Implement cone-beam geometry calibration

doc_sources/apidocs/corrct/corrct.alignment.cone_beam.md

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+# {py:mod}`corrct.alignment.cone_beam`
+
+```{py:module} corrct.alignment.cone_beam
+```
+
+```{autodoc2-docstring} corrct.alignment.cone_beam
+:allowtitles:
+```
+
+## Module Contents
+
+### Classes
+
+````{list-table}
+:class: autosummary longtable
+:align: left
+
+* - {py:obj}`ConeBeamGeometry <corrct.alignment.cone_beam.ConeBeamGeometry>`
+  - ```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry
+    :summary:
+    ```
+* - {py:obj}`FitConeBeamGeometry <corrct.alignment.cone_beam.FitConeBeamGeometry>`
+  - ```{autodoc2-docstring} corrct.alignment.cone_beam.FitConeBeamGeometry
+    :summary:
+    ```
+````
+
+### Functions
+
+````{list-table}
+:class: autosummary longtable
+:align: left
+
+* - {py:obj}`_class_to_json <corrct.alignment.cone_beam._class_to_json>`
+  - ```{autodoc2-docstring} corrct.alignment.cone_beam._class_to_json
+    :summary:
+    ```
+* - {py:obj}`_get_rot_axis_angle_deg <corrct.alignment.cone_beam._get_rot_axis_angle_deg>`
+  - ```{autodoc2-docstring} corrct.alignment.cone_beam._get_rot_axis_angle_deg
+    :summary:
+    ```
+* - {py:obj}`tune_acquisition_geometry <corrct.alignment.cone_beam.tune_acquisition_geometry>`
+  - ```{autodoc2-docstring} corrct.alignment.cone_beam.tune_acquisition_geometry
+    :summary:
+    ```
+````
+
+### API
+
+````{py:function} _class_to_json(obj: object) -> str
+:canonical: corrct.alignment.cone_beam._class_to_json
+
+```{autodoc2-docstring} corrct.alignment.cone_beam._class_to_json
+```
+````
+
+````{py:function} _get_rot_axis_angle_deg(center_1_vu: collections.abc.Sequence[float] | numpy.typing.NDArray, center_2_vu: collections.abc.Sequence[float] | numpy.typing.NDArray, decimals: int | None = 4, dtype: numpy.typing.DTypeLike = np.float32) -> float
+:canonical: corrct.alignment.cone_beam._get_rot_axis_angle_deg
+
+```{autodoc2-docstring} corrct.alignment.cone_beam._get_rot_axis_angle_deg
+```
+````
+
+`````{py:class} ConeBeamGeometry
+:canonical: corrct.alignment.cone_beam.ConeBeamGeometry
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry
+```
+
+````{py:attribute} theta_deg
+:canonical: corrct.alignment.cone_beam.ConeBeamGeometry.theta_deg
+:type: float
+:value: >
+   0.0
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry.theta_deg
+```
+
+````
+
+````{py:attribute} phi_deg
+:canonical: corrct.alignment.cone_beam.ConeBeamGeometry.phi_deg
+:type: float
+:value: >
+   0.0
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry.phi_deg
+```
+
+````
+
+````{py:attribute} eta_deg
+:canonical: corrct.alignment.cone_beam.ConeBeamGeometry.eta_deg
+:type: float
+:value: >
+   0.0
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry.eta_deg
+```
+
+````
+
+````{py:attribute} D_pix
+:canonical: corrct.alignment.cone_beam.ConeBeamGeometry.D_pix
+:type: float
+:value: >
+   0.0
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry.D_pix
+```
+
+````
+
+````{py:attribute} R_pix
+:canonical: corrct.alignment.cone_beam.ConeBeamGeometry.R_pix
+:type: float
+:value: >
+   0.0
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry.R_pix
+```
+
+````
+
+````{py:attribute} v0_pix
+:canonical: corrct.alignment.cone_beam.ConeBeamGeometry.v0_pix
+:type: float
+:value: >
+   0.0
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry.v0_pix
+```
+
+````
+
+````{py:attribute} u0_pix
+:canonical: corrct.alignment.cone_beam.ConeBeamGeometry.u0_pix
+:type: float
+:value: >
+   0.0
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry.u0_pix
+```
+
+````
+
+````{py:attribute} det_size_v_pix
+:canonical: corrct.alignment.cone_beam.ConeBeamGeometry.det_size_v_pix
+:type: int
+:value: >
+   0
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry.det_size_v_pix
+```
+
+````
+
+````{py:attribute} det_size_u_pix
+:canonical: corrct.alignment.cone_beam.ConeBeamGeometry.det_size_u_pix
+:type: int
+:value: >
+   0
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry.det_size_u_pix
+```
+
+````
+
+````{py:attribute} pix_size_um
+:canonical: corrct.alignment.cone_beam.ConeBeamGeometry.pix_size_um
+:type: float
+:value: >
+   0.0
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry.pix_size_um
+```
+
+````
+
+````{py:method} __str__() -> str
+:canonical: corrct.alignment.cone_beam.ConeBeamGeometry.__str__
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry.__str__
+```
+
+````
+
+````{py:method} get_prj_geom(translate_z_to_center: bool = True) -> corrct.models.ProjectionGeometry
+:canonical: corrct.alignment.cone_beam.ConeBeamGeometry.get_prj_geom
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry.get_prj_geom
+```
+
+````
+
+````{py:method} get_vol_geom(up_sampling: int = 1) -> corrct.models.VolumeGeometry
+:canonical: corrct.alignment.cone_beam.ConeBeamGeometry.get_vol_geom
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry.get_vol_geom
+```
+
+````
+
+````{py:method} update(field: str, val: float, is_relative: bool = True, decimals: int | None = 3) -> corrct.alignment.cone_beam.ConeBeamGeometry
+:canonical: corrct.alignment.cone_beam.ConeBeamGeometry.update
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry.update
+```
+
+````
+
+````{py:method} get_tuning_params(field: str, val_range: collections.abc.Sequence[float] | numpy.typing.NDArray, is_relative: bool = True) -> collections.abc.Sequence[corrct.alignment.cone_beam.ConeBeamGeometry]
+:canonical: corrct.alignment.cone_beam.ConeBeamGeometry.get_tuning_params
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry.get_tuning_params
+```
+
+````
+
+````{py:method} to_json() -> str
+:canonical: corrct.alignment.cone_beam.ConeBeamGeometry.to_json
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry.to_json
+```
+
+````
+
+````{py:method} from_json(data_json: str) -> None
+:canonical: corrct.alignment.cone_beam.ConeBeamGeometry.from_json
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.ConeBeamGeometry.from_json
+```
+
+````
+
+`````
+
+`````{py:class} FitConeBeamGeometry(prj_size_vu: collections.abc.Sequence[int] | numpy.typing.NDArray, points_ell1: collections.abc.Sequence[collections.abc.Sequence[float]] | numpy.typing.NDArray, points_ell2: collections.abc.Sequence[collections.abc.Sequence[float]] | numpy.typing.NDArray, points_axis: collections.abc.Sequence[collections.abc.Sequence[float]] | numpy.typing.NDArray | None = None, pix_size_um: float | None = None, use_l1_norm: bool = False, verbose: bool = True, plot_result: bool = False)
+:canonical: corrct.alignment.cone_beam.FitConeBeamGeometry
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.FitConeBeamGeometry
+```
+
+```{rubric} Initialization
+```
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.FitConeBeamGeometry.__init__
+```
+
+````{py:attribute} acq_geom
+:canonical: corrct.alignment.cone_beam.FitConeBeamGeometry.acq_geom
+:type: corrct.alignment.cone_beam.ConeBeamGeometry
+:value: >
+   None
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.FitConeBeamGeometry.acq_geom
+```
+
+````
+
+````{py:method} _initialize(use_l1_norm: bool) -> None
+:canonical: corrct.alignment.cone_beam.FitConeBeamGeometry._initialize
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.FitConeBeamGeometry._initialize
+```
+
+````
+
+````{py:method} fit(r: float, e: float = 1, meas_D_pix: float | None = None) -> corrct.alignment.cone_beam.ConeBeamGeometry
+:canonical: corrct.alignment.cone_beam.FitConeBeamGeometry.fit
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.FitConeBeamGeometry.fit
+```
+
+````
+
+````{py:method} _fit_distance_det2src(ellipse_1: corrct.alignment.fitting.Ellipse, ellipse_2: corrct.alignment.fitting.Ellipse, e: float = 1) -> float
+:canonical: corrct.alignment.cone_beam.FitConeBeamGeometry._fit_distance_det2src
+:staticmethod:
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.FitConeBeamGeometry._fit_distance_det2src
+```
+
+````
+
+`````
+
+````{py:function} tune_acquisition_geometry(acq_geom_init: corrct.alignment.cone_beam.ConeBeamGeometry, data: numpy.typing.NDArray, angles_rot_rad: collections.abc.Sequence[float] | numpy.typing.NDArray, params: dict[str, collections.abc.Sequence[float] | numpy.typing.NDArray], data_mask: numpy.typing.NDArray | None = None, verbose: bool = True) -> corrct.alignment.cone_beam.ConeBeamGeometry
+:canonical: corrct.alignment.cone_beam.tune_acquisition_geometry
+
+```{autodoc2-docstring} corrct.alignment.cone_beam.tune_acquisition_geometry
+```
+````