ngio 0.4.0b1__tar.gz → 0.4.1__tar.gz

{ngio-0.4.0b1 → ngio-0.4.1}/.github/workflows/build_docs.yml

@@ -22,7 +22,7 @@ jobs:
         with:
           fetch-depth: 0
       - name: 🐍 Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.13"
           cache-dependency-path: "pyproject.toml"

{ngio-0.4.0b1 → ngio-0.4.1}/.github/workflows/ci.yml

@@ -40,7 +40,7 @@ jobs:
       - uses: actions/checkout@v5
 
       - name: 🐍 Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
           cache-dependency-path: "pyproject.toml"
@@ -103,7 +103,7 @@ jobs:
           fetch-depth: 0
 
       - name: 🐍 Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.x"
 

{ngio-0.4.0b1 → ngio-0.4.1}/CHANGELOG.md

@@ -1,13 +1,22 @@
 # Changelog
 
-## [v0.4.0a1]
+## [v0.4.1]
+
+### Bug Fixes
+- Fix bug in zoom transform when input axes contain unknown axes (e.g. virtual axes). Now unknown axes are treated as virtual axes and set to 1 in the target shape.
+
+## [v0.4.0]
 
 ### Features
 
-- add support for time in rois and roi-tables
+- Add Iterators for image processing pipelines
+- Add support for time in rois and roi-tables
 - Building masking roi tables expanded to time series data
-- add experimental support for Iterators
-- add support for rescaling on-the-fly masks for masked images
+- Add zoom transformation
+- Add support for rescaling on-the-fly masks for masked images
+- Big refactor of the io pipeline to support iterators and lazy loading
+- Add support for customize dimension separators and compression codecs
+- Simplify AxesHandler and Dataset Classes
 
 ### API Changes
 
@@ -19,15 +28,12 @@
 - Image like objects now have a more clean API to load data. Instead of `get_array` and `set_array`, they now use `get_as_numpy`, and `get_as_dask` for delayed arrays.
 - Also for `get_roi` now specific methods are available. For ROI objects, the `get_roi_as_numpy`, and `get_roi_as_dask` methods.
 - Table ops moved to `ngio.images`
-- Make `label` an explicit attribute in `Roi` objects.
+- int `label` as an explicit attribute in `Roi` objects (previously only in stored in name and relying on convention)
+- Slight changes to `Image` and `Label` objects. Some minor attributes have been renamed for consistency.
 
 ### Table specs
 
-- add `t_second` and `len_t_second` to ROI tables and masking ROI tables
-
-### Bug Fixes
-
-- improve type consistency and remove non-necessary "type: ignore"
+- Add `t_second` and `len_t_second` to ROI tables and masking ROI tables
 
 ## [v0.3.5]
 

{ngio-0.4.0b1 → ngio-0.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.4.0b1
+Version: 0.4.1
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio
@@ -28,7 +28,6 @@ Requires-Dist: pooch
 Requires-Dist: pyarrow
 Requires-Dist: pydantic
 Requires-Dist: requests
-Requires-Dist: xarray
 Requires-Dist: zarr<3
 Provides-Extra: dev
 Requires-Dist: devtools; extra == 'dev'
@@ -83,20 +82,22 @@ Ngio's mission is to streamline working with OME-Zarr files by providing a simpl
 
 ## Key Features
 
-### 📊 Simple Object-Based API
+### 🔍 Simple Object-Based API
 
 - Easily open, explore, and manipulate OME-Zarr images and HCS plates
 - Create and derive new images and labels with minimal boilerplate code
 
-### 🔍 Rich Tables and Regions of Interest (ROI) Support
+### 📊 Rich Tables and Regions of Interest (ROI) Support
 
+- Tight integration with [tabular data](https://biovisioncenter.github.io/ngio/stable/table_specs/overview/)
 - Extract and analyze specific regions of interest
-- Tight integration with [Tabular Data](https://BioVisionCenter.github.io/ngio/stable/table_specs/overview/)
+- Store measurements and other metadata in the OME-Zarr container
+- Extensible & modular allowing users to define custom table schemas and on disk serialization
 
-### 🔄 Scalable Data Processing (Coming Soon)
+### 🔄 Scalable Data Processing
 
-- Powerful iterators for processing data at scale
-- Efficient memory management for large datasets
+- Powerful iterators for building scalable and generalizable image processing pipelines
+- Extensible mapping mechanism for custom parallelization strategies
 
 ## Installation
 
@@ -114,23 +115,22 @@ Currently, ngio only supports OME-Zarr v0.4. Support for version 0.5 and higher
 
 ## Development Status
 
-!!! warning
-    Ngio is under active development and is not yet stable. The API is subject to change, and bugs and breaking changes are expected.
-    We follow [Semantic Versioning](https://semver.org/). Which means for 0.x releases potentially breaking changes can be introduced in minor releases.
+Ngio is under active development and is not yet stable. The API is subject to change, and bugs and breaking changes are expected.
+We follow [Semantic Versioning](https://semver.org/). Which means for 0.x releases potentially breaking changes can be introduced in minor releases.
 
 ### Available Features
 
 - ✅ OME-Zarr metadata handling and validation
 - ✅ Image and label access across pyramid levels
 - ✅ ROI and table support
+- ✅ Image processing iterators
 - ✅ Streaming from remote sources
 - ✅ Documentation and examples
 
 ### Upcoming Features
 
-- Advanced image processing iterators
-- Parallel processing capabilities
-- Support for OME-Zarr v0.5 and Zarr v3
+- Support for OME-Zarr v0.5 and Zarr v3 (via `zarr-python` v3)
+- Enhanced performance optimizations (parallel iterators, optimized io strategies)
 
 ## Contributors
 

{ngio-0.4.0b1 → ngio-0.4.1}/README.md

@@ -16,20 +16,22 @@ Ngio's mission is to streamline working with OME-Zarr files by providing a simpl
 
 ## Key Features
 
-### 📊 Simple Object-Based API
+### 🔍 Simple Object-Based API
 
 - Easily open, explore, and manipulate OME-Zarr images and HCS plates
 - Create and derive new images and labels with minimal boilerplate code
 
-### 🔍 Rich Tables and Regions of Interest (ROI) Support
+### 📊 Rich Tables and Regions of Interest (ROI) Support
 
+- Tight integration with [tabular data](https://biovisioncenter.github.io/ngio/stable/table_specs/overview/)
 - Extract and analyze specific regions of interest
-- Tight integration with [Tabular Data](https://BioVisionCenter.github.io/ngio/stable/table_specs/overview/)
+- Store measurements and other metadata in the OME-Zarr container
+- Extensible & modular allowing users to define custom table schemas and on disk serialization
 
-### 🔄 Scalable Data Processing (Coming Soon)
+### 🔄 Scalable Data Processing
 
-- Powerful iterators for processing data at scale
-- Efficient memory management for large datasets
+- Powerful iterators for building scalable and generalizable image processing pipelines
+- Extensible mapping mechanism for custom parallelization strategies
 
 ## Installation
 
@@ -47,23 +49,22 @@ Currently, ngio only supports OME-Zarr v0.4. Support for version 0.5 and higher
 
 ## Development Status
 
-!!! warning
-    Ngio is under active development and is not yet stable. The API is subject to change, and bugs and breaking changes are expected.
-    We follow [Semantic Versioning](https://semver.org/). Which means for 0.x releases potentially breaking changes can be introduced in minor releases.
+Ngio is under active development and is not yet stable. The API is subject to change, and bugs and breaking changes are expected.
+We follow [Semantic Versioning](https://semver.org/). Which means for 0.x releases potentially breaking changes can be introduced in minor releases.
 
 ### Available Features
 
 - ✅ OME-Zarr metadata handling and validation
 - ✅ Image and label access across pyramid levels
 - ✅ ROI and table support
+- ✅ Image processing iterators
 - ✅ Streaming from remote sources
 - ✅ Documentation and examples
 
 ### Upcoming Features
 
-- Advanced image processing iterators
-- Parallel processing capabilities
-- Support for OME-Zarr v0.5 and Zarr v3
+- Support for OME-Zarr v0.5 and Zarr v3 (via `zarr-python` v3)
+- Enhanced performance optimizations (parallel iterators, optimized io strategies)
 
 ## Contributors
 

{ngio-0.4.0b1 → ngio-0.4.1}/docs/index.md

@@ -8,15 +8,16 @@ Ngio's mission is to streamline working with OME-Zarr files by providing a simpl
 
 ## Key Features
 
-### 📊 Simple Object-Based API
+### 🔍 Simple Object-Based API
 
 - Easily open, explore, and manipulate OME-Zarr images and HCS plates
 - Create and derive new images and labels with minimal boilerplate code
 
-### 🔍 Rich Tables and Regions of Interest (ROI) Support
+### 📊 Rich Tables and Regions of Interest (ROI) Support
 
+- Tight integration with [tabular data](https://biovisioncenter.github.io/ngio/stable/table_specs/overview/)
 - Extract and analyze specific regions of interest
-- Tight integration with [Fractal's table framework](https://BioVisionCenter.github.io/fractal-tasks-core/tables/)
+- Store measurements and other metadata in the OME-Zarr container
 - Extensible & modular allowing users to define custom table schemas and on disk serialization
 
 ### 🔄 Scalable Data Processing

{ngio-0.4.0b1 → ngio-0.4.1}/pyproject.toml

@@ -43,7 +43,7 @@ dependencies = [
     "aiohttp",
     "dask[array]",
     "dask[distributed]",
-    "xarray",
+    # "xarray", still not used
     "ome-zarr-models",
     "pooch",
     "polars",

{ngio-0.4.0b1 → ngio-0.4.1}/src/ngio/io_pipes/_zoom_transform.py

@@ -60,7 +60,12 @@ class BaseZoomTransform:
         target_shape = []
         for shape, ax_name in zip(array_shape, axes_ops.output_axes, strict=True):
             ax_type = self._input_dimensions.axes_handler.get_axis(ax_name)
-            if ax_type is not None and ax_type.axis_type == "channel":
+            if ax_type is None:
+                # Unknown axis can only be a virtual axis
+                # So we set it to 1
+                target_shape.append(1)
+                continue
+            elif ax_type.axis_type == "channel":
                 # Do not scale channel axis
                 target_shape.append(shape)
                 continue

{ngio-0.4.0b1 → ngio-0.4.1}/tests/unit/images/test_images.py

@@ -187,3 +187,36 @@ def test_image_require_can_be_rescaled2(
     # Roi data should match exactly
     assert img1_data.shape == img2_roi_data.shape
     img2.set_roi(roi=roi, patch=img2_roi_data, transforms=[zoom])
+
+
+def test_zoom_virtual_axes(
+    tmp_path: Path,
+):
+    path1 = tmp_path / "image1.zarr"
+    path2 = tmp_path / "image2.zarr"
+    create_empty_ome_zarr(
+        store=path1, shape=(3, 16, 16, 16), axes_names="czyx", xy_pixelsize=1.0
+    )
+    create_empty_ome_zarr(
+        store=path2, shape=(16, 32, 32), axes_names="zyx", xy_pixelsize=0.5
+    )
+    img1 = open_image(path1)
+    img2 = open_image(path2)
+
+    # Also test with transforms
+    zoom = ZoomTransform(
+        input_image=img2,
+        target_image=img1,
+        order="nearest",
+    )
+
+    img1_data = img1.get_as_numpy()
+    img2_data = img2.get_as_numpy(transforms=[zoom], axes_order="czyx")
+    img2.set_array(patch=img2_data, transforms=[zoom], axes_order="czyx")
+    assert img2_data.shape[0] == 1  # Virtual channel axis
+
+    roi = img1.build_image_roi_table().rois()[0]
+    img2_roi_data = img2.get_roi_as_numpy(roi, transforms=[zoom], axes_order="czyx")
+    # Roi data should match exactly except for virtual axis
+    assert img1_data.shape[1:] == img2_roi_data.shape[1:]
+    img2.set_roi(roi=roi, patch=img2_roi_data, transforms=[zoom], axes_order="czyx")