Update orthoviewer (#7)

* intermediate transparenecy ui

* add startup logging

* improve GUI

* add perf monitoring

* initial multichannel support

* improve multiscale support

* asyncio compat

* compat with 0.0.18

* bump cellier

* add lod bias control

* update api

Author: kevinyamauchi

README.md

@@ -8,6 +8,15 @@
 
 A viewer for ome-zarr images.
 
+## Orthoviewer startup performance diagnostics
+
+Use the orthoviewer performance flags to print startup timings
+with step and cumulative durations:
+
+```sh
+oz-viewer ortho /path/to/data.zarr --perf-startup --perf-table --perf-table-title "My Startup Profile"
+```
+
 ## Development
 
 The easiest way to get started is to use the [github cli](https://cli.github.com)

pyproject.toml

@@ -38,7 +38,7 @@ dependencies = [
     "typer >= 0.12",
     "rich >= 13",
     "numpy >= 1.24",
-    "cellier[pyside]>=0.0.13",
+    "cellier[pyside]>=0.0.18",
     "jupyterlab>=4.5.6",
     "aiohttp >= 3.9",
     "zarr >= 3.0",
@@ -155,3 +155,5 @@ OME = "OME"
 ome = "ome"
 # lod = Level of Detail (graphics term), not a typo for "load"
 lod = "lod"
+# nd = N-dimensional (numpy/array convention), not a typo for "and"
+nd = "nd"

src/oz_viewer/_cli.py

@@ -18,6 +18,11 @@
     print_ping_results,
     print_success_panel,
 )
+from oz_viewer._perf import (
+    StartupPerfTracer,
+    configure_perf_logging,
+    perf_enabled_from_env,
+)
 
 app = typer.Typer(
     name="oz-viewer",
@@ -141,6 +146,17 @@ def ortho(
             help="Create a synthetic anisotropic OME-Zarr and open it in the viewer.",
         ),
     ] = False,
+    multichannel: Annotated[
+        int | None,
+        typer.Option(
+            "--multichannel",
+            help=(
+                "Dimension index to treat as the channel axis, enabling multichannel"
+                " mode. If omitted, single-channel mode is used."
+            ),
+            show_default=False,
+        ),
+    ] = None,
     theme: Annotated[
         str,
         typer.Option(
@@ -151,15 +167,57 @@ def ortho(
             ),
         ),
     ] = "dark",
+    perf_startup: Annotated[
+        bool,
+        typer.Option(
+            "--perf-startup/--no-perf-startup",
+            help="Enable startup performance logging diagnostics.",
+        ),
+    ] = False,
+    perf_log_file: Annotated[
+        Path | None,
+        typer.Option(
+            "--perf-log-file",
+            help="Write startup performance logs to a file instead of stderr.",
+            show_default=False,
+        ),
+    ] = None,
+    perf_table: Annotated[
+        bool,
+        typer.Option(
+            "--perf-table/--no-perf-table",
+            help="Display startup timings as a Rich table at startup completion.",
+        ),
+    ] = False,
+    perf_table_title: Annotated[
+        str,
+        typer.Option(
+            "--perf-table-title",
+            help="Title used for the startup performance Rich table.",
+        ),
+    ] = "Orthoviewer startup timings",
 ) -> None:
     """Open an OME-Zarr store in the 4-panel orthoviewer."""
     from oz_viewer.viewer import launch_orthoviewer
 
+    perf_enabled = perf_startup or perf_enabled_from_env()
+    configure_perf_logging(
+        enabled=perf_enabled,
+        log_file=str(perf_log_file) if perf_log_file is not None else None,
+    )
+    perf = StartupPerfTracer(
+        enabled=perf_enabled,
+        show_table=perf_table,
+        table_title=perf_table_title,
+    )
+    perf.mark("cli.ortho.start", make_example=make_example, theme=theme)
+
     if make_example:
         from oz_viewer.data._blobs import make_example_zarr
 
         zarr_path = make_example_zarr()
         zarr_uri = f"file://{zarr_path}"
+        perf.mark("cli.ortho.example_created", zarr_path=zarr_path)
     else:
         raw = path or path_option
         if raw is None:
@@ -176,8 +234,10 @@ def ortho(
             )
             raise typer.Exit(code=1)
         zarr_uri = _resolve_zarr_uri(raw)
+        perf.mark("cli.ortho.uri_resolved", zarr_uri=zarr_uri)
 
-    launch_orthoviewer(zarr_uri, theme=theme)
+    perf.mark("cli.ortho.launch")
+    launch_orthoviewer(zarr_uri, channel_axis=multichannel, theme=theme, perf=perf)
 
 
 @app.command(name="theme")

src/oz_viewer/_perf.py

@@ -0,0 +1,122 @@
+"""Performance logging utilities for opt-in startup diagnostics."""
+
+from __future__ import annotations
+
+import logging
+import os
+from dataclasses import dataclass, field
+from time import perf_counter
+from uuid import uuid4
+
+_PERF_LOGGER_NAME = "oz_viewer.perf"
+_ENV_VAR_PERF = "OZ_VIEWER_PERF"
+_TRUTHY = {"1", "true", "yes", "on"}
+
+
+@dataclass(slots=True)
+class _PerfEvent:
+    step: str
+    elapsed_s: float
+    delta_s: float
+    fields: dict[str, object]
+
+
+def perf_enabled_from_env() -> bool:
+    """Return whether performance logging is enabled through an env var."""
+    return os.getenv(_ENV_VAR_PERF, "").strip().lower() in _TRUTHY
+
+
+def configure_perf_logging(
+    *, enabled: bool, log_file: str | None = None
+) -> logging.Logger:
+    """Configure the dedicated performance logger.
+
+    The logger is isolated from the default logging tree so users only see
+    performance output when this explicit configuration is enabled.
+    """
+    logger = logging.getLogger(_PERF_LOGGER_NAME)
+    logger.propagate = False
+
+    for handler in list(logger.handlers):
+        handler.close()
+        logger.removeHandler(handler)
+
+    if not enabled:
+        logger.setLevel(logging.CRITICAL + 1)
+        return logger
+
+    logger.setLevel(logging.INFO)
+    handler: logging.Handler
+    if log_file:
+        handler = logging.FileHandler(log_file)
+    else:
+        handler = logging.StreamHandler()
+    handler.setFormatter(logging.Formatter("[%(name)s] %(message)s"))
+    logger.addHandler(handler)
+    return logger
+
+
+@dataclass(slots=True)
+class StartupPerfTracer:
+    """Lightweight startup milestone tracer for perf diagnostics."""
+
+    enabled: bool
+    show_table: bool = False
+    table_title: str = "Orthoviewer startup timings"
+    run_id: str = field(default_factory=lambda: uuid4().hex[:8])
+    _t0: float = field(default_factory=perf_counter)
+    _last_elapsed_s: float = 0.0
+    _events: list[_PerfEvent] = field(default_factory=list)
+    _table_reported: bool = False
+
+    def mark(self, step: str, /, **fields: object) -> None:
+        """Emit a perf milestone with elapsed startup time."""
+        if not self.enabled:
+            return
+
+        logger = logging.getLogger(_PERF_LOGGER_NAME)
+        if not logger.isEnabledFor(logging.INFO):
+            return
+
+        elapsed = perf_counter() - self._t0
+        delta = max(0.0, elapsed - self._last_elapsed_s)
+        self._last_elapsed_s = elapsed
+        self._events.append(
+            _PerfEvent(step=step, elapsed_s=elapsed, delta_s=delta, fields=dict(fields))
+        )
+
+        suffix = ""
+        if fields:
+            details = " ".join(f"{key}={value}" for key, value in fields.items())
+            suffix = f" {details}"
+        logger.info("run=%s +%.3fs step=%s%s", self.run_id, elapsed, step, suffix)
+
+    def report_rich_table(self, *, title: str | None = None) -> None:
+        """Render a Rich table of step and cumulative startup timings."""
+        if not self.enabled or not self.show_table or self._table_reported:
+            return
+
+        from rich.console import Console
+        from rich.table import Table
+
+        table = Table(title=title or self.table_title)
+        table.add_column("#", justify="right", no_wrap=True)
+        table.add_column("Step")
+        table.add_column("Step (ms)", justify="right")
+        table.add_column("Cumulative (ms)", justify="right")
+        table.add_column("Details")
+
+        for idx, event in enumerate(self._events, start=1):
+            details = " ".join(
+                f"{key}={value}" for key, value in sorted(event.fields.items())
+            )
+            table.add_row(
+                str(idx),
+                event.step,
+                f"{event.delta_s * 1000:.1f}",
+                f"{event.elapsed_s * 1000:.1f}",
+                details,
+            )
+
+        Console(stderr=True).print(table)
+        self._table_reported = True