diff --git a/src/cryo_sbi/inference/priors.py b/src/cryo_sbi/inference/priors.py index f8fbb29..6342b1f 100644 --- a/src/cryo_sbi/inference/priors.py +++ b/src/cryo_sbi/inference/priors.py @@ -15,7 +15,7 @@ def gen_quat() -> torch.Tensor: count = 0 while count < 1: quat = 2 * torch.rand(size=(4,)) - 1 - norm = torch.sqrt(torch.sum(quat**2)) + norm = torch.sqrt(torch.sum(quat ** 2)) if 0.2 <= norm <= 1.0: quat /= norm count += 1 @@ -207,7 +207,7 @@ class PriorLoader(DataLoader): def __init__( self, prior: Distribution, - batch_size: int = 2**8, # 256 + batch_size: int = 2 ** 8, # 256 **kwargs, ): super().__init__( diff --git a/src/cryo_sbi/utils/image_utils.py b/src/cryo_sbi/utils/image_utils.py index 0699b59..6080fde 100644 --- a/src/cryo_sbi/utils/image_utils.py +++ b/src/cryo_sbi/utils/image_utils.py @@ -25,9 +25,9 @@ def circular_mask(n_pixels: int, radius: int, inside: bool = True) -> torch.Tens r_2d = grid[None, :] ** 2 + grid[:, None] ** 2 if inside is True: - mask = r_2d < radius**2 + mask = r_2d < radius ** 2 else: - mask = r_2d > radius**2 + mask = r_2d > radius ** 2 return mask @@ -183,7 +183,7 @@ def __init__(self, image_size: int, sigma: int): -0.5 * (image_size - 1), 0.5 * (image_size - 1), image_size ) self._r_2d = self._grid[None, :] ** 2 + self._grid[:, None] ** 2 - self._mask = torch.exp(-self._r_2d / (2 * sigma**2)) + self._mask = torch.exp(-self._r_2d / (2 * sigma ** 2)) def __call__(self, image: torch.Tensor) -> torch.Tensor: """ diff --git a/src/cryo_sbi/wpa_simulator/ctf.py b/src/cryo_sbi/wpa_simulator/ctf.py index 35a4a81..9717e67 100644 --- a/src/cryo_sbi/wpa_simulator/ctf.py +++ b/src/cryo_sbi/wpa_simulator/ctf.py @@ -21,7 +21,7 @@ def apply_ctf(image: torch.Tensor, defocus, b_factor, amp, pixel_size) -> torch. freq_pix_1d = torch.fft.fftfreq(num_pixels, d=pixel_size, device=image.device) x, y = torch.meshgrid(freq_pix_1d, freq_pix_1d, indexing="ij") - freq2_2d = x**2 + y**2 + freq2_2d = x ** 2 + y ** 2 freq2_2d = freq2_2d.expand(num_batch, -1, -1) imag = torch.zeros_like(freq2_2d, device=image.device) * 1j @@ -30,7 +30,7 @@ def apply_ctf(image: torch.Tensor, defocus, b_factor, amp, pixel_size) -> torch. ctf = ( -amp * torch.cos(phase * freq2_2d * 0.5) - - torch.sqrt(1 - amp**2) * torch.sin(phase * freq2_2d * 0.5) + - torch.sqrt(1 - amp ** 2) * torch.sin(phase * freq2_2d * 0.5) + imag ) ctf = ctf * env / amp diff --git a/src/cryo_sbi/wpa_simulator/image_generation.py b/src/cryo_sbi/wpa_simulator/image_generation.py index 3e9bc00..c19a18b 100644 --- a/src/cryo_sbi/wpa_simulator/image_generation.py +++ b/src/cryo_sbi/wpa_simulator/image_generation.py @@ -13,7 +13,7 @@ def gen_quat() -> torch.Tensor: count = 0 while count < 1: quat = 2 * torch.rand(size=(4,)) - 1 - norm = torch.sqrt(torch.sum(quat**2)) + norm = torch.sqrt(torch.sum(quat ** 2)) if 0.2 <= norm <= 1.0: quat /= norm count += 1 @@ -72,7 +72,7 @@ def project_density( """ num_batch, _, num_atoms = coords.shape - norm = 1 / (2 * torch.pi * sigma**2 * num_atoms) + norm = 1 / (2 * torch.pi * sigma ** 2 * num_atoms) grid_min = -pixel_size * num_pixels * 0.5 grid_max = pixel_size * num_pixels * 0.5 diff --git a/src/cryo_sbi/wpa_simulator/noise.py b/src/cryo_sbi/wpa_simulator/noise.py index a763bb2..013c066 100644 --- a/src/cryo_sbi/wpa_simulator/noise.py +++ b/src/cryo_sbi/wpa_simulator/noise.py @@ -19,7 +19,7 @@ def circular_mask(n_pixels: int, radius: int, device: str = "cpu") -> torch.Tens -0.5 * (n_pixels - 1), 0.5 * (n_pixels - 1), n_pixels, device=device ) r_2d = grid[None, :] ** 2 + grid[:, None] ** 2 - mask = r_2d < radius**2 + mask = r_2d < radius ** 2 return mask diff --git a/tests/test_image_utils.py b/tests/test_image_utils.py index ff21436..dadef69 100644 --- a/tests/test_image_utils.py +++ b/tests/test_image_utils.py @@ -11,9 +11,9 @@ def test_circular_mask(): assert inside_mask.shape == (n_pixels, n_pixels) assert outside_mask.shape == (n_pixels, n_pixels) - assert inside_mask.sum().item() == pytest.approx(radius**2 * 3.14159, abs=10) + assert inside_mask.sum().item() == pytest.approx(radius ** 2 * 3.14159, abs=10) assert outside_mask.sum().item() == pytest.approx( - n_pixels**2 - radius**2 * 3.14159, abs=10 + n_pixels ** 2 - radius ** 2 * 3.14159, abs=10 ) @@ -27,7 +27,7 @@ def test_mask_class(): masked_image = mask(image) assert masked_image.shape == (image_size, image_size) assert masked_image[inside].sum().item() == pytest.approx( - image_size**2 - radius**2 * 3.14159, abs=10 + image_size ** 2 - radius ** 2 * 3.14159, abs=10 ) diff --git a/tests/test_simulator.py b/tests/test_simulator.py index ed88cdc..54e8be8 100644 --- a/tests/test_simulator.py +++ b/tests/test_simulator.py @@ -80,6 +80,7 @@ def test_get_snr(noise_std, num_images): snr.flatten(), noise_std * torch.ones(images.shape[0]), atol=1e-01 ), "SNR is not correct" + @pytest.mark.parametrize(("num_images"), [2, 3, 10]) def test_simulator_default_settings(num_images): sim = CryoEmSimulator("tests/config_files/image_params_testing.json") @@ -94,5 +95,3 @@ def test_simulator_custom_indices(): assert (parameters[0] == test_indices).all().item() assert images.shape == torch.Size([6, 64, 64]) - -