nabu 2024.1.0rc3__py3-none-any.whl → 2024.1.1__py3-none-any.whl

build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/reconstruction/sinogram.py

@@ -0,0 +1,467 @@
+import numpy as np
+from scipy.interpolate import interp1d
+from ..utils import get_2D_3D_shape, check_supported, deprecated_class, deprecated
+
+
+class SinoBuilder:
+    """
+    A class to build sinograms.
+    """
+
+    def __init__(
+        self, sinos_shape=None, radios_shape=None, rot_center=None, halftomo=False, angles=None, interpolate=False
+    ):
+        """
+        Initialize a SinoBuilder instance.
+
+        Parameters
+        ----------
+        sinos_shape: tuple of int
+            Shape of the stack of sinograms, in the form `(n_z, n_angles, n_x)`.
+            If not provided, it is derived from `radios_shape`.
+        radios_shape: tuple of int
+            Shape of the chunk of radios, in the form `(n_angles, n_z, n_x)`.
+            If not provided, it is derived from `sinos_shape`.
+        rot_center: int or array
+            Rotation axis position. A scalar indicates the same rotation axis position
+            for all the projections.
+        halftomo: bool
+            Whether "half tomography" is enabled. Default is False.
+        interpolate: bool, optional
+            Only used if halftomo=True.
+            Whether to re-grid the second part of sinograms to match projection k with projection k + n_a/2.
+            This forces each pair of projection (k, k + n_a/2) to be separated by exactly 180 degrees.
+        angles: array, optional
+            Rotation angles (in radians). Used and required only when halftomo and interpolate are True.
+        """
+        self._get_shapes(sinos_shape, radios_shape)
+        self.set_rot_center(rot_center)
+        self._configure_halftomo(halftomo, interpolate, angles)
+
+    def _get_shapes(self, sinos_shape, radios_shape=None):
+        if (sinos_shape is None) and (radios_shape is None):
+            raise ValueError("Need to provide sinos_shape and/or radios_shape")
+        if sinos_shape is None:
+            n_a, n_z, n_x = get_2D_3D_shape(radios_shape)
+            sinos_shape = (n_z, n_a, n_x)
+        elif len(sinos_shape) == 2:
+            sinos_shape = (1,) + sinos_shape
+        if radios_shape is None:
+            n_z, n_a, n_x = get_2D_3D_shape(sinos_shape)
+            radios_shape = (n_a, n_z, n_x)
+        elif len(radios_shape) == 2:
+            radios_shape = (1,) + radios_shape
+
+        self.sinos_shape = sinos_shape
+        self.radios_shape = radios_shape
+        n_a, n_z, n_x = radios_shape
+        self.n_angles = n_a
+        self.n_z = n_z
+        self.n_x = n_x
+
+    def set_rot_center(self, rot_center):
+        """
+        Set the rotation axis position for the current radios/sinos stack.
+
+        rot_center: int or array
+            Rotation axis position. A scalar indicates the same rotation axis position
+            for all the projections.
+        """
+        if rot_center is None:
+            rot_center = (self.n_x - 1) / 2.0
+        if not (np.isscalar(rot_center)):
+            rot_center = np.array(rot_center)
+            if rot_center.size != self.n_angles:
+                raise ValueError(
+                    "Expected rot_center to have %d elements but got %d" % (self.n_angles, rot_center.size)
+                )
+        self.rot_center = rot_center
+
+    def _configure_halftomo(self, halftomo, interpolate, angles):
+        self.halftomo = halftomo
+        self.interpolate = interpolate
+        self.angles = angles
+        self._halftomo_flip = False
+        if not self.halftomo:
+            return
+        if interpolate and (angles is None):
+            raise ValueError("The parameter 'angles' has to be provided when using halftomo=True and interpolate=True")
+        self.extended_sino_width = get_extended_sinogram_width(self.n_x, self.rot_center)
+        # If CoR is on the left: "flip" the logic
+        if self.rot_center < (self.n_x - 1) / 2:
+            self.rot_center = self.n_x - 1 - self.rot_center
+            self._halftomo_flip = True
+        #
+
+        if abs(self.rot_center - ((self.n_x - 1) / 2.0)) < 1:  # which tol ?
+            raise ValueError("Half tomography: incompatible rotation axis position: %.2f" % self.rot_center)
+        self.sinos_halftomo_shape = (self.n_z, (self.n_angles + 1) // 2, self.extended_sino_width)
+
+    def _check_array_shape(self, array, kind="radio"):
+        expected_shape = self.radios_shape if "radio" in kind else self.sinos_shape
+        assert array.shape == expected_shape, "Expected radios shape %s, but got %s" % (expected_shape, array.shape)
+
+    @property
+    def output_shape(self):
+        """
+        Get the output sinograms shape.
+        """
+        if self.halftomo:
+            return self.sinos_halftomo_shape
+        return self.sinos_shape
+
+    #
+    # 2D
+    #
+
+    def _get_sino_simple(self, radios, i):
+        return radios[:, i, :]  # view
+
+    def _get_sino_halftomo(self, sino, output=None):
+        # TODO output is ignored for now
+        if self.interpolate:
+            match_half_sinos_parts(sino, self.angles)
+        elif self.n_angles & 1:
+            # Odd number of projections - add one line in the end
+            sino = np.vstack([sino, np.zeros_like(sino[-1])])
+        if self._halftomo_flip:
+            sino = sino[:, ::-1]
+
+        if self.rot_center > self.n_x:
+            # (hopefully rare) case where CoR is outside FoV
+            result = _convert_halftomo_right(sino, self.extended_sino_width)
+        else:
+            # Standard case
+            result = convert_halftomo(sino, self.extended_sino_width)
+
+        if self._halftomo_flip:
+            result = result[:, ::-1]
+        return result
+
+    def get_sino(self, radios, i, output=None):
+        """
+        The the sinogram at a given index.
+
+        Parameters
+        ----------
+        radios: array
+            3D array with shape (n_z, n_angles, n_x)
+        i: int
+            Sinogram index
+
+        Returns
+        -------
+        sino: array
+            Two dimensional array with shape (n_angles2, n_x2) where the dimensions
+            are determined by the current settings.
+        """
+        sino = self._get_sino_simple(radios, i)
+        if self.halftomo:
+            return self._get_sino_halftomo(sino, output=None)
+        else:
+            return sino
+
+    def convert_sino(self, sino, output=None):
+        if not self.halftomo:
+            return sino
+        return self._get_sino_halftomo(sino, output=output)
+
+    #
+    # 3D
+    #
+
+    def _get_sinos_simple(self, radios, output=None):
+        res = np.rollaxis(radios, 1, 0)  # view
+        if output is not None:
+            output[...] = res[...]  # copy
+            return output
+        return res
+
+    def _get_sinos_halftomo(self, radios, output=None):
+        n_a, n_z, n_x = radios.shape
+        if output is None:
+            output = np.zeros(self.sinos_halftomo_shape, dtype=np.float32)
+        elif output.shape != self.output_shape:
+            raise ValueError("Expected output shape to be %s, but got %s" % (str(output.shape), str(self.output_shape)))
+        for i in range(n_z):
+            sino = self._get_sino_simple(radios, i)
+            output[i] = self._get_sino_halftomo(sino)
+        return output
+
+    def get_sinos(self, radios, output=None):
+        if self.halftomo:
+            return self._get_sinos_halftomo(radios, output=output)
+        else:
+            return self._get_sinos_simple(radios, output=output)
+
+    @deprecated("Use get_sino() or get_sinos() instead", do_print=True)
+    def radios_to_sinos(self, radios, output=None, copy=False):
+        """
+        DEPRECATED. Use get_sinos() or get_sino() instead.
+        """
+        return self.get_sinos(radios, output=output)
+
+
+SinoProcessing = deprecated_class("'SinoProcessing' was renamed 'SinoBuilder'", do_print=True)(SinoBuilder)
+
+
+class SinoMult:
+    """
+    A class for preparing a sinogram for half-tomography reconstruction, without stitching the two parts
+    """
+
+    def __init__(self, sino_shape, rot_center):
+        self._set_shape(sino_shape)
+        self._prepare_weights(rot_center)
+
+    def _set_shape(self, sino_shape):
+        _, self.n_a, self.n_x = get_2D_3D_shape(sino_shape)
+
+    def _prepare_weights(self, rot_center):
+        n_x = self.n_x
+        middle = (n_x - 1) / 2.0
+        if rot_center >= middle:
+            overlap_width = int(2 * (n_x - 1 - rot_center))
+            self.overlap_region = slice(-overlap_width, None)
+            self.pad_left, self.pad_right = 0, n_x - overlap_width
+        else:
+            overlap_width = int(2 * rot_center)
+            self.overlap_region = slice(0, overlap_width)
+            self.pad_left, self.pad_right = n_x - overlap_width, 0
+        weights = np.linspace(0, 1, overlap_width, endpoint=True)
+        if rot_center >= middle:
+            weights = weights[::-1]
+        self.weights = np.ascontiguousarray(weights, dtype="f")
+        overlap_region_indices = np.arange(self.n_x)[self.overlap_region]
+        self.start_x = overlap_region_indices[0]
+        self.end_x = overlap_region_indices[-1]
+        self.extended_width = n_x + self.pad_left + self.pad_right
+
+    def prepare_sino(self, sino):
+        sino[:, self.overlap_region] *= self.weights
+        return sino
+
+
+def convert_halftomo(sino, extended_width, transition_width=None):
+    """
+    Converts a sinogram into a sinogram with extended FOV with the "half tomography"
+    setting.
+    """
+    assert sino.ndim == 2
+    assert (sino.shape[0] % 2) == 0
+    na, nx = sino.shape
+
+    na2 = na // 2
+    r = extended_width // 2
+    d = transition_width or nx - r
+    res = np.zeros((na2, 2 * r), dtype="f")
+
+    sino1 = sino[:na2, :]
+    sino2 = sino[na2:, ::-1]
+    res[:, : r - d] = sino1[:, : r - d]
+    #
+    w1 = np.linspace(0, 1, 2 * d, endpoint=True)
+    res[:, r - d : r + d] = (1 - w1) * sino1[:, r - d :] + w1 * sino2[:, 0 : 2 * d]
+    #
+    res[:, r + d :] = sino2[:, 2 * d :]
+
+    return res
+
+
+# This function can have a cuda counterpart, see test_interpolation.py
+def match_half_sinos_parts(sino, angles, output=None):
+    """
+    Modifies the lower part of the half-acquisition sinogram so that each projection pair is
+    separated by exactly 180 degrees.
+    This means that `new_sino[k]` and `new_sino[k + n_angles//2]` will be 180 degrees apart.
+
+    Parameters
+    ----------
+    sino: numpy.ndarray
+        Two dimensional array with the sinogram in the form (n_angles, n_x)
+    angles: numpy.ndarray
+        One dimensional array with the rotation angles.
+    output: numpy.array, optional
+        Output sinogram. By default, the array 'sino' is modified in-place.
+
+    Notes
+    -----
+    This function assumes that the angles are in an increasing order.
+    """
+    n_a = angles.size
+    n_a_2 = n_a // 2
+    sino_part1 = sino[:n_a_2, :]
+    sino_part2 = sino[n_a_2:, :]
+    angles = np.rad2deg(angles)  # more numerically stable ?
+    angles_1 = angles[:n_a_2]
+    angles_2 = angles[n_a_2:]
+    angles_2_target = angles_1 + 180.0
+    interpolator = interp1d(angles_2, sino_part2, axis=0, kind="linear", copy=False, fill_value="extrapolate")
+    if output is None:
+        output = sino
+    else:
+        output[:n_a_2, :] = sino[:n_a_2, :]
+    output[n_a_2:, :] = interpolator(angles_2_target)
+    return output
+
+
+# EXPERIMENTAL
+def _convert_halftomo_right(sino, extended_width):
+    """
+    Converts a sinogram into a sinogram with extended FOV with the "half tomography"
+    setting, with a CoR outside the image support.
+    """
+    assert sino.ndim == 2
+    na, nx = sino.shape
+    assert (na % 2) == 0
+    rotation_axis_position = extended_width // 2
+    assert rotation_axis_position > nx
+
+    sino2 = np.pad(sino, ((0, 0), (0, rotation_axis_position - nx)), mode="reflect")
+    return convert_halftomo(sino2, extended_width)
+
+
+def get_extended_sinogram_width(sino_width, rotation_axis_position):
+    """
+    Compute the width (in pixels) of the extended sinogram for half-acquisition setting.
+    """
+    middle = (sino_width - 1) / 2.0
+    if rotation_axis_position >= middle:
+        overlap_width = int(2 * (sino_width - 1 - rotation_axis_position))
+    else:
+        overlap_width = int(2 * rotation_axis_position)
+    return 2 * sino_width - overlap_width
+
+
+def prepare_half_tomo_sinogram(sino, rot_center, get_extended_sino=True):
+    if get_extended_sino:
+        sino = sino.copy()
+    n_angles, n_x = sino.shape
+    middle = (n_x - 1) / 2.0
+    if rot_center >= middle:
+        overlap_width = int(2 * (n_x - 1 - rot_center))
+        overlap_region = slice(-overlap_width, None)
+        pad_left, pad_right = 0, n_x - overlap_width
+    else:
+        overlap_width = int(2 * rot_center)
+        overlap_region = slice(0, overlap_width)
+        pad_left, pad_right = n_x - overlap_width, 0
+    weights = np.linspace(0, 1, overlap_width, endpoint=True)
+    if rot_center >= middle:
+        weights = weights[::-1]
+    sino[:, overlap_region] *= weights
+    if get_extended_sino:
+        return np.pad(sino, ((0, 0), (pad_left, pad_right)), mode="constant")
+    return sino
+
+
+class SinoNormalization:
+    """
+    A class for sinogram normalization utilities.
+    """
+
+    kinds = [
+        "chebyshev",
+        "subtraction",
+        "division",
+    ]
+    operations = {"subtraction": np.subtract, "division": np.divide}
+
+    def __init__(self, kind="chebyshev", sinos_shape=None, radios_shape=None, normalization_array=None):
+        """
+        Initialize a SinoNormalization class.
+
+        Parameters
+        -----------
+        kind: str, optional
+            Normalization type. They can be the following:
+               - chebyshev: Each sinogram line is estimated by a Chebyshev polynomial
+               of degree 2. This estimation is then subtracted from the sinogram.
+               - subtraction: Each sinogram is subtracted with a user-provided array.
+                 The array can be 1D (angle-independent) and 2D (angle-dependent)
+               - division: same as previously, but with a division operation.
+            Default is "chebyshev"
+        sinos_shape: tuple, optional
+            Shape of the sinogram or sinogram stack.
+            Either this parameter or 'radios_shape' has to be provided.
+        radios_shape: tuple, optional
+            Shape of the projections or projections stack.
+            Either this parameter or 'sinos_shape' has to be provided.
+        normalization_array: numpy.ndarray, optional
+            Normalization array when kind='subtraction' or kind='division'.
+        """
+        self._get_shapes(sinos_shape, radios_shape)
+        self._set_kind(kind, normalization_array)
+
+    _get_shapes = SinoBuilder._get_shapes
+
+    def _set_kind(self, kind, normalization_array):
+        check_supported(kind, self.kinds, "sinogram normalization kind")
+        self.normalization_kind = kind
+        self._normalization_instance_method = self._normalize_chebyshev  # default
+        if kind in ["subtraction", "division"]:
+            if not isinstance(normalization_array, np.ndarray):
+                raise ValueError(
+                    "Expected 'normalization_array' to be provided as a numpy array for normalization kind='%s'" % kind
+                )
+            if normalization_array.shape[-1] != self.sinos_shape[-1]:
+                n_a, n_x = self.sinos_shape[-2:]
+                raise ValueError("Expected normalization_array to have shape (%d, %d) or (%d, )" % (n_a, n_x, n_x))
+            self.norm_operation = self.operations[kind]
+            self._normalization_instance_method = self._normalize_op
+        self.normalization_array = normalization_array
+
+    #
+    # Chebyshev normalization
+    #
+
+    def _normalize_chebyshev_2D(self, sino):
+        output = sino  # inplace
+        Nr, Nc = sino.shape
+        J = np.arange(Nc)
+        x = 2.0 * (J + 0.5 - Nc / 2) / Nc
+        sum0 = Nc
+        f2 = 3.0 * x * x - 1.0
+        sum1 = (x**2).sum()
+        sum2 = (f2**2).sum()
+        for i in range(Nr):
+            ff0 = sino[i, :].sum()
+            ff1 = (x * sino[i, :]).sum()
+            ff2 = (f2 * sino[i, :]).sum()
+            output[i, :] = sino[i, :] - (ff0 / sum0 + ff1 * x / sum1 + ff2 * f2 / sum2)
+        return output
+
+    def _normalize_chebyshev_3D(self, sino):
+        for i in range(sino.shape[0]):
+            self._normalize_chebyshev_2D(sino[i])
+        return sino
+
+    def _normalize_chebyshev(self, sino):
+        if sino.ndim == 2:
+            self._normalize_chebyshev_2D(sino)
+        else:
+            self._normalize_chebyshev_3D(sino)
+        return sino
+
+    #
+    # Array subtraction/division
+    #
+
+    def _normalize_op(self, sino):
+        if sino.ndim == 2:
+            self.norm_operation(sino, self.normalization_array, out=sino)
+        else:
+            for i in range(sino.shape[0]):
+                self.norm_operation(sino[i], self.normalization_array, out=sino[i])
+        return sino
+
+    #
+    # Dispatch
+    #
+
+    def normalize(self, sino):
+        """
+        Normalize a sinogram or stack of sinogram.
+        The process is done in-place, meaning that the sinogram content is overwritten.
+        """
+        return self._normalization_instance_method(sino)