Merge branch 'main' into implementation/stereonet-equal-area/seaborn

Author: github-actions[bot]

plots/column-stratigraphic/implementations/bokeh.py

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+""" pyplots.ai
+column-stratigraphic: Stratigraphic Column with Lithology Patterns
+Library: bokeh 3.9.0 | Python 3.14.3
+Quality: 89/100 | Created: 2026-03-15
+"""
+
+from bokeh.io import export_png
+from bokeh.models import ColumnDataSource, HoverTool, Label, Legend, LegendItem, Range1d, Span
+from bokeh.plotting import figure, output_file, save
+
+
+# Data: Synthetic sedimentary section with 10 layers (varied thicknesses)
+layers = [
+    {"top": 0, "bottom": 12, "lithology": "Sandstone", "formation": "Dakota Fm", "age": "Late Cretaceous"},
+    {"top": 12, "bottom": 38, "lithology": "Shale", "formation": "Mancos Fm", "age": "Late Cretaceous"},
+    {"top": 38, "bottom": 52, "lithology": "Limestone", "formation": "Niobrara Fm", "age": "Late Cretaceous"},
+    {"top": 52, "bottom": 60, "lithology": "Siltstone", "formation": "Pierre Fm", "age": "Late Cretaceous"},
+    {"top": 60, "bottom": 88, "lithology": "Sandstone", "formation": "Fox Hills Fm", "age": "Late Cretaceous"},
+    {"top": 88, "bottom": 112, "lithology": "Conglomerate", "formation": "Dawson Fm", "age": "Paleocene"},
+    {"top": 112, "bottom": 140, "lithology": "Shale", "formation": "Green River Fm", "age": "Eocene"},
+    {"top": 140, "bottom": 158, "lithology": "Limestone", "formation": "Leadville Fm", "age": "Eocene"},
+    {"top": 158, "bottom": 180, "lithology": "Sandstone", "formation": "Wasatch Fm", "age": "Eocene"},
+    {"top": 180, "bottom": 200, "lithology": "Siltstone", "formation": "Uinta Fm", "age": "Eocene"},
+]
+
+# Lithology style mapping: improved colorblind-safe palette
+# Sandstone: warm yellow, Siltstone: olive green (high contrast vs sandstone)
+lithology_styles = {
+    "Sandstone": {"color": "#F5DEB3", "hatch_pattern": ".", "hatch_color": "#8B7355"},
+    "Shale": {"color": "#A9A9A9", "hatch_pattern": "-", "hatch_color": "#4A4A4A"},
+    "Limestone": {"color": "#87CEEB", "hatch_pattern": "+", "hatch_color": "#2E5A88"},
+    "Siltstone": {"color": "#7B9971", "hatch_pattern": "/", "hatch_color": "#3B5335"},
+    "Conglomerate": {"color": "#E8923F", "hatch_pattern": "o", "hatch_color": "#6B3A00"},
+}
+
+# K-Pg boundary depth
+KPG_DEPTH = 88
+
+# Column geometry — wider for better canvas fill
+col_center = 0.55
+col_width = 1.1
+
+# Plot — tighter x_range for better horizontal utilization
+p = figure(
+    width=4800,
+    height=2700,
+    title="column-stratigraphic · bokeh · pyplots.ai",
+    y_axis_label="Depth (m)",
+    toolbar_location=None,
+    x_range=Range1d(-0.55, 1.85),
+    y_range=Range1d(210, -10),
+)
+
+# Draw each layer as a rectangle with hatch pattern
+legend_items_dict = {}
+for layer in layers:
+    source = ColumnDataSource(
+        data={
+            "x": [col_center],
+            "y": [(layer["top"] + layer["bottom"]) / 2],
+            "width": [col_width],
+            "height": [layer["bottom"] - layer["top"]],
+            "lithology": [layer["lithology"]],
+            "formation": [layer["formation"]],
+            "age": [layer["age"]],
+            "top_depth": [layer["top"]],
+            "bottom_depth": [layer["bottom"]],
+            "thickness": [layer["bottom"] - layer["top"]],
+        }
+    )
+
+    style = lithology_styles[layer["lithology"]]
+    renderer = p.rect(
+        x="x",
+        y="y",
+        width="width",
+        height="height",
+        source=source,
+        fill_color=style["color"],
+        line_color="#2C2C2C",
+        line_width=2,
+        hatch_pattern=style["hatch_pattern"],
+        hatch_color=style["hatch_color"],
+        hatch_alpha=0.7,
+        hatch_scale=16,
+        hatch_weight=2,
+    )
+
+    lith = layer["lithology"]
+    if lith not in legend_items_dict:
+        legend_items_dict[lith] = renderer
+
+    hover = HoverTool(
+        renderers=[renderer],
+        tooltips=[
+            ("Lithology", "@lithology"),
+            ("Formation", "@formation"),
+            ("Age", "@age"),
+            ("Top", "@top_depth{0.0} m"),
+            ("Bottom", "@bottom_depth{0.0} m"),
+            ("Thickness", "@thickness{0.0} m"),
+        ],
+    )
+    p.add_tools(hover)
+
+# Depth tick marks at each layer boundary for polished geological appearance
+boundary_depths = sorted({layer["top"] for layer in layers} | {layer["bottom"] for layer in layers})
+for depth in boundary_depths:
+    x_left = col_center - col_width / 2
+    p.line(x=[x_left - 0.04, x_left], y=[depth, depth], line_color="#555555", line_width=1.5, line_alpha=0.6)
+    # Small depth label at boundary
+    label = Label(
+        x=x_left - 0.06,
+        y=depth,
+        text=f"{depth:.0f}",
+        text_font_size="13pt",
+        text_align="right",
+        text_baseline="middle",
+        text_color="#777777",
+    )
+    p.add_layout(label)
+
+# K-Pg boundary emphasis — bold red dashed line with prominent annotation
+kpg_span = Span(location=KPG_DEPTH, dimension="width", line_color="#CC0000", line_width=5, line_dash="dashed")
+p.add_layout(kpg_span)
+
+kpg_label = Label(
+    x=col_center,
+    y=KPG_DEPTH,
+    text="K-Pg Boundary (~66 Ma)",
+    text_font_size="20pt",
+    text_font_style="bold",
+    text_color="#CC0000",
+    text_align="center",
+    text_baseline="bottom",
+    y_offset=10,
+    background_fill_color="white",
+    background_fill_alpha=0.8,
+)
+p.add_layout(kpg_label)
+
+# Formation labels on the right side — closer to column
+for layer in layers:
+    mid_y = (layer["top"] + layer["bottom"]) / 2
+    label = Label(
+        x=col_center + col_width / 2 + 0.04,
+        y=mid_y,
+        text=layer["formation"],
+        text_font_size="19pt",
+        text_font_style="bold",
+        text_align="left",
+        text_baseline="middle",
+        text_color="#2C2C2C",
+    )
+    p.add_layout(label)
+
+# Age labels on the left side with brackets
+age_groups = {}
+for layer in layers:
+    age = layer["age"]
+    if age not in age_groups:
+        age_groups[age] = {"top": layer["top"], "bottom": layer["bottom"]}
+    else:
+        age_groups[age]["bottom"] = max(age_groups[age]["bottom"], layer["bottom"])
+        age_groups[age]["top"] = min(age_groups[age]["top"], layer["top"])
+
+bracket_x = -0.12
+for age, bounds in age_groups.items():
+    mid_y = (bounds["top"] + bounds["bottom"]) / 2
+    label = Label(
+        x=bracket_x - 0.04,
+        y=mid_y,
+        text=age,
+        text_font_size="19pt",
+        text_align="right",
+        text_baseline="middle",
+        text_color="#2C2C2C",
+        text_font_style="italic",
+    )
+    p.add_layout(label)
+
+    # Bracket lines
+    p.line(x=[bracket_x, bracket_x], y=[bounds["top"] + 1, bounds["bottom"] - 1], line_color="#2C2C2C", line_width=2.5)
+    p.line(
+        x=[bracket_x - 0.025, bracket_x], y=[bounds["top"] + 1, bounds["top"] + 1], line_color="#2C2C2C", line_width=2.5
+    )
+    p.line(
+        x=[bracket_x - 0.025, bracket_x],
+        y=[bounds["bottom"] - 1, bounds["bottom"] - 1],
+        line_color="#2C2C2C",
+        line_width=2.5,
+    )
+
+# Legend — positioned adjacent to column on right side
+legend_items = [LegendItem(label=lith, renderers=[rend]) for lith, rend in legend_items_dict.items()]
+legend = Legend(
+    items=legend_items,
+    location="top_right",
+    label_text_font_size="20pt",
+    spacing=14,
+    padding=20,
+    margin=10,
+    background_fill_color="#F5F5F0",
+    background_fill_alpha=0.9,
+    border_line_color="#CCCCCC",
+    border_line_width=1,
+    glyph_height=32,
+    glyph_width=32,
+    title="Lithology",
+    title_text_font_size="22pt",
+    title_text_font_style="bold",
+)
+p.add_layout(legend, "right")
+
+# Typography hierarchy
+p.title.text_font_size = "36pt"
+p.title.text_color = "#1A1A1A"
+p.title.offset = 10
+p.yaxis.axis_label_text_font_size = "28pt"
+p.yaxis.axis_label_text_font_style = "bold"
+p.yaxis.axis_label_text_color = "#333333"
+p.yaxis.major_label_text_font_size = "22pt"
+p.yaxis.major_label_text_color = "#444444"
+
+# Visual refinement
+p.xaxis.visible = False
+p.xgrid.grid_line_color = None
+p.ygrid.grid_line_alpha = 0.12
+p.ygrid.grid_line_dash = [4, 4]
+p.ygrid.grid_line_color = "#999999"
+
+p.yaxis.minor_tick_line_color = None
+p.yaxis.major_tick_line_color = "#AAAAAA"
+p.yaxis.axis_line_color = "#888888"
+p.outline_line_color = None
+p.background_fill_color = "#FAFAF6"
+p.border_fill_color = "#FFFFFF"
+
+# Padding
+p.min_border_left = 100
+p.min_border_right = 40
+p.min_border_top = 60
+p.min_border_bottom = 60
+
+# Save
+export_png(p, filename="plot.png")
+output_file("plot.html", title="column-stratigraphic · bokeh · pyplots.ai")
+save(p)