Unverified Commit 26630279 authored by Zhang, Chen's avatar Zhang, Chen Committed by GitHub
Browse files

Merge pull request #271 from ornlneutronimaging/IMG444_update_default_atol 

[IMG444] atol can be inferred during 180 deg pair finding for sorted array
parents 7c6079da 0b7b8fb8

docs/api/imars3d.backend.corrections.rst

+2 −2
Original line number Diff line number Diff line
@@ -34,7 +34,7 @@ imars3d.backend.corrections.intensity\_fluctuation\_correction module 
   :members:

   :undoc-members:

   :show-inheritance:

   :exclude-members: ct, air_pixels, max_workers, name, sigma, tqdm_class

   :exclude-members: ct, air_pixels, max_workers, name, sigma, tqdm_class, roi



imars3d.backend.corrections.ring\_removal module

------------------------------------------------
@@ -43,4 +43,4 @@ imars3d.backend.corrections.ring\_removal module 
   :members:

   :undoc-members:

   :show-inheritance:

   :exclude-members: arrays, correction_range, kernel_size, max_workers, name, sub_division, tqdm_class, sinogram
 
   :exclude-members: arrays, correction_range, kernel_size, max_workers, name, sub_division, tqdm_class, sinogram, extreme_streak_iterations, extreme_detect_lambda, extreme_detect_size, extreme_replace_size, max_bin_iter_horizontal, bin_vertical, filter_strength, use_slices, slice_sizes, slice_step_sizes, denoise_indices

src/imars3d/backend/diagnostics/rotation.py

+7 −7
Original line number Diff line number Diff line
@@ -26,8 +26,8 @@ class find_rotation_center(param.ParameterizedFunction): 
        array of angles in degrees or radians, which must match the order of arrays

    in_degrees: bool = True

        whether angles are in degrees or radians, default is True (degrees)

    atol_deg: float = 1e-3

        tolerance for the search of 180 deg paris, default is 0.1 degrees

    atol_deg: Optional[float] = None

        tolerance for the search of 180 deg paris, default is None ("auto")

    num_pairs: int = 1

        Number of pairs to look for. Specifying -1 means as many pairs as possible.

    max_workers: int = 0
@@ -46,8 +46,8 @@ class find_rotation_center(param.ParameterizedFunction): 
    )

    in_degrees = param.Boolean(default=True, doc="whether angles are in degrees or radians, default is True (degrees)")

    atol_deg = param.Number(

        default=1e-3,

        doc="tolerance for the search of 180 deg paris, default is 0.1 degrees",

        default=None,

        doc="tolerance for the search of 180 deg paris, default is None (auto)",

    )

    num_pairs = param.Integer(

        default=1, bounds=(-1, None), doc="Number of pairs to look for. Specifying -1 means as many pairs as possible."
@@ -72,7 +72,7 @@ class find_rotation_center(param.ParameterizedFunction): 
            arrays=params.arrays,

            angles=params.angles,

            in_degrees=params.in_degrees,

            atol_deg=params.atol_deg,

            atol=params.atol_deg,

            num_pairs=params.num_pairs,

            max_workers=self.max_workers,

            tqdm_class=params.tqdm_class,
@@ -85,7 +85,7 @@ class find_rotation_center(param.ParameterizedFunction): 
        arrays: np.ndarray,

        angles: np.ndarray,

        in_degrees: bool = True,

        atol_deg: float = 1e-3,

        atol: float = None,

        num_pairs: int = 1,

        max_workers: int = -1,

        tqdm_class=None,
@@ -96,8 +96,8 @@ class find_rotation_center(param.ParameterizedFunction): 
            logger.error(msg)

            raise ValueError(msg)

        # locate 180 degree pairs

        atol = atol_deg if in_degrees else np.radians(atol_deg)

        idx_low, idx_hgh = find_180_deg_pairs_idx(angles, atol=atol, in_degrees=in_degrees)

        # decide how many pairs to use

        if num_pairs <= 0 or num_pairs >= idx_low.size:

            logger.info("Using all pairs of angles")

        elif num_pairs == 1:

src/imars3d/backend/diagnostics/tilt.py

+10 −2
Original line number Diff line number Diff line
@@ -20,7 +20,7 @@ logger = logging.getLogger(__name__) 


def find_180_deg_pairs_idx(

    angles: np.ndarray,

    atol: float = 1e-3,

    atol: float = None,

    in_degrees: bool = True,

) -> Tuple[np.ndarray, np.ndarray]:

    """
@@ -31,7 +31,7 @@ def find_180_deg_pairs_idx( 
    angles:

        The list of angles as a 1d array.

    atol:

        The absolute tolerance in degree for the 180 degree pairs.

        The absolute tolerance for the 180 degree pairs.

    in_degrees:

        Whether the angles are in degrees or radians, default is in degrees.
@@ -45,6 +45,14 @@ def find_180_deg_pairs_idx( 
        raise ValueError("angles must be a 1d array")

    # ensure angles are in degrees

    angles = angles if in_degrees else np.degrees(angles)

    # compute atol if not specified

    if atol is None:

        sorted_indices = np.argsort(angles)

        atol = np.min(np.diff(angles[sorted_indices])) / 2.0

        del sorted_indices

        logger.debug(f"use computed atol = {atol}")

    else:

        atol = atol if in_degrees else np.degrees(atol)

    # compute the self difference matrix

    angles = angles[..., np.newaxis]

    diff_matrix = angles.T - angles

tests/unit/backend/diagnostics/test_rotation.py

+3 −0
Original line number Diff line number Diff line
@@ -72,10 +72,13 @@ def test_differrent_centers(center_ref): 
    projs = get_synthetic_stack(center_ref)

    # this is using default number of pairs (1)

    center_calc = find_rotation_center(arrays=projs, angles=OMEGAS, in_degrees=False)

    # with atol

    center_calc2 = find_rotation_center(arrays=projs, angles=OMEGAS, in_degrees=False, atol=0.5)

    # verify

    # NOTE:

    # answer within the same pixel should be sufficient for most cases

    np.testing.assert_allclose(center_calc, center_ref, atol=0.2)

    np.testing.assert_allclose(center_calc2, center_ref, atol=0.2)





def test_wrong_dimension():

tests/unit/backend/diagnostics/test_tilt.py

+7 −0
Original line number Diff line number Diff line
@@ -227,6 +227,13 @@ def test_find_180_deg_pairs(): 
    # verify

    np.testing.assert_equal(low_range_idx, np.array([0, 1, 2, 3, 4]))

    np.testing.assert_equal(high_range_idx, np.array([5, 6, 7, 8, 9]))

    # test explicit atol

    # NOTE: use the same formula to compute atol outside the function

    sorted_indices = np.argsort(omegas)

    atol = np.min(np.diff(omegas[sorted_indices])) / 2.0

    low_range_idx, high_range_idx = find_180_deg_pairs_idx(omegas, in_degrees=False, atol=atol)

    np.testing.assert_equal(low_range_idx, np.array([0, 1, 2, 3, 4]))

    np.testing.assert_equal(high_range_idx, np.array([5, 6, 7, 8, 9]))

    # test incorrect input

    omegas = np.random.random(5 * 5) * np.pi

    omegas = omegas.reshape(5, 5)