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Running on Zero
Running on Zero
File size: 4,701 Bytes
5d31c67 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 | 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
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