def test_synthetic_spot_creation_raises_error_with_coords_too_small(
synthetic_intensity_table):
num_z = 0
height = 40
width = 50
with pytest.raises(ValueError):
ImageStack.synthetic_spots(synthetic_intensity_table, num_z, height,
width)
def test_synthetic_spot_creation_produces_an_imagestack(
synthetic_intensity_table):
num_z = 12
height = 50
width = 40
image = ImageStack.synthetic_spots(synthetic_intensity_table, num_z,
height, width)
assert isinstance(image, ImageStack)
def synthetic_spot_pass_through_stack(synthetic_dataset_with_truth_values):
codebook, true_intensities, _ = synthetic_dataset_with_truth_values
true_intensities = true_intensities[:2]
# transfer the intensities to the stack but don't do anything to them.
img_stack = ImageStack.synthetic_spots(
true_intensities, num_z=12, height=50, width=45, n_photons_background=0,
point_spread_function=(0, 0, 0), camera_detection_efficiency=1.0,
background_electrons=0, graylevel=1)
return codebook, true_intensities, img_stack
def spots(self, intensities=None) -> ImageStack:
if intensities is None:
intensities = self.intensities()
stack = ImageStack.synthetic_spots(
intensities, self.n_z, self.height, self.width,
self.n_photons_background, self.point_spread_function,
self.camera_detection_efficiency, self.background_electrons,
self.gray_level, self.ad_coversion_bits)
assert stack.xarray.dtype == np.float32
return stack