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Move root experiment scripts into their papers' experiments/ folders

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Relocate the standalone Python scripts from the repo root into the
experiments/ folder of the paper each one belongs to:

  plane_depth_sequencing/experiments/
    plane_depth_sequencing.py, draw_quad_sequence.py,
    draw_quad_sequence_diagram.py, extract_sequence.py,
    plane_depth_sequencing_figure.py, quad_sequence_coloring_check.py
  colored_edge_flip_classes/experiments/   colored_edge_flip_class_survey.py
  colored_pentagon_contractions/experiments/ colored_pentagon_contractions.py
  plane_diamond_coloring/experiments/       plane_diamond_coloring.py

Each file that imports lib.* (still in the repo root) or the sibling
plane_depth_sequencing module gets a sys.path shim that prepends the
repo root (computed three levels up) and, where needed, its own dir.
Imports verified to resolve from a neutral working directory.

flip_symmetric_census.py is intentionally left in the root.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
This commit is contained in:
didericis
2026-05-22 10:40:39 -04:00
parent 1a71658349
commit ad3f95fa39
9 changed files with 480 additions and 1 deletions
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papers/plane_depth_sequencing/experiments/draw_quad_sequence_diagram.py
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"""Draw a labeled quadrilateral sequence diagram for the plane depth sequencing paper."""
import matplotlib.pyplot as plt
import matplotlib.patches as patches
from matplotlib.patches import FancyArrowPatch
import numpy as np
sequence_data = [
{"vertices": [-2, -1, 3, 7], "ordered": [-2, 7, -1, 3], "depths": [0, 1, 0, 1], "move": "Q_1", "type": "deep_diamond"},
{"vertices": [-1, 3, 4, 8], "ordered": [3, -1, 4, 8], "depths": [1, 0, 1, 2], "move": "Q_2^{AD}", "type": "s_quad"},
{"vertices": [2, 4, 5, 8], "ordered": [4, 2, 5, 8], "depths": [1, 0, 1, 2], "move": "Q_3^{AD}", "type": "s_quad"},
{"vertices": [-1, 2, 4, 6], "ordered": [4, 2, 6, -1], "depths": [1, 0, 1, 0], "move": "Q_4^{LA}", "type": "shallow_diamond"},
]
COLORS = {
"deep_diamond": "#B2DFDB",
"shallow_diamond": "#FFE0B2",
"s_quad": "#F8BBD0",
}
def draw_sequence_diagram(sequence_data: list[dict], output_path: str = "quad_sequence_diagram.png"):
"""Draw the full quadrilateral sequence diagram."""
fig, ax = plt.subplots(figsize=(16, 5.5))
step_width = 4.0
y_center = 1.0
x_positions = [i * step_width for i in range(len(sequence_data))]
# Store vertex positions for connecting matching vertices
quad_vertex_positions = []
for i, quad_data in enumerate(sequence_data):
x = x_positions[i]
quad_type = quad_data["type"]
ordered_verts = quad_data["ordered"]
depths = quad_data["depths"]
# Standard positions: top, right, bottom, left (or tweezers variant)
if quad_type == "s_quad":
# Tweezers shape: top, left-pinched-upper, right, left-pinched-lower
r = 0.45
pinch = 0.25
std_positions = [
(x, y_center + r), # e1: top
(x - r + pinch, y_center + r * 0.35), # a: left-upper
(x + r, y_center), # e2: right
(x - r + pinch, y_center - r * 0.35), # b: left-lower
]
else:
# Diamond shape: top, right, bottom, left
r = 0.45
std_positions = [
(x, y_center + r), # e1: top
(x + r, y_center), # a: right
(x, y_center - r), # e2: bottom
(x - r, y_center), # b: left
]
# Draw polygon
polygon = patches.Polygon(
std_positions,
closed=True,
facecolor=COLORS.get(quad_type, "#CCCCCC"),
edgecolor="black",
linewidth=1.5,
alpha=0.75,
)
ax.add_patch(polygon)
# Draw vertices and labels
vertex_positions = {}
for vert_idx, (vertex_id, (vx, vy), depth) in enumerate(zip(ordered_verts, std_positions, depths)):
# Draw vertex point
ax.plot(vx, vy, "ko", markersize=7, zorder=5)
vertex_positions[vertex_id] = (vx, vy)
# Draw vertex label below
ax.text(vx, vy - 0.2, str(vertex_id), ha="center", va="top", fontsize=8, fontweight="bold",
bbox=dict(boxstyle="round,pad=0.15", facecolor="lightyellow", alpha=0.9, edgecolor="none"))
# Draw quad label in center
center_x = np.mean([p[0] for p in std_positions])
center_y = np.mean([p[1] for p in std_positions])
ax.text(center_x, center_y, f"${quad_data['move']}$", ha="center", va="center",
fontsize=11, fontweight="bold",
bbox=dict(boxstyle="round,pad=0.3", facecolor="white", edgecolor="black", alpha=0.85))
# Draw depth labels on the left (only for first quad)
if i == 0:
unique_depths = sorted(set(depths))
for d in unique_depths:
label_y = y_center + 0.5 - d * 0.5
ax.text(x - 1.0, label_y, f"d={d}", ha="right", va="center", fontsize=9, style="italic")
quad_vertex_positions.append(vertex_positions)
# Draw arrows connecting matching vertices to next quad
if i < len(sequence_data) - 1:
next_quad_verts = set(sequence_data[i + 1]["vertices"])
for vertex_id, (vx, vy) in vertex_positions.items():
if vertex_id in next_quad_verts:
next_quad_data = sequence_data[i + 1]
next_x = x_positions[i + 1]
next_idx = next_quad_data["ordered"].index(vertex_id)
if next_quad_data["type"] == "s_quad":
r = 0.45
pinch = 0.25
next_std_positions = [
(next_x, y_center + r),
(next_x - r + pinch, y_center + r * 0.35),
(next_x + r, y_center),
(next_x - r + pinch, y_center - r * 0.35),
]
else:
r = 0.45
next_std_positions = [
(next_x, y_center + r),
(next_x + r, y_center),
(next_x, y_center - r),
(next_x - r, y_center),
]
next_vx, next_vy = next_std_positions[next_idx]
# Draw connecting arrow
arrow = FancyArrowPatch(
(vx, vy), (next_vx, next_vy),
arrowstyle="->", color="gray", linewidth=0.8, alpha=0.5, zorder=1,
connectionstyle="arc3,rad=0.15"
)
ax.add_patch(arrow)
# Set axis properties
ax.set_xlim(-1.8, x_positions[-1] + 1.2)
ax.set_ylim(-1.0, 2.2)
ax.set_aspect("equal")
ax.axis("off")
plt.tight_layout()
plt.savefig(output_path, dpi=150, bbox_inches="tight")
print(f"Saved diagram to {output_path}")
plt.show()
if __name__ == "__main__":
draw_sequence_diagram(sequence_data, "quad_sequence_diagram.png")