test: add demo data workflow coverage

tests/test_config_workspace.py

@@ -0,0 +1,178 @@
+import autoflow.api as api
+from autoflow import AutoFlowConfig, build_workspace
+
+
+def test_autoflow_config_defaults_cover_workspace_and_rendering_contract():
+    cfg = AutoFlowConfig()
+
+    assert cfg.inputs == []
+    assert cfg.output_dir == "./results"
+
+    assert cfg.skip_derived is False
+    assert cfg.skip_plane_metrics is False
+    assert cfg.use_multithread is True
+    assert cfg.reuse_planes == ""
+
+    assert cfg.use_center_plane is True
+    assert cfg.cross_section_dist == 5.0
+    assert cfg.start_dist == 5.0
+    assert cfg.end_dist == 0.0
+
+    assert cfg.remove_small_cc is True
+    assert cfg.min_cc_volume == 50.0
+
+    assert cfg.seed_ratio == 0.02
+    assert cfg.tube_radius == 0.05
+
+    assert cfg.fps == 12
+    assert cfg.plane_rotation_frames == 180
+    assert cfg.make_plane_video is False
+    assert cfg.make_wss_video is False
+    assert cfg.make_streamlines_video is False
+    assert cfg.make_tke_video is False
+
+    assert cfg.camera_view == "right"
+    assert cfg.camera_distance_scale == 1.5
+    assert cfg.rotate_dynamic_video is True
+    assert cfg.dynamic_rotation_frames == 180
+    assert cfg.dynamic_rotation_elevation_deg == 10.0
+    assert cfg.dynamic_time_repeat == 3
+
+    assert cfg.add_plane_idx is False
+    assert cfg.add_path_idx is False
+
+    assert cfg.wss_clim == (0.0, 10.0)
+    assert cfg.wss_bar_cfg == api.DEFAULT_WSS_BAR_CFG
+    assert cfg.wss_bar_cfg is not api.DEFAULT_WSS_BAR_CFG
+
+    assert cfg.tke_clim == (0.0, 100.0)
+    assert cfg.tke_bar_cfg == api.DEFAULT_TKE_BAR_CFG
+    assert cfg.tke_bar_cfg is not api.DEFAULT_TKE_BAR_CFG
+
+    assert cfg.streamline_clim == (0.0, 1)
+    assert cfg.streamline_bar_cfg == api.DEFAULT_STREAMLINE_BAR_CFG
+    assert cfg.streamline_bar_cfg is not api.DEFAULT_STREAMLINE_BAR_CFG
+
+
+def test_build_workspace_maps_default_config_values():
+    ws = build_workspace()
+
+    assert ws.plane_gen_params.to_dict() == {
+        "use_center_plane": True,
+        "cross_section_distance": 5.0,
+        "start_distance": 5.0,
+        "end_distance": 0.0,
+        "smoothing_window": 15,
+        "smoothing_polyorder": 2,
+        "inter_time": 10,
+    }
+    assert ws.skeleton_params.to_dict() == {
+        "remove_small_cc": True,
+        "min_cc_volume_mm3": 50.0,
+        "do_closing": True,
+        "do_opening": False,
+        "gaussian_sigma": 0.5,
+        "gaussian_enabled": True,
+    }
+    assert ws.streamline_params.to_dict() == {
+        "seed_ratio": 0.02,
+        "max_steps": 2000,
+        "min_seeds": 50,
+        "terminal_speed": 0.01,
+        "rng_seed": 0,
+    }
+    assert getattr(ws.streamline_params, "tube_radius") == 0.05
+
+
+def test_build_workspace_maps_custom_plane_generation_parameters():
+    config = AutoFlowConfig(
+        use_center_plane=False,
+        cross_section_dist=12.5,
+        start_dist=1.5,
+        end_dist=2.5,
+    )
+
+    ws = build_workspace(config)
+
+    assert ws.plane_gen_params.to_dict() == {
+        "use_center_plane": False,
+        "cross_section_distance": 12.5,
+        "start_distance": 1.5,
+        "end_distance": 2.5,
+        "smoothing_window": 15,
+        "smoothing_polyorder": 2,
+        "inter_time": 10,
+    }
+
+
+def test_build_workspace_maps_skeleton_and_streamline_parameters():
+    config = AutoFlowConfig(
+        remove_small_cc=False,
+        min_cc_volume=42.0,
+        seed_ratio=0.03,
+        tube_radius=0.12,
+    )
+
+    ws = build_workspace(config)
+
+    assert ws.skeleton_params.to_dict() == {
+        "remove_small_cc": False,
+        "min_cc_volume_mm3": 42.0,
+        "do_closing": True,
+        "do_opening": False,
+        "gaussian_sigma": 0.5,
+        "gaussian_enabled": True,
+    }
+    assert ws.streamline_params.to_dict() == {
+        "seed_ratio": 0.03,
+        "max_steps": 2000,
+        "min_seeds": 50,
+        "terminal_speed": 0.01,
+        "rng_seed": 0,
+    }
+    assert getattr(ws.streamline_params, "tube_radius") == 0.12
+
+
+def test_run_case_forwards_rendering_defaults_to_process_single(monkeypatch, tmp_path):
+    captured = {}
+
+    def fake_process_single(input_path, case_dir, **kwargs):
+        captured["input_path"] = input_path
+        captured["case_dir"] = case_dir
+        captured.update(kwargs)
+        return {"status": "ok", "case_dir": case_dir}
+
+    monkeypatch.setattr(api, "process_single", fake_process_single)
+
+    cfg = AutoFlowConfig()
+    out_dir = tmp_path / "case"
+    summary = api.run_case("demo_input.h5", output_dir=str(out_dir), config=cfg)
+
+    assert summary == {"status": "ok", "case_dir": str(out_dir)}
+    assert captured["input_path"] == "demo_input.h5"
+    assert captured["case_dir"] == str(out_dir)
+
+    assert captured["workspace"].plane_gen_params.cross_section_distance == 5.0
+    assert captured["fps"] == 12
+    assert captured["plane_rotation_frames"] == 180
+    assert captured["make_plane_video"] is False
+    assert captured["make_wss_video"] is False
+    assert captured["make_streamlines_video"] is False
+    assert captured["make_tke_video"] is False
+    assert captured["camera_view"] == "right"
+    assert captured["camera_distance_scale"] == 1.5
+    assert captured["rotate_dynamic_video"] is True
+    assert captured["dynamic_rotation_frames"] == 180
+    assert captured["dynamic_rotation_elevation_deg"] == 10.0
+    assert captured["dynamic_time_repeat"] == 3
+    assert captured["add_plane_idx"] is False
+    assert captured["add_path_idx"] is False
+    assert captured["wss_clim"] == (0.0, 10.0)
+    assert captured["tke_clim"] == (0.0, 100.0)
+    assert captured["streamline_clim"] == (0.0, 1)
+    assert captured["wss_bar_cfg"] == api.DEFAULT_WSS_BAR_CFG
+    assert captured["tke_bar_cfg"] == api.DEFAULT_TKE_BAR_CFG
+    assert captured["streamline_bar_cfg"] == api.DEFAULT_STREAMLINE_BAR_CFG
+    assert captured["wss_bar_cfg"] is not cfg.wss_bar_cfg
+    assert captured["tke_bar_cfg"] is not cfg.tke_bar_cfg
+    assert captured["streamline_bar_cfg"] is not cfg.streamline_bar_cfg

tests/test_demo_workflows.py

@@ -0,0 +1,130 @@
+import json
+import os
+from pathlib import Path
+import subprocess
+import sys
+
+import numpy as np
+
+from autoflow import AutoFlowConfig, run_batch
+
+
+REPO_ROOT = Path(__file__).resolve().parents[1]
+DEMO_INPUT = REPO_ROOT / "data" / "demo_data.h5"
+EXPECTED_PIXELWISE_KEYS = {"origin", "spacing", "tke", "tke_time", "wss"}
+NOTEBOOK_VIDEO_KEYS = {"streamlines", "tke", "wss"}
+
+
+def _run_cli(*args: str) -> subprocess.CompletedProcess[str]:
+    env = os.environ.copy()
+    existing = env.get("PYTHONPATH", "")
+    env["PYTHONPATH"] = str(REPO_ROOT) if not existing else os.pathsep.join((str(REPO_ROOT), existing))
+    return subprocess.run(
+        [sys.executable, "-m", "autoflow.cli", *args],
+        cwd=REPO_ROOT,
+        env=env,
+        capture_output=True,
+        text=True,
+        check=False,
+    )
+
+
+def _assert_demo_outputs(output_root: Path, expected_video_keys: set[str]) -> dict:
+    case_dir = output_root / "demo_data"
+    summary_path = case_dir / "summary.json"
+    plane_positions_path = case_dir / "plane_positions.json"
+    planes_path = case_dir / "planes.json"
+    plane_metrics_path = case_dir / "plane_metrics.json"
+    plane_qc_path = case_dir / "plane_qc.json"
+    pixelwise_path = case_dir / "derived_metrics_pixelwise.npz"
+    batch_report_path = output_root / "batch_report.json"
+    time_summary_path = output_root / "time_summary.txt"
+
+    for path in (
+        summary_path,
+        plane_positions_path,
+        planes_path,
+        plane_metrics_path,
+        plane_qc_path,
+        pixelwise_path,
+        batch_report_path,
+        time_summary_path,
+    ):
+        assert path.is_file(), path
+
+    summary = json.loads(summary_path.read_text(encoding="utf-8"))
+    assert summary["input"].endswith("data/demo_data.h5")
+    assert summary["output_dir"] == str(case_dir)
+    assert summary["n_planes"] >= 1
+    assert summary["n_paths"] >= 1
+    assert summary["n_forks"] >= 1
+    assert len(summary["plane_metrics"]) == summary["n_planes"]
+    assert set(summary["pixelwise_export"]) == EXPECTED_PIXELWISE_KEYS
+    assert Path(summary["plane_positions_file"]).is_file()
+    assert summary["reused_planes_file"] == ""
+
+    batch_report = json.loads(batch_report_path.read_text(encoding="utf-8"))
+    assert len(batch_report) == 1
+    assert batch_report[0]["status"] == "ok"
+    assert batch_report[0]["file"].endswith("data/demo_data.h5")
+
+    assert set(summary["videos"]) == expected_video_keys
+    for key in expected_video_keys:
+        video_path = Path(summary["videos"][key])
+        assert video_path.is_file(), video_path
+        assert video_path.suffix in {".gif", ".mp4"}
+
+    pixelwise = np.load(pixelwise_path)
+    assert set(pixelwise.files) == EXPECTED_PIXELWISE_KEYS
+
+    return summary
+
+
+def test_cli_demo_command_processes_demo_data(tmp_path):
+    output_root = tmp_path / "cli_demo"
+
+    result = _run_cli(str(DEMO_INPUT), "--output-dir", str(output_root))
+
+    assert result.returncode == 0, result.stderr or result.stdout
+    assert "Found 1 file(s) to process." in result.stdout
+    assert "Done: 1/1 succeeded." in result.stdout
+
+    summary = _assert_demo_outputs(output_root, expected_video_keys=set())
+    assert summary["videos"] == {}
+
+
+def test_library_demo_notebook_workflow_processes_demo_data(tmp_path):
+    output_root = tmp_path / "library_demo"
+    config = AutoFlowConfig(
+        inputs=[str(DEMO_INPUT)],
+        output_dir=str(output_root),
+        skip_derived=False,
+        use_multithread=True,
+        reuse_planes="",
+        use_center_plane=True,
+        cross_section_dist=15.0,
+        start_dist=5.0,
+        end_dist=0.0,
+        remove_small_cc=True,
+        min_cc_volume=50.0,
+        make_plane_video=False,
+        make_wss_video=True,
+        make_streamlines_video=True,
+        make_tke_video=True,
+        camera_view="right",
+        camera_distance_scale=1.5,
+        rotate_dynamic_video=True,
+        dynamic_rotation_frames=180,
+        dynamic_rotation_elevation_deg=10.0,
+        dynamic_time_repeat=3,
+        add_path_idx=False,
+    )
+
+    results, case_out = run_batch(config)
+
+    assert len(results) == 1
+    assert results[0]["status"] == "ok"
+    assert case_out == str(output_root / "demo_data")
+
+    summary = _assert_demo_outputs(output_root, expected_video_keys=NOTEBOOK_VIDEO_KEYS)
+    assert set(summary["videos"]) == NOTEBOOK_VIDEO_KEYS