def test_slice_plate_image(self, image_circle):
plates = PlateCollection(shape=(1, 1))
plates.add(id=1, diameter=180, edge_cut=20, center=(102, 102))
images = plates.slice_plate_image(image_circle)
assert len(images) == 1
assert images[1].shape == (141, 141)
def test_centers(self):
centers = list()
collection = PlateCollection()
for i in range(1, 10):
center = (i, i)
centers.append(center)
collection.add(id=i, diameter=1, center=center)
assert collection.count == len(centers)
assert collection.centers == centers
def test_plates_from_image(self, image_circle):
label = "label"
plates = PlateCollection(shape=(1, 1))
plates.plates_from_image(image=image_circle,
diameter=180,
labels={1: label})
assert plates.count == 1
assert plates.centers == [(102, 102)]
assert plates.items[0].diameter == 160
assert plates.items[0].name == label
def test_from_image(self, image_circle):
plates = PlateCollection.from_image(
shape=(1, 1),
image=image_circle,
diameter=180,
)
assert plates is not None
assert isinstance(plates, PlateCollection)
def test_plates_to_csv(self, image_circle, tmp_path):
import csv
plates = PlateCollection.from_image(
shape=(1, 1),
image=image_circle,
diameter=180,
)
result = plates.plates_to_csv(tmp_path)
# Check all rows were written correctly
with open(result, 'r') as csvfile:
reader = list(csv.reader(csvfile))
assert len(reader) == plates.count + 1
assert reader[1] == [
"1", "", "(102, 102)", "160", "0", "0", "0", "0.0", "0.0",
"0.0", "0.0", "0.0", "0.0", "0.0", "0.0"
]
def test_coordinate_to_index_invalid(self, coordinate):
with pytest.raises(ValueError):
PlateCollection.coordinate_to_index(coordinate)
def test_coordinate_to_index(self, coordinate, expected):
result = PlateCollection.coordinate_to_index(coordinate)
assert result == expected
def test_index_to_coordinate_invalid(self, index, shape):
with pytest.raises(ValueError):
PlateCollection.index_to_coordinate(index, shape)
with pytest.raises(IndexError):
PlateCollection.index_to_coordinate(100, (1, 1))
def test_index_to_coordinate(self, index, shape, expected):
result = PlateCollection.index_to_coordinate(index, shape)
assert result == expected
def test_plates_from_image_invalid(self, image_circle):
plates = PlateCollection()
with pytest.raises(ValueError):
plates.plates_from_image(image=image_circle, diameter=180)
def test_add(self, id, diameter):
collection = PlateCollection()
item_new = collection.add(id=id, diameter=diameter)
assert collection.count == 1
assert item_new in collection.items
def test_init_invalid(self, shape):
with pytest.raises(ValueError):
PlateCollection(shape=shape)
def test_init(self, shape):
collection = PlateCollection(shape=shape)
assert collection.shape == shape
# Output a plate image with plate locations outlined
image_files = [
["./images/outlined/3_1_95.tif", (3, 1), 95],
["./images/outlined/3_2_35_empty.tif", (3, 2), 35],
["./images/outlined/3_2_35.tif", (3, 2), 35],
["./images/outlined/3_2_90_empty.tif", (3, 2), 90],
["./images/outlined/3_2_90.tif", (3, 2), 90],
["./images/outlined/6_4_35_empty.tif", (6, 4), 35],
["./images/outlined/6_4_35.tif", (6, 4), 35],
]
for image in image_files:
image_file, lattice, size = image
size = int(mm_to_pixels(size, dots_per_inch = 300))
# Load the image
img = imread(image_file, as_gray = False, plugin = "pil")
# Locate plates in the image and store as Plate instances
plates = PlateCollection.from_image(
shape = lattice,
image = rgb2gray(img),
diameter = size,
search_radius = size // 20,
edge_cut = int(round(size * (5 / 100))),
labels = []
)
# Plot the locations on the plate image
plot_plate_map(img, plates.items, Path(image_file))