@pikaa-ai/pikaa 0.3.22 → 0.3.24

package/skills/openpiv/SKILL.md

@@ -1,469 +0,0 @@
----
-name: openpiv
-description: Particle Image Velocimetry (PIV) analysis with OpenPIV. Use when extracting velocity fields from PIV image pairs, analyzing fluid dynamics or flow visualization experiments, cross-correlating interrogation windows, validating and replacing spurious PIV vectors, or computing vorticity, strain rate, and turbulence statistics from measured velocity fields.
-license: BSD-3-Clause
-compatibility: Requires Python 3.10+ with openpiv installed (uv pip install openpiv). numpy, scipy, scikit-image, and matplotlib arrive as dependencies. No network access needed after install.
-allowed-tools: Read Write Edit Bash
-metadata:
-  version: "1.1"
-  skill-author: OpenPIV Team
-  tested-against: "openpiv 0.25.4"
----
-
-# OpenPIV
-
-## Overview
-
-OpenPIV (Open Particle Image Velocimetry) analyzes fluid flow from PIV image pairs. It covers
-preprocessing, cross-correlation, vector validation, outlier replacement, smoothing, and scaling to
-physical units.
-
-Everything below is verified against **openpiv 0.25.4**. The API moves between releases — check
-`inspect.signature()` before trusting a snippet against a different version.
-
-## When to use
-
-Use this skill when working with experimental PIV or flow-visualization image pairs: measuring 2D
-velocity fields, tuning interrogation-window parameters, validating vectors, or deriving vorticity,
-strain rate, and turbulence statistics. For *simulating* flow rather than measuring it, use a CFD
-skill instead.
-
-## Quick Start
-
-Install OpenPIV:
-
-```bash
-uv pip install openpiv
-
-# Pin it when the analysis needs to be reproducible -- this is the version every
-# snippet below was checked against.
-uv pip install "openpiv==0.25.4"
-```
-
-Run PIV analysis on an image pair:
-
-```python
-import numpy as np
-from openpiv import tools, pyprocess, validation, filters, scaling
-
-frame_a = tools.imread("image_a.bmp")
-frame_b = tools.imread("image_b.bmp")
-
-# Cross-correlate. Returns (u, v, s2n) whenever sig2noise_method is not None.
-u, v, s2n = pyprocess.extended_search_area_piv(
-    frame_a.astype(np.int32),
-    frame_b.astype(np.int32),
-    window_size=32,
-    overlap=12,
-    dt=0.02,
-    search_area_size=38,
-    correlation_method="linear",   # required for search_area_size > window_size
-    sig2noise_method="peak2peak",
-)
-
-x, y = pyprocess.get_coordinates(
-    image_size=frame_a.shape,
-    search_area_size=38,
-    overlap=12,
-)
-
-# flags is a boolean array: True marks a spurious vector.
-flags = validation.sig2noise_val(s2n, threshold=1.05)
-u, v = filters.replace_outliers(u, v, flags, method="localmean", max_iter=3, kernel_size=2)
-
-# Scale to physical units, then flip to image coordinates for plotting.
-x, y, u, v = scaling.uniform(x, y, u, v, scaling_factor=96.52)
-x, y, u, v = tools.transform_coordinates(x, y, u, v)
-
-tools.save("vectors.txt", x, y, u, v, flags)
-```
-
-Or use the bundled CLI, which wraps exactly that pipeline:
-
-```bash
-python skills/openpiv/scripts/runner.py \
-    --image frame_a.bmp --image frame_b.bmp --output_dir results --verbose
-```
-
-## Core Concepts
-
-### PIV Fundamentals
-
-Particle Image Velocimetry is an optical method for measuring fluid velocity by tracking illuminated
-tracer particles between two images.
-
-**Process flow:**
-
-1. Capture an image pair (`frame_a`, `frame_b`) separated by a known time `dt`.
-2. Divide the images into interrogation windows.
-3. Cross-correlate matching windows to find peak displacement.
-4. Validate vectors (signal-to-noise, global range, local median).
-5. Replace spurious vectors with interpolated values.
-6. Scale pixel displacements to physical units.
-
-### Interrogation Window Parameters
-
-**`window_size`** — correlation window in pixels (typically 16–128). Larger windows give better
-correlation but coarser spatial resolution.
-
-**`overlap`** — pixels shared between adjacent windows (typically 50–75% of `window_size`). Higher
-overlap raises vector density and cost, but adjacent vectors become correlated rather than
-independent.
-
-**`search_area_size`** — the window searched in the second frame. Must be ≥ `window_size`; a few
-pixels larger accommodates larger displacements. Pair an extended search area with
-`correlation_method="linear"` — the default `"circular"` relies on FFT wrap-around and aliases large
-displacements into small ones. See `references/advanced_algorithms.md`.
-
-Rules of thumb: keep the largest displacement under about a quarter of `window_size`, and aim for
-5–10 particles per window.
-
-### Signal-to-Noise Ratio
-
-`s2n` measures how distinct the correlation peak is. `sig2noise_method` controls how it is computed —
-`"peak2mean"` (the function default) or `"peak2peak"`. **The two are on different scales**, so a
-threshold tuned for one is meaningless for the other. Typical `peak2peak` thresholds are 1.05–1.3.
-
-```python
-flags = validation.sig2noise_val(s2n, threshold=1.05)
-# flags is bool: True == spurious. `~flags` selects the good vectors.
-```
-
-## Common Operations
-
-### Dynamic Masking
-
-Masking lives in `openpiv.preprocess`, **not** in an `openpiv.masking` module. It returns an
-`(image, mask)` tuple and expects a float image.
-
-```python
-from openpiv import preprocess
-
-# method="edges" for dark, sharp-edged objects; "intensity" for high-contrast objects.
-frame_a_masked, mask_a = preprocess.dynamic_masking(
-    frame_a.astype(np.float64), method="intensity", filter_size=7, threshold=0.005
-)
-frame_b_masked, mask_b = preprocess.dynamic_masking(
-    frame_b.astype(np.float64), method="intensity", filter_size=7, threshold=0.005
-)
-```
-
-Feed the **returned image** into the correlation step — it already has the masked region zeroed. Do
-not multiply the original frame by `mask`: masking is already applied, and for `method="edges"` the
-mask comes back as `uint8` 0/255 rather than boolean, so multiplying rescales the image by 255.
-
-### Multi-Pass Processing
-
-Multi-pass (window deformation) lives in `openpiv.windef`, driven by a `PIVSettings` dataclass.
-`pyprocess` has no multi-pass entry point.
-
-```python
-import numpy as np
-from openpiv import scaling, windef
-
-settings = windef.PIVSettings()
-settings.windowsizes = (64, 32, 16)   # one entry per pass, decreasing (this is also the default)
-settings.overlap = (32, 16, 8)        # same length as windowsizes
-settings.num_iterations = 3           # number of passes to actually run
-settings.sig2noise_threshold = 1.05
-
-x, y, u, v, flags = windef.simple_multipass(
-    frame_a.astype(np.int32), frame_b.astype(np.int32), settings
-)
-
-# Output is in PIXELS PER FRAME -- convert yourself. scaling.uniform only divides
-# by scaling_factor, so apply dt separately.
-dt = 0.02
-x, y, u, v = scaling.uniform(x, y, u, v, scaling_factor=96.52)
-u, v = u / dt, v / dt
-```
-
-`simple_multipass` already validates, replaces outliers, fills remaining NaNs with zeros, and calls
-`transform_coordinates` — do not repeat those steps.
-
-**Units trap:** `PIVSettings` has `dt` and `scaling_factor` fields, but `windef` never uses either —
-`first_pass` calls `extended_search_area_piv` without `dt`, so the whole multi-pass chain works in
-pixels per frame. Setting `settings.dt = 0.02` changes nothing about the returned values. Convert
-after the fact, as above.
-
-For control over individual passes, `windef.first_pass` and `windef.multipass_img_deform` are the
-lower-level building blocks.
-
-## Validation and Post-Processing
-
-### Validation Methods
-
-Every validator returns a boolean array where **True marks a spurious vector**.
-
-```python
-# Signal-to-noise
-flags = validation.sig2noise_val(s2n, threshold=1.05)
-
-# Global range -- takes (min, max) TUPLES, positionally or as u_thresholds/v_thresholds.
-flags = validation.global_val(u, v, (-300, 300), (-300, 300))
-
-# Local median -- u_threshold and v_threshold are REQUIRED; size is the neighbourhood half-width.
-flags = validation.local_median_val(u, v, u_threshold=30.0, v_threshold=30.0, size=1)
-
-# Combine with boolean OR (not np.maximum -- these are bool arrays).
-flags = (
-    validation.sig2noise_val(s2n, threshold=1.05)
-    | validation.global_val(u, v, (-300, 300), (-300, 300))
-    | validation.local_median_val(u, v, u_threshold=30.0, v_threshold=30.0)
-)
-```
-
-**Set these thresholds in the units of `u` and `v`, not in pixels per frame.**
-`extended_search_area_piv` divides by `dt`, so with `dt=0.02` a 3 px/frame displacement arrives as
-150 px/s. The thresholds above suit that case; the `(-30, 30)` figure that PIV literature and
-`PIVSettings.min_max_u_disp` use is a px/frame limit, and applying it to px/s output rejects the
-entire field. Either validate before scaling, or scale the thresholds by `1/dt` too.
-
-### Outlier Replacement
-
-```python
-u, v = filters.replace_outliers(
-    u, v, flags, method="localmean", max_iter=3, tol=1e-3, kernel_size=2
-)
-```
-
-`method` accepts `"localmean"`, `"disk"`, or `"distance"` — and only those three. An unrecognized
-name is not rejected; it falls through to an all-zero kernel and silently returns a useless field.
-Note that replacement *fills* the flagged
-positions with interpolated values — if you then overwrite them with NaN, the replacement was
-wasted. Choose one or the other:
-
-```python
-# Keep flagged vectors out of the analysis entirely, instead of interpolating them.
-u = np.where(flags, np.nan, u)
-v = np.where(flags, np.nan, v)
-```
-
-### Smoothing
-
-Smoothing is `openpiv.smoothn.smoothn`; there is no `openpiv.smooth` module. It returns a tuple
-whose first element is the smoothed field, and it does not accept NaN input.
-
-```python
-from openpiv.smoothn import smoothn
-
-u_smooth, *_ = smoothn(np.nan_to_num(u), s=0.5)  # s: larger == smoother
-v_smooth, *_ = smoothn(np.nan_to_num(v), s=0.5)
-u_smooth = np.asarray(u_smooth)
-```
-
-## Visualization
-
-### Vector Field Plotting
-
-`display_vector_field` reads a saved vectors file and calls `plt.show()` internally, so select a
-non-interactive backend for batch runs.
-
-```python
-import matplotlib
-matplotlib.use("Agg")
-import matplotlib.pyplot as plt
-from openpiv import tools
-
-fig, ax = plt.subplots(figsize=(8, 8))
-tools.display_vector_field(
-    "vectors.txt",
-    ax=ax,
-    scaling_factor=96.52,   # same factor used in scaling.uniform, to map back onto the image
-    scale=50,
-    width=0.0035,
-    on_img=True,
-    image_name="frame_a.bmp",
-)
-fig.savefig("vector_field.png", dpi=150, bbox_inches="tight")
-plt.close(fig)
-```
-
-### Custom Visualization
-
-```python
-import numpy as np
-import matplotlib.pyplot as plt
-
-fig, axes = plt.subplots(1, 3, figsize=(15, 5))
-
-mag = np.sqrt(u**2 + v**2)
-for ax, field, title, cmap in [
-    (axes[0], mag, "Velocity Magnitude", "viridis"),
-    (axes[1], u, "U Velocity", "RdBu_r"),
-    (axes[2], v, "V Velocity", "RdBu_r"),
-]:
-    im = ax.imshow(field, cmap=cmap)
-    ax.set_title(title)
-    plt.colorbar(im, ax=ax)
-
-fig.tight_layout()
-fig.savefig("velocity_components.png")
-plt.close(fig)
-```
-
-## Analysis Functions
-
-`scripts/analyze.py` bundles these against a `params.npz` written by `runner.py`. It infers the
-physical grid spacing from the saved coordinates, so the derivatives come out per unit length:
-
-```python
-import sys
-sys.path.insert(0, "skills/openpiv/scripts")
-from analyze import PIVAnalyzer
-
-piv = PIVAnalyzer("results/params.npz")
-vorticity = piv.compute_vorticity()          # dv/dx - du/dy
-exx, eyy, exy = piv.compute_strain()
-stats = piv.compute_statistics()             # u_mean, v_mean, rms_u, rms_v, tke
-piv.plot_vector_field(save_path="quiver.png")
-```
-
-The standalone forms, if you would rather compute them inline:
-
-### Vorticity
-
-```python
-def compute_vorticity(u, v, dx=1.0, dy=None):
-    """Out-of-plane vorticity dv/dx - du/dy. Pass the physical grid spacing, not 1.0."""
-    dy = dx if dy is None else dy
-    return np.gradient(v, dx, axis=1) - np.gradient(u, dy, axis=0)
-```
-
-The grid spacing is `(window_size - overlap) / scaling_factor` in physical units, so leaving `dx=1.0`
-yields vorticity per grid cell, not per unit length.
-
-**Sign convention:** `runner.py` ends with `transform_coordinates`, which relabels the grid into a
-right-handed y-up frame but leaves the rows in image order, so the saved `y` *decreases* as the row
-index grows. The standalone forms above assume the opposite, so on a `params.npz` field they return
-`-du/dy` and flip the sign of the vorticity and the shear strain — negate the `axis=0` derivatives, or
-use `PIVAnalyzer`, which reads the orientation off the saved coordinates.
-
-### Strain Rate
-
-```python
-def compute_strain(u, v, dx=1.0, dy=None):
-    """Return (exx, eyy, exy) of the 2D strain-rate tensor."""
-    dy = dx if dy is None else dy
-    du_dx = np.gradient(u, dx, axis=1)
-    du_dy = np.gradient(u, dy, axis=0)
-    dv_dx = np.gradient(v, dx, axis=1)
-    dv_dy = np.gradient(v, dy, axis=0)
-    return du_dx, dv_dy, 0.5 * (du_dy + dv_dx)
-```
-
-### Turbulence Statistics
-
-```python
-def compute_statistics(u, v):
-    """Single-frame spatial statistics. NOT Reynolds decomposition."""
-    u_prime = u - np.nanmean(u)
-    v_prime = v - np.nanmean(v)
-    rms_u, rms_v = np.nanstd(u_prime), np.nanstd(v_prime)
-    return {
-        "u_mean": np.nanmean(u),
-        "v_mean": np.nanmean(v),
-        "rms_u": rms_u,
-        "rms_v": rms_v,
-        "tke": 0.5 * (rms_u**2 + rms_v**2),
-    }
-```
-
-**Caveat:** subtracting the *spatial* mean of one frame measures spatial variance, which equals
-turbulent intensity only for a homogeneous field. Genuine Reynolds decomposition needs an ensemble of
-image pairs: average over the time axis, then subtract that mean field from each realization.
-
-## CLI Usage
-
-```bash
-# Basic run
-python skills/openpiv/scripts/runner.py \
-    --image img1.bmp --image img2.bmp --output_dir results --verbose
-
-# Tuned parameters with dynamic masking
-python skills/openpiv/scripts/runner.py \
-    --image frame_a.bmp \
-    --image frame_b.bmp \
-    --output_dir results \
-    --window_size 32 \
-    --overlap 12 \
-    --search_area 38 \
-    --dt 0.02 \
-    --scaling 96.52 \
-    --threshold 1.05 \
-    --mask dynamic \
-    --mask_method intensity \
-    --verbose
-```
-
-### CLI Options
-
-| Option | Default | Description |
-|--------|---------|-------------|
-| `--image` | required | Image file; specify exactly twice for the pair |
-| `--output_dir` | `results` | Output directory (created if absent) |
-| `--window_size` | 32 | Interrogation window size (px) |
-| `--overlap` | 12 | Window overlap (px) |
-| `--search_area` | 38 | Search area size (px), must be ≥ `--window_size` |
-| `--dt` | 0.02 | Time between frames (s) |
-| `--scaling` | 96.52 | Scaling factor, pixels per physical unit (e.g. px/mm) |
-| `--threshold` | 1.05 | `peak2peak` signal-to-noise threshold |
-| `--mask` | `none` | `none` or `dynamic` (`openpiv.preprocess.dynamic_masking`) |
-| `--mask_method` | `intensity` | `edges` or `intensity`, used only with `--mask dynamic` |
-| `--drop_invalid` | off | NaN out flagged vectors instead of keeping interpolated values |
-| `--verbose` | off | Print progress messages |
-
-Verify an install end to end against OpenPIV's own bundled image pair:
-
-```bash
-python skills/openpiv/scripts/run_example.py --output_dir /tmp/openpiv-demo
-```
-
-## Output Files
-
-- **vectors.txt** — tab-delimited, `%.4e` formatted, with a `# x y u v flags mask` comment header
-- **params.npz** — NumPy archive with `x`, `y`, `u`, `v`, `flags` arrays
-- **vector_field.png** — vector field drawn over the first frame
-
-```text
-# x	y	u	v	flags	mask
-2.1757e-01	3.5226e+00	-6.2220e-02	-2.7081e+00	0.0000e+00	0.0000e+00
-4.8695e-01	3.5226e+00	-3.1587e-01	-2.9800e+00	0.0000e+00	0.0000e+00
-```
-
-`flags` is written as a float, `0` for a valid vector and `1` for a flagged one.
-
-## Best Practices
-
-### Parameter Selection
-
-1. **Window size** — 32×32 suits most cases. 64/128 for better correlation at coarser resolution;
-   16/24 for finer resolution at the cost of noise.
-2. **Overlap** — 50–75% of window size.
-3. **Threshold** — raise it to reject more vectors; always re-tune after switching
-   `sig2noise_method`.
-4. **Scaling factor** — calibrate against a known reference such as a calibration grid, and keep the
-   units straight (`96.52` in OpenPIV's `test1` tutorial data is px/mm).
-
-### Image Quality
-
-- Particles visible and evenly distributed, 5–10 per interrogation window
-- No saturated or overexposed regions
-- Minimal background noise; consider background subtraction across a run
-
-### Processing Tips
-
-1. Start from the defaults, then tune against the vector field you get.
-2. Inspect the `s2n` distribution — a low median means poor correlation, not a bad threshold.
-3. Visualize early; obvious problems (uniform vectors, edge artifacts) show up immediately.
-4. Use multi-pass (`windef`) for flows with large velocity gradients or displacements.
-5. Mask reflections and solid boundaries rather than letting them generate vectors.
-
-## Resources
-
-### references/
-
-- `advanced_algorithms.md` — correlation and subpixel methods, multi-pass window deformation,
-  `PIVSettings` fields, 3D and phase-separation modules
-
-Load the reference when detailed algorithm or settings information is needed.