Rebuild as SoftwareX reproducibility capsule

Per-case ready-to-run configs derived from the published run snapshots, split per-pipeline for planar_noisy and experimental (instantaneous: ssmin/time-free split; every ensemble config runs on raw images). Three-tier README: plot-only from reference_results, full CLI reprocess, calibration re-derivation, plus a pivtools-bench performance section. reference_results refreshed to the published runs (figure scripts regenerate the paper figures byte-identically). Calibration models + settings sidecars shipped under calibration/{planar,stereo,experimental} with corrected planar dt (0.0057553 s). Minimal hot-wire extract hotwire/hwa.mat replaces the Hutchins-corrected file. scripts/ reduced to the three paper scripts; analysis tooling moved to python-PIVTOOLs manual_tools; generation/SIG configs removed (kept in git history). Stereo image folders renamed camera{1,2} -> Cam{1,2} to match the pivtools loader convention; stale masks and in-case board sets removed.

README.md

@@ -11,6 +11,7 @@ tags:
 - validation
 - benchmark
 - synthetic-data
+- hot-wire-anemometry
 pretty_name: PIVtools Turbulent Channel Validation Dataset
 size_categories:
 - 10K<n<100K
@@ -18,218 +19,315 @@ size_categories:
 
 # PIVtools Turbulent Channel Validation Dataset
 
-Synthetic particle-image-velocimetry (PIV) images of a turbulent channel flow at Re_τ ≈ 1000, paired with DNS-derived ground-truth statistics. Designed to benchmark PIV algorithms end-to-end against a reference dataset of known answer.
+Reproducibility capsule for the PIVtools software paper (SoftwareX, submitted). It contains
+everything needed to regenerate the paper's validation figures, at three levels of effort:
 
-Two cases are provided:
+1. **Plot only** — run two scripts against the shipped `reference_results/`. No PIV processing.
+2. **Reprocess** — run PIV → calibration → statistics from the shipped images and configs,
+   then plot from your own outputs.
+3. **Re-derive calibration** — recompute the camera models from the shipped calibration
+   board images before reprocessing.
 
-- **Case A (clean)**: 85 000 particles per 2048 × 2048 image (≈ 5.2 ppw at 16 × 16 windows), no noise. Sets an upper bound on PIV accuracy.
-- **Case B (noisy)**: 22 000 particles per image (≈ 1.3 ppw), Gaussian sensor noise (mean 80, std 16, SNR ≈ 8). Realistic experimental conditions.
+Two synthetic cases and one experimental case:
 
-Each case contains 4 000 image pairs in both planar and stereo geometries. The stereo cameras are placed symmetrically at ± 45° from the sheet normal, in a side-scatter arrangement. Ground truth is provided separately for each case — both derive from the same underlying JHTDB channel snapshots but with their respective particle counts, so finite-sample statistics are self-consistent.
+- **Case A (clean, synthetic)**: 85 000 particles per 2048 × 2048 image (≈ 5.2 ppw at
+  16 × 16 windows), no noise. Upper bound on PIV accuracy. Planar + stereo geometries.
+- **Case B (noisy, synthetic)**: 22 000 particles per image (≈ 1.3 ppw), Gaussian sensor
+  noise (mean 80, std 16, SNR ≈ 8, independent per frame). Planar + stereo geometries.
+- **Experimental**: 2 100 pairs of cropped, gain-normalised Cam4 images of a turbulent
+  channel/boundary-layer facility, compared against a hot-wire profile from the same
+  facility (shipped in `hotwire/hwa.mat`).
 
-Companion to the PIVtools software paper (SoftwareX, submitted). The dataset is self-contained: drop it next to a [PIVtools](https://github.com/MTT69/python-PIVtools) install and the benchmark scripts reproduce every validation figure in the paper.
-
-## Quickstart
-
-```bash
-# 1. Install pivtools (C extensions are pre-built in the PyPI wheel)
-pip install pivtools
-
-# 2. Download this dataset
-hf download MTT69/TurbulentChannel --repo-type dataset --local-dir ./tc
-
-# 3. Process the planar noisy images (ensemble PIV — example)
-pivtools-cli init --output ./work/config.yaml
-# edit config.yaml to point sources at ./tc/planar_noisy
-pivtools-cli ensemble --config ./work/config.yaml
-
-# 4. Benchmark against DNS  (use ground_truth/clean for Case A, ground_truth/noisy for Case B)
-python ./tc/scripts/benchmark_comparison.py \
-    --mode ensemble \
-    --gt-dir ./tc/ground_truth/noisy \
-    --ensemble-dir ./work/calibrated_piv/4000/Cam1/ensemble \
-    --num-frames 4000 \
-    --output-dir ./work/validation
-```
+Each synthetic case has 4 000 image pairs. The stereo cameras sit symmetrically at ± 45°
+from the sheet normal in a side-scatter arrangement. Ground truth comes from
+DNS-derived particle statistics (JHTDB channel flow, Re_τ ≈ 1000); both cases derive from
+the same snapshots at their respective particle counts, so finite-sample statistics are
+self-consistent.
 
 ## Contents
 
 ```
 MTT69/TurbulentChannel/
-├── README.md                         (this file)
-├── LICENSE                           (CC-BY-4.0)
+├── README.md                          (this file)
+├── LICENSE                            (CC-BY-4.0)
+├── configs/                           ready-to-run PIVtools configs (edit the
+│   │                                   C:/EDIT_ME/... paths at the top, nothing else)
+│   ├── planar_clean.yaml              one config: clean case uses no preprocessing anywhere
+│   ├── planar_noisy_instantaneous.yaml   noisy case ships PER-PIPELINE configs: the
+│   ├── planar_noisy_ensemble.yaml        instantaneous ran with ssmin, the ensemble on RAW images
+│   ├── stereo_clean.yaml
+│   ├── stereo_noisy.yaml
+│   ├── experimental_instantaneous.yaml   experimental likewise: ssmin for instantaneous,
+│   └── experimental_ensemble.yaml        no filters for the ensemble
 ├── ground_truth/
-│   ├── clean/direct_stats.mat        DNS statistics for Case A (85k particles)
-│   └── noisy/direct_stats.mat        DNS statistics for Case B (22k particles)
-├── planar_clean/                     Case A planar images (4000 pairs, 85k particles)
-│   └── B00001_A.tif … B04000_B.tif   2048 × 2048 TIFF, flat at root
-├── planar_noisy/                     Case B planar images (4000 pairs, 22k particles)
-│   ├── B00001_A.tif … B04000_B.tif
-│   └── calibration_boards/           20 synthetic dotboard calibration images
-│                                     (shared between Case A and Case B)
-├── stereo_clean/                     Case A stereo images (4000 pairs × 2 cameras)
-│   ├── camera1/                      cam 1 TIFFs
-│   ├── camera2/                      cam 2 TIFFs
-│   ├── mask_Cam1.mat                 pixel-space masks
-│   └── mask_Cam2.mat
-├── stereo_noisy/                     Case B stereo images (4000 pairs × 2 cameras)
-│   ├── camera1/
-│   ├── camera2/
-│   ├── calibration/
-│   │   ├── cam1/                     20 stereo dotboard images, cam 1
-│   │   └── cam2/                     20 stereo dotboard images, cam 2
-│   │                                 (shared between Case A and Case B)
-│   ├── mask_Cam1.mat
-│   └── mask_Cam2.mat
+│   ├── clean/direct_stats.mat         DNS statistics for Case A (85k particles)
+│   └── noisy/direct_stats.mat         DNS statistics for Case B (22k particles)
+├── hotwire/
+│   └── hwa.mat                        hot-wire profile (uncorrected variance) + u_tau, l+, nu
+├── calibration/
+│   ├── planar/                        ChArUco boards (calib%05d.tif, 20 views)
+│   │   └── calibration/               + fitted model and settings sidecar (dt = 0.0057553 s)
+│   ├── stereo/                        board view-pairs under Cam1/, Cam2/ + ground_truth.npz
+│   │   └── calibration/               + fitted stereo model and sidecar (dt = 0.0057553 s)
+│   └── experimental/                  single board view (calib_Cam_B00001_crop.tif)
+│       └── calibration/               + scale-factor model (16.72 px/mm, wall origin,
+│                                        axis signs) and sidecar (dt = 4.96e-05 s)
+├── reference_results/                 final calibrated outputs of the published runs
+│   ├── planar_clean/                  mean_stats.mat + ensemble_result.mat + coordinates.mat
+│   ├── planar_noisy/                  (same three files)
+│   ├── stereo_clean/                  mean_stats.mat (stereo Cam1_Cam2 statistics)
+│   ├── stereo_noisy/                  mean_stats.mat
+│   └── experimental/                  mean_stats.mat + ensemble_result.mat + coordinates.mat
+├── planar_clean/                      Case A planar images: B00001_A.tif ... B04000_B.tif
+├── planar_noisy/                      Case B planar images (same naming)
+├── stereo_clean/Cam1/, Cam2/          Case A stereo images (4000 pairs per camera)
+├── stereo_noisy/Cam1/, Cam2/          Case B stereo images
+├── experimental/cam4_normalised/      2100 pairs of cropped, gain-normalised TIFFs
 └── scripts/
-    ├── benchmark_comparison.py       Planar + ensemble vs DNS
-    ├── stereo_benchmark_comparison.py Stereo 3-component + 6 stresses vs DNS
-    ├── cross_method_comparison.py    Multi-method overlay figures
-    ├── paper_figures.py              Combined clean + noisy paper figures
-    ├── tcf_direct_stats.py           Recompute ground truth from JHTDB particles
-    └── sig_configs/                  EUROSIG configuration files (.cdl)
+    ├── paper_figures.py               synthetic validation figures (Cases A + B vs DNS)
+    ├── piv_vs_hwa_paper.py            experimental figure (PIV vs hot wire)
+    └── benchmark_comparison.py        shared library (GT loading, wall-unit conversion)
 ```
 
-**Calibration boards are shared.** To avoid duplicate uploads, the calibration images for both Case A and Case B live at `planar_noisy/calibration_boards/` (planar) and `stereo_noisy/calibration/{cam1,cam2}/` (stereo). When processing Case A, point your PIVtools config at those same calibration paths.
+## Tier 1 — regenerate the paper figures (no PIV processing)
 
-## Image specifications
+Only needs standard scientific Python — no PIVtools install:
 
-| Parameter | Value |
-|-----------|-------|
-| Image size | 2048 × 2048 px, 16-bit TIFF |
-| Particle diameter | 3 px |
-| Laser sheet thickness | 16 px (1.2 mm physical) |
-| Number of pairs | 4000 |
-| Case A particle count | 85 000 per image (≈ 5.2 ppw at 16 × 16 windows), no noise |
-| Case B particle count | 22 000 per image (≈ 1.3 ppw at 16 × 16 windows) |
-| Case B noise | Gaussian, mean = 80, std = 16, SNR ≈ 8 |
-| Stereo geometry | Two cameras at ± 45° from the sheet normal (side-scatter arrangement) |
-| dt | Matches JHTDB snapshot spacing (see CDL configs) |
+```bash
+pip install numpy scipy h5py matplotlib
+hf download MTT69/TurbulentChannel --repo-type dataset --local-dir tc
+cd tc
+
+# synthetic figures (mean velocity, stresses, combined stresses)
+python scripts/paper_figures.py -o figs \
+    --gt-clean-dir ground_truth/clean --gt-noisy-dir ground_truth/noisy \
+    --inst-clean-stats reference_results/planar_clean/mean_stats.mat \
+    --ens-clean-dir   reference_results/planar_clean \
+    --stereo-clean-stats reference_results/stereo_clean/mean_stats.mat \
+    --inst-noisy-stats reference_results/planar_noisy/mean_stats.mat \
+    --ens-noisy-dir   reference_results/planar_noisy \
+    --stereo-noisy-stats reference_results/stereo_noisy/mean_stats.mat
+
+# experimental figure (PIV vs hot wire)
+python scripts/piv_vs_hwa_paper.py \
+    --ens-dir reference_results/experimental \
+    --inst-stats reference_results/experimental/mean_stats.mat \
+    --hwa hotwire/hwa.mat \
+    --ens-pass 2 --inst-pass 2 3 \
+    --inst-labels '16$\times$96 px' '8$\times$96 px' \
+    --utau-piv 0.7 --utau-hwa 0.68138107 --y-lo 0.640 \
+    --out figs/piv_vs_hwa_comparison.png
+```
 
-## Ground truth
+These exact commands, run against the shipped `reference_results/`, reproduce the paper
+figures byte-for-byte on the authors' machine (fonts permitting: the scripts prefer
+CMU Serif and fall back to DejaVu). Quote the `--inst-labels` arguments exactly as shown
+(single quotes) so your shell does not eat the `$` characters.
 
-Two ground-truth files are provided, one per case, each in its own subdirectory so the benchmark scripts can point at them directly via `--gt-dir`:
+## Tier 2 — reprocess from images
 
-- `ground_truth/clean/direct_stats.mat` — Case A reference (85 000 particle trajectories)
-- `ground_truth/noisy/direct_stats.mat` — Case B reference (22 000 trajectories)
+Install PIVtools, then run one case per working directory. The CLI reads `config.yaml`
+from the current working directory — no flags, no fallbacks.
 
-Both are computed directly from the JHTDB particle position snapshots used to render the corresponding images. Benchmark Case A PIV against the clean file and Case B against the noisy one — finite-sample statistics are self-consistent within each case. Both share this schema:
+```bash
+pip install pivtools
+mkdir work_planar_clean && cd work_planar_clean
+cp ../tc/configs/planar_clean.yaml config.yaml
+# open config.yaml, replace every C:/EDIT_ME/... path (instructions in the header),
+# then:
+```
 
-| Key | Shape | Description |
-|-----|-------|-------------|
-| `y_plus` | (N,) | wall-normal coordinate, wall units |
-| `U_plus` | (N, 3) | mean velocity [U, V, W] in wall units |
-| `stress_plus` | (N, 3, 3) | Reynolds stress tensor in wall units |
-| `stress_ci_lo`, `stress_ci_hi` | (N, 3, 3) | 95% confidence interval |
-| `umean_ci_lo`, `umean_ci_hi` | (N, 3) | 95% CI for mean velocity |
-| `u_tau` | scalar | friction velocity (mm/s) |
-| `delta_nu` | scalar | viscous length scale (mm) |
-| `Re_tau` | scalar | friction Reynolds number |
+**planar_clean** (one config, both pipelines):
 
-The Case B ground truth is self-consistent with the 22 000-particle rendering — finite-sample statistics from the subsampled particle set, not the full DNS. Benchmark Case B PIV against Case B ground truth.
+```bash
+pivtools-cli instantaneous
+pivtools-cli ensemble
+pivtools-cli apply-calibration --all-paths --type-name instantaneous
+pivtools-cli apply-calibration --all-paths --type-name ensemble
+pivtools-cli statistics
+```
+
+**planar_noisy and experimental** ship TWO configs each, because the published runs
+used different preprocessing per pipeline (instantaneous: ssmin 7×7;
+ensemble: raw images — adding a filter corrupts the ensemble stresses). Use one
+working directory per config, with the SAME `base_paths` in both so outputs merge:
 
-## How this was generated
+```bash
+# directory 1: <case>_instantaneous.yaml as config.yaml
+pivtools-cli instantaneous
+pivtools-cli apply-calibration --all-paths --type-name instantaneous
+pivtools-cli statistics
+
+# directory 2: <case>_ensemble.yaml as config.yaml
+pivtools-cli ensemble
+pivtools-cli apply-calibration --all-paths --type-name ensemble
+```
 
-Synthetic images are rendered from JHTDB turbulent-channel particle trajectories using the **EUROSIG / EUROPIV synthetic image generator**. The configuration files in `scripts/sig_configs/` are the authoritative build instructions:
+**Stereo cases** (instantaneous only — the paper uses no stereo ensemble):
 
-| Configuration | Role |
-|---------------|------|
-| `sigconf_planar_noisy_A.cdl` | Planar frame A, 22k particles, noise pattern A |
-| `sigconf_planar_noisy_B.cdl` | Planar frame B, 22k particles, noise pattern B |
-| `SIGconf_Stereo_cam1_noisy_A.cdl`, `..._B.cdl` | Stereo cam 1, frames A and B |
-| `SIGconf_Stereo_cam2_noisy_A.cdl`, `..._B.cdl` | Stereo cam 2, frames A and B |
-| `sigconf_planar.cdl`, `SIGconf_Stereo_cam{1,2}.cdl` | Case A planar + stereo (85k particles, no noise) |
+```bash
+pivtools-cli instantaneous
+pivtools-cli apply-stereo --all-paths
+pivtools-cli statistics --source-endpoint stereo
+```
 
-To regenerate images bit-for-bit, install EUROSIG and invoke each `.cdl` with its associated particle-position files from JHTDB. See the SIG documentation for build instructions.
+Outputs land under the `base_paths` folder you set:
+calibrated vectors in `calibrated_piv/<n>/...`, statistics in
+`statistics/<n>/.../mean_stats/mean_stats.mat` (stereo: `statistics/<n>/stereo/Cam1_Cam2/...`).
+Point the Tier-1 figure commands at your own outputs instead of `reference_results/`
+(the `--ens-*-dir` arguments want the folder holding `ensemble_result.mat` +
+`coordinates.mat`; the `--*-stats` arguments want a `mean_stats.mat`).
 
-## Scripts
+**GUI instead of CLI:** load the same `config.yaml` in the PIVtools GUI and run the same
+stages from their tabs (Process → Calibration → Statistics) — identical engine, identical
+outputs. The calibration tab picks up the shipped model through the same
+`calibration_sources` path in the config.
 
-### `benchmark_comparison.py` — single-method benchmark
+## Performance benchmark (optional)
 
-Compares planar or ensemble PIV against the DNS ground truth; produces U+, Reynolds stress, residual, trace invariant, and noise-decomposition plots.
+The paper's strong-scaling benchmark is packaged with PIVtools as the
+`pivtools-bench` console command — no scheduler scripts required. From the same
+path-edited `planar_clean` working directory as Tier 2:
 
 ```bash
-python scripts/benchmark_comparison.py \
-    --mode ensemble \
-    --gt-dir ./ground_truth/noisy \
-    --ensemble-dir <path/to/your/ensemble_result_directory> \
-    --num-frames 4000 \
-    --output-dir ./out
+pivtools-bench scaling --config config.yaml \
+    --dataset <your download of TurbulentChannel/planar_clean> \
+    --n-images 3840 --sweep workers            # add --dry-run to preview the matrix
 ```
 
-| Flag | Description |
-|------|-------------|
-| `--mode` / `-m` | `instantaneous` or `ensemble` |
-| `--runs` / `-r` | Comma-separated 0-based pass indices (e.g. `2,3`) |
-| `--windows` / `-w` | Labels for those passes (e.g. `32,16`) |
-| `--gt-dir` / `-g` | Directory containing `direct_stats.mat` — e.g. `./ground_truth/noisy` or `./ground_truth/clean` (required) |
-| `--base-dir` / `-b` | PIV results base (instantaneous mode) |
-| `--ensemble-dir` / `-e` | Direct path to ensemble result directory |
-| `--num-frames` / `-n` | Frame count subdirectory (default 1000; use 4000 for this dataset) |
-| `--output-dir` / `-o` | Output directory |
-| `--y-plus-offset` / `-y` | Additional y+ offset on top of hardcoded +1 |
-| `--show-fit-lines` | Overlay log-law and viscous sublayer curves |
+This runs the full production pipeline (Dask cluster, load, correlate, save) at a
+geometric sweep of worker counts sized to your machine's cores, two OpenMP threads
+per worker, at fixed total workload — a strong-scaling measurement. Add
+`--iterations 3` for error bars. Three outputs land in `bench_results/` under the
+working directory:
 
-### `stereo_benchmark_comparison.py` — stereo 3C + 6-stress benchmark
+| Output | Contents |
+|---|---|
+| `scaling_<ts>.csv` | one row per run: timings, throughput, full provenance (git SHA, FFT backend, host, CPU) |
+| `scaling_<ts>_summary.csv` | per-config median/IQR statistics plus speedup and parallel efficiency |
+| `scaling_<ts>_paper.png` | throughput vs the ideal linear bound + parallel efficiency — the same two-panel layout as the paper's scaling figure |
 
-Uses LaTeX for labels (`text.usetex=True`); requires MiKTeX / TeXLive.
+(Two additional diagnostic figures are also written; the `matrix`/`oversub` sweep
+modes explore worker×thread trade-offs beyond the paper's sweep — see
+`pivtools-bench scaling --help`.)
 
-```bash
-python scripts/stereo_benchmark_comparison.py \
-    --gt-dir ./ground_truth/noisy \
-    --stereo-base <path/to/your/stereo_results> \
-    --num-frames 4000 \
-    --output-dir ./out
-```
+Throughput numbers are hardware-dependent: the paper's peak of 117 pairs/s was
+measured on a 192-core dual-EPYC node, and your core count sets your ceiling. The
+scaling *shape* — near-linear until the memory bandwidth of the machine saturates —
+is the reproducible claim. On a cluster, wrap this same command in your scheduler
+of choice; nothing about it is scheduler-specific.
 
-### `cross_method_comparison.py` — multi-method overlay
+## Tier 3 — re-derive the calibration models
 
-Publication-quality plots comparing one pass from each of instantaneous, ensemble, and stereo against DNS on the same axes. Okabe-Ito colourblind palette.
+The shipped models under `calibration/*/calibration/` reproduce the paper as-is. To rebuild
+them from the board images instead:
 
 ```bash
-python scripts/cross_method_comparison.py \
-    --gt-dir ./ground_truth/noisy \
-    --output-dir ./out \
-    --inst-stats <path/to/instantaneous/mean_stats.mat> \
-    --ens-dir <path/to/ensemble_dir> \
-    --stereo-stats <path/to/stereo/mean_stats.mat>
+# planar (single camera; ChArUco 10 x 7 squares, 12 mm, DICT_4X4_1000)
+pivtools-cli detect-charuco --source ./tc/calibration/planar \
+    --camera 1 --image-format "calib%05d.tif" --n-views 20 --square-size 0.012
+
+# stereo pair (boards under Cam1/, Cam2/)
+pivtools-cli detect-stereo --source ./tc/calibration/stereo --camera-pair 1,2 \
+    --image-format "calib%05d.tif" --n-views 20 --square-size 0.012
 ```
 
-### `paper_figures.py` — combined Case A + Case B figures
+The synthetic boards are rendered through the same camera models that rendered the
+particle images, so the recovered calibration corresponds exactly to the imaging system
+(`calibration/stereo/ground_truth.npz` holds the true cameras; expected recovery:
+stereo angle ≈ 89.9° vs the true 90.0°, RMS < 0.1 px). Detection writes proof figures
+beside the model.
+
+The experimental case uses a uniform scale-factor model rather than a fitted camera. The
+shipped model (`calibration/experimental/calibration/Cam1/scale_factor_planar/model/`)
+carries everything: 16.72 px/mm, the wall origin (origin_px [254.41, 1626.65] →
+origin_mm [0, 11.17]) and the axis directions (col_sign −1, row_sign −1). Rebuilding it
+requires clicking the origin on the board image — use the GUI Scale Factor tab, or
+`pivtools-cli scale-factor --help` with the constants above.
+
+## Key constants
+
+| Quantity | Synthetic | Experimental |
+|---|---|---|
+| dt | 0.0057553 s | 4.96e-05 s |
+| Scale factor | 13.6533 px/mm | 16.72 px/mm |
+| u_τ | 8.4206 mm/s (DNS) | 0.700 m/s (PIV, freestream-matched); 0.68138 m/s (hot wire, OFI) |
+| ν | — | 1.4943e-05 m²/s |
+| Re_τ | 998 | — |
+| δ_ν | 0.15030 mm | — |
+| Hot-wire l+ | — | 45.6 |
+
+## Image specifications (synthetic)
 
-Reproduces the figures in the PIVtools paper: Case A (open symbols) and Case B (filled symbols) overlaid. Any combination of paths may be supplied — the script plots whichever it receives.
+| Parameter | Value |
+|-----------|-------|
+| Image size | planar 2048 × 2048 px; stereo 1440 × 2080 px — 8-bit TIFF |
+| Scale factor (planar) | 13.6533 px/mm (2048 px over the 150 mm half-height) |
+| Particle diameter | ≈ 3 px |
+| Laser sheet thickness | 1.2 mm (≈ 16 px at the planar scale) |
+| Number of pairs | 4000 per case and geometry |
+| Case A particle count | 85 000 per image (≈ 5.2 ppw at 16 × 16 windows), no noise |
+| Case B particle count | 22 000 per image (≈ 1.3 ppw) |
+| Case B noise | Gaussian, mean = 80, std = 16, SNR ≈ 8 — independent per frame |
+| Stereo geometry | ± 45° side-scatter, Scheimpflug ± 2.39°, full-frame domain (no masks) |
 
-```bash
-# Case B only (what this dataset ships today)
-python scripts/paper_figures.py \
-    --gt-noisy-dir ./ground_truth \
-    --inst-noisy-stats <path/to/noisy/instantaneous/mean_stats.mat> \
-    --ens-noisy-dir <path/to/noisy/ensemble_dir> \
-    --stereo-noisy-stats <path/to/noisy/stereo/mean_stats.mat> \
-    --output-dir ./out
-```
+## Ground truth
 
-### `tcf_direct_stats.py` — recompute ground truth
+One file per case, each in its own subdirectory so the figure script can point at them
+via `--gt-clean-dir` / `--gt-noisy-dir`:
 
-If you regenerate the synthetic images via EUROSIG, this script recomputes `direct_stats.mat` from the underlying JHTDB particle position files (`B*_A.data`, `B*_B.data`).
+- `ground_truth/clean/direct_stats.mat` — Case A reference (85 000 particle trajectories)
+- `ground_truth/noisy/direct_stats.mat` — Case B reference (22 000 trajectories)
 
-```bash
-python scripts/tcf_direct_stats.py \
-    --data-dir <path/to/particle_positions> \
-    --output-dir ./ground_truth
-```
+Both are computed directly from the JHTDB particle position snapshots used to render the
+corresponding images (the truth derives from the particle files, not the rendered images).
+The stereo cases share the same files. Schema:
+
+| Key | Shape | Description |
+|-----|-------|-------------|
+| `y_plus` | (N,) | wall-normal coordinate, wall units |
+| `U_plus` | (N, 3) | mean velocity [U, V, W] in wall units |
+| `stress_plus` | (N, 3, 3) | Reynolds stress tensor in wall units |
+| `stress_ci_lo`, `stress_ci_hi` | (N, 3, 3) | 95% confidence interval |
+| `umean_ci_lo`, `umean_ci_hi` | (N, 3) | 95% CI for mean velocity |
+| `u_tau` | scalar | friction velocity (mm/s) |
+| `delta_nu` | scalar | viscous length scale (mm) |
+| `Re_tau` | scalar | friction Reynolds number |
+
+## Hot-wire data
+
+`hotwire/hwa.mat` is an HDF5 file with a `caseData` group holding exactly what the
+experimental figure needs:
+
+| Field | Description |
+|---|---|
+| `y_corrected_poly` | wall-normal positions (m), wall-origin corrected |
+| `meanvel_poly_corrected` | mean velocity (m/s) |
+| `variance_poly_corrected` | streamwise variance (m²/s²) — wall-origin corrected, **not** spatial-resolution corrected |
+| `utau_ofi` | friction velocity from oil-film interferometry (0.68138 m/s) |
+| `lplus` | wire length in wall units (45.6) |
+| `nu_air` | kinematic viscosity (m²/s) |
+
+The figure plots the uncorrected variance deliberately: at l+ ≈ 46 the wire attenuates
+the near-wall peak, and the comparison discusses that rather than hiding it behind a
+correction.
 
-## Unit conventions
+## Image orientation
 
-| Quantity | PIVtools storage | Benchmark display |
-|----------|-----------------|-------------------|
-| Velocity | m/s | mm/s (× 1000) |
-| Reynolds stress | (m/s)² | (mm/s)² (× 1e6) |
-| Spatial coordinates | mm | wall units y⁺ = y / δ_ν |
+There are no masks: the stereo renders fill the full frame and the planar images are
+full-field. Both synthetic geometries read physically — the channel wall is at the bottom
+row, fast flow at the top. The stereo renders have a single deterministic vertical flip
+composed into both the images and the calibration boards, so calibration and images are
+consistent. Do not flip anything downstream.
 
-## Masks
+## Provenance
 
-`stereo_noisy/mask_Cam{1,2}.mat` hold pixel-space boolean masks (same shape as images) that exclude regions outside the valid field of view. PIVtools loads them automatically when configured with `masking.enabled: true` and `mask_file_pattern: mask_Cam{cam}.mat`.
+The synthetic images were rendered from JHTDB turbulent-channel particle trajectories with
+the EUROPIV Synthetic Image Generator; noise was added post-render with independent
+per-frame seeds. The full generation chain (JHTDB download, particle conversion,
+85k → 22k downsampling, SIG configs, render recipes, noise and ground-truth scripts) was
+removed from the current tree to keep the capsule focused, but remains available in this
+repository's git history.
 
 ## Citation
 
@@ -264,4 +362,6 @@ DNS reference data is from the **Johns Hopkins Turbulence Database** (JHTDB).
 
 CC-BY-4.0 — free to use, modify, and redistribute with attribution to the PIVtools paper.
 
-The DNS ground truth is derived from publicly accessible JHTDB data and is redistributed here under the same permissive terms; consult the JHTDB usage policy (http://turbulence.pha.jhu.edu) for their citation requirements.
+The DNS ground truth is derived from publicly accessible JHTDB data and is redistributed
+here under the same permissive terms; consult the JHTDB usage policy
+(http://turbulence.pha.jhu.edu) for their citation requirements.

calibration/experimental/calibration/Cam1/scale_factor_planar/model/model_scale_factor.mat

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a69e79d958598d967e1b9e8248323fa44359191bf271d065aa45e15e0346f988
+size 2344

calibration/experimental/calibration/settings.yaml

@@ -0,0 +1,58 @@
+schema_version: 1
+image:
+  image_format: calib_Cam_B00001_crop.tif
+  image_type: standard
+  n_views: null
+  start_index: 1
+  zero_based_indexing: false
+  use_camera_subfolders: false
+  camera_subfolders: []
+rig:
+  camera: 1
+  camera_pair:
+  - 1
+  - 2
+  dt: 4.96e-05
+  datum_frame: 1
+  interpolator: lanczos
+  piv_type: instantaneous
+fit:
+  distortion_model: standard
+  fix_aspect_ratio: true
+  self_cal_n_images: 20
+  world_frame: default
+  world_frame_cam2: null
+  world_frame_grid: null
+  world_frame_grid_cam2: null
+global_coordinates:
+  enabled: false
+  datum_camera: 1
+  datum_pixel: null
+  datum_physical:
+  - 0.0
+  - 0.0
+  datum_frame: 1
+  overlap_pairs: []
+methods:
+  dotboard:
+    dot_spacing_mm: null
+    k_neighbors: 9
+    model_type: pinhole
+  charuco:
+    squares_h: null
+    squares_v: null
+    square_size: null
+    marker_ratio: 0.5
+    aruco_dict: DICT_4X4_1000
+    min_corners: 6
+    model_type: pinhole
+  stepped:
+    dot_spacing_mm: null
+    step_height_mm: null
+    board_thickness_mm: null
+    level_offset_mm: null
+  stepped_stereo:
+    stereo_config: auto
+    model_type: pinhole
+  scale_factor:
+    px_per_mm: 16.72

calibration/planar/calibration/Cam1/charuco_planar/model/inputs.mat

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:fe382296114160595739e985d3cda31b79422e181b55655cf3022a6c5def2926
+size 92368

calibration/planar/calibration/Cam1/charuco_planar/model/model_pinhole.mat

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:851cf5c7626735af602b4e333bf74c75d5bbb94619b7f6d5d79c10fb9f55ded5
+size 5672

calibration/planar/calibration/settings.yaml

@@ -0,0 +1,58 @@
+schema_version: 1
+image:
+  image_format: calib%05d.tif
+  image_type: standard
+  n_views: 20
+  start_index: 1
+  zero_based_indexing: false
+  use_camera_subfolders: false
+  camera_subfolders: []
+rig:
+  camera: 1
+  camera_pair:
+  - 1
+  - 2
+  dt: 0.0057553
+  datum_frame: 1
+  interpolator: lanczos
+  piv_type: ensemble
+fit:
+  distortion_model: standard
+  fix_aspect_ratio: true
+  self_cal_n_images: 20
+  world_frame: default
+  world_frame_cam2: null
+  world_frame_grid: null
+  world_frame_grid_cam2: null
+global_coordinates:
+  enabled: false
+  datum_camera: 1
+  datum_pixel: null
+  datum_physical:
+  - 0.0
+  - 0.0
+  datum_frame: 1
+  overlap_pairs: []
+methods:
+  dotboard:
+    dot_spacing_mm: null
+    k_neighbors: 9
+    model_type: pinhole
+  charuco:
+    squares_h: 10
+    squares_v: 7
+    square_size: 0.012
+    marker_ratio: 0.5
+    aruco_dict: DICT_4X4_1000
+    min_corners: 6
+    model_type: pinhole
+  stepped:
+    dot_spacing_mm: null
+    step_height_mm: null
+    board_thickness_mm: null
+    level_offset_mm: null
+  stepped_stereo:
+    stereo_config: auto
+    model_type: pinhole
+  scale_factor:
+    px_per_mm: null

calibration/stereo/calibration/settings.yaml

@@ -0,0 +1,58 @@
+schema_version: 1
+image:
+  image_format: calib%05d.tif
+  image_type: standard
+  n_views: 20
+  start_index: 1
+  zero_based_indexing: false
+  use_camera_subfolders: true
+  camera_subfolders: []
+rig:
+  camera: 1
+  camera_pair:
+  - 1
+  - 2
+  dt: 0.0057553
+  datum_frame: 1
+  interpolator: lanczos
+  piv_type: instantaneous
+fit:
+  distortion_model: standard
+  fix_aspect_ratio: true
+  self_cal_n_images: 20
+  world_frame: default
+  world_frame_cam2: null
+  world_frame_grid: null
+  world_frame_grid_cam2: null
+global_coordinates:
+  enabled: false
+  datum_camera: 1
+  datum_pixel: null
+  datum_physical:
+  - 0.0
+  - 0.0
+  datum_frame: 1
+  overlap_pairs: []
+methods:
+  dotboard:
+    dot_spacing_mm: null
+    k_neighbors: 9
+    model_type: pinhole
+  charuco:
+    squares_h: 10
+    squares_v: 7
+    square_size: 0.012
+    marker_ratio: 0.5
+    aruco_dict: DICT_4X4_1000
+    min_corners: 6
+    model_type: pinhole
+  stepped:
+    dot_spacing_mm: null
+    step_height_mm: null
+    board_thickness_mm: null
+    level_offset_mm: null
+  stepped_stereo:
+    stereo_config: auto
+    model_type: pinhole
+  scale_factor:
+    px_per_mm: null

calibration/stereo/calibration/stereo_cam1_cam2/model/inputs.mat

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+version https://git-lfs.github.com/spec/v1
+oid sha256:8dd4c0a738222c7d0af4ed2118679f044f3cb0dd7c6c08368a1773d7e6976c82
+size 178608

calibration/stereo/calibration/stereo_cam1_cam2/model/stereo_model_pinhole.mat

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:18f03b2a5cbac067b3456f4ec3248dc2dd5bba8d32e2d711c9f7994647baf8f1
+size 9864

calibration/stereo/ground_truth.npz

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+version https://git-lfs.github.com/spec/v1
+oid sha256:2576c01319059af28e0361285cb18aef45050e5d7bf5d81db4e5bf311a54b73c
+size 7154

configs/experimental_ensemble.yaml

@@ -0,0 +1,234 @@
+# =============================================================================
+# PIVtools config -- EXPERIMENTAL Cam4, ENSEMBLE pipeline only
+# Reproduces: ensemble 8x96 x2 vs 32x32 sum windows (paper plots pass 2)
+# The experimental case needs DIFFERENT preprocessing per pipeline, so it ships
+# as TWO configs. Run from this one:
+#   pivtools-cli ensemble
+#   pivtools-cli apply-calibration --all-paths --type-name ensemble
+# (run the instantaneous from experimental_instantaneous.yaml in its own directory)
+# -----------------------------------------------------------------------------
+# EDIT BEFORE RUNNING (search for EDIT_ME):
+#   paths.source_paths            -> your download of
+#                                    TurbulentChannel/experimental/cam4_normalised
+#   paths.base_paths              -> any writable output folder (SAME folder in
+#                                    both experimental configs -- outputs merge)
+#   calibration.calibration_sources + calibration.source
+#                                 -> your download of TurbulentChannel/calibration/experimental
+# DO NOT CHANGE:
+#   filters: []                   the ensemble runs on RAW images. Verified
+#                                 2026-07-30: adding ssmin or time preprocessing
+#                                 corrupts the ensemble stresses.
+#   ensemble_piv.envelope_divide: true and kspace_shape: gaussian (published run)
+#   The scale-factor calibration sidecar carries dt = 4.96e-05 s.
+# =============================================================================
+paths:
+  base_paths:
+  - C:/EDIT_ME/Results/experimental
+  source_paths:
+  - C:/EDIT_ME/TurbulentChannel/experimental/cam4_normalised
+  active_paths:
+  - 0
+  camera_numbers:
+  - 1
+  camera_count: 1
+  camera_subfolders: []
+images:
+  image_format:
+  - B%05d_A.tif
+  - B%05d_B.tif
+  vector_format:
+  - '%05d.mat'
+  dtype: float32
+  image_type: standard
+  use_camera_subfolders: false
+  start_index: 1
+  frame_stride: 0
+  pair_stride: 1
+  pairing_preset: ab_format
+  num_loops: 1
+  num_images: 2100
+  image_shape:
+  - 1836
+  - 512
+batches:
+  size: 5
+logging:
+  file: pypiv.log
+  level: INFO
+  console: true
+processing:
+  backend: cpu
+  debug: false
+  auto_compute_params: false
+  omp_threads: 4
+  dask_workers_per_node: 5
+  dask_memory_limit: 10GB
+  dask_max_in_flight_per_worker: 2
+  open_dashboard: false
+  dask_nanny: false
+  post_processing_workers: 16
+  always_batch: true
+  instantaneous: false
+  ensemble: true
+outlier_detection:
+  enabled: true
+  methods:
+  - threshold: 0.25
+    type: peak_mag
+  - type: median_2d
+    epsilon: 0.1
+    threshold: 2
+infilling:
+  mid_pass:
+    method: nearest
+    parameters: {}
+  final_pass:
+    enabled: true
+    method: biharmonic
+    parameters: {}
+ensemble_outlier_detection:
+  enabled: true
+  methods:
+  - type: median_2d
+    epsilon: 0.1
+    threshold: 2
+    size: 5
+ensemble_infilling:
+  mid_pass:
+    method: biharmonic
+    parameters: {}
+  final_pass:
+    enabled: true
+    method: biharmonic
+    parameters: {}
+plots:
+  save_extension: .png
+  save_pickle: true
+  fontsize: 14
+  title_fontsize: 16
+video:
+  base_path_idx: 0
+  camera: 1
+  data_source: stereo
+  variable: mag
+  run: 3
+  piv_type: ensemble
+  cmap: default
+  lower: ''
+  upper: ''
+  fps: 30
+  crf: 15
+  resolution: 4k
+  source_endpoint: regular
+statistics:
+  enabled_methods:
+    inst_gamma: false
+    inst_stresses: false
+    mean_stresses: true
+    mean_velocity: true
+    inst_divergence: false
+    fluctuating_velocity: false
+    mean_divergence: false
+    correlation_quality: true
+    vorticity: false
+    divergence: false
+    gamma1: false
+    gamma2: false
+    inst_vorticity: false
+    mean_vorticity: false
+    mean_tke: false
+    tke: false
+    inst_velocity: false
+  gamma_radius: 4
+  save_figures: true
+  type_name: ensemble
+  source_endpoint: regular
+instantaneous_piv:
+  window_size:
+  - - 8
+    - 96
+  - - 8
+    - 96
+  overlap:
+  - 50
+  - 50
+  runs:
+  - 2
+  time_resolved: false
+  window_type: gaussian
+  num_peaks: 1
+  peak_finder: gauss6
+  secondary_peak: false
+  predictor_smoothing: false
+  save_mode: full
+  save_compression: false
+  image_warp_interpolation: lanczos
+  dump_correlation_planes: false
+ensemble_piv:
+  fit_method: kspace
+  kspace_shape: gaussian
+  kspace_floor: coloured
+  skip_background_subtraction: false
+  gradient_correction: true
+  persist_images: false
+  predictor_smoothing: false
+  image_warp_interpolation: lanczos
+  mask_center_pixel: true
+  background_subtraction_method: correlation+dc_zero
+  window_size:
+  - - 8
+    - 96
+  - - 8
+    - 96
+  overlap:
+  - 50
+  - 50
+  type:
+  - std
+  - std
+  runs:
+  - 1
+  - 2
+  store_planes: true
+  save_diagnostics: true
+  sum_window:
+  - 32
+  - 32
+  sum_fitting_window_enabled: true
+  sum_fitting_window:
+  - 16
+  - 16
+  resume_from_pass: 0
+  window_type: square
+  predictor_boundary_conditions: []
+  per_pair_normalization: false
+  predictor_rounding: false
+  envelope_divide: true
+calibration:
+  calibration_sources:
+  - C:/EDIT_ME/TurbulentChannel/calibration/experimental
+  source: C:/EDIT_ME/TurbulentChannel/calibration/experimental
+  source_idx: 0
+  active: scale_factor
+filters: []
+masking:
+  enabled: false
+  mask_file_pattern: mask_Cam%d.mat
+  mask_threshold: 0.01
+  mode: rectangular
+  rectangular:
+    top: 0
+    bottom: 0
+    left: 0
+    right: 0
+merging:
+  type_name: ensemble
+  base_path_idx: 0
+  cameras: null
+transforms:
+  base_path_idx: 0
+  type_name: ensemble
+  cameras:
+    1:
+      operations: []
+  source_endpoint: regular

configs/experimental_instantaneous.yaml

@@ -0,0 +1,186 @@
+# =============================================================================
+# PIVtools config -- EXPERIMENTAL Cam4, INSTANTANEOUS pipeline only
+# Reproduces: instantaneous 32x96 -> 16x96 -> 8x96 (paper plots passes 2 AND 3)
+# The experimental case needs DIFFERENT preprocessing per pipeline, so it ships
+# as TWO configs. Run from this one:
+#   pivtools-cli instantaneous
+#   pivtools-cli apply-calibration --all-paths --type-name instantaneous
+#   pivtools-cli statistics
+# (run the ensemble from experimental_ensemble.yaml in its own directory)
+# -----------------------------------------------------------------------------
+# EDIT BEFORE RUNNING (search for EDIT_ME):
+#   paths.source_paths            -> your download of
+#                                    TurbulentChannel/experimental/cam4_normalised
+#   paths.base_paths              -> any writable output folder (SAME folder in
+#                                    both experimental configs -- outputs merge)
+#   calibration.calibration_sources + calibration.source
+#                                 -> your download of TurbulentChannel/calibration/experimental
+# DO NOT CHANGE:
+#   filters: ssmin 7x7            sliding-minimum background subtraction -- the
+#                                 published instantaneous preprocessing.
+#   The scale-factor calibration sidecar carries dt = 4.96e-05 s.
+# =============================================================================
+paths:
+  base_paths:
+  - C:/EDIT_ME/Results/experimental
+  source_paths:
+  - C:/EDIT_ME/TurbulentChannel/experimental/cam4_normalised
+  active_paths:
+  - 0
+  camera_numbers:
+  - 1
+  camera_count: 1
+  camera_subfolders: []
+images:
+  image_format:
+  - B%05d_A.tif
+  - B%05d_B.tif
+  vector_format:
+  - '%05d.mat'
+  dtype: float32
+  image_type: standard
+  use_camera_subfolders: false
+  start_index: 1
+  frame_stride: 0
+  pair_stride: 1
+  pairing_preset: ab_format
+  num_loops: 1
+  num_images: 2100
+  image_shape:
+  - 1836
+  - 512
+batches:
+  size: 20
+logging:
+  file: pypiv.log
+  level: INFO
+  console: true
+processing:
+  backend: cpu
+  debug: false
+  auto_compute_params: false
+  omp_threads: 4
+  dask_workers_per_node: 5
+  dask_memory_limit: 10GB
+  dask_max_in_flight_per_worker: 2
+  open_dashboard: false
+  dask_nanny: false
+  post_processing_workers: 16
+  always_batch: true
+  instantaneous: true
+  ensemble: false
+outlier_detection:
+  enabled: true
+  methods:
+  - threshold: 0.25
+    type: peak_mag
+  - type: median_2d
+    epsilon: 0.1
+    threshold: 2
+infilling:
+  mid_pass:
+    method: nearest
+    parameters: {}
+  final_pass:
+    enabled: true
+    method: biharmonic
+    parameters: {}
+plots:
+  save_extension: .png
+  save_pickle: true
+  fontsize: 14
+  title_fontsize: 16
+video:
+  base_path_idx: 0
+  camera: 1
+  data_source: stereo
+  variable: mag
+  run: 3
+  piv_type: instantaneous
+  cmap: default
+  lower: ''
+  upper: ''
+  fps: 30
+  crf: 15
+  resolution: 4k
+  source_endpoint: regular
+statistics:
+  enabled_methods:
+    inst_vorticity: false
+    gamma2: false
+    inst_divergence: false
+    mean_velocity: true
+    vorticity: false
+    mean_vorticity: false
+    tke: false
+    inst_gamma: false
+    mean_tke: false
+    correlation_quality: true
+    inst_stresses: false
+    divergence: false
+    inst_velocity: false
+    gamma1: false
+    mean_stresses: true
+    mean_divergence: false
+    fluctuating_velocity: false
+  gamma_radius: 4
+  save_figures: true
+  type_name: instantaneous
+  source_endpoint: regular
+instantaneous_piv:
+  window_size:
+  - - 32
+    - 96
+  - - 16
+    - 96
+  - - 8
+    - 96
+  overlap:
+  - 50
+  - 50
+  - 50
+  runs:
+  - 2
+  - 3
+  time_resolved: false
+  window_type: gaussian
+  num_peaks: 1
+  peak_finder: gauss6
+  secondary_peak: false
+  predictor_smoothing: false
+  save_mode: full
+  save_compression: false
+  image_warp_interpolation: lanczos
+  dump_correlation_planes: false
+calibration:
+  calibration_sources:
+  - C:/EDIT_ME/TurbulentChannel/calibration/experimental
+  source: C:/EDIT_ME/TurbulentChannel/calibration/experimental
+  source_idx: 0
+  active: scale_factor
+filters:
+- type: ssmin
+  size:
+  - 7
+  - 7
+masking:
+  enabled: false
+  mask_file_pattern: mask_Cam%d.mat
+  mask_threshold: 0.01
+  mode: rectangular
+  rectangular:
+    top: 0
+    bottom: 0
+    left: 0
+    right: 0
+merging:
+  type_name: instantaneous
+  base_path_idx: 0
+  cameras: null
+transforms:
+  base_path_idx: 0
+  type_name: instantaneous
+  cameras:
+    1:
+      operations: []
+  source_endpoint: regular

configs/planar_clean.yaml

@@ -0,0 +1,236 @@
+# =============================================================================
+# PIVtools config -- SYNTHETIC PLANAR, CLEAN (paper Case A, planar arm)
+# Reproduces: instantaneous 64x64 -> 32x32 -> 16x16 (stats on the 16x16 pass)
+#             ensemble      64x64 -> 32x32 -> 8x8 single-mode vs 32x32 sum windows
+# -----------------------------------------------------------------------------
+# EDIT BEFORE RUNNING (search for EDIT_ME):
+#   paths.source_paths            -> your download of TurbulentChannel/planar_clean
+#   paths.base_paths              -> any writable output folder
+#   calibration.calibration_sources + calibration.source
+#                                 -> your download of TurbulentChannel/calibration/planar
+# DO NOT CHANGE (these are the published-run settings):
+#   ensemble_piv.envelope_divide: false   (true corrupts uu+ by 10-20% at 8x8)
+#   ensemble_piv.kspace_shape: kx4, kspace_floor: coloured
+#   The calibration sidecar carries dt = 0.0057553 s -- no dt entry here.
+# Run order (see README): instantaneous PIV -> ensemble PIV -> apply calibration
+#                         -> statistics (instantaneous) -> figure scripts.
+# =============================================================================
+paths:
+  base_paths:
+  - C:/EDIT_ME/Results/planar_clean
+  source_paths:
+  - C:/EDIT_ME/TurbulentChannel/planar_clean
+  active_paths:
+  - 0
+  camera_numbers:
+  - 1
+  camera_count: 1
+  camera_subfolders: []
+images:
+  image_format:
+  - B%05d_A.tif
+  - B%05d_B.tif
+  vector_format:
+  - '%05d.mat'
+  dtype: float32
+  image_type: standard
+  use_camera_subfolders: false
+  start_index: 1
+  frame_stride: 0
+  pair_stride: 1
+  pairing_preset: ab_format
+  num_loops: 1
+  num_images: 4000
+  image_shape:
+  - 2048
+  - 2048
+batches:
+  size: 5
+logging:
+  file: pypiv.log
+  level: INFO
+  console: true
+processing:
+  backend: cpu
+  debug: false
+  auto_compute_params: false
+  omp_threads: 4
+  dask_workers_per_node: 5
+  dask_memory_limit: 10GB
+  dask_max_in_flight_per_worker: 2
+  open_dashboard: false
+  dask_nanny: false
+  post_processing_workers: 16
+  always_batch: true
+  instantaneous: true
+  ensemble: true
+outlier_detection:
+  enabled: true
+  methods:
+  - threshold: 0.25
+    type: peak_mag
+  - type: median_2d
+    epsilon: 0.1
+    threshold: 2
+infilling:
+  mid_pass:
+    method: nearest
+    parameters: {}
+  final_pass:
+    enabled: true
+    method: biharmonic
+    parameters: {}
+ensemble_outlier_detection:
+  enabled: true
+  methods:
+  - type: median_2d
+    epsilon: 0.1
+    threshold: 2
+    size: 5
+ensemble_infilling:
+  mid_pass:
+    method: biharmonic
+    parameters: {}
+  final_pass:
+    enabled: true
+    method: biharmonic
+    parameters: {}
+plots:
+  save_extension: .png
+  save_pickle: true
+  fontsize: 14
+  title_fontsize: 16
+video:
+  base_path_idx: 0
+  camera: 1
+  data_source: stereo
+  variable: mag
+  run: 3
+  piv_type: instantaneous
+  cmap: default
+  lower: ''
+  upper: ''
+  fps: 30
+  crf: 15
+  resolution: 4k
+  source_endpoint: regular
+statistics:
+  enabled_methods:
+    inst_vorticity: false
+    gamma2: false
+    inst_divergence: false
+    mean_velocity: true
+    vorticity: false
+    mean_vorticity: false
+    tke: false
+    inst_gamma: false
+    mean_tke: false
+    correlation_quality: true
+    inst_stresses: false
+    divergence: false
+    inst_velocity: false
+    gamma1: false
+    mean_stresses: true
+    mean_divergence: false
+    fluctuating_velocity: false
+  gamma_radius: 4
+  save_figures: true
+  type_name: instantaneous
+  source_endpoint: regular
+instantaneous_piv:
+  window_size:
+  - - 64
+    - 64
+  - - 32
+    - 32
+  - - 16
+    - 16
+  overlap:
+  - 50
+  - 50
+  - 50
+  runs:
+  - 3
+  time_resolved: false
+  window_type: gaussian
+  num_peaks: 1
+  peak_finder: gauss6
+  secondary_peak: false
+  predictor_smoothing: false
+  save_mode: full
+  save_compression: false
+  image_warp_interpolation: lanczos
+  dump_correlation_planes: false
+ensemble_piv:
+  fit_method: kspace
+  kspace_shape: kx4  # LOCKED: synthetic fitter shape
+  kspace_floor: coloured
+  skip_background_subtraction: false
+  gradient_correction: true
+  persist_images: false
+  predictor_smoothing: false
+  image_warp_interpolation: lanczos
+  mask_center_pixel: true
+  background_subtraction_method: correlation+dc_zero
+  window_size:
+  - - 64
+    - 64
+  - - 32
+    - 32
+  - - 8
+    - 8
+  overlap:
+  - 50
+  - 50
+  - 50
+  type:
+  - std
+  - std
+  - single
+  runs:
+  - 1
+  - 2
+  - 3
+  store_planes: true
+  save_diagnostics: true
+  sum_window:
+  - 32
+  - 32
+  sum_fitting_window_enabled: true
+  sum_fitting_window:
+  - 16
+  - 16
+  resume_from_pass: 0
+  window_type: square
+  predictor_boundary_conditions: []
+  per_pair_normalization: false
+  predictor_rounding: false
+  envelope_divide: false  # LOCKED: true corrupts uu+ at 8x8
+calibration:
+  calibration_sources:
+  - C:/EDIT_ME/TurbulentChannel/calibration/planar
+  source: C:/EDIT_ME/TurbulentChannel/calibration/planar
+  source_idx: 0
+  active: charuco
+filters: []
+masking:
+  enabled: false
+  mask_file_pattern: mask_Cam%d.mat
+  mask_threshold: 0.01
+  mode: rectangular
+  rectangular:
+    top: 0
+    bottom: 0
+    left: 0
+    right: 0
+merging:
+  type_name: instantaneous
+  base_path_idx: 0
+  cameras: null
+transforms:
+  base_path_idx: 0
+  type_name: instantaneous
+  cameras:
+    1:
+      operations: []
+  source_endpoint: regular

configs/planar_noisy_ensemble.yaml

@@ -0,0 +1,242 @@
+# =============================================================================
+# PIVtools config -- SYNTHETIC PLANAR, NOISY (Case B), ENSEMBLE pipeline only
+# Reproduces: ensemble 64x64 -> 32x32 -> 8x8 single-mode vs 32x32 sum windows
+# The noisy case needs DIFFERENT preprocessing per pipeline, so it ships as TWO
+# configs. Run from this one:
+#   pivtools-cli ensemble
+#   pivtools-cli apply-calibration --all-paths --type-name ensemble
+# (run the instantaneous from planar_noisy_instantaneous.yaml in its own directory)
+# -----------------------------------------------------------------------------
+# EDIT BEFORE RUNNING (search for EDIT_ME):
+#   paths.source_paths            -> your download of TurbulentChannel/planar_noisy
+#   paths.base_paths              -> any writable output folder (SAME folder in
+#                                    both planar_noisy configs -- outputs merge)
+#   calibration.calibration_sources + calibration.source
+#                                 -> your download of TurbulentChannel/calibration/planar
+# DO NOT CHANGE:
+#   filters: []                   the ensemble runs on RAW images (verified: the
+#                                 published run used no preprocessing; adding
+#                                 ssmin corrupts the ensemble stresses)
+#   ensemble_piv.envelope_divide: false, kspace_shape: kx4, kspace_floor: coloured
+#   The ChArUco calibration sidecar carries dt = 0.0057553 s.
+# =============================================================================
+paths:
+  base_paths:
+  - C:/EDIT_ME/Results/planar_noisy
+  source_paths:
+  - C:/EDIT_ME/TurbulentChannel/planar_noisy
+  active_paths:
+  - 0
+  camera_numbers:
+  - 1
+  camera_count: 1
+  camera_subfolders: []
+images:
+  image_format:
+  - B%05d_A.tif
+  - B%05d_B.tif
+  vector_format:
+  - '%05d.mat'
+  dtype: float32
+  image_type: standard
+  use_camera_subfolders: false
+  start_index: 1
+  frame_stride: 0
+  pair_stride: 1
+  pairing_preset: ab_format
+  num_loops: 1
+  num_images: 4000
+  image_shape:
+  - 2048
+  - 2048
+batches:
+  size: 5
+logging:
+  file: pypiv.log
+  level: INFO
+  console: true
+processing:
+  backend: cpu
+  debug: false
+  auto_compute_params: false
+  omp_threads: 4
+  dask_workers_per_node: 5
+  dask_memory_limit: 10GB
+  dask_max_in_flight_per_worker: 2
+  open_dashboard: false
+  dask_nanny: false
+  post_processing_workers: 16
+  always_batch: true
+  instantaneous: false
+  ensemble: true
+outlier_detection:
+  enabled: true
+  methods:
+  - threshold: 0.25
+    type: peak_mag
+  - type: median_2d
+    epsilon: 0.1
+    threshold: 2
+infilling:
+  mid_pass:
+    method: nearest
+    parameters: {}
+  final_pass:
+    enabled: true
+    method: biharmonic
+    parameters: {}
+ensemble_outlier_detection:
+  enabled: true
+  methods:
+  - type: median_2d
+    epsilon: 0.1
+    threshold: 2
+    size: 5
+ensemble_infilling:
+  mid_pass:
+    method: biharmonic
+    parameters: {}
+  final_pass:
+    enabled: true
+    method: biharmonic
+    parameters: {}
+plots:
+  save_extension: .png
+  save_pickle: true
+  fontsize: 14
+  title_fontsize: 16
+video:
+  base_path_idx: 0
+  camera: 1
+  data_source: stereo
+  variable: mag
+  run: 3
+  piv_type: instantaneous
+  cmap: default
+  lower: ''
+  upper: ''
+  fps: 30
+  crf: 15
+  resolution: 4k
+  source_endpoint: regular
+statistics:
+  enabled_methods:
+    inst_vorticity: false
+    gamma2: false
+    inst_divergence: false
+    mean_velocity: true
+    vorticity: false
+    mean_vorticity: false
+    tke: false
+    inst_gamma: false
+    mean_tke: false
+    correlation_quality: true
+    inst_stresses: false
+    divergence: false
+    inst_velocity: false
+    gamma1: false
+    mean_stresses: true
+    mean_divergence: false
+    fluctuating_velocity: false
+  gamma_radius: 4
+  save_figures: true
+  type_name: instantaneous
+  source_endpoint: regular
+instantaneous_piv:
+  window_size:
+  - - 64
+    - 64
+  - - 32
+    - 32
+  - - 16
+    - 16
+  overlap:
+  - 50
+  - 50
+  - 50
+  runs:
+  - 2
+  - 3
+  time_resolved: false
+  window_type: gaussian
+  num_peaks: 1
+  peak_finder: gauss6
+  secondary_peak: false
+  predictor_smoothing: false
+  save_mode: full
+  save_compression: false
+  image_warp_interpolation: lanczos
+  dump_correlation_planes: false
+ensemble_piv:
+  fit_method: kspace
+  kspace_shape: kx4
+  kspace_floor: coloured
+  skip_background_subtraction: false
+  gradient_correction: true
+  persist_images: false
+  predictor_smoothing: false
+  image_warp_interpolation: lanczos
+  mask_center_pixel: true
+  background_subtraction_method: correlation+dc_zero
+  window_size:
+  - - 64
+    - 64
+  - - 32
+    - 32
+  - - 8
+    - 8
+  overlap:
+  - 50
+  - 50
+  - 50
+  type:
+  - std
+  - std
+  - single
+  runs:
+  - 1
+  - 2
+  - 3
+  store_planes: true
+  save_diagnostics: true
+  sum_window:
+  - 32
+  - 32
+  sum_fitting_window_enabled: true
+  sum_fitting_window:
+  - 16
+  - 16
+  resume_from_pass: 0
+  window_type: square
+  predictor_boundary_conditions: []
+  per_pair_normalization: false
+  predictor_rounding: false
+  envelope_divide: false
+calibration:
+  calibration_sources:
+  - C:/EDIT_ME/TurbulentChannel/calibration/planar
+  source: C:/EDIT_ME/TurbulentChannel/calibration/planar
+  source_idx: 0
+  active: charuco
+filters: []
+masking:
+  enabled: false
+  mask_file_pattern: mask_Cam%d.mat
+  mask_threshold: 0.01
+  mode: rectangular
+  rectangular:
+    top: 0
+    bottom: 0
+    left: 0
+    right: 0
+merging:
+  type_name: instantaneous
+  base_path_idx: 0
+  cameras: null
+transforms:
+  base_path_idx: 0
+  type_name: instantaneous
+  cameras:
+    1:
+      operations: []
+  source_endpoint: regular

configs/planar_noisy_instantaneous.yaml

@@ -0,0 +1,180 @@
+# =============================================================================
+# PIVtools config -- SYNTHETIC PLANAR, NOISY (Case B), INSTANTANEOUS pipeline only
+# Reproduces: instantaneous 64x64 -> 32x32 (stats on the 32x32 pass, ssmin preproc)
+# The noisy case needs DIFFERENT preprocessing per pipeline, so it ships as TWO
+# configs. Run from this one:
+#   pivtools-cli instantaneous
+#   pivtools-cli apply-calibration --all-paths --type-name instantaneous
+#   pivtools-cli statistics
+# (run the ensemble from planar_noisy_ensemble.yaml in its own directory)
+# -----------------------------------------------------------------------------
+# EDIT BEFORE RUNNING (search for EDIT_ME):
+#   paths.source_paths            -> your download of TurbulentChannel/planar_noisy
+#   paths.base_paths              -> any writable output folder (SAME folder in
+#                                    both planar_noisy configs -- outputs merge)
+#   calibration.calibration_sources + calibration.source
+#                                 -> your download of TurbulentChannel/calibration/planar
+# DO NOT CHANGE:
+#   filters: ssmin 7x7            (instantaneous preprocessing for the noisy case)
+#   The ChArUco calibration sidecar carries dt = 0.0057553 s.
+# =============================================================================
+paths:
+  base_paths:
+  - C:/EDIT_ME/Results/planar_noisy
+  source_paths:
+  - C:/EDIT_ME/TurbulentChannel/planar_noisy
+  active_paths:
+  - 0
+  camera_numbers:
+  - 1
+  camera_count: 1
+  camera_subfolders: []
+images:
+  image_format:
+  - B%05d_A.tif
+  - B%05d_B.tif
+  vector_format:
+  - '%05d.mat'
+  dtype: float32
+  image_type: standard
+  use_camera_subfolders: false
+  start_index: 1
+  frame_stride: 0
+  pair_stride: 1
+  pairing_preset: ab_format
+  num_loops: 1
+  num_images: 4000
+  image_shape:
+  - 2048
+  - 2048
+batches:
+  size: 5
+logging:
+  file: pypiv.log
+  level: INFO
+  console: true
+processing:
+  backend: cpu
+  debug: false
+  auto_compute_params: false
+  omp_threads: 4
+  dask_workers_per_node: 5
+  dask_memory_limit: 10GB
+  dask_max_in_flight_per_worker: 2
+  open_dashboard: false
+  dask_nanny: false
+  post_processing_workers: 16
+  always_batch: true
+  instantaneous: true
+  ensemble: false
+outlier_detection:
+  enabled: true
+  methods:
+  - threshold: 0.25
+    type: peak_mag
+  - type: median_2d
+    epsilon: 0.1
+    threshold: 2
+infilling:
+  mid_pass:
+    method: nearest
+    parameters: {}
+  final_pass:
+    enabled: true
+    method: biharmonic
+    parameters: {}
+plots:
+  save_extension: .png
+  save_pickle: true
+  fontsize: 14
+  title_fontsize: 16
+video:
+  base_path_idx: 0
+  camera: 1
+  data_source: stereo
+  variable: mag
+  run: 3
+  piv_type: instantaneous
+  cmap: default
+  lower: ''
+  upper: ''
+  fps: 30
+  crf: 15
+  resolution: 4k
+  source_endpoint: regular
+statistics:
+  enabled_methods:
+    inst_vorticity: false
+    gamma2: false
+    inst_divergence: false
+    mean_velocity: true
+    vorticity: false
+    mean_vorticity: false
+    tke: false
+    inst_gamma: false
+    mean_tke: false
+    correlation_quality: true
+    inst_stresses: false
+    divergence: false
+    inst_velocity: false
+    gamma1: false
+    mean_stresses: true
+    mean_divergence: false
+    fluctuating_velocity: false
+  gamma_radius: 4
+  save_figures: true
+  type_name: instantaneous
+  source_endpoint: regular
+instantaneous_piv:
+  window_size:
+  - - 64
+    - 64
+  - - 32
+    - 32
+  overlap:
+  - 50
+  - 50
+  runs:
+  - 2
+  time_resolved: false
+  window_type: gaussian
+  num_peaks: 1
+  peak_finder: gauss6
+  secondary_peak: false
+  predictor_smoothing: false
+  save_mode: full
+  save_compression: false
+  image_warp_interpolation: lanczos
+  dump_correlation_planes: false
+calibration:
+  calibration_sources:
+  - C:/EDIT_ME/TurbulentChannel/calibration/planar
+  source: C:/EDIT_ME/TurbulentChannel/calibration/planar
+  source_idx: 0
+  active: charuco
+filters:
+- type: ssmin
+  size:
+  - 7
+  - 7
+masking:
+  enabled: false
+  mask_file_pattern: mask_Cam%d.mat
+  mask_threshold: 0.01
+  mode: rectangular
+  rectangular:
+    top: 0
+    bottom: 0
+    left: 0
+    right: 0
+merging:
+  type_name: instantaneous
+  base_path_idx: 0
+  cameras: null
+transforms:
+  base_path_idx: 0
+  type_name: instantaneous
+  cameras:
+    1:
+      operations: []
+  source_endpoint: regular

configs/stereo_clean.yaml

@@ -0,0 +1,176 @@
+# =============================================================================
+# PIVtools config -- SYNTHETIC STEREO, CLEAN (paper Case A, stereo arm)
+# Reproduces: instantaneous stereo 64x64 -> 32x32 -> 16x16 (stats on 16x16 pass).
+# The paper uses NO stereo ensemble -- this config is instantaneous-only.
+# -----------------------------------------------------------------------------
+# EDIT BEFORE RUNNING (search for EDIT_ME):
+#   paths.source_paths            -> your download of TurbulentChannel/stereo_clean
+#                                    (camera1/ + camera2/ subfolders live inside it)
+#   paths.base_paths              -> any writable output folder
+#   calibration.calibration_sources
+#                                 -> your download of TurbulentChannel/calibration/stereo
+# DO NOT CHANGE: stereo ChArUco calibration (active: stereo_charuco); the
+#   calibration sidecar carries dt = 0.0057553 s -- no dt entry here.
+# Run order (see README): instantaneous PIV -> apply calibration
+#                         -> statistics (source_endpoint stereo) -> figure scripts.
+# =============================================================================
+paths:
+  base_paths:
+  - C:/EDIT_ME/Results/stereo_clean
+  source_paths:
+  - C:/EDIT_ME/TurbulentChannel/stereo_clean
+  active_paths:
+  - 0
+  camera_numbers:
+  - 1
+  - 2
+  camera_count: 2
+  camera_subfolders: []
+images:
+  image_format:
+  - B%05d_A.tif
+  - B%05d_B.tif
+  vector_format:
+  - '%05d.mat'
+  dtype: float32
+  image_type: standard
+  use_camera_subfolders: false
+  start_index: 1
+  frame_stride: 0
+  pair_stride: 1
+  pairing_preset: ab_format
+  num_loops: 1
+  num_images: 4000
+  image_shape:
+  - 2080
+  - 1440
+batches:
+  size: 5
+logging:
+  file: pypiv.log
+  level: INFO
+  console: true
+processing:
+  backend: cpu
+  debug: false
+  auto_compute_params: false
+  omp_threads: 4
+  dask_workers_per_node: 5
+  dask_memory_limit: 10GB
+  dask_max_in_flight_per_worker: 2
+  open_dashboard: false
+  dask_nanny: false
+  post_processing_workers: 16
+  always_batch: true
+  instantaneous: true
+  ensemble: false
+outlier_detection:
+  enabled: true
+  methods:
+  - threshold: 0.25
+    type: peak_mag
+  - type: median_2d
+    epsilon: 0.1
+    threshold: 3
+infilling:
+  mid_pass:
+    method: nearest
+    parameters: {}
+  final_pass:
+    enabled: true
+    method: biharmonic
+    parameters: {}
+plots:
+  save_extension: .png
+  save_pickle: true
+  fontsize: 14
+  title_fontsize: 16
+video:
+  base_path_idx: 0
+  camera: 1
+  data_source: stereo
+  variable: mag
+  run: 3
+  piv_type: instantaneous
+  cmap: default
+  lower: ''
+  upper: ''
+  fps: 30
+  crf: 15
+  resolution: 4k
+  source_endpoint: stereo
+statistics:
+  enabled_methods:
+    vorticity: false
+    gamma2: false
+    mean_divergence: false
+    inst_vorticity: false
+    fluctuating_velocity: false
+    mean_tke: false
+    inst_divergence: false
+    mean_velocity: true
+    inst_velocity: false
+    inst_gamma: false
+    mean_vorticity: false
+    inst_stresses: false
+    mean_stresses: true
+    tke: false
+    divergence: false
+    gamma1: false
+    correlation_quality: true
+  gamma_radius: 4
+  save_figures: true
+  type_name: instantaneous
+  source_endpoint: stereo
+instantaneous_piv:
+  window_size:
+  - - 64
+    - 64
+  - - 32
+    - 32
+  - - 16
+    - 16
+  overlap:
+  - 50
+  - 50
+  - 50
+  runs:
+  - 1
+  - 2
+  - 3
+  time_resolved: false
+  window_type: gaussian
+  num_peaks: 1
+  peak_finder: gauss6
+  secondary_peak: false
+  predictor_smoothing: false
+  save_mode: full
+  save_compression: false
+  image_warp_interpolation: lanczos
+  dump_correlation_planes: false
+calibration:
+  calibration_sources:
+  - C:/EDIT_ME/TurbulentChannel/calibration/stereo
+  active: stereo_charuco
+filters: []
+masking:
+  enabled: false
+  mask_file_pattern: mask_Cam%d.mat
+  mask_threshold: 0.01
+  mode: rectangular
+  rectangular:
+    top: 0
+    bottom: 0
+    left: 0
+    right: 0
+merging:
+  type_name: instantaneous
+  base_path_idx: 0
+  cameras: null
+transforms:
+  base_path_idx: 0
+  type_name: instantaneous
+  cameras:
+    1:
+      operations: []
+  source_endpoint: stereo

configs/stereo_noisy.yaml

@@ -0,0 +1,178 @@
+# =============================================================================
+# PIVtools config -- SYNTHETIC STEREO, NOISY (paper Case B, stereo arm)
+# Reproduces: instantaneous stereo 64x64 -> 32x32 (stats on 32x32 pass, ssmin).
+# The paper uses NO stereo ensemble -- this config is instantaneous-only.
+# -----------------------------------------------------------------------------
+# EDIT BEFORE RUNNING (search for EDIT_ME):
+#   paths.source_paths            -> your download of TurbulentChannel/stereo_noisy
+#                                    (camera1/ + camera2/ subfolders live inside it)
+#   paths.base_paths              -> any writable output folder
+#   calibration.calibration_sources
+#                                 -> your download of TurbulentChannel/calibration/stereo
+# DO NOT CHANGE:
+#   filters: ssmin 7x7            (the only preprocessing for the noisy case)
+#   stereo ChArUco calibration (active: stereo_charuco); the calibration sidecar
+#   carries dt = 0.0057553 s -- no dt entry here.
+# Run order (see README): instantaneous PIV -> apply calibration
+#                         -> statistics (source_endpoint stereo) -> figure scripts.
+# =============================================================================
+paths:
+  base_paths:
+  - C:/EDIT_ME/Results/stereo_noisy
+  source_paths:
+  - C:/EDIT_ME/TurbulentChannel/stereo_noisy
+  active_paths:
+  - 0
+  camera_numbers:
+  - 1
+  - 2
+  camera_count: 2
+  camera_subfolders: []
+images:
+  image_format:
+  - B%05d_A.tif
+  - B%05d_B.tif
+  vector_format:
+  - '%05d.mat'
+  dtype: float32
+  image_type: standard
+  use_camera_subfolders: false
+  start_index: 1
+  frame_stride: 0
+  pair_stride: 1
+  pairing_preset: ab_format
+  num_loops: 1
+  num_images: 4000
+  image_shape:
+  - 2080
+  - 1440
+batches:
+  size: 5
+logging:
+  file: pypiv.log
+  level: INFO
+  console: true
+processing:
+  backend: cpu
+  debug: false
+  auto_compute_params: false
+  omp_threads: 4
+  dask_workers_per_node: 5
+  dask_memory_limit: 10GB
+  dask_max_in_flight_per_worker: 2
+  open_dashboard: false
+  dask_nanny: false
+  post_processing_workers: 16
+  always_batch: true
+  instantaneous: true
+  ensemble: false
+outlier_detection:
+  enabled: true
+  methods:
+  - threshold: 0.25
+    type: peak_mag
+  - type: median_2d
+    epsilon: 0.1
+    threshold: 3
+infilling:
+  mid_pass:
+    method: nearest
+    parameters: {}
+  final_pass:
+    enabled: true
+    method: biharmonic
+    parameters: {}
+plots:
+  save_extension: .png
+  save_pickle: true
+  fontsize: 14
+  title_fontsize: 16
+video:
+  base_path_idx: 0
+  camera: 1
+  data_source: stereo
+  variable: mag
+  run: 3
+  piv_type: instantaneous
+  cmap: default
+  lower: ''
+  upper: ''
+  fps: 30
+  crf: 15
+  resolution: 4k
+  source_endpoint: stereo
+statistics:
+  enabled_methods:
+    mean_vorticity: false
+    mean_stresses: true
+    divergence: false
+    mean_tke: false
+    gamma2: false
+    inst_vorticity: false
+    inst_divergence: false
+    mean_velocity: true
+    inst_stresses: false
+    inst_velocity: false
+    gamma1: false
+    mean_divergence: false
+    tke: false
+    correlation_quality: true
+    fluctuating_velocity: false
+    inst_gamma: false
+    vorticity: false
+  gamma_radius: 4
+  save_figures: true
+  type_name: instantaneous
+  source_endpoint: stereo
+instantaneous_piv:
+  window_size:
+  - - 64
+    - 64
+  - - 32
+    - 32
+  overlap:
+  - 50
+  - 50
+  runs:
+  - 1
+  - 2
+  time_resolved: false
+  window_type: gaussian
+  num_peaks: 1
+  peak_finder: gauss6
+  secondary_peak: false
+  predictor_smoothing: false
+  save_mode: full
+  save_compression: false
+  image_warp_interpolation: lanczos
+  dump_correlation_planes: false
+calibration:
+  calibration_sources:
+  - C:/EDIT_ME/TurbulentChannel/calibration/stereo
+  active: stereo_charuco
+filters:
+- type: ssmin
+  size:
+  - 7
+  - 7
+masking:
+  enabled: false
+  mask_file_pattern: mask_Cam%d.mat
+  mask_threshold: 0.01
+  mode: rectangular
+  rectangular:
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+    bottom: 0
+    left: 0
+    right: 0
+merging:
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+  base_path_idx: 0
+  cameras: null
+transforms:
+  base_path_idx: 0
+  type_name: instantaneous
+  cameras:
+    1:
+      operations: []
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