7 +25,7 @@ Instead of requiring users to be storage experts, MLArray introduces a **patch s
    * element size (bytes per pixel),
    * CPU cache sizes (L1 / L3 per core),
    * your patch size (2D or 3D),
-   * channel layout (via `channel_axis`),
+   * non-spatial axes layout (via `axis_labels`),
    * and then chooses block/chunk sizes that aim to keep decompression and reads cache-friendly.
 
 Practically: this means *reading a training patch should tend to require as few chunk/block touches as possible*, while keeping the decompressed working set aligned with CPU caches.
@@ -201,8 +201,6 @@ When to use:
 
 ## Notes and practical tips
 
-* **Patch optimization is currently implemented for 2D and 3D images** (and common channel handling). If your data falls outside that, you can still set `chunk_size`/`block_size` manually or let Blosc2 decide.
+* **Patch optimization is currently implemented for 2D and 3D images** (with at most one further non-spatial axis). If your data falls outside that, you can still set `chunk_size`/`block_size` manually or let Blosc2 decide.
 * The best patch size to use is usually the **patch size your dataloader requests most often** (training patch, not necessarily inference tile size).
 * If you’re unsure: start with the default (`patch_size='default'`) and only tune if profiling shows I/O bottlenecks.
-
-If you want, I can also help you add a short “How to pick patch_size” subsection tailored to typical pipelines (nnU-Net, 2D slice training, multi-channel inputs).

{mlarray-0.0.32 → mlarray-0.0.39}/docs/schema.md

@@ -13,7 +13,7 @@ All fields in the schema are **JSON-serializable** unless otherwise noted. Field
 
 ### Representation notes
 
-Many namespaces are implemented as **single-key dataclasses** (subclasses of `SingleKeyBaseMeta`). In Python, these behave like their wrapped value (e.g., `meta.is_seg` is a `bool`, `meta.original` is a `dict`). When serialized via `Meta.to_mapping()`, they appear as a one-field object keyed by their internal field name (e.g., `is_seg: {"is_seg": true}` or `original: {"data": {...}}`). `Meta.from_mapping()` accepts either the one-field object or the raw value and will coerce it to the correct class.
+Many namespaces are implemented as **single-key dataclasses** (subclasses of `SingleKeyBaseMeta`). In Python, these behave like their wrapped value (e.g., `meta.is_seg` is a `bool`, `meta.source` is a `dict`). When serialized via `Meta.to_mapping()`, they appear as a one-field object keyed by their internal field name (e.g., `is_seg: {"is_seg": true}` or `source: {"data": {...}}`). `Meta.from_mapping()` accepts either the one-field object or the raw value and will coerce it to the correct class.
 
 ---
 
@@ -23,16 +23,16 @@ Top-level metadata container.
 
 ### Overview
 
-`Meta` is the root object that groups all metadata into well-defined namespaces. Some namespaces are **standardized** (e.g., `spatial`, `stats`), while others are intentionally **free-form** (`original`, `extra`) to support arbitrary metadata and long-term extensibility. Several entries are single-key dataclasses that wrap a primitive value while still allowing schema-aware validation.
+`Meta` is the root object that groups all metadata into well-defined namespaces. Some namespaces are **standardized** (e.g., `spatial`, `stats`), while others are intentionally **free-form** (`source`, `extra`) to support arbitrary metadata and long-term extensibility. Several entries are single-key dataclasses that wrap a primitive value while still allowing schema-aware validation.
 
 ---
 
-### original
+### source
 
 * **Description:** Arbitrary JSON-serializable dictionary for metadata from the original image source.
   Stores information from image sources such as DICOM, NIfTI, NRRD,
   or other imaging formats.
-* **Dataclass:** `MetaOriginal` (single-key wrapper).
+* **Dataclass:** `MetaSource` (single-key wrapper).
 
 | field | type                  | description                                  |
 | ----- | --------------------- | -------------------------------------------- |
@@ -58,15 +58,34 @@ Top-level metadata container.
 * **Description:** Spatial metadata for the image.
 * **Dataclass:** `MetaSpatial`.
 
-This section stores the information needed to interpret the array in physical space (e.g., voxel spacing, coordinate origin, and orientation). It also optionally captures array shape and channel layout to make downstream consumers more robust.
+This section stores the information needed to interpret the array in physical space (e.g., voxel spacing, coordinate origin, and orientation). It also optionally captures array shape and axes layout to make downstream consumers more robust.
 
 | field        | type                        | description                                                                              |
 | ------------ | --------------------------- | ---------------------------------------------------------------------------------------- |
 | spacing      | Optional[List[float]]       | Voxel spacing per spatial axis, length = `ndims`.                                        |
 | origin       | Optional[List[float]]       | Origin per spatial axis, length = `ndims`.                                               |
 | direction    | Optional[List[List[float]]] | Direction matrix, shape `[ndims][ndims]`.                                                |
-| shape        | Optional[List[int]]         | Array shape. If `channel_axis` is set, length = `ndims + 1`, otherwise length = `ndims`. |
-| channel_axis | Optional[int]               | Index of channel dimension in the full array, if present.                                |
+| shape        | Optional[List[int]]         | Full array shape, length = spatial + non-spatial axes.                                   |
+| axis_labels  | Optional[List[str,AxisLabel]]   | Per-axis labels or roles, length = full array `ndims`.                                   |
+| axis_units   | Optional[List[str]]         | Per-axis units, length = full array `ndims`.                                             |
+
+---
+
+#### AxisLabel
+
+Axis labels describe the semantic role of each axis. They may be provided as strings or enum values.
+
+| value         | description                                              |
+| ------------- | -------------------------------------------------------- |
+| spatial       | Generic spatial axis (used when no axis-specific label). |
+| spatial_x     | Spatial axis representing X.                             |
+| spatial_y     | Spatial axis representing Y.                             |
+| spatial_z     | Spatial axis representing Z.                             |
+| non_spatial   | Generic non-spatial axis.                                |
+| channel       | Channel axis (e.g., color channels or feature maps).     |
+| temporal      | Time axis.                                               |
+| continuous    | Continuous-valued axis (non-spatial).                    |
+| components    | Component axis (e.g., vector components).                |
 
 ---
 
@@ -97,15 +116,17 @@ This section stores precomputed global statistics for the array, which can be us
 ### bbox
 
 * **Description:** Bounding boxes for objects/regions in the image.
-* **Dataclass:** `MetaBbox` (single-key wrapper).
+* **Dataclass:** `MetaBbox`.
 * **Structure:** List of bboxes, each bbox is a list with length equal to image `ndims`,
   and each entry is `[min, max]`.
 
 Bounding boxes are stored in a normalized, axis-aligned representation that works across dimensionalities (2D, 3D, …). This is especially useful for detection-style workflows, ROI cropping, dataset summaries, and interactive visualization.
 
-| field  | type                            | description                                                          |
-| ------ | ------------------------------- | -------------------------------------------------------------------- |
-| bboxes | Optional[List[List[List[int]]]] | Bounding boxes shaped `[num_bboxes][ndims][2]` (min/max), ints only. |
+| field  | type                                            | description                                                                 |
+| ------ | ----------------------------------------------- | --------------------------------------------------------------------------- |
+| bboxes | Optional[List[List[List[Union[int, float]]]]]   | Bounding boxes shaped `[num_bboxes][ndims][2]` (min/max), ints or floats.   |
+| scores | Optional[List[Union[int, float]]]               | Optional confidence scores aligned with `bboxes`.                           |
+| labels | Optional[List[Union[str, int, float]]]          | Optional labels aligned with `bboxes`.                                      |
 
 ---
 
@@ -129,9 +150,9 @@ This section records how the array was laid out on disk (chunking, blocking, pat
 
 | field      | type                  | description                                                            |
 | ---------- | --------------------- | ---------------------------------------------------------------------- |
-| chunk_size | Optional[List[float]] | Chunk size per axis, length = full array `ndims` (including channels). |
-| block_size | Optional[List[float]] | Block size per axis, length = full array `ndims` (including channels). |
-| patch_size | Optional[List[float]] | Patch size per spatial axis, length = `ndims` (channels excluded).     |
+| chunk_size | Optional[List[float]] | Chunk size per axis, length = full array `ndims` (including non-spatial axes). |
+| block_size | Optional[List[float]] | Block size per axis, length = full array `ndims` (including non-spatial axes). |
+| patch_size | Optional[List[float]] | Patch size per spatial axis, length = `ndims` (non-spatial axes excluded).     |
 
 ---
 
@@ -154,7 +175,7 @@ This section records how the array was laid out on disk (chunking, blocking, pat
 
 | field             | type           | description                                   |
 | ----------------- | -------------- | --------------------------------------------- |
-| image_meta_format | Optional[str]  | Identifier for the original metadata format. |
+| image_meta_format | Optional[str]  | Identifier for the source metadata format. |
 
 ---
 

{mlarray-0.0.32 → mlarray-0.0.39}/docs/usage.md

@@ -51,7 +51,7 @@ image[...] = array  # Modify image in memory and disk
 
 ## Metadata inspection and manipulation
 
-MLArray provides first-class support for common image metadata (spacing, origin, direction), and also lets you attach arbitrary metadata from the original image source via `meta=...` (e.g., raw DICOM fields, acquisition parameters, dataset identifiers).
+MLArray provides first-class support for common image metadata (spacing, origin, direction), and also lets you attach arbitrary metadata from the source image source via `meta=...` (e.g., raw DICOM fields, acquisition parameters, dataset identifiers).
 
 ```python
 import numpy as np
@@ -68,15 +68,15 @@ image = MLArray(
 
 print(image.spacing)  # [1.0, 1.0, 1.5]
 print(image.origin)  # [10.0, 10.0, 30.0]
-print(image.meta.original)  # {"patient_id": "123", "modality": "CT"}
+print(image.meta.source)  # {"patient_id": "123", "modality": "CT"}
 
 image.spacing[1] = 5.3
-image.meta.original["study_id"] = "study-001"
+image.meta.source["study_id"] = "study-001"
 image.save("with-metadata.mla")
 
 # Open memory-mapped
 image = MLArray.open("with-metadata.mla", mmap='r+')  
-image.meta.original["study_id"] = "new-study"  # Modify metadata
+image.meta.source["study_id"] = "new-study"  # Modify metadata
 image.close()  # Close and save metadata, only necessary to save modified metadata
 ```
 
@@ -115,19 +115,56 @@ from mlarray import MLArray, Meta
 array = np.random.random((64, 128, 128))
 image = MLArray(
     array,
-    meta=Meta(original={"patient_id": "123", "modality": "CT"}, is_seg=True),  # Add metadata in a pre-defined format
+    meta=Meta(source={"patient_id": "123", "modality": "CT"}, is_seg=True),  # Add metadata in a pre-defined format
 )
 
-print(image.meta.original)  # {"patient_id": "123", "modality": "CT"}
+print(image.meta.source)  # {"patient_id": "123", "modality": "CT"}
 print(image.meta.is_seg)  # True
 
-image.meta.original["study_id"] = "study-001"
+image.meta.source["study_id"] = "study-001"
 image.meta.is_seg = False
 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 strings 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-0.0.32 → mlarray-0.0.39}/docs/why.md

@@ -13,8 +13,8 @@ MLArray is designed to bridge that gap: a machine-learning-friendly array format
 * **A standardized, extensible metadata schema**
   MLArray defines a metadata schema that balances *standardization* and *flexibility*: software that supports MLArray has a consistent way to access relevant metadata, while users can still attach arbitrary custom metadata when needed.
 
-* **Preserve original metadata across conversions**
-  Users can convert images from arbitrary formats to MLArray while preserving the original metadata *in a structured and reproducible way*. Tools that integrate MLArray can still access metadata according to the original format’s conventions, which makes MLArray a practical alternative for ML pipelines without breaking downstream analysis or visualization workflows.
+* **Preserve source metadata across conversions**
+  Users can convert images from arbitrary formats to MLArray while preserving the source metadata *in a structured and reproducible way*. Tools that integrate MLArray can still access metadata according to the source format’s conventions, which makes MLArray a practical alternative for ML pipelines without breaking downstream analysis or visualization workflows.
 
 * **Machine learning–specific metadata support**
   In addition to format-preserving metadata, MLArray includes a dedicated schema for machine-learning-relevant information, and it also supports storing dynamic metadata outside predefined schemas.

{mlarray-0.0.32 → mlarray-0.0.39}/examples/example_channel.py

@@ -1,18 +1,18 @@
 import numpy as np
 import os
 from pathlib import Path
-from mlarray import MLArray, Meta
+from mlarray import MLArray, Meta, MetaBbox, MetaSpatial
 import json
 
 
 if __name__ == '__main__':
     print("Creating array...")
     array = np.random.random((32, 64, 64, 3))
-    channel_axis = 3
+    axis_labels = (MetaSpatial.AxisLabel.spatial_z, MetaSpatial.AxisLabel.spatial_y, MetaSpatial.AxisLabel.spatial_x, MetaSpatial.AxisLabel.channel)
     spacing = np.array((2, 2.5, 4))
     origin = (1, 1, 1)
     direction = [[1, 2, 3], [4, 5, 6], [7, 8, 9]]
-    image_meta = {"tmp1": "This is an image", "tmp2": 5, "tmp3": {"test1": 16.4587, "test2": [1, 2, 3, 4, 5, 6]}}
+    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"
 
@@ -20,7 +20,7 @@ if __name__ == '__main__':
         os.remove(filepath)
 
     print("Initializing image...")
-    image = MLArray(array, spacing=spacing, origin=origin, direction=direction, channel_axis=channel_axis, meta=Meta(original=image_meta, bbox=bboxes))
+    image = MLArray(array, spacing=spacing, origin=origin, direction=direction, axis_labels=axis_labels, meta=Meta(source=source_meta, bbox=MetaBbox(bboxes)))
     print("Saving image...")
     image.save(filepath)
 

{mlarray-0.0.32 → mlarray-0.0.39}/examples/example_metadata_only.py

@@ -1,7 +1,7 @@
 import numpy as np
 import os
 from pathlib import Path
-from mlarray import MLArray, Meta
+from mlarray import MLArray, Meta, MetaBbox
 import json
 
 
@@ -11,7 +11,7 @@ if __name__ == '__main__':
     spacing = np.array((2, 2.5, 4))
     origin = (1, 1, 1)
     direction = [[1, 2, 3], [4, 5, 6], [7, 8, 9]]
-    image_meta = {"tmp1": "This is an image", "tmp2": 5, "tmp3": {"test1": 16.4587, "test2": [1, 2, 3, 4, 5, 6]}}
+    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"
 
@@ -19,7 +19,7 @@ if __name__ == '__main__':
         os.remove(filepath)
 
     print("Initializing image...")
-    image = MLArray(spacing=spacing, origin=origin, direction=direction, meta=Meta(original=image_meta, bbox=bboxes))
+    image = MLArray(spacing=spacing, origin=origin, direction=direction, meta=Meta(source=source_meta, bbox=MetaBbox(bboxes)))
     print("Saving image...")
     image.save(filepath)
 

mlarray-0.0.39/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 strings 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-0.0.32 → mlarray-0.0.39}/examples/example_open.py

@@ -1,7 +1,7 @@
 import numpy as np
 import os
 from pathlib import Path
-from mlarray import MLArray, Meta, MetaSpatial
+from mlarray import MLArray, Meta, MetaSpatial, MetaBbox
 import json
 
 
@@ -11,7 +11,7 @@ if __name__ == '__main__':
     spacing = np.array((2, 2.5, 4))
     origin = (1, 1, 1)
     direction = [[1, 2, 3], [4, 5, 6], [7, 8, 9]]
-    image_meta = {"tmp1": "This is an image", "tmp2": 5, "tmp3": {"test1": 16.4587, "test2": [1, 2, 3, 4, 5, 6]}}
+    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"
 
@@ -22,7 +22,7 @@ if __name__ == '__main__':
     image = MLArray.open(filepath, shape=array.shape, dtype=array.dtype, mmap='w+')
     print("Saving image...")
     image[...] = array
-    image.meta.copy_from(Meta(original=image_meta, spatial=MetaSpatial(spacing=spacing, origin=origin, direction=direction), bbox=bboxes))
+    image.meta.copy_from(Meta(source=source_meta, spatial=MetaSpatial(spacing=spacing, origin=origin, direction=direction), bbox=MetaBbox(bboxes)))
     image.meta.is_seg = True
     image.close()
 

{mlarray-0.0.32 → mlarray-0.0.39}/examples/example_save_load.py

@@ -1,8 +1,7 @@
 import numpy as np
 import os
 from pathlib import Path
-from mlarray import MLArray, Meta
-from mlarray.meta import MetaOriginal, MetaIsSeg
+from mlarray import MLArray, Meta, MetaBbox
 import json
 
 
@@ -12,7 +11,7 @@ if __name__ == '__main__':
     spacing = np.array((2, 2.5, 4))
     origin = (1, 1, 1)
     direction = [[1, 2, 3], [4, 5, 6], [7, 8, 9]]
-    image_meta = {"tmp1": "This is an image", "tmp2": 5, "tmp3": {"test1": 16.4587, "test2": [1, 2, 3, 4, 5, 6]}}
+    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"
 
@@ -20,7 +19,7 @@ if __name__ == '__main__':
         os.remove(filepath)
 
     print("Initializing image...")
-    image = MLArray(array, spacing=spacing, origin=origin, direction=direction, meta=Meta(original=image_meta, bbox=bboxes, is_seg=True))
+    image = MLArray(array, spacing=spacing, origin=origin, direction=direction, meta=Meta(source=source_meta, bbox=MetaBbox(bboxes), is_seg=True))
     print("Saving image...")
     image.save(filepath)
 

{mlarray-0.0.32 → mlarray-0.0.39}/mlarray/__init__.py

@@ -11,12 +11,13 @@ if TYPE_CHECKING:
         MetaBlosc2,
         MetaExtra,
         MetaHasArray,
-        MetaOriginal,
+        MetaSource,
         MetaImageFormat,
         MetaIsSeg,
         MetaSpatial,
         MetaStatistics,
         MetaVersion,
+        AxisLabel
     )
     from mlarray.utils import is_serializable
     from mlarray.cli import cli_print_header, cli_convert_to_mlarray
@@ -30,12 +31,13 @@ __all__ = [
     "MetaBlosc2",
     "MetaExtra",
     "MetaHasArray",
-    "MetaOriginal",
+    "MetaSource",
     "MetaImageFormat",
     "MetaIsSeg",
     "MetaSpatial",
     "MetaStatistics",
     "MetaVersion",
+    "AxisLabel",
     "is_serializable",
     "cli_print_header",
     "cli_convert_to_mlarray",
@@ -55,12 +57,13 @@ _LAZY_ATTRS = {
     "MetaBlosc2": ("mlarray.meta", "MetaBlosc2"),
     "MetaExtra": ("mlarray.meta", "MetaExtra"),
     "MetaHasArray": ("mlarray.meta", "MetaHasArray"),
-    "MetaOriginal": ("mlarray.meta", "MetaOriginal"),
+    "MetaSource": ("mlarray.meta", "MetaSource"),
     "MetaImageFormat": ("mlarray.meta", "MetaImageFormat"),
     "MetaIsSeg": ("mlarray.meta", "MetaIsSeg"),
     "MetaSpatial": ("mlarray.meta", "MetaSpatial"),
     "MetaStatistics": ("mlarray.meta", "MetaStatistics"),
     "MetaVersion": ("mlarray.meta", "MetaVersion"),
+    "AxisLabel": ("mlarray.meta", "AxisLabel"),
     "is_serializable": ("mlarray.utils", "is_serializable"),
     "cli_print_header": ("mlarray.cli", "cli_print_header"),
     "cli_convert_to_mlarray": ("mlarray.cli", "cli_convert_to_mlarray"),