ngio 0.3.0a0__py3-none-any.whl → 0.3.1__py3-none-any.whl

ngio/tables/v1/_feature_table.py

@@ -6,21 +6,14 @@ https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/
 
 from typing import Literal
 
-from pydantic import BaseModel
+from pydantic import BaseModel, Field
 
-from ngio.tables.abstract_table import AbstractBaseTable
-from ngio.tables.backends import BackendMeta, TableBackendProtocol, TabularData
+from ngio.tables._abstract_table import AbstractBaseTable
+from ngio.tables.backends import BackendMeta, TableBackend, TabularData
 from ngio.utils import NgioValueError
 from ngio.utils._zarr_utils import ZarrGroupHandler
 
 
-class GenericTableMeta(BackendMeta):
-    """Metadata for the ROI table."""
-
-    fractal_table_version: str | None = None
-    type: str | None = None
-
-
 class RegionMeta(BaseModel):
     """Metadata for the region."""
 
@@ -30,12 +23,17 @@ class RegionMeta(BaseModel):
 class FeatureTableMeta(BackendMeta):
     """Metadata for the ROI table."""
 
-    fractal_table_version: Literal["1"] = "1"
+    table_version: Literal["1"] = "1"
     type: Literal["feature_table"] = "feature_table"
     region: RegionMeta | None = None
-    instance_key: str = "label"
+    instance_key: str = "label"  # Legacy field, kept for compatibility
+    # Backend metadata
     index_key: str | None = "label"
     index_type: Literal["int", "str"] | None = "int"
+    # Columns optional types
+    categorical_columns: list[str] = Field(default_factory=list)
+    measurement_columns: list[str] = Field(default_factory=list)
+    metadata_columns: list[str] = Field(default_factory=list)
 
 
 class FeatureTableV1(AbstractBaseTable):
@@ -85,7 +83,7 @@ class FeatureTableV1(AbstractBaseTable):
     def from_handler(
         cls,
         handler: ZarrGroupHandler,
-        backend: str | TableBackendProtocol | None = None,
+        backend: TableBackend | None = None,
     ) -> "FeatureTableV1":
         return cls._from_handler(
             handler=handler,

ngio/tables/v1/_generic_table.py

@@ -1,10 +1,21 @@
 """Implementation of a generic table class."""
 
-from ngio.tables.abstract_table import AbstractBaseTable
-from ngio.tables.backends import BackendMeta, TableBackendProtocol
+from ngio.tables._abstract_table import AbstractBaseTable
+from ngio.tables.backends import BackendMeta, TableBackend
 from ngio.utils import ZarrGroupHandler
 
 
+class GenericTableMeta(BackendMeta):
+    """Metadata for the generic table.
+
+    This is used to store metadata for a generic table.
+    It does not have a specific definition.
+    """
+
+    table_version: str | None = "1"
+    type: str | None = "generic_table"
+
+
 class GenericTable(AbstractBaseTable):
     """Class to a non-specific table.
 
@@ -29,7 +40,7 @@ class GenericTable(AbstractBaseTable):
     def from_handler(
         cls,
         handler: ZarrGroupHandler,
-        backend: str | TableBackendProtocol | None = None,
+        backend: TableBackend | None = None,
     ) -> "GenericTable":
         return cls._from_handler(
             handler=handler,

ngio/tables/v1/_roi_table.py

@@ -13,12 +13,16 @@ import pandas as pd
 from pydantic import BaseModel
 
 from ngio.common import Roi
-from ngio.tables.abstract_table import (
+from ngio.tables._abstract_table import (
     AbstractBaseTable,
-    TableBackendProtocol,
     TabularData,
 )
-from ngio.tables.backends import BackendMeta, convert_to_pandas, normalize_pandas_df
+from ngio.tables.backends import (
+    BackendMeta,
+    TableBackend,
+    convert_to_pandas,
+    normalize_pandas_df,
+)
 from ngio.utils import (
     NgioTableValidationError,
     NgioValueError,
@@ -302,7 +306,7 @@ class GenericRoiTableV1(AbstractBaseTable):
 class RoiTableV1Meta(BackendMeta):
     """Metadata for the ROI table."""
 
-    fractal_table_version: Literal["1"] = "1"
+    table_version: Literal["1"] = "1"
     type: Literal["roi_table"] = "roi_table"
     index_key: str | None = "FieldIndex"
     index_type: Literal["str", "int"] | None = "str"
@@ -334,7 +338,7 @@ class RoiTableV1(GenericRoiTableV1):
     def from_handler(
         cls,
         handler: ZarrGroupHandler,
-        backend: str | TableBackendProtocol | None = None,
+        backend: TableBackend | None = None,
     ) -> "RoiTableV1":
         table = cls._from_handler(
             handler=handler,
@@ -358,7 +362,7 @@ class RegionMeta(BaseModel):
 class MaskingRoiTableV1Meta(BackendMeta):
     """Metadata for the ROI table."""
 
-    fractal_table_version: Literal["1"] = "1"
+    table_version: Literal["1"] = "1"
     type: Literal["masking_roi_table"] = "masking_roi_table"
     region: RegionMeta | None = None
     instance_key: str = "label"
@@ -409,7 +413,7 @@ class MaskingRoiTableV1(GenericRoiTableV1):
     def from_handler(
         cls,
         handler: ZarrGroupHandler,
-        backend: str | TableBackendProtocol | None = None,
+        backend: TableBackend | None = None,
     ) -> "MaskingRoiTableV1":
         table = cls._from_handler(
             handler=handler,

ngio/utils/_fractal_fsspec_store.py

@@ -37,6 +37,6 @@ def fractal_fsspec_store(
         raise NgioValueError(
             f"Store {url} can not be read. Possible problems are: \n"
             "- The url does not exist. \n"
-            f"- The url is not a valid .zarr. \n"
+            "- The url is not a valid .zarr. \n"
         )
     return store

{ngio-0.3.0a0.dist-info → ngio-0.3.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.3.0a0
+Version: 0.3.1
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/fractal-analytics-platform/ngio
 Project-URL: repository, https://github.com/fractal-analytics-platform/ngio
@@ -50,6 +50,7 @@ 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-include-markdown-plugin; extra == 'docs'
 Requires-Dist: mkdocs-jupyter; extra == 'docs'
 Requires-Dist: mkdocs-material; extra == 'docs'
 Requires-Dist: mkdocstrings[python]; extra == 'docs'
@@ -62,7 +63,7 @@ Requires-Dist: pytest-cov; extra == 'test'
 Requires-Dist: scikit-image; extra == 'test'
 Description-Content-Type: text/markdown
 
-# NGIO - Next Generation file format IO
+# 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)
@@ -70,36 +71,69 @@ Description-Content-Type: text/markdown
 [![CI](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/fractal-analytics-platform/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
-- Powerful 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/)
-- Validation of 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 is a Python library designed to simplify bioimage analysis workflows, offering an intuitive interface for working with OME-Zarr files.
+
+## What is Ngio?
+
+Ngio is built for the [OME-Zarr](https://ngff.openmicroscopy.org/) file format, a modern, cloud-optimized format for biological imaging data. OME-Zarr stores large, multi-dimensional microscopy images and metadata in an efficient and scalable way.
+
+Ngio's mission is to streamline working with OME-Zarr files by providing a simple, object-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates. It also offers comprehensive support for labels, tables and regions of interest (ROIs), making it easy to extract and analyze specific regions in your data.
+
+## Key Features
+
+### 📊 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
+
+- Extract and analyze specific regions of interest
+- Tight integration with [Tabular Data](https://fractal-analytics-platform.github.io/ngio/stable/table_specs/overview/)
+
+### 🔄 Scalable Data Processing (Coming Soon)
+
+- Powerful iterators for processing data at scale
+- Efficient memory management for large datasets
+
+## Installation
+
+You can install ngio via pip:
+
+```bash
+pip install ngio
+```
+
+To get started check out the [Quickstart Guide](https://fractal-analytics-platform.github.io/ngio/stable/getting_started/0_quickstart/).
+
+## Supported OME-Zarr versions
+
+Currently, ngio only supports OME-Zarr v0.4. Support for version 0.5 and higher is planned for future releases.
+
+## 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.
+
+### Available Features
+
+- ✅ OME-Zarr metadata handling and validation
+- ✅ Image and label access across pyramid levels
+- ✅ ROI and table support
+- ✅ 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
+
+## Contributors
+
+Ngio is developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html), University of Zurich, by [@lorenzocerrone](https://github.com/lorenzocerrone) and [@jluethi](https://github.com/jluethi).
+
+## License
+
+Ngio is released under the BSD-3-Clause License. See [LICENSE](https://github.com/fractal-analytics-platform/ngio/blob/main/LICENSE) for details.

ngio-0.3.1.dist-info/RECORD

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ngio-0.3.0a0.dist-info/RECORD

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