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"
]
# 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))