ngio 0.2.0a2__py3-none-any.whl → 0.2.0a3__py3-none-any.whl

ngio/images/image.py

@@ -170,17 +170,20 @@ class ImagesContainer:
                 be shown by default.
             omero_kwargs(dict): Extra fields to store in the omero attributes.
         """
-        ref = self.get()
+        low_res_dataset = self.meta.get_lowest_resolution_dataset()
+        ref_image = self.get(path=low_res_dataset.path)
 
         if percentiles is not None:
             start, end = compute_image_percentile(
-                ref, start_percentile=percentiles[0], end_percentile=percentiles[1]
+                ref_image,
+                start_percentile=percentiles[0],
+                end_percentile=percentiles[1],
             )
         else:
             start, end = None, None
 
         if labels is None:
-            labels = ref.num_channels
+            labels = ref_image.num_channels
 
         channel_meta = ChannelsMeta.default_init(
             labels=labels,
@@ -189,7 +192,7 @@ class ImagesContainer:
             start=start,
             end=end,
             active=active,
-            data_type=ref.dtype,
+            data_type=ref_image.dtype,
             **omero_kwargs,
         )
 
@@ -206,9 +209,10 @@ class ImagesContainer:
         if self.meta._channels_meta is None:
             raise NgioValidationError("The channels meta is not initialized.")
 
-        image = self.get()
+        low_res_dataset = self.meta.get_lowest_resolution_dataset()
+        ref_image = self.get(path=low_res_dataset.path)
         starts, ends = compute_image_percentile(
-            image, start_percentile=start_percentile, end_percentile=end_percentile
+            ref_image, start_percentile=start_percentile, end_percentile=end_percentile
         )
 
         channels = []
@@ -256,13 +260,20 @@ class ImagesContainer:
         self,
         path: str | None = None,
         pixel_size: PixelSize | None = None,
-        highest_resolution: bool = True,
+        strict: bool = False,
     ) -> Image:
-        """Get an image at a specific level."""
-        if path is not None or pixel_size is not None:
-            highest_resolution = False
+        """Get an image at a specific level.
+
+        Args:
+            path (str | None): The path to the image in the omezarr file.
+            pixel_size (PixelSize | None): The pixel size of the image.
+            strict (bool): Only used if the pixel size is provided. If True, the
+                pixel size must match the image pixel size exactly. If False, the
+                closest pixel size level will be returned.
+
+        """
         dataset = self._meta_handler.meta.get_dataset(
-            path=path, pixel_size=pixel_size, highest_resolution=highest_resolution
+            path=path, pixel_size=pixel_size, strict=strict
         )
         return Image(
             group_handler=self._group_handler,

ngio/images/label.py

@@ -10,6 +10,7 @@ from ngio.ome_zarr_meta import (
     ImplementedLabelMetaHandlers,
     LabelMetaHandler,
     NgioLabelMeta,
+    PixelSize,
 )
 from ngio.ome_zarr_meta.ngio_specs import SpaceUnits, TimeUnits
 from ngio.utils import (
@@ -86,11 +87,38 @@ class LabelsContainer:
         attrs = self._group_handler.load_attrs()
         return attrs.get("labels", [])
 
-    def get(self, name: str, path: str) -> Label:
+    def _get(self, name: str, path: str) -> Label:
         """Get a label from the group."""
         group_handler = self._group_handler.derive_handler(name)
         return Label(group_handler, path, None)
 
+    def get(
+        self,
+        name: str,
+        path: str | None = None,
+        pixel_size: PixelSize | None = None,
+        strict: bool = False,
+    ) -> Label:
+        """Get a label from the group.
+
+        Args:
+            name (str): The name of the label.
+            path (str | None): The path to the image in the omezarr file.
+            pixel_size (PixelSize | None): The pixel size of the image.
+            strict (bool): Only used if the pixel size is provided. If True, the
+                pixel size must match the image pixel size exactly. If False, the
+                closest pixel size level will be returned.
+
+        """
+        group_handler = self._group_handler.derive_handler(name)
+        label_meta_handler = ImplementedLabelMetaHandlers().find_meta_handler(
+            group_handler
+        )
+        path = label_meta_handler.meta.get_dataset(
+            path=path, pixel_size=pixel_size, strict=strict
+        ).path
+        return Label(group_handler, path, label_meta_handler)
+
     def derive(
         self,
         name: str,

ngio/images/omezarr_container.py

@@ -160,13 +160,20 @@ class OmeZarrContainer:
         self,
         path: str | None = None,
         pixel_size: PixelSize | None = None,
-        highest_resolution: bool = True,
+        strict: bool = False,
     ) -> Image:
-        """Get an image at a specific level."""
+        """Get an image at a specific level.
+
+        Args:
+            path (str | None): The path to the image in the omezarr file.
+            pixel_size (PixelSize | None): The pixel size of the image.
+            strict (bool): Only used if the pixel size is provided. If True, the
+                pixel size must match the image pixel size exactly. If False, the
+                closest pixel size level will be returned.
+
+        """
         return self._images_container.get(
-            path=path,
-            pixel_size=pixel_size,
-            highest_resolution=highest_resolution,
+            path=path, pixel_size=pixel_size, strict=strict
         )
 
     def derive_image(
@@ -279,11 +286,28 @@ class OmeZarrContainer:
             return []
         return self._labels_container.list()
 
-    def get_label(self, name: str, path: str) -> Label:
-        """Get a label from the image."""
+    def get_label(
+        self,
+        name: str,
+        path: str | None = None,
+        pixel_size: PixelSize | None = None,
+        strict: bool = False,
+    ) -> Label:
+        """Get a label from the group.
+
+        Args:
+            name (str): The name of the label.
+            path (str | None): The path to the image in the omezarr file.
+            pixel_size (PixelSize | None): The pixel size of the image.
+            strict (bool): Only used if the pixel size is provided. If True, the
+                pixel size must match the image pixel size exactly. If False, the
+                closest pixel size level will be returned.
+        """
         if self._labels_container is None:
             raise NgioValidationError("No labels found in the image.")
-        return self._labels_container.get(name=name, path=path)
+        return self._labels_container.get(
+            name=name, path=path, pixel_size=pixel_size, strict=strict
+        )
 
     def derive_label(
         self,
@@ -334,17 +358,29 @@ def open_image(
     store: StoreOrGroup,
     path: str | None = None,
     pixel_size: PixelSize | None = None,
-    highest_resolution: bool = False,
+    strict: bool = True,
     cache: bool = False,
     mode: AccessModeLiteral = "r+",
 ) -> Image:
-    """Open a single level image from an OME-Zarr image."""
+    """Open a single level image from an OME-Zarr image.
+
+    Args:
+        store (StoreOrGroup): The Zarr store or group to create the image in.
+        path (str | None): The path to the image in the omezarr file.
+        pixel_size (PixelSize | None): The pixel size of the image.
+        strict (bool): Only used if the pixel size is provided. If True, the
+                pixel size must match the image pixel size exactly. If False, the
+                closest pixel size level will be returned.
+        cache (bool): Whether to use a cache for the zarr group metadata.
+        mode (AccessModeLiteral): The
+            access mode for the image. Defaults to "r+".
+    """
     group_handler = ZarrGroupHandler(store, cache, mode)
     images_container = ImagesContainer(group_handler)
     return images_container.get(
         path=path,
         pixel_size=pixel_size,
-        highest_resolution=highest_resolution,
+        strict=strict,
     )
 
 

ngio/ome_zarr_meta/ngio_specs/_ngio_image.py

@@ -138,16 +138,16 @@ class AbstractNgioImageMeta:
         path: str | None = None,
         idx: int | None = None,
         pixel_size: PixelSize | None = None,
-        highest_resolution: bool = False,
         strict: bool = False,
     ) -> Dataset:
         """Get a dataset by its path, index or pixel size.
 
+        If all arguments are None, the dataset with the highest resolution is returned.
+
         Args:
             path(str): The path of the dataset.
             idx(int): The index of the dataset.
             pixel_size(PixelSize): The pixel size to search for.
-            highest_resolution(bool): If True, the dataset with the highest resolution
             strict(bool): If True, the pixel size must be exactly the same.
                 If pixel_size is None, strict is ignored.
         """
@@ -158,12 +158,11 @@ class AbstractNgioImageMeta:
                     path is not None,
                     idx is not None,
                     pixel_size is not None,
-                    highest_resolution,
                 ]
             )
-            != 1
+            > 1
         ):
-            raise NgioValueError("get_dataset must receive only one argument.")
+            raise NgioValueError("get_dataset must receive only one argument or None.")
 
         if path is not None:
             return self._get_dataset_by_path(path)
@@ -171,10 +170,8 @@ class AbstractNgioImageMeta:
             return self._get_dataset_by_index(idx)
         elif pixel_size is not None:
             return self._get_dataset_by_pixel_size(pixel_size, strict=strict)
-        elif highest_resolution:
-            return self.get_highest_resolution_dataset()
         else:
-            raise NgioValueError("get_dataset has no valid arguments.")
+            return self.get_highest_resolution_dataset()
 
     @classmethod
     def default_init(
@@ -237,6 +234,20 @@ class AbstractNgioImageMeta:
             strict=False,
         )
 
+    def get_lowest_resolution_dataset(self) -> Dataset:
+        """Get the dataset with the lowest resolution."""
+        return self._get_dataset_by_pixel_size(
+            pixel_size=PixelSize(
+                x=1000.0,
+                y=1000.0,
+                z=1000.0,
+                t=1000.0,
+                space_unit=SpaceUnits.micrometer,
+                time_unit=TimeUnits.s,
+            ),
+            strict=False,
+        )
+
     def get_scaling_factor(self, axis_name: str) -> float:
         """Get the scaling factors of the dataset."""
         scaling_factors = []

ngio/utils/__init__.py

@@ -11,6 +11,7 @@ from ngio.utils._errors import (
     NgioValidationError,
     NgioValueError,
 )
+from ngio.utils._fractal_fsspec_store import fractal_fsspec_store
 from ngio.utils._logger import ngio_logger, set_logger_level
 from ngio.utils._zarr_utils import (
     AccessModeLiteral,
@@ -35,6 +36,8 @@ __all__ = [
     "ZarrGroupHandler",
     # Datasets
     "download_ome_zarr_dataset",
+    # Fractal
+    "fractal_fsspec_store",
     "list_ome_zarr_datasets",
     # Logger
     "ngio_logger",

ngio/utils/_fractal_fsspec_store.py

@@ -0,0 +1,12 @@
+import fsspec.implementations.http
+
+
+def fractal_fsspec_store(
+    url: str, fractal_token: str, client_kwargs: dict | None = None
+) -> fsspec.mapping.FSMap:
+    """Simple function to get an http fsspec store from a url."""
+    client_kwargs = {} if client_kwargs is None else client_kwargs
+    client_kwargs["headers"] = {"Authorization": f"Bearer {fractal_token}"}
+    fs = fsspec.implementations.http.HTTPFileSystem(client_kwargs=client_kwargs)
+    store = fs.get_mapper(url)
+    return store

{ngio-0.2.0a2.dist-info → ngio-0.2.0a3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.2.0a2
+Version: 0.2.0a3
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/lorenzocerrone/ngio
 Project-URL: repository, https://github.com/lorenzocerrone/ngio

{ngio-0.2.0a2.dist-info → ngio-0.2.0a3.dist-info}/RECORD

@@ -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=QiSdOaZSLWtAweecMj69hXXAdVnPIkO3Qfjvs8QII3o,12586
-ngio/images/label.py,sha256=wzpIsIFuKdTOcTU57PHpIf_U4Fh6TwRhM-tLpEt4GbI,7520
-ngio/images/omezarr_container.py,sha256=E0uDyBM1vZ8kCwXI6tIyPDl7QEdi5e91hI5AIWf8kFY,19161
+ngio/images/image.py,sha256=zdrOVFlalUMdBwQTzDY6gy-BejttBHHkjJd2oOeEWLE,13101
+ngio/images/label.py,sha256=6DgliUcTUNUXNIDRGF7lfCp_eyQ2aCys6l-bnHQeAs8,8558
+ngio/images/omezarr_container.py,sha256=Et9FFJmgyqVm7hZsTPB5xBLRsGlGyL65tXdUs2Z4dE8,20695
 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
@@ -23,7 +23,7 @@ ngio/ome_zarr_meta/ngio_specs/_axes.py,sha256=zgAE0-2DHzJfqGqBhyjY7y_6qAgDLdV9iu
 ngio/ome_zarr_meta/ngio_specs/_channels.py,sha256=KLQAo7eerBXa5NN3-QWSFxeAfM_bvXXaxFjFNM6OMoA,13762
 ngio/ome_zarr_meta/ngio_specs/_dataset.py,sha256=xT4GY2mdIsm6nAP8bXRj5E9-P6rS-iwzcXT_o3pZajo,4696
 ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py,sha256=Gk29MJ4Vn4TLFK4M7X_33BumCLiZWRuXtSeLX6H56s4,115
-ngio/ome_zarr_meta/ngio_specs/_ngio_image.py,sha256=FnVSupNHHsUxlQOfDXQP2fBZqL8BOX7bB_c1gHP0iWk,14703
+ngio/ome_zarr_meta/ngio_specs/_ngio_image.py,sha256=Bf2DyGuVmFqA4zQROYpjGxAcquXkGyztPkHuHh7586Y,14966
 ngio/ome_zarr_meta/ngio_specs/_pixel_size.py,sha256=Ny4F0Wa7uVCKdDQhvFJPCQFUEtKP_DpwId8vdVxkVyQ,2777
 ngio/ome_zarr_meta/v04/__init__.py,sha256=0sb_CaJNgC1AOYeR6LDB91oUmSk6edJyQTTo3Lnh5Y4,226
 ngio/ome_zarr_meta/v04/_meta_handlers.py,sha256=aRvuq9ofzQQCB-CJehD3e2T1eKBtZwKg6r2OkpTG1Oo,1768
@@ -42,12 +42,13 @@ ngio/tables/v1/_feature_table.py,sha256=WOkFOb0UDxwM-MPZGdv-nLIiqfiGL8etVkMett9i
 ngio/tables/v1/_generic_table.py,sha256=KOVzbeUs8AwVvI83Os5gBZky948ucEKjxXl2CGzSQqQ,3483
 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/__init__.py,sha256=r3nuLWgp6-cQlS4ODjYSBrfgdTLkCOVke9jKbn1NpkA,1129
 ngio/utils/_datasets.py,sha256=Ir5-DUaplJoWXIsFCVp6yaJNfEKXKygj6RbGsy275uE,1669
 ngio/utils/_errors.py,sha256=pKQ12LUjQLYE1nUawemA5h7HsgznjaSvV1n2PQU33N0,759
+ngio/utils/_fractal_fsspec_store.py,sha256=KxIu37EUJgiKI92qmJKfZtCjNdfMmfNbYez2LAK3dxg,496
 ngio/utils/_logger.py,sha256=zvFG-Ta3ZIJxTyY93zYoPGp2A6TTUf7mSO0zr_uFy4A,837
 ngio/utils/_zarr_utils.py,sha256=5Mo8Nfb7oww7rGVqEWUH29VvOkhD3-Despb3c1SlENM,12172
-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,,
+ngio-0.2.0a3.dist-info/METADATA,sha256=L6dq7gPr76J0FFjE0K6mFTm5UFFpOaHVpi8mKS15hRk,4804
+ngio-0.2.0a3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ngio-0.2.0a3.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.2.0a3.dist-info/RECORD,,