MolloiLab · Dale-Black · Jun 18, 2026 · Jun 18, 2026 · Jun 18, 2026
diff --git a/.gitignore b/.gitignore
@@ -46,6 +46,10 @@ docs/package-lock.json
 # the .bin into docs/notebooks/data/xcat/ (default path, symlink-friendly).
 docs/notebooks/data/
 
+# Pluto cell-output caches written by PlutoSpace / pluto-collab — large
+# (tens of MB), regenerated on every run, never tracked.
+*.pluto-cache.toml
+
 # File generated by Pkg, the package manager, based on a corresponding Project.toml
 # It records a fixed state of all packages used by the project. As such, it should not be
 # committed for packages, but should be committed for applications that require a static

diff --git a/docs/assets/dual_kvp_vmi_projection_grid.png b/docs/assets/dual_kvp_vmi_projection_grid.png
diff --git a/docs/assets/dual_kvp_vmi_projection_monoplus.png b/docs/assets/dual_kvp_vmi_projection_monoplus.png
diff --git a/docs/assets/dual_kvp_vmi_water_noise_vs_energy.png b/docs/assets/dual_kvp_vmi_water_noise_vs_energy.png
diff --git a/docs/assets/pcct_vmi_projection_grid.png b/docs/assets/pcct_vmi_projection_grid.png
diff --git a/docs/assets/pcct_vmi_projection_monoplus.png b/docs/assets/pcct_vmi_projection_monoplus.png
diff --git a/docs/assets/pcct_vmi_regression.png b/docs/assets/pcct_vmi_regression.png
diff --git a/docs/assets/pcct_vmi_vs_theoretical.png b/docs/assets/pcct_vmi_vs_theoretical.png
diff --git a/docs/assets/pcct_vmi_water_noise_vs_energy.png b/docs/assets/pcct_vmi_water_noise_vs_energy.png
diff --git a/docs/assets/pcct_vmi_water_roi_check.png b/docs/assets/pcct_vmi_water_roi_check.png
diff --git a/docs/assets/qrm_thorax_vmi_noise_roi.png b/docs/assets/qrm_thorax_vmi_noise_roi.png
diff --git a/docs/assets/qrm_thorax_vmi_vs_theoretical.png b/docs/assets/qrm_thorax_vmi_vs_theoretical.png
diff --git a/docs/assets/qrm_thorax_vmi_water_roi_check.png b/docs/assets/qrm_thorax_vmi_water_roi_check.png
diff --git a/docs/assets/recon_compare_4panel.png b/docs/assets/recon_compare_4panel.png
diff --git a/docs/assets/sinogram_standard.png b/docs/assets/sinogram_standard.png
diff --git a/docs/assets/vmi_regression.png b/docs/assets/vmi_regression.png
diff --git a/docs/assets/vmi_vs_theoretical.png b/docs/assets/vmi_vs_theoretical.png
diff --git a/docs/assets/vmi_water_roi_check.png b/docs/assets/vmi_water_roi_check.png
diff --git a/docs/assets/xcat_fbp_vs_hir.png b/docs/assets/xcat_fbp_vs_hir.png
diff --git a/docs/notebooks/01_five_struct_api.jl b/docs/notebooks/01_five_struct_api.jl
@@ -1,5 +1,8 @@
 ### A Pluto.jl notebook ###
-# v0.19.0
+# v0.1.0
+
+using Markdown
+using InteractiveUtils
 
 # ╔═╡ 01000003-0000-4000-8000-000000000001
 begin
@@ -47,6 +50,7 @@ detect a GPU backend.
 import BasisSimulator as BS
 
 # ╔═╡ 01000003-0000-4000-8000-000000000003
+# ╠═╡ show_logs = false
 import CairoMakie as CM
 
 # ╔═╡ 01000004-0000-4000-8000-000000000001

diff --git a/docs/notebooks/02_xcat_custom_materials.jl b/docs/notebooks/02_xcat_custom_materials.jl
@@ -1,5 +1,5 @@
 ### A Pluto.jl notebook ###
-# v0.20.24
+# v0.1.0
 
 using Markdown
 using InteractiveUtils

diff --git a/docs/notebooks/03_dual_kvp_switching_vmi.jl b/docs/notebooks/03_dual_kvp_switching_vmi.jl
@@ -1,5 +1,8 @@
 ### A Pluto.jl notebook ###
-# v0.19.0
+# v0.1.0
+
+using Markdown
+using InteractiveUtils
 
 # ╔═╡ 05000001-0000-4000-8000-000000000001
 begin
@@ -307,7 +310,7 @@ subspace `U[:,2]` with a small separable Gaussian.  One knob:
 """
 
 # ╔═╡ 05000007-0000-4000-8000-000000000005
-SVD_SIGMA_PX = 1.0;   # Gaussian σ (px) for U[:,2]; 0 = passthrough (no denoising)
+SVD_SIGMA_PX = 0.0;   # Gaussian σ (px) for U[:,2]; 0 = passthrough (no denoising)
 
 # ╔═╡ 05000007-0000-4000-8000-000000000010
 # 2-channel joint projection-domain SVD denoise (BS.apply_sino_svd_denoise).

diff --git a/docs/notebooks/04_pcct_vmi.jl b/docs/notebooks/04_pcct_vmi.jl
@@ -1,5 +1,8 @@
 ### A Pluto.jl notebook ###
-# v0.19.0
+# v0.1.0
+
+using Markdown
+using InteractiveUtils
 
 # ╔═╡ 06000001-0000-4000-8000-000000000001
 begin

diff --git a/docs/notebooks/07_qrm_thorax_pure_material_vmi.jl b/docs/notebooks/07_qrm_thorax_pure_material_vmi.jl
@@ -1,5 +1,8 @@
 ### A Pluto.jl notebook ###
-# v0.19.0
+# v0.1.0
+
+using Markdown
+using InteractiveUtils
 
 # ╔═╡ 07010003-0000-4000-8000-000000000001
 begin

diff --git a/src/BasisSimulator.jl b/src/BasisSimulator.jl
@@ -79,6 +79,11 @@ include("geometry/affine.jl")
 # Reference: CERN/TIGRE/Common/CUDA/Siddon_projection.cu
 include("projection/siddon.jl")
 
+# Distance-driven forward projection (CatSim/XCIST DD3, gather form)
+# Reference: De Man & Basu 2004; gecatsim DD3Proj_roi_notrans_mm.cpp
+# Drop-in replacement for Siddon (same signatures, cm units, Σμ·l output).
+include("projection/dd.jl")
+
 # =============================================================================
 # Detector (ALL detector effects + noise)
 # =============================================================================

diff --git a/src/api/driver.jl b/src/api/driver.jl
@@ -1321,7 +1321,7 @@ function reconstruct!(
             # Forward project with subset geometry → subset_Ax_buf
             ax_view = view(ws.subset_Ax_buf, :, :, 1:n_sub)
             fill!(ax_view, zero(T))
-            siddon_forward_project!(
+            dd_forward_project!(
                 ax_view, ws.volume, geom_s;
                 ws_source_positions = ws.subset_geom_source_positions[s],
                 ws_detector_centers = ws.subset_geom_detector_centers[s],

diff --git a/src/correction/bhc_image_domain.jl b/src/correction/bhc_image_domain.jl
@@ -107,7 +107,7 @@ function apply_bhc_image_domain(
     # Use geom's recon FOV (no volume_extent override) so this matches Step 3's
     # FDK back-projection grid exactly — same physical box on both halves of
     # the round-trip.
-    ξ_gpu = siddon_forward_project(high_atten_μ, geom)
+    ξ_gpu = dd_forward_project(high_atten_μ, geom)
 
     # Step 3: FDK-reconstruct the error sinogram → error image.
     error_image = fdk_reconstruct(ξ_gpu, geom, matrix_size)

diff --git a/src/correction/bhc_sinogram.jl b/src/correction/bhc_sinogram.jl
@@ -603,7 +603,7 @@ function apply_bhc_two_material(
         end
     end
 
-    p_b_gpu = siddon_forward_project(bone_μ_gpu, geom)
+    p_b_gpu = dd_forward_project(bone_μ_gpu, geom)
 
     p_s_gpu = similar(sino_water)
     copyto!(p_s_gpu, sino_water)

diff --git a/src/detector/photon_counting.jl b/src/detector/photon_counting.jl
@@ -495,15 +495,15 @@ function pcct_forward_project(
 
             if has_src
                 copyto!(bt_sub, @view ws_source_spectral[:, :, ts:te])
-                siddon_fused_spectral_project!(
+                dd_fused_spectral_project!(
                     _pilot, _outputs_flat, Int32(n_bins), mask, _proj_geom,
                     μ_sub, W_sub, Val(TILE_K), Int32(1);
                     volume_extent=volume_extent,
                     ws_source_positions=_ws_src, ws_detector_centers=_ws_det,
                     ws_detector_u=_ws_u, ws_detector_v=_ws_v,
                     ws_bowtie_spectral=bt_sub)
             else
-                siddon_fused_spectral_project!(
+                dd_fused_spectral_project!(
                     _pilot, _outputs_flat, Int32(n_bins), mask, _proj_geom,
                     μ_sub, W_sub, Val(TILE_K), Int32(1);
                     volume_extent=volume_extent,
@@ -636,7 +636,7 @@ function pcct_forward_project(
 
         # Forward project at this energy (native or binned resolution)
         fill!(sino_buf, zero(T))
-        siddon_forward_project!(sino_buf, μ_volume, proj_geom;
+        dd_forward_project!(sino_buf, μ_volume, proj_geom;
             ws_source_positions=_ws_src,
             ws_detector_centers=_ws_det,
             ws_detector_u=_ws_u,