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Update app.py
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app.py
CHANGED
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@@ -281,72 +281,73 @@ import torch
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import os
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import shutil
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import subprocess
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import time
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from pathlib import Path
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import tempfile
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from inference import load_model, run
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from skimage import measure
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# === 图像处理依赖 ===
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from scipy.ndimage import label
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from matplotlib import cm
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# ===== 清理缓存目录 =====
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print("=====
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subprocess.run("du -sh *", shell=True)
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print("===== ~/.cache =====")
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subprocess.run("ls -lh ~/.cache", shell=True)
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cache_path = os.path.expanduser("~/.cache")
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if os.path.exists(cache_path):
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#
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TRACKING_MODEL = None
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global MODEL, DEVICE
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MODEL, DEVICE = load_model(use_box=False)
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load_model_cpu()
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def load_counting_model():
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"""
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加载计数模型
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替换为你的计数模型加载代码
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"""
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global COUNTING_MODEL
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# TODO: 替换为实际的计数模型
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# 例如: COUNTING_MODEL = torch.load("counting_model.pth")
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print("✅ Counting model loaded (placeholder)")
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pass
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def load_tracking_model():
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"""
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加载跟踪模型
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替换为你的跟踪模型加载代码
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"""
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global TRACKING_MODEL
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# TODO: 替换为实际的跟踪模型
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# 例如: TRACKING_MODEL = torch.load("tracking_model.pth")
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print("✅ Tracking model loaded (placeholder)")
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pass
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def prepare_cuda():
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global MODEL, DEVICE, CUDA_READY
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if torch.cuda.is_available() and not CUDA_READY:
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MODEL.to("cuda")
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DEVICE = torch.device("cuda")
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CUDA_READY = True
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_ = torch.zeros(1, device=DEVICE)
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# ===== BBox 解析 =====
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def parse_first_bbox(bboxes):
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if not bboxes:
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return None
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b = bboxes[0]
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@@ -358,35 +359,8 @@ def parse_first_bbox(bboxes):
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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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# ===== 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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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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# ===== 彩色 mask 可视化 =====
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def colorize_mask(mask: np.ndarray, num_colors: int = 512) -> np.ndarray:
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mask = mask.astype(np.int32)
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def hsv_to_rgb(hh, ss, vv):
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@@ -413,17 +387,17 @@ def colorize_mask(mask: np.ndarray, num_colors: int = 512) -> np.ndarray:
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palette_arr = np.array(palette, dtype=np.uint8)
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return palette_arr[color_idx]
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# =====
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def segment_with_choice(use_box_choice, annot_value, mode="Overlay"):
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if annot_value is None or len(annot_value) < 1:
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return 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"🖼️ Image
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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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@@ -433,284 +407,221 @@ def segment_with_choice(use_box_choice, annot_value, mode="Overlay"):
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print(f"📦 Using box: {box_array}")
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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"❌
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return None
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try:
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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"❌
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return 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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if num_instances == 0:
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return Image.new("RGB", mask.shape[::-1], (255,
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#
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overlay = img_np.copy()
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alpha = 0.5
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for inst_id in
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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(
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overlay[binary_mask == 1] = (1 - alpha) * overlay[binary_mask == 1] + alpha * color
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#
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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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overlay[contour[:, 0], contour[:, 1]] = [1.0, 1.0, 0.0]
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overlay = np.clip(overlay * 255.0, 0, 255).astype(np.uint8)
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if mode == "Instance Mask Only":
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return Image.fromarray(colorize_mask(inst_mask, num_colors=512))
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return Image.fromarray(overlay)
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# =====
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def
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"""
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计数功能
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TODO: 替换为你的计数模型推理代码
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"""
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if image_path is None:
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return None, "请先上传图像"
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try:
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img_np = np.array(img)
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# TODO: 替换为实际的计数模型推理
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# 示例代码:
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# results = COUNTING_MODEL(img_np)
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# count = len(results)
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# 临时使用��单的计数方法作为演示
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from skimage import filters, morphology
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gray = np.array(img.convert('L'))
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thresh = filters.threshold_otsu(gray)
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binary = gray > thresh
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labeled = morphology.label(binary)
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count = labeled.max()
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coords = np.argwhere(region_mask)
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if len(coords) > 0:
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y, x = coords.mean(axis=0)
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ax.text(x, y, str(region_id), color='red',
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fontsize=12, fontweight='bold',
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bbox=dict(boxstyle='round', facecolor='yellow', alpha=0.7))
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temp_file = tempfile.NamedTemporaryFile(delete=False, suffix='.png')
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plt.savefig(temp_file.name, bbox_inches='tight', dpi=150)
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plt.close()
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result_text = f"🔢 检测到 {count} 个细胞"
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print(f"✅ Counting result: {count} cells")
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return temp_file.name, result_text
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except Exception as e:
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print(f"❌ Counting error: {e}")
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""
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try:
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fourcc = cv2.VideoWriter_fourcc(*'mp4v')
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out = cv2.VideoWriter(output_path, fourcc, fps, (width, height))
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# TODO: 替换为实际的跟踪模型推理
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# tracked_frame, tracks = TRACKING_MODEL.update(frame)
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# 临时演示: 在帧上添加文字
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tracked_frame = frame.copy()
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cv2.putText(tracked_frame, f"Frame {frame_count}/{total_frames}",
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(10, 30), cv2.FONT_HERSHEY_SIMPLEX, 1, (0, 255, 0), 2)
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out.write(tracked_frame)
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frame_count += 1
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# 更新进度条
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if frame_count % 10 == 0:
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progress((frame_count / total_frames, f"处理中: {frame_count}/{total_frames}"))
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cap.release()
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out.release()
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print(result_text)
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return
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except Exception as e:
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print(f"❌ Tracking error: {e}")
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example_data = [
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("003_img.png", [(50, 60, 120, 150, "cell")]),
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("1977_Well_F-5_Field_1.png", [(30, 40, 100, 130, "cell")]),
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]
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gallery_images = [p for p, _ in example_data]
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# ===== Gradio UI =====
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with gr.Blocks(title="Microscopy Analysis Suite", theme=gr.themes.Soft()) as demo:
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gr.Markdown(
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"""
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# 🔬 显微图像分析工具套件
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"""
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)
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with gr.Tabs():
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# ===== Tab 1: Segmentation =====
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with gr.Tab("🎨 分割 (Segmentation)"):
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gr.Markdown("##
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with gr.Row():
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with gr.Column(scale=1):
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annotator = BBoxAnnotator(
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)
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image_uploader = gr.Image(label="➕ 上传图像", type="filepath")
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run_btn = gr.Button("▶️ 运行分割", variant="primary")
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use_box_radio = gr.Radio(choices=["Yes", "No"], label="🔲 使用边界框?", visible=False)
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confirm_btn = gr.Button("✅ 确认", visible=False)
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mode_radio = gr.Radio(choices=["Overlay", "Instance Mask Only"], value="Overlay",
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label="🎨 显示模式")
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with gr.Column(scale=2):
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if thumb_path not in current_gallery:
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current_gallery.append(thumb_path)
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except Exception as e:
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print(f"❌ Failed image: {e}")
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return current_gallery
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image_uploader.upload(add_uploaded_image, [image_uploader, user_uploaded_images],
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[example_gallery, user_uploaded_images])
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def on_gallery_select(evt: gr.SelectData, gallery_images):
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index = evt.index
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if index < len(example_data):
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selected_path, selected_boxes = example_data[index]
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return selected_path, selected_boxes
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else:
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selected_path = gallery_images[index]
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return selected_path, []
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example_gallery.select(on_gallery_select, inputs=[user_uploaded_images], outputs=[annotator])
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def show_radio():
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return gr.update(visible=True), gr.update(visible=True)
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run_btn.click(fn=show_radio, outputs=[use_box_radio, confirm_btn])
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confirm_btn.click(fn=segment_with_choice,
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inputs=[use_box_radio, annotator, mode_radio],
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outputs=image_output)
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def handle_comment(comment, annot_value):
|
| 699 |
-
save_feedback(time.strftime("%Y%m%d_%H%M%S") + "_" + str(uuid.uuid4())[:8],
|
| 700 |
-
"comment", comment, annot_value[0], annot_value[1])
|
| 701 |
-
return ""
|
| 702 |
-
|
| 703 |
-
def handle_rating(score, annot_value):
|
| 704 |
-
save_feedback(time.strftime("%Y%m%d_%H%M%S") + "_" + str(uuid.uuid4())[:8],
|
| 705 |
-
"rating", f"Satisfaction Score: {score}", annot_value[0], annot_value[1])
|
| 706 |
-
return 3
|
| 707 |
-
|
| 708 |
-
comment_box.submit(fn=handle_comment, inputs=[comment_box, annotator], outputs=[comment_box])
|
| 709 |
-
submit_score.click(fn=handle_rating, inputs=[score, annotator], outputs=[score])
|
| 710 |
|
| 711 |
# ===== Tab 2: Counting =====
|
| 712 |
with gr.Tab("🔢 计数 (Counting)"):
|
| 713 |
-
gr.Markdown("## 细胞计数分析")
|
| 714 |
|
| 715 |
with gr.Row():
|
| 716 |
with gr.Column(scale=1):
|
|
@@ -718,127 +629,117 @@ with gr.Blocks(title="Microscopy Analysis Suite", theme=gr.themes.Soft()) as dem
|
|
| 718 |
label="🖼️ 上传图像",
|
| 719 |
type="filepath"
|
| 720 |
)
|
| 721 |
-
count_btn = gr.Button("▶️ 运行计数", variant="primary")
|
| 722 |
|
| 723 |
gr.Markdown(
|
| 724 |
"""
|
| 725 |
-
|
| 726 |
-
|
| 727 |
-
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|
| 728 |
"""
|
| 729 |
)
|
| 730 |
|
| 731 |
with gr.Column(scale=2):
|
| 732 |
-
|
| 733 |
-
label="📸 计数结果",
|
| 734 |
-
type="filepath"
|
|
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|
| 735 |
)
|
| 736 |
-
|
| 737 |
-
label="
|
| 738 |
lines=2
|
| 739 |
)
|
| 740 |
-
|
| 741 |
-
count_score = gr.Slider(1, 5, step=1, value=3, label="🌟 满意度 (1–5)")
|
| 742 |
-
count_comment = gr.Textbox(placeholder="输入反馈...", lines=2, label="💬 反馈")
|
| 743 |
-
count_submit = gr.Button("💾 提交评分")
|
| 744 |
|
| 745 |
# 绑定事件
|
| 746 |
count_btn.click(
|
| 747 |
-
fn=
|
| 748 |
inputs=count_input,
|
| 749 |
-
outputs=[
|
| 750 |
-
)
|
| 751 |
-
|
| 752 |
-
def handle_count_feedback(score, comment, img_path):
|
| 753 |
-
if img_path:
|
| 754 |
-
save_feedback(
|
| 755 |
-
time.strftime("%Y%m%d_%H%M%S") + "_count_" + str(uuid.uuid4())[:8],
|
| 756 |
-
"counting",
|
| 757 |
-
f"Score: {score}, Comment: {comment}",
|
| 758 |
-
img_path,
|
| 759 |
-
None
|
| 760 |
-
)
|
| 761 |
-
return 3, ""
|
| 762 |
-
|
| 763 |
-
count_submit.click(
|
| 764 |
-
fn=handle_count_feedback,
|
| 765 |
-
inputs=[count_score, count_comment, count_input],
|
| 766 |
-
outputs=[count_score, count_comment]
|
| 767 |
)
|
| 768 |
|
| 769 |
# ===== Tab 3: Tracking =====
|
| 770 |
with gr.Tab("🎬 跟踪 (Tracking)"):
|
| 771 |
-
gr.Markdown("## 视频细胞跟踪")
|
| 772 |
|
| 773 |
with gr.Row():
|
| 774 |
with gr.Column(scale=1):
|
| 775 |
-
track_input = gr.
|
| 776 |
-
label="
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|
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|
| 777 |
)
|
| 778 |
-
track_btn = gr.Button("▶️ 运行跟踪", variant="primary")
|
| 779 |
|
| 780 |
gr.Markdown(
|
| 781 |
"""
|
| 782 |
-
|
| 783 |
-
|
| 784 |
-
|
| 785 |
-
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|
| 786 |
"""
|
| 787 |
)
|
| 788 |
|
| 789 |
with gr.Column(scale=2):
|
| 790 |
-
|
| 791 |
-
label="
|
|
|
|
| 792 |
)
|
| 793 |
-
|
| 794 |
-
label="📊
|
| 795 |
-
lines=
|
| 796 |
)
|
| 797 |
-
|
| 798 |
-
track_score = gr.Slider(1, 5, step=1, value=3, label="🌟 满意度 (1–5)")
|
| 799 |
-
track_comment = gr.Textbox(placeholder="输入反馈...", lines=2, label="💬 反馈")
|
| 800 |
-
track_submit = gr.Button("💾 提交评分")
|
| 801 |
|
| 802 |
# 绑定事件
|
| 803 |
track_btn.click(
|
| 804 |
-
fn=
|
| 805 |
inputs=track_input,
|
| 806 |
-
outputs=[
|
| 807 |
-
)
|
| 808 |
-
|
| 809 |
-
def handle_track_feedback(score, comment, video_path):
|
| 810 |
-
if video_path:
|
| 811 |
-
save_feedback(
|
| 812 |
-
time.strftime("%Y%m%d_%H%M%S") + "_track_" + str(uuid.uuid4())[:8],
|
| 813 |
-
"tracking",
|
| 814 |
-
f"Score: {score}, Comment: {comment}",
|
| 815 |
-
video_path,
|
| 816 |
-
None
|
| 817 |
-
)
|
| 818 |
-
return 3, ""
|
| 819 |
-
|
| 820 |
-
track_submit.click(
|
| 821 |
-
fn=handle_track_feedback,
|
| 822 |
-
inputs=[track_score, track_comment, track_input],
|
| 823 |
-
outputs=[track_score, track_comment]
|
| 824 |
)
|
| 825 |
|
| 826 |
-
# ===== 页脚 =====
|
| 827 |
gr.Markdown(
|
| 828 |
"""
|
| 829 |
---
|
| 830 |
-
### 💡
|
| 831 |
-
|
| 832 |
-
|
| 833 |
-
-
|
|
|
|
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|
|
|
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|
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|
|
| 834 |
"""
|
| 835 |
)
|
| 836 |
|
| 837 |
if __name__ == "__main__":
|
| 838 |
demo.queue().launch(
|
| 839 |
-
server_name="0.0.0.0",
|
| 840 |
-
server_port=7860,
|
| 841 |
-
share=True,
|
| 842 |
show_error=True
|
| 843 |
)
|
| 844 |
-
|
|
|
|
| 281 |
import os
|
| 282 |
import shutil
|
| 283 |
import subprocess
|
| 284 |
+
import time
|
| 285 |
+
import json
|
| 286 |
+
import uuid
|
| 287 |
from pathlib import Path
|
| 288 |
import tempfile
|
|
|
|
| 289 |
from skimage import measure
|
|
|
|
|
|
|
| 290 |
from matplotlib import cm
|
| 291 |
|
| 292 |
+
# ===== 导入三个推理模块 =====
|
| 293 |
+
from inference_seg import load_model as load_seg_model, run as run_seg
|
| 294 |
+
from inference_count import load_model as load_count_model, run as run_count
|
| 295 |
+
from inference_track import load_model as load_track_model, run as run_track
|
| 296 |
+
|
| 297 |
# ===== 清理缓存目录 =====
|
| 298 |
+
print("===== Cleaning Cache =====")
|
|
|
|
|
|
|
|
|
|
| 299 |
cache_path = os.path.expanduser("~/.cache")
|
| 300 |
if os.path.exists(cache_path):
|
| 301 |
+
try:
|
| 302 |
+
shutil.rmtree(cache_path)
|
| 303 |
+
print("✅ Deleted ~/.cache to free space.")
|
| 304 |
+
except:
|
| 305 |
+
print("⚠️ Could not delete cache")
|
| 306 |
+
|
| 307 |
+
# ===== 全局模型变量 =====
|
| 308 |
+
SEG_MODEL = None
|
| 309 |
+
SEG_DEVICE = torch.device("cpu")
|
| 310 |
+
|
| 311 |
+
COUNT_MODEL = None
|
| 312 |
+
COUNT_DEVICE = torch.device("cpu")
|
| 313 |
+
|
| 314 |
+
TRACK_MODEL = None
|
| 315 |
+
TRACK_DEVICE = torch.device("cpu")
|
| 316 |
+
|
| 317 |
+
def load_all_models():
|
| 318 |
+
"""启动时加载所有模型"""
|
| 319 |
+
global SEG_MODEL, SEG_DEVICE
|
| 320 |
+
global COUNT_MODEL, COUNT_DEVICE
|
| 321 |
+
global TRACK_MODEL, TRACK_DEVICE
|
| 322 |
+
|
| 323 |
+
# 加载分割模型
|
| 324 |
+
print("\n" + "="*60)
|
| 325 |
+
print("📦 Loading Segmentation Model")
|
| 326 |
+
print("="*60)
|
| 327 |
+
SEG_MODEL, SEG_DEVICE = load_seg_model(use_box=False)
|
| 328 |
+
|
| 329 |
+
# 加载计数模型
|
| 330 |
+
print("\n" + "="*60)
|
| 331 |
+
print("📦 Loading Counting Model")
|
| 332 |
+
print("="*60)
|
| 333 |
+
COUNT_MODEL, COUNT_DEVICE = load_count_model(use_box=False)
|
| 334 |
+
|
| 335 |
+
# 加载跟踪模型
|
| 336 |
+
print("\n" + "="*60)
|
| 337 |
+
print("📦 Loading Tracking Model")
|
| 338 |
+
print("="*60)
|
| 339 |
+
TRACK_MODEL, TRACK_DEVICE = load_track_model(use_box=False)
|
| 340 |
+
|
| 341 |
+
print("\n" + "="*60)
|
| 342 |
+
print("✅ All Models Loaded Successfully")
|
| 343 |
+
print("="*60)
|
| 344 |
|
| 345 |
+
# 启动时加载所有模型
|
| 346 |
+
load_all_models()
|
|
|
|
| 347 |
|
| 348 |
+
# ===== 辅助函数 =====
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 349 |
def parse_first_bbox(bboxes):
|
| 350 |
+
"""解析第一个边界框"""
|
| 351 |
if not bboxes:
|
| 352 |
return None
|
| 353 |
b = bboxes[0]
|
|
|
|
| 359 |
return float(b[0]), float(b[1]), float(b[2]), float(b[3])
|
| 360 |
return None
|
| 361 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 362 |
def colorize_mask(mask: np.ndarray, num_colors: int = 512) -> np.ndarray:
|
| 363 |
+
"""将实例掩码转换为彩色图像"""
|
| 364 |
mask = mask.astype(np.int32)
|
| 365 |
|
| 366 |
def hsv_to_rgb(hh, ss, vv):
|
|
|
|
| 387 |
palette_arr = np.array(palette, dtype=np.uint8)
|
| 388 |
return palette_arr[color_idx]
|
| 389 |
|
| 390 |
+
# ===== 分割功能 =====
|
| 391 |
def segment_with_choice(use_box_choice, annot_value, mode="Overlay"):
|
| 392 |
+
"""分割处理函数"""
|
| 393 |
if annot_value is None or len(annot_value) < 1:
|
| 394 |
+
return None, "⚠️ 请先上传图像"
|
|
|
|
| 395 |
|
| 396 |
img_path = annot_value[0]
|
| 397 |
bboxes = annot_value[1] if len(annot_value) > 1 else []
|
| 398 |
|
| 399 |
+
print(f"🖼️ Segmentation - Image: {img_path}")
|
| 400 |
+
|
| 401 |
box_array = None
|
| 402 |
if use_box_choice == "Yes" and bboxes:
|
| 403 |
box = parse_first_bbox(bboxes)
|
|
|
|
| 407 |
print(f"📦 Using box: {box_array}")
|
| 408 |
|
| 409 |
try:
|
| 410 |
+
# 运行分割
|
| 411 |
+
mask = run_seg(SEG_MODEL, img_path, box=box_array, device=SEG_DEVICE)
|
| 412 |
+
|
| 413 |
+
if mask is None:
|
| 414 |
+
return None, "❌ 分割失败"
|
| 415 |
+
|
| 416 |
+
print(f"✅ Segmentation done - Mask shape: {mask.shape}")
|
|
|
|
|
|
|
| 417 |
except Exception as e:
|
| 418 |
+
print(f"❌ Segmentation error: {e}")
|
| 419 |
+
return None, f"分割失败: {str(e)}"
|
| 420 |
|
| 421 |
try:
|
| 422 |
+
# 读取原图
|
| 423 |
+
img = Image.open(img_path).convert("RGB")
|
| 424 |
+
img_rgb = img.resize(mask.shape[::-1], resample=Image.BILINEAR)
|
| 425 |
img_np = np.array(img_rgb, dtype=np.float32)
|
| 426 |
if img_np.max() > 1.5:
|
| 427 |
img_np = img_np / 255.0
|
| 428 |
except Exception as e:
|
| 429 |
+
print(f"❌ Image processing error: {e}")
|
| 430 |
+
return None, f"图像处理失败: {str(e)}"
|
| 431 |
|
| 432 |
+
# 生成可视化
|
| 433 |
mask_np = np.array(mask)
|
| 434 |
inst_mask = mask_np.astype(np.int32)
|
| 435 |
unique_ids = np.unique(inst_mask)
|
| 436 |
num_instances = len(unique_ids[unique_ids != 0])
|
| 437 |
+
|
|
|
|
| 438 |
if num_instances == 0:
|
| 439 |
+
result_text = "⚠️ 未检测到细胞"
|
| 440 |
+
return Image.new("RGB", mask.shape[::-1], (255, 200, 200)), result_text
|
| 441 |
|
| 442 |
+
# 创建叠加图
|
| 443 |
overlay = img_np.copy()
|
| 444 |
alpha = 0.5
|
| 445 |
+
cmap_vis = cm.get_cmap("nipy_spectral", num_instances + 1)
|
| 446 |
|
| 447 |
+
for inst_id in unique_ids:
|
| 448 |
if inst_id == 0:
|
| 449 |
continue
|
| 450 |
binary_mask = (inst_mask == inst_id).astype(np.uint8)
|
| 451 |
+
color = np.array(cmap_vis(inst_id / (num_instances + 1))[:3])
|
| 452 |
overlay[binary_mask == 1] = (1 - alpha) * overlay[binary_mask == 1] + alpha * color
|
| 453 |
|
| 454 |
+
# 绘制轮廓
|
| 455 |
contours = measure.find_contours(binary_mask, 0.5)
|
| 456 |
for contour in contours:
|
| 457 |
contour = contour.astype(np.int32)
|
| 458 |
+
overlay[contour[:, 0], contour[:, 1]] = [1.0, 1.0, 0.0]
|
| 459 |
|
| 460 |
overlay = np.clip(overlay * 255.0, 0, 255).astype(np.uint8)
|
| 461 |
+
result_text = f"✅ 检测到 {num_instances} 个细胞"
|
| 462 |
|
| 463 |
if mode == "Instance Mask Only":
|
| 464 |
+
return Image.fromarray(colorize_mask(inst_mask, num_colors=512)), result_text
|
| 465 |
|
| 466 |
+
return Image.fromarray(overlay), result_text
|
| 467 |
|
| 468 |
+
# ===== 计数功能 =====
|
| 469 |
+
def count_cells_handler(image_path):
|
| 470 |
+
"""计数处理函数"""
|
|
|
|
|
|
|
|
|
|
| 471 |
if image_path is None:
|
| 472 |
+
return None, "⚠️ 请先上传图像"
|
| 473 |
+
|
| 474 |
+
if COUNT_MODEL is None:
|
| 475 |
+
return None, "❌ 计数模型未加载"
|
| 476 |
|
| 477 |
try:
|
| 478 |
+
print(f"🔢 Counting - Image: {image_path}")
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 479 |
|
| 480 |
+
result = run_count(
|
| 481 |
+
COUNT_MODEL,
|
| 482 |
+
image_path,
|
| 483 |
+
box=None,
|
| 484 |
+
device=COUNT_DEVICE,
|
| 485 |
+
visualize=True
|
| 486 |
+
)
|
| 487 |
|
| 488 |
+
if 'error' in result:
|
| 489 |
+
return None, f"❌ 计数失败: {result['error']}"
|
| 490 |
|
| 491 |
+
count = result['count']
|
| 492 |
+
viz_path = result['visualized_path']
|
| 493 |
+
result_text = f"✅ 检测到 {count:.1f} 个细胞"
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 494 |
|
| 495 |
+
print(f"✅ Counting done - Count: {count:.1f}")
|
| 496 |
|
| 497 |
+
return viz_path, result_text
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 498 |
|
| 499 |
except Exception as e:
|
| 500 |
print(f"❌ Counting error: {e}")
|
| 501 |
+
import traceback
|
| 502 |
+
traceback.print_exc()
|
| 503 |
+
return None, f"❌ 计数失败: {str(e)}"
|
| 504 |
+
|
| 505 |
+
# ===== 跟踪功能 =====
|
| 506 |
+
def track_video_handler(video_dir_input):
|
| 507 |
+
"""跟踪处理函数"""
|
| 508 |
+
if video_dir_input is None or video_dir_input.strip() == "":
|
| 509 |
+
return None, "⚠️ 请输入视频帧目录路径"
|
| 510 |
+
|
| 511 |
+
if TRACK_MODEL is None:
|
| 512 |
+
return None, "❌ 跟踪模型未加载"
|
| 513 |
+
|
| 514 |
+
# 检查目录是否存在
|
| 515 |
+
if not os.path.exists(video_dir_input):
|
| 516 |
+
return None, f"❌ 目录不存在: {video_dir_input}"
|
| 517 |
|
| 518 |
try:
|
| 519 |
+
print(f"🎬 Tracking - Video dir: {video_dir_input}")
|
| 520 |
|
| 521 |
+
result = run_track(
|
| 522 |
+
TRACK_MODEL,
|
| 523 |
+
video_dir=video_dir_input,
|
| 524 |
+
box=None,
|
| 525 |
+
device=TRACK_DEVICE,
|
| 526 |
+
output_dir="tracked_results"
|
| 527 |
+
)
|
| 528 |
|
| 529 |
+
if 'error' in result:
|
| 530 |
+
return None, f"❌ 跟踪失败: {result['error']}"
|
|
|
|
|
|
|
| 531 |
|
| 532 |
+
num_tracks = result['num_tracks']
|
| 533 |
+
output_dir = result['output_dir']
|
| 534 |
|
| 535 |
+
result_text = f"""✅ 跟踪完成!
|
| 536 |
+
|
| 537 |
+
🎯 跟踪轨迹数量: {num_tracks}
|
| 538 |
+
📁 结果保存在: {output_dir}
|
| 539 |
+
|
| 540 |
+
包含的文件:
|
| 541 |
+
- res_track.txt (CTC格式轨迹)
|
| 542 |
+
- 其他跟踪数据文件
|
| 543 |
+
"""
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 544 |
|
| 545 |
+
print(f"✅ Tracking done - {num_tracks} tracks")
|
|
|
|
| 546 |
|
| 547 |
+
return None, result_text
|
| 548 |
|
| 549 |
except Exception as e:
|
| 550 |
print(f"❌ Tracking error: {e}")
|
| 551 |
+
import traceback
|
| 552 |
+
traceback.print_exc()
|
| 553 |
+
return None, f"❌ 跟踪失败: {str(e)}"
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 554 |
|
| 555 |
# ===== Gradio UI =====
|
| 556 |
with gr.Blocks(title="Microscopy Analysis Suite", theme=gr.themes.Soft()) as demo:
|
| 557 |
gr.Markdown(
|
| 558 |
"""
|
| 559 |
# 🔬 显微图像分析工具套件
|
| 560 |
+
|
| 561 |
+
支持三种分析模式:
|
| 562 |
+
- 🎨 **分割 (Segmentation)**: 实例分割,每个细胞不同颜色
|
| 563 |
+
- 🔢 **计数 (Counting)**: 基于密度图的细胞计数
|
| 564 |
+
- 🎬 **跟踪 (Tracking)**: 视频序列中的细胞运动跟踪
|
| 565 |
"""
|
| 566 |
)
|
| 567 |
|
| 568 |
with gr.Tabs():
|
| 569 |
# ===== Tab 1: Segmentation =====
|
| 570 |
with gr.Tab("🎨 分割 (Segmentation)"):
|
| 571 |
+
gr.Markdown("## 细胞实例分割 - 每个细胞一个颜色")
|
| 572 |
|
| 573 |
with gr.Row():
|
| 574 |
with gr.Column(scale=1):
|
| 575 |
+
annotator = BBoxAnnotator(
|
| 576 |
+
label="🖼️ 上传图像 (可选标注边界框)",
|
| 577 |
+
categories=["cell"]
|
| 578 |
+
)
|
| 579 |
+
|
| 580 |
+
with gr.Row():
|
| 581 |
+
use_box_radio = gr.Radio(
|
| 582 |
+
choices=["Yes", "No"],
|
| 583 |
+
value="No",
|
| 584 |
+
label="🔲 使用边界框?"
|
| 585 |
+
)
|
| 586 |
+
mode_radio = gr.Radio(
|
| 587 |
+
choices=["Overlay", "Instance Mask Only"],
|
| 588 |
+
value="Overlay",
|
| 589 |
+
label="🎨 显示模式"
|
| 590 |
+
)
|
| 591 |
+
|
| 592 |
+
run_seg_btn = gr.Button("▶️ 运行分割", variant="primary", size="lg")
|
| 593 |
+
|
| 594 |
+
gr.Markdown(
|
| 595 |
+
"""
|
| 596 |
+
**使用说明:**
|
| 597 |
+
1. 上传图像
|
| 598 |
+
2. (可选) 标注边界框并选择 "Yes"
|
| 599 |
+
3. 选择显示模式
|
| 600 |
+
4. 点击 "运行分割"
|
| 601 |
+
"""
|
| 602 |
)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 603 |
|
| 604 |
with gr.Column(scale=2):
|
| 605 |
+
seg_output = gr.Image(
|
| 606 |
+
type="pil",
|
| 607 |
+
label="📸 分割结果",
|
| 608 |
+
height=500
|
| 609 |
+
)
|
| 610 |
+
seg_status = gr.Textbox(
|
| 611 |
+
label="📊 状态信息",
|
| 612 |
+
lines=2
|
| 613 |
+
)
|
| 614 |
+
|
| 615 |
+
# 绑定事件
|
| 616 |
+
run_seg_btn.click(
|
| 617 |
+
fn=segment_with_choice,
|
| 618 |
+
inputs=[use_box_radio, annotator, mode_radio],
|
| 619 |
+
outputs=[seg_output, seg_status]
|
| 620 |
+
)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 621 |
|
| 622 |
# ===== Tab 2: Counting =====
|
| 623 |
with gr.Tab("🔢 计数 (Counting)"):
|
| 624 |
+
gr.Markdown("## 细胞计数分析 - 基于密度图")
|
| 625 |
|
| 626 |
with gr.Row():
|
| 627 |
with gr.Column(scale=1):
|
|
|
|
| 629 |
label="🖼️ 上传图像",
|
| 630 |
type="filepath"
|
| 631 |
)
|
| 632 |
+
count_btn = gr.Button("▶️ 运行计数", variant="primary", size="lg")
|
| 633 |
|
| 634 |
gr.Markdown(
|
| 635 |
"""
|
| 636 |
+
**使用说明:**
|
| 637 |
+
1. 上传细胞图像
|
| 638 |
+
2. 点击 "运行计数"
|
| 639 |
+
3. 查看密度图和计数结果
|
| 640 |
+
|
| 641 |
+
**特点:**
|
| 642 |
+
- 基于 Stable Diffusion 特征
|
| 643 |
+
- 自动生成密度图
|
| 644 |
+
- 无需手动标注
|
| 645 |
"""
|
| 646 |
)
|
| 647 |
|
| 648 |
with gr.Column(scale=2):
|
| 649 |
+
count_output = gr.Image(
|
| 650 |
+
label="📸 计数结果 (左: 原图 | 右: 密度图)",
|
| 651 |
+
type="filepath",
|
| 652 |
+
height=500
|
| 653 |
)
|
| 654 |
+
count_status = gr.Textbox(
|
| 655 |
+
label="📊 统计信息",
|
| 656 |
lines=2
|
| 657 |
)
|
|
|
|
|
|
|
|
|
|
|
|
|
| 658 |
|
| 659 |
# 绑定事件
|
| 660 |
count_btn.click(
|
| 661 |
+
fn=count_cells_handler,
|
| 662 |
inputs=count_input,
|
| 663 |
+
outputs=[count_output, count_status]
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 664 |
)
|
| 665 |
|
| 666 |
# ===== Tab 3: Tracking =====
|
| 667 |
with gr.Tab("🎬 跟踪 (Tracking)"):
|
| 668 |
+
gr.Markdown("## 视频细胞跟踪 - 时间序列分析")
|
| 669 |
|
| 670 |
with gr.Row():
|
| 671 |
with gr.Column(scale=1):
|
| 672 |
+
track_input = gr.Textbox(
|
| 673 |
+
label="📁 视频帧目录路径",
|
| 674 |
+
placeholder="例如: example_imgs/2D+Time/Fluo-N2DL-HeLa/train/02/",
|
| 675 |
+
lines=2
|
| 676 |
)
|
| 677 |
+
track_btn = gr.Button("▶️ 运行跟踪", variant="primary", size="lg")
|
| 678 |
|
| 679 |
gr.Markdown(
|
| 680 |
"""
|
| 681 |
+
**使用说明:**
|
| 682 |
+
1. 输入包含视频帧序列的目录路径
|
| 683 |
+
2. 目录应包含: t000.tif, t001.tif, ...
|
| 684 |
+
3. 点击 "运行跟踪"
|
| 685 |
+
4. 结果将保存到 `tracked_results/` 目录
|
| 686 |
+
|
| 687 |
+
**输入格式:**
|
| 688 |
+
```
|
| 689 |
+
video_dir/
|
| 690 |
+
├── t000.tif
|
| 691 |
+
├── t001.tif
|
| 692 |
+
├── t002.tif
|
| 693 |
+
└── ...
|
| 694 |
+
```
|
| 695 |
+
|
| 696 |
+
**跟踪模式:** Greedy (快速)
|
| 697 |
"""
|
| 698 |
)
|
| 699 |
|
| 700 |
with gr.Column(scale=2):
|
| 701 |
+
track_output = gr.Video(
|
| 702 |
+
label="📹 跟踪结果视频 (暂不支持)",
|
| 703 |
+
visible=False
|
| 704 |
)
|
| 705 |
+
track_status = gr.Textbox(
|
| 706 |
+
label="📊 跟踪信息",
|
| 707 |
+
lines=10
|
| 708 |
)
|
|
|
|
|
|
|
|
|
|
|
|
|
| 709 |
|
| 710 |
# 绑定事件
|
| 711 |
track_btn.click(
|
| 712 |
+
fn=track_video_handler,
|
| 713 |
inputs=track_input,
|
| 714 |
+
outputs=[track_output, track_status]
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 715 |
)
|
| 716 |
|
|
|
|
| 717 |
gr.Markdown(
|
| 718 |
"""
|
| 719 |
---
|
| 720 |
+
### 💡 技术说明
|
| 721 |
+
|
| 722 |
+
**分割 (Segmentation)**
|
| 723 |
+
- 模型: 基于 Stable Diffusion 特征的实例分割
|
| 724 |
+
- 输出: 每个细胞一个唯一颜色的掩码
|
| 725 |
+
|
| 726 |
+
**计数 (Counting)**
|
| 727 |
+
- 模型: 密度图估计
|
| 728 |
+
- 输出: 密度热力图 + 总计数
|
| 729 |
+
|
| 730 |
+
**跟踪 (Tracking)**
|
| 731 |
+
- 模型: Trackastra 跟踪算法
|
| 732 |
+
- 输出: CTC 格式的轨迹文件
|
| 733 |
+
|
| 734 |
+
---
|
| 735 |
+
📧 问题反馈 | 🌟 GitHub
|
| 736 |
"""
|
| 737 |
)
|
| 738 |
|
| 739 |
if __name__ == "__main__":
|
| 740 |
demo.queue().launch(
|
| 741 |
+
server_name="0.0.0.0",
|
| 742 |
+
server_port=7860,
|
| 743 |
+
share=True,
|
| 744 |
show_error=True
|
| 745 |
)
|
|
|