def test_save_cell_images(tmp_path):
cells = segment_cells(locate_module_and_cells(datasets.poly10x6(1)[0]))
save_images(tmp_path, cells)
for cell in cells:
p = tmp_path / "{}_row{:02d}_col{:02d}{}".format(
cell.path.stem, cell.row, cell.col, cell.path.suffix)
img_read = read_module_image(p, EL_IMAGE)
def test_segment_cells_single_image():
seq = data.datasets.poly10x6(1)
seq = detection.locate_module_and_cells(seq, True)
cells = detection.segment_cells(seq[0])
assert isinstance(cells, CellImageSequence)
assert len(cells) == 60
assert isinstance(cells[0], CellImage)
def test_save_images_filename_hook(tmp_path: Path):
cells = segment_cells(locate_module_and_cells(datasets.poly10x6(1)[0]))
hook = lambda x: "{}_{:02d}{:02d}{}".format(x.path.stem, x.row, x.col, x.
path.suffix)
save_images(tmp_path, cells)
for cell in cells:
p = tmp_path / "{}_{:02d}{:02d}{}".format(cell.path.stem, cell.row,
cell.col, cell.path.suffix)
# try read
img_read = read_module_image(p, EL_IMAGE)
def test_segment_cells():
seq = data.datasets.poly10x6(2)
seq = detection.locate_module_and_cells(seq, True)
cells = detection.segment_cells(seq)
assert isinstance(cells, CellImageSequence)
assert len(cells) == 120
assert isinstance(cells[0], CellImage)
assert cells[0].row == 0
assert cells[0].col == 0
assert cells[1].col == 1
assert cells[11].row == 1
assert cells[0].has_meta("segment_module_original")
assert (cells[0].get_meta("segment_module_original").has_meta(
"segment_module_original_box"))
def test_single_segmentation():
# load images
img = datasets.poly10x6(N=1)[0]
# perform detection
module = locate_module_and_cells(img)
# check result
assert module.has_meta("transform")
# check that show result does not fail
module.show()
# perform segmentation into cells
cells = segment_cells(module)
# check
assert len(cells) == 60
def test_multi_segmentation():
# load images
_, imgs = datasets.multi_module_detection(N=2)
# perform multi module segmentation
modules = locate_multiple_modules(imgs, rows=6, cols=10)
# check result
assert len(modules) == 12
assert isinstance(modules[0].get_meta("multimodule_original"), Image)
assert modules[0].get_meta("multimodule_original").path == imgs[0].path
# check that plotting does not fail
modules[0].get_meta("multimodule_original").show()
# perform precise module localization and segmentation
modules = locate_module_and_cells(modules)
modules_crop = segment_modules(modules)
# check result
assert len(modules) == 12
assert_equal(
modules_crop[0].get_meta("transform")(np.array([[0.0, 0.0]])),
np.array([0.0, 0.0]),
)
# make sure that original is preserved
assert isinstance(modules_crop[0].get_meta("multimodule_original"), Image)
assert modules_crop[0].get_meta(
"multimodule_original").path == imgs[0].path
# check show
modules_crop.head()
# check segmentation into cells
cells = segment_cells(modules_crop[0])
assert len(cells) == 60
# make sure that original is preserved
assert isinstance(cells[0].get_meta("multimodule_original"), Image)
assert cells[0].get_meta("multimodule_original").path == imgs[0].path