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'