ChessAnalysisPipeline 0.0.17.dev3__py3-none-any.whl

CHAP/tomo/models.py

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+"""Tomography Pydantic model classes."""
+
+# Third party imports
+from typing import (
+    Literal,
+    Optional,
+)
+from pydantic import (
+    conint,
+    conlist,
+    confloat,
+    constr,
+)
+
+# Local modules
+from CHAP.models import CHAPBaseModel
+
+
+class Detector(CHAPBaseModel):
+    """
+    Detector class to represent the detector used in the experiment.
+    The image origin is assumed to be in the top-left corner, with
+    rows down (-z in lab frame) and columns sideways (+x in lab frame).
+
+    :ivar prefix: Prefix of the detector in the SPEC file.
+    :type prefix: str
+    :ivar rows: Number of pixel rows on the detector.
+    :type rows: int
+    :ivar columns: Number of pixel columns on the detector.
+    :type columns: int
+    :ivar pixel_size: Pixel size of the detector in mm.
+    :type pixel_size: int or list[int]
+    :ivar lens_magnification: Lens magnification for the detector,
+        defaults to `1.0`.
+    :type lens_magnification: float, optional
+    """
+    prefix: constr(strip_whitespace=True, min_length=1)
+    rows: conint(gt=0)
+    columns: conint(gt=0)
+    pixel_size: conlist(
+        item_type=confloat(gt=0, allow_inf_nan=False),
+        min_length=1, max_length=2)
+    lens_magnification: confloat(gt=0, allow_inf_nan=False) = 1.0
+
+
+class TomoReduceConfig(CHAPBaseModel):
+    """
+    Class representing the configuration for the tomography image
+    reduction processor.
+
+    :ivar img_row_bounds: Detector image bounds in the row-direction
+        (ignored for id1a3 and id3a).
+    :type img_row_bounds: list[int], optional
+    :ivar delta_theta: Rotation angle increment in image reduction
+        in degrees.
+    :type delta_theta: float, optional
+    """
+    img_row_bounds: Optional[
+        conlist(item_type=conint(ge=-1), min_length=2, max_length=2)] = None
+    delta_theta: Optional[confloat(gt=0, allow_inf_nan=False)] = None
+
+
+class TomoFindCenterConfig(CHAPBaseModel):
+    """
+    Class representing the configuration for the tomography center axis
+    finding processor.
+
+    :ivar center_stack_index: Stack index of the tomography set to find
+        the center axis.
+    :type center_stack_index: int, optional
+    :ivar center_rows: Row indices for the center finding processor.
+    :type center_rows: list[int, int], optional
+    :ivar center_offsets: Centers at the center finding row indices in
+        pixels.
+    :type center_offsets: list[float, float], optional
+    :ivar center_offset_min: Minimum value of center_offset in center
+        axis finding search in pixels.
+    :type center_offset_min: float, optional
+    :ivar center_offset_max: Maximum value of center_offset in center
+        axis finding search in pixels.
+    :type center_offset_max: float, optional
+    :ivar gaussian_sigma: Standard deviation for the Gaussian filter
+        applied to image reconstruction visualizations, defaults to no
+        filtering performed.
+    :type gaussian_sigma: float, optional
+    :ivar ring_width: Maximum width of rings to be filtered in the image
+        reconstruction in pixels, defaults to no filtering performed.
+    :type ring_width: float, optional
+    """
+    center_stack_index: Optional[conint(ge=0)] = None
+    center_rows: Optional[conlist(
+        item_type=conint(ge=0), min_length=2, max_length=2)] = None
+    center_offsets: Optional[conlist(
+        item_type=confloat(allow_inf_nan=False),
+        min_length=2, max_length=2)] = None
+    center_offset_min: Optional[confloat(allow_inf_nan=False)] = None
+    center_offset_max: Optional[confloat(allow_inf_nan=False)] = None
+    center_search_range: Optional[conlist(
+        item_type=confloat(allow_inf_nan=False),
+        min_length=1, max_length=3)] = None
+    gaussian_sigma: Optional[confloat(ge=0, allow_inf_nan=False)] = None
+    ring_width: Optional[confloat(ge=0, allow_inf_nan=False)] = None
+
+
+class TomoReconstructConfig(CHAPBaseModel):
+    """
+    Class representing the configuration for the tomography image
+    reconstruction processor.
+
+    :ivar x_bounds: Reconstructed image bounds in the x-direction.
+    :type x_bounds: list[int], optional
+    :ivar y_bounds: Reconstructed image bounds in the y-direction.
+    :type y_bounds: list[int], optional
+    :ivar z_bounds: Reconstructed image bounds in the z-direction.
+    :type z_bounds: list[int], optional
+    :ivar secondary_iters: Number of secondary iterations in the tomopy
+        image reconstruction algorithm, defaults to `0`.
+    :type secondary_iters: int, optional
+    :ivar gaussian_sigma: Standard deviation for the Gaussian filter
+        applied to image reconstruction visualizations, defaults to no
+        filtering performed.
+    :type gaussian_sigma: float, optional
+    :ivar remove_stripe_sigma: Damping parameter in Fourier space in
+        tomopy's horizontal stripe removal tool, defaults to no
+        correction performed.
+    :type remove_stripe_sigma: float, optional
+    :ivar ring_width: Maximum width of rings to be filtered in the image
+        reconstruction in pixels, defaults to no filtering performed.
+    :type ring_width: float, optional
+    """
+    x_bounds: Optional[
+        conlist(item_type=conint(ge=-1), min_length=2, max_length=2)] = None
+    y_bounds: Optional[
+        conlist(item_type=conint(ge=-1), min_length=2, max_length=2)] = None
+    z_bounds: Optional[
+        conlist(item_type=conint(ge=-1), min_length=2, max_length=2)] = None
+    secondary_iters: conint(ge=0) = 0
+    gaussian_sigma: Optional[confloat(ge=0, allow_inf_nan=False)] = None
+    remove_stripe_sigma: Optional[confloat(ge=0, allow_inf_nan=False)] = None
+    ring_width: Optional[confloat(ge=0, allow_inf_nan=False)] = None
+
+
+class TomoCombineConfig(CHAPBaseModel):
+    """
+    Class representing the configuration for the combined tomography
+    stacks processor.
+
+    :ivar x_bounds: Combined image bounds in the x-direction.
+    :type x_bounds: list[int], optional
+    :ivar y_bounds: Combined image bounds in the y-direction.
+    :type y_bounds: list[int], optional
+    :ivar z_bounds: Combined image bounds in the z-direction.
+    :type z_bounds: list[int], optional
+    """
+    x_bounds: Optional[
+        conlist(item_type=conint(ge=-1), min_length=2, max_length=2)] = None
+    y_bounds: Optional[
+        conlist(item_type=conint(ge=-1), min_length=2, max_length=2)] = None
+    z_bounds: Optional[
+        conlist(item_type=conint(ge=-1), min_length=2, max_length=2)] = None
+
+
+class TomoSimConfig(CHAPBaseModel):
+    """
+    Class representing the configuration for the tomography simulator.
+
+    :ivar station: The station name (in 'idxx' format).
+    :type station: Literal['id1a3', 'id3a', 'id3b']
+    :ivar detector: Detector used in the tomography experiment.
+    :type detector: Detector
+    :ivar sample_type: Sample type for the tomography simulator.
+    :type sample_type: Literal['square_rod', 'square_pipe',
+        'hollow_cube', 'hollow_brick', 'hollow_pyramid']
+    :ivar sample_size: Size of each sample dimension in mm (internally
+        converted to an integer number of pixels). Enter three values
+        for sample_type == `'hollow_pyramid'`, the height and the side
+        at the respective bottom and the top of the pyramid.
+    :type sample_size: list[float]
+    :ivar wall_thickness: Wall thickness for pipe, cube, and brick in
+        mm (internally converted to an integer number of pixels).
+    :type wall_thickness: float
+    :ivar mu: Linear attenuation coefficient in mm^-1, defaults to
+        `0.05`.
+    :type mu: float, optional
+    :ivar theta_step: Rotation angle increment in the tomography
+        simulation in degrees.
+    :type theta_step: float
+    :ivar beam_intensity: Initial beam intensity in counts,
+        defaults to `1.e9`.
+    :type beam_intensity: float, optional
+    :ivar background_intensity: Background intensity in counts,
+        defaults to `20`.
+    :type background_intensity: float, optional
+    :ivar slit_size: Vertical beam height in mm, defaults to `1.0`.
+    :type slit_size: float, optional
+    """
+    station: Literal['id1a3', 'id3a', 'id3b']
+    detector: Detector.model_construct()
+    sample_type: Literal[
+        'square_rod', 'square_pipe', 'hollow_cube', 'hollow_brick',
+        'hollow_pyramid']
+    sample_size: conlist(
+        item_type=confloat(gt=0, allow_inf_nan=False),
+        min_length=1, max_length=3)
+    wall_thickness: Optional[confloat(ge=0, allow_inf_nan=False)] = None
+    mu: Optional[confloat(gt=0, allow_inf_nan=False)] = 0.05
+    theta_step: confloat(gt=0, allow_inf_nan=False)
+    beam_intensity: Optional[confloat(gt=0, allow_inf_nan=False)] = 1.e9
+    background_intensity: Optional[confloat(gt=0, allow_inf_nan=False)] = 20
+    slit_size: Optional[confloat(gt=0, allow_inf_nan=False)] = 1.0