def intensities(self, codebook=None) -> IntensityTable:
if codebook is None:
codebook = self.codebook()
intensities = IntensityTable.synthetic_intensities(
codebook, self.n_z, self.height, self.width, self.n_spots,
self.mean_fluor_per_spot, self.mean_photons_per_fluor)
assert intensities.dtype == np.float32 and intensities.max() <= 1
return intensities
def test_synthetic_intensities_generates_correct_number_of_features(
loaded_codebook):
n_spots = 2
intensities = IntensityTable.synthetic_intensities(loaded_codebook,
n_spots=n_spots)
assert isinstance(intensities, IntensityTable)
# shape should have n_spots and channels and hybridization rounds equal to the codebook's shape
assert intensities.shape == (n_spots, *loaded_codebook.shape[1:])
def test_synthetic_intensities_have_correct_number_of_on_features(
loaded_codebook):
n_spots = 2
intensities = IntensityTable.synthetic_intensities(loaded_codebook,
n_spots=n_spots)
on_features = np.sum(intensities.values != 0)
# this asserts that the number of features "on" in intensities should be equal to the
# number of "on" features in the codewords, times the total number of spots in intensities.
assert on_features == loaded_codebook.sum(
(Indices.CH, Indices.HYB)).values.mean() * n_spots
def intensities(self, codebook=None) -> IntensityTable:
if codebook is None:
codebook = self.codebook()
return IntensityTable.synthetic_intensities(
codebook, self.n_z, self.height, self.width, self.n_spots,
self.mean_fluor_per_spot, self.mean_photons_per_fluor)
def synthetic_intensity_table(loaded_codebook) -> IntensityTable:
return IntensityTable.synthetic_intensities(loaded_codebook, n_spots=2)