datalab-platform 0.0.1.dev0__py3-none-any.whl → 1.0.0__py3-none-any.whl

datalab/__init__.py

@@ -1,2 +1,35 @@
-"""Placeholder for future datalab-platform package."""
-__version__ = "0.0.1.dev0"
+# Copyright (c) DataLab Platform Developers, BSD 3-Clause license, see LICENSE file.
+
+"""
+DataLab
+=======
+
+DataLab is a generic signal and image processing software based on Python
+scientific libraries (such as NumPy, SciPy or scikit-image) and Qt graphical
+user interfaces (thanks to `PlotPyStack`_ libraries).
+
+.. _PlotPyStack: https://github.com/PlotPyStack
+"""
+
+import multiprocessing
+import os
+
+# Set multiprocessing start method to 'spawn' early to avoid fork-related warnings
+# on Linux systems when using Qt and multithreading. This must be done before
+# any multiprocessing.Pool is created.
+try:
+    multiprocessing.set_start_method("spawn")
+except RuntimeError:
+    # This exception is raised if the method is already set (this may happen because
+    # this module is imported more than once, e.g. when running tests)
+    pass
+
+__version__ = "1.0.0"
+__docurl__ = __homeurl__ = "https://datalab-platform.com/"
+__supporturl__ = "https://github.com/DataLab-Platform/DataLab/issues/new/choose"
+
+os.environ["DATALAB_VERSION"] = __version__
+
+# Dear (Debian, RPM, ...) package makers, please feel free to customize the
+# following path to module's data (images) and translations:
+DATAPATH = LOCALEPATH = ""

datalab/adapters_metadata/__init__.py

@@ -0,0 +1,31 @@
+# Copyright (c) DataLab Platform Developers, BSD 3-Clause license, see LICENSE file.
+
+"""
+Adapters for Sigima's TableResult and GeometryResult, providing features
+for storing and retrieving those objects as metadata for DataLab's signal
+and image objects.
+"""
+
+from .base_adapter import BaseResultAdapter
+from .common import (
+    ResultData,
+    create_resultdata_dict,
+    have_geometry_results,
+    have_results,
+    resultadapter_to_html,
+    show_resultdata,
+)
+from .geometry_adapter import GeometryAdapter
+from .table_adapter import TableAdapter
+
+__all__ = [
+    "BaseResultAdapter",
+    "GeometryAdapter",
+    "ResultData",
+    "TableAdapter",
+    "create_resultdata_dict",
+    "have_geometry_results",
+    "have_results",
+    "resultadapter_to_html",
+    "show_resultdata",
+]

datalab/adapters_metadata/base_adapter.py

@@ -0,0 +1,316 @@
+# Copyright (c) DataLab Platform Developers, BSD 3-Clause license, see LICENSE file.
+
+"""
+Base adapter class for result objects, providing common functionality
+for storing and retrieving result objects as metadata for DataLab's signal
+and image objects.
+"""
+
+from __future__ import annotations
+
+from abc import ABC, abstractmethod
+from typing import TYPE_CHECKING, Any, ClassVar, Generator
+
+import guidata.dataset as gds
+from sigima.objects import ImageObj, SignalObj
+
+if TYPE_CHECKING:
+    import pandas as pd
+    from sigima.objects.scalar import GeometryResult, TableResult
+
+
+class BaseResultAdapter(ABC):
+    """Base adapter for result objects.
+
+    This base class provides common functionality for working with result objects,
+    including metadata storage/retrieval and various data representations.
+
+    Args:
+        result: Result object to adapt
+    """
+
+    # Class constants for metadata storage - to be overridden by subclasses
+    META_PREFIX: ClassVar[str] = ""
+    META_SUFFIX: ClassVar[str] = "_dict"
+
+    def __init__(self, result: TableResult | GeometryResult) -> None:
+        self.result = result
+
+    def set_applicative_attr(self, key: str, value: Any) -> None:
+        """Set an applicative attribute for the result.
+
+        Args:
+            key: Attribute key
+            value: Attribute value
+        """
+        self.result.attrs[key] = value
+
+    def get_applicative_attr(self, key: str, default: Any = None) -> Any:
+        """Get an applicative attribute for the result.
+
+        Args:
+            key: Attribute key
+            default: Default value to return if key not found
+
+        Returns:
+            Attribute value, or default if not set. If default is not None, assign it
+            to the attribute if it was not already set.
+        """
+        if key not in self.result.attrs and default is not None:
+            self.result.attrs[key] = default
+        return self.result.attrs.get(key, default)
+
+    @property
+    def title(self) -> str:
+        """Get the title.
+
+        Returns:
+            Title
+        """
+        return self.result.title
+
+    @property
+    def name(self) -> str:
+        """Get the result kind name.
+
+        Returns:
+            The string value of the kind attribute (e.g., "segment", "circle",
+            "statistics"). This is NOT unique - multiple results can share the
+            same kind.
+        """
+        return self.result.name
+
+    @property
+    def func_name(self) -> str:
+        """Get the computation function name.
+
+        Returns:
+            The name of the computation function that produced this result.
+        """
+        return self.result.func_name
+
+    @property
+    @abstractmethod
+    def headers(self) -> list[str]:
+        """Get column headers.
+
+        Returns:
+            List of column headers
+        """
+
+    @property
+    @abstractmethod
+    def category(self) -> str:
+        """Get the category.
+
+        Returns:
+            Category
+        """
+
+    def get_roi_data(self, roi_index: int) -> "pd.DataFrame":
+        """Get data for a specific ROI index.
+
+        Args:
+            roi_index: ROI index to filter by
+
+        Returns:
+            DataFrame containing only data for the specified ROI
+        """
+        df = self.to_dataframe()
+        if "roi_index" in df.columns:
+            return df[df["roi_index"] == roi_index].drop(columns=["roi_index"])
+        return df
+
+    def get_column_values(self, column_name: str, roi_index: int = None) -> list:
+        """Get values for a specific column, optionally filtered by ROI.
+
+        Args:
+            column_name: Name of the column to retrieve
+            roi_index: Optional ROI index to filter by
+
+        Returns:
+            List of values for the specified column
+        """
+        df = self.to_dataframe()
+        if roi_index is not None and "roi_index" in df.columns:
+            df = df[df["roi_index"] == roi_index]
+        return df[column_name].tolist()
+
+    def get_unique_roi_indices(self) -> list[int]:
+        """Get unique ROI indices present in the data.
+
+        Returns:
+            List of unique ROI indices
+        """
+        df = self.to_dataframe()
+        if "roi_index" in df.columns:
+            return sorted(df["roi_index"].unique().tolist())
+        return [] if len(df) == 0 else [0]  # Default ROI index for result data
+
+    @property
+    def metadata_key(self) -> str:
+        """Get the metadata key used to store this result.
+
+        Returns:
+            Metadata key based on the result's title
+        """
+        return f"{self.META_PREFIX}{self.func_name}{self.META_SUFFIX}"
+
+    def add_to(
+        self, obj: SignalObj | ImageObj, param: gds.DataSet | None = None
+    ) -> None:
+        """Add result to object metadata.
+
+        Args:
+            obj: Signal or image object
+            param: Optional parameter dataset associated with this result
+        """
+        assert self.func_name, "func_name must be set before adding to object metadata"
+        # Store parameter in result attrs (will be serialized with result)
+        if param is not None:
+            self.result.attrs["param_json"] = gds.dataset_to_json(param)
+        obj.metadata[self.metadata_key] = self.result.to_dict()
+
+    def get_param(self) -> gds.DataSet | None:
+        """Get parameter dataset associated with this result.
+
+        Returns:
+            Parameter dataset if present, None otherwise
+        """
+        param_json = self.result.attrs.get("param_json")
+        if param_json is not None:
+            return gds.json_to_dataset(param_json)
+        return None
+
+    def remove_from(self, obj: SignalObj | ImageObj) -> None:
+        """Remove result from object metadata.
+
+        Args:
+            obj: Signal or image object
+        """
+        obj.metadata.pop(self.metadata_key, None)
+
+    @classmethod
+    def remove_all_from(cls, obj: SignalObj | ImageObj) -> None:
+        """Remove all results of this type from object metadata.
+
+        Args:
+            obj: Signal or image object
+        """
+        # Find all results in the object and remove them
+        for adapter in list(cls.iterate_from_obj(obj)):
+            adapter.remove_from(obj)
+
+    @classmethod
+    def match(cls, key: str, _value: Any) -> bool:
+        """Check if the key matches the pattern for this result type.
+
+        Args:
+            key: Metadata key
+            _value: Metadata value (unused)
+
+        Returns:
+            True if the key matches the pattern
+        """
+        return key.startswith(cls.META_PREFIX) and key.endswith(cls.META_SUFFIX)
+
+    @classmethod
+    @abstractmethod
+    def from_metadata_entry(cls, obj: SignalObj | ImageObj, key: str):
+        """Create a result adapter from a metadata entry.
+
+        Args:
+            obj: Object containing the metadata
+            key: Metadata key for the result data
+
+        Returns:
+            Adapter object
+
+        Raises:
+            ValueError: Invalid metadata entry
+        """
+
+    @classmethod
+    def from_obj(
+        cls, obj: SignalObj | ImageObj, func_name: str
+    ) -> BaseResultAdapter | None:
+        """Create a result adapter from an object's metadata entry.
+
+        Args:
+            obj: Signal or image object
+            func_name: Function name to look for
+
+        Returns:
+            Adapter object if found, None otherwise
+        """
+        for adapter in cls.iterate_from_obj(obj):
+            if adapter.func_name == func_name:
+                return adapter
+        return None
+
+    @classmethod
+    def iterate_from_obj(
+        cls, obj: SignalObj | ImageObj
+    ) -> Generator["BaseResultAdapter", None, None]:
+        """Iterate over results stored in an object's metadata.
+
+        Args:
+            obj: Signal or image object
+
+        Yields:
+            Adapter objects
+        """
+        for key, value in obj.metadata.items():
+            if cls.match(key, value):
+                try:
+                    yield cls.from_metadata_entry(obj, key)
+                except (ValueError, TypeError):
+                    # Skip invalid entries
+                    pass
+
+    def to_dataframe(self, visible_only: bool = False):
+        """Convert the result to a pandas DataFrame.
+
+        Args:
+            visible_only: If True, include only visible headers based on display
+             preferences. Default is False.
+
+        Returns:
+            DataFrame with an optional 'roi_index' column.
+             If visible_only is True, only columns with visible headers are included.
+        """
+        return self.result.to_dataframe(visible_only=visible_only)
+
+    def to_html(
+        self,
+        obj=None,
+        visible_only: bool = True,
+        transpose_single_row: bool = True,
+        **kwargs,
+    ) -> str:
+        """Convert the result to HTML format.
+
+        Args:
+            obj: Optional SignalObj or ImageObj for ROI title extraction
+            visible_only: If True, include only visible headers based on display
+             preferences. Default is False.
+            transpose_single_row: If True, transpose the table when there's only one row
+            **kwargs: Additional arguments passed to DataFrame.to_html()
+
+        Returns:
+            HTML representation of the result
+        """
+        return self.result.to_html(
+            obj=obj,
+            visible_only=visible_only,
+            transpose_single_row=transpose_single_row,
+            **kwargs,
+        )
+
+    def get_visible_headers(self) -> list[str]:
+        """Get list of currently visible headers based on display preferences.
+
+        Returns:
+            List of header names that should be displayed
+        """
+        return self.result.get_visible_headers()