Spaces:
Running on Zero
Running on Zero
| import os | |
| import zipfile | |
| import numpy as np | |
| import pytest | |
| from cellquant.annotations import ( | |
| ImageAnnotation, | |
| Shape, | |
| discover, | |
| image_key, | |
| load_annotation_file, | |
| parse_cvat_xml, | |
| rasterize, | |
| to_rgb_uint8, | |
| ) | |
| XML = """<?xml version="1.0" encoding="utf-8"?> | |
| <annotations> | |
| <version>1.1</version> | |
| <meta><task><size>1</size></task></meta> | |
| <image id="0" name="K1 demo - RGB copy.tif" width="100" height="80"> | |
| <polyline label="Cell, Antibody +" source="manual" occluded="0" points="10.0,10.0;30.0,10.0;30.0,30.0;10.0,30.0;10.0,10.0" z_order="0"></polyline> | |
| <polygon label="Cell, Nostril, Antibody -" source="manual" occluded="0" points="50,50;70,50;70,70;50,70" z_order="0"></polygon> | |
| <ellipse label="Nostril in Nucleus" source="manual" occluded="0" cx="60" cy="60" rx="3" ry="2" z_order="0"></ellipse> | |
| <polyline label="Nostril External of Nucleus" source="manual" occluded="0" points="90.2,5.1;90.4,5.3;90.6,5.1" z_order="0"></polyline> | |
| <box label="Cell, Antibody -" source="manual" occluded="0" xtl="80" ytl="60" xbr="95" ybr="75" z_order="0"></box> | |
| </image> | |
| </annotations> | |
| """ | |
| def test_parse_xml_shapes_and_counts(): | |
| anns = parse_cvat_xml(XML.encode()) | |
| assert len(anns) == 1 | |
| a = anns[0] | |
| assert (a.width, a.height) == (100, 80) | |
| assert a.key == "K1" | |
| c = a.counts() | |
| assert c["Cell, Antibody +"] == 1 and c["Cell, Nostril, Antibody -"] == 1 and c["Cell, Antibody -"] == 1 | |
| assert c["Nostril in Nucleus"] == 1 and c["Nostril External of Nucleus"] == 1 | |
| def test_rasterize_areas_and_attributes(): | |
| a = parse_cvat_xml(XML.encode())[0] | |
| R = rasterize(a) | |
| assert R.cell_inst.shape == (80, 100) | |
| assert R.n_cells == 3 and R.n_nostrils == 2 | |
| areas = np.bincount(R.cell_inst.ravel())[1:] | |
| # 20x20 squares rasterise to ~21x21 pixels (inclusive edges) -> 400..441 | |
| assert all(380 <= x <= 450 for x in areas[:2]) or all(380 <= x <= 450 for x in sorted(areas)[-2:]) | |
| # tiny polyline (sub-pixel) keeps its centroid pixel | |
| nareas = np.bincount(R.nostril_inst.ravel())[1:] | |
| assert nareas.min() >= 1 | |
| # ellipse rx=3, ry=2 -> pi*6 ~ 19 px | |
| assert 10 <= nareas.max() <= 30 | |
| ab = R.cell_antibody() | |
| hn = R.cell_has_nostril() | |
| labels = R.cell_labels | |
| for i, lab in enumerate(labels): | |
| if i == 0: | |
| continue | |
| assert ab[i] == lab.endswith("+") | |
| assert hn[i] == ("Nostril" in lab) | |
| assert R.nostril_inside().sum() == 1 | |
| def test_image_key_handles_copies_and_double_spaces(): | |
| assert image_key("F114 F 35D SC Iba W002 - Focused EDF Document_RGB.tif") == "F114" | |
| assert image_key("C110 F 35D SC Iba W001 - Focused EDF Document_RGB copy (1).tif") == "C110" | |
| def test_discover_pairs_by_internal_name(tmp_path): | |
| from PIL import Image | |
| Image.fromarray(np.zeros((80, 100, 3), np.uint8)).save(tmp_path / "K1 demo - RGB copy (1).png") | |
| Image.fromarray(np.zeros((80, 100, 3), np.uint8)).save(tmp_path / "K2 other.png") # unannotated | |
| with zipfile.ZipFile(tmp_path / "WRONGNAME_Annotated.zip", "w") as zf: | |
| zf.writestr("annotations.xml", XML) | |
| samples, unann = discover(str(tmp_path), verbose=False) | |
| assert [s.key for s in samples] == ["K1"] | |
| assert len(unann) == 1 and unann[0].endswith("K2 other.png") | |
| assert samples[0].annotation.count("Cell, Antibody +") == 1 | |
| def test_load_annotation_file_zip_and_xml(tmp_path): | |
| (tmp_path / "a.xml").write_text(XML) | |
| with zipfile.ZipFile(tmp_path / "a.zip", "w") as zf: | |
| zf.writestr("annotations.xml", XML) | |
| assert len(load_annotation_file(str(tmp_path / "a.xml"))[0].shapes) == 5 | |
| assert len(load_annotation_file(str(tmp_path / "a.zip"))[0].shapes) == 5 | |
| with pytest.raises(ValueError): | |
| load_annotation_file(str(tmp_path / "nothing.txt")) | |
| def test_to_rgb_uint8_variants(): | |
| g = np.full((4, 5), 7, np.uint8) | |
| assert to_rgb_uint8(g).shape == (4, 5, 3) | |
| chw = np.zeros((3, 4, 5), np.uint8) | |
| assert to_rgb_uint8(chw).shape == (4, 5, 3) | |
| rgba = np.zeros((4, 5, 4), np.uint8) | |
| assert to_rgb_uint8(rgba).shape == (4, 5, 3) | |
| u16 = np.full((4, 5, 3), 4000, np.uint16) | |
| out = to_rgb_uint8(u16) | |
| assert out.dtype == np.uint8 and out.max() == 255 | |
| f01 = np.full((4, 5, 3), 0.5, np.float32) | |
| assert to_rgb_uint8(f01).max() in (127, 128) | |
| with pytest.raises(ValueError): | |
| to_rgb_uint8(np.zeros((40, 50, 2), np.uint8)) | |
| with pytest.raises(ValueError): | |
| to_rgb_uint8(np.zeros((4, 50, 2), np.uint8)) # 4 rows is not "RGBA channel-first" | |
| def test_shape_area_shoelace(): | |
| s = Shape("Cell, Antibody +", "polygon", np.array([[0, 0], [10, 0], [10, 10], [0, 10]], np.float32)) | |
| assert abs(s.area - 100) < 1e-6 | |