feat: dpc3d reconstruction

.gitignore

@@ -297,6 +297,7 @@ dask-worker-space/
 
 # temporary files
 *.*~
+build/**
 
 # scratch space
 examples/data/**
@@ -308,4 +309,6 @@ expt_ctrl/temp*.cfg
 *.hdf5
 
 # documentation
-docs/_*
+docs/_*
+
+.codex/**

examples/build_dpc_mie_stack.py

@@ -0,0 +1,112 @@
+#!/usr/bin/env python3
+"""
+Generate the default DPC Mie simulation stack used by the example scripts.
+"""
+
+from __future__ import annotations
+
+from pathlib import Path
+from dataclasses import dataclass
+
+import numpy as np
+
+try:
+    import cupy as cp  # type: ignore
+except Exception:
+    cp = None
+
+from simulate_dpc_microsphere import SphereSpec, simulate_dpc_images_sphere_to_zarr
+
+
+@dataclass(frozen=True)
+class SimParams:
+    wavelength_um: float = 0.515
+    na_obj: float = 0.8
+    led_grid_shape: tuple[int, int] = (64, 64)
+    pitch_mm: float = 2.5
+    camera_pixel_um: float = 2.4
+    magnification: float = 20.0
+    camera_oversample: int = 1
+    esize_camera: tuple[int, int] = (256, 256)
+    z_plane_um: float = 0.0
+    sphere: SphereSpec = SphereSpec(radius_um=1., n_sphere=1.59, n_medium=1.55)
+    inner_na: float = 0.0
+    include_center_led: bool = False
+    pattern_order: tuple[str, str, str, str] = ("left", "right", "up", "down")
+    normalize_by_led_count: bool = True
+    led_subsample: int = 1
+    mie_kwargs: dict | None = None
+    camera_gains: float = 2.0
+    camera_offsets: float = 100.0
+    camera_readout_noise_sds: float = 3.0
+    camera_photon_shot_noise: bool = True
+    camera_saturation: float | None = None
+    camera_image_is_integer: bool = True
+    exposure_time_ms: float = 10.0
+    illumination_photons_per_s_per_um2: float = 1e7
+    focal_stack_planes: int = 31
+    focal_stack_step_um: float = 0.325
+
+    @property
+    def z_planes_um(self) -> np.ndarray:
+        return (
+            np.arange(self.focal_stack_planes) - self.focal_stack_planes // 2
+        ) * self.focal_stack_step_um
+
+
+def ensure_dpc_mie_stack(zarr_path: Path, *, use_gpu: bool) -> None:
+    """
+    Ensure the default DPC Mie simulation stack exists at the provided path.
+    """
+    if zarr_path.exists():
+        return
+    params = SimParams()
+    zarr_path.parent.mkdir(parents=True, exist_ok=True)
+    simulate_dpc_images_sphere_to_zarr(
+        zarr_path,
+        wavelength_um=params.wavelength_um,
+        na_obj=params.na_obj,
+        led_grid_shape=params.led_grid_shape,
+        pitch_mm=params.pitch_mm,
+        camera_pixel_um=params.camera_pixel_um,
+        magnification=params.magnification,
+        camera_oversample=params.camera_oversample,
+        esize_camera=params.esize_camera,
+        z_plane_um=params.z_plane_um,
+        sphere=params.sphere,
+        inner_na=params.inner_na,
+        include_center_led=params.include_center_led,
+        pattern_order=params.pattern_order,
+        normalize_by_led_count=params.normalize_by_led_count,
+        led_subsample=params.led_subsample,
+        use_gpu=use_gpu,
+        mie_kwargs=params.mie_kwargs,
+        camera_gains=params.camera_gains,
+        camera_offsets=params.camera_offsets,
+        camera_readout_noise_sds=params.camera_readout_noise_sds,
+        camera_photon_shot_noise=params.camera_photon_shot_noise,
+        camera_saturation=params.camera_saturation,
+        camera_image_is_integer=params.camera_image_is_integer,
+        exposure_time_ms=params.exposure_time_ms,
+        illumination_photons_per_s_per_um2=params.illumination_photons_per_s_per_um2,
+        focal_stack_planes=params.focal_stack_planes,
+        focal_stack_step_um=params.focal_stack_step_um,
+        overwrite=True,
+        reuse_cache=True,
+    )
+
+
+def main() -> None:
+    default_path = Path("build/dpc_mie_stack.zarr")
+    use_gpu = False
+    if cp is not None:
+        try:
+            use_gpu = bool(cp.is_available())
+        except Exception:
+            use_gpu = False
+    ensure_dpc_mie_stack(default_path, use_gpu=use_gpu)
+    print(f"Simulation written to {default_path}")
+
+
+if __name__ == "__main__":
+    main()