mlarray 0.0.24__tar.gz → 0.0.32__tar.gz

{mlarray-0.0.24 → mlarray-0.0.32}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: mlarray
-Version: 0.0.24
-Summary: A standardized blosc2 image reader and writer for medical images.
+Version: 0.0.32
+Summary: Array format specialized for Machine Learning with Blosc2 backend and standardized metadata.
 Author-email: Karol Gotkowski <karol.gotkowski@dkfz.de>
 License: MIT
 Project-URL: Homepage, https://github.com/MIC-DKFZ/mlarray
@@ -41,7 +41,7 @@ Dynamic: license-file
   <a href="https://pypi.org/project/mlarray/"><img src="https://img.shields.io/pypi/pyversions/mlarray?logo=python&cacheSeconds=300&v" alt="Python Version" align="middle" /></a>
   <a href="https://github.com/MIC-DKFZ/mlarray/actions"><img src="https://img.shields.io/github/actions/workflow/status/MIC-DKFZ/mlarray/workflow.yml?branch=main&logo=github" alt="Tests" align="middle" /></a>
   <a href="https://MIC-DKFZ.github.io/mlarray/"><img src="https://img.shields.io/badge/docs-mlarray-blue?logo=readthedocs&logoColor=white" alt="Docs" align="middle" /></a>
-  <a href="https://github.com/MIC-DKFZ/mlarray/blob/main/LICENSE"><img src="https://img.shields.io/github/license/MIC-DKFZmlarray" alt="License" align="middle" /></a>
+  <a href="https://github.com/MIC-DKFZ/mlarray/blob/main/LICENSE"><img src="https://img.shields.io/github/license/MIC-DKFZ/mlarray" alt="License" align="middle" /></a>
 </p>
 
 **tl;dr:** Working with large medical or scientific images for machine learning? -> Use MLArray.
@@ -88,16 +88,16 @@ from mlarray import MLArray
 import numpy as np
 
 # read-only, partial access (default)
-image = MLArray().open("sample.mla", mmap='r')  
+image = MLArray.open("sample.mla", mmap='r')  
 crop = image[10:20, 50:60]  # Read crop
 
 # read/write, partial access
-image = MLArray().open("sample.mla", mmap='r+')  
+image = MLArray.open("sample.mla", mmap='r+')  
 image[10:20, 50:60] *= 5  # Modify crop in memory and disk
 
 # read/write, partial access, create/overwrite
 array = np.random.random((128, 256, 256))
-image = MLArray().open("sample.mla", shape=array.shape, dtype=array.dtype, mmap='w+')  
+image = MLArray.open("sample.mla", shape=array.shape, dtype=array.dtype, mmap='w+')  
 image[...] = array  # Modify image in memory and disk
 ```
 
@@ -113,20 +113,20 @@ image = MLArray(
     spacing=(1.0, 1.0, 1.5),
     origin=(10.0, 10.0, 30.0),
     direction=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
-    meta={"patient_id": "123", "modality": "CT"},  # Any image metadata (for example raw DICOM metadata)
+    meta={"patient_id": "123", "modality": "CT"},  # Any metadata from the original image source (for example raw DICOM metadata)
 )
 
 print(image.spacing)  # [1.0, 1.0, 1.5]
 print(image.origin)  # [10.0, 10.0, 30.0]
-print(image.meta.image)  # {"patient_id": "123", "modality": "CT"}
+print(image.meta.original)  # {"patient_id": "123", "modality": "CT"}
 
 image.spacing[1] = 5.3
-image.meta.image["study_id"] = "study-001"
+image.meta.original["study_id"] = "study-001"
 image.save("with-metadata.mla")
 
 # Open memory-mapped
-image = MLArray().open("with-metadata.mla", mmap='r+')  
-image.meta.image["study_id"] = "new-study"  # Modify metadata
+image = MLArray.open("with-metadata.mla", mmap='r+')  
+image.meta.original["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(image={"patient_id": "123", "modality": "CT"}, is_seg=True),  # Add metadata in a pre-defined format
+    meta=Meta(original={"patient_id": "123", "modality": "CT"}, is_seg=True),  # Add metadata in a pre-defined format
 )
 
-print(image.meta.image)  # {"patient_id": "123", "modality": "CT"}
+print(image.meta.original)  # {"patient_id": "123", "modality": "CT"}
 print(image.meta.is_seg)  # True
 
-image.meta.image["study_id"] = "study-001"
+image.meta.original["study_id"] = "study-001"
 image.meta.is_seg = False
 image.save("with-metadata.mla")
 ```

{mlarray-0.0.24 → mlarray-0.0.32}/README.md

@@ -7,7 +7,7 @@
   <a href="https://pypi.org/project/mlarray/"><img src="https://img.shields.io/pypi/pyversions/mlarray?logo=python&cacheSeconds=300&v" alt="Python Version" align="middle" /></a>
   <a href="https://github.com/MIC-DKFZ/mlarray/actions"><img src="https://img.shields.io/github/actions/workflow/status/MIC-DKFZ/mlarray/workflow.yml?branch=main&logo=github" alt="Tests" align="middle" /></a>
   <a href="https://MIC-DKFZ.github.io/mlarray/"><img src="https://img.shields.io/badge/docs-mlarray-blue?logo=readthedocs&logoColor=white" alt="Docs" align="middle" /></a>
-  <a href="https://github.com/MIC-DKFZ/mlarray/blob/main/LICENSE"><img src="https://img.shields.io/github/license/MIC-DKFZmlarray" alt="License" align="middle" /></a>
+  <a href="https://github.com/MIC-DKFZ/mlarray/blob/main/LICENSE"><img src="https://img.shields.io/github/license/MIC-DKFZ/mlarray" alt="License" align="middle" /></a>
 </p>
 
 **tl;dr:** Working with large medical or scientific images for machine learning? -> Use MLArray.
@@ -54,16 +54,16 @@ from mlarray import MLArray
 import numpy as np
 
 # read-only, partial access (default)
-image = MLArray().open("sample.mla", mmap='r')  
+image = MLArray.open("sample.mla", mmap='r')  
 crop = image[10:20, 50:60]  # Read crop
 
 # read/write, partial access
-image = MLArray().open("sample.mla", mmap='r+')  
+image = MLArray.open("sample.mla", mmap='r+')  
 image[10:20, 50:60] *= 5  # Modify crop in memory and disk
 
 # read/write, partial access, create/overwrite
 array = np.random.random((128, 256, 256))
-image = MLArray().open("sample.mla", shape=array.shape, dtype=array.dtype, mmap='w+')  
+image = MLArray.open("sample.mla", shape=array.shape, dtype=array.dtype, mmap='w+')  
 image[...] = array  # Modify image in memory and disk
 ```
 
@@ -79,20 +79,20 @@ image = MLArray(
     spacing=(1.0, 1.0, 1.5),
     origin=(10.0, 10.0, 30.0),
     direction=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
-    meta={"patient_id": "123", "modality": "CT"},  # Any image metadata (for example raw DICOM metadata)
+    meta={"patient_id": "123", "modality": "CT"},  # Any metadata from the original image source (for example raw DICOM metadata)
 )
 
 print(image.spacing)  # [1.0, 1.0, 1.5]
 print(image.origin)  # [10.0, 10.0, 30.0]
-print(image.meta.image)  # {"patient_id": "123", "modality": "CT"}
+print(image.meta.original)  # {"patient_id": "123", "modality": "CT"}
 
 image.spacing[1] = 5.3
-image.meta.image["study_id"] = "study-001"
+image.meta.original["study_id"] = "study-001"
 image.save("with-metadata.mla")
 
 # Open memory-mapped
-image = MLArray().open("with-metadata.mla", mmap='r+')  
-image.meta.image["study_id"] = "new-study"  # Modify metadata
+image = MLArray.open("with-metadata.mla", mmap='r+')  
+image.meta.original["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(image={"patient_id": "123", "modality": "CT"}, is_seg=True),  # Add metadata in a pre-defined format
+    meta=Meta(original={"patient_id": "123", "modality": "CT"}, is_seg=True),  # Add metadata in a pre-defined format
 )
 
-print(image.meta.image)  # {"patient_id": "123", "modality": "CT"}
+print(image.meta.original)  # {"patient_id": "123", "modality": "CT"}
 print(image.meta.is_seg)  # True
 
-image.meta.image["study_id"] = "study-001"
+image.meta.original["study_id"] = "study-001"
 image.meta.is_seg = False
 image.save("with-metadata.mla")
 ```

mlarray-0.0.32/docs/api.md

@@ -0,0 +1,33 @@
+# API Reference
+
+## MLArray Module
+
+::: mlarray.mlarray.MLArray
+
+## Metadata Module
+
+::: mlarray.meta.BaseMeta
+
+::: mlarray.meta.SingleKeyBaseMeta
+
+::: mlarray.meta.Meta
+
+::: mlarray.meta.MetaOriginal
+
+::: mlarray.meta.MetaExtra
+
+::: mlarray.meta.MetaSpatial
+
+::: mlarray.meta.MetaStatistics
+
+::: mlarray.meta.MetaBbox
+
+::: mlarray.meta.MetaIsSeg
+
+::: mlarray.meta.MetaBlosc2
+
+::: mlarray.meta.MetaHasArray
+
+::: mlarray.meta.MetaImageFormat
+
+::: mlarray.meta.MetaVersion

{mlarray-0.0.24 → mlarray-0.0.32}/docs/optimization.md

@@ -96,7 +96,7 @@ For large files, you typically want **mmap reads** so random patches don’t req
 from mlarray import MLArray
 
 # read-only mmap: fast random access without loading the full volume
-image = MLArray().open("patch-non-iso.mla", mmap='r')
+image = MLArray.open("patch-non-iso.mla", mmap='r')
 
 patch = image[10:20, 50:60]  # Read a crop/patch (partial read)
 ```
@@ -119,7 +119,7 @@ You can modify regions in-place with `mmap='r+'`. This is useful for workflows l
 ```python
 from mlarray import MLArray
 
-image = MLArray().open("patch-non-iso.mla", mmap='r+')
+image = MLArray.open("patch-non-iso.mla", mmap='r+')
 image[10:20, 50:60] *= 5  # Modify crop in memory and on disk
 image.close()
 ```
@@ -137,7 +137,7 @@ from mlarray import MLArray
 shape = (128, 256, 256)
 dtype = np.float32
 
-image = MLArray().open(
+image = MLArray.open(
     "streamed-write.mla",
     shape=shape,
     dtype=dtype,

{mlarray-0.0.24 → mlarray-0.0.32}/docs/schema.md

@@ -11,6 +11,10 @@ The schema is designed around a few core goals:
 
 All fields in the schema are **JSON-serializable** unless otherwise noted. Fields marked as `Optional[...]` may be omitted if unknown or not applicable.
 
+### 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.
+
 ---
 
 ## Meta
@@ -19,16 +23,20 @@ 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** (`image`, `extra`) to support arbitrary metadata and long-term extensibility.
+`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.
 
 ---
 
-### image
+### original
+
+* **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).
 
-* **Description:** Arbitrary JSON-serializable dictionary for image-level metadata.
-  Stores information from medical image sources such as DICOM, NIfTI, NRRD,
-  or other medical imaging formats.
-* **Dataclass:** None (plain dict).
+| field | type                  | description                                  |
+| ----- | --------------------- | -------------------------------------------- |
+| data  | Dict[str, Any]        | JSON-serializable metadata from the source. |
 
 ---
 
@@ -37,7 +45,11 @@ Top-level metadata container.
 * **Description:** Flexible container for arbitrary, JSON-serializable metadata
   when no schema exists. Intended for experimental or application-specific
   fields that are not part of the standard.
-* **Dataclass:** None (plain dict).
+* **Dataclass:** `MetaExtra` (single-key wrapper).
+
+| field | type           | description                                  |
+| ----- | -------------- | -------------------------------------------- |
+| data  | Dict[str, Any]  | JSON-serializable metadata for extra fields. |
 
 ---
 
@@ -53,18 +65,11 @@ This section stores the information needed to interpret the array in physical sp
 | 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`. |
+| 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.                                |
 
 ---
 
-### is_seg
-
-* **Description:** Whether the image is a segmentation mask.
-* **Dataclass:** None (boolean).
-
----
-
 ### stats
 
 * **Description:** Summary statistics for the image.
@@ -84,13 +89,15 @@ This section stores precomputed global statistics for the array, which can be us
 | percentile_mean   | Optional[float] | Mean within a selected percentile range.               |
 | percentile_median | Optional[float] | Median within a selected percentile range.             |
 | percentile_std    | Optional[float] | Standard deviation within a selected percentile range. |
+| percentile_min_key    | Optional[float] | Minimum percentile key used to determine percentile_min (for example 0.05).            |
+| percentile_max_key    | Optional[float] | Maximum percentile key used to determine percentile_max (for example 0.95).            |
 
 ---
 
 ### bbox
 
 * **Description:** Bounding boxes for objects/regions in the image.
-* **Dataclass:** `MetaBbox`.
+* **Dataclass:** `MetaBbox` (single-key wrapper).
 * **Structure:** List of bboxes, each bbox is a list with length equal to image `ndims`,
   and each entry is `[min, max]`.
 
@@ -102,18 +109,14 @@ Bounding boxes are stored in a normalized, axis-aligned representation that work
 
 ---
 
-### _has_array
-
-* **Description:** Whether this metadata instance represents an on-disk array.
-* **Dataclass:** None (boolean).
-
----
+### is_seg
 
-### _image_meta_format
+* **Description:** Whether the image is a segmentation mask.
+* **Dataclass:** `MetaIsSeg` (single-key wrapper).
 
-* **Description:** Source format identifier for the `image` metadata (e.g., "dicom",
-  "nifti", "nrrd"). This is advisory and application-defined.
-* **Dataclass:** None (string).
+| field  | type           | description                                     |
+| ------ | -------------- | ----------------------------------------------- |
+| is_seg | Optional[bool] | True/False when known, None when unknown.       |
 
 ---
 
@@ -132,7 +135,34 @@ This section records how the array was laid out on disk (chunking, blocking, pat
 
 ---
 
+### _has_array
+
+* **Description:** Whether this metadata instance represents an on-disk array.
+* **Dataclass:** `MetaHasArray` (single-key wrapper).
+
+| field     | type | description                           |
+| --------- | ---- | ------------------------------------- |
+| has_array | bool | True when an array payload is stored. |
+
+---
+
+### _image_meta_format
+
+* **Description:** Source format identifier for the `image` metadata (e.g., "dicom",
+  "nifti", "nrrd"). This is advisory and application-defined.
+* **Dataclass:** `MetaImageFormat` (single-key wrapper).
+
+| field             | type           | description                                   |
+| ----------------- | -------------- | --------------------------------------------- |
+| image_meta_format | Optional[str]  | Identifier for the original metadata format. |
+
+---
+
 ### _mlarray_version
 
 * **Description:** MLArray version string used to write the file.
-* **Dataclass:** None (string).
+* **Dataclass:** `MetaVersion` (single-key wrapper).
+
+| field           | type           | description                          |
+| --------------- | -------------- | ------------------------------------ |
+| mlarray_version | Optional[str]  | Version string for the writer.       |

{mlarray-0.0.24 → mlarray-0.0.32}/docs/usage.md

@@ -34,16 +34,16 @@ from mlarray import MLArray
 import numpy as np
 
 # read-only, partial access (default)
-image = MLArray().open("sample.mla", mmap='r')  
+image = MLArray.open("sample.mla", mmap='r')  
 crop = image[10:20, 50:60]  # Read crop
 
 # read/write, partial access
-image = MLArray().open("sample.mla", mmap='r+')  
+image = MLArray.open("sample.mla", mmap='r+')  
 image[10:20, 50:60] *= 5  # Modify crop in memory and disk
 
 # read/write, partial access, create/overwrite
 array = np.random.random((128, 256, 256))
-image = MLArray().open("sample.mla", shape=array.shape, dtype=array.dtype, mmap='w+')  
+image = MLArray.open("sample.mla", shape=array.shape, dtype=array.dtype, mmap='w+')  
 image[...] = array  # Modify image in memory and disk
 ```
 
@@ -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 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 original image source via `meta=...` (e.g., raw DICOM fields, acquisition parameters, dataset identifiers).
 
 ```python
 import numpy as np
@@ -63,20 +63,20 @@ image = MLArray(
     spacing=(1.0, 1.0, 1.5),
     origin=(10.0, 10.0, 30.0),
     direction=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
-    meta={"patient_id": "123", "modality": "CT"},  # Any image metadata (for example raw DICOM metadata)
+    meta={"patient_id": "123", "modality": "CT"},  # Any metadata from the original image source (for example raw DICOM metadata)
 )
 
 print(image.spacing)  # [1.0, 1.0, 1.5]
 print(image.origin)  # [10.0, 10.0, 30.0]
-print(image.meta.image)  # {"patient_id": "123", "modality": "CT"}
+print(image.meta.original)  # {"patient_id": "123", "modality": "CT"}
 
 image.spacing[1] = 5.3
-image.meta.image["study_id"] = "study-001"
+image.meta.original["study_id"] = "study-001"
 image.save("with-metadata.mla")
 
 # Open memory-mapped
-image = MLArray().open("with-metadata.mla", mmap='r+')  
-image.meta.image["study_id"] = "new-study"  # Modify metadata
+image = MLArray.open("with-metadata.mla", mmap='r+')  
+image.meta.original["study_id"] = "new-study"  # Modify metadata
 image.close()  # Close and save metadata, only necessary to save modified metadata
 ```
 
@@ -115,13 +115,13 @@ from mlarray import MLArray, Meta
 array = np.random.random((64, 128, 128))
 image = MLArray(
     array,
-    meta=Meta(image={"patient_id": "123", "modality": "CT"}, is_seg=True),  # Add metadata in a pre-defined format
+    meta=Meta(original={"patient_id": "123", "modality": "CT"}, is_seg=True),  # Add metadata in a pre-defined format
 )
 
-print(image.meta.image)  # {"patient_id": "123", "modality": "CT"}
+print(image.meta.original)  # {"patient_id": "123", "modality": "CT"}
 print(image.meta.is_seg)  # True
 
-image.meta.image["study_id"] = "study-001"
+image.meta.original["study_id"] = "study-001"
 image.meta.is_seg = False
 image.save("with-metadata.mla")
 ```

{mlarray-0.0.24 → mlarray-0.0.32}/examples/example_channel.py

@@ -20,13 +20,13 @@ if __name__ == '__main__':
         os.remove(filepath)
 
     print("Initializing image...")
-    image = MLArray(array, spacing=spacing, origin=origin, direction=direction, channel_axis=channel_axis, meta=Meta(image=image_meta, bbox=bboxes))
+    image = MLArray(array, spacing=spacing, origin=origin, direction=direction, channel_axis=channel_axis, meta=Meta(original=image_meta, bbox=bboxes))
     print("Saving image...")
     image.save(filepath)
 
     print("Loading image...")
     image = MLArray(filepath)
-    print(json.dumps(image.meta.to_dict(), indent=2, sort_keys=True))
+    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])
 

{mlarray-0.0.24 → mlarray-0.0.32}/examples/example_metadata_only.py

@@ -19,13 +19,13 @@ if __name__ == '__main__':
         os.remove(filepath)
 
     print("Initializing image...")
-    image = MLArray(spacing=spacing, origin=origin, direction=direction, meta=Meta(image=image_meta, bbox=bboxes))
+    image = MLArray(spacing=spacing, origin=origin, direction=direction, meta=Meta(original=image_meta, bbox=bboxes))
     print("Saving image...")
     image.save(filepath)
 
     print("Loading image...")
     image = MLArray(filepath)
-    print(json.dumps(image.meta.to_dict(), indent=2, sort_keys=True))
+    print(json.dumps(image.meta.to_mapping(), indent=2, sort_keys=True))
 
     if Path(filepath).is_file():
         os.remove(filepath)

{mlarray-0.0.24 → mlarray-0.0.32}/examples/example_open.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, MetaSpatial
 import json
 
 
@@ -19,17 +19,16 @@ if __name__ == '__main__':
         os.remove(filepath)
 
     print("Initializing image...")
-    image = MLArray(spacing=spacing, origin=origin, direction=direction, meta=Meta(image=image_meta, bbox=bboxes))
-    image.open(filepath, shape=array.shape, dtype=array.dtype, mmap='w+')
+    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.is_seg = True
     image.close()
 
     print("Loading image...")
-    image = MLArray()
-    image.open(filepath)
-    print(json.dumps(image.meta.to_dict(), indent=2, sort_keys=True))
+    image = MLArray.open(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])
 

{mlarray-0.0.24 → mlarray-0.0.32}/examples/example_save_load.py

@@ -2,6 +2,7 @@ import numpy as np
 import os
 from pathlib import Path
 from mlarray import MLArray, Meta
+from mlarray.meta import MetaOriginal, MetaIsSeg
 import json
 
 
@@ -19,13 +20,14 @@ if __name__ == '__main__':
         os.remove(filepath)
 
     print("Initializing image...")
-    image = MLArray(array, spacing=spacing, origin=origin, direction=direction, meta=Meta(image=image_meta, bbox=bboxes))
+    image = MLArray(array, spacing=spacing, origin=origin, direction=direction, meta=Meta(original=image_meta, bbox=bboxes, is_seg=True))
     print("Saving image...")
     image.save(filepath)
 
     print("Loading image...")
     image = MLArray(filepath)
-    print(json.dumps(image.meta.to_dict(), indent=2, sort_keys=True))
+    image = MLArray.load(filepath)  # Just testing both load methods
+    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])
 

mlarray-0.0.32/mlarray/__init__.py

@@ -0,0 +1,79 @@
+"""A standardized blosc2 image reader and writer for medical images."""
+
+from importlib import metadata as _metadata
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from mlarray.mlarray import MLArray, MLARRAY_DEFAULT_PATCH_SIZE
+    from mlarray.meta import (
+        Meta,
+        MetaBbox,
+        MetaBlosc2,
+        MetaExtra,
+        MetaHasArray,
+        MetaOriginal,
+        MetaImageFormat,
+        MetaIsSeg,
+        MetaSpatial,
+        MetaStatistics,
+        MetaVersion,
+    )
+    from mlarray.utils import is_serializable
+    from mlarray.cli import cli_print_header, cli_convert_to_mlarray
+
+__all__ = [
+    "__version__",
+    "MLArray",
+    "MLARRAY_DEFAULT_PATCH_SIZE",
+    "Meta",
+    "MetaBbox",
+    "MetaBlosc2",
+    "MetaExtra",
+    "MetaHasArray",
+    "MetaOriginal",
+    "MetaImageFormat",
+    "MetaIsSeg",
+    "MetaSpatial",
+    "MetaStatistics",
+    "MetaVersion",
+    "is_serializable",
+    "cli_print_header",
+    "cli_convert_to_mlarray",
+]
+
+try:
+    __version__ = _metadata.version(__name__)
+except _metadata.PackageNotFoundError:  # pragma: no cover - during editable installs pre-build
+    __version__ = "0.0.0"
+
+
+_LAZY_ATTRS = {
+    "MLArray": ("mlarray.mlarray", "MLArray"),
+    "MLARRAY_DEFAULT_PATCH_SIZE": ("mlarray.mlarray", "MLARRAY_DEFAULT_PATCH_SIZE"),
+    "Meta": ("mlarray.meta", "Meta"),
+    "MetaBbox": ("mlarray.meta", "MetaBbox"),
+    "MetaBlosc2": ("mlarray.meta", "MetaBlosc2"),
+    "MetaExtra": ("mlarray.meta", "MetaExtra"),
+    "MetaHasArray": ("mlarray.meta", "MetaHasArray"),
+    "MetaOriginal": ("mlarray.meta", "MetaOriginal"),
+    "MetaImageFormat": ("mlarray.meta", "MetaImageFormat"),
+    "MetaIsSeg": ("mlarray.meta", "MetaIsSeg"),
+    "MetaSpatial": ("mlarray.meta", "MetaSpatial"),
+    "MetaStatistics": ("mlarray.meta", "MetaStatistics"),
+    "MetaVersion": ("mlarray.meta", "MetaVersion"),
+    "is_serializable": ("mlarray.utils", "is_serializable"),
+    "cli_print_header": ("mlarray.cli", "cli_print_header"),
+    "cli_convert_to_mlarray": ("mlarray.cli", "cli_convert_to_mlarray"),
+}
+
+
+def __getattr__(name: str):
+    if name in _LAZY_ATTRS:
+        module_name, attr_name = _LAZY_ATTRS[name]
+        module = __import__(module_name, fromlist=[attr_name])
+        return getattr(module, attr_name)
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+
+def __dir__():
+    return sorted(__all__)

{mlarray-0.0.24 → mlarray-0.0.32}/mlarray/cli.py

@@ -20,7 +20,7 @@ def print_header(filepath: Union[str, Path]) -> None:
     if meta is None:
         print("null")
         return
-    print(json.dumps(meta.to_dict(include_none=True), indent=2, sort_keys=True))
+    print(json.dumps(meta.to_plain(include_none=True), indent=2, sort_keys=True))
 
 
 def convert_to_mlarray(load_filepath: Union[str, Path], save_filepath: Union[str, Path]):