Update docs/api.md for the CameraModel geometry redesign

Documents CameraModel/CameraModelTolerance, the rewritten
GeometryCalibration, z_tolerance, the two pointing angles, and every
downstream signature change (ModalFitter, SyntheticBeamGenerator,
PhaseRetriever, BeamReconstructor) introduced by the redesign.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

docs/api.md

@@ -15,11 +15,33 @@ Every class/function below is exported from the top-level `he11lib` package
 ## Quick start
 
 ```python
-from he11lib import BeamReconstructor, MeasurementPlane
+from he11lib import (
+    BeamReconstructor,
+    CameraModel,
+    CameraModelTolerance,
+    MeasurementPlane,
+)
 
 # planes: a list of >=3 MeasurementPlane objects built from your own
 # flux arrays (see MeasurementPlane below).
-reconstructor = BeamReconstructor(w0=5e-3, z0=0.5, wavelength=1.76e-3)
+
+# Nominal camera pose/intrinsics from calibration; every field here is
+# refined jointly with the mode fit because its tolerance is nonzero.
+camera = CameraModel(
+    focal_length_px=2000.0,
+    position=(0.0, 0.0, -2.0),
+    orientation_deg=(0.0, 0.0, 0.0),
+)
+camera_tolerance = CameraModelTolerance(
+    focal_length_px=20.0,
+    position=(0.01, 0.01, 0.05),
+    orientation_deg=(2.0, 2.0, 2.0),
+)
+
+reconstructor = BeamReconstructor(
+    w0=5e-3, z0=0.5, wavelength=1.76e-3,
+    camera=camera, camera_tolerance=camera_tolerance,
+)
 result = reconstructor.reconstruct(planes)
 
 for mode, (power_fraction, phase_rad) in result.purity.items():
@@ -28,19 +50,22 @@ for mode, (power_fraction, phase_rad) in result.purity.items():
 
 ## `data` — `MeasurementPlane`, `ReconstructionResult`
 
-### `MeasurementPlane(flux, z, pixel_scale=None, viewing_angle_deg=None, label=None)`
+### `MeasurementPlane(flux, z, z_tolerance=0.0, label=None)`
 
 One measurement: a 2D flux array plus its acquisition metadata.
 
 - `flux` — 2D `np.ndarray` of flux values. Dead-pixel correction, background
   subtraction, and saturation clipping are assumed already handled upstream.
 - `z` — nominal distance from the output window, in meters. Must be `> 0`.
-- `pixel_scale` — known meters/pixel, or `None` if unknown (then jointly
+- `z_tolerance` — `+/-` bound, in meters, around the nominal `z` within
-  fit by `ModalFitter`/`BeamReconstructor`).
+  which the true distance is jointly refined by `ModalFitter`. Must be
-- `viewing_angle_deg` — known camera viewing angle relative to the beam
+  `>= 0`; `0` (the default) means `z` is trusted exactly and held fixed.
-  axis, in degrees, or `None` if unknown (also jointly fit).
 - `label` — optional human-readable identifier.
 
+Per-plane camera geometry (`pixel_scale`/`viewing_angle_deg`) no longer
+lives on `MeasurementPlane` — camera pose/intrinsics are a single shared
+`CameraModel` for the whole reconstruction (see `geometry` below).
+
 ### `validate_planes(planes)`
 
 Raises `ValueError` if there are fewer than 3 planes, planes have
@@ -58,9 +83,14 @@ and `BeamReconstructor.reconstruct`):
 - `purity: dict[(p, l), (power_fraction, phase_rad)]`
 - `reconstructed_field: np.ndarray` — reconstructed complex field.
 - `centers: list[(x, y)]` — fitted beam transverse center per plane, meters.
-- `pointing_angle_deg: float` — fitted shared beam pointing angle (tilt).
+- `pointing_angle_horizontal_deg`, `pointing_angle_vertical_deg: float` —
-- `geometry: dict[str, float]` — geometry parameters used or fitted (keys
+  fitted shared beam pointing (tilt) angles, independent horizontal and
-  `pixel_scale_{i}`, `viewing_angle_deg_{i}` per plane index `i`).
+  vertical.
+- `geometry: dict[str, float]` — geometry parameters used or fitted: the 9
+  `CameraModel` field names from `he11lib.geometry.CAMERA_FIELD_NAMES`
+  (`focal_length_px`, `position_x`, `position_y`, `position_z`, `yaw_deg`,
+  `pitch_deg`, `roll_deg`, `principal_point_x`, `principal_point_y`), plus
+  `z_{i}` per plane index `i` (that plane's fitted/held distance).
 - `residuals: list[np.ndarray]` — per-plane (measured − modeled) flux maps.
   Empty when `used_phase_retrieval` is `True`.
 - `coefficient_uncertainty: dict[(p, l), float]` — 1-sigma uncertainty on
@@ -87,17 +117,55 @@ waist radius `w0` (m), waist location `z0` (m), and radiation `wavelength`
   onto each `(p, l)` in `modes`, returning `dict[(p, l), complex]`
   coefficients (Riemann-sum inner product; `dx` is the grid spacing).
 
-## `geometry` — `GeometryCalibration`
+## `geometry` — `CameraModel`, `CameraModelTolerance`, `GeometryCalibration`
 
-`GeometryCalibration(plane)` wraps a single `MeasurementPlane` and resolves
+### `CameraModel(focal_length_px, position, orientation_deg, principal_point=(0.0, 0.0))`
-its pixel-to-physical-coordinate mapping.
 
-- `pixel_scale_known` / `viewing_angle_known` — `bool` properties.
+A nominal pinhole camera pose/intrinsics shared across every plane in one
-- `physical_coordinates(pixel_scale=None, viewing_angle_deg=None)` —
+reconstruction. Always a point estimate — never trusted as exact by
-  returns `(x, y)` physical coordinate grids matching the plane's flux
+itself; trust is expressed via the paired `CameraModelTolerance`.
-  shape. Values known on the `MeasurementPlane` take precedence over the
+
-  `override` arguments; raises `ValueError` if a value is neither known nor
+- `focal_length_px` — focal length in pixel units.
-  overridden.
+- `position` — `(x, y, z)` camera position in the beam-axis world frame,
+  meters; `z=0` is the output window.
+- `orientation_deg` — `(yaw, pitch, roll)`, degrees. All-zero means the
+  boresight is normal to every `z=const` target plane with no in-plane
+  rotation.
+- `principal_point` — `(px, px)` offset from the frame center.
+
+### `CameraModelTolerance(focal_length_px, position, orientation_deg, principal_point=(0.0, 0.0))`
+
+Per-field `+/-` refinement bound, same shape as `CameraModel`. Every field
+must be `>= 0` (raises `ValueError` otherwise). A field's tolerance of `0`
+holds that `CameraModel` field fixed at its nominal value during fitting;
+`> 0` lets `ModalFitter` refine it within `[nominal - tolerance, nominal +
+tolerance]`.
+
+### `GeometryCalibration(camera)`
+
+Wraps a `CameraModel` and resolves pixel <-> physical coordinate mappings
+via true pinhole projection (not a uniform affine/cosine approximation).
+
+- `pixel_coordinates(x, y, z) -> (row, col)` — forward-projects physical
+  `(x, y)` at depth `z` to pixel coordinates. Raises `ValueError` if the
+  point is behind the camera (`Z_cam <= 0`).
+- `physical_coordinates(image_shape, z) -> (x, y)` — inverse-projects every
+  pixel in a frame of `image_shape` to physical `(x, y)` on the `z=const`
+  plane, via ray-plane intersection (this is what produces genuine
+  keystoning — non-uniform spacing across the frame — for tilted/off-axis
+  poses). Raises `ValueError` if the plane is edge-on to or behind the
+  camera.
+- `effective_pixel_scale(image_shape, z) -> float` — a single isotropic
+  meters/pixel figure (finite-difference approximation at the frame
+  center), for callers like `DiffusionDeconvolver` that assume one
+  isotropic pixel-space kernel.
+
+### `CAMERA_FIELD_NAMES`, `camera_to_values`, `tolerance_to_values`, `camera_from_values`
+
+Module-level helpers used internally by `ModalFitter` to flatten/unflatten
+`CameraModel`/`CameraModelTolerance` into the optimizer's parameter vector.
+Not usually needed by application code, but exported for advanced use
+(e.g. inspecting `CAMERA_FIELD_NAMES` to interpret `ReconstructionResult.geometry` keys).
 
 ## `noise` — `NoiseEstimator`
 
@@ -121,25 +189,30 @@ pass a `deconvolver` to `BeamReconstructor`.
 - `deconvolve(image, pixel_scale, noise_to_signal_ratio=1e-3)` — regularized
   (Wiener) removal of the blur.
 
-Note: the blur/deconvolution kernel is isotropic in pixel space. If a
+Note: the blur/deconvolution kernel is isotropic in pixel space. A tilted
-plane has a nonzero `viewing_angle_deg`, its `x` and `y` pixel axes have
+or off-axis `CameraModel` produces a pixel scale that varies across the
-different physical scales (see `SyntheticBeamGenerator` below), so
+frame and between `x`/`y` (keystoning), so `deconvolve` uses
-deconvolution is only exact for `viewing_angle_deg == 0`; at oblique
+`GeometryCalibration.effective_pixel_scale` — a single isotropic
-angles it is an approximation.
+approximation evaluated at the frame center. This is exact only for an
+on-axis, untilted camera; at oblique poses it is an accepted
+approximation (see `CLAUDE.md`).
 
 ## `synthetic` — `SyntheticBeamGenerator`
 
-`SyntheticBeamGenerator(basis, image_shape, pixel_scale)` — forward model
+`SyntheticBeamGenerator(basis, camera)` — forward model used to validate
-used to validate the pipeline against known ground truth, and to evaluate
+the pipeline against known ground truth, and to evaluate experimental
-experimental design (e.g. "would these distances separate my modes?").
+design. `camera` is the ground-truth `CameraModel` (position/orientation/
-`pixel_scale` is the physical pixel size, in meters, along the non-tilted
+intrinsics) used to render each plane via true perspective projection.
-`y` axis; the `x` axis is compressed by `1/cos(viewing_angle_deg)` to model
-an oblique camera view.
 
-- `generate(coefficients, z_list, *, center=(0, 0), pointing_angle_deg=0.0, viewing_angle_deg=0.0, noise_std=0.0, seed=None)`
+- `generate(coefficients, z_list, image_shape, *, center=(0.0, 0.0), pointing_angle_horizontal_deg=0.0, pointing_angle_vertical_deg=0.0, z_tolerance=0.0, nominal_z_offsets=None, noise_std=0.0, seed=None) -> list[MeasurementPlane]`
-  — returns one `MeasurementPlane` per `z` in `z_list`. The beam's
+  — returns one `MeasurementPlane` per (true) `z` in `z_list`. The beam's
-  transverse center drifts linearly with `z` according to
+  transverse center drifts linearly with `z` according to the two
-  `pointing_angle_deg`, starting from `center` at `z0`.
+  independent pointing angles, starting from `center` at the basis's
+  `z0`. `nominal_z_offsets`, if given, maps a true `z` to an offset
+  applied to that plane's *nominal* `z` — letting a reconstruction be
+  tested against a deliberately-offset nominal input while the plane's
+  flux is still rendered at the true `z`. Every resulting plane shares
+  `z_tolerance`.
 
 ## `fitting` — `ModalFitter`, `generate_mode_shells`
 
@@ -152,16 +225,22 @@ Groups candidate `LG_{p,l}` modes into shells of increasing order
 ### `ModalFitter(basis, noise_estimator=None)`
 
 Core reconstruction path: a joint nonlinear least-squares fit of complex LG
-coefficients, beam center/pointing, and (if unknown) geometry.
+coefficients, beam center/pointing, and any nonzero-tolerance camera/`z`
+geometry.
 
-- `fit(planes, modes, initial_coefficients=None, initial_center=(0.0, 0.0), initial_tilt_deg=(0.0, 0.0), initial_pixel_scale=None, initial_viewing_angle_deg=0.0) -> ReconstructionResult`
+- `fit(planes, modes, camera, camera_tolerance, initial_coefficients=None, initial_center=(0.0, 0.0), initial_pointing_deg=(0.0, 0.0)) -> ReconstructionResult`
-  — fits exactly the given candidate `modes`.
+  — fits exactly the given candidate `modes`. Every `CameraModel` field
-- `fit_auto(planes, max_order=4, bic_improvement_threshold=10.0) -> ReconstructionResult`
+  with a nonzero `camera_tolerance` entry, and every plane whose
+  `z_tolerance` is nonzero, is refined within `[nominal - tolerance,
+  nominal + tolerance]`; zero-tolerance fields are held fixed at their
+  nominal value.
+- `fit_auto(planes, camera, camera_tolerance, max_order=4, bic_improvement_threshold=10.0) -> ReconstructionResult`
   — starts from `LG_00` and grows the candidate mode set shell-by-shell
   (via `generate_mode_shells`), stopping once BIC no longer improves by
   more than `bic_improvement_threshold`, capped at `max_order`. Emits a
   `UserWarning` (does not raise) if the cap is reached while the fit is
-  still improving.
+  still improving, or if the number of free camera+`z` parameters is large
+  relative to the number of planes (see `CLAUDE.md`'s degeneracy pitfall).
 
 ## `phase_retrieval` — `PhaseRetriever`, `propagate_angular_spectrum`
 
@@ -176,11 +255,12 @@ model implicitly assumed by `LGBasis`'s closed-form paraxial modes.
 
 ### `PhaseRetriever(wavelength)`
 
-- `retrieve(planes, pixel_scale=None, viewing_angle_deg=None, max_iterations=200) -> PhaseRetrievalResult`
+- `retrieve(planes, camera, max_iterations=200) -> PhaseRetrievalResult`
   — multi-plane Gerchberg-Saxton phase retrieval: propagates a trial
   complex field back and forth between planes, enforcing the measured
   amplitude (`sqrt(flux)`) at each plane, without assuming a finite mode
-  basis.
+  basis. All planes are propagated on one common physical grid, derived
+  from `camera` at the smallest-`z` plane's depth.
 
 ### `PhaseRetrievalResult`
 
@@ -192,23 +272,27 @@ table, as `BeamReconstructor` does internally for its fallback path.
 
 ## `reconstruct` — `BeamReconstructor`
 
-`BeamReconstructor(w0, z0, wavelength, max_order=4, noise_estimator=None, deconvolver=None, force_phase_retrieval=False, phase_retrieval_residual_threshold=None)`
+`BeamReconstructor(w0, z0, wavelength, camera, camera_tolerance, max_order=4, noise_estimator=None, deconvolver=None, force_phase_retrieval=False, phase_retrieval_residual_threshold=None)`
 
 High-level orchestrator wiring together the full pipeline: optional
 diffusion deblurring → `ModalFitter.fit_auto` → optional
-`PhaseRetriever` fallback.
+`PhaseRetriever` fallback. `camera`/`camera_tolerance` are the nominal
+shared `CameraModel` and its per-field refinement bounds for this
+reconstruction.
 
 - `reconstruct(planes) -> ReconstructionResult`
   1. Validates `planes` (see `validate_planes`).
-  2. If `deconvolver` is set, deblurs each plane (raises `ValueError` if a
+  2. If `deconvolver` is set, deblurs each plane using
-     plane's `pixel_scale` isn't known).
+     `GeometryCalibration(camera).effective_pixel_scale(plane.flux.shape, plane.z)`.
-  3. Runs `ModalFitter(basis, noise_estimator).fit_auto(planes, max_order)`.
+  3. Runs `ModalFitter(basis, noise_estimator).fit_auto(planes, camera, camera_tolerance, max_order)`.
   4. Runs the `PhaseRetriever` fallback instead, projecting its recovered
      field onto all modes up to `max_order`, if `force_phase_retrieval` is
      `True`, or if `phase_retrieval_residual_threshold` is set and the
      modal fit's noise-weighted RMS residual exceeds it. In that case
-     `result.residuals` is empty and `coefficient_uncertainty` is `NaN`
+     `result.residuals` is empty, `coefficient_uncertainty` is `NaN` per
-     per mode (phase retrieval doesn't produce a fit covariance).
+     mode, `geometry` is empty, and both pointing-angle fields are `NaN`
+     (phase retrieval doesn't fit geometry/pointing or produce a fit
+     covariance).
 
 ## `plotting` — diagnostic visualizations