ngio 0.2.0a2__py3-none-any.whl → 0.5.0b4__py3-none-any.whl

ngio/tables/tables_container.py

@@ -1,300 +0,0 @@
-"""Module for handling the /tables group in an OME-NGFF file."""
-
-from typing import Literal, Protocol
-
-from ngio.tables.v1 import FeatureTableV1, MaskingROITableV1, RoiTableV1
-from ngio.tables.v1._generic_table import GenericTable
-from ngio.utils import (
-    AccessModeLiteral,
-    NgioValidationError,
-    NgioValueError,
-    StoreOrGroup,
-    ZarrGroupHandler,
-)
-
-RoiTable = RoiTableV1
-MaskingROITable = MaskingROITableV1
-FeatureTable = FeatureTableV1
-
-
-class Table(Protocol):
-    """Placeholder class for a table."""
-
-    @staticmethod
-    def type() -> str | None:
-        """Return the type of the table."""
-        ...
-
-    @staticmethod
-    def version() -> str | None:
-        """Return the version of the table."""
-        ...
-
-    @property
-    def backend_name(self) -> str | None:
-        """The name of the backend."""
-        ...
-
-    @classmethod
-    def _from_handler(
-        cls, handler: ZarrGroupHandler, backend_name: str | None = None
-    ) -> "Table":
-        """Create a new table from a Zarr group handler."""
-        ...
-
-    def _set_backend(
-        self,
-        handler: ZarrGroupHandler,
-        backend_name: str | None = None,
-    ) -> None:
-        """Set the backend store and path for the table."""
-        ...
-
-    def consolidate(self) -> None:
-        """Consolidate the table on disk."""
-        ...
-
-
-TypedTable = Literal["roi_table", "masking_roi_table", "feature_table"]
-
-
-def _unique_table_name(type_name, version) -> str:
-    """Return the unique name for a table."""
-    return f"{type_name}_v{version}"
-
-
-class ImplementedTables:
-    """A singleton class to manage the available table handler plugins."""
-
-    _instance = None
-    _implemented_tables: dict[str, type[Table]]
-
-    def __new__(cls):
-        """Create a new instance of the class if it does not exist."""
-        if cls._instance is None:
-            cls._instance = super().__new__(cls)
-            cls._instance._implemented_tables = {}
-        return cls._instance
-
-    def available_implementations(self) -> list[str]:
-        """Get the available table handler versions."""
-        return list(self._implemented_tables.keys())
-
-    def get_table(
-        self,
-        type: str,
-        version: str,
-        handler: ZarrGroupHandler,
-        backend_name: str | None = None,
-    ) -> Table:
-        """Try to get a handler for the given store based on the metadata version."""
-        _errors = {}
-        for name, table_cls in self._implemented_tables.items():
-            if name != _unique_table_name(type, version):
-                continue
-            try:
-                table = table_cls._from_handler(
-                    handler=handler, backend_name=backend_name
-                )
-                return table
-            except Exception as e:
-                _errors[name] = e
-        print(_errors)
-        # If no table was found, we can try to load the table from a generic table
-        try:
-            table = GenericTable._from_handler(
-                handler=handler, backend_name=backend_name
-            )
-            return table
-        except Exception as e:
-            _errors["generic"] = e
-
-        if len(_errors) == 0:
-            raise NgioValidationError(
-                f"Could not find a table implementation for {type} v{version}. "
-                f"Available tables: {self.available_implementations()}"
-            )
-
-        raise NgioValidationError(
-            f"Could not load table from any known version. Errors: {_errors}"
-        )
-
-    def add_implementation(self, handler: type[Table], overwrite: bool = False):
-        """Register a new table handler."""
-        table_type = handler.type()
-        version = handler.version()
-        if table_type is None:
-            raise NgioValueError("Table handler must have a type.")
-
-        if version is None:
-            raise NgioValueError("Table handler must have a version.")
-
-        table_unique_name = _unique_table_name(table_type, version)
-        if table_unique_name in self._implemented_tables and not overwrite:
-            raise NgioValueError(
-                f"Table handler for {table_unique_name} already exists. "
-                "Use overwrite=True to replace it."
-            )
-        self._implemented_tables[table_unique_name] = handler
-
-
-def _get_table_type(handler: ZarrGroupHandler) -> str:
-    """Get the type of the table from the handler."""
-    attrs = handler.load_attrs()
-    return attrs.get("type", "None")
-
-
-def _get_table_version(handler: ZarrGroupHandler) -> str:
-    """Get the version of the table from the handler."""
-    attrs = handler.load_attrs()
-    return attrs.get("fractal_table_version", "None")
-
-
-class TablesContainer:
-    """A class to handle the /labels group in an OME-NGFF file."""
-
-    def __init__(self, group_handler: ZarrGroupHandler) -> None:
-        """Initialize the LabelGroupHandler."""
-        self._group_handler = group_handler
-
-        # Validate the group
-        # Either contains a tables attribute or is empty
-        attrs = self._group_handler.load_attrs()
-        if len(attrs) == 0:
-            # It's an empty group
-            pass
-        elif "tables" in attrs and isinstance(attrs["tables"], list):
-            # It's a valid group
-            pass
-        else:
-            raise NgioValidationError(
-                f"Invalid /tables group. "
-                f"Expected a single tables attribute with a list of table names. "
-                f"Found: {attrs}"
-            )
-
-    def _get_tables_list(self) -> list[str]:
-        """Create the /tables group if it doesn't exist."""
-        attrs = self._group_handler.load_attrs()
-        return attrs.get("tables", [])
-
-    def _get_table_group_handler(self, name: str) -> ZarrGroupHandler:
-        """Get the group handler for a table."""
-        handler = self._group_handler.derive_handler(path=name)
-        return handler
-
-    def list(self, filter_types: str | None = None) -> list[str]:
-        """List all labels in the group."""
-        tables = self._get_tables_list()
-        if filter_types is None:
-            return tables
-
-        filtered_tables = []
-        for table_name in tables:
-            tb_handler = self._get_table_group_handler(table_name)
-            table_type = _get_table_type(tb_handler)
-            if table_type == filter_types:
-                filtered_tables.append(table_name)
-        return filtered_tables
-
-    def get(self, name: str, backend_name: str | None = None) -> Table:
-        """Get a label from the group."""
-        if name not in self.list():
-            raise KeyError(f"Table '{name}' not found in the group.")
-
-        table_handler = self._get_table_group_handler(name)
-        table_type = _get_table_type(table_handler)
-        table_version = _get_table_version(table_handler)
-        return ImplementedTables().get_table(
-            type=table_type,
-            version=table_version,
-            handler=table_handler,
-            backend_name=backend_name,
-        )
-
-    def add(
-        self,
-        name: str,
-        table: Table,
-        backend: str | None = None,
-        overwrite: bool = False,
-    ) -> None:
-        """Add a table to the group."""
-        existing_tables = self._get_tables_list()
-        if name in existing_tables and not overwrite:
-            raise NgioValueError(
-                f"Table '{name}' already exists in the group. "
-                "Use overwrite=True to replace it."
-            )
-
-        table_handler = self._group_handler.derive_handler(path=name)
-
-        if backend is None:
-            backend = table.backend_name
-
-        table._set_backend(
-            handler=table_handler,
-            backend_name=backend,
-        )
-        table.consolidate()
-        if name not in existing_tables:
-            existing_tables.append(name)
-            self._group_handler.write_attrs({"tables": existing_tables})
-
-
-ImplementedTables().add_implementation(RoiTableV1)
-ImplementedTables().add_implementation(MaskingROITableV1)
-ImplementedTables().add_implementation(FeatureTableV1)
-
-###################################################################################
-#
-# Utility functions to open and write tables
-#
-###################################################################################
-
-
-def open_tables_container(
-    store: StoreOrGroup,
-    cache: bool = False,
-    mode: AccessModeLiteral = "a",
-    parallel_safe: bool = False,
-) -> TablesContainer:
-    """Open a table handler from a Zarr store."""
-    handler = ZarrGroupHandler(
-        store=store, cache=cache, mode=mode, parallel_safe=parallel_safe
-    )
-    return TablesContainer(handler)
-
-
-def open_table(
-    store: StoreOrGroup,
-    cache: bool = False,
-    mode: AccessModeLiteral = "a",
-    parallel_safe: bool = False,
-) -> Table:
-    """Open a table from a Zarr store."""
-    handler = ZarrGroupHandler(
-        store=store, cache=cache, mode=mode, parallel_safe=parallel_safe
-    )
-    return ImplementedTables().get_table(
-        _get_table_type(handler), _get_table_version(handler), handler
-    )
-
-
-def write_table(
-    store: StoreOrGroup,
-    table: Table,
-    backend: str | None = None,
-    cache: bool = False,
-    mode: AccessModeLiteral = "a",
-    parallel_safe: bool = False,
-) -> None:
-    """Write a table to a Zarr store."""
-    handler = ZarrGroupHandler(
-        store=store, cache=cache, mode=mode, parallel_safe=parallel_safe
-    )
-    table._set_backend(
-        handler=handler,
-        backend_name=backend,
-    )
-    table.consolidate()

ngio/tables/v1/_masking_roi_table.py

@@ -1,175 +0,0 @@
-"""Implementation of the Masking ROI table class.
-
-This class follows the roi_table specification at:
-https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/
-"""
-
-from collections.abc import Iterable
-from typing import Literal
-
-from pydantic import BaseModel
-
-from ngio.common import WorldCooROI
-from ngio.tables._validators import validate_columns
-from ngio.tables.backends import ImplementedTableBackends
-from ngio.tables.v1._roi_table import (
-    OPTIONAL_COLUMNS,
-    REQUIRED_COLUMNS,
-    _dataframe_to_rois,
-    _rois_to_dataframe,
-)
-from ngio.utils import NgioValueError, ZarrGroupHandler
-
-
-class RegionMeta(BaseModel):
-    """Metadata for the region."""
-
-    path: str
-
-
-class MaskingROITableV1Meta(BaseModel):
-    """Metadata for the ROI table."""
-
-    fractal_table_version: Literal["1"] = "1"
-    type: Literal["masking_roi_table"] = "masking_roi_table"
-    backend: str | None = None
-    region: RegionMeta | None = None
-    instance_key: str = "label"
-
-
-class MaskingROITableV1:
-    """Class to handle fractal ROI tables.
-
-    To know more about the ROI table format, please refer to the
-    specification at:
-    https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/
-    """
-
-    def __init__(
-        self,
-        rois: Iterable[WorldCooROI] | None = None,
-        reference_label: str | None = None,
-    ) -> None:
-        """Create a new ROI table."""
-        if reference_label is None:
-            self._meta = MaskingROITableV1Meta()
-        else:
-            path = f"../labels/{reference_label}"
-            self._meta = MaskingROITableV1Meta(region=RegionMeta(path=path))
-        self._table_backend = None
-
-        self._rois = {}
-        if rois is not None:
-            self.add(rois)
-
-    @staticmethod
-    def type() -> Literal["masking_roi_table"]:
-        """Return the type of the table."""
-        return "masking_roi_table"
-
-    @staticmethod
-    def version() -> Literal["1"]:
-        """Return the version of the fractal table."""
-        return "1"
-
-    @property
-    def backend_name(self) -> str | None:
-        """Return the name of the backend."""
-        if self._table_backend is None:
-            return None
-        return self._table_backend.backend_name()
-
-    @classmethod
-    def _from_handler(
-        cls, handler: ZarrGroupHandler, backend_name: str | None = None
-    ) -> "MaskingROITableV1":
-        """Create a new ROI table from a Zarr store."""
-        meta = MaskingROITableV1Meta(**handler.load_attrs())
-
-        if backend_name is None:
-            backend = ImplementedTableBackends().get_backend(
-                backend_name=meta.backend,
-                group_handler=handler,
-                index_key="label",
-                index_type="int",
-            )
-        else:
-            backend = ImplementedTableBackends().get_backend(
-                backend_name=backend_name,
-                group_handler=handler,
-                index_key="label",
-                index_type="int",
-            )
-            meta.backend = backend_name
-
-        if not backend.implements_dataframe:
-            raise NgioValueError(
-                "The backend does not implement the dataframe protocol."
-            )
-
-        table = cls()
-        table._meta = meta
-        table._table_backend = backend
-
-        dataframe = backend.load_as_dataframe()
-        dataframe = validate_columns(
-            dataframe,
-            required_columns=REQUIRED_COLUMNS,
-            optional_columns=OPTIONAL_COLUMNS,
-        )
-        table._rois = _dataframe_to_rois(dataframe)
-        return table
-
-    def _set_backend(
-        self,
-        handler: ZarrGroupHandler,
-        backend_name: str | None = None,
-    ) -> None:
-        """Set the backend of the table."""
-        backend = ImplementedTableBackends().get_backend(
-            backend_name=backend_name,
-            group_handler=handler,
-            index_key="label",
-            index_type="int",
-        )
-        self._meta.backend = backend_name
-        self._table_backend = backend
-
-    def rois(self) -> list[WorldCooROI]:
-        """List all ROIs in the table."""
-        return list(self._rois.values())
-
-    def get(self, label: int) -> WorldCooROI:
-        """Get an ROI from the table."""
-        _label = str(label)
-        if _label not in self._rois:
-            raise KeyError(f"ROI {_label} not found in the table.")
-        return self._rois[_label]
-
-    def add(self, roi: WorldCooROI | Iterable[WorldCooROI]) -> None:
-        """Append ROIs to the current table."""
-        if isinstance(roi, WorldCooROI):
-            roi = [roi]
-
-        for _roi in roi:
-            if _roi.name in self._rois:
-                raise NgioValueError(f"ROI {_roi.name} already exists in the table.")
-            self._rois[_roi.name] = _roi
-
-    def consolidate(self) -> None:
-        """Write the current state of the table to the Zarr file."""
-        if self._table_backend is None:
-            raise NgioValueError(
-                "No backend set for the table. "
-                "Please add the table to a OME-Zarr Image before calling consolidate."
-            )
-
-        dataframe = _rois_to_dataframe(self._rois, index_key="label")
-        dataframe = validate_columns(
-            dataframe,
-            required_columns=REQUIRED_COLUMNS,
-            optional_columns=OPTIONAL_COLUMNS,
-        )
-        self._table_backend.write_from_dataframe(
-            dataframe, metadata=self._meta.model_dump(exclude_none=True)
-        )

ngio/utils/_logger.py

@@ -1,29 +0,0 @@
-import logging
-
-# 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 ValueError(f"Invalid log level: {level}")
-
-    ngio_logger.setLevel(level)

ngio-0.2.0a2.dist-info/METADATA

@@ -1,95 +0,0 @@
-Metadata-Version: 2.4
-Name: ngio
-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
-Author-email: Lorenzo Cerrone <lorenzo.cerrone@uzh.ch>
-License: BSD-3-Clause
-License-File: LICENSE
-Classifier: Development Status :: 3 - Alpha
-Classifier: License :: OSI Approved :: BSD License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Classifier: Typing :: Typed
-Requires-Python: <3.14,>=3.11
-Requires-Dist: aiohttp
-Requires-Dist: anndata>=0.8.0
-Requires-Dist: dask[array]
-Requires-Dist: dask[distributed]
-Requires-Dist: filelock
-Requires-Dist: numpy
-Requires-Dist: ome-zarr-models
-Requires-Dist: pandas>=1.2.0
-Requires-Dist: pooch
-Requires-Dist: pydantic
-Requires-Dist: requests
-Requires-Dist: xarray
-Requires-Dist: zarr<3
-Provides-Extra: dev
-Requires-Dist: matplotlib; extra == 'dev'
-Requires-Dist: mypy; extra == 'dev'
-Requires-Dist: napari; extra == 'dev'
-Requires-Dist: notebook; extra == 'dev'
-Requires-Dist: pdbpp; extra == 'dev'
-Requires-Dist: pre-commit; extra == 'dev'
-Requires-Dist: pyqt5; extra == 'dev'
-Requires-Dist: rich; extra == 'dev'
-Requires-Dist: ruff; extra == 'dev'
-Provides-Extra: docs
-Requires-Dist: mkdocs; extra == 'docs'
-Requires-Dist: mkdocs-autorefs; extra == 'docs'
-Requires-Dist: mkdocs-git-committers-plugin-2; extra == 'docs'
-Requires-Dist: mkdocs-git-revision-date-localized-plugin; extra == 'docs'
-Requires-Dist: mkdocs-jupyter; extra == 'docs'
-Requires-Dist: mkdocs-material; extra == 'docs'
-Requires-Dist: mkdocstrings[python]; extra == 'docs'
-Requires-Dist: scikit-image; extra == 'docs'
-Provides-Extra: test
-Requires-Dist: pytest; extra == 'test'
-Requires-Dist: pytest-cov; extra == 'test'
-Description-Content-Type: text/markdown
-
-# NGIO - Next Generation file format IO
-
-[![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/lorenzocerrone/ngio/raw/main/LICENSE)
-[![PyPI](https://img.shields.io/pypi/v/ngio.svg?color=green)](https://pypi.org/project/ngio)
-[![Python Version](https://img.shields.io/pypi/pyversions/ngio.svg?color=green)](https://python.org)
-[![CI](https://github.com/lorenzocerrone/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/lorenzocerrone/ngio/actions/workflows/ci.yml)
-[![codecov](https://codecov.io/gh/fractal-analytics-platform/ngio/graph/badge.svg?token=FkmF26FZki)](https://codecov.io/gh/fractal-analytics-platform/ngio)
-
-NGIO is a Python library to streamline OME-Zarr image analysis workflows.
-
-**Main Goals:**
-
-- Abstract object base API for handling OME-Zarr files
-- Powefull iterators for processing data using common access patterns
-- Tight integration with [Fractal's Table Fractal](https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/)
-- Validate OME-Zarr files
-
-To get started, check out the [Getting Started](https://fractal-analytics-platform.github.io/ngio/getting-started/) guide. Or checkout our [Documentation](https://fractal-analytics-platform.github.io/ngio/)
-
-## 🚧 Ngio is Under active Development 🚧
-
-### Roadmap
-
-| Feature | Status | ETA | Description |
-|---------|--------|-----|-------------|
-| Metadata Handling | ✅ | | Read, Write, Validate OME-Zarr Metadata (0.4 supported, 0.5 ready) |
-| OME-Zarr Validation | ✅ | | Validate OME-Zarr files for compliance with the OME-Zarr Specification + Compliance between Metadata and Data |
-| Base Image Handling | ✅ | | Load data from OME-Zarr files, retrieve basic metadata, and write data |
-| ROI Handling | ✅ | | Common ROI models |
-| Label Handling | ✅ | Mid-September | Based on Image Handling |
-| Table Validation | ✅ | Mid-September | Validate Table fractal V1 + Compliance between Metadata and Data |
-| Table Handling | ✅ | Mid-September | Read, Write ROI, Features, and Masked Tables |
-| Basic Iterators | Ongoing | End-September | Read and Write Iterators for common access patterns |
-| Base Documentation | ✅ | End-September | API Documentation and Examples |
-| Beta Ready Testing | ✅ | End-September | Beta Testing; Library is ready for testing, but the API is not stable |
-| Streaming from Fractal | Ongoing | December | Ngio can stream ome-zarr from fractal |
-| Mask Iterators | Ongoing | Early 2025 | Iterators over Masked Tables |
-| Advanced Iterators | Not started | mid-2025 | Iterators for advanced access patterns |
-| Parallel Iterators | Not started | mid-2025 | Concurrent Iterators for parallel read and write |
-| Full Documentation | Not started | 2025 | Complete Documentation |
-| Release 1.0 (Commitment to API) | Not started | 2025 | API is stable; breaking changes will be avoided |

ngio-0.2.0a2.dist-info/RECORD

@@ -1,53 +0,0 @@
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-ngio/common/__init__.py,sha256=1vyK1i1ueu2BKKI-gaUhEyERVtHOtfKjQuPJOKDbrLA,1140
-ngio/common/_array_pipe.py,sha256=DyYjGTy2L74zBtD6S2jGPsFG4zj7KaY39TwPGWsSf8g,4877
-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=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
-ngio/hcs/__init__.py,sha256=ugnRl22hM9dic5XRsqQr-HCyyyY1qXTqYOAOzyOZm4M,1624
-ngio/images/__init__.py,sha256=aijqG14eyqVgHtnlcKVNx37FRfT6QvKt8V6bwBpX_r8,526
-ngio/images/abstract_image.py,sha256=n4akBHWQul7vmo4OlYtKWZwpsYl8IYg82AThJrvDrxc,7113
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