Basic camera simulation

pyproject.toml

@@ -55,6 +55,7 @@ dependencies = [
     "tqdm >= 4.41.1",
     "virtualbox >= 2.0.0",
     "pyserialem >= 0.3.2",
+    "diffpy.structure",
 ]
 
 [project.urls]

src/instamatic/simulation/camera.py

@@ -0,0 +1,105 @@
+from __future__ import annotations
+
+from typing import Tuple
+
+from numpy import ndarray
+
+from instamatic.camera.camera_base import CameraBase
+from instamatic.simulation.stage import Stage
+
+
+class CameraSimulation(CameraBase):
+    streamable = True
+
+    def __init__(self, name: str = 'simulate'):
+        super().__init__(name)
+
+        self.ready = False
+
+        # TODO put parameters into config
+        self.stage = Stage()
+        self.mag = None
+
+    def establish_connection(self):
+        pass
+
+    def actually_establish_connection(self):
+        if self.ready:
+            return
+        import time
+
+        time.sleep(2)
+        from instamatic.controller import get_instance
+
+        ctrl = get_instance()
+        self.tem = ctrl.tem
+
+        ctrl.stage.set(z=0, a=0, b=0)
+        print(self.tem.getStagePosition())
+        print(self.stage.samples[0].x, self.stage.samples[0].y)
+
+        self.ready = True
+
+    def release_connection(self):
+        self.tem = None
+        self.ready = False
+
+    def get_image(self, exposure: float = None, binsize: int = None, **kwargs) -> ndarray:
+        self.actually_establish_connection()
+
+        if exposure is None:
+            exposure = self.default_exposure
+        if binsize is None:
+            binsize = self.default_binsize
+
+        # TODO this has inconsistent units. Assume m, deg
+        pos = self.tem.getStagePosition()
+        if pos is not None and len(pos) == 5:
+            x, y, z, alpha, beta = pos
+            self.stage.set_position(x=x, y=y, z=z, alpha_tilt=alpha, beta_tilt=beta)
+
+        mode = self.tem.getFunctionMode()
+
+        # Get real-space extent
+        if mode == 'diff':
+            # TODO this has inconsistent units. Assume mm
+            self.camera_length = self.tem.getMagnification()
+        else:
+            mag = self.tem.getMagnification()
+            if isinstance(mag, (float, int)):
+                self.mag = mag
+            else:
+                print(mag, type(mag))
+        if self.mag is None:
+            raise ValueError('Must start in image mode')
+
+        # TODO consider beam shift, tilt ect.
+        x_min, x_max, y_min, y_max = self._mag_to_ranges(self.mag)
+        x_min += self.stage.x
+        x_max += self.stage.x
+        y_min += self.stage.y
+        y_max += self.stage.y
+
+        # TODO I mean properly considering them, this has no regard for units ect
+        bx, by = self.tem.getBeamShift()
+        x_min += bx
+        x_max += bx
+        y_min += by
+        y_max += by
+
+        shape_x, shape_y = self.get_camera_dimensions()
+        shape = (shape_x // binsize, shape_y // binsize)
+
+        if mode == 'diff':
+            return self.stage.get_diffraction_pattern(
+                shape=shape, x_min=x_min, x_max=x_max, y_min=y_min, y_max=y_max
+            )
+        else:
+            return self.stage.get_image(
+                shape=shape, x_min=x_min, x_max=x_max, y_min=y_min, y_max=y_max
+            )
+
+    def _mag_to_ranges(self, mag: float) -> Tuple[float, float, float, float]:
+        # assume 50x = 2mm full size
+        half_width = 50 * 1e6 / mag  # 2mm/2 in nm is 1e6
+        return -half_width, half_width, -half_width, half_width

src/instamatic/simulation/crystal.py

@@ -0,0 +1,255 @@
+from __future__ import annotations
+
+from typing import Type, TypeVar
+
+import numpy as np
+from diffpy import structure as diffpy
+
+Crystal_T = TypeVar('Crystal_T', bound='Crystal')
+
+
+class Crystal:
+    def __init__(
+        self, a: float, b: float, c: float, alpha: float, beta: float, gamma: float
+    ) -> None:
+        """Simulate a primitive crystal given the unit cell. No additional
+        symmetry is imposed.
+
+        Standard orientation as defined in diffpy.
+
+        Parameters
+        ----------
+        a : float
+            Unit cell length a, in Å
+        b : float
+            Unit cell length b, in Å
+        c : float
+            Unit cell length c, in Å
+        alpha : float
+            Angle between b and c, in degrees
+        beta : float
+            Angle between a and c, in degrees
+        gamma : float
+            Angle between a and b, in degrees
+        """
+        self.a = a
+        self.b = b
+        self.c = c
+        self.alpha = alpha
+        self.beta = beta
+        self.gamma = gamma
+
+        self.lattice = diffpy.Lattice(self.a, self.b, self.c, self.alpha, self.beta, self.gamma)
+        self.structure = diffpy.Structure(
+            atoms=[diffpy.Atom(xyz=[0, 0, 0])],
+            lattice=self.lattice,
+        )
+
+    @property
+    def a_vec(self) -> np.ndarray:
+        return self.lattice.cartesian((1, 0, 0))
+
+    @property
+    def b_vec(self) -> np.ndarray:
+        return self.lattice.cartesian((0, 1, 0))
+
+    @property
+    def c_vec(self) -> np.ndarray:
+        return self.lattice.cartesian((0, 0, 1))
+
+    @property
+    def a_star_vec(self) -> np.ndarray:
+        return self.lattice.reciprocal().cartesian((1, 0, 0))
+
+    @property
+    def b_star_vec(self) -> np.ndarray:
+        return self.lattice.reciprocal().cartesian((0, 1, 0))
+
+    @property
+    def c_star_vec(self) -> np.ndarray:
+        return self.lattice.reciprocal().cartesian((0, 0, 1))
+
+    @classmethod
+    def default(cls: Type[Crystal_T]) -> Crystal_T:
+        return cls(1, 2, 3, 90, 100, 110)
+
+    def real_space_lattice(self, d_max: float) -> np.ndarray:
+        """Get the real space lattice as a (n, 3) shape array.
+
+        Parameters
+        ----------
+        d_max: float
+            The maximum d-spacing
+
+        Returns
+        -------
+        np.ndarray
+            Shape (n, 3), lattice points
+        """
+        max_h = int(d_max // self.a)
+        max_k = int(d_max // self.b)
+        max_l = int(d_max // self.c)
+        hkls = np.array(
+            [
+                (h, k, l)
+                for h in range(-max_h, max_h + 1)  # noqa: E741
+                for k in range(-max_k, max_k + 1)  # noqa: E741
+                for l in range(-max_l, max_l + 1)  # noqa: E741
+            ]
+        )
+        vecs = self.lattice.cartesian(hkls)
+        return vecs
+
+    def reciprocal_space_lattice(self, d_min: float) -> np.ndarray:
+        """Get the reciprocal space lattice as a (n, 3) shape array for input
+        n.
+
+        Parameters
+        ----------
+        d_min: float
+            Minimum d-spacing included
+
+        Returns
+        -------
+        np.ndarray
+            Shape (n, 3), lattice points
+        """
+        max_h = int(d_min // self.lattice.ar)
+        max_k = int(d_min // self.lattice.br)
+        max_l = int(d_min // self.lattice.cr)
+        hkls = np.array(
+            [
+                (h, k, l)
+                for h in range(-max_h, max_h + 1)  # noqa: E741
+                for k in range(-max_k, max_k + 1)  # noqa: E741
+                for l in range(-max_l, max_l + 1)  # noqa: E741
+            ]
+        )
+        vecs = self.lattice.reciprocal().cartesian(hkls)
+        return vecs
+
+    def diffraction_pattern_mask(
+        self,
+        shape: tuple[int, int],
+        d_min: float,
+        rotation_matrix: np.ndarray,
+        wavelength: float,
+        excitation_error: float,
+    ) -> np.ndarray:
+        """Get a diffraction pattern with a given shape, up to a given
+        resolution, in a given orientation and wavelength.
+
+        Parameters
+        ----------
+        shape : tuple[int, int]
+            Output shape
+        d_min : float
+            Minimum d-spacing, in Å
+        rotation_matrix : np.ndarray
+            Orientation
+        wavelength : float
+            Wavelength of incident beam, in Å
+        excitation_error : float
+            Excitation error used for intensity calculation, in reciprocal Å
+
+        Returns
+        -------
+        np.ndarray
+            Diffraction pattern
+        """
+        # TODO calibration
+        out = np.zeros(shape, dtype=bool)
+
+        # TODO this depends on convergence angle
+        spot_radius = 3  # pixels
+
+        vecs = self.reciprocal_space_lattice(d_min)
+        d = np.sum(vecs**2, axis=1)
+        vecs = vecs[d < d_min**2]
+
+        k = 2 * np.pi / wavelength
+        k_vec = rotation_matrix @ np.array([0, 0, -k])
+
+        # Find intersect with Ewald's sphere
+        q_squared = np.sum((vecs - k_vec) ** 2, axis=1)
+        vecs = vecs[
+            (q_squared > (k - excitation_error) ** 2)
+            & (q_squared < (k + excitation_error) ** 2)
+        ]
+
+        # Project onto screen
+        vecs_xy = (rotation_matrix.T @ vecs.T).T[:, :-1]  # ignoring curvature
+
+        # Make image
+        for vec in vecs_xy:
+            x = int(vec[0] * d_min * shape[1] / 2) + shape[1] // 2
+            y = int(vec[1] * d_min * shape[0] / 2) + shape[0] // 2
+            min_x = max(0, x - spot_radius)
+            max_x = min(shape[1], x + spot_radius)
+            min_y = max(0, y - spot_radius)
+            max_y = min(shape[0], y + spot_radius)
+            out[min_y:max_y, min_x:max_x] = 1
+        return out
+
+    def __str__(self) -> str:
+        return f'{self.__class__.__name__}(a = {self.a}, b = {self.b}, c = {self.c}, alpha = {self.alpha}, beta = {self.beta}, gamma = {self.gamma})'
+
+
+class CubicCrystal(Crystal):
+    def __init__(self, a: float) -> None:
+        super().__init__(a, a, a, 90, 90, 90)
+
+    @classmethod
+    def default(cls: Type[Crystal_T]) -> Crystal_T:
+        return cls(1)
+
+
+class HexagonalCrystal(Crystal):
+    def __init__(self, a: float, c: float) -> None:
+        super().__init__(a, a, c, 90, 90, 120)
+
+    @classmethod
+    def default(cls: Type[Crystal_T]) -> Crystal_T:
+        return cls(1, 2)
+
+
+class TrigonalCrystal(Crystal):
+    def __init__(self, a: float, alpha: float) -> None:
+        super().__init__(a, a, a, alpha, alpha, alpha)
+
+    @classmethod
+    def default(cls: Type[Crystal_T]) -> Crystal_T:
+        return cls(1, 100)
+
+
+class TetragonalCrystal(Crystal):
+    def __init__(self, a: float, c: float) -> None:
+        super().__init__(a, a, c, 90, 90, 90)
+
+    @classmethod
+    def default(cls: Type[Crystal_T]) -> Crystal_T:
+        return cls(1, 2)
+
+
+class OrthorhombicCrystal(Crystal):
+    def __init__(self, a: float, b: float, c: float) -> None:
+        super().__init__(a, b, c, 90, 90, 90)
+
+    @classmethod
+    def default(cls: Type[Crystal_T]) -> Crystal_T:
+        return cls(1, 2, 3)
+
+
+class MonoclinicCrystal(Crystal):
+    def __init__(self, a: float, b: float, c: float, beta: float) -> None:
+        super().__init__(a, b, c, 90, beta, 90)
+
+    @classmethod
+    def default(cls: Type[Crystal_T]) -> Crystal_T:
+        return cls(1, 2, 3, 100)
+
+
+class TriclinicCrystal(Crystal):
+    @classmethod
+    def default(cls: Type[Crystal_T]) -> Crystal_T:
+        return cls(1, 2, 3, 90, 100, 110)