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Running on Zero
Running on Zero
| import os | |
| import numpy as np | |
| import pytest | |
| from PIL import Image | |
| WEIGHTS = os.environ.get("CELLQUANT_WEIGHTS", os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "weights", "cellquant.pt")) | |
| def test_analyze_files_end_to_end(tmp_path, monkeypatch): | |
| monkeypatch.delenv("GEMINI_API_KEY", raising=False) # never call Gemini from the tests | |
| import app | |
| rng = np.random.default_rng(0) | |
| img = (rng.random((200, 240, 3)) * 50).astype(np.uint8) | |
| p1 = tmp_path / "a.png" | |
| Image.fromarray(img).save(p1) | |
| import tifffile | |
| p2 = tmp_path / "b.tif" | |
| tifffile.imwrite(str(p2), img) | |
| rows, gallery, zip_path, summary = app.analyze_files([str(p1), str(p2)], 0.5, 0.5, 50, "head", "contains") | |
| from cellquant.labels import COUNT_COLUMNS | |
| assert len(rows) == 2 and rows[0][0] == "a.png" and len(rows[0]) == 1 + len(COUNT_COLUMNS) == 9 | |
| for r in rows: # "All nuclei" after the four nucleus labels, "All puncta" after the two punctum labels | |
| assert r[5] == sum(r[1:5]) and r[8] == sum(r[6:8]) | |
| assert len(gallery) == 2 and os.path.exists(gallery[0][0]) | |
| assert gallery[0][1] == f"a.png: {rows[0][5]} nuclei, {rows[0][8]} puncta" | |
| assert os.path.exists(zip_path) and summary.startswith("Analysed 2 images in ") and "on the CPU" in summary | |
| assert "Gemini summary is off" in summary # no key: the write-up is replaced by a one-line notice | |
| assert app._gpu_seconds(3) == 15 + 3 * {1: 4, 4: 6, 8: 10}[app.TTA] and app._gpu_seconds(0) == 15 + {1: 4, 4: 6, 8: 10}[app.TTA] | |
| with pytest.raises(Exception): | |
| app.analyze_files([], 0.5, 0.5, 50, "head", "contains") | |
| import csv | |
| import io | |
| import json | |
| import zipfile | |
| with zipfile.ZipFile(zip_path) as zf: | |
| names = zf.namelist() | |
| counts_csv = list(csv.reader(io.StringIO(zf.read("counts.csv").decode()))) | |
| results = json.loads(zf.read("results.json")) | |
| assert "counts.csv" in names and "objects.csv" in names and "results.json" in names | |
| assert counts_csv[0] == ["image"] + list(COUNT_COLUMNS) | |
| assert counts_csv[0][5] == "All nuclei" and counts_csv[0][8] == "All puncta" | |
| assert [[r[0]] + [int(v) for v in r[1:]] for r in counts_csv[1:]] == rows | |
| assert results["cellquant_version"] == app.__version__ | |
| assert results["images"]["a.png"]["totals"] == {"All nuclei": rows[0][5], "All puncta": rows[0][8]} | |
| assert results["images"]["a.png"]["totals"]["All nuclei"] == sum(results["images"]["a.png"]["counts"][lab] for lab in COUNT_COLUMNS[:4]) | |
| def test_build_demo_constructs(): | |
| pytest.importorskip("gradio") | |
| import app | |
| demo = app.build_demo() | |
| assert demo is not None | |