vis/utils_data.py

import torch
import numpy as np
import plotly.graph_objects as go
from stl import mesh as stl_mesh
from matplotlib import cm


def _cm2px(cm, dpi):
    return int(cm / 2.54 * dpi)

def _pt2px(pt, dpi):
    return int(pt / 72 * dpi)

def _rgb_colorscale(cmap_name):
    cmap = cm.get_cmap(cmap_name) if isinstance(cmap_name, str) else cmap_name
    return [[i / 255, "rgb({},{},{})".format(*[int(c * 255) for c in cmap(i / 255)[:3]])] for i in range(256)]

def _alpha_colorscale(cmap_name, a_min, a_max):
    cmap = cm.get_cmap(cmap_name) if isinstance(cmap_name, str) else cmap_name
    scale = []
    for i in range(256):
        t = i / 255
        r, g, b, _ = cmap(t)
        a = a_min + (a_max - a_min) * t ** 5
        scale.append([t, f"rgba({int(r*255)},{int(g*255)},{int(b*255)},{a:.3f})"])
    return scale


def plot_2d(
    data, heatmap_width_cm=2., heatmap_height_cm=2., dpi=300, scale=1.0,
    use_colorbar=True, colorbar_thickness=24, text_font_size=7,
    ticklabel_font_size=5, show_x_ticks=True, show_x_ticklabels=True,
    show_y_ticks=True, show_y_ticklabels=True, x_unit=0.004, y_unit=0.004,
    x_ticks=[0, 250, 500], y_ticks=[0, 250, 500], boundary_linewidth=1,
    tick_width=1, x_label='x [μm]', y_label='y [μm]', cmap="Jet",
    ticklen=16, colorbar_min=None, colorbar_max=None, outer_margin_cm=0.2,
    colorbar_title=None,
):
    is_grid = data.ndim == 4 and data.shape[:2] == (2, 2)
    panels = data if is_grid else data[np.newaxis, np.newaxis]
    rows, cols = (2, 2) if is_grid else (1, 1)

    def cm2px(v): return v / 2.54 * dpi

    N = panels[0, 0].shape[0]
    if N > 1000:
        x_ticks = [0, 500, 1000]; y_ticks = [0, 500, 1000]
        heatmap_width_cm *= 2; heatmap_height_cm *= 2
        colorbar_thickness *= 2

    data_w = cm2px(heatmap_width_cm)
    data_h = cm2px(heatmap_height_cm)
    text_px = int(text_font_size / 72 * dpi * scale)
    tick_px = int(ticklabel_font_size / 72 * dpi * scale)
    pad = int(5 * scale)
    gap = pad * 5
    outer = cm2px(outer_margin_cm)
    cb_gap = pad * 4
    cb_tick_w = tick_px * 8

    ml = outer + boundary_linewidth + show_y_ticks * ticklen + show_y_ticklabels * tick_px + (1 if y_label else 0) * text_px + pad
    mr = outer + boundary_linewidth + pad + use_colorbar * (cb_gap + colorbar_thickness + cb_tick_w)
    mb = outer + boundary_linewidth + show_x_ticks * ticklen + show_x_ticklabels * tick_px + (1 if x_label else 0) * text_px * 3 + pad
    mt = outer + boundary_linewidth + pad

    fig_w = ml + mr + cols * data_w + (cols - 1) * gap
    fig_h = mt + mb + rows * data_h + (rows - 1) * gap
    grid_y0 = mb / fig_h
    grid_y1 = (mb + rows * data_h + (rows - 1) * gap) / fig_h

    vmin = float(colorbar_min if colorbar_min is not None else min(panels[r, c].min() for r in range(rows) for c in range(cols)))
    vmax = float(colorbar_max if colorbar_max is not None else max(panels[r, c].max() for r in range(rows) for c in range(cols)))

    border = dict(showline=True, linecolor='lightgray', linewidth=boundary_linewidth, mirror=True, fixedrange=True)

    def xname(i): return 'x' if i == 0 else f'x{i+1}'
    def yname(i): return 'y' if i == 0 else f'y{i+1}'

    def make_xaxis(domain, anchor, is_bottom):
        ax = dict(domain=domain, anchor=anchor, **border)
        if is_bottom:
            ax.update(
                ticks='outside' if show_x_ticks else '', ticklen=ticklen, tickwidth=tick_width,
                tickcolor='black', tickfont=dict(size=tick_px, color='black'),
                showticklabels=show_x_ticklabels,
                title=dict(text=x_label or '', font=dict(size=text_px, color='black'), standoff=tick_px + ticklen),
                tickmode='array', tickvals=x_ticks, ticktext=[f"{v * x_unit:.1f}" for v in x_ticks],
            )
        else:
            ax.update(ticks='', ticklen=0, showticklabels=False, title=dict(text=''), showgrid=False)
        return ax

    def make_yaxis(domain, anchor, is_left):
        ax = dict(domain=domain, anchor=anchor, **border)
        if is_left:
            ax.update(
                ticks='outside' if show_y_ticks else '', ticklen=ticklen, tickwidth=tick_width,
                tickcolor='black', tickfont=dict(size=tick_px, color='black'),
                showticklabels=show_y_ticklabels,
                title=dict(text=y_label or '', font=dict(size=text_px, color='black'), standoff=tick_px + ticklen),
                tickmode='array', tickvals=y_ticks, ticktext=[f"{v * y_unit:.1f}" for v in y_ticks],
            )
        else:
            ax.update(ticks='', ticklen=0, showticklabels=False, title=dict(text=''), showgrid=False)
        return ax

    fig = go.Figure()

    for r in range(rows):
        for c in range(cols):
            idx = r * cols + c
            x0 = (ml + c * (data_w + gap)) / fig_w
            x1 = (ml + c * (data_w + gap) + data_w) / fig_w
            y0 = (mb + (rows - 1 - r) * (data_h + gap)) / fig_h
            y1 = (mb + (rows - 1 - r) * (data_h + gap) + data_h) / fig_h

            fig.add_trace(go.Heatmap(
                z=panels[r, c], colorscale=cmap, showscale=False,
                zmin=vmin, zmax=vmax, xaxis=xname(idx), yaxis=yname(idx),
            ))
            fig.update_layout(**{
                f'xaxis{"" if idx == 0 else idx+1}': make_xaxis([x0, x1], anchor=yname(idx), is_bottom=(r == rows - 1)),
                f'yaxis{"" if idx == 0 else idx+1}': make_yaxis([y0, y1], anchor=xname(idx), is_left=(c == 0)),
            })

    if use_colorbar:
        n_cb = 256
        cb_idx = rows * cols
        cb_data = np.linspace(vmin, vmax, n_cb).reshape(n_cb, 1)
        cb_x0 = (ml + cols * data_w + (cols - 1) * gap + cb_gap) / fig_w
        cb_x1 = cb_x0 + colorbar_thickness / fig_w
        cb_tickvals = np.linspace(0, n_cb - 1, 5)
        cb_ticktext = [f"{v:.2f}" for v in np.linspace(vmin, vmax, 5)]

        fig.add_trace(go.Heatmap(
            z=cb_data, colorscale=cmap, showscale=False,
            zmin=vmin, zmax=vmax, xaxis=xname(cb_idx), yaxis=yname(cb_idx),
        ))
        fig.update_layout(**{
            f'xaxis{"" if cb_idx == 0 else cb_idx+1}': dict(
                domain=[cb_x0, cb_x1], anchor=yname(cb_idx), visible=False, fixedrange=True,
                showline=True, linecolor='black', linewidth=boundary_linewidth, mirror=True,
            ),
            f'yaxis{"" if cb_idx == 0 else cb_idx+1}': dict(
                domain=[grid_y0, grid_y1], anchor=xname(cb_idx), side='right', fixedrange=True,
                tickmode='array', tickvals=cb_tickvals, ticktext=cb_ticktext,
                tickfont=dict(size=tick_px, color='black'), tickcolor='black',
                tickwidth=tick_width, ticklen=ticklen // 2,
                showline=True, linecolor='black', linewidth=boundary_linewidth,
                showgrid=False, mirror=False,
                title=dict(text=colorbar_title or '', font=dict(size=text_px, color='black'), standoff=tick_px + ticklen // 2),
            ),
        })

    fig.update_layout(
        autosize=False, width=int(fig_w), height=int(fig_h),
        margin=dict(l=0, r=0, t=0, b=0),
        paper_bgcolor='rgba(0,0,0,0)', plot_bgcolor='rgba(0,0,0,0)',
        font=dict(family="Arial, sans-serif", size=text_px, color='black'),
    )
    return fig


def vis_mask(data, cmap='gray'):
    return plot_2d(torch.flip(data, dims=(0,)), cmap=cmap, use_colorbar=False)

def vis_sc(data, cmap='jet'):
    return plot_2d(torch.flip(data, dims=(2,)), cmap=cmap, use_colorbar=True, colorbar_title='Amplitude [-]')


def plot_tensor_slices(
    data, slice_indices=None, opacity=None, colorscale="jet",
    vmin=None, vmax=None, alpha_at_cmin=0.1, alpha_at_cmax=1,
    use_colorbar=True, colorbar_thickness=20, colorbar_title=None,
    colorbar_title_side="right", use_dummy_colorbar=True, colorbar_length=0.6,
    colorbar_font="Arial, sans-serif", colorbar_fontsize=7, colorbar_tick_fontsize=5,
    colorbar_nticks=None, show_axes=True, isotropic_view=True,
    camera_distance=1.5, fig_width_cm=6.0, fig_height_cm=4.0, dpi=300, png_path=None,
):
    if data.ndim != 3:
        raise ValueError("`data` must be a 3-D array (Nx, Ny, Nz).")

    N = data.shape[0]
    sf = 2 if N >= 513 else 1
    s, e = N // 2 - 128 * sf, N // 2 + 128 * sf
    data = data[s:e, s:e, :]
    fig_width_cm *= sf; fig_height_cm *= sf
    camera_distance /= sf
    colorbar_thickness = int(colorbar_thickness * sf)

    Nx, Ny, Nz = data.shape
    ix, iy, iz = map(int, slice_indices) if slice_indices else (Nx // 2, Ny // 2, Nz // 2)
    vmin = float(np.nanmin(data)) if vmin is None else float(vmin)
    vmax = float(np.nanmax(data)) if vmax is None else float(vmax)

    custom_scale = _alpha_colorscale(colorscale, alpha_at_cmin, alpha_at_cmax)
    dummy_scale = _rgb_colorscale(colorscale)

    x, y, z = np.arange(Nx), np.arange(Ny), np.arange(Nz)

    def cb_cfg():
        cb = dict(
            lenmode="fraction", len=colorbar_length, thickness=colorbar_thickness,
            x=0.85, y=0.45,
            tickfont=dict(family=colorbar_font, size=_pt2px(colorbar_tick_fontsize, dpi), color="black"),
            tickwidth=1, tickcolor="black", outlinewidth=1, outlinecolor="black",
            nticks=colorbar_nticks or 5,
        )
        if colorbar_title is not None:
            cb["title"] = dict(
                text=colorbar_title, side=colorbar_title_side,
                font=dict(family=colorbar_font, size=_pt2px(colorbar_fontsize, dpi), color="black"),
            )
        return cb

    surf_kw = dict(
        colorscale=custom_scale, cmin=vmin, cmax=vmax,
        lighting=dict(ambient=1.0), opacity=1.0 if opacity is None else opacity,
    )

    surfaces = []
    for k_z in range(0, Nz, 4):
        show_scale = use_colorbar and not use_dummy_colorbar and len(surfaces) == 0
        surfaces.append(go.Surface(
            x=np.tile(x[:, None], (1, Ny)), y=np.tile(y[None, :], (Nx, 1)),
            z=np.full((Nx, Ny), k_z), surfacecolor=data[:, :, k_z],
            showscale=show_scale, colorbar=cb_cfg() if show_scale else None,
            name=f"XY @ z={k_z}", **surf_kw,
        ))

    surfaces.append(go.Surface(
        x=np.full((Ny, Nz), Nx - 1), y=np.tile(y[:, None], (1, Nz)),
        z=np.tile(z[None, :], (Ny, 1)), surfacecolor=data[Nx - 1, :, :],
        showscale=False, name=f"YZ @ x={Nx-1}", **surf_kw,
    ))
    surfaces.append(go.Surface(
        x=np.tile(x[:, None], (1, Nz)), y=np.full((Nx, Nz), Ny - 1),
        z=np.tile(z[None, :], (Nx, 1)), surfacecolor=data[:, Ny - 1, :],
        showscale=False, name=f"XZ @ y={Ny-1}", **surf_kw,
    ))

    fig = go.Figure(data=surfaces)

    if use_colorbar and use_dummy_colorbar:
        fig.add_trace(go.Scatter3d(
            x=[0.0, 0.0], y=[0.0, 0.0], z=[0.0, 0.0],
            mode="markers", showlegend=False, hoverinfo="skip",
            marker=dict(
                size=0.001, opacity=0.0, color=[vmin, vmax],
                cmin=vmin, cmax=vmax, colorscale=dummy_scale,
                showscale=True, colorbar=cb_cfg(),
            ),
        ))

    bbox_x = [0, Nx-1, Nx-1, 0, 0, None, 0, Nx-1, Nx-1, 0, 0, None, 0, 0, None, Nx-1, Nx-1, None, Nx-1, Nx-1, None, 0, 0]
    bbox_y = [0, 0, Ny-1, Ny-1, 0, None, 0, 0, Ny-1, Ny-1, 0, None, 0, 0, None, 0, 0, None, Ny-1, Ny-1, None, Ny-1, Ny-1]
    bbox_z = [0, 0, 0, 0, 0, None, Nz-1, Nz-1, Nz-1, Nz-1, Nz-1, None, 0, Nz-1, None, 0, Nz-1, None, 0, Nz-1, None, 0, Nz-1]
    fig.add_trace(go.Scatter3d(
        x=bbox_x, y=bbox_y, z=bbox_z, mode="lines",
        line=dict(color="black", width=1.5), showlegend=False,
    ))

    tick_px = int(2.5 / 72 * dpi)
    unit = 0.004
    sz = 1 if Nx < 257 else 2
    axis_style = dict(visible=show_axes, showbackground=False, mirror=True, linecolor="black", linewidth=0, tickwidth=0, tickcolor="black")
    title_font = dict(family="Arial, sans-serif", size=tick_px * 1.5, color="black")
    tick_font = dict(family="Arial, sans-serif", size=tick_px, color="black")

    centre = np.array([Nx / 2, Ny / 2, Nz / 2])
    diag_len = np.linalg.norm([Nx, Ny, Nz]) / 2

    if isotropic_view:
        eye_dir = np.array([1.0, 1.0, 1.7 * (2.5 if sf == 2 else 1.0)])
        eye_pos = centre + camera_distance * diag_len * eye_dir / np.linalg.norm(eye_dir) / 1.1
    else:
        eye_pos = centre + camera_distance * np.array([0.0, 0.0, diag_len])

    fig.update_layout(
        scene=dict(
            xaxis=dict(**axis_style, title=dict(text="x", font=title_font), tickfont=tick_font,
                       tickmode="array", tickvals=[0, Nx//2, Nx-1],
                       ticktext=[f"{abs(sz - v * unit):.1f}" for v in [0, Nx//2, Nx-1]]),
            yaxis=dict(**axis_style, title=dict(text="y", font=title_font), tickfont=tick_font,
                       tickmode="array", tickvals=[0, Ny//2, Ny-1],
                       ticktext=[f"{abs(sz - v * unit):.1f}" for v in [0, Ny//2, Ny-1]]),
            zaxis=dict(**axis_style, title=dict(text="z", font=title_font), tickfont=tick_font,
                       tickmode="array", tickvals=[Nz-1], ticktext=[f"{abs(Nz * unit):.2f}"]),
            aspectmode="data",
            camera=dict(eye=dict(x=float(eye_pos[0]*0.01), y=float(eye_pos[1]*0.01), z=float(eye_pos[2]*0.01))),
        ),
        width=_cm2px(fig_width_cm, dpi), height=_cm2px(fig_height_cm, dpi),
        paper_bgcolor="rgba(0,0,0,0)",
        legend=dict(orientation="h", yanchor="bottom", y=1.02, xanchor="right", x=1),
    )

    if png_path is not None:
        fig.write_image(png_path, width=_cm2px(fig_width_cm, dpi), height=_cm2px(fig_height_cm, dpi), scale=1.0)

    return fig


def vis_field(data, cmap="jet", colorbar_title=None):
    data = data.permute(2, 1, 0).flip(dims=(0, 2))
    return plot_tensor_slices(data, colorscale=cmap, colorbar_title=colorbar_title)


def _make_ground_plane(xmin, xmax, ymin, ymax, z0=0.0, color="#1653D0", grid_color="black", grid_size=10):
    return go.Surface(
        x=[[xmin, xmax]] * 2, y=[[ymin, ymin], [ymax, ymax]], z=[[z0, z0]] * 2,
        showscale=False, colorscale=[[0, color], [1, color]],
        contours=dict(
            x=dict(show=True, color=grid_color, start=xmin, end=xmax, size=(xmax - xmin) / grid_size, width=16),
            y=dict(show=True, color=grid_color, start=ymin, end=ymax, size=(ymax - ymin) / grid_size, width=16),
            z=dict(show=False),
        ),
    )


def plot_stl(
    stl_path, z_th=0.5, scale_mode="auto", isotropic_view=True,
    camera_distance=0.9, below_color="rgba(0,0,0,0)", above_color="#86CDFF",
    flat_shading=False, ambient=0.20, diffuse=0.70, specular=0.45,
    roughness=0.35, fresnel=0.06, light_xyz=None, width=800, height=600, margin=0,
):
    tri = stl_mesh.Mesh.from_file(str(stl_path)).vectors
    vertices, reindex = np.unique(tri.reshape(-1, 3), axis=0, return_inverse=True)
    i, j, k = reindex.reshape(-1, 3).T

    if scale_mode == "auto":
        diag_len = np.linalg.norm(np.ptp(vertices, axis=0))
        vertices = vertices / diag_len
    elif isinstance(scale_mode, (int, float)):
        vertices = vertices * float(scale_mode)

    vmin, vmax = vertices.min(0), vertices.max(0)
    center, diag_vec = (vmin + vmax) / 2, vmax - vmin
    diag_len = np.linalg.norm(diag_vec)

    z_centroids = tri.mean(axis=1)[:, 2]
    if scale_mode == "auto":
        z_centroids = z_centroids / diag_len
    face_colors = np.where(z_centroids < z_th, below_color, above_color)

    light_pos = light_xyz or (center + 2 * diag_vec)
    mesh3d = go.Mesh3d(
        x=vertices[:, 0], y=vertices[:, 1], z=vertices[:, 2],
        i=i, j=j, k=k, facecolor=face_colors, flatshading=flat_shading,
        lighting=dict(ambient=ambient, diffuse=diffuse, specular=specular, roughness=roughness, fresnel=fresnel),
        lightposition=dict(x=light_pos[0], y=light_pos[1], z=light_pos[2]),
        showscale=False, name="",
    )

    p = 0.05 * vmax[0]
    ground = _make_ground_plane(p, vmax[0] - p, p, vmax[1] - p, z0=0.003, color="rgba(200,200,255,1)", grid_color="black")

    eye_pos = center + camera_distance * diag_len * (
        np.array([1.5, -2, 1.7]) / 4 * 5 if isotropic_view else np.array([0, 0, 1])
    )

    fig = go.Figure(mesh3d)
    fig.add_trace(ground)
    fig.update_layout(
        width=width, height=height,
        margin=dict(l=margin, r=margin, t=margin, b=margin),
        paper_bgcolor="rgba(0,0,0,0)",
        scene=dict(
            aspectmode="data",
            camera=dict(eye=dict(x=eye_pos[0], y=eye_pos[1], z=eye_pos[2])),
            xaxis=dict(visible=False), yaxis=dict(visible=False), zaxis=dict(visible=False),
        ),
    )
    return fig


_default_layout = [
    {'row': 1, 'col': 1, 'title': 'Photomask (M)'},
    {'row': 1, 'col': 2, 'title': 'Diffracted near field (E)'},
    {'row': 2, 'col': 1, 'title': 'Photoacid (h)'},
    {'row': 2, 'col': 2, 'title': 'Deprotection image (m)'},
    {'row': 3, 'col': 1, 'title': 'Development rate (R)'},
    {'row': 3, 'col': 2, 'title': 'Development time (T)'},
]

def save_html(figures, filepath, title="Dashboard", layout=_default_layout, cols=2):
    import plotly.io as pio

    html_parts = [pio.to_html(fig, full_html=False, include_plotlyjs=(i == 0)) for i, fig in enumerate(figures)]

    items_html = ""
    for i, part in enumerate(html_parts):
        L = layout[i] if layout and i < len(layout) else {}
        row, col = L.get("row", "auto"), L.get("col", "auto")
        rowspan, colspan = L.get("rowspan", 1), L.get("colspan", 1)
        fig_title = L.get("title", "")
        style = f"grid-row: {row} / span {rowspan}; grid-column: {col} / span {colspan};"
        title_html = f'<div class="fig-title">{fig_title}</div>' if fig_title else ""
        items_html += f'<div class="fig-item" style="{style}">{title_html}<div class="fig-inner">{part}</div></div>\n'

    full_html = f"""<!DOCTYPE html>
<html>
<head>
  <meta charset="utf-8">
  <title>{title}</title>
  <style>
    body {{ font-family: Arial, sans-serif; margin: 20px; background: #f5f5f5; }}
    h1 {{ margin-bottom: 20px; }}
    .grid-container {{ display: grid; grid-template-columns: repeat({cols}, 1fr); gap: 16px; }}
    .fig-item {{ background: white; border-radius: 8px; padding: 12px; box-shadow: 0 2px 8px rgba(0,0,0,0.1); }}
    .fig-title {{ font-size: 1em; font-weight: bold; color: #333; margin-bottom: 8px; padding-bottom: 6px; border-bottom: 2px solid #e0e0e0; }}
    .fig-inner {{ width: 100%; }}
  </style>
</head>
<body>
  <h1>{title}</h1>
  <div class="grid-container">{items_html}</div>
</body>
</html>"""

    with open(filepath, "w", encoding="utf-8") as f:
        f.write(full_html)
    print(f"Saved → {filepath}")