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app_cn.py
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import gradio as gr
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from gradio_bbox_annotator import BBoxAnnotator
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from PIL import Image
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import numpy as np
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import torch
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import os
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import shutil
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import time
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import json
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import uuid
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from pathlib import Path
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import tempfile
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import zipfile
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from skimage import measure
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from matplotlib import cm
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from glob import glob
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from natsort import natsorted
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# ===== 导入三个推理模块 =====
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from inference_seg import load_model as load_seg_model, run as run_seg
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from inference_count import load_model as load_count_model, run as run_count
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from inference_track import load_model as load_track_model, run as run_track
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# ===== 清理缓存目录 =====
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print("===== 清理缓存 =====")
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# cache_path = os.path.expanduser("~/.cache/")
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cache_path = os.path.expanduser("~/.cache/huggingface/gradio")
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if os.path.exists(cache_path):
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try:
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shutil.rmtree(cache_path)
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# print("✅ Deleted ~/.cache/")
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print("✅ Deleted ~/.cache/huggingface/gradio")
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except:
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pass
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# ===== 全局模型变量 =====
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SEG_MODEL = None
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SEG_DEVICE = torch.device("cpu")
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COUNT_MODEL = None
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COUNT_DEVICE = torch.device("cpu")
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TRACK_MODEL = None
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TRACK_DEVICE = torch.device("cpu")
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def load_all_models():
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"""启动时加载所有模型"""
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global SEG_MODEL, SEG_DEVICE
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global COUNT_MODEL, COUNT_DEVICE
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global TRACK_MODEL, TRACK_DEVICE
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print("\n" + "="*60)
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print("📦 Loading Segmentation Model")
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print("="*60)
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SEG_MODEL, SEG_DEVICE = load_seg_model(use_box=False)
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print("\n" + "="*60)
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print("📦 Loading Counting Model")
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print("="*60)
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COUNT_MODEL, COUNT_DEVICE = load_count_model(use_box=False)
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print("\n" + "="*60)
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print("📦 Loading Tracking Model")
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print("="*60)
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TRACK_MODEL, TRACK_DEVICE = load_track_model(use_box=False)
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print("\n" + "="*60)
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print("✅ All Models Loaded Successfully")
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print("="*60)
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load_all_models()
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# ===== 保存用户反馈 =====
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DATASET_DIR = Path("solver_cache")
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DATASET_DIR.mkdir(parents=True, exist_ok=True)
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def save_feedback(query_id, feedback_type, feedback_text=None, img_path=None, bboxes=None):
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"""保存用户反馈到JSON文件"""
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feedback_data = {
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"query_id": query_id,
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"feedback_type": feedback_type,
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"feedback_text": feedback_text,
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"image": img_path,
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"bboxes": bboxes,
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"datetime": time.strftime("%Y%m%d_%H%M%S")
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}
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feedback_file = DATASET_DIR / query_id / "feedback.json"
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feedback_file.parent.mkdir(parents=True, exist_ok=True)
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if feedback_file.exists():
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with feedback_file.open("r") as f:
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existing = json.load(f)
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if not isinstance(existing, list):
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existing = [existing]
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existing.append(feedback_data)
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feedback_data = existing
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else:
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feedback_data = [feedback_data]
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with feedback_file.open("w") as f:
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json.dump(feedback_data, f, indent=4, ensure_ascii=False)
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# ===== 辅助函数 =====
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def parse_first_bbox(bboxes):
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"""解析第一个边界框"""
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if not bboxes:
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return None
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b = bboxes[0]
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if isinstance(b, dict):
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x, y = float(b.get("x", 0)), float(b.get("y", 0))
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w, h = float(b.get("width", 0)), float(b.get("height", 0))
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return x, y, x + w, y + h
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if isinstance(b, (list, tuple)) and len(b) >= 4:
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return float(b[0]), float(b[1]), float(b[2]), float(b[3])
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return None
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def colorize_mask(mask: np.ndarray, num_colors: int = 512) -> np.ndarray:
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"""将实例掩码转换为彩色图像"""
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def hsv_to_rgb(h, s, v):
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i = int(h * 6.0)
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f = h * 6.0 - i
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i = i % 6
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p = v * (1 - s)
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q = v * (1 - f * s)
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t = v * (1 - (1 - f) * s)
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if i == 0: r, g, b = v, t, p
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elif i == 1: r, g, b = q, v, p
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elif i == 2: r, g, b = p, v, t
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elif i == 3: r, g, b = p, q, v
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elif i == 4: r, g, b = t, p, v
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else: r, g, b = v, p, q
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return int(r * 255), int(g * 255), int(b * 255)
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palette = [(0, 0, 0)]
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for i in range(1, num_colors):
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h = (i % num_colors) / float(num_colors)
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palette.append(hsv_to_rgb(h, 1.0, 0.95))
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palette_arr = np.array(palette, dtype=np.uint8)
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color_idx = mask % num_colors
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return palette_arr[color_idx]
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# ===== 分割功能 =====
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def segment_with_choice(use_box_choice, annot_value):
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print("边界框选择:", use_box_choice)
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print("注释值:", annot_value)
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"""分割主函数 - 每个实例不同颜色+轮廓"""
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if annot_value is None or len(annot_value) < 1:
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print("❌ No annotation input")
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return None, None
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img_path = annot_value[0]
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bboxes = annot_value[1] if len(annot_value) > 1 else []
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print(f"🖼️ 图像路径: {img_path}")
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box_array = None
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if use_box_choice == "Yes" and bboxes:
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box = parse_first_bbox(bboxes)
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if box:
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xmin, ymin, xmax, ymax = map(int, box)
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box_array = [[xmin, ymin, xmax, ymax]]
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print(f"📦 使用边界框: {box_array}")
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# 运行分割模型
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try:
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mask = run_seg(SEG_MODEL, img_path, box=box_array, device=SEG_DEVICE)
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print("📏 mask shape:", mask.shape, "dtype:", mask.dtype, "unique:", np.unique(mask))
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except Exception as e:
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print(f"❌ 推理失败: {str(e)}")
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return None, None
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# 保存原始mask为TIF文件
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temp_mask_file = tempfile.NamedTemporaryFile(delete=False, suffix=".tif")
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mask_img = Image.fromarray(mask.astype(np.uint16))
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mask_img.save(temp_mask_file.name)
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print(f"💾 原始mask保存到: {temp_mask_file.name}")
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# 读取原图
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try:
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img = Image.open(img_path)
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print("📷 Image mode:", img.mode, "size:", img.size)
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except Exception as e:
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print(f"❌ Failed to open image: {e}")
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return None, None
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try:
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img_rgb = img.convert("RGB").resize(mask.shape[::-1], resample=Image.BILINEAR)
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img_np = np.array(img_rgb, dtype=np.float32)
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if img_np.max() > 1.5:
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img_np = img_np / 255.0
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except Exception as e:
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print(f"❌ Error in image conversion/resizing: {e}")
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return None, None
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mask_np = np.array(mask)
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inst_mask = mask_np.astype(np.int32)
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unique_ids = np.unique(inst_mask)
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num_instances = len(unique_ids[unique_ids != 0])
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print(f"✅ Instance IDs found: {unique_ids}, Total instances: {num_instances}")
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if num_instances == 0:
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print("⚠️ No instance found, returning dummy red image")
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return Image.new("RGB", mask.shape[::-1], (255, 0, 0)), None
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# ==== Color Overlay (每个实例一个颜色) ====
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overlay = img_np.copy()
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alpha = 0.5
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# cmap = cm.get_cmap("hsv", num_instances + 1)
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for inst_id in np.unique(inst_mask):
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if inst_id == 0:
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continue
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binary_mask = (inst_mask == inst_id).astype(np.uint8)
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# color = np.array(cmap(inst_id / (num_instances + 1))[:3]) # RGB only, ignore alpha
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color = get_well_spaced_color(inst_id)
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overlay[binary_mask == 1] = (1 - alpha) * overlay[binary_mask == 1] + alpha * color
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# 绘制轮廓
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contours = measure.find_contours(binary_mask, 0.5)
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for contour in contours:
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contour = contour.astype(np.int32)
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# 确保坐标在范围内
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valid_y = np.clip(contour[:, 0], 0, overlay.shape[0] - 1)
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valid_x = np.clip(contour[:, 1], 0, overlay.shape[1] - 1)
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overlay[valid_y, valid_x] = [1.0, 1.0, 0.0] # 黄色轮廓
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overlay = np.clip(overlay * 255.0, 0, 255).astype(np.uint8)
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return Image.fromarray(overlay), temp_mask_file.name
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# ===== 计数功能 =====
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def count_cells_handler(use_box_choice, annot_value):
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"""计数处理函数 - 支持边界框,只返回密度图"""
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if annot_value is None or len(annot_value) < 1:
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return None, "⚠️ 请先上传图像"
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image_path = annot_value[0]
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bboxes = annot_value[1] if len(annot_value) > 1 else []
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print(f"🖼️ 图像路径: {image_path}")
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box_array = None
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if use_box_choice == "Yes" and bboxes:
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box = parse_first_bbox(bboxes)
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if box:
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xmin, ymin, xmax, ymax = map(int, box)
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box_array = [[xmin, ymin, xmax, ymax]]
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print(f"📦 使用边界框: {box_array}")
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try:
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print(f"🔢 Counting - Image: {image_path}")
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result = run_count(
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COUNT_MODEL,
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image_path,
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box=box_array,
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device=COUNT_DEVICE,
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visualize=True
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)
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if 'error' in result:
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return None, f"❌ 计数失败: {result['error']}"
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count = result['count']
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density_map = result['density_map']
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# save density map as temp file
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temp_density_file = tempfile.NamedTemporaryFile(delete=False, suffix=".npy")
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np.save(temp_density_file.name, density_map)
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print(f"💾 Density map saved to {temp_density_file.name}")
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# 只提取密度图部分(假设visualized_path是拼接图,我们只要右半部分)
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# viz_path = result.get('visualized_path')
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# 如果有density_map_path,直接使用
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# if 'density_map_path' in result:
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# density_path = result['density_map_path']
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# elif viz_path and os.path.exists(viz_path):
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# # 如果是拼接图,提取右半部分(密度图)
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# try:
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# viz_img = Image.open(viz_path)
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# w, h = viz_img.size
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# # 取右半部分
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# density_img = viz_img
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# # 保存为新文件
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# temp_density = tempfile.NamedTemporaryFile(delete=False, suffix=".png")
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# density_img.save(temp_density.name)
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# density_path = temp_density.name
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# except:
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# density_path = viz_path
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# else:
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# density_path = viz_path
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# 读取原图
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try:
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img = Image.open(image_path)
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print("📷 Image mode:", img.mode, "size:", img.size)
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except Exception as e:
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print(f"❌ Failed to open image: {e}")
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return None, None
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try:
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img_rgb = img.convert("RGB").resize(density_map.shape[::-1], resample=Image.BILINEAR)
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img_np = np.array(img_rgb, dtype=np.float32)
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img_np = (img_np - img_np.min()) / (img_np.max() - img_np.min() + 1e-8)
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if img_np.max() > 1.5:
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img_np = img_np / 255.0
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except Exception as e:
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print(f"❌ Error in image conversion/resizing: {e}")
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return None, None
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# Normalize density map to [0, 1]
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density_normalized = density_map.copy()
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if density_normalized.max() > 0:
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density_normalized = (density_normalized - density_normalized.min()) / (density_normalized.max() - density_normalized.min())
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# Apply colormap
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cmap = cm.get_cmap("jet")
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alpha = 0.3
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density_colored = cmap(density_normalized)[:, :, :3] # RGB only, ignore alpha
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# Create overlay
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overlay = img_np.copy()
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# Blend only where density is significant (optional: threshold)
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threshold = 0.01 # Only overlay where density > 1% of max
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significant_mask = density_normalized > threshold
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overlay[significant_mask] = (1 - alpha) * overlay[significant_mask] + alpha * density_colored[significant_mask]
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# Clip and convert to uint8
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overlay = np.clip(overlay * 255.0, 0, 255).astype(np.uint8)
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result_text = f"✅ 检测到 {round(count)} 个细胞"
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print(f"✅ Counting done - Count: {count:.1f}")
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return Image.fromarray(overlay), temp_density_file.name, result_text
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# return density_path, result_text
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except Exception as e:
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print(f"❌ Counting error: {e}")
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import traceback
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traceback.print_exc()
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return None, f"❌ 计数失败: {str(e)}"
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# ===== 跟踪功能 =====
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def find_tif_dir(root_dir):
|
| 353 |
-
"""递归查找第一个包含 .tif 文件的目录"""
|
| 354 |
-
for dirpath, _, filenames in os.walk(root_dir):
|
| 355 |
-
if '__MACOSX' in dirpath:
|
| 356 |
-
continue
|
| 357 |
-
if any(f.lower().endswith('.tif') for f in filenames):
|
| 358 |
-
return dirpath
|
| 359 |
-
return None
|
| 360 |
-
|
| 361 |
-
def is_valid_tiff(filepath):
|
| 362 |
-
"""Check if a file is a valid TIFF image"""
|
| 363 |
-
try:
|
| 364 |
-
with Image.open(filepath) as img:
|
| 365 |
-
img.verify()
|
| 366 |
-
return True
|
| 367 |
-
except Exception as e:
|
| 368 |
-
return False
|
| 369 |
-
|
| 370 |
-
def find_valid_tif_dir(root_dir):
|
| 371 |
-
"""递归查找第一个包含有效 .tif 文件的目录"""
|
| 372 |
-
for dirpath, dirnames, filenames in os.walk(root_dir):
|
| 373 |
-
if '__MACOSX' in dirpath:
|
| 374 |
-
continue
|
| 375 |
-
|
| 376 |
-
potential_tifs = [
|
| 377 |
-
os.path.join(dirpath, f)
|
| 378 |
-
for f in filenames
|
| 379 |
-
if f.lower().endswith(('.tif', '.tiff')) and not f.startswith('._')
|
| 380 |
-
]
|
| 381 |
-
|
| 382 |
-
if not potential_tifs:
|
| 383 |
-
continue
|
| 384 |
-
|
| 385 |
-
valid_tifs = [f for f in potential_tifs if is_valid_tiff(f)]
|
| 386 |
-
|
| 387 |
-
if valid_tifs:
|
| 388 |
-
print(f"✅ Found {len(valid_tifs)} valid TIFF files in: {dirpath}")
|
| 389 |
-
return dirpath
|
| 390 |
-
|
| 391 |
-
return None
|
| 392 |
-
|
| 393 |
-
def create_ctc_results_zip(output_dir):
|
| 394 |
-
"""
|
| 395 |
-
Create a ZIP file with CTC format results
|
| 396 |
-
|
| 397 |
-
Parameters:
|
| 398 |
-
-----------
|
| 399 |
-
output_dir : str
|
| 400 |
-
Directory containing tracking results (res_track.txt, etc.)
|
| 401 |
-
|
| 402 |
-
Returns:
|
| 403 |
-
--------
|
| 404 |
-
zip_path : str
|
| 405 |
-
Path to created ZIP file
|
| 406 |
-
"""
|
| 407 |
-
# Create temp directory for ZIP
|
| 408 |
-
temp_zip_dir = tempfile.mkdtemp()
|
| 409 |
-
zip_filename = f"tracking_results_{time.strftime('%Y%m%d_%H%M%S')}.zip"
|
| 410 |
-
zip_path = os.path.join(temp_zip_dir, zip_filename)
|
| 411 |
-
|
| 412 |
-
print(f"📦 Creating results ZIP: {zip_path}")
|
| 413 |
-
|
| 414 |
-
# Create ZIP with all tracking results
|
| 415 |
-
with zipfile.ZipFile(zip_path, 'w', zipfile.ZIP_DEFLATED) as zipf:
|
| 416 |
-
# Add all files from output directory
|
| 417 |
-
for root, dirs, files in os.walk(output_dir):
|
| 418 |
-
for file in files:
|
| 419 |
-
file_path = os.path.join(root, file)
|
| 420 |
-
arcname = os.path.relpath(file_path, output_dir)
|
| 421 |
-
zipf.write(file_path, arcname)
|
| 422 |
-
print(f" 📄 Added: {arcname}")
|
| 423 |
-
|
| 424 |
-
# Add a README with summary
|
| 425 |
-
readme_content = f"""Tracking Results Summary
|
| 426 |
-
========================
|
| 427 |
-
|
| 428 |
-
Generated: {time.strftime('%Y-%m-%d %H:%M:%S')}
|
| 429 |
-
|
| 430 |
-
Files:
|
| 431 |
-
------
|
| 432 |
-
- res_track.txt: CTC format tracking data
|
| 433 |
-
Format: track_id start_frame end_frame parent_id
|
| 434 |
-
|
| 435 |
-
- Segmentation masks
|
| 436 |
-
|
| 437 |
-
For more information on CTC format:
|
| 438 |
-
http://celltrackingchallenge.net/
|
| 439 |
-
"""
|
| 440 |
-
zipf.writestr("README.txt", readme_content)
|
| 441 |
-
|
| 442 |
-
print(f"✅ ZIP created: {zip_path} ({os.path.getsize(zip_path) / 1024:.1f} KB)")
|
| 443 |
-
return zip_path
|
| 444 |
-
|
| 445 |
-
# 使用更智能的颜色分配 - 让相邻的ID颜色差异更大
|
| 446 |
-
def get_well_spaced_color(track_id, num_colors=256):
|
| 447 |
-
"""生成间隔良好的颜色,相邻ID使用对比色"""
|
| 448 |
-
# 使用质数跳跃来分散颜色
|
| 449 |
-
golden_ratio = 0.618033988749895
|
| 450 |
-
hue = (track_id * golden_ratio) % 1.0
|
| 451 |
-
|
| 452 |
-
# 使用高饱和度和明度
|
| 453 |
-
import colorsys
|
| 454 |
-
rgb = colorsys.hsv_to_rgb(hue, 0.9, 0.95)
|
| 455 |
-
return np.array(rgb)
|
| 456 |
-
|
| 457 |
-
|
| 458 |
-
def extract_first_frame(tif_dir):
|
| 459 |
-
"""
|
| 460 |
-
Extract the first frame from a directory of TIF files
|
| 461 |
-
|
| 462 |
-
Returns:
|
| 463 |
-
--------
|
| 464 |
-
first_frame_path : str
|
| 465 |
-
Path to the first TIF frame
|
| 466 |
-
"""
|
| 467 |
-
tif_files = natsorted(glob(os.path.join(tif_dir, "*.tif")) +
|
| 468 |
-
glob(os.path.join(tif_dir, "*.tiff")))
|
| 469 |
-
valid_tif_files = [f for f in tif_files
|
| 470 |
-
if not os.path.basename(f).startswith('._') and is_valid_tiff(f)]
|
| 471 |
-
|
| 472 |
-
if valid_tif_files:
|
| 473 |
-
return valid_tif_files[0]
|
| 474 |
-
return None
|
| 475 |
-
|
| 476 |
-
def create_tracking_visualization(tif_dir, output_dir, valid_tif_files):
|
| 477 |
-
"""
|
| 478 |
-
Create an animated GIF/video showing tracked objects with consistent colors
|
| 479 |
-
|
| 480 |
-
Parameters:
|
| 481 |
-
-----------
|
| 482 |
-
tif_dir : str
|
| 483 |
-
Directory containing input TIF frames
|
| 484 |
-
output_dir : str
|
| 485 |
-
Directory containing tracking results (masks)
|
| 486 |
-
valid_tif_files : list
|
| 487 |
-
List of valid TIF file paths
|
| 488 |
-
|
| 489 |
-
Returns:
|
| 490 |
-
--------
|
| 491 |
-
video_path : str
|
| 492 |
-
Path to generated visualization (GIF or first frame)
|
| 493 |
-
"""
|
| 494 |
-
import numpy as np
|
| 495 |
-
from matplotlib import colormaps
|
| 496 |
-
from skimage import measure
|
| 497 |
-
import tifffile
|
| 498 |
-
|
| 499 |
-
# Look for tracking mask files in output directory
|
| 500 |
-
# Common CTC formats: man_track*.tif, mask*.tif, or numbered masks
|
| 501 |
-
mask_files = natsorted(glob(os.path.join(output_dir, "mask*.tif")) +
|
| 502 |
-
glob(os.path.join(output_dir, "man_track*.tif")) +
|
| 503 |
-
glob(os.path.join(output_dir, "*.tif")))
|
| 504 |
-
|
| 505 |
-
if not mask_files:
|
| 506 |
-
print("⚠️ No mask files found in output directory")
|
| 507 |
-
# Return first frame as fallback
|
| 508 |
-
return valid_tif_files[0]
|
| 509 |
-
|
| 510 |
-
print(f"📊 Found {len(mask_files)} mask files")
|
| 511 |
-
|
| 512 |
-
# Create color map for consistent track IDs
|
| 513 |
-
# Use a colormap with many distinct colors
|
| 514 |
-
# try:
|
| 515 |
-
# cmap = colormaps.get_cmap("hsv")
|
| 516 |
-
# except:
|
| 517 |
-
# from matplotlib import cm
|
| 518 |
-
# cmap = cm.get_cmap("hsv")
|
| 519 |
-
|
| 520 |
-
frames = []
|
| 521 |
-
alpha = 0.3 # Transparency for overlay
|
| 522 |
-
|
| 523 |
-
# Process each frame
|
| 524 |
-
num_frames = min(len(valid_tif_files), len(mask_files))
|
| 525 |
-
for i in range(num_frames):
|
| 526 |
-
try:
|
| 527 |
-
# Load original image using tifffile (handles ZSTD compression)
|
| 528 |
-
try:
|
| 529 |
-
img_np = tifffile.imread(valid_tif_files[i])
|
| 530 |
-
|
| 531 |
-
# Normalize to [0, 1] range based on actual data type and values
|
| 532 |
-
if img_np.dtype == np.uint8:
|
| 533 |
-
img_np = img_np.astype(np.float32) / 255.0
|
| 534 |
-
elif img_np.dtype == np.uint16:
|
| 535 |
-
# Normalize uint16 to [0, 1] using actual min/max
|
| 536 |
-
img_min, img_max = img_np.min(), img_np.max()
|
| 537 |
-
if img_max > img_min:
|
| 538 |
-
img_np = (img_np.astype(np.float32) - img_min) / (img_max - img_min)
|
| 539 |
-
else:
|
| 540 |
-
img_np = img_np.astype(np.float32) / 65535.0
|
| 541 |
-
else:
|
| 542 |
-
# For float or other types, normalize based on actual range
|
| 543 |
-
img_np = img_np.astype(np.float32)
|
| 544 |
-
img_min, img_max = img_np.min(), img_np.max()
|
| 545 |
-
if img_max > img_min:
|
| 546 |
-
img_np = (img_np - img_min) / (img_max - img_min)
|
| 547 |
-
else:
|
| 548 |
-
img_np = np.clip(img_np, 0, 1)
|
| 549 |
-
|
| 550 |
-
# Convert to RGB if grayscale
|
| 551 |
-
if img_np.ndim == 2:
|
| 552 |
-
img_np = np.stack([img_np]*3, axis=-1)
|
| 553 |
-
img_np = img_np.astype(np.float32)
|
| 554 |
-
if img_np.max() > 1.5:
|
| 555 |
-
img_np = img_np / 255.0
|
| 556 |
-
except Exception as e:
|
| 557 |
-
print(f"⚠️ Error loading image frame {i}: {e}")
|
| 558 |
-
# Fallback to PIL
|
| 559 |
-
img = Image.open(valid_tif_files[i]).convert("RGB")
|
| 560 |
-
img_np = np.array(img, dtype=np.float32) / 255.0
|
| 561 |
-
|
| 562 |
-
# Load tracking mask using tifffile (handles ZSTD compression)
|
| 563 |
-
try:
|
| 564 |
-
mask = tifffile.imread(mask_files[i])
|
| 565 |
-
except Exception as e:
|
| 566 |
-
print(f"⚠️ Error loading mask frame {i}: {e}")
|
| 567 |
-
# Fallback to PIL
|
| 568 |
-
mask = np.array(Image.open(mask_files[i]))
|
| 569 |
-
|
| 570 |
-
# Resize mask to match image if needed
|
| 571 |
-
if mask.shape[:2] != img_np.shape[:2]:
|
| 572 |
-
from scipy.ndimage import zoom
|
| 573 |
-
zoom_factors = [img_np.shape[0] / mask.shape[0], img_np.shape[1] / mask.shape[1]]
|
| 574 |
-
mask = zoom(mask, zoom_factors, order=0).astype(mask.dtype)
|
| 575 |
-
|
| 576 |
-
# Create overlay
|
| 577 |
-
overlay = img_np.copy()
|
| 578 |
-
|
| 579 |
-
# Get unique track IDs (excluding background 0)
|
| 580 |
-
track_ids = np.unique(mask)
|
| 581 |
-
track_ids = track_ids[track_ids != 0]
|
| 582 |
-
|
| 583 |
-
# Color each tracked object
|
| 584 |
-
for track_id in track_ids:
|
| 585 |
-
# Create binary mask for this track
|
| 586 |
-
binary_mask = (mask == track_id)
|
| 587 |
-
|
| 588 |
-
# Get consistent color for this track ID
|
| 589 |
-
# color = np.array(cmap(int(track_id) % 256)[:3])
|
| 590 |
-
color = get_well_spaced_color(int(track_id))
|
| 591 |
-
|
| 592 |
-
# Blend color onto image
|
| 593 |
-
overlay[binary_mask] = (1 - alpha) * overlay[binary_mask] + alpha * color
|
| 594 |
-
|
| 595 |
-
# Draw contours (optional, adds yellow boundaries)
|
| 596 |
-
try:
|
| 597 |
-
contours = measure.find_contours(binary_mask.astype(np.uint8), 0.5)
|
| 598 |
-
for contour in contours:
|
| 599 |
-
contour = contour.astype(np.int32)
|
| 600 |
-
valid_y = np.clip(contour[:, 0], 0, overlay.shape[0] - 1)
|
| 601 |
-
valid_x = np.clip(contour[:, 1], 0, overlay.shape[1] - 1)
|
| 602 |
-
overlay[valid_y, valid_x] = [1.0, 1.0, 0.0] # Yellow contour
|
| 603 |
-
except:
|
| 604 |
-
pass # Skip contours if they fail
|
| 605 |
-
|
| 606 |
-
# Convert to uint8
|
| 607 |
-
overlay_uint8 = np.clip(overlay * 255.0, 0, 255).astype(np.uint8)
|
| 608 |
-
frames.append(Image.fromarray(overlay_uint8))
|
| 609 |
-
|
| 610 |
-
if i % 10 == 0 or i == num_frames - 1:
|
| 611 |
-
print(f" 📸 Processed frame {i+1}/{num_frames}")
|
| 612 |
-
|
| 613 |
-
except Exception as e:
|
| 614 |
-
print(f"⚠️ Error processing frame {i}: {e}")
|
| 615 |
-
import traceback
|
| 616 |
-
traceback.print_exc()
|
| 617 |
-
continue
|
| 618 |
-
|
| 619 |
-
if not frames:
|
| 620 |
-
print("⚠️ No frames were processed successfully")
|
| 621 |
-
return valid_tif_files[0]
|
| 622 |
-
|
| 623 |
-
# Save as animated GIF
|
| 624 |
-
try:
|
| 625 |
-
temp_gif = tempfile.NamedTemporaryFile(delete=False, suffix=".gif")
|
| 626 |
-
frames[0].save(
|
| 627 |
-
temp_gif.name,
|
| 628 |
-
save_all=True,
|
| 629 |
-
append_images=frames[1:],
|
| 630 |
-
duration=200, # 200ms per frame = 5fps
|
| 631 |
-
loop=0
|
| 632 |
-
)
|
| 633 |
-
temp_gif.close() # Close the file handle
|
| 634 |
-
print(f"✅ Created tracking visualization GIF: {temp_gif.name}")
|
| 635 |
-
print(f" Size: {os.path.getsize(temp_gif.name)} bytes, Frames: {len(frames)}")
|
| 636 |
-
return temp_gif.name
|
| 637 |
-
except Exception as e:
|
| 638 |
-
print(f"⚠️ Failed to create GIF: {e}")
|
| 639 |
-
import traceback
|
| 640 |
-
traceback.print_exc()
|
| 641 |
-
# Return first frame as static image fallback
|
| 642 |
-
try:
|
| 643 |
-
temp_img = tempfile.NamedTemporaryFile(delete=False, suffix=".png")
|
| 644 |
-
frames[0].save(temp_img.name)
|
| 645 |
-
temp_img.close()
|
| 646 |
-
return temp_img.name
|
| 647 |
-
except:
|
| 648 |
-
return valid_tif_files[0]
|
| 649 |
-
|
| 650 |
-
|
| 651 |
-
def track_video_handler(use_box_choice, first_frame_annot, zip_file_obj):
|
| 652 |
-
"""
|
| 653 |
-
支持 ZIP 压缩包上传的 Tracking 处理函数 - 支持首帧边界框
|
| 654 |
-
|
| 655 |
-
Parameters:
|
| 656 |
-
-----------
|
| 657 |
-
use_box_choice : str
|
| 658 |
-
"Yes" or "No" - 是否使用边界框
|
| 659 |
-
first_frame_annot : tuple or None
|
| 660 |
-
(image_path, bboxes) from BBoxAnnotator, only used if user annotated first frame
|
| 661 |
-
zip_file_obj : File
|
| 662 |
-
Uploaded ZIP file containing TIF sequence
|
| 663 |
-
"""
|
| 664 |
-
if zip_file_obj is None:
|
| 665 |
-
return None, "⚠️ 请上传包含视频帧的压缩包 (.zip)", None, None
|
| 666 |
-
|
| 667 |
-
temp_dir = None
|
| 668 |
-
output_temp_dir = None
|
| 669 |
-
|
| 670 |
-
try:
|
| 671 |
-
# Parse bounding box if provided
|
| 672 |
-
box_array = None
|
| 673 |
-
if use_box_choice == "Yes" and first_frame_annot is not None:
|
| 674 |
-
if isinstance(first_frame_annot, (list, tuple)) and len(first_frame_annot) > 1:
|
| 675 |
-
bboxes = first_frame_annot[1]
|
| 676 |
-
if bboxes:
|
| 677 |
-
box = parse_first_bbox(bboxes)
|
| 678 |
-
if box:
|
| 679 |
-
xmin, ymin, xmax, ymax = map(int, box)
|
| 680 |
-
box_array = [[xmin, ymin, xmax, ymax]]
|
| 681 |
-
print(f"📦 使用边界框: {box_array}")
|
| 682 |
-
|
| 683 |
-
# Extract input ZIP
|
| 684 |
-
temp_dir = tempfile.mkdtemp()
|
| 685 |
-
print(f"\n📦 解压到临时目录: {temp_dir}")
|
| 686 |
-
|
| 687 |
-
with zipfile.ZipFile(zip_file_obj.name, 'r') as zip_ref:
|
| 688 |
-
extracted_count = 0
|
| 689 |
-
skipped_count = 0
|
| 690 |
-
|
| 691 |
-
for member in zip_ref.namelist():
|
| 692 |
-
basename = os.path.basename(member)
|
| 693 |
-
|
| 694 |
-
if ('__MACOSX' in member or
|
| 695 |
-
basename.startswith('._') or
|
| 696 |
-
basename.startswith('.DS_Store') or
|
| 697 |
-
member.endswith('/')):
|
| 698 |
-
skipped_count += 1
|
| 699 |
-
continue
|
| 700 |
-
|
| 701 |
-
try:
|
| 702 |
-
zip_ref.extract(member, temp_dir)
|
| 703 |
-
extracted_count += 1
|
| 704 |
-
if basename.lower().endswith(('.tif', '.tiff')):
|
| 705 |
-
print(f"📄 Extracted TIFF: {basename}")
|
| 706 |
-
except Exception as e:
|
| 707 |
-
print(f"⚠️ Failed to extract {member}: {e}")
|
| 708 |
-
|
| 709 |
-
print(f"\n📊 提取: {extracted_count} 文件, 跳过: {skipped_count} 文件")
|
| 710 |
-
|
| 711 |
-
# Find valid TIFF directory
|
| 712 |
-
tif_dir = find_valid_tif_dir(temp_dir)
|
| 713 |
-
|
| 714 |
-
if tif_dir is None:
|
| 715 |
-
return None, "❌ 未找到有效的TIFF文件", None, None
|
| 716 |
-
|
| 717 |
-
# Validate TIFF files
|
| 718 |
-
tif_files = sorted(glob(os.path.join(tif_dir, "*.tif")) +
|
| 719 |
-
glob(os.path.join(tif_dir, "*.tiff")))
|
| 720 |
-
valid_tif_files = [f for f in tif_files
|
| 721 |
-
if not os.path.basename(f).startswith('._') and is_valid_tiff(f)]
|
| 722 |
-
|
| 723 |
-
if len(valid_tif_files) == 0:
|
| 724 |
-
return None, "❌ 没有有效的TIFF文件", None, None
|
| 725 |
-
|
| 726 |
-
print(f"📈 使用 {len(valid_tif_files)} 个TIFF文件")
|
| 727 |
-
|
| 728 |
-
# Store paths for later visualization
|
| 729 |
-
first_frame_path = valid_tif_files[0]
|
| 730 |
-
|
| 731 |
-
# Create temporary output directory for CTC results
|
| 732 |
-
output_temp_dir = tempfile.mkdtemp()
|
| 733 |
-
print(f"💾 CTC结果将保存到: {output_temp_dir}")
|
| 734 |
-
|
| 735 |
-
# Run tracking with optional bounding box
|
| 736 |
-
result = run_track(
|
| 737 |
-
TRACK_MODEL,
|
| 738 |
-
video_dir=tif_dir,
|
| 739 |
-
box=box_array, # Pass bounding box if specified
|
| 740 |
-
device=TRACK_DEVICE,
|
| 741 |
-
output_dir=output_temp_dir
|
| 742 |
-
)
|
| 743 |
-
|
| 744 |
-
if 'error' in result:
|
| 745 |
-
return None, f"❌ 跟踪失败: {result['error']}", None, None
|
| 746 |
-
|
| 747 |
-
# Create visualization video of tracked objects
|
| 748 |
-
print("\n🎬 Creating tracking visualization...")
|
| 749 |
-
try:
|
| 750 |
-
tracking_video = create_tracking_visualization(
|
| 751 |
-
tif_dir,
|
| 752 |
-
output_temp_dir,
|
| 753 |
-
valid_tif_files
|
| 754 |
-
)
|
| 755 |
-
except Exception as e:
|
| 756 |
-
print(f"⚠️ Failed to create visualization: {e}")
|
| 757 |
-
import traceback
|
| 758 |
-
traceback.print_exc()
|
| 759 |
-
# Fallback to first frame if visualization fails
|
| 760 |
-
try:
|
| 761 |
-
tracking_video = Image.open(first_frame_path)
|
| 762 |
-
except:
|
| 763 |
-
tracking_video = None
|
| 764 |
-
|
| 765 |
-
# Create downloadable ZIP with results
|
| 766 |
-
try:
|
| 767 |
-
results_zip = create_ctc_results_zip(output_temp_dir)
|
| 768 |
-
except Exception as e:
|
| 769 |
-
print(f"⚠️ Failed to create ZIP: {e}")
|
| 770 |
-
results_zip = None
|
| 771 |
-
|
| 772 |
-
bbox_info = ""
|
| 773 |
-
if box_array:
|
| 774 |
-
bbox_info = f"\n🔲 使用边界框: [{box_array[0][0]}, {box_array[0][1]}, {box_array[0][2]}, {box_array[0][3]}]"
|
| 775 |
-
|
| 776 |
-
result_text = f"""✅ 跟踪完成!
|
| 777 |
-
|
| 778 |
-
🖼️ 处理帧数: {len(valid_tif_files)}{bbox_info}
|
| 779 |
-
|
| 780 |
-
📥 点击下方按钮下载CTC格式结果
|
| 781 |
-
结果包含:
|
| 782 |
-
- res_track.txt (CTC格式轨迹数据)
|
| 783 |
-
- 其他跟踪相关文件
|
| 784 |
-
- README.txt (结果说明)
|
| 785 |
-
"""
|
| 786 |
-
|
| 787 |
-
print(f"\n✅ Tracking完成")
|
| 788 |
-
|
| 789 |
-
# Clean up input temp directory (keep output temp for download)
|
| 790 |
-
if temp_dir:
|
| 791 |
-
try:
|
| 792 |
-
shutil.rmtree(temp_dir)
|
| 793 |
-
print(f"🗑️ 清理输入临时目录")
|
| 794 |
-
except:
|
| 795 |
-
pass
|
| 796 |
-
|
| 797 |
-
return results_zip, result_text, gr.update(visible=True), tracking_video
|
| 798 |
-
|
| 799 |
-
except zipfile.BadZipFile:
|
| 800 |
-
return None, "❌ 不是有效的ZIP文件", None, None
|
| 801 |
-
except Exception as e:
|
| 802 |
-
import traceback
|
| 803 |
-
traceback.print_exc()
|
| 804 |
-
|
| 805 |
-
# Clean up on error
|
| 806 |
-
for d in [temp_dir, output_temp_dir]:
|
| 807 |
-
if d:
|
| 808 |
-
try:
|
| 809 |
-
shutil.rmtree(d)
|
| 810 |
-
except:
|
| 811 |
-
pass
|
| 812 |
-
|
| 813 |
-
return None, f"❌ 跟踪失败: {str(e)}", None, None
|
| 814 |
-
|
| 815 |
-
|
| 816 |
-
|
| 817 |
-
# ===== 示例图像 =====
|
| 818 |
-
example_images_seg = [f for f in glob("example_imgs/seg/*")]
|
| 819 |
-
# ["example_imgs/seg/003_img.png", "example_imgs/seg/1977_Well_F-5_Field_1.png"]
|
| 820 |
-
example_images_cnt = [f for f in glob("example_imgs/cnt/*")]
|
| 821 |
-
example_tracking_zips = [f for f in glob("example_imgs/tra/*.zip")]
|
| 822 |
-
|
| 823 |
-
# ===== Gradio UI =====
|
| 824 |
-
with gr.Blocks(
|
| 825 |
-
title="Microscopy Analysis Suite",
|
| 826 |
-
theme=gr.themes.Soft(),
|
| 827 |
-
css="""
|
| 828 |
-
.tabs button {
|
| 829 |
-
font-size: 20px !important;
|
| 830 |
-
font-weight: 600 !important;
|
| 831 |
-
padding: 12px 20px !important;
|
| 832 |
-
}
|
| 833 |
-
"""
|
| 834 |
-
) as demo:
|
| 835 |
-
gr.Markdown(
|
| 836 |
-
"""
|
| 837 |
-
# 🔬 显微图像分析工具套件
|
| 838 |
-
|
| 839 |
-
支持三种分析模式:
|
| 840 |
-
- 🎨 **分割 (Segmentation)**: 实例分割显微镜物体
|
| 841 |
-
- 🔢 **计数 (Counting)**: 基于密度图的显微镜物体计数
|
| 842 |
-
- 🎬 **跟踪 (Tracking)**: 视频序列中的显微镜物体跟踪
|
| 843 |
-
"""
|
| 844 |
-
)
|
| 845 |
-
|
| 846 |
-
# 全局状态
|
| 847 |
-
current_query_id = gr.State(str(uuid.uuid4()))
|
| 848 |
-
user_uploaded_examples = gr.State(example_images_seg.copy()) # 初始化时包含原始示例
|
| 849 |
-
|
| 850 |
-
with gr.Tabs():
|
| 851 |
-
# ===== Tab 1: Segmentation =====
|
| 852 |
-
with gr.Tab("🎨 分割 (Segmentation)"):
|
| 853 |
-
gr.Markdown("## 显微镜物体实例分割")
|
| 854 |
-
gr.Markdown(
|
| 855 |
-
"""
|
| 856 |
-
**使用说明:**
|
| 857 |
-
1. 上传图像或选择示例图片(支持多种格式: .png, .jpg, .tif)
|
| 858 |
-
2. (可选) 标注一个目标物体的边界框并选择 "Yes",或直接点击 "运行分割"
|
| 859 |
-
3. 点击 "运行分割"
|
| 860 |
-
4. 查看分割结果,下载原始预测mask (.tif格式);如果需要,点击 "清空重选" 选择新图像运行
|
| 861 |
-
5. 评分并提交反馈以帮助我们改进模型!
|
| 862 |
-
"""
|
| 863 |
-
)
|
| 864 |
-
|
| 865 |
-
with gr.Row():
|
| 866 |
-
with gr.Column(scale=1):
|
| 867 |
-
annotator = BBoxAnnotator(
|
| 868 |
-
label="🖼️ 上传图像 (可选标注边界框)",
|
| 869 |
-
categories=["cell"]
|
| 870 |
-
)
|
| 871 |
-
|
| 872 |
-
# 示例图片Gallery
|
| 873 |
-
example_gallery = gr.Gallery(
|
| 874 |
-
label="📁 示例图片",
|
| 875 |
-
columns=len(example_images_seg),
|
| 876 |
-
rows=1,
|
| 877 |
-
height=120,
|
| 878 |
-
object_fit="cover",
|
| 879 |
-
show_download_button=False
|
| 880 |
-
)
|
| 881 |
-
|
| 882 |
-
|
| 883 |
-
with gr.Row():
|
| 884 |
-
use_box_radio = gr.Radio(
|
| 885 |
-
choices=["Yes", "No"],
|
| 886 |
-
value="No",
|
| 887 |
-
label="🔲 使用边界框?"
|
| 888 |
-
)
|
| 889 |
-
with gr.Row():
|
| 890 |
-
run_seg_btn = gr.Button("▶️ 运行分割", variant="primary", size="lg")
|
| 891 |
-
clear_btn = gr.Button("🔄 清空重选", variant="secondary")
|
| 892 |
-
|
| 893 |
-
# 上传示例图片
|
| 894 |
-
image_uploader = gr.Image(
|
| 895 |
-
label="➕ 上传新示例到Gallery",
|
| 896 |
-
type="filepath"
|
| 897 |
-
)
|
| 898 |
-
|
| 899 |
-
|
| 900 |
-
with gr.Column(scale=2):
|
| 901 |
-
seg_output = gr.Image(
|
| 902 |
-
type="pil",
|
| 903 |
-
label="📸 分割结果",
|
| 904 |
-
height=400
|
| 905 |
-
)
|
| 906 |
-
|
| 907 |
-
# 下载原始预测结果
|
| 908 |
-
download_mask_btn = gr.File(
|
| 909 |
-
label="📥 下载原始预测 (.tif 格式)",
|
| 910 |
-
visible=True,
|
| 911 |
-
height=40,
|
| 912 |
-
)
|
| 913 |
-
|
| 914 |
-
# 满意度评分
|
| 915 |
-
score_slider = gr.Slider(
|
| 916 |
-
minimum=1,
|
| 917 |
-
maximum=5,
|
| 918 |
-
step=1,
|
| 919 |
-
value=5,
|
| 920 |
-
label="🌟 满意度评分 (1-5)"
|
| 921 |
-
)
|
| 922 |
-
|
| 923 |
-
# 反馈文本框
|
| 924 |
-
feedback_box = gr.Textbox(
|
| 925 |
-
placeholder="请输入您的反馈意见...",
|
| 926 |
-
lines=2,
|
| 927 |
-
label="💬 反馈意见"
|
| 928 |
-
)
|
| 929 |
-
|
| 930 |
-
# 提交按钮
|
| 931 |
-
submit_feedback_btn = gr.Button("💾 提交反馈", variant="secondary")
|
| 932 |
-
|
| 933 |
-
feedback_status = gr.Textbox(
|
| 934 |
-
label="✅ 提交状态",
|
| 935 |
-
lines=1,
|
| 936 |
-
visible=False
|
| 937 |
-
)
|
| 938 |
-
|
| 939 |
-
# 绑定事件: 运行分割
|
| 940 |
-
run_seg_btn.click(
|
| 941 |
-
fn=segment_with_choice,
|
| 942 |
-
inputs=[use_box_radio, annotator],
|
| 943 |
-
outputs=[seg_output, download_mask_btn]
|
| 944 |
-
)
|
| 945 |
-
|
| 946 |
-
# 清空按钮事件
|
| 947 |
-
clear_btn.click(
|
| 948 |
-
fn=lambda: None,
|
| 949 |
-
inputs=None,
|
| 950 |
-
outputs=annotator
|
| 951 |
-
)
|
| 952 |
-
|
| 953 |
-
# 初始化Gallery显示
|
| 954 |
-
demo.load(
|
| 955 |
-
fn=lambda: example_images_seg.copy(),
|
| 956 |
-
outputs=example_gallery
|
| 957 |
-
)
|
| 958 |
-
|
| 959 |
-
# 绑定事件: 上传示例图片
|
| 960 |
-
def add_to_gallery(img_path, current_imgs):
|
| 961 |
-
if not img_path:
|
| 962 |
-
return current_imgs
|
| 963 |
-
try:
|
| 964 |
-
if img_path not in current_imgs:
|
| 965 |
-
current_imgs.append(img_path)
|
| 966 |
-
return current_imgs
|
| 967 |
-
except:
|
| 968 |
-
return current_imgs
|
| 969 |
-
|
| 970 |
-
image_uploader.change(
|
| 971 |
-
fn=add_to_gallery,
|
| 972 |
-
inputs=[image_uploader, user_uploaded_examples],
|
| 973 |
-
outputs=user_uploaded_examples
|
| 974 |
-
).then(
|
| 975 |
-
fn=lambda imgs: imgs,
|
| 976 |
-
inputs=user_uploaded_examples,
|
| 977 |
-
outputs=example_gallery
|
| 978 |
-
)
|
| 979 |
-
|
| 980 |
-
# 绑定事件: 点击Gallery加载
|
| 981 |
-
def load_from_gallery(evt: gr.SelectData, all_imgs):
|
| 982 |
-
if evt.index is not None and evt.index < len(all_imgs):
|
| 983 |
-
return all_imgs[evt.index]
|
| 984 |
-
return None
|
| 985 |
-
|
| 986 |
-
example_gallery.select(
|
| 987 |
-
fn=load_from_gallery,
|
| 988 |
-
inputs=user_uploaded_examples,
|
| 989 |
-
outputs=annotator
|
| 990 |
-
)
|
| 991 |
-
|
| 992 |
-
# 绑定事件: 提交反馈
|
| 993 |
-
def submit_user_feedback(query_id, score, comment, annot_val):
|
| 994 |
-
try:
|
| 995 |
-
img_path = annot_val[0] if annot_val and len(annot_val) > 0 else None
|
| 996 |
-
bboxes = annot_val[1] if annot_val and len(annot_val) > 1 else []
|
| 997 |
-
|
| 998 |
-
save_feedback(
|
| 999 |
-
query_id=query_id,
|
| 1000 |
-
feedback_type=f"score_{int(score)}",
|
| 1001 |
-
feedback_text=comment,
|
| 1002 |
-
img_path=img_path,
|
| 1003 |
-
bboxes=bboxes
|
| 1004 |
-
)
|
| 1005 |
-
return "✅ 反馈已提交,感谢您的评价!", gr.update(visible=True)
|
| 1006 |
-
except Exception as e:
|
| 1007 |
-
return f"❌ 提交失败: {str(e)}", gr.update(visible=True)
|
| 1008 |
-
|
| 1009 |
-
submit_feedback_btn.click(
|
| 1010 |
-
fn=submit_user_feedback,
|
| 1011 |
-
inputs=[current_query_id, score_slider, feedback_box, annotator],
|
| 1012 |
-
outputs=[feedback_status, feedback_status]
|
| 1013 |
-
)
|
| 1014 |
-
|
| 1015 |
-
# ===== Tab 2: Counting =====
|
| 1016 |
-
with gr.Tab("🔢 计数 (Counting)"):
|
| 1017 |
-
gr.Markdown("## 显微镜物体计数分析")
|
| 1018 |
-
gr.Markdown(
|
| 1019 |
-
"""
|
| 1020 |
-
**使用说明:**
|
| 1021 |
-
1. 上传图像或选择示例图片(支持多种格式: .png, .jpg, .tif)
|
| 1022 |
-
2. (可选) 标注边界框并选择 "Yes",或直接点击 "运行计数"
|
| 1023 |
-
3. 点击 "运行计数"
|
| 1024 |
-
4. 查看密度图,下载原始预测 (.npy格式);如果需要,点击 "清空重选" 选择新图像运行
|
| 1025 |
-
5. 评分并提交反馈以帮助我们改进模型!
|
| 1026 |
-
"""
|
| 1027 |
-
)
|
| 1028 |
-
|
| 1029 |
-
with gr.Row():
|
| 1030 |
-
with gr.Column(scale=1):
|
| 1031 |
-
count_annotator = BBoxAnnotator(
|
| 1032 |
-
label="🖼️ 上传图像 (可选标注边界框)",
|
| 1033 |
-
categories=["cell"]
|
| 1034 |
-
)
|
| 1035 |
-
|
| 1036 |
-
# Example gallery with "add" functionality
|
| 1037 |
-
with gr.Row():
|
| 1038 |
-
count_example_gallery = gr.Gallery(
|
| 1039 |
-
label="📁 示例图片",
|
| 1040 |
-
columns=len(example_images_cnt),
|
| 1041 |
-
rows=1,
|
| 1042 |
-
object_fit="cover",
|
| 1043 |
-
height=120,
|
| 1044 |
-
value=example_images_cnt.copy(), # Initialize with examples
|
| 1045 |
-
show_download_button=False
|
| 1046 |
-
)
|
| 1047 |
-
|
| 1048 |
-
|
| 1049 |
-
with gr.Row():
|
| 1050 |
-
count_use_box_radio = gr.Radio(
|
| 1051 |
-
choices=["Yes", "No"],
|
| 1052 |
-
value="No",
|
| 1053 |
-
label="🔲 使用边界框?"
|
| 1054 |
-
)
|
| 1055 |
-
|
| 1056 |
-
with gr.Row():
|
| 1057 |
-
count_btn = gr.Button("▶️ 运行计数", variant="primary", size="lg")
|
| 1058 |
-
clear_btn = gr.Button("🔄 清空重选", variant="secondary")
|
| 1059 |
-
|
| 1060 |
-
# Add button to upload new examples
|
| 1061 |
-
with gr.Row():
|
| 1062 |
-
count_image_uploader = gr.File(
|
| 1063 |
-
label="➕ 添加示例图片",
|
| 1064 |
-
file_types=["image"],
|
| 1065 |
-
type="filepath"
|
| 1066 |
-
)
|
| 1067 |
-
|
| 1068 |
-
|
| 1069 |
-
with gr.Column(scale=2):
|
| 1070 |
-
count_output = gr.Image(
|
| 1071 |
-
label="📸 密度图",
|
| 1072 |
-
type="filepath",
|
| 1073 |
-
height=400
|
| 1074 |
-
)
|
| 1075 |
-
count_status = gr.Textbox(
|
| 1076 |
-
label="📊 统计信息",
|
| 1077 |
-
lines=2
|
| 1078 |
-
)
|
| 1079 |
-
download_density_btn = gr.File(
|
| 1080 |
-
label="📥 下载原始预测 (.npy 格式)",
|
| 1081 |
-
visible=True
|
| 1082 |
-
)
|
| 1083 |
-
|
| 1084 |
-
# 满意度评分
|
| 1085 |
-
score_slider = gr.Slider(
|
| 1086 |
-
minimum=1,
|
| 1087 |
-
maximum=5,
|
| 1088 |
-
step=1,
|
| 1089 |
-
value=5,
|
| 1090 |
-
label="🌟 满意度评分 (1-5)"
|
| 1091 |
-
)
|
| 1092 |
-
|
| 1093 |
-
# 反馈文本框
|
| 1094 |
-
feedback_box = gr.Textbox(
|
| 1095 |
-
placeholder="请输入您的反馈意见...",
|
| 1096 |
-
lines=2,
|
| 1097 |
-
label="💬 反馈意见"
|
| 1098 |
-
)
|
| 1099 |
-
|
| 1100 |
-
# 提交按钮
|
| 1101 |
-
submit_feedback_btn = gr.Button("💾 提交反馈", variant="secondary")
|
| 1102 |
-
|
| 1103 |
-
feedback_status = gr.Textbox(
|
| 1104 |
-
label="✅ 提交状态",
|
| 1105 |
-
lines=1,
|
| 1106 |
-
visible=False
|
| 1107 |
-
)
|
| 1108 |
-
|
| 1109 |
-
# State for managing gallery images
|
| 1110 |
-
count_user_examples = gr.State(example_images_cnt.copy())
|
| 1111 |
-
|
| 1112 |
-
# Function to add image to gallery
|
| 1113 |
-
def add_to_count_gallery(new_img_file, current_imgs):
|
| 1114 |
-
"""Add uploaded image to gallery"""
|
| 1115 |
-
if new_img_file is None:
|
| 1116 |
-
return current_imgs, current_imgs
|
| 1117 |
-
|
| 1118 |
-
try:
|
| 1119 |
-
# Add new image path to list
|
| 1120 |
-
if new_img_file not in current_imgs:
|
| 1121 |
-
current_imgs.append(new_img_file)
|
| 1122 |
-
print(f"✅ Added image to gallery: {new_img_file}")
|
| 1123 |
-
except Exception as e:
|
| 1124 |
-
print(f"⚠️ Failed to add image: {e}")
|
| 1125 |
-
|
| 1126 |
-
return current_imgs, current_imgs
|
| 1127 |
-
|
| 1128 |
-
# When user uploads a new image file
|
| 1129 |
-
count_image_uploader.upload(
|
| 1130 |
-
fn=add_to_count_gallery,
|
| 1131 |
-
inputs=[count_image_uploader, count_user_examples],
|
| 1132 |
-
outputs=[count_user_examples, count_example_gallery]
|
| 1133 |
-
)
|
| 1134 |
-
|
| 1135 |
-
# When user selects from gallery, load into annotator
|
| 1136 |
-
def load_from_count_gallery(evt: gr.SelectData, all_imgs):
|
| 1137 |
-
"""Load selected image from gallery into annotator"""
|
| 1138 |
-
if evt.index is not None and evt.index < len(all_imgs):
|
| 1139 |
-
selected_img = all_imgs[evt.index]
|
| 1140 |
-
print(f"📸 Loading image from gallery: {selected_img}")
|
| 1141 |
-
return selected_img
|
| 1142 |
-
return None
|
| 1143 |
-
|
| 1144 |
-
count_example_gallery.select(
|
| 1145 |
-
fn=load_from_count_gallery,
|
| 1146 |
-
inputs=count_user_examples,
|
| 1147 |
-
outputs=count_annotator
|
| 1148 |
-
)
|
| 1149 |
-
|
| 1150 |
-
# Run counting
|
| 1151 |
-
count_btn.click(
|
| 1152 |
-
fn=count_cells_handler,
|
| 1153 |
-
inputs=[count_use_box_radio, count_annotator],
|
| 1154 |
-
outputs=[count_output, download_density_btn, count_status]
|
| 1155 |
-
)
|
| 1156 |
-
|
| 1157 |
-
# 清空按钮事件
|
| 1158 |
-
clear_btn.click(
|
| 1159 |
-
fn=lambda: None,
|
| 1160 |
-
inputs=None,
|
| 1161 |
-
outputs=count_annotator
|
| 1162 |
-
)
|
| 1163 |
-
|
| 1164 |
-
# 绑定事件: 提交反馈
|
| 1165 |
-
def submit_user_feedback(query_id, score, comment, annot_val):
|
| 1166 |
-
try:
|
| 1167 |
-
img_path = annot_val[0] if annot_val and len(annot_val) > 0 else None
|
| 1168 |
-
bboxes = annot_val[1] if annot_val and len(annot_val) > 1 else []
|
| 1169 |
-
|
| 1170 |
-
save_feedback(
|
| 1171 |
-
query_id=query_id,
|
| 1172 |
-
feedback_type=f"score_{int(score)}",
|
| 1173 |
-
feedback_text=comment,
|
| 1174 |
-
img_path=img_path,
|
| 1175 |
-
bboxes=bboxes
|
| 1176 |
-
)
|
| 1177 |
-
return "✅ 反馈已提交,感谢您的评价!", gr.update(visible=True)
|
| 1178 |
-
except Exception as e:
|
| 1179 |
-
return f"❌ 提交失败: {str(e)}", gr.update(visible=True)
|
| 1180 |
-
|
| 1181 |
-
submit_feedback_btn.click(
|
| 1182 |
-
fn=submit_user_feedback,
|
| 1183 |
-
inputs=[current_query_id, score_slider, feedback_box, annotator],
|
| 1184 |
-
outputs=[feedback_status, feedback_status]
|
| 1185 |
-
)
|
| 1186 |
-
|
| 1187 |
-
# ===== Tab 3: Tracking =====
|
| 1188 |
-
with gr.Tab("🎬 跟踪 (Tracking)"):
|
| 1189 |
-
gr.Markdown("## 显微镜物体视频跟踪 - 支持 ZIP 压缩包上传")
|
| 1190 |
-
gr.Markdown(
|
| 1191 |
-
"""
|
| 1192 |
-
**使用说明:**
|
| 1193 |
-
1. 上传ZIP文件或从示例库选择,ZIP内应包含按时间顺序命名的TIF图像序列 (如: t000.tif, t001.tif...)
|
| 1194 |
-
2. (可选) 在首帧上���注边界框并选择 "Yes"
|
| 1195 |
-
3. 点击 "运行跟踪"
|
| 1196 |
-
4. 下载CTC格式结果;如果需要,点击 "清空重选" 选择新ZIP文件运行
|
| 1197 |
-
5. 评分并提交反馈以帮助我们改进模型!
|
| 1198 |
-
|
| 1199 |
-
"""
|
| 1200 |
-
)
|
| 1201 |
-
|
| 1202 |
-
with gr.Row():
|
| 1203 |
-
with gr.Column(scale=1):
|
| 1204 |
-
track_zip_upload = gr.File(
|
| 1205 |
-
label="📦 上传视频帧 ZIP 文件",
|
| 1206 |
-
file_types=[".zip"]
|
| 1207 |
-
)
|
| 1208 |
-
|
| 1209 |
-
# First frame annotation for bounding box
|
| 1210 |
-
track_first_frame_annotator = BBoxAnnotator(
|
| 1211 |
-
label="🖼️ 首帧边界框标注 (可选)",
|
| 1212 |
-
categories=["cell"],
|
| 1213 |
-
visible=False # Hidden initially
|
| 1214 |
-
)
|
| 1215 |
-
|
| 1216 |
-
# Example ZIP gallery
|
| 1217 |
-
track_example_gallery = gr.Gallery(
|
| 1218 |
-
label="📁 示例视频库 (点击选择)",
|
| 1219 |
-
columns=10,
|
| 1220 |
-
rows=1,
|
| 1221 |
-
height=120,
|
| 1222 |
-
object_fit="contain",
|
| 1223 |
-
show_download_button=False
|
| 1224 |
-
)
|
| 1225 |
-
|
| 1226 |
-
with gr.Row():
|
| 1227 |
-
track_use_box_radio = gr.Radio(
|
| 1228 |
-
choices=["Yes", "No"],
|
| 1229 |
-
value="No",
|
| 1230 |
-
label="🔲 使用边界框?"
|
| 1231 |
-
)
|
| 1232 |
-
|
| 1233 |
-
with gr.Row():
|
| 1234 |
-
track_btn = gr.Button("▶️ 运行跟踪", variant="primary", size="lg")
|
| 1235 |
-
clear_btn = gr.Button("🔄 清空重选", variant="secondary")
|
| 1236 |
-
|
| 1237 |
-
# Add to gallery button
|
| 1238 |
-
track_gallery_upload = gr.File(
|
| 1239 |
-
label="➕ 添加ZIP到示例库",
|
| 1240 |
-
file_types=[".zip"],
|
| 1241 |
-
type="filepath"
|
| 1242 |
-
)
|
| 1243 |
-
|
| 1244 |
-
with gr.Column(scale=2):
|
| 1245 |
-
track_first_frame_preview = gr.Image(
|
| 1246 |
-
label="📸 跟踪可视化 (动画预览)",
|
| 1247 |
-
type="filepath",
|
| 1248 |
-
height=400,
|
| 1249 |
-
interactive=False
|
| 1250 |
-
)
|
| 1251 |
-
|
| 1252 |
-
track_output = gr.Textbox(
|
| 1253 |
-
label="📊 跟踪信息",
|
| 1254 |
-
lines=8,
|
| 1255 |
-
interactive=False
|
| 1256 |
-
)
|
| 1257 |
-
|
| 1258 |
-
track_download = gr.File(
|
| 1259 |
-
label="📥 下载跟踪结果 (CTC格式)",
|
| 1260 |
-
visible=False
|
| 1261 |
-
)
|
| 1262 |
-
|
| 1263 |
-
# 满意度评分
|
| 1264 |
-
score_slider = gr.Slider(
|
| 1265 |
-
minimum=1,
|
| 1266 |
-
maximum=5,
|
| 1267 |
-
step=1,
|
| 1268 |
-
value=5,
|
| 1269 |
-
label="🌟 满意度评分 (1-5)"
|
| 1270 |
-
)
|
| 1271 |
-
|
| 1272 |
-
# 反馈文本框
|
| 1273 |
-
feedback_box = gr.Textbox(
|
| 1274 |
-
placeholder="请输入您的反馈意见...",
|
| 1275 |
-
lines=2,
|
| 1276 |
-
label="💬 反馈意见"
|
| 1277 |
-
)
|
| 1278 |
-
|
| 1279 |
-
# 提交按钮
|
| 1280 |
-
submit_feedback_btn = gr.Button("💾 提交反馈", variant="secondary")
|
| 1281 |
-
|
| 1282 |
-
feedback_status = gr.Textbox(
|
| 1283 |
-
label="✅ 提交状态",
|
| 1284 |
-
lines=1,
|
| 1285 |
-
visible=False
|
| 1286 |
-
)
|
| 1287 |
-
|
| 1288 |
-
# State for tracking examples
|
| 1289 |
-
track_user_examples = gr.State(example_tracking_zips.copy())
|
| 1290 |
-
|
| 1291 |
-
# Function to get preview image from ZIP
|
| 1292 |
-
def get_zip_preview(zip_path):
|
| 1293 |
-
"""Extract first frame from ZIP for gallery preview"""
|
| 1294 |
-
try:
|
| 1295 |
-
temp_dir = tempfile.mkdtemp()
|
| 1296 |
-
with zipfile.ZipFile(zip_path, 'r') as zip_ref:
|
| 1297 |
-
for member in zip_ref.namelist():
|
| 1298 |
-
basename = os.path.basename(member)
|
| 1299 |
-
if ('__MACOSX' not in member and
|
| 1300 |
-
not basename.startswith('._') and
|
| 1301 |
-
basename.lower().endswith(('.tif', '.tiff', '.png', '.jpg'))):
|
| 1302 |
-
zip_ref.extract(member, temp_dir)
|
| 1303 |
-
extracted_path = os.path.join(temp_dir, member)
|
| 1304 |
-
|
| 1305 |
-
# Load and normalize for preview
|
| 1306 |
-
import tifffile
|
| 1307 |
-
import numpy as np
|
| 1308 |
-
|
| 1309 |
-
img_np = tifffile.imread(extracted_path)
|
| 1310 |
-
if img_np.dtype == np.uint16:
|
| 1311 |
-
img_min, img_max = img_np.min(), img_np.max()
|
| 1312 |
-
if img_max > img_min:
|
| 1313 |
-
img_np = ((img_np.astype(np.float32) - img_min) / (img_max - img_min) * 255).astype(np.uint8)
|
| 1314 |
-
|
| 1315 |
-
if img_np.ndim == 2:
|
| 1316 |
-
img_np = np.stack([img_np]*3, axis=-1)
|
| 1317 |
-
|
| 1318 |
-
# Save preview
|
| 1319 |
-
preview_path = tempfile.NamedTemporaryFile(delete=False, suffix=".png")
|
| 1320 |
-
Image.fromarray(img_np).save(preview_path.name)
|
| 1321 |
-
return preview_path.name
|
| 1322 |
-
except:
|
| 1323 |
-
pass
|
| 1324 |
-
return None
|
| 1325 |
-
|
| 1326 |
-
# Initialize gallery with previews
|
| 1327 |
-
def init_tracking_gallery():
|
| 1328 |
-
"""Create preview images for ZIP examples"""
|
| 1329 |
-
previews = []
|
| 1330 |
-
for zip_path in example_tracking_zips:
|
| 1331 |
-
if os.path.exists(zip_path):
|
| 1332 |
-
preview = get_zip_preview(zip_path)
|
| 1333 |
-
if preview:
|
| 1334 |
-
previews.append(preview)
|
| 1335 |
-
return previews
|
| 1336 |
-
|
| 1337 |
-
# Load gallery on startup
|
| 1338 |
-
demo.load(
|
| 1339 |
-
fn=init_tracking_gallery,
|
| 1340 |
-
outputs=track_example_gallery
|
| 1341 |
-
)
|
| 1342 |
-
|
| 1343 |
-
# Add ZIP to gallery
|
| 1344 |
-
def add_zip_to_gallery(zip_path, current_zips):
|
| 1345 |
-
if not zip_path:
|
| 1346 |
-
return current_zips, track_example_gallery
|
| 1347 |
-
try:
|
| 1348 |
-
if zip_path not in current_zips:
|
| 1349 |
-
current_zips.append(zip_path)
|
| 1350 |
-
print(f"✅ Added ZIP to gallery: {zip_path}")
|
| 1351 |
-
# Regenerate previews
|
| 1352 |
-
previews = []
|
| 1353 |
-
for zp in current_zips:
|
| 1354 |
-
preview = get_zip_preview(zp)
|
| 1355 |
-
if preview:
|
| 1356 |
-
previews.append(preview)
|
| 1357 |
-
return current_zips, previews
|
| 1358 |
-
except Exception as e:
|
| 1359 |
-
print(f"⚠️ Error: {e}")
|
| 1360 |
-
return current_zips, []
|
| 1361 |
-
|
| 1362 |
-
track_gallery_upload.upload(
|
| 1363 |
-
fn=add_zip_to_gallery,
|
| 1364 |
-
inputs=[track_gallery_upload, track_user_examples],
|
| 1365 |
-
outputs=[track_user_examples, track_example_gallery]
|
| 1366 |
-
)
|
| 1367 |
-
|
| 1368 |
-
# Select ZIP from gallery
|
| 1369 |
-
def load_zip_from_gallery(evt: gr.SelectData, all_zips):
|
| 1370 |
-
if evt.index is not None and evt.index < len(all_zips):
|
| 1371 |
-
selected_zip = all_zips[evt.index]
|
| 1372 |
-
print(f"📁 Selected ZIP from gallery: {selected_zip}")
|
| 1373 |
-
return selected_zip
|
| 1374 |
-
return None
|
| 1375 |
-
|
| 1376 |
-
track_example_gallery.select(
|
| 1377 |
-
fn=load_zip_from_gallery,
|
| 1378 |
-
inputs=track_user_examples,
|
| 1379 |
-
outputs=track_zip_upload
|
| 1380 |
-
)
|
| 1381 |
-
|
| 1382 |
-
# Load first frame when ZIP is uploaded
|
| 1383 |
-
def load_first_frame_for_annotation(zip_file_obj):
|
| 1384 |
-
'''Load and normalize first frame from ZIP for annotation'''
|
| 1385 |
-
if zip_file_obj is None:
|
| 1386 |
-
return None, gr.update(visible=False)
|
| 1387 |
-
|
| 1388 |
-
import tifffile
|
| 1389 |
-
import numpy as np
|
| 1390 |
-
|
| 1391 |
-
try:
|
| 1392 |
-
temp_dir = tempfile.mkdtemp()
|
| 1393 |
-
with zipfile.ZipFile(zip_file_obj.name, 'r') as zip_ref:
|
| 1394 |
-
for member in zip_ref.namelist():
|
| 1395 |
-
basename = os.path.basename(member)
|
| 1396 |
-
if ('__MACOSX' not in member and
|
| 1397 |
-
not basename.startswith('._') and
|
| 1398 |
-
basename.lower().endswith(('.tif', '.tiff'))):
|
| 1399 |
-
zip_ref.extract(member, temp_dir)
|
| 1400 |
-
|
| 1401 |
-
tif_dir = find_valid_tif_dir(temp_dir)
|
| 1402 |
-
if tif_dir:
|
| 1403 |
-
first_frame = extract_first_frame(tif_dir)
|
| 1404 |
-
if first_frame:
|
| 1405 |
-
# Load and normalize the first frame
|
| 1406 |
-
try:
|
| 1407 |
-
img_np = tifffile.imread(first_frame)
|
| 1408 |
-
|
| 1409 |
-
# Normalize to [0, 255] uint8 range for display
|
| 1410 |
-
if img_np.dtype == np.uint8:
|
| 1411 |
-
pass # Already uint8
|
| 1412 |
-
elif img_np.dtype == np.uint16:
|
| 1413 |
-
# Normalize uint16 using actual min/max
|
| 1414 |
-
img_min, img_max = img_np.min(), img_np.max()
|
| 1415 |
-
if img_max > img_min:
|
| 1416 |
-
img_np = ((img_np.astype(np.float32) - img_min) / (img_max - img_min) * 255).astype(np.uint8)
|
| 1417 |
-
else:
|
| 1418 |
-
img_np = (img_np.astype(np.float32) / 65535.0 * 255).astype(np.uint8)
|
| 1419 |
-
else:
|
| 1420 |
-
# Float or other types
|
| 1421 |
-
img_np = img_np.astype(np.float32)
|
| 1422 |
-
img_min, img_max = img_np.min(), img_np.max()
|
| 1423 |
-
if img_max > img_min:
|
| 1424 |
-
img_np = ((img_np - img_min) / (img_max - img_min) * 255).astype(np.uint8)
|
| 1425 |
-
else:
|
| 1426 |
-
img_np = np.clip(img_np * 255, 0, 255).astype(np.uint8)
|
| 1427 |
-
|
| 1428 |
-
# Convert to RGB if grayscale
|
| 1429 |
-
if img_np.ndim == 2:
|
| 1430 |
-
img_np = np.stack([img_np]*3, axis=-1)
|
| 1431 |
-
elif img_np.ndim == 3 and img_np.shape[2] > 3:
|
| 1432 |
-
img_np = img_np[:, :, :3]
|
| 1433 |
-
|
| 1434 |
-
# Save normalized image to temp file
|
| 1435 |
-
temp_img = tempfile.NamedTemporaryFile(delete=False, suffix=".png")
|
| 1436 |
-
Image.fromarray(img_np).save(temp_img.name)
|
| 1437 |
-
|
| 1438 |
-
print(f"✅ Loaded and normalized first frame: {first_frame}")
|
| 1439 |
-
print(f" Original dtype: {tifffile.imread(first_frame).dtype}")
|
| 1440 |
-
print(f" Normalized to uint8 RGB for annotation")
|
| 1441 |
-
|
| 1442 |
-
return temp_img.name, gr.update(visible=True)
|
| 1443 |
-
except Exception as e:
|
| 1444 |
-
print(f"⚠️ Error normalizing first frame: {e}")
|
| 1445 |
-
import traceback
|
| 1446 |
-
traceback.print_exc()
|
| 1447 |
-
# Fallback to original file
|
| 1448 |
-
return first_frame, gr.update(visible=True)
|
| 1449 |
-
except Exception as e:
|
| 1450 |
-
print(f"⚠️ Error loading first frame: {e}")
|
| 1451 |
-
import traceback
|
| 1452 |
-
traceback.print_exc()
|
| 1453 |
-
return None, gr.update(visible=False)
|
| 1454 |
-
|
| 1455 |
-
# Load first frame when ZIP is uploaded
|
| 1456 |
-
track_zip_upload.change(
|
| 1457 |
-
fn=load_first_frame_for_annotation,
|
| 1458 |
-
inputs=track_zip_upload,
|
| 1459 |
-
outputs=[track_first_frame_annotator, track_first_frame_annotator]
|
| 1460 |
-
)
|
| 1461 |
-
|
| 1462 |
-
# Run tracking
|
| 1463 |
-
track_btn.click(
|
| 1464 |
-
fn=track_video_handler,
|
| 1465 |
-
inputs=[track_use_box_radio, track_first_frame_annotator, track_zip_upload],
|
| 1466 |
-
outputs=[track_download, track_output, track_download, track_first_frame_preview]
|
| 1467 |
-
)
|
| 1468 |
-
|
| 1469 |
-
# 清空按钮事件
|
| 1470 |
-
clear_btn.click(
|
| 1471 |
-
fn=lambda: None,
|
| 1472 |
-
inputs=None,
|
| 1473 |
-
outputs=track_first_frame_annotator
|
| 1474 |
-
)
|
| 1475 |
-
|
| 1476 |
-
# 绑定事件: 提交反馈
|
| 1477 |
-
def submit_user_feedback(query_id, score, comment, annot_val):
|
| 1478 |
-
try:
|
| 1479 |
-
img_path = annot_val[0] if annot_val and len(annot_val) > 0 else None
|
| 1480 |
-
bboxes = annot_val[1] if annot_val and len(annot_val) > 1 else []
|
| 1481 |
-
|
| 1482 |
-
save_feedback(
|
| 1483 |
-
query_id=query_id,
|
| 1484 |
-
feedback_type=f"score_{int(score)}",
|
| 1485 |
-
feedback_text=comment,
|
| 1486 |
-
img_path=img_path,
|
| 1487 |
-
bboxes=bboxes
|
| 1488 |
-
)
|
| 1489 |
-
return "✅ 反馈已提交,感谢您的评价!", gr.update(visible=True)
|
| 1490 |
-
except Exception as e:
|
| 1491 |
-
return f"❌ 提交失败: {str(e)}", gr.update(visible=True)
|
| 1492 |
-
|
| 1493 |
-
submit_feedback_btn.click(
|
| 1494 |
-
fn=submit_user_feedback,
|
| 1495 |
-
inputs=[current_query_id, score_slider, feedback_box, annotator],
|
| 1496 |
-
outputs=[feedback_status, feedback_status]
|
| 1497 |
-
)
|
| 1498 |
-
|
| 1499 |
-
gr.Markdown(
|
| 1500 |
-
"""
|
| 1501 |
-
---
|
| 1502 |
-
### 💡 技术说明
|
| 1503 |
-
|
| 1504 |
-
**MicroscopyMatching** - 基于 Stable Diffusion 的显微图像分析工具套件
|
| 1505 |
-
"""
|
| 1506 |
-
)
|
| 1507 |
-
|
| 1508 |
-
if __name__ == "__main__":
|
| 1509 |
-
demo.queue().launch(
|
| 1510 |
-
server_name="0.0.0.0",
|
| 1511 |
-
server_port=7862,
|
| 1512 |
-
share=False,
|
| 1513 |
-
ssr_mode=False,
|
| 1514 |
-
show_error=True,
|
| 1515 |
-
)
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