refactoring the graph visualizer

bump version

format

format
This commit is contained in:
ArnoChen
2025-02-03 22:08:25 +08:00
parent c07b5522fe
commit 460a2cda02
6 changed files with 1340 additions and 666 deletions

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"""
3D GraphML Viewer
Author: LoLLMs
Description: An interactive 3D GraphML viewer using PyQt5 and pyqtgraph
Version: 2.2
"""
from pathlib import Path
from typing import Optional, Tuple, Dict, List, Any
import pipmaster as pm
# Install all required dependencies
REQUIRED_PACKAGES = [
"PyQt5",
"pyqtgraph",
"numpy",
"PyOpenGL",
"PyOpenGL_accelerate",
"networkx",
"matplotlib",
"python-louvain",
"ascii_colors",
]
def setup_dependencies():
"""
Ensure all required packages are installed
"""
for package in REQUIRED_PACKAGES:
if not pm.is_installed(package):
print(f"Installing {package}...")
pm.install(package)
# Install dependencies
setup_dependencies()
import networkx as nx
import numpy as np
import matplotlib.pyplot as plt
import community
from PyQt5.QtWidgets import (
QApplication,
QMainWindow,
QWidget,
QVBoxLayout,
QHBoxLayout,
QPushButton,
QFileDialog,
QLabel,
QMessageBox,
QSpinBox,
QComboBox,
QCheckBox,
QTableWidget,
QTableWidgetItem,
QSplitter,
QDockWidget,
QTextEdit,
)
from PyQt5.QtCore import Qt
import pyqtgraph.opengl as gl
from ascii_colors import trace_exception
class Point:
"""Simple point class to handle coordinates"""
def __init__(self, x: float, y: float):
self.x = x
self.y = y
class NodeState:
"""Data class for node visual state"""
NORMAL_SCALE = 1.0
HOVER_SCALE = 1.2
SELECTED_SCALE = 1.3
NORMAL_OPACITY = 0.8
HOVER_OPACITY = 1.0
SELECTED_OPACITY = 1.0
# Increase base node size (was 0.05)
BASE_SIZE = 0.2
SELECTED_COLOR = (1.0, 1.0, 0.0, 1.0)
HOVER_COLOR = (1.0, 0.8, 0.0, 1.0)
class Node3D:
"""Class representing a 3D node in the graph"""
def __init__(
self,
position: np.ndarray,
color: Tuple[float, float, float, float],
label: str,
node_type: str,
size: float,
):
self.position = position
self.base_color = color
self.color = color
self.label = label
self.node_type = node_type
self.size = size
self.mesh_item = None
self.label_item = None
self.is_highlighted = False
self.is_selected = False
def highlight(self):
"""Highlight the node"""
if not self.is_highlighted and not self.is_selected:
self.color = NodeState.HOVER_COLOR
self.update_appearance(NodeState.HOVER_SCALE)
self.is_highlighted = True
def unhighlight(self):
"""Remove highlight from node"""
if self.is_highlighted and not self.is_selected:
self.color = self.base_color
self.update_appearance(NodeState.NORMAL_SCALE)
self.is_highlighted = False
def select(self):
"""Select the node"""
self.is_selected = True
self.color = NodeState.SELECTED_COLOR
self.update_appearance(NodeState.SELECTED_SCALE)
def deselect(self):
"""Deselect the node"""
self.is_selected = False
self.color = self.base_color
self.update_appearance(NodeState.NORMAL_SCALE)
def update_appearance(self, scale: float = 1.0):
"""Update node visual appearance"""
if self.mesh_item:
self.mesh_item.setData(
color=np.array([self.color]), size=np.array([self.size * scale * 5])
)
class NodeDetailsWidget(QWidget):
"""Widget to display node details"""
def __init__(self, parent=None):
super().__init__(parent)
self.init_ui()
def init_ui(self):
"""Initialize the UI"""
layout = QVBoxLayout(self)
# Properties text edit
self.properties = QTextEdit()
self.properties.setReadOnly(True)
layout.addWidget(QLabel("Properties:"))
layout.addWidget(self.properties)
# Connections table
self.connections = QTableWidget()
self.connections.setColumnCount(3)
self.connections.setHorizontalHeaderLabels(
["Connected Node", "Relationship", "Direction"]
)
layout.addWidget(QLabel("Connections:"))
layout.addWidget(self.connections)
def update_node_info(self, node_data: Dict, connections: Dict):
"""Update the display with node information"""
# Update properties
properties_text = "Node Properties:\n"
for key, value in node_data.items():
properties_text += f"{key}: {value}\n"
self.properties.setText(properties_text)
# Update connections
self.connections.setRowCount(len(connections))
for idx, (neighbor, edge_data) in enumerate(connections.items()):
self.connections.setItem(idx, 0, QTableWidgetItem(str(neighbor)))
self.connections.setItem(
idx, 1, QTableWidgetItem(edge_data.get("relationship", "unknown"))
)
self.connections.setItem(idx, 2, QTableWidgetItem("outgoing"))
class GraphMLViewer3D(QMainWindow):
"""Main window class for 3D GraphML visualization"""
def __init__(self):
super().__init__()
self.graph: Optional[nx.Graph] = None
self.nodes: Dict[str, Node3D] = {}
self.edges: List[gl.GLLinePlotItem] = []
self.edge_labels: List[gl.GLTextItem] = []
self.selected_node = None
self.communities = None
self.community_colors = None
self.mouse_pos_last = None
self.mouse_buttons_pressed = set()
self.distance = 20 # Initial camera distance
self.center = np.array([0, 0, 0]) # View center point
self.elevation = 30 # Initial camera elevation
self.azimuth = 45 # Initial camera azimuth
self.init_ui()
def init_ui(self):
"""Initialize the user interface"""
self.setWindowTitle("3D GraphML Viewer")
self.setGeometry(100, 100, 1600, 900)
# Create main splitter
self.main_splitter = QSplitter(Qt.Horizontal)
self.setCentralWidget(self.main_splitter)
# Create left panel for 3D view
left_widget = QWidget()
left_layout = QVBoxLayout(left_widget)
# Create controls
self.create_toolbar(left_layout)
# Create 3D view
self.view = gl.GLViewWidget()
self.view.setMouseTracking(True)
# Connect mouse events
self.view.mousePressEvent = self.on_mouse_press
self.view.mouseMoveEvent = self.on_mouse_move
left_layout.addWidget(self.view)
self.main_splitter.addWidget(left_widget)
# Create details widget
self.details = NodeDetailsWidget()
details_dock = QDockWidget("Node Details", self)
details_dock.setWidget(self.details)
self.addDockWidget(Qt.RightDockWidgetArea, details_dock)
# Add status bar
self.statusBar().showMessage("Ready")
# Add initial grid
grid = gl.GLGridItem()
grid.setSize(x=20, y=20, z=20)
grid.setSpacing(x=1, y=1, z=1)
self.view.addItem(grid)
# Set initial camera position
self.view.setCameraPosition(
distance=self.distance, elevation=self.elevation, azimuth=self.azimuth
)
# Connect all mouse events
self.view.mousePressEvent = self.on_mouse_press
self.view.mouseReleaseEvent = self.on_mouse_release
self.view.mouseMoveEvent = self.on_mouse_move
self.view.wheelEvent = self.on_mouse_wheel
def calculate_node_sizes(self) -> Dict[str, float]:
"""Calculate node sizes based on number of connections"""
if not self.graph:
return {}
# Get degree (number of connections) for each node
degrees = dict(self.graph.degree())
# Calculate size scaling
max_degree = max(degrees.values())
min_degree = min(degrees.values())
# Normalize sizes between 0.5 and 2.0
sizes = {}
for node, degree in degrees.items():
if max_degree == min_degree:
sizes[node] = 1.0
else:
# Normalize and scale size
normalized = (degree - min_degree) / (max_degree - min_degree)
sizes[node] = 0.5 + normalized * 1.5
return sizes
def create_toolbar(self, layout: QVBoxLayout):
"""Create the toolbar with controls"""
toolbar = QHBoxLayout()
# Load button
load_btn = QPushButton("Load GraphML")
load_btn.clicked.connect(self.load_graphml)
toolbar.addWidget(load_btn)
# Reset view button
reset_btn = QPushButton("Reset View")
reset_btn.clicked.connect(lambda: self.view.setCameraPosition(distance=20))
toolbar.addWidget(reset_btn)
# Layout selector
self.layout_combo = QComboBox()
self.layout_combo.addItems(["Spring", "Circular", "Shell", "Random"])
self.layout_combo.currentTextChanged.connect(self.refresh_layout)
toolbar.addWidget(QLabel("Layout:"))
toolbar.addWidget(self.layout_combo)
# Node size control
self.node_size = QSpinBox()
self.node_size.setRange(1, 100)
self.node_size.setValue(20)
self.node_size.valueChanged.connect(self.refresh_layout)
toolbar.addWidget(QLabel("Node Size:"))
toolbar.addWidget(self.node_size)
# Show labels checkbox
self.show_labels = QCheckBox("Show Labels")
self.show_labels.setChecked(True)
self.show_labels.stateChanged.connect(self.refresh_layout)
toolbar.addWidget(self.show_labels)
layout.addLayout(toolbar)
# Reset view button
reset_btn = QPushButton("Reset View")
reset_btn.clicked.connect(self.reset_view) # Use the new reset_view method
toolbar.addWidget(reset_btn)
def load_graphml(self) -> None:
"""Load and visualize a GraphML file"""
try:
file_path, _ = QFileDialog.getOpenFileName(
self, "Open GraphML file", "", "GraphML files (*.graphml)"
)
if file_path:
self.graph = nx.read_graphml(Path(file_path))
self.refresh_layout()
self.statusBar().showMessage(f"Loaded: {file_path}")
except Exception as e:
trace_exception(e)
QMessageBox.critical(self, "Error", f"Error loading file: {str(e)}")
def calculate_layout(self) -> Dict[str, np.ndarray]:
"""Calculate node positions based on selected layout"""
layout_type = self.layout_combo.currentText().lower()
# Detect communities for coloring
self.communities = community.best_partition(self.graph)
num_communities = len(set(self.communities.values()))
self.community_colors = plt.cm.rainbow(np.linspace(0, 1, num_communities))
if layout_type == "spring":
pos = nx.spring_layout(
self.graph, dim=3, k=2.0, iterations=100, weight=None
)
elif layout_type == "circular":
pos_2d = nx.circular_layout(self.graph)
pos = {node: np.array([x, y, 0.0]) for node, (x, y) in pos_2d.items()}
elif layout_type == "shell":
comm_lists = [[] for _ in range(num_communities)]
for node, comm in self.communities.items():
comm_lists[comm].append(node)
pos_2d = nx.shell_layout(self.graph, comm_lists)
pos = {node: np.array([x, y, 0.0]) for node, (x, y) in pos_2d.items()}
else: # random
pos = {node: np.random.rand(3) * 2 - 1 for node in self.graph.nodes()}
# Scale positions
positions = np.array(list(pos.values()))
if len(positions) > 0:
scale = 10.0 / max(1.0, np.max(np.abs(positions)))
return {node: coords * scale for node, coords in pos.items()}
return pos
def get_node_color(self, node_id: str) -> Tuple[float, float, float, float]:
"""Get RGBA color based on community"""
if hasattr(self, "communities") and node_id in self.communities:
comm_id = self.communities[node_id]
color = self.community_colors[comm_id]
return tuple(color)
return (0.5, 0.5, 0.5, 0.8)
def create_node(self, node_id: str, position: np.ndarray, node_type: str) -> Node3D:
"""Create a 3D node with interaction capabilities"""
color = self.get_node_color(node_id)
# Get size multiplier based on connections
size_multiplier = self.node_sizes.get(node_id, 1.0)
size = NodeState.BASE_SIZE * self.node_size.value() / 50.0 * size_multiplier
node = Node3D(position, color, str(node_id), node_type, size)
node.mesh_item = gl.GLScatterPlotItem(
pos=np.array([position]),
size=np.array([size * 8]),
color=np.array([color]),
pxMode=False,
)
# Enable picking and set node ID
node.mesh_item.setGLOptions("translucent")
node.mesh_item.node_id = node_id
if self.show_labels.isChecked():
node.label_item = gl.GLTextItem(
pos=position,
text=str(node_id),
color=(1, 1, 1, 1),
)
return node
def mapToView(self, pos) -> Point:
"""Convert screen coordinates to world coordinates"""
# Get the viewport size
width = self.view.width()
height = self.view.height()
# Normalize coordinates
x = (pos.x() / width - 0.5) * 20 # Scale factor of 20 matches the grid size
y = -(pos.y() / height - 0.5) * 20
return Point(x, y)
def on_mouse_move(self, event):
"""Handle mouse movement for pan, rotate and hover"""
if self.mouse_pos_last is None:
self.mouse_pos_last = event.pos()
return
pos = event.pos()
dx = pos.x() - self.mouse_pos_last.x()
dy = pos.y() - self.mouse_pos_last.y()
# Handle right button drag for panning
if Qt.RightButton in self.mouse_buttons_pressed:
# Scale the pan amount based on view distance
scale = self.distance / 1000.0
# Calculate pan in view coordinates
right = np.cross([0, 0, 1], self.view.cameraPosition())
right = right / np.linalg.norm(right)
up = np.cross(self.view.cameraPosition(), right)
up = up / np.linalg.norm(up)
pan = -right * dx * scale + up * dy * scale
self.center += pan
self.view.pan(dx, dy, 0)
# Handle middle button drag for rotation
elif Qt.MiddleButton in self.mouse_buttons_pressed:
self.azimuth += dx * 0.5 # Adjust rotation speed as needed
self.elevation -= dy * 0.5
# Clamp elevation to prevent gimbal lock
self.elevation = np.clip(self.elevation, -89, 89)
self.view.setCameraPosition(
distance=self.distance, elevation=self.elevation, azimuth=self.azimuth
)
# Handle hover events when no buttons are pressed
elif not self.mouse_buttons_pressed:
# Get the mouse position in world coordinates
mouse_pos = self.mapToView(pos)
# Check for hover
min_dist = float("inf")
hovered_node = None
for node_id, node in self.nodes.items():
# Calculate distance to mouse in world coordinates
dx = mouse_pos.x - node.position[0]
dy = mouse_pos.y - node.position[1]
dist = np.sqrt(dx * dx + dy * dy)
if dist < min_dist and dist < 0.5: # Adjust threshold as needed
min_dist = dist
hovered_node = node_id
# Update hover states
for node_id, node in self.nodes.items():
if node_id == hovered_node:
node.highlight()
self.statusBar().showMessage(f"Node: {node_id} ({node.node_type})")
else:
if not node.is_selected:
node.unhighlight()
self.mouse_pos_last = pos
def on_mouse_press(self, event):
"""Handle mouse press events"""
self.mouse_pos_last = event.pos()
self.mouse_buttons_pressed.add(event.button())
# Handle left click for node selection
if event.button() == Qt.LeftButton:
pos = event.pos()
mouse_pos = self.mapToView(pos)
# Find closest node
min_dist = float("inf")
clicked_node = None
for node_id, node in self.nodes.items():
dx = mouse_pos.x - node.position[0]
dy = mouse_pos.y - node.position[1]
dist = np.sqrt(dx * dx + dy * dy)
if dist < min_dist and dist < 0.5: # Adjust threshold as needed
min_dist = dist
clicked_node = node_id
# Handle selection
if clicked_node:
if self.selected_node and self.selected_node in self.nodes:
self.nodes[self.selected_node].deselect()
self.nodes[clicked_node].select()
self.selected_node = clicked_node
if self.graph:
self.details.update_node_info(
self.graph.nodes[clicked_node], self.graph[clicked_node]
)
def on_mouse_release(self, event):
"""Handle mouse release events"""
self.mouse_buttons_pressed.discard(event.button())
self.mouse_pos_last = None
def on_mouse_wheel(self, event):
"""Handle mouse wheel for zooming"""
delta = event.angleDelta().y()
# Adjust zoom speed based on current distance
zoom_speed = self.distance / 100.0
# Update distance with limits
self.distance -= delta * zoom_speed
self.distance = np.clip(self.distance, 1.0, 100.0)
self.view.setCameraPosition(
distance=self.distance, elevation=self.elevation, azimuth=self.azimuth
)
def reset_view(self):
"""Reset camera to default position"""
self.distance = 20
self.elevation = 30
self.azimuth = 45
self.center = np.array([0, 0, 0])
self.view.setCameraPosition(
distance=self.distance, elevation=self.elevation, azimuth=self.azimuth
)
def create_edge(
self,
start_pos: np.ndarray,
end_pos: np.ndarray,
color: Tuple[float, float, float, float] = (0.3, 0.3, 0.3, 0.2),
) -> gl.GLLinePlotItem:
"""Create a 3D edge between nodes"""
return gl.GLLinePlotItem(
pos=np.array([start_pos, end_pos]),
color=color,
width=1,
antialias=True,
mode="lines",
)
def handle_node_hover(self, event: Any, node_id: str) -> None:
"""Handle node hover events"""
if node_id in self.nodes:
node = self.nodes[node_id]
if event.isEnter():
node.highlight()
self.statusBar().showMessage(f"Node: {node_id} ({node.node_type})")
elif event.isExit():
node.unhighlight()
self.statusBar().showMessage("")
def handle_node_click(self, event: Any, node_id: str) -> None:
"""Handle node click events"""
if event.button() != Qt.LeftButton or node_id not in self.nodes:
return
if self.selected_node and self.selected_node in self.nodes:
self.nodes[self.selected_node].deselect()
node = self.nodes[node_id]
node.select()
self.selected_node = node_id
if self.graph:
self.details.update_node_info(
self.graph.nodes[node_id], self.graph[node_id]
)
def refresh_layout(self) -> None:
"""Refresh the graph visualization"""
if not self.graph:
return
self.positions = self.calculate_layout()
self.node_sizes = self.calculate_node_sizes()
self.view.clear()
self.nodes.clear()
self.edges.clear()
self.edge_labels.clear()
grid = gl.GLGridItem()
grid.setSize(x=20, y=20, z=20)
grid.setSpacing(x=1, y=1, z=1)
self.view.addItem(grid)
positions = self.calculate_layout()
for node_id in self.graph.nodes():
node_type = self.graph.nodes[node_id].get("type", "default")
node = self.create_node(node_id, positions[node_id], node_type)
self.view.addItem(node.mesh_item)
if node.label_item:
self.view.addItem(node.label_item)
self.nodes[node_id] = node
for source, target in self.graph.edges():
edge = self.create_edge(positions[source], positions[target])
self.view.addItem(edge)
self.edges.append(edge)
if self.show_labels.isChecked():
mid_point = (positions[source] + positions[target]) / 2
relationship = self.graph.edges[source, target].get("relationship", "")
if relationship:
label = gl.GLTextItem(
pos=mid_point,
text=relationship,
color=(0.8, 0.8, 0.8, 0.8),
)
self.view.addItem(label)
self.edge_labels.append(label)
def main():
"""Application entry point"""
import sys
app = QApplication(sys.argv)
viewer = GraphMLViewer3D()
viewer.show()
sys.exit(app.exec_())
if __name__ == "__main__":
main()

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# 3D GraphML Viewer
一个基于 Dear ImGui 和 ModernGL 的交互式 3D 图可视化工具。
## 功能特点
- **3D 交互式可视化**: 使用 ModernGL 实现高性能的 3D 图形渲染
- **多种布局算法**: 支持多种图布局方式
- Spring 布局
- Circular 布局
- Shell 布局
- Random 布局
- **社区检测**: 支持图社区结构的自动检测和可视化
- **交互控制**:
- WASD + QE 键控制相机移动
- 鼠标右键拖拽控制视角
- 节点选择和高亮
- 可调节节点大小和边宽度
- 可控制标签显示
- 可在节点的Connections间快速跳转
- **社区检测**: 支持图社区结构的自动检测和可视化
- **交互控制**:
- WASD + QE 键控制相机移动
- 鼠标右键拖拽控制视角
- 节点选择和高亮
- 可调节节点大小和边宽度
- 可控制标签显示
## 技术栈
- **imgui_bundle**: 用户界面
- **ModernGL**: OpenGL 图形渲染
- **NetworkX**: 图数据结构和算法
- **NumPy**: 数值计算
- **community**: 社区检测
## 使用方法
1. **启动程序**:
```bash
python -m pip install -r requirements.txt
python graph_visualizer.py
```
2. **加载字体**:
- 将中文字体文件 `font.ttf` 放置在 `assets` 目录下
- 或者修改 `CUSTOM_FONT` 常量来使用其他字体文件
3. **加载图文件**:
- 点击界面上的 "Load GraphML" 按钮
- 选择 GraphML 格式的图文件
4. **交互控制**:
- **相机移动**:
- W: 前进
- S: 后退
- A: 左移
- D: 右移
- Q: 上升
- E: 下降
- **视角控制**:
- 按住鼠标右键拖动来旋转视角
- **节点交互**:
- 鼠标悬停可高亮节点
- 点击可选中节点
5. **可视化设置**:
- 可通过 UI 控制面板调整:
- 布局类型
- 节点大小
- 边的宽度
- 标签显示
- 标签大小
- 背景颜色
## 自定义设置
- **节点缩放**: 通过 `node_scale` 参数调整节点大小
- **边宽度**: 通过 `edge_width` 参数调整边的宽度
- **标签显示**: 可通过 `show_labels` 开关标签显示
- **标签大小**: 使用 `label_size` 调整标签大小
- **标签颜色**: 通过 `label_color` 设置标签颜色
- **视距控制**: 使用 `label_culling_distance` 控制标签显示的最大距离
## 性能优化
- 使用 ModernGL 进行高效的图形渲染
- 视距裁剪优化标签显示
- 社区检测算法优化大规模图的可视化效果
## 系统要求
- Python 3.10+
- OpenGL 3.3+ 兼容的显卡
- 支持的操作系统Windows/Linux/MacOS

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# 3D GraphML Viewer
An interactive 3D graph visualization tool based on Dear ImGui and ModernGL.
## Features
- **3D Interactive Visualization**: High-performance 3D graphics rendering using ModernGL
- **Multiple Layout Algorithms**: Support for various graph layouts
- Spring layout
- Circular layout
- Shell layout
- Random layout
- **Community Detection**: Automatic detection and visualization of graph community structures
- **Interactive Controls**:
- WASD + QE keys for camera movement
- Right mouse drag for view angle control
- Node selection and highlighting
- Adjustable node size and edge width
- Configurable label display
- Quick navigation between node connections
## Tech Stack
- **imgui_bundle**: User interface
- **ModernGL**: OpenGL graphics rendering
- **NetworkX**: Graph data structures and algorithms
- **NumPy**: Numerical computations
- **community**: Community detection
## Usage
1. **Launch the Program**:
```bash
python -m pip install -r requirements.txt
python graph_visualizer.py
```
2. **Load Font**:
- Place the font file `font.ttf` in the `assets` directory
- Or modify the `CUSTOM_FONT` constant to use a different font file
3. **Load Graph File**:
- Click the "Load GraphML" button in the interface
- Select a graph file in GraphML format
4. **Interactive Controls**:
- **Camera Movement**:
- W: Move forward
- S: Move backward
- A: Move left
- D: Move right
- Q: Move up
- E: Move down
- **View Control**:
- Hold right mouse button and drag to rotate view
- **Node Interaction**:
- Hover mouse to highlight nodes
- Click to select nodes
5. **Visualization Settings**:
- Adjustable via UI control panel:
- Layout type
- Node size
- Edge width
- Label visibility
- Label size
- Background color
## Customization Options
- **Node Scaling**: Adjust node size via `node_scale` parameter
- **Edge Width**: Modify edge width using `edge_width` parameter
- **Label Display**: Toggle label visibility with `show_labels`
- **Label Size**: Adjust label size using `label_size`
- **Label Color**: Set label color through `label_color`
- **View Distance**: Control maximum label display distance with `label_culling_distance`
## Performance Optimizations
- Efficient graphics rendering using ModernGL
- View distance culling for label display optimization
- Community detection algorithms for optimized visualization of large-scale graphs
## System Requirements
- Python 3.10+
- Graphics card with OpenGL 3.3+ support
- Supported Operating Systems: Windows/Linux/MacOS

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imgui_bundle
moderngl
networkx
numpy
pyglm
python-louvain
scipy
tk