ngio 0.5.0__py3-none-any.whl → 0.5.0a2__py3-none-any.whl

ngio/utils/__init__.py

@@ -1,12 +1,13 @@
 """Various utilities for the ngio package."""
 
+import os
+
 from ngio.utils._datasets import (
     download_ome_zarr_dataset,
     list_ome_zarr_datasets,
     print_datasets_infos,
 )
 from ngio.utils._errors import (
-    NgioError,
     NgioFileExistsError,
     NgioFileNotFoundError,
     NgioTableValidationError,
@@ -14,32 +15,37 @@ from ngio.utils._errors import (
     NgioValueError,
 )
 from ngio.utils._fractal_fsspec_store import fractal_fsspec_store
+from ngio.utils._logger import ngio_logger, ngio_warn, set_logger_level
 from ngio.utils._zarr_utils import (
     AccessModeLiteral,
     NgioCache,
-    NgioSupportedStore,
     StoreOrGroup,
     ZarrGroupHandler,
-    copy_group,
     open_group_wrapper,
 )
 
+set_logger_level(os.getenv("NGIO_LOGGER_LEVEL", "WARNING"))
+
 __all__ = [
+    # Zarr
     "AccessModeLiteral",
     "NgioCache",
-    "NgioError",
+    # Errors
     "NgioFileExistsError",
     "NgioFileNotFoundError",
-    "NgioSupportedStore",
     "NgioTableValidationError",
     "NgioValidationError",
     "NgioValueError",
     "StoreOrGroup",
     "ZarrGroupHandler",
-    "copy_group",
+    # Other
     "download_ome_zarr_dataset",
     "fractal_fsspec_store",
     "list_ome_zarr_datasets",
+    # Logger
+    "ngio_logger",
+    "ngio_warn",
     "open_group_wrapper",
     "print_datasets_infos",
+    "set_logger_level",
 ]

ngio/utils/_datasets.py

@@ -155,11 +155,5 @@ def download_ome_zarr_dataset(
         path=download_dir,
         processor=processor,
         progressbar=progressbar,
-        # Add User-Agent to avoid 403 errors from Zenodo
-        downloader=pooch.HTTPDownloader(
-            headers={
-                "User-Agent": f"pooch/{pooch.__version__} (https://github.com/BioVisionCenter/ngio)"
-            }
-        ),
     )
     return processor.output_file()

ngio/utils/_logger.py

@@ -0,0 +1,50 @@
+import logging
+import time
+from functools import cache
+
+from ngio.utils._errors import NgioValueError
+
+# Configure the logger
+ngio_logger = logging.getLogger("NgioLogger")
+ngio_logger.setLevel(logging.ERROR)
+
+# Set up a console handler with a custom format
+console_handler = logging.StreamHandler()
+formatter = logging.Formatter(
+    "%(asctime)s - %(levelname)s - %(name)s - "
+    "[%(module)s.%(funcName)s:%(lineno)d]: %(message)s"
+)
+console_handler.setFormatter(formatter)
+
+# Add the handler to the logger
+ngio_logger.addHandler(console_handler)
+
+
+def set_logger_level(level: str) -> None:
+    """Set the logger level.
+
+    Args:
+        level: The level to set the logger to.
+            Must be one of "DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL".
+    """
+    if level not in ["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]:
+        raise NgioValueError(f"Invalid log level: {level}")
+
+    ngio_logger.setLevel(level)
+
+
+@cache
+def _warn(message: str, ttl_hash: int) -> None:
+    """Log a warning message with a time-to-live (TTL) hash."""
+    ngio_logger.warning(message, stacklevel=3)
+
+
+def ngio_warn(message: str, cooldown: int = 2) -> None:
+    """Log a warning message.
+
+    Args:
+        message: The warning message to log.
+        cooldown: The cooldown period in seconds to avoid repeated logging.
+    """
+    ttl_hash = time.time() // cooldown
+    _warn(message, ttl_hash)

ngio/utils/_zarr_utils.py

@@ -1,22 +1,19 @@
 """Common utilities for working with Zarr groups in consistent ways."""
 
-import json
 import warnings
 from pathlib import Path
-from typing import Literal, TypeAlias
+from typing import Literal
 
-import dask.array as da
 import fsspec
 import zarr
 from filelock import BaseFileLock, FileLock
-from pydantic_zarr.v2 import ArraySpec as AnyArraySpecV2
-from pydantic_zarr.v3 import ArraySpec as AnyArraySpecV3
 from zarr.abc.store import Store
 from zarr.errors import ContainsGroupError
-from zarr.storage import FsspecStore, LocalStore, MemoryStore, ZipStore
+from zarr.storage import FsspecStore, LocalStore, MemoryStore
 
 from ngio.utils._cache import NgioCache
 from ngio.utils._errors import (
+    NgioError,
     NgioFileExistsError,
     NgioFileNotFoundError,
     NgioValueError,
@@ -26,11 +23,11 @@ AccessModeLiteral = Literal["r", "r+", "w", "w-", "a"]
 # StoreLike is more restrictive than it could be
 # but to make sure we can handle the store correctly
 # we need to be more restrictive
-NgioSupportedStore: TypeAlias = (
-    str | Path | fsspec.mapping.FSMap | FsspecStore | MemoryStore | dict | LocalStore
+NgioSupportedStore = (
+    str | Path | fsspec.mapping.FSMap | FsspecStore | MemoryStore | LocalStore
 )
-GenericStore: TypeAlias = NgioSupportedStore | Store
-StoreOrGroup: TypeAlias = NgioSupportedStore | zarr.Group
+GenericStore = Store | NgioSupportedStore
+StoreOrGroup = GenericStore | zarr.Group
 
 
 def _check_store(store) -> NgioSupportedStore:
@@ -114,6 +111,7 @@ class ZarrGroupHandler:
 
         Args:
             store (StoreOrGroup): The Zarr store or group containing the image data.
+            meta_mode (str): The mode of the metadata handler.
             zarr_format (int | None): The Zarr format version to use.
             cache (bool): Whether to cache the metadata.
             mode (str | None): The mode of the store.
@@ -127,7 +125,6 @@ class ZarrGroupHandler:
 
         self._group_cache: NgioCache[zarr.Group] = NgioCache(use_cache=cache)
         self._array_cache: NgioCache[zarr.Array] = NgioCache(use_cache=cache)
-        self._handlers_cache: NgioCache[ZarrGroupHandler] = NgioCache(use_cache=cache)
         self._lock: tuple[Path, BaseFileLock] | None = None
 
     def __repr__(self) -> str:
@@ -147,17 +144,8 @@ class ZarrGroupHandler:
         """Return the store path."""
         if isinstance(self.store, LocalStore):
             return (self.store.root / self.group.path).as_posix()
-        elif isinstance(self.store, FsspecStore):
-            return f"{self.store.path}/{self.group.path}"
-        elif isinstance(self.store, ZipStore):
-            return (self.store.path / self.group.path).as_posix()
-        elif isinstance(self.store, MemoryStore):
-            return None
-        warnings.warn(
-            f"Cannot determine full URL for store type {type(self.store)}. ",
-            UserWarning,
-            stacklevel=2,
-        )
+        if isinstance(self.store, FsspecStore):
+            return self.store.fs.map.root_path
         return None
 
     @property
@@ -337,6 +325,25 @@ class ZarrGroupHandler:
         self._group_cache.set(path, group, overwrite=overwrite)
         return group
 
+    def safe_get_group(
+        self, path: str, create_mode: bool = False
+    ) -> tuple[bool, zarr.Group | NgioError]:
+        """Get a group from the group.
+
+        Args:
+            path (str): The path to the group.
+            create_mode (bool): If True, create the group if it does not exist.
+
+        Returns:
+            zarr.Group | None: The Zarr group or None if it does not exist
+                or an error occurs.
+
+        """
+        try:
+            return True, self.get_group(path, create_mode)
+        except NgioError as e:
+            return False, e
+
     def get_array(self, path: str) -> zarr.Array:
         """Get an array from the group."""
         array = self._array_cache.get(path)
@@ -351,55 +358,47 @@ class ZarrGroupHandler:
             raise NgioValueError(f"The object at {path} is not an array, but a group.")
         raise NgioFileNotFoundError(f"No array found at {path}")
 
-    def get_handler(
+    def derive_handler(
         self,
         path: str,
-        create_mode: bool = True,
         overwrite: bool = False,
     ) -> "ZarrGroupHandler":
-        """Get a new handler for a group in the current handler group.
+        """Derive a new handler from the current handler.
 
         Args:
             path (str): The path to the group.
-            create_mode (bool): If True, create the group if it does not exist.
             overwrite (bool): If True, overwrite the group if it exists.
         """
-        handler = self._handlers_cache.get(path)
-        if handler is not None:
-            return handler
-        group = self.get_group(path, create_mode=create_mode, overwrite=overwrite)
-        mode = "r" if group.read_only else "r+"
-        handler = ZarrGroupHandler(
-            store=group, zarr_format=self.zarr_format, cache=self.use_cache, mode=mode
+        group = self.get_group(path, create_mode=True, overwrite=overwrite)
+        return ZarrGroupHandler(
+            store=group, zarr_format=self.zarr_format, cache=self.use_cache, mode="r+"
         )
-        self._handlers_cache.set(path, handler)
-        return handler
-
-    @property
-    def is_listable(self) -> bool:
-        return is_group_listable(self.group)
-
-    def delete_group(self, path: str) -> None:
-        """Delete a group from the current group.
 
-        Args:
-            path (str): The path to the group to delete.
-        """
-        if self.group.read_only:
-            raise NgioValueError("Cannot delete a group in read only mode.")
-        self.group.__delitem__(path)
-        self._group_cache._cache.pop(path, None)
-        self._handlers_cache._cache.pop(path, None)
-
-    def delete_self(self) -> None:
-        """Delete the current group."""
-        if self.group.read_only:
-            raise NgioValueError("Cannot delete a group in read only mode.")
-        self.group.__delitem__("/")
+    def safe_derive_handler(
+        self,
+        path: str,
+        overwrite: bool = False,
+    ) -> tuple[bool, "ZarrGroupHandler | NgioError"]:
+        """Derive a new handler from the current handler."""
+        try:
+            return True, self.derive_handler(path, overwrite=overwrite)
+        except NgioError as e:
+            return False, e
 
-    def copy_group(self, dest_group: zarr.Group):
+    def copy_handler(self, handler: "ZarrGroupHandler") -> None:
         """Copy the group to a new store."""
-        copy_group(self.group, dest_group)
+        _, n_skipped, _ = zarr.copy_store(
+            source=self.group.store,
+            dest=handler.group.store,
+            source_path=self.group.path,
+            dest_path=handler.group.path,
+            if_exists="replace",
+        )
+        if n_skipped > 0:
+            raise NgioValueError(
+                f"Error copying group to {handler.full_url}, "
+                f"#{n_skipped} files where skipped."
+            )
 
 
 def find_dimension_separator(array: zarr.Array) -> Literal[".", "/"]:
@@ -418,116 +417,8 @@ def find_dimension_separator(array: zarr.Array) -> Literal[".", "/"]:
     else:
         separator = array.metadata.chunk_key_encoding
         if not isinstance(separator, DefaultChunkKeyEncoding):
-            raise NgioValueError(
+            raise ValueError(
                 "Only DefaultChunkKeyEncoding is supported in this example."
             )
         separator = separator.separator
     return separator
-
-
-def is_group_listable(group: zarr.Group) -> bool:
-    """Check if a Zarr group is listable.
-
-    A group is considered listable if it contains at least one array or subgroup.
-
-    Args:
-        group (zarr.Group): The Zarr group to check.
-
-    Returns:
-        bool: True if the group is listable, False otherwise.
-    """
-    if not group.store.supports_listing:
-        # If the store does not support listing
-        # then for sure it is not listable
-        return False
-    try:
-        next(group.keys())
-        return True
-    except StopIteration:
-        # Group is listable but empty
-        return True
-    except Exception as _:
-        # Some stores may raise errors when listing
-        # consider those not listable
-        return False
-
-
-def _make_sync_fs(fs: fsspec.AbstractFileSystem) -> fsspec.AbstractFileSystem:
-    fs_dict = json.loads(fs.to_json())
-    fs_dict["asynchronous"] = False
-    return fsspec.AbstractFileSystem.from_json(json.dumps(fs_dict))
-
-
-def _get_mapper(store: LocalStore | FsspecStore, path: str):
-    if isinstance(store, LocalStore):
-        fs = fsspec.filesystem("file")
-        full_path = (store.root / path).as_posix()
-    else:
-        fs = _make_sync_fs(store.fs)
-        full_path = f"{store.path}/{path}"
-    return fs.get_mapper(full_path)
-
-
-def _fsspec_copy(
-    src_fs: LocalStore | FsspecStore,
-    src_path: str,
-    dest_fs: LocalStore | FsspecStore,
-    dest_path: str,
-):
-    src_mapper = _get_mapper(src_fs, src_path)
-    dest_mapper = _get_mapper(dest_fs, dest_path)
-    for key in src_mapper.keys():
-        dest_mapper[key] = src_mapper[key]
-
-
-def _zarr_python_copy(src_group: zarr.Group, dest_group: zarr.Group):
-    # Copy attributes
-    dest_group.attrs.put(src_group.attrs.asdict())
-    # Copy arrays
-    for name, array in src_group.arrays():
-        if array.metadata.zarr_format == 2:
-            spec = AnyArraySpecV2.from_zarr(array)
-        else:
-            spec = AnyArraySpecV3.from_zarr(array)
-        dst = spec.to_zarr(
-            store=dest_group.store,
-            path=f"{dest_group.path}/{name}",
-            overwrite=True,
-        )
-        if array.ndim > 0:
-            dask_array = da.from_zarr(array)
-            da.to_zarr(dask_array, dst, overwrite=False)
-    # Copy subgroups
-    for name, subgroup in src_group.groups():
-        dest_subgroup = dest_group.create_group(name, overwrite=True)
-        _zarr_python_copy(subgroup, dest_subgroup)
-
-
-def copy_group(
-    src_group: zarr.Group, dest_group: zarr.Group, suppress_warnings: bool = False
-):
-    if src_group.metadata.zarr_format != dest_group.metadata.zarr_format:
-        raise NgioValueError(
-            "Different Zarr format versions between source and destination, "
-            "cannot copy."
-        )
-
-    if not is_group_listable(src_group):
-        raise NgioValueError("Source group is not listable, cannot copy.")
-
-    if dest_group.read_only:
-        raise NgioValueError("Destination group is read only, cannot copy.")
-    if isinstance(src_group.store, LocalStore | FsspecStore) and isinstance(
-        dest_group.store, LocalStore | FsspecStore
-    ):
-        _fsspec_copy(src_group.store, src_group.path, dest_group.store, dest_group.path)
-        return
-    if not suppress_warnings:
-        warnings.warn(
-            "Fsspec copy not possible, falling back to Zarr Python API for the copy. "
-            "This will preserve some tabular data non-zarr native (parquet, and csv), "
-            "and it will be slower for large datasets.",
-            UserWarning,
-            stacklevel=2,
-        )
-    _zarr_python_copy(src_group, dest_group)

{ngio-0.5.0.dist-info → ngio-0.5.0a2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.5.0
+Version: 0.5.0a2
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio
@@ -13,9 +13,8 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Classifier: Programming Language :: Python :: 3.14
 Classifier: Typing :: Typed
-Requires-Python: <3.15,>=3.11
+Requires-Python: <3.14,>=3.11
 Requires-Dist: aiohttp
 Requires-Dist: anndata
 Requires-Dist: dask[array]<2025.11.0
@@ -23,7 +22,7 @@ Requires-Dist: dask[distributed]<2025.11.0
 Requires-Dist: filelock
 Requires-Dist: numpy
 Requires-Dist: ome-zarr-models
-Requires-Dist: pandas<3.0.0,>=1.2.0
+Requires-Dist: pandas>=1.2.0
 Requires-Dist: pillow
 Requires-Dist: polars
 Requires-Dist: pooch
@@ -32,6 +31,7 @@ Requires-Dist: pydantic
 Requires-Dist: requests
 Requires-Dist: zarr>3
 Provides-Extra: dev
+Requires-Dist: devtools; extra == 'dev'
 Requires-Dist: matplotlib; extra == 'dev'
 Requires-Dist: mypy; extra == 'dev'
 Requires-Dist: napari; extra == 'dev'
@@ -43,7 +43,6 @@ Requires-Dist: pyqt5; extra == 'dev'
 Requires-Dist: rich; extra == 'dev'
 Requires-Dist: ruff; extra == 'dev'
 Requires-Dist: scikit-image; extra == 'dev'
-Requires-Dist: zarrs; extra == 'dev'
 Provides-Extra: docs
 Requires-Dist: griffe-typingdoc; extra == 'docs'
 Requires-Dist: markdown-exec[ansi]; extra == 'docs'
@@ -58,17 +57,11 @@ Requires-Dist: mkdocs-jupyter; extra == 'docs'
 Requires-Dist: mkdocs-material; extra == 'docs'
 Requires-Dist: mkdocstrings[python]; extra == 'docs'
 Requires-Dist: rich; extra == 'docs'
-Requires-Dist: ruff; extra == 'docs'
 Requires-Dist: scikit-image; extra == 'docs'
 Requires-Dist: tabulate; extra == 'docs'
 Provides-Extra: test
-Requires-Dist: boto; extra == 'test'
-Requires-Dist: devtools; extra == 'test'
-Requires-Dist: moto[server]; extra == 'test'
 Requires-Dist: pytest; extra == 'test'
 Requires-Dist: pytest-cov; extra == 'test'
-Requires-Dist: pytest-httpserver; extra == 'test'
-Requires-Dist: s3fs; extra == 'test'
 Requires-Dist: scikit-image; extra == 'test'
 Description-Content-Type: text/markdown
 

ngio-0.5.0a2.dist-info/RECORD

@@ -0,0 +1,89 @@
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+ngio/common/__init__.py,sha256=aPSuUbdGryrxbnlWrsVNe3LZoBAWC4GijR1BNH1UwuU,612
+ngio/common/_dimensions.py,sha256=w8PYgyWxA8hgJETjFbw5CXf7WrasCL5FbzgfL1in86M,11361
+ngio/common/_masking_roi.py,sha256=ZZTXordEZoq_ADk0OzADvq-5dPOwUBSuNobzFR8fpTw,5697
+ngio/common/_pyramid.py,sha256=loQbtoGWs0g5Ke2s1tSBDsvos0235F-ElhFspsMsIr0,9238
+ngio/common/_roi.py,sha256=9fKFTHoUiP0xmxvQiFkNmIuwWg3bFuRaAx-froCSqvA,11487
+ngio/common/_synt_images_utils.py,sha256=B6uYOW1NyrM06YMR-csca3_YnAAkPRTbvnbLdy9tk9E,3188
+ngio/common/_zoom.py,sha256=U01c-vqXjzZkrpd9Yvs24frVfTls_xPJeeaFCGmUwYI,6727
+ngio/experimental/__init__.py,sha256=3pmBtHi-i8bKjTsvrOJM56ZyRX3Pv_dceCdt88-8COQ,147
+ngio/experimental/iterators/__init__.py,sha256=TECOMGb5PEEZ0yXxt8pqIGvLKG41g_L1fTJU-zGPeV8,488
+ngio/experimental/iterators/_abstract_iterator.py,sha256=7aAoMI-6vYGCMKxO3M10WpuBMTdqX4zr0K-TutAOp88,13195
+ngio/experimental/iterators/_feature.py,sha256=g03yHIzYpTVeD3KUq2a4TwX29Dt48XaaGdZNSykYy7M,6749
+ngio/experimental/iterators/_image_processing.py,sha256=cM7sL7xgdcjSOKAu-6367Aov89o6wgiJ_wqCGkU2Bsw,5091
+ngio/experimental/iterators/_mappers.py,sha256=VVVsjems57wJUnWeufUFcgqa23k7VPeFL4Nc04HVw4o,1399
+ngio/experimental/iterators/_rois_utils.py,sha256=Q-8lQ26neYn63h_RvfypYqvrq2UUN2O3xqVe57k_ufU,4363
+ngio/experimental/iterators/_segmentation.py,sha256=xzotGvTn04HPeMeXZ_URnQqWco6d2lH6Ng6vkCUh9NM,9153
+ngio/hcs/__init__.py,sha256=G8j9vD-liLeB_UeGtKYIgshWvJnUA6ks9GwjvWBLdHs,357
+ngio/hcs/_plate.py,sha256=9kvvI_qu946xbRqWeY9q1bp45duREyOx-3a-QeKkrGU,43376
+ngio/images/__init__.py,sha256=9Whvt7GTiCgT_vXaEEqGnDaY1-UsRk3dhLTv091F_g4,1211
+ngio/images/_abstract_image.py,sha256=hrB9xn4MFRxnxE1d7HKnM8SXVPUGhMD9u32yBHTsFiU,18517
+ngio/images/_create.py,sha256=IIdX0vER9J3c3aJYZRB7bDGMGv_kv0CbaJjGJM7yjyY,10536
+ngio/images/_create_synt_container.py,sha256=HeRscNNWYHY3rJTO-oKDr5mMuQD6RHWThrv9Rc9yZdg,5539
+ngio/images/_image.py,sha256=LP_XZrL0OLSasPTxaySldKSysyMZvznhFm-E3YLN5Tg,33488
+ngio/images/_label.py,sha256=o7dFDfn-vAgBA80g-vR54M64av_tNebduQqtnG0AkIw,11926
+ngio/images/_masked_image.py,sha256=YhbBzgPZMav6rX0WYue1BaxAzEIsfaQrxUIOK6ZWZcw,18848
+ngio/images/_ome_zarr_container.py,sha256=IlXZojr9HDnfGboLAWD0TlV5Bv7J5fvzKqYc8U43WdU,38777
+ngio/images/_table_ops.py,sha256=jFv_AMqoB4JBpoWsMtZppZVW7dAOC_u-JpfNm8b33kY,15292
+ngio/io_pipes/__init__.py,sha256=arW_7GWzZs82kPNKdm_6B1sIDFV0lWwp-ZaORr9Q1FQ,2412
+ngio/io_pipes/_io_pipes.py,sha256=KuwMYofE11EKx0iplWXBQZ-eE1A9YpGDprWh98cUlAI,10710
+ngio/io_pipes/_io_pipes_masked.py,sha256=077j1XNgyCNOHlOsbjPOWcLtb2ccFvbLp-cPzWL1j3c,16999
+ngio/io_pipes/_io_pipes_roi.py,sha256=cu_vd4MTDuyiabCWQ5ieMLI4v3tu_twSEe4X5-3bp84,4543
+ngio/io_pipes/_io_pipes_types.py,sha256=xCeUd9rZe2wsgoZR1pUq6L4LSeawoPsb-9pmz5C6ztA,1393
+ngio/io_pipes/_match_shape.py,sha256=eDy_Eqzld08m9zDuIjAvJnIhWh_HVjQS-5Pw9BMjdbw,13200
+ngio/io_pipes/_ops_axes.py,sha256=Geg4ZXxB0njWWopX9YeiwRJJ9Ef2GKfG0NIUafOmi2c,10043
+ngio/io_pipes/_ops_slices.py,sha256=hHMIOQ_niUSK9uFl8P2-10dP_K4GX3Do6vivN4fGRE0,14520
+ngio/io_pipes/_ops_slices_utils.py,sha256=xjDaCVGmtME5Q0XSmGrY3nUKYgw5jOBQZW4YDq5s4vE,6580
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 Tag: py3-none-any