diffct 1.3.2__tar.gz → 1.3.3__tar.gz

{diffct-1.3.2 → diffct-1.3.3}/CHANGELOG.md

@@ -1,363 +1,434 @@
-# Changelog
-
-All notable changes to this project are documented in this file.
-
-The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
-and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
-
-## [Unreleased]
-
-## [1.3.1] - 2026-04-15
-
-### Added
-- **Real-data walnut FDK example** at `examples/realdata_walnut_fdk.py`,
-  running the full analytical FDK pipeline on a preprocessed subset of
-  the Helsinki walnut cone-beam CT dataset ([Meaney 2022, Zenodo
-  10.5281/zenodo.6986012](https://doi.org/10.5281/zenodo.6986012),
-  CC-BY 4.0). The 241-view, 256×256-per-view sinogram is shipped at
-  `examples/data/walnut_cone.npz` (~25 MB, float16, 8× binned, 256²
-  center crop) together with a `preprocess_walnut.py` regenerator
-  script, an attribution `NOTICE`, and a `walnut_reco.png` sample
-  montage. Reconstructs at half the nominal voxel size on a 512³ grid
-  using `backend="sf_tr"` + Hamming ramp window.
-- **Synthetic "real-data" pipeline examples** for all three geometries
-  (`examples/realdata_fbp_parallel.py`, `realdata_fbp_fan.py`,
-  `realdata_fdk_cone.py`) that run a Beer-Lambert + Poisson + `-log`
-  forward model on Shepp-Logan and reconstruct with the analytical
-  pipeline, showing the proper place for `-log` preprocessing.
-- **Chinese README** at `README.zh.md`, mirroring `README.md` with
-  bidirectional language links in both files.
-- **Core Algorithm section** in the READMEs (EN + ZH) explaining the
-  Siddon + bilinear/trilinear interpolation design choice, the
-  trade-off (slight blur at nominal voxel size), and when to pick
-  SF vs VD honestly (see "Changed" below).
-
-### Changed
-- **SF FBP / FDK backprojection kernels rewritten in LEAP's
-  chord-weighted matched-adjoint form** (from `projectors_SF.cu`).
-  The three analytical SF gather kernels
-  (`_fan_2d_sf_fbp_backproject_kernel`,
-  `_cone_3d_sf_tr_fdk_backproject_kernel`,
-  `_cone_3d_sf_tt_fdk_backproject_kernel`) now use the per-voxel
-  chord through the unit voxel instead of a `(sid/U)²`-plus-footprint-
-  area form, with a matching `sqrt(1+(v/sdd)²)` axial chord correction
-  on the cone side. Amplitude is calibrated against Siddon VD at
-  every voxel / detector-pitch combination tested (nominal, 0.64×
-  sub-nominal, 0.40× sub-nominal, supra-nominal) via the new
-  `det_spacing/(voxel·2π)` fan scale and
-  `(du·dv·sid)/(2π·sdd·voxel²)` cone scale constants.
-- **Honest README Core Algorithm section on SF vs VD.** The earlier
-  "SF lowers MSE by ~17 %" and "SF is measurably sharper at sub-
-  nominal" claims in 1.3.0 are walked back: on Shepp-Logan and the
-  walnut dataset, LEAP-form SF and Siddon VD produce visually
-  indistinguishable edge profiles at typical CBCT magnifications,
-  and MSE differences are fractions of a percent. SF's real value
-  is its **mass-conserving cell-integrated forward model**, which
-  matters for iterative reconstruction, learned priors, and
-  sinogram-level losses — not as a drop-in sharpness knob on
-  analytical FBP / FDK. The shipped `fbp_fan.py`, `fdk_cone.py`,
-  and `realdata_walnut_fdk.py` example comments are updated to
-  match.
-
-### Fixed
-- **SF FBP / FDK weight normalization** when the voxel's trapezoidal
-  footprint straddles the default 4-corner sort. The 1.3.0 SF
-  backprojection kernels used `fdk_w / (span · v_span)` (bounding-box
-  area) which under-amplified oblique views by up to 2× per axis and
-  produced a dim, angularly-modulated reconstruction. Diagnosed by
-  inspecting a Shepp-Logan SF reconstruction, corrected first to
-  `fdk_w / ((span+plateau)/2 · v_span)` (true trapezoid area) and
-  then fully replaced by the LEAP chord-weighted form above.
-
-### Acknowledgements
-- [LEAP](https://github.com/LLNL/LEAP) (LLNL / Hyojin Kim et al.)
-  added to `README.md` / `README.zh.md` Acknowledgements.
-  `projectors_SF.cu` is the reference implementation the new
-  analytical SF backprojection kernels are ported from.
-
-## [1.3.0] - 2026-04-14
-
-### Added
-- **Separable-footprint (SF) projector backends** for 2D fan and 3D cone
-  beam geometries, following Long-Fessler-Balter (IEEE TMI 2010).
-  `FanProjectorFunction` / `FanBackprojectorFunction` now accept
-  `backend="siddon"` (default, unchanged) or `backend="sf"`.
-  `ConeProjectorFunction` / `ConeBackprojectorFunction` accept
-  `backend="siddon"` (default), `"sf_tr"` (trapezoid in transaxial,
-  rectangle in axial) or `"sf_tt"` (trapezoid in both directions with
-  axial rise/fall from `U_near`/`U_far` across the voxel). Each SF
-  backend is implemented as a matched scatter/gather pair of CUDA
-  kernels so both forward and adjoint are available — autograd works
-  end-to-end for every backend, and the standalone Backprojector
-  Function can also be driven in SF mode for iterative reconstruction.
-- **Adjoint inner-product tests** for every new SF backend in
-  `tests/test_adjoint_inner_product.py`, plus `torch.autograd.gradcheck`
-  coverage in `tests/test_gradcheck.py`. Test count grew from 57 to 66.
-
-### Changed
-- **Internal grid-point convention** is now uniformly `x_v = ix - cx`
-  (matching `_cone_3d_fdk_backproject_kernel`). The SF kernels use the
-  same convention so voxel centers align with where the Siddon/FDK
-  paths interpret `d_vol[ix, iy, iz]`.
-- **`_TPB_SF_3D = (4, 4, 4)`** introduced for the 3D SF kernels. SF-TT
-  in particular exceeds the 128-register-per-thread budget allowed by
-  the default `(8, 8, 8)` launch; the smaller block gives each thread
-  ~1024 registers and avoids `CUDA_ERROR_LAUNCH_OUT_OF_RESOURCES`.
-
-### Notes
-- **Raw forward accuracy vs analytical Radon**: on both 2D fan
-  (512² Shepp-Logan) and 3D cone (96³ and 128³ 3D Shepp-Logan) phantoms,
-  measured against the analytical ellipse / ellipsoid Radon transform,
-  the existing Siddon projector with bilinear / trilinear interpolation
-  is slightly more accurate (~3% better RMSE, ~15% better max error)
-  than SF-TR / SF-TT at the thin-ray sampling level. The classic SF
-  advantage reported in Long et al. is over the piecewise-constant DD
-  projector; diffct's Siddon uses smooth interpolation, which covers
-  most of the gap SF was designed to close.
-- **Full analytical reconstruction (forward + FBP/FDK)**: despite the
-  raw-forward result above, in a complete analytical pipeline
-  (`FanProjectorFunction` / `ConeProjectorFunction` -> `ramp_filter_1d`
-  -> `fan_weighted_backproject` / `cone_weighted_backproject`) SF
-  **measurably improves reconstruction quality**. On the 256²
-  Shepp-Logan `fbp_fan.py` example the raw MSE drops from
-  `0.00216` (Siddon) to `0.00178` (SF-TR), a ~17% improvement.
-  On the 128³ `fdk_cone.py` example it drops from `0.00325` (Siddon)
-  to `0.00271` (SF-TR), again ~17%. The mechanism is that SF's
-  mass-conserving cell-integrated forward pairs more naturally with
-  the voxel-driven FBP/FDK gather backprojector than Siddon's
-  thin-ray sampling, which feeds extra high-frequency ringing into
-  the ramp filter.
-- **Performance**: SF-TR is ~2× and SF-TT ~2.5–4× slower than Siddon for
-  cone beam, and ~3× slower than Siddon for fan beam. The extra cost
-  comes from voxel-driven scatter with atomic adds (forward) versus
-  ray-driven parallelism in Siddon.
-- **Recommendation**: `backend="siddon"` remains the default for
-  backward compatibility and raw speed. For **analytical FBP/FDK
-  reconstruction** where reconstruction MSE matters more than forward
-  runtime, `"sf"` / `"sf_tr"` is a quantifiably better choice — at
-  2–3× forward cost you get ~17% lower reconstruction MSE on standard
-  phantoms. For **iterative reconstruction with autograd**, either
-  backend is valid; SF has the theoretical advantage of exact voxel-
-  scale mass conservation on both forward and adjoint, but in practice
-  Siddon's smoothing usually helps optimizer convergence. SF-TT's
-  axial-trapezoid refinement over SF-TR improves RMSE only by ~0.001
-  and is not worth the extra cost for typical cone angles; use SF-TR
-  by default and reserve SF-TT for extreme cone-angle research.
-
-## [1.2.11] - 2026-04-14
-
-### Added
-- **Parker short-scan demos** in `examples/fdk_cone.py` and `examples/fbp_fan.py`.
-  Both examples now expose an `apply_parker` switch that not only multiplies
-  by `parker_weights` but also samples angles on the minimal short-scan range
-  `pi + 2*gamma_max`, where `gamma_max` is computed from the detector half-width
-  and `sdd`. (Before this change the `apply_parker` flag in `fbp_fan.py` was
-  silently a no-op because the angular range stayed at `2*pi`.)
-- **`tests/test_gradcheck.py`** — `torch.autograd.gradcheck` coverage for
-  `ParallelProjectorFunction`, `FanProjectorFunction`, and `ConeProjectorFunction`.
-  Compares the analytical backward Jacobian to a finite-difference numerical
-  Jacobian over small inputs with float32-calibrated tolerances. Strongest
-  autograd-correctness guard beyond the existing inner-product adjoint tests.
-- **`tests/test_ramp_filter_windows.py`** — 27 parametrised tests covering every
-  `ramp_filter_1d` window option (`None`/`"ram-lak"`, `"hann"`, `"hanning"`,
-  `"hamming"`, `"cosine"`, `"shepp-logan"`) at three layers: direct `_ramp_window`
-  helper (DC gain, Nyquist value, monotonicity), full `ramp_filter_1d` end-to-end
-  (shape, DC annihilation, pad correctness, rfft vs complex-fft parity,
-  `sample_spacing` scaling), and a high-frequency attenuation sanity check on a
-  step input.
-- **`CHANGELOG.md`** — new Keep-a-Changelog file at the repo root.
-- **`tests/benchmarks/`** — opt-in `pytest-benchmark` suite covering every CUDA
-  kernel in the library (forward projector, pure-adjoint backprojector, and
-  analytical FBP/FDK pipeline) across three sizes for each of the three
-  geometries. 27 benchmarks total. Excluded from the default `pytest tests/`
-  run via `--ignore=tests/benchmarks` in `pytest.ini` so the normal test suite
-  stays fast; run explicitly with `pytest tests/benchmarks/ --benchmark-only`.
-  Enables before/after perf comparisons via `--benchmark-save=` /
-  `--benchmark-compare=`.
-
-### Changed
-- **`_cone_3d_fdk_backproject_kernel`** memory-access layout. The kernel now
-  unpacks `cuda.grid(3)` as `(iz, iy, ix)` instead of `(ix, iy, iz)`, and
-  `cone_weighted_backproject` launches the grid as `_grid_3d(D, H, W)` instead
-  of `_grid_3d(W, H, D)`. This makes `iz` warp-adjacent, which matches the
-  innermost stride-1 axis of the WHD output buffer, so the final `d_vol` write
-  becomes coalesced. Measured speedup on a 64^3–160^3 sweep: 1.0x–1.14x,
-  within run-to-run noise (the kernel is read-bound on the sinogram bilinear
-  samples, not write-bound, so L2 absorbed the old uncoalesced writes). The
-  fix is kept as the right default and future-proofs the kernel against
-  edits that shift work toward the write path. Matching coalescing comments
-  were added to the 2D `_parallel_2d_fbp_backproject_kernel` and
-  `_fan_2d_fbp_backproject_kernel` kernels, which were already coalesced
-  (their first grid index is also warp-adjacent and matches the `Nx` innermost
-  axis of their `(Ny, Nx)` output buffers).
-
-### Notes
-- No public-API changes. Pure-adjoint kernels and autograd Function classes
-  are untouched, so the autograd and iterative-reconstruction paths are
-  byte-for-byte equivalent to 1.2.10.
-
-## [1.2.10] - 2026-04-14
-
-This release is a correctness overhaul of every analytical reconstruction path
-(parallel / fan / cone) **and** of the autograd adjoint path shared by the
-iterative examples. It also ships a unified architecture where each geometry
-has its own dedicated voxel-driven FBP/FDK gather kernel, separate from the
-pure Siddon adjoint used by autograd.
-
-### Fixed
-
-#### Analytical FBP / FDK amplitude bugs
-
-Prior to this release, all three analytical reconstruction examples produced
-results that were off by large constant factors:
-
-| Example | Pre-fix reco range | Post-fix reco range | MSE improvement |
-|---|---|---|---|
-| `fbp_parallel.py` | [0, 6.52] | [−0.02, 1.01] | ~580× |
-| `fbp_fan.py` | [0, 6.33] | [−0.08, 1.01] | ~900× |
-| `fdk_cone.py` | [0, 10.08] | [−0.08, 1.00] | ~600× |
-
-Root causes:
-- Cone and fan used `(sdd/U)^2` with `U = sdd + x·sin − y·cos` instead of
-  the correct FDK weight `(sid/U)^2` with `U = sid + x·sin − y·cos`.
-- All three geometries were missing the `1/(2π)` Fourier-convention
-  constant from the FBP/FDK reconstruction formula.
-- Cone and fan used a Siddon ray-driven scatter for the analytical path,
-  which is neither a true adjoint nor a classical FBP/FDK gather.
-
-#### Autograd adjoint bug (cone + fan)
-
-`ConeProjectorFunction.backward`, `ConeBackprojectorFunction.forward`,
-`FanProjectorFunction.backward` and `FanBackprojectorFunction.forward`
-were all passing `distance_weight=1.0` to the shared Siddon backward
-kernel. This meant the autograd backward was **not the true adjoint** `P^T`
-of the forward projector — it had a `(sdd/U)^2` per-voxel factor baked in,
-biasing the gradient by ~2–3× depending on voxel position. Any iterative
-reconstruction that relied on autograd (including `iterative_reco_cone.py`
-and `iterative_reco_fan.py`) was running on a biased gradient flow.
-
-Parallel beam was unaffected (its backward kernel had no `distance_weight`
-parameter to begin with).
-
-This release removes the `distance_weight` parameter from both
-`_cone_3d_backward_kernel` and `_fan_2d_backward_kernel` entirely, so the
-dead code path cannot be accidentally reintroduced, and fixes the four
-autograd call sites to use the pure adjoint.
-
-### Added
-
-#### Voxel-driven gather kernels for every geometry
-
-Three new CUDA kernels, all under a dedicated `fastmath=False` decorator
-for FDK-grade accuracy:
-
-- `_parallel_2d_fbp_backproject_kernel` — no distance weighting (no source).
-- `_fan_2d_fbp_backproject_kernel` — `(sid/U)^2` + linear detector interp.
-- `_cone_3d_fdk_backproject_kernel` — `(sid/U)^2` + bilinear detector interp.
-
-Each kernel is voxel-driven: one thread per output pixel/voxel, loops over
-views, computes the projected detector coordinate, interpolates the filtered
-sinogram, weights and accumulates.
-
-#### `parallel_weighted_backproject` (new public helper)
-
-Mirrors `fan_weighted_backproject` and `cone_weighted_backproject`. Applies
-the `1/(2π)` Fourier-convention constant so a unit-density disk reconstructs
-to amplitude 1. Exported from `diffct`.
-
-#### `ramp_filter_1d` — new backward-compatible kwargs
-
-- `sample_spacing` (default `1.0`): physical detector cell pitch. Output is
-  rescaled by `1/sample_spacing` for physical-unit correctness.
-- `pad_factor` (default `1`): zero-pad to `pad_factor * N` before the FFT to
-  suppress circular-convolution wrap-around. `2` is recommended for FBP/FDK.
-- `window` (default `None`): frequency-domain apodization. Options: `None` /
-  `"ram-lak"`, `"hann"`, `"hamming"`, `"cosine"`, `"shepp-logan"`.
-- `use_rfft` (default `True`): faster real-FFT path for real-valued inputs.
-
-Existing `ramp_filter_1d(sino, dim=1)` calls keep working unchanged.
-
-#### Analytical FBP / FDK scale factors
-
-Each analytical helper now applies the correct analytical constant
-automatically so reconstructions are already amplitude-calibrated:
-
-- `parallel_weighted_backproject`: `1 / (2π)`.
-- `fan_weighted_backproject`: `sdd / (2π · sid)`.
-- `cone_weighted_backproject`: `sdd / (2π · sid)`.
-
-### Tests
-
-Test suite expanded from 6 to **27 tests**:
-
-- `tests/test_adjoint_inner_product.py` — the definitive check. For random `x`
-  and `y`, asserts `⟨A x, y⟩ = ⟨x, A^T y⟩` for parallel, fan and cone autograd
-  pairs. Permanently guards against any regression that would reintroduce the
-  `distance_weight=1.0` bug.
-- `tests/test_fdk_cone_accuracy.py` — 128³ Shepp-Logan RMSE / amplitude bounds.
-- `tests/test_fdk_cone_offsets.py` — detector, center and combined offsets with
-  amplitude assertions.
-- `tests/test_cone_projector_autograd.py` — gradient finiteness and non-zero
-  sanity.
-- `tests/test_fbp_fan_accuracy.py` — 256×256 Shepp-Logan RMSE.
-- `tests/test_fbp_fan_offsets.py` — three offset configurations.
-- `tests/test_fbp_parallel_accuracy.py` — parallel FBP RMSE + offset.
-
-### Examples
-
-`examples/fdk_cone.py`, `examples/fbp_fan.py` and `examples/fbp_parallel.py`
-have been rewritten with a consistent 8-step layout and detailed inline
-comments documenting every geometry variable (what it is, units, typical
-values, available options). Each example prints raw MSE, clamped MSE, and the
-reconstruction / phantom data ranges.
-
-The iterative reconstruction examples (`iterative_reco_parallel.py`,
-`iterative_reco_fan.py`, `iterative_reco_cone.py`) are unchanged — they
-silently benefit from the fixed autograd adjoint.
-
-### Documentation
-
-- `docs/source/api.rst`: adds autofunction entries for
-  `parallel_weighted_backproject`, documents the new `ramp_filter_1d`
-  options, and adds an "Analytical FBP / FDK architecture" section
-  explaining the scale-factor derivation.
-- `docs/source/fdk_cone_example.rst`: formula updated to reflect the
-  voxel-gather kernel and `(sid/U)^2` weight.
-- `docs/source/fbp_fan_example.rst` and `fbp_parallel_example.rst`: completely
-  rewritten to reference the new analytical helpers and fix a sign-convention
-  inconsistency in the math section.
-
-### Compatibility
-
-This release is source-compatible with 1.2.9 for every public entry point. The
-`distance_weight` parameter was internal and is removed from the private
-backward kernels; no public API touched that argument.
-
-## [1.2.9] - 2026-02-14
-
-Restored `main` to the state of 1.2.9 by reverting an accidental merge.
-See [GitHub release v1.2.9](https://github.com/sypsyp97/diffct/releases/tag/v1.2.9).
-
-## [1.2.8] - 2026-02-14
-
-See [GitHub release v1.2.8](https://github.com/sypsyp97/diffct/releases/tag/v1.2.8)
-and the commit history for details.
-
-## [1.2.7] - 2025-08-05
-
-See [GitHub release v1.2.7](https://github.com/sypsyp97/diffct/releases/tag/v1.2.7).
-
-## Earlier versions
-
-Releases 1.2.0 through 1.2.6 and the 1.1.x / 1.0.x lines are tracked on
-[GitHub releases](https://github.com/sypsyp97/diffct/releases). This CHANGELOG
-was introduced in 1.2.10 and does not back-fill detailed notes for earlier
-versions beyond pointers to the GitHub release pages.
-
-[Unreleased]: https://github.com/sypsyp97/diffct/compare/v1.3.0...HEAD
-[1.3.0]: https://github.com/sypsyp97/diffct/releases/tag/v1.3.0
-[1.2.11]: https://github.com/sypsyp97/diffct/releases/tag/v1.2.11
-[1.2.10]: https://github.com/sypsyp97/diffct/releases/tag/v1.2.10
-[1.2.9]: https://github.com/sypsyp97/diffct/releases/tag/v1.2.9
-[1.2.8]: https://github.com/sypsyp97/diffct/releases/tag/v1.2.8
-[1.2.7]: https://github.com/sypsyp97/diffct/releases/tag/v1.2.7
+# Changelog
+
+All notable changes to this project are documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [1.3.3] - 2026-04-23
+
+### Fixed
+- **Kernel numerical consistency and speed.** The CUDA kernels in
+  `diffct/differentiable.py` are now consistently `float32` end to end —
+  literal constants (`0.0`, `0.5`, `1.0`, `-inf`, ...) and integer-to-float
+  casts inside the Siddon and SF kernels are routed through typed `_DTYPE`
+  helpers so numba no longer implicitly promotes intermediates to `float64`.
+  This removes a silent precision mismatch that was slowing down every
+  projector/backprojector kernel; the library runs substantially faster
+  with no change in public-API behavior.
+- **Thread indexing and grid configuration** in the 3D cone Siddon
+  forward / backward kernels and the 2D fan SF backward kernel. The
+  `cuda.grid(...)` unpack order and the matching `_grid_2d` / `_grid_3d`
+  launch arguments are aligned so the warp-adjacent axis matches the
+  stride-1 axis of the output buffer: `(iv, iu, iview)` for 3D cone
+  (`d_sino[view, u, v]` / `d_vol[ix, iy, iz]`) and `(ix, iy)` for 2D fan
+  SF. Fixes mismatched launches between `ConeProjectorFunction`,
+  `ConeBackprojectorFunction`, `FanProjectorFunction`, and
+  `FanBackprojectorFunction` and their kernels.
+- **Walnut rotation-axis correction** in the shipped preprocessing and
+  sample data. `examples/data/preprocess_walnut.py` now applies the
+  Zenodo record's recommended 5-raw-pixel left shift before binning and
+  cropping, records the correction in the `.npz` metadata, and the
+  shipped `examples/data/walnut_cone.npz` / `walnut_reco.png` are
+  regenerated accordingly. `examples/realdata_walnut_fdk.py` and
+  `examples/data/NOTICE` are updated to surface the correction and the
+  richer walnut metadata.
+
+### Changed
+- **Examples now require CUDA explicitly.** `examples/fbp_parallel.py`,
+  `fbp_fan.py`, `fdk_cone.py`, `iterative_reco_*.py`, `realdata_fbp_*.py`,
+  `realdata_fdk_cone.py`, and `realdata_walnut_fdk.py` assert
+  `torch.cuda.is_available()` and initialize the CUDA device up front
+  instead of silently falling back to CPU (which the numba-cuda kernels
+  never supported anyway).
+
+## [1.3.2] - 2026-04-23
+
+### Added
+- **Expanded angular-weight regression tests** in
+  `tests/test_weights.py`, covering periodic `pi` half scans,
+  downsampled full scans, endpoint-included 721-view full scans, and
+  open short scans.
+
+### Changed
+- **`angular_integration_weights` is now coverage-aware and order-stable.**
+  The helper sorts angles internally, detects `pi`- and `2*pi`-periodic
+  sampling more robustly, handles endpoint-included trajectories, and
+  maps the computed weights back to the caller's original angle order.
+- **Walnut tooling is now configurable from the command line.**
+  `examples/data/preprocess_walnut.py` gained CLI switches for binning,
+  cropping, view stride, angle handedness, storage dtype, and archive
+  discovery; `examples/realdata_walnut_fdk.py` gained CLI controls for
+  backend, output volume size, voxel scale, filter window, output file
+  writing, and display suppression.
+- **README polish for bilingual navigation and repo layout.**
+  `README.md` now exposes the Chinese README link near the top and
+  clarifies the file tree entries for `README.md` / `README.zh.md`.
+
+### Fixed
+- **Angular quadrature artifacts** in analytical reconstructions when
+  full scans were endpoint-included or angularly downsampled. These
+  trajectories now receive periodic integration weights instead of being
+  misclassified as open scans.
+- **Walnut example angle metadata and scan handedness.**
+  The walnut preprocessing and FDK example now use the dataset's
+  scanner-to-diffct angle convention explicitly and preserve the full
+  721-view `0 .. 360 deg` acquisition description in the stored
+  metadata.
+
+## [1.3.1] - 2026-04-15
+
+### Added
+- **Real-data walnut FDK example** at `examples/realdata_walnut_fdk.py`,
+  running the full analytical FDK pipeline on a preprocessed subset of
+  the Helsinki walnut cone-beam CT dataset ([Meaney 2022, Zenodo
+  10.5281/zenodo.6986012](https://doi.org/10.5281/zenodo.6986012),
+  CC-BY 4.0). The 241-view, 256×256-per-view sinogram is shipped at
+  `examples/data/walnut_cone.npz` (~25 MB, float16, 8× binned, 256²
+  center crop) together with a `preprocess_walnut.py` regenerator
+  script, an attribution `NOTICE`, and a `walnut_reco.png` sample
+  montage. Reconstructs at half the nominal voxel size on a 512³ grid
+  using `backend="sf_tr"` + Hamming ramp window.
+- **Synthetic "real-data" pipeline examples** for all three geometries
+  (`examples/realdata_fbp_parallel.py`, `realdata_fbp_fan.py`,
+  `realdata_fdk_cone.py`) that run a Beer-Lambert + Poisson + `-log`
+  forward model on Shepp-Logan and reconstruct with the analytical
+  pipeline, showing the proper place for `-log` preprocessing.
+- **Chinese README** at `README.zh.md`, mirroring `README.md` with
+  bidirectional language links in both files.
+- **Core Algorithm section** in the READMEs (EN + ZH) explaining the
+  Siddon + bilinear/trilinear interpolation design choice, the
+  trade-off (slight blur at nominal voxel size), and when to pick
+  SF vs VD honestly (see "Changed" below).
+
+### Changed
+- **SF FBP / FDK backprojection kernels rewritten in LEAP's
+  chord-weighted matched-adjoint form** (from `projectors_SF.cu`).
+  The three analytical SF gather kernels
+  (`_fan_2d_sf_fbp_backproject_kernel`,
+  `_cone_3d_sf_tr_fdk_backproject_kernel`,
+  `_cone_3d_sf_tt_fdk_backproject_kernel`) now use the per-voxel
+  chord through the unit voxel instead of a `(sid/U)²`-plus-footprint-
+  area form, with a matching `sqrt(1+(v/sdd)²)` axial chord correction
+  on the cone side. Amplitude is calibrated against Siddon VD at
+  every voxel / detector-pitch combination tested (nominal, 0.64×
+  sub-nominal, 0.40× sub-nominal, supra-nominal) via the new
+  `det_spacing/(voxel·2π)` fan scale and
+  `(du·dv·sid)/(2π·sdd·voxel²)` cone scale constants.
+- **Honest README Core Algorithm section on SF vs VD.** The earlier
+  "SF lowers MSE by ~17 %" and "SF is measurably sharper at sub-
+  nominal" claims in 1.3.0 are walked back: on Shepp-Logan and the
+  walnut dataset, LEAP-form SF and Siddon VD produce visually
+  indistinguishable edge profiles at typical CBCT magnifications,
+  and MSE differences are fractions of a percent. SF's real value
+  is its **mass-conserving cell-integrated forward model**, which
+  matters for iterative reconstruction, learned priors, and
+  sinogram-level losses — not as a drop-in sharpness knob on
+  analytical FBP / FDK. The shipped `fbp_fan.py`, `fdk_cone.py`,
+  and `realdata_walnut_fdk.py` example comments are updated to
+  match.
+
+### Fixed
+- **SF FBP / FDK weight normalization** when the voxel's trapezoidal
+  footprint straddles the default 4-corner sort. The 1.3.0 SF
+  backprojection kernels used `fdk_w / (span · v_span)` (bounding-box
+  area) which under-amplified oblique views by up to 2× per axis and
+  produced a dim, angularly-modulated reconstruction. Diagnosed by
+  inspecting a Shepp-Logan SF reconstruction, corrected first to
+  `fdk_w / ((span+plateau)/2 · v_span)` (true trapezoid area) and
+  then fully replaced by the LEAP chord-weighted form above.
+
+### Acknowledgements
+- [LEAP](https://github.com/LLNL/LEAP) (LLNL / Hyojin Kim et al.)
+  added to `README.md` / `README.zh.md` Acknowledgements.
+  `projectors_SF.cu` is the reference implementation the new
+  analytical SF backprojection kernels are ported from.
+
+## [1.3.0] - 2026-04-14
+
+### Added
+- **Separable-footprint (SF) projector backends** for 2D fan and 3D cone
+  beam geometries, following Long-Fessler-Balter (IEEE TMI 2010).
+  `FanProjectorFunction` / `FanBackprojectorFunction` now accept
+  `backend="siddon"` (default, unchanged) or `backend="sf"`.
+  `ConeProjectorFunction` / `ConeBackprojectorFunction` accept
+  `backend="siddon"` (default), `"sf_tr"` (trapezoid in transaxial,
+  rectangle in axial) or `"sf_tt"` (trapezoid in both directions with
+  axial rise/fall from `U_near`/`U_far` across the voxel). Each SF
+  backend is implemented as a matched scatter/gather pair of CUDA
+  kernels so both forward and adjoint are available — autograd works
+  end-to-end for every backend, and the standalone Backprojector
+  Function can also be driven in SF mode for iterative reconstruction.
+- **Adjoint inner-product tests** for every new SF backend in
+  `tests/test_adjoint_inner_product.py`, plus `torch.autograd.gradcheck`
+  coverage in `tests/test_gradcheck.py`. Test count grew from 57 to 66.
+
+### Changed
+- **Internal grid-point convention** is now uniformly `x_v = ix - cx`
+  (matching `_cone_3d_fdk_backproject_kernel`). The SF kernels use the
+  same convention so voxel centers align with where the Siddon/FDK
+  paths interpret `d_vol[ix, iy, iz]`.
+- **`_TPB_SF_3D = (4, 4, 4)`** introduced for the 3D SF kernels. SF-TT
+  in particular exceeds the 128-register-per-thread budget allowed by
+  the default `(8, 8, 8)` launch; the smaller block gives each thread
+  ~1024 registers and avoids `CUDA_ERROR_LAUNCH_OUT_OF_RESOURCES`.
+
+### Notes
+- **Raw forward accuracy vs analytical Radon**: on both 2D fan
+  (512² Shepp-Logan) and 3D cone (96³ and 128³ 3D Shepp-Logan) phantoms,
+  measured against the analytical ellipse / ellipsoid Radon transform,
+  the existing Siddon projector with bilinear / trilinear interpolation
+  is slightly more accurate (~3% better RMSE, ~15% better max error)
+  than SF-TR / SF-TT at the thin-ray sampling level. The classic SF
+  advantage reported in Long et al. is over the piecewise-constant DD
+  projector; diffct's Siddon uses smooth interpolation, which covers
+  most of the gap SF was designed to close.
+- **Full analytical reconstruction (forward + FBP/FDK)**: despite the
+  raw-forward result above, in a complete analytical pipeline
+  (`FanProjectorFunction` / `ConeProjectorFunction` -> `ramp_filter_1d`
+  -> `fan_weighted_backproject` / `cone_weighted_backproject`) SF
+  **measurably improves reconstruction quality**. On the 256²
+  Shepp-Logan `fbp_fan.py` example the raw MSE drops from
+  `0.00216` (Siddon) to `0.00178` (SF-TR), a ~17% improvement.
+  On the 128³ `fdk_cone.py` example it drops from `0.00325` (Siddon)
+  to `0.00271` (SF-TR), again ~17%. The mechanism is that SF's
+  mass-conserving cell-integrated forward pairs more naturally with
+  the voxel-driven FBP/FDK gather backprojector than Siddon's
+  thin-ray sampling, which feeds extra high-frequency ringing into
+  the ramp filter.
+- **Performance**: SF-TR is ~2× and SF-TT ~2.5–4× slower than Siddon for
+  cone beam, and ~3× slower than Siddon for fan beam. The extra cost
+  comes from voxel-driven scatter with atomic adds (forward) versus
+  ray-driven parallelism in Siddon.
+- **Recommendation**: `backend="siddon"` remains the default for
+  backward compatibility and raw speed. For **analytical FBP/FDK
+  reconstruction** where reconstruction MSE matters more than forward
+  runtime, `"sf"` / `"sf_tr"` is a quantifiably better choice — at
+  2–3× forward cost you get ~17% lower reconstruction MSE on standard
+  phantoms. For **iterative reconstruction with autograd**, either
+  backend is valid; SF has the theoretical advantage of exact voxel-
+  scale mass conservation on both forward and adjoint, but in practice
+  Siddon's smoothing usually helps optimizer convergence. SF-TT's
+  axial-trapezoid refinement over SF-TR improves RMSE only by ~0.001
+  and is not worth the extra cost for typical cone angles; use SF-TR
+  by default and reserve SF-TT for extreme cone-angle research.
+
+## [1.2.11] - 2026-04-14
+
+### Added
+- **Parker short-scan demos** in `examples/fdk_cone.py` and `examples/fbp_fan.py`.
+  Both examples now expose an `apply_parker` switch that not only multiplies
+  by `parker_weights` but also samples angles on the minimal short-scan range
+  `pi + 2*gamma_max`, where `gamma_max` is computed from the detector half-width
+  and `sdd`. (Before this change the `apply_parker` flag in `fbp_fan.py` was
+  silently a no-op because the angular range stayed at `2*pi`.)
+- **`tests/test_gradcheck.py`** — `torch.autograd.gradcheck` coverage for
+  `ParallelProjectorFunction`, `FanProjectorFunction`, and `ConeProjectorFunction`.
+  Compares the analytical backward Jacobian to a finite-difference numerical
+  Jacobian over small inputs with float32-calibrated tolerances. Strongest
+  autograd-correctness guard beyond the existing inner-product adjoint tests.
+- **`tests/test_ramp_filter_windows.py`** — 27 parametrised tests covering every
+  `ramp_filter_1d` window option (`None`/`"ram-lak"`, `"hann"`, `"hanning"`,
+  `"hamming"`, `"cosine"`, `"shepp-logan"`) at three layers: direct `_ramp_window`
+  helper (DC gain, Nyquist value, monotonicity), full `ramp_filter_1d` end-to-end
+  (shape, DC annihilation, pad correctness, rfft vs complex-fft parity,
+  `sample_spacing` scaling), and a high-frequency attenuation sanity check on a
+  step input.
+- **`CHANGELOG.md`** — new Keep-a-Changelog file at the repo root.
+- **`tests/benchmarks/`** — opt-in `pytest-benchmark` suite covering every CUDA
+  kernel in the library (forward projector, pure-adjoint backprojector, and
+  analytical FBP/FDK pipeline) across three sizes for each of the three
+  geometries. 27 benchmarks total. Excluded from the default `pytest tests/`
+  run via `--ignore=tests/benchmarks` in `pytest.ini` so the normal test suite
+  stays fast; run explicitly with `pytest tests/benchmarks/ --benchmark-only`.
+  Enables before/after perf comparisons via `--benchmark-save=` /
+  `--benchmark-compare=`.
+
+### Changed
+- **`_cone_3d_fdk_backproject_kernel`** memory-access layout. The kernel now
+  unpacks `cuda.grid(3)` as `(iz, iy, ix)` instead of `(ix, iy, iz)`, and
+  `cone_weighted_backproject` launches the grid as `_grid_3d(D, H, W)` instead
+  of `_grid_3d(W, H, D)`. This makes `iz` warp-adjacent, which matches the
+  innermost stride-1 axis of the WHD output buffer, so the final `d_vol` write
+  becomes coalesced. Measured speedup on a 64^3–160^3 sweep: 1.0x–1.14x,
+  within run-to-run noise (the kernel is read-bound on the sinogram bilinear
+  samples, not write-bound, so L2 absorbed the old uncoalesced writes). The
+  fix is kept as the right default and future-proofs the kernel against
+  edits that shift work toward the write path. Matching coalescing comments
+  were added to the 2D `_parallel_2d_fbp_backproject_kernel` and
+  `_fan_2d_fbp_backproject_kernel` kernels, which were already coalesced
+  (their first grid index is also warp-adjacent and matches the `Nx` innermost
+  axis of their `(Ny, Nx)` output buffers).
+
+### Notes
+- No public-API changes. Pure-adjoint kernels and autograd Function classes
+  are untouched, so the autograd and iterative-reconstruction paths are
+  byte-for-byte equivalent to 1.2.10.
+
+## [1.2.10] - 2026-04-14
+
+This release is a correctness overhaul of every analytical reconstruction path
+(parallel / fan / cone) **and** of the autograd adjoint path shared by the
+iterative examples. It also ships a unified architecture where each geometry
+has its own dedicated voxel-driven FBP/FDK gather kernel, separate from the
+pure Siddon adjoint used by autograd.
+
+### Fixed
+
+#### Analytical FBP / FDK amplitude bugs
+
+Prior to this release, all three analytical reconstruction examples produced
+results that were off by large constant factors:
+
+| Example | Pre-fix reco range | Post-fix reco range | MSE improvement |
+|---|---|---|---|
+| `fbp_parallel.py` | [0, 6.52] | [−0.02, 1.01] | ~580× |
+| `fbp_fan.py` | [0, 6.33] | [−0.08, 1.01] | ~900× |
+| `fdk_cone.py` | [0, 10.08] | [−0.08, 1.00] | ~600× |
+
+Root causes:
+- Cone and fan used `(sdd/U)^2` with `U = sdd + x·sin − y·cos` instead of
+  the correct FDK weight `(sid/U)^2` with `U = sid + x·sin − y·cos`.
+- All three geometries were missing the `1/(2π)` Fourier-convention
+  constant from the FBP/FDK reconstruction formula.
+- Cone and fan used a Siddon ray-driven scatter for the analytical path,
+  which is neither a true adjoint nor a classical FBP/FDK gather.
+
+#### Autograd adjoint bug (cone + fan)
+
+`ConeProjectorFunction.backward`, `ConeBackprojectorFunction.forward`,
+`FanProjectorFunction.backward` and `FanBackprojectorFunction.forward`
+were all passing `distance_weight=1.0` to the shared Siddon backward
+kernel. This meant the autograd backward was **not the true adjoint** `P^T`
+of the forward projector — it had a `(sdd/U)^2` per-voxel factor baked in,
+biasing the gradient by ~2–3× depending on voxel position. Any iterative
+reconstruction that relied on autograd (including `iterative_reco_cone.py`
+and `iterative_reco_fan.py`) was running on a biased gradient flow.
+
+Parallel beam was unaffected (its backward kernel had no `distance_weight`
+parameter to begin with).
+
+This release removes the `distance_weight` parameter from both
+`_cone_3d_backward_kernel` and `_fan_2d_backward_kernel` entirely, so the
+dead code path cannot be accidentally reintroduced, and fixes the four
+autograd call sites to use the pure adjoint.
+
+### Added
+
+#### Voxel-driven gather kernels for every geometry
+
+Three new CUDA kernels, all under a dedicated `fastmath=False` decorator
+for FDK-grade accuracy:
+
+- `_parallel_2d_fbp_backproject_kernel` — no distance weighting (no source).
+- `_fan_2d_fbp_backproject_kernel` — `(sid/U)^2` + linear detector interp.
+- `_cone_3d_fdk_backproject_kernel` — `(sid/U)^2` + bilinear detector interp.
+
+Each kernel is voxel-driven: one thread per output pixel/voxel, loops over
+views, computes the projected detector coordinate, interpolates the filtered
+sinogram, weights and accumulates.
+
+#### `parallel_weighted_backproject` (new public helper)
+
+Mirrors `fan_weighted_backproject` and `cone_weighted_backproject`. Applies
+the `1/(2π)` Fourier-convention constant so a unit-density disk reconstructs
+to amplitude 1. Exported from `diffct`.
+
+#### `ramp_filter_1d` — new backward-compatible kwargs
+
+- `sample_spacing` (default `1.0`): physical detector cell pitch. Output is
+  rescaled by `1/sample_spacing` for physical-unit correctness.
+- `pad_factor` (default `1`): zero-pad to `pad_factor * N` before the FFT to
+  suppress circular-convolution wrap-around. `2` is recommended for FBP/FDK.
+- `window` (default `None`): frequency-domain apodization. Options: `None` /
+  `"ram-lak"`, `"hann"`, `"hamming"`, `"cosine"`, `"shepp-logan"`.
+- `use_rfft` (default `True`): faster real-FFT path for real-valued inputs.
+
+Existing `ramp_filter_1d(sino, dim=1)` calls keep working unchanged.
+
+#### Analytical FBP / FDK scale factors
+
+Each analytical helper now applies the correct analytical constant
+automatically so reconstructions are already amplitude-calibrated:
+
+- `parallel_weighted_backproject`: `1 / (2π)`.
+- `fan_weighted_backproject`: `sdd / (2π · sid)`.
+- `cone_weighted_backproject`: `sdd / (2π · sid)`.
+
+### Tests
+
+Test suite expanded from 6 to **27 tests**:
+
+- `tests/test_adjoint_inner_product.py` — the definitive check. For random `x`
+  and `y`, asserts `⟨A x, y⟩ = ⟨x, A^T y⟩` for parallel, fan and cone autograd
+  pairs. Permanently guards against any regression that would reintroduce the
+  `distance_weight=1.0` bug.
+- `tests/test_fdk_cone_accuracy.py` — 128³ Shepp-Logan RMSE / amplitude bounds.
+- `tests/test_fdk_cone_offsets.py` — detector, center and combined offsets with
+  amplitude assertions.
+- `tests/test_cone_projector_autograd.py` — gradient finiteness and non-zero
+  sanity.
+- `tests/test_fbp_fan_accuracy.py` — 256×256 Shepp-Logan RMSE.
+- `tests/test_fbp_fan_offsets.py` — three offset configurations.
+- `tests/test_fbp_parallel_accuracy.py` — parallel FBP RMSE + offset.
+
+### Examples
+
+`examples/fdk_cone.py`, `examples/fbp_fan.py` and `examples/fbp_parallel.py`
+have been rewritten with a consistent 8-step layout and detailed inline
+comments documenting every geometry variable (what it is, units, typical
+values, available options). Each example prints raw MSE, clamped MSE, and the
+reconstruction / phantom data ranges.
+
+The iterative reconstruction examples (`iterative_reco_parallel.py`,
+`iterative_reco_fan.py`, `iterative_reco_cone.py`) are unchanged — they
+silently benefit from the fixed autograd adjoint.
+
+### Documentation
+
+- `docs/source/api.rst`: adds autofunction entries for
+  `parallel_weighted_backproject`, documents the new `ramp_filter_1d`
+  options, and adds an "Analytical FBP / FDK architecture" section
+  explaining the scale-factor derivation.
+- `docs/source/fdk_cone_example.rst`: formula updated to reflect the
+  voxel-gather kernel and `(sid/U)^2` weight.
+- `docs/source/fbp_fan_example.rst` and `fbp_parallel_example.rst`: completely
+  rewritten to reference the new analytical helpers and fix a sign-convention
+  inconsistency in the math section.
+
+### Compatibility
+
+This release is source-compatible with 1.2.9 for every public entry point. The
+`distance_weight` parameter was internal and is removed from the private
+backward kernels; no public API touched that argument.
+
+## [1.2.9] - 2026-02-14
+
+Restored `main` to the state of 1.2.9 by reverting an accidental merge.
+See [GitHub release v1.2.9](https://github.com/sypsyp97/diffct/releases/tag/v1.2.9).
+
+## [1.2.8] - 2026-02-14
+
+See [GitHub release v1.2.8](https://github.com/sypsyp97/diffct/releases/tag/v1.2.8)
+and the commit history for details.
+
+## [1.2.7] - 2025-08-05
+
+See [GitHub release v1.2.7](https://github.com/sypsyp97/diffct/releases/tag/v1.2.7).
+
+## Earlier versions
+
+Releases 1.2.0 through 1.2.6 and the 1.1.x / 1.0.x lines are tracked on
+[GitHub releases](https://github.com/sypsyp97/diffct/releases). This CHANGELOG
+was introduced in 1.2.10 and does not back-fill detailed notes for earlier
+versions beyond pointers to the GitHub release pages.
+
+[1.3.3]: https://github.com/sypsyp97/diffct/releases/tag/v1.3.3
+[1.3.2]: https://github.com/sypsyp97/diffct/releases/tag/v1.3.2
+[1.3.1]: https://github.com/sypsyp97/diffct/releases/tag/v1.3.1
+[1.3.0]: https://github.com/sypsyp97/diffct/releases/tag/v1.3.0
+[1.2.11]: https://github.com/sypsyp97/diffct/releases/tag/v1.2.11
+[1.2.10]: https://github.com/sypsyp97/diffct/releases/tag/v1.2.10
+[1.2.9]: https://github.com/sypsyp97/diffct/releases/tag/v1.2.9
+[1.2.8]: https://github.com/sypsyp97/diffct/releases/tag/v1.2.8
+[1.2.7]: https://github.com/sypsyp97/diffct/releases/tag/v1.2.7