ngio 0.2.0a1__py3-none-any.whl → 0.2.0a2__py3-none-any.whl

ngio/common/_pyramid.py

@@ -203,6 +203,7 @@ def init_empty_pyramid(
             dtype=dtype,
             chunks=chunks,
             dimension_separator="/",
+            overwrite=True,
         )
 
         # Todo redo this with when a proper build of pyramid is implemented

ngio/images/image.py

@@ -236,6 +236,8 @@ class ImagesContainer:
         ref_path: str | None = None,
         shape: Collection[int] | None = None,
         chunks: Collection[int] | None = None,
+        xy_scaling_factor: float = 2.0,
+        z_scaling_factor: float = 1.0,
         overwrite: bool = False,
     ) -> "ImagesContainer":
         """Create an OME-Zarr image from a numpy array."""
@@ -245,6 +247,8 @@ class ImagesContainer:
             ref_path=ref_path,
             shape=shape,
             chunks=chunks,
+            xy_scaling_factor=xy_scaling_factor,
+            z_scaling_factor=z_scaling_factor,
             overwrite=overwrite,
         )
 
@@ -314,6 +318,8 @@ def derive_image_container(
     ref_path: str | None = None,
     shape: Collection[int] | None = None,
     chunks: Collection[int] | None = None,
+    xy_scaling_factor: float = 2.0,
+    z_scaling_factor: float = 1.0,
     overwrite: bool = False,
 ) -> ImagesContainer:
     """Create an OME-Zarr image from a numpy array."""
@@ -347,8 +353,8 @@ def derive_image_container(
         z_spacing=ref_image.pixel_size.z,
         time_spacing=ref_image.pixel_size.t,
         levels=ref_meta.levels,
-        xy_scaling_factor=2.0,  # will need to be fixed
-        z_scaling_factor=1.0,  # will need to be fixed
+        xy_scaling_factor=xy_scaling_factor,
+        z_scaling_factor=z_scaling_factor,
         time_unit=ref_image.pixel_size.time_unit,
         space_unit=ref_image.pixel_size.space_unit,
         axes_names=ref_image.dataset.axes_mapper.on_disk_axes_names,

ngio/images/label.py

@@ -1,15 +1,21 @@
 """A module for handling label images in OME-NGFF files."""
 
+from collections.abc import Collection
 from typing import Literal
 
 from ngio.images.abstract_image import AbstractImage, consolidate_image
+from ngio.images.create import _create_empty_label
+from ngio.images.image import Image
 from ngio.ome_zarr_meta import (
     ImplementedLabelMetaHandlers,
     LabelMetaHandler,
     NgioLabelMeta,
 )
+from ngio.ome_zarr_meta.ngio_specs import SpaceUnits, TimeUnits
 from ngio.utils import (
     NgioValidationError,
+    NgioValueError,
+    StoreOrGroup,
     ZarrGroupHandler,
 )
 
@@ -88,9 +94,143 @@ class LabelsContainer:
     def derive(
         self,
         name: str,
-        reference_image: AbstractImage,
+        ref_image: Image,
+        shape: Collection[int] | None = None,
+        chunks: Collection[int] | None = None,
+        dtype: str = "uint16",
+        xy_scaling_factor=2.0,
+        z_scaling_factor=1.0,
         overwrite: bool = False,
-        **kwargs,
-    ) -> Label:
-        """Derive a label from an image."""
-        raise NotImplementedError
+    ) -> None:
+        """Add a label to the group."""
+        existing_labels = self.list()
+        if name in existing_labels and not overwrite:
+            raise NgioValueError(
+                f"Table '{name}' already exists in the group. "
+                "Use overwrite=True to replace it."
+            )
+
+        label_group = self._group_handler.get_group(name, create_mode=True)
+
+        _derive_label(
+            ref_image=ref_image,
+            store=label_group,
+            shape=shape,
+            chunks=chunks,
+            dtype=dtype,
+            xy_scaling_factor=xy_scaling_factor,
+            z_scaling_factor=z_scaling_factor,
+            overwrite=overwrite,
+        )
+
+        if name not in existing_labels:
+            existing_labels.append(name)
+            self._group_handler.write_attrs({"labels": existing_labels})
+
+    def new(
+        self,
+        name: str,
+        shape: Collection[int],
+        xy_pixelsize: float,
+        z_spacing: float = 1.0,
+        time_spacing: float = 1.0,
+        levels: "int | list[str]" = 5,
+        xy_scaling_factor: float = 2.0,
+        z_scaling_factor: float = 1.0,
+        space_unit: SpaceUnits | str | None = None,
+        time_unit: TimeUnits | str | None = None,
+        axes_names: Collection[str] | None = None,
+        chunks: Collection[int] | None = None,
+        dtype: str = "uint16",
+        overwrite: bool = False,
+        version: str = "0.4",
+    ) -> None:
+        """Add a label to the group."""
+        existing_labels = self.list()
+        if name in existing_labels and not overwrite:
+            raise NgioValueError(
+                f"Table '{name}' already exists in the group. "
+                "Use overwrite=True to replace it."
+            )
+
+        label_group = self._group_handler.get_group(name, create_mode=True)
+
+        _create_empty_label(
+            store=label_group,
+            shape=shape,
+            xy_pixelsize=xy_pixelsize,
+            z_spacing=z_spacing,
+            time_spacing=time_spacing,
+            levels=levels,
+            xy_scaling_factor=xy_scaling_factor,
+            z_scaling_factor=z_scaling_factor,
+            space_unit=space_unit,
+            time_unit=time_unit,
+            axes_names=axes_names,
+            chunks=chunks,
+            dtype=dtype,
+            overwrite=overwrite,
+            version=version,
+        )
+
+        if name not in existing_labels:
+            existing_labels.append(name)
+            self._group_handler.write_attrs({"labels": existing_labels})
+
+
+def _derive_label(
+    ref_image: Image,
+    store: StoreOrGroup,
+    shape: Collection[int] | None = None,
+    chunks: Collection[int] | None = None,
+    dtype: str = "uint16",
+    xy_scaling_factor=2.0,
+    z_scaling_factor=1.0,
+    overwrite: bool = False,
+) -> None:
+    """Create an OME-Zarr image from a numpy array."""
+    ref_meta = ref_image.meta
+    # remove channls if present
+    shape_ref = ref_image.shape
+    chunks_ref = ref_image.chunks
+    axes_names_ref = ref_image.dataset.axes_mapper.on_disk_axes_names
+    c_axis = ref_image.dataset.axes_mapper.get_index("c")
+    if c_axis is not None:
+        shape_ref = shape_ref[:c_axis] + shape_ref[c_axis + 1 :]
+        chunks_ref = chunks_ref[:c_axis] + chunks_ref[c_axis + 1 :]
+        axes_names_ref = axes_names_ref[:c_axis] + axes_names_ref[c_axis + 1 :]
+
+    if shape is None:
+        shape = shape_ref
+
+    if chunks is None:
+        chunks = chunks_ref
+
+    if len(shape) != len(shape_ref):
+        raise NgioValidationError(
+            "The shape of the new image does not match the reference image."
+        )
+
+    if len(chunks) != len(chunks_ref):
+        raise NgioValidationError(
+            "The chunks of the new image does not match the reference image."
+        )
+
+    _ = _create_empty_label(
+        store=store,
+        shape=shape,
+        xy_pixelsize=ref_image.pixel_size.x,
+        z_spacing=ref_image.pixel_size.z,
+        time_spacing=ref_image.pixel_size.t,
+        levels=ref_meta.levels,
+        xy_scaling_factor=xy_scaling_factor,
+        z_scaling_factor=z_scaling_factor,
+        time_unit=ref_image.pixel_size.time_unit,
+        space_unit=ref_image.pixel_size.space_unit,
+        axes_names=axes_names_ref,
+        chunks=chunks,
+        dtype=dtype,
+        overwrite=overwrite,
+        version=ref_meta.version,
+    )
+    return None

ngio/images/omezarr_container.py

@@ -175,6 +175,8 @@ class OmeZarrContainer:
         ref_path: str | None = None,
         shape: Collection[int] | None = None,
         chunks: Collection[int] | None = None,
+        xy_scaling_factor: float = 2.0,
+        z_scaling_factor: float = 1.0,
         copy_tables: bool = False,
         copy_labels: bool = False,
         overwrite: bool = False,
@@ -191,6 +193,8 @@ class OmeZarrContainer:
             ref_path=ref_path,
             shape=shape,
             chunks=chunks,
+            xy_scaling_factor=xy_scaling_factor,
+            z_scaling_factor=z_scaling_factor,
             overwrite=overwrite,
         )
         return OmeZarrContainer(
@@ -281,15 +285,34 @@ class OmeZarrContainer:
             raise NgioValidationError("No labels found in the image.")
         return self._labels_container.get(name=name, path=path)
 
-    def derive_label(self, name: str, **kwargs) -> Label:
+    def derive_label(
+        self,
+        name: str,
+        ref_image: Image | None = None,
+        shape: Collection[int] | None = None,
+        chunks: Collection[int] | None = None,
+        dtype: str = "uint16",
+        xy_scaling_factor=2.0,
+        z_scaling_factor=1.0,
+        overwrite: bool = False,
+    ) -> Label:
         """Derive a label from an image."""
         if self._labels_container is None:
             raise NgioValidationError("No labels found in the image.")
 
-        ref_image = self.get_image()
-        return self._labels_container.derive(
-            name=name, reference_image=ref_image, **kwargs
+        if ref_image is None:
+            ref_image = self.get_image()
+        self._labels_container.derive(
+            name=name,
+            ref_image=ref_image,
+            shape=shape,
+            chunks=chunks,
+            dtype=dtype,
+            xy_scaling_factor=xy_scaling_factor,
+            z_scaling_factor=z_scaling_factor,
+            overwrite=overwrite,
         )
+        return self.get_label(name, path="0")
 
 
 def open_omezarr_container(

ngio/utils/_datasets.py

@@ -28,7 +28,7 @@ def list_ome_zarr_datasets() -> list[str]:
 def download_ome_zarr_dataset(
     dataset_name: str,
     download_dir: str = "data",
-) -> str:
+) -> Path:
     """Download an OME-Zarr dataset.
 
     To list available datasets, use `list_ome_zarr_datasets`.

{ngio-0.2.0a1.dist-info → ngio-0.2.0a2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.2.0a1
+Version: 0.2.0a2
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/lorenzocerrone/ngio
 Project-URL: repository, https://github.com/lorenzocerrone/ngio

{ngio-0.2.0a1.dist-info → ngio-0.2.0a2.dist-info}/RECORD

@@ -4,7 +4,7 @@ ngio/common/_array_pipe.py,sha256=DyYjGTy2L74zBtD6S2jGPsFG4zj7KaY39TwPGWsSf8g,48
 ngio/common/_axes_transforms.py,sha256=Dmrta3ZT1IgZAWomdUeTZVje8TBF_oU3RMKBv1r4EvM,1989
 ngio/common/_common_types.py,sha256=OkAYNSNjZkixL1MI-HPBVuXamheFBr862uJ4PvTxmhk,129
 ngio/common/_dimensions.py,sha256=t3X2wzqCl3-UeocqIpQgKRdcWYagijtKsaHTQz5bfT4,3680
-ngio/common/_pyramid.py,sha256=rFFIrOtgcDLsUvUX5WMQkQx9ce2MBqyk-hcXHXxxTqY,7203
+ngio/common/_pyramid.py,sha256=aBxRBjW7y6D-Rj8f9B3dtqIErxk2eq20O58C33NBU0Q,7231
 ngio/common/_roi.py,sha256=q7HZg2lPbnJ6flKRgK9e4nfOIgkGpDjDcdz-tE8F0Ys,2869
 ngio/common/_slicer.py,sha256=Qk7XXmd4W9T3w55LvFTjAyloyIcS9tt9NTXiDZNwOx8,3076
 ngio/common/_zoom.py,sha256=z2UjgotoDw7pvpeZVrxiGx4PXx65nk1vwQH3osTFACI,5422
@@ -12,9 +12,9 @@ ngio/hcs/__init__.py,sha256=ugnRl22hM9dic5XRsqQr-HCyyyY1qXTqYOAOzyOZm4M,1624
 ngio/images/__init__.py,sha256=aijqG14eyqVgHtnlcKVNx37FRfT6QvKt8V6bwBpX_r8,526
 ngio/images/abstract_image.py,sha256=n4akBHWQul7vmo4OlYtKWZwpsYl8IYg82AThJrvDrxc,7113
 ngio/images/create.py,sha256=DMyiNVmj3uaJmJQqsL9ftzZNvXxeqgZ0-Pjo63WqWoM,8991
-ngio/images/image.py,sha256=23rrwR2rUN9WA_YFoPrlcsSdETQlW6dwNsOeGxu1qRo,12363
-ngio/images/label.py,sha256=fhxMC_pL_BbyE5IyS_86mMuzRWzKckSwUX8_oXHQ3Qk,2871
-ngio/images/omezarr_container.py,sha256=QEcPPX4-dgAY4oEWJAq3KhtMN5yo4R78_ulc9Zvjeis,18439
+ngio/images/image.py,sha256=QiSdOaZSLWtAweecMj69hXXAdVnPIkO3Qfjvs8QII3o,12586
+ngio/images/label.py,sha256=wzpIsIFuKdTOcTU57PHpIf_U4Fh6TwRhM-tLpEt4GbI,7520
+ngio/images/omezarr_container.py,sha256=E0uDyBM1vZ8kCwXI6tIyPDl7QEdi5e91hI5AIWf8kFY,19161
 ngio/ome_zarr_meta/__init__.py,sha256=9kYdyuCc3ouQCLDyUCB_lCVXUJ69Ls0fYwtodk3GtYI,798
 ngio/ome_zarr_meta/_generic_handlers.py,sha256=4zRm3P1CRKgUQgD5Z2C9j8VVv659DZIifrmzkQ7o31I,10987
 ngio/ome_zarr_meta/_meta_handlers.py,sha256=b6r1zX3SBBTKoQdKfEqvJaSnTOen5t1EPO3rh0I9VH4,4925
@@ -43,11 +43,11 @@ ngio/tables/v1/_generic_table.py,sha256=KOVzbeUs8AwVvI83Os5gBZky948ucEKjxXl2CGzS
 ngio/tables/v1/_masking_roi_table.py,sha256=vPlUWGQalxDJ7G4NcSmzsOFqSEIJFXbuCLD_ucBj7ew,5492
 ngio/tables/v1/_roi_table.py,sha256=UMwJEMkOAgDf-80z0qPfIiB6fsQInjzjDlR4OkBYH4o,7147
 ngio/utils/__init__.py,sha256=fhT4CUTk3obQHzjfTcZYOwjZrSuuI1uXQ8qJmyH17iY,1021
-ngio/utils/_datasets.py,sha256=o6-CGwK7tEUtlwrTOayrg08Yc_nYBuKxWCu1K3dAgm4,1668
+ngio/utils/_datasets.py,sha256=Ir5-DUaplJoWXIsFCVp6yaJNfEKXKygj6RbGsy275uE,1669
 ngio/utils/_errors.py,sha256=pKQ12LUjQLYE1nUawemA5h7HsgznjaSvV1n2PQU33N0,759
 ngio/utils/_logger.py,sha256=zvFG-Ta3ZIJxTyY93zYoPGp2A6TTUf7mSO0zr_uFy4A,837
 ngio/utils/_zarr_utils.py,sha256=5Mo8Nfb7oww7rGVqEWUH29VvOkhD3-Despb3c1SlENM,12172
-ngio-0.2.0a1.dist-info/METADATA,sha256=7IwTK3iOC_hzeIa2Q7n7TXvROIboYJjjUMGkW9oFf5c,4804
-ngio-0.2.0a1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ngio-0.2.0a1.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.2.0a1.dist-info/RECORD,,
+ngio-0.2.0a2.dist-info/METADATA,sha256=-NUZl0xeZ-rFEqPilWo_hFfbQ-uuyCFa2cv2bLxkABo,4804
+ngio-0.2.0a2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ngio-0.2.0a2.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.2.0a2.dist-info/RECORD,,