oscura 0.7.0__py3-none-any.whl → 0.8.0__py3-none-any.whl

oscura/__init__.py

@@ -53,7 +53,7 @@ try:
     __version__ = version("oscura")
 except Exception:
     # Fallback for development/testing when package not installed
-    __version__ = "0.7.0"
+    __version__ = "0.8.0"
 
 __author__ = "Oscura Contributors"
 

oscura/analyzers/eye/__init__.py

@@ -15,7 +15,9 @@ References:
     OIF CEI: Common Electrical I/O
 """
 
-from oscura.analyzers.eye.diagram import (
+# Backward compatibility
+from oscura.analyzers.eye import generation as diagram
+from oscura.analyzers.eye.generation import (
     EyeDiagram,
     generate_eye,
     generate_eye_from_edges,
@@ -36,6 +38,8 @@ __all__ = [
     # Metrics
     "EyeMetrics",
     "crossing_percentage",
+    # Backward compatibility
+    "diagram",
     "eye_contour",
     "eye_height",
     "eye_width",

oscura/analyzers/eye/generation.py

@@ -0,0 +1,501 @@
+"""Eye diagram generation from serial data.
+
+This module generates eye diagrams by folding waveform data
+at the unit interval boundary.
+
+Example:
+    >>> from oscura.analyzers.eye.diagram import generate_eye
+    >>> eye = generate_eye(trace, unit_interval=1e-9)
+    >>> print(f"Eye diagram: {eye.n_traces} traces, {eye.samples_per_ui} samples/UI")
+
+References:
+    IEEE 802.3: Ethernet Physical Layer Specifications
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass
+from typing import TYPE_CHECKING
+
+import numpy as np
+
+from oscura.core.exceptions import AnalysisError, InsufficientDataError
+
+if TYPE_CHECKING:
+    from numpy.typing import NDArray
+
+    from oscura.core.types import WaveformTrace
+
+
+@dataclass
+class EyeDiagram:
+    """Eye diagram data structure.
+
+    Attributes:
+        data: 2D array of eye traces (n_traces x samples_per_ui).
+        time_axis: Time axis in UI (0.0 to 2.0 for 2-UI eye).
+        unit_interval: Unit interval in seconds.
+        samples_per_ui: Number of samples per unit interval.
+        n_traces: Number of overlaid traces.
+        sample_rate: Original sample rate in Hz.
+        histogram: Optional 2D histogram (voltage x time bins).
+        voltage_bins: Bin edges for voltage axis.
+        time_bins: Bin edges for time axis.
+    """
+
+    data: NDArray[np.float64]
+    time_axis: NDArray[np.float64]
+    unit_interval: float
+    samples_per_ui: int
+    n_traces: int
+    sample_rate: float
+    histogram: NDArray[np.float64] | None = None
+    voltage_bins: NDArray[np.float64] | None = None
+    time_bins: NDArray[np.float64] | None = None
+
+
+def generate_eye(
+    trace: WaveformTrace,
+    unit_interval: float,
+    *,
+    n_ui: int = 2,
+    trigger_level: float = 0.5,
+    trigger_edge: str = "rising",
+    max_traces: int | None = None,
+    generate_histogram: bool = True,
+    histogram_bins: tuple[int, int] = (100, 100),
+) -> EyeDiagram:
+    """Generate eye diagram from waveform data.
+
+    Folds the waveform at unit interval boundaries to create
+    an overlaid eye pattern for signal quality analysis.
+
+    Args:
+        trace: Input waveform trace.
+        unit_interval: Unit interval (bit period) in seconds.
+        n_ui: Number of unit intervals to display (1 or 2).
+        trigger_level: Trigger level as fraction of amplitude.
+        trigger_edge: Trigger on "rising" or "falling" edges.
+        max_traces: Maximum number of traces to include.
+        generate_histogram: Generate 2D histogram for persistence.
+        histogram_bins: (voltage_bins, time_bins) for histogram.
+
+    Returns:
+        EyeDiagram with overlaid traces and optional histogram.
+
+    Raises:
+        AnalysisError: If unit interval is too short.
+        InsufficientDataError: If not enough data for eye generation.
+
+    Example:
+        >>> eye = generate_eye(trace, unit_interval=1e-9)
+        >>> print(f"Generated {eye.n_traces} traces")
+
+    References:
+        OIF CEI: Common Electrical I/O Eye Diagram Methodology
+    """
+    data = trace.data
+    sample_rate = trace.metadata.sample_rate
+
+    samples_per_ui = _validate_unit_interval(unit_interval, sample_rate)
+    total_ui_samples = samples_per_ui * n_ui
+    _validate_data_length(len(data), total_ui_samples)
+
+    trigger_indices = _find_trigger_points(data, trigger_level, trigger_edge)
+    eye_traces = _extract_eye_traces(
+        data, trigger_indices, samples_per_ui, total_ui_samples, max_traces
+    )
+    eye_data = np.array(eye_traces, dtype=np.float64)
+    time_axis = np.linspace(0, n_ui, total_ui_samples, endpoint=False)
+
+    histogram, voltage_bins, time_bins = _generate_histogram_if_requested(
+        eye_data, time_axis, n_ui, generate_histogram, histogram_bins
+    )
+
+    return EyeDiagram(
+        data=eye_data,
+        time_axis=time_axis,
+        unit_interval=unit_interval,
+        samples_per_ui=samples_per_ui,
+        n_traces=len(eye_traces),
+        sample_rate=sample_rate,
+        histogram=histogram,
+        voltage_bins=voltage_bins,
+        time_bins=time_bins,
+    )
+
+
+def _validate_unit_interval(unit_interval: float, sample_rate: float) -> int:
+    """Validate unit interval and calculate samples per UI."""
+    samples_per_ui = round(unit_interval * sample_rate)
+    if samples_per_ui < 4:
+        raise AnalysisError(
+            f"Unit interval too short: {samples_per_ui} samples/UI. Need at least 4 samples per UI."
+        )
+    return samples_per_ui
+
+
+def _validate_data_length(n_samples: int, total_ui_samples: int) -> None:
+    """Validate that we have enough data for eye generation."""
+    if n_samples < total_ui_samples * 2:
+        raise InsufficientDataError(
+            f"Need at least {total_ui_samples * 2} samples for eye diagram",
+            required=total_ui_samples * 2,
+            available=n_samples,
+            analysis_type="eye_diagram_generation",
+        )
+
+
+def _find_trigger_points(
+    data: NDArray[np.float64],
+    trigger_level: float,
+    trigger_edge: str,
+) -> NDArray[np.intp]:
+    """Find trigger points in the data."""
+    low = np.percentile(data, 10)
+    high = np.percentile(data, 90)
+    threshold = low + trigger_level * (high - low)
+
+    if trigger_edge == "rising":
+        trigger_mask = (data[:-1] < threshold) & (data[1:] >= threshold)
+    else:
+        trigger_mask = (data[:-1] >= threshold) & (data[1:] < threshold)
+
+    trigger_indices = np.where(trigger_mask)[0]
+
+    if len(trigger_indices) < 2:
+        raise InsufficientDataError(
+            "Not enough trigger events for eye diagram",
+            required=2,
+            available=len(trigger_indices),
+            analysis_type="eye_diagram_generation",
+        )
+
+    return trigger_indices
+
+
+def _extract_eye_traces(
+    data: NDArray[np.float64],
+    trigger_indices: NDArray[np.intp],
+    samples_per_ui: int,
+    total_ui_samples: int,
+    max_traces: int | None,
+) -> list[NDArray[np.float64]]:
+    """Extract eye traces from data using trigger points."""
+    eye_traces = []
+    half_ui = samples_per_ui // 2
+    n_samples = len(data)
+
+    for trig_idx in trigger_indices:
+        start_idx = trig_idx - half_ui
+        end_idx = start_idx + total_ui_samples
+
+        if start_idx >= 0 and end_idx <= n_samples:
+            eye_traces.append(data[start_idx:end_idx])
+
+        if max_traces is not None and len(eye_traces) >= max_traces:
+            break
+
+    if len(eye_traces) == 0:
+        raise InsufficientDataError(
+            "Could not extract any complete eye traces",
+            required=1,
+            available=0,
+            analysis_type="eye_diagram_generation",
+        )
+
+    return eye_traces
+
+
+def _generate_histogram_if_requested(
+    eye_data: NDArray[np.float64],
+    time_axis: NDArray[np.float64],
+    n_ui: int,
+    generate_histogram: bool,
+    histogram_bins: tuple[int, int],
+) -> tuple[NDArray[np.float64] | None, NDArray[np.float64] | None, NDArray[np.float64] | None]:
+    """Generate 2D histogram if requested."""
+    if not generate_histogram:
+        return None, None, None
+
+    all_voltages = eye_data.flatten()
+    all_times = np.tile(time_axis, len(eye_data))
+
+    voltage_range = (np.min(all_voltages), np.max(all_voltages))
+    time_range = (0, n_ui)
+
+    histogram, voltage_edges, time_edges = np.histogram2d(
+        all_voltages,
+        all_times,
+        bins=histogram_bins,
+        range=[voltage_range, time_range],
+    )
+
+    return histogram, voltage_edges, time_edges
+
+
+def generate_eye_from_edges(
+    trace: WaveformTrace,
+    edge_timestamps: NDArray[np.float64],
+    *,
+    n_ui: int = 2,
+    samples_per_ui: int = 100,
+    max_traces: int | None = None,
+) -> EyeDiagram:
+    """Generate eye diagram using recovered clock edges.
+
+    Uses pre-recovered clock edges for triggering, which can provide
+    more accurate alignment than threshold-based triggering.
+
+    Args:
+        trace: Input waveform trace.
+        edge_timestamps: Array of clock edge timestamps in seconds.
+        n_ui: Number of unit intervals to display.
+        samples_per_ui: Samples per UI in resampled eye.
+        max_traces: Maximum traces to include.
+
+    Returns:
+        EyeDiagram with overlaid traces.
+
+    Raises:
+        InsufficientDataError: If not enough edge timestamps or traces.
+
+    Example:
+        >>> edges = recover_clock_edges(trace)
+        >>> eye = generate_eye_from_edges(trace, edges)
+    """
+    data = trace.data
+    sample_rate = trace.metadata.sample_rate
+
+    if len(edge_timestamps) < 3:
+        raise InsufficientDataError(
+            "Need at least 3 edge timestamps",
+            required=3,
+            available=len(edge_timestamps),
+            analysis_type="eye_diagram_generation",
+        )
+
+    # Calculate unit interval from edges
+    periods = np.diff(edge_timestamps)
+    unit_interval = float(np.median(periods))
+
+    # Create time vector for original data
+    original_time = np.arange(len(data)) / sample_rate
+
+    # Extract and resample traces around each edge
+    eye_traces = []
+    total_samples = samples_per_ui * n_ui
+    half_ui = unit_interval / 2
+
+    for edge_time in edge_timestamps:
+        # Define window around edge
+        start_time = edge_time - half_ui
+        end_time = start_time + unit_interval * n_ui
+
+        if start_time < 0 or end_time > original_time[-1]:
+            continue
+
+        # Find samples within window
+        mask = (original_time >= start_time) & (original_time <= end_time)
+        window_time = original_time[mask] - start_time
+        window_data = data[mask]
+
+        if len(window_data) < 4:
+            continue
+
+        # Resample to consistent samples_per_ui
+        resample_time = np.linspace(0, unit_interval * n_ui, total_samples)
+        resampled = np.interp(resample_time, window_time, window_data)
+
+        eye_traces.append(resampled)
+
+        if max_traces is not None and len(eye_traces) >= max_traces:
+            break
+
+    if len(eye_traces) == 0:
+        raise InsufficientDataError(
+            "Could not extract any eye traces",
+            required=1,
+            available=0,
+            analysis_type="eye_diagram_generation",
+        )
+
+    eye_data = np.array(eye_traces, dtype=np.float64)
+    time_axis = np.linspace(0, n_ui, total_samples, endpoint=False)
+
+    return EyeDiagram(
+        data=eye_data,
+        time_axis=time_axis,
+        unit_interval=unit_interval,
+        samples_per_ui=samples_per_ui,
+        n_traces=len(eye_traces),
+        sample_rate=sample_rate,
+    )
+
+
+def _calculate_trigger_threshold(data: NDArray[np.float64], trigger_fraction: float) -> float:
+    """Calculate trigger threshold from data amplitude.
+
+    Args:
+        data: Eye diagram data.
+        trigger_fraction: Trigger level as fraction of amplitude.
+
+    Returns:
+        Threshold value.
+    """
+    low = np.percentile(data, 10)
+    high = np.percentile(data, 90)
+    amplitude_range = high - low
+    threshold: float = float(low + trigger_fraction * amplitude_range)
+    return threshold
+
+
+def _find_trace_crossings(data: NDArray[np.float64], threshold: float) -> list[int]:
+    """Find crossing indices for all traces.
+
+    Args:
+        data: Eye diagram trace data (n_traces x samples_per_trace).
+        threshold: Crossing threshold.
+
+    Returns:
+        List of crossing indices for traces with crossings.
+    """
+    n_traces, _samples_per_trace = data.shape
+    crossing_indices = []
+
+    for trace_idx in range(n_traces):
+        trace = data[trace_idx, :]
+        crossings = np.where((trace[:-1] < threshold) & (trace[1:] >= threshold))[0]
+
+        if len(crossings) > 0:
+            crossing_indices.append(crossings[0])
+
+    return crossing_indices
+
+
+def _align_traces_to_target(
+    data: NDArray[np.float64], threshold: float, target_crossing: int
+) -> NDArray[np.float64]:
+    """Align all traces to target crossing position.
+
+    Args:
+        data: Eye diagram trace data.
+        threshold: Crossing threshold.
+        target_crossing: Target crossing position.
+
+    Returns:
+        Aligned trace data.
+    """
+    n_traces, _samples_per_trace = data.shape
+    aligned_data = np.zeros_like(data)
+
+    for trace_idx in range(n_traces):
+        trace = data[trace_idx, :]
+        crossings = np.where((trace[:-1] < threshold) & (trace[1:] >= threshold))[0]
+
+        if len(crossings) > 0:
+            crossing = crossings[0]
+            shift = target_crossing - crossing
+
+            if shift != 0:
+                aligned_data[trace_idx, :] = np.roll(trace, shift)
+            else:
+                aligned_data[trace_idx, :] = trace
+        else:
+            aligned_data[trace_idx, :] = trace
+
+    return aligned_data
+
+
+def _apply_symmetric_centering(data: NDArray[np.float64]) -> NDArray[np.float64]:
+    """Apply symmetric amplitude centering if enabled.
+
+    Args:
+        data: Aligned trace data.
+
+    Returns:
+        Symmetrically centered data.
+    """
+    max_abs = np.max(np.abs(data))
+    if max_abs > 0:
+        data = data - np.mean(data)
+    return data
+
+
+def auto_center_eye_diagram(
+    eye: EyeDiagram,
+    *,
+    trigger_fraction: float = 0.5,
+    symmetric_range: bool = True,
+) -> EyeDiagram:
+    """Auto-center eye diagram on optimal crossing point.
+
+    Automatically centers eye diagrams on the optimal trigger point
+    and scales amplitude for maximum eye opening visibility with
+    symmetric vertical centering.
+
+    Args:
+        eye: Input EyeDiagram to center.
+        trigger_fraction: Trigger level as fraction of amplitude (default 0.5 = 50%).
+        symmetric_range: Use symmetric amplitude range ±max(abs(signal)).
+
+    Returns:
+        Centered EyeDiagram with adjusted data.
+
+    Raises:
+        ValueError: If trigger_fraction is not in [0, 1].
+
+    Example:
+        >>> eye = generate_eye(trace, unit_interval=1e-9)
+        >>> centered = auto_center_eye_diagram(eye)
+        >>> # Centered at 50% crossing with symmetric amplitude
+
+    References:
+        VIS-021: Eye Diagram Auto-Centering
+    """
+    if not 0 <= trigger_fraction <= 1:
+        raise ValueError(f"trigger_fraction must be in [0, 1], got {trigger_fraction}")
+
+    # Setup: calculate threshold and find crossings
+    data = eye.data
+    threshold = _calculate_trigger_threshold(data, trigger_fraction)
+    crossing_indices = _find_trace_crossings(data, threshold)
+
+    if len(crossing_indices) == 0:
+        import warnings
+
+        warnings.warn(
+            "No crossing points found, cannot auto-center eye diagram",
+            UserWarning,
+            stacklevel=2,
+        )
+        return eye
+
+    # Processing: align traces to target crossing point
+    _n_traces, samples_per_trace = data.shape
+    target_crossing = samples_per_trace // 2
+    aligned_data = _align_traces_to_target(data, threshold, target_crossing)
+
+    # Result building: apply symmetric centering and create result
+    if symmetric_range:
+        aligned_data = _apply_symmetric_centering(aligned_data)
+
+    return EyeDiagram(
+        data=aligned_data,
+        time_axis=eye.time_axis,
+        unit_interval=eye.unit_interval,
+        samples_per_ui=eye.samples_per_ui,
+        n_traces=eye.n_traces,
+        sample_rate=eye.sample_rate,
+        histogram=None,
+        voltage_bins=None,
+        time_bins=None,
+    )
+
+
+__all__ = [
+    "EyeDiagram",
+    "auto_center_eye_diagram",
+    "generate_eye",
+    "generate_eye_from_edges",
+]

oscura/analyzers/jitter/__init__.py

@@ -40,7 +40,12 @@ from oscura.analyzers.jitter.decomposition import (
     extract_pj,
     extract_rj,
 )
-from oscura.analyzers.jitter.measurements import (
+from oscura.analyzers.jitter.spectrum import (
+    JitterSpectrumResult,
+    identify_periodic_components,
+    jitter_spectrum,
+)
+from oscura.analyzers.jitter.timing import (
     CycleJitterResult,
     DutyCycleDistortionResult,
     cycle_to_cycle_jitter,
@@ -48,11 +53,6 @@ from oscura.analyzers.jitter.measurements import (
     period_jitter,
     tie_from_edges,
 )
-from oscura.analyzers.jitter.spectrum import (
-    JitterSpectrumResult,
-    identify_periodic_components,
-    jitter_spectrum,
-)
 
 __all__ = [
     "BathtubCurveResult",