geopyv-dev 0.1.0__cp39-cp39-win_amd64.whl

geopyv_dev/__init__.py

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+from ._geopyv_dev import *
+from .plots import (
+    inspect_subset,
+    inspect_mesh,
+    inspect_sequence,
+    inspect_particle,
+    inspect_field,
+    convergence_subset,
+    convergence_mesh,
+    convergence_sequence,
+    contour_mesh,
+    contour_field,
+)
+from .wrappers import SubsetWrapper, MeshWrapper, ParticleWrapper, FieldWrapper

geopyv_dev/plots.py

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+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.tri as tri
+from scipy.spatial import Delaunay
+
+
+def _imshow_or_blank(ax, img_path, **kwargs):
+    """Helper: show image from path, or blank background if path is None."""
+    kwargs.setdefault("cmap", "gist_gray")
+    if img_path is not None:
+        import cv2
+        img = cv2.imread(img_path, cv2.IMREAD_COLOR)
+        img_gs = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY).astype(float)
+        ax.imshow(img_gs, **kwargs)
+    else:
+        blank = np.zeros((50, 50), dtype=float)
+        ax.imshow(blank, **kwargs)
+
+
+def _show_save_close(fig, show, block, save):
+    if save:
+        plt.savefig(save, dpi=600)
+    if show:
+        plt.show(block=block)
+    else:
+        plt.close(fig)
+
+
+def inspect_subset(subset, show=True, block=True, save=False, **kwargs):
+    coord = subset.coord
+    f_coords = np.asarray(subset.f_coords)
+    f = np.asarray(subset.f)
+    sssig = subset.sssig
+    sigma_intensity = subset.sigma_intensity
+
+    f_img_path = getattr(subset, 'f_img_path', None)
+    template_size = getattr(subset, 'template_size', None)
+    if template_size is None:
+        template_size = int(np.ceil(np.sqrt(len(f) / np.pi)))
+
+    # Build display image
+    if f_img_path is not None:
+        import cv2
+        img = cv2.imread(f_img_path, cv2.IMREAD_COLOR)
+        img_gs = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY).astype(float)
+        x, y = coord
+        r = template_size
+        x0, x1 = max(0, int(round(x)) - r), min(img_gs.shape[1], int(round(x)) + r + 1)
+        y0, y1 = max(0, int(round(y)) - r), min(img_gs.shape[0], int(round(y)) + r + 1)
+        display = img_gs[y0:y1, x0:x1]
+    else:
+        xi = f_coords[:, 0]
+        yi = f_coords[:, 1]
+        x_min = int(np.floor(xi.min()))
+        y_min = int(np.floor(yi.min()))
+        x_max = int(np.ceil(xi.max()))
+        y_max = int(np.ceil(yi.max()))
+        h = y_max - y_min + 1
+        w = x_max - x_min + 1
+        display = np.full((h, w), float(np.mean(f)))
+        for k in range(len(f)):
+            ix = int(round(float(xi[k]))) - x_min
+            iy = int(round(float(yi[k]))) - y_min
+            if 0 <= iy < h and 0 <= ix < w:
+                display[iy, ix] = float(f[k])
+
+    imshow_kwargs = {"cmap": "gist_gray"}
+    imshow_kwargs.update(kwargs)
+
+    fig, ax = plt.subplots()
+    ax.imshow(display, **imshow_kwargs)
+    ax.text(0.5, -0.05,
+            f"Size: {template_size} px; \u03c3_s = {sigma_intensity:.2f}; SSSIG = {sssig:.2E}",
+            transform=ax.transAxes, ha="center")
+    ax.set_axis_off()
+    plt.tight_layout()
+    _show_save_close(fig, show, block, save)
+    return fig, ax
+
+
+def inspect_mesh(mesh, subset_idx=None, show_areas=False, show=True, block=True, save=False, **kwargs):
+    nodes = np.asarray(mesh.nodes)
+    elements = np.asarray(mesh.elements)
+    f_img_path = getattr(mesh, 'f_img_path', None)
+
+    fig, ax = plt.subplots()
+
+    imshow_kwargs = {"cmap": "gist_gray"}
+    imshow_kwargs.update(kwargs)
+    _imshow_or_blank(ax, f_img_path, **imshow_kwargs)
+
+    # Element edges
+    n_corner = 3
+    for elem in elements:
+        corners = nodes[elem[:n_corner]]
+        for i in range(n_corner):
+            j = (i + 1) % n_corner
+            ax.plot([corners[i, 0], corners[j, 0]], [corners[i, 1], corners[j, 1]],
+                    'b-', linewidth=0.5)
+
+    # Element index annotations
+    for i, elem in enumerate(elements):
+        cx = nodes[elem[:3], 0].mean()
+        cy = nodes[elem[:3], 1].mean()
+        ax.text(cx, cy, str(i), ha='center', va='center', color='red', fontsize=8)
+
+    if show_areas:
+        from matplotlib.patches import Circle as MplCircle
+        radius = 10
+        for nd in nodes:
+            ax.add_patch(MplCircle((nd[0], nd[1]), radius, alpha=0.2, color='blue'))
+
+    plt.tight_layout()
+    _show_save_close(fig, show, block, save)
+    return fig, ax
+
+
+def inspect_sequence(sequence, mesh_idx=None, subset_idx=None, show=True, block=True, save=False, **kwargs):
+    if mesh_idx is None:
+        raise ValueError("mesh_idx is required")
+    mesh = sequence.mesh_solutions[mesh_idx]
+    return inspect_mesh(mesh, subset_idx=subset_idx, show=show, block=block, save=save, **kwargs)
+
+
+def inspect_particle(particle, show=True, block=True, save=False, **kwargs):
+    coords = np.asarray(particle.coordinates)
+    initial = coords[0]
+    img_path = getattr(particle, 'image_0_path', None)
+
+    fig, ax = plt.subplots()
+    _imshow_or_blank(ax, img_path)
+    ax.scatter([initial[0]], [initial[1]], marker='x', color='red', s=100, zorder=10, **kwargs)
+    plt.tight_layout()
+    _show_save_close(fig, show, block, save)
+    return fig, ax
+
+
+def inspect_field(field, particle_idx=None, show=True, block=True, save=False, **kwargs):
+    coords = np.asarray(field.coordinates)
+    img_path = getattr(field, 'image_0_path', None)
+
+    fig, ax = plt.subplots()
+    _imshow_or_blank(ax, img_path)
+    ax.scatter(coords[:, 0], coords[:, 1], **kwargs)
+    if particle_idx is not None:
+        ax.scatter([coords[particle_idx, 0]], [coords[particle_idx, 1]],
+                   color='red', s=100, zorder=10)
+    plt.tight_layout()
+    _show_save_close(fig, show, block, save)
+    return fig, ax
+
+
+def convergence_subset(subset, show=True, block=True, save=False, **kwargs):
+    solve_result = getattr(subset, 'solve_result', None)
+    if solve_result is None:
+        raise ValueError("Subset has not been solved.")
+    history = solve_result["history"]
+    max_norm = solve_result.get("max_norm", 1e-3)
+    max_iterations = solve_result.get("max_iterations", 50)
+
+    iters = [h[0] for h in history]
+    norms = [h[1] for h in history]
+    znccs = [h[2] for h in history]
+
+    fig, ax = plt.subplots(2, 1, sharex=True)
+    ax[0].semilogy(iters, norms, marker="o", **kwargs)
+    ax[0].semilogy([min(iters), max(iters)], [max_norm, max_norm], "--r")
+    ax[0].set_ylabel(r"$\Delta$ Norm (-)")
+    ax[1].plot(iters, znccs, marker="o", **kwargs)
+    ax[1].plot([min(iters), max(iters)], [0.75, 0.75], "--r")
+    ax[1].set_ylabel(r"$C_{ZNCC}$ (-)")
+    ax[1].set_xlabel("Iteration (-)")
+    plt.tight_layout()
+    _show_save_close(fig, show, block, save)
+    return fig, np.array(ax)
+
+
+def convergence_mesh(mesh, quantity, show=True, block=True, save=False, **kwargs):
+    valid = {"C_ZNCC", "iterations", "norm"}
+    if quantity not in valid:
+        raise ValueError(f"quantity must be one of {sorted(valid)!r}, got {quantity!r}")
+
+    if quantity == "C_ZNCC":
+        data = np.asarray(mesh.c_zncc)
+        xlabel = r"$C_{ZNCC}$ (-)"
+    elif quantity == "iterations":
+        data = np.asarray(mesh.iterations, dtype=float)
+        xlabel = "Iterations (-)"
+    else:
+        data = np.asarray(mesh.norms)
+        xlabel = r"$\Delta$ Norm (-)"
+
+    fig, ax = plt.subplots()
+    ax.hist(data, **kwargs)
+    ax.set_xlabel(xlabel)
+    ax.set_ylabel("Count (-)")
+    plt.tight_layout()
+    _show_save_close(fig, show, block, save)
+    return fig, ax
+
+
+def convergence_sequence(sequence, mesh_idx=None, subset_idx=None, quantity="C_ZNCC",
+                          show=True, block=True, save=False, **kwargs):
+    if mesh_idx is not None:
+        mesh = sequence.mesh_solutions[mesh_idx]
+        return convergence_mesh(mesh, quantity, show=show, block=block, save=save, **kwargs)
+    else:
+        all_data = np.concatenate([np.asarray(m.c_zncc) for m in sequence.mesh_solutions])
+        fig, ax = plt.subplots()
+        ax.hist(all_data, **kwargs)
+        ax.set_xlabel(r"$C_{ZNCC}$ (-)")
+        ax.set_ylabel("Count (-)")
+        plt.tight_layout()
+        _show_save_close(fig, show, block, save)
+        return fig, ax
+
+
+def contour_mesh(mesh, quantity, show=True, block=True, save=False, **kwargs):
+    valid = {"C_ZNCC", "iterations", "norm", "u", "v", "R"}
+    if quantity not in valid:
+        raise ValueError(f"quantity must be one of {sorted(valid)!r}, got {quantity!r}")
+
+    nodes = np.asarray(mesh.nodes)
+    elements = np.asarray(mesh.elements)
+    displacements = np.asarray(mesh.displacements)
+
+    labels = {
+        "C_ZNCC": r"$C_{ZNCC}$ (-)",
+        "iterations": "Iterations (-)",
+        "norm": r"$\Delta$ Norm (-)",
+        "u": "u (px)",
+        "v": "v (px)",
+        "R": "R (px)",
+    }
+    if quantity == "C_ZNCC":
+        values = np.asarray(mesh.c_zncc)
+    elif quantity == "iterations":
+        values = np.asarray(mesh.iterations, dtype=float)
+    elif quantity == "norm":
+        values = np.asarray(mesh.norms)
+    elif quantity == "u":
+        values = displacements[:, 0]
+    elif quantity == "v":
+        values = displacements[:, 1]
+    elif quantity == "R":
+        values = np.sqrt(displacements[:, 0]**2 + displacements[:, 1]**2)
+
+    fig, ax = plt.subplots()
+    f_img_path = getattr(mesh, 'f_img_path', None)
+    _imshow_or_blank(ax, f_img_path)
+
+    tri_obj = tri.Triangulation(nodes[:, 0], nodes[:, 1], elements[:, :3])
+    cf = ax.tricontourf(tri_obj, values, **kwargs)
+    cbar = fig.colorbar(cf, ax=ax)
+    cbar.set_label(labels[quantity])
+
+    plt.tight_layout()
+    _show_save_close(fig, show, block, save)
+    return fig, ax
+
+
+def contour_field(field, quantity, window=None, dt=None, absolute=False,
+                   show=True, block=True, save=False, **kwargs):
+    valid = {"u", "v", "R", "ep_xx", "ep_yy", "ep_xy", "ep_vol"}
+    if quantity not in valid:
+        raise ValueError(f"quantity must be one of {sorted(valid)!r}, got {quantity!r}")
+
+    particles = field.particles
+    n = len(particles)
+    coords = np.array([[p.coordinates[0, 0], p.coordinates[0, 1]] for p in particles])
+
+    strain_col = {"ep_xx": 0, "ep_yy": 1, "ep_xy": 2}
+
+    # Build window slice
+    if window is not None:
+        if isinstance(window, (list, tuple)) and len(window) == 2:
+            w = slice(window[0], window[1])
+        else:
+            w = window
+    else:
+        w = slice(None)
+
+    values = np.zeros(n)
+    for i, p in enumerate(particles):
+        warps = np.asarray(p.warps)  # (inc_no, warp_len)
+        vol_strains = np.asarray(p.vol_strains)
+        strains = np.asarray(p.strains)  # (inc_no, 6)
+
+        if quantity == "u":
+            v = warps[w, 0]
+        elif quantity == "v":
+            v = warps[w, 1]
+        elif quantity == "R":
+            v = np.sqrt(warps[w, 0]**2 + warps[w, 1]**2)
+        elif quantity in strain_col:
+            v = strains[w, strain_col[quantity]]
+        elif quantity == "ep_vol":
+            v = vol_strains[w]
+
+        v = np.atleast_1d(v)
+        if dt is None:
+            if absolute:
+                values[i] = float(np.sum(np.abs(np.diff(v)))) if len(v) > 1 else 0.0
+            else:
+                values[i] = float(v[-1] - v[0]) if len(v) > 1 else float(v[-1])
+        else:
+            if len(v) > 1:
+                values[i] = float((v[-1] - v[0]) / (len(v) * dt))
+            else:
+                values[i] = 0.0
+
+    # Delaunay triangulation
+    if n >= 3:
+        delaunay = Delaunay(coords)
+        triangles = delaunay.simplices
+    else:
+        triangles = None
+
+    fig, ax = plt.subplots()
+    img_path = getattr(field, 'image_0_path', None)
+    _imshow_or_blank(ax, img_path)
+
+    if triangles is not None and len(triangles) > 0:
+        mpl_tri = tri.Triangulation(coords[:, 0], coords[:, 1], triangles)
+        cf = ax.tricontourf(mpl_tri, values, **kwargs)
+    else:
+        cf = ax.scatter(coords[:, 0], coords[:, 1], c=values, **kwargs)
+
+    if dt is None:
+        label = f"{quantity}" + (" (abs)" if absolute else "")
+    else:
+        label = f"{quantity} /s"
+
+    cbar = fig.colorbar(cf, ax=ax)
+    cbar.set_label(label)
+
+    plt.tight_layout()
+    _show_save_close(fig, show, block, save)
+    return fig, ax

geopyv_dev/wrappers.py

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+from geopyv_dev import plots
+
+
+class SubsetWrapper:
+    def __init__(self, inner):
+        self._inner = inner
+
+    def __getattr__(self, name):
+        return getattr(self._inner, name)
+
+    def inspect(self, **kwargs):
+        return plots.inspect_subset(self._inner, **kwargs)
+
+    def convergence(self, **kwargs):
+        return plots.convergence_subset(self._inner, **kwargs)
+
+
+class MeshWrapper:
+    def __init__(self, inner):
+        self._inner = inner
+
+    def __getattr__(self, name):
+        return getattr(self._inner, name)
+
+    def inspect(self, **kwargs):
+        return plots.inspect_mesh(self._inner, **kwargs)
+
+    def convergence(self, quantity="C_ZNCC", **kwargs):
+        return plots.convergence_mesh(self._inner, quantity, **kwargs)
+
+    def contour(self, quantity, **kwargs):
+        return plots.contour_mesh(self._inner, quantity, **kwargs)
+
+
+class ParticleWrapper:
+    def __init__(self, inner):
+        self._inner = inner
+
+    def __getattr__(self, name):
+        return getattr(self._inner, name)
+
+    def inspect(self, **kwargs):
+        return plots.inspect_particle(self._inner, **kwargs)
+
+
+class FieldWrapper:
+    def __init__(self, inner):
+        self._inner = inner
+
+    def __getattr__(self, name):
+        return getattr(self._inner, name)
+
+    def inspect(self, **kwargs):
+        return plots.inspect_field(self._inner, **kwargs)
+
+    def contour(self, quantity, **kwargs):
+        return plots.contour_field(self._inner, quantity, **kwargs)

geopyv_dev-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: geopyv_dev
+Version: 0.1.0
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Rust
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering
+License-File: LICENSE
+Summary: A PIV/DIC analysis package for geotechnics.
+Author-email: Sam Stanier <sas229@cam.ac.uk>, Jonathan Smith <jdks2@cam.ac.uk>
+License: GPL-3.0-or-later
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: Bug Tracker, https://github.com/jdks2/geopyv-dev/issues
+Project-URL: Homepage, https://github.com/jdks2/geopyv-dev
+
+# geopyv-dev
+PIV/DIC package for geotechnics. Under active development.
+

geopyv_dev-0.1.0.dist-info/RECORD

@@ -0,0 +1,9 @@
+geopyv_dev/__init__.py,sha256=zZ22CcRbt9vlLjmdfOQPTnTAvl0TCVpD6H0rhfSJcN4,354
+geopyv_dev/_geopyv_dev.cp39-win_amd64.pyd,sha256=v6DkvaQo_7HbHIkeH-42KPYJx2QziuUj2Xaw7rD_-uc,4067840
+geopyv_dev/plots.py,sha256=TIxO5gr5AzZyjl_qYNyk3pw9du8uKuPpNHWPDo5aVJA,11989
+geopyv_dev/wrappers.py,sha256=u3vsgrDd3Hc8MffLn8oKGdnBUlYEzNGqCgN92Vl9KhQ,1540
+geopyv_dev-0.1.0.dist-info/METADATA,sha256=VDAfBzOUQv3DGwJ1JnMwUAoj2Hyi_Ve4c3yq2ecNuE8,786
+geopyv_dev-0.1.0.dist-info/WHEEL,sha256=DJX_XFogDpLjEnUqFWUEworxKj63T7Pk_Z9glsI6giw,95
+geopyv_dev-0.1.0.dist-info/licenses/LICENSE,sha256=IwGE9guuL-ryRPEKi6wFPI_zOhg7zDZbTYuHbSt_SAk,35823
+geopyv_dev-0.1.0.dist-info/sboms/geopyv-dev-python.cyclonedx.json,sha256=cIqL2mcOySKIUE5QqA2x9fNQ9waz9PR469tECun1yuQ,178931
+geopyv_dev-0.1.0.dist-info/RECORD,,

geopyv_dev-0.1.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: maturin (1.13.1)
+Root-Is-Purelib: false
+Tag: cp39-cp39-win_amd64