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Commit ·
c204e64
1
Parent(s): f6846ac
update interface functions
Browse files- .gitattributes +1 -0
- app.py +352 -114
- example_imgs/{1977_Well_F-5_Field_1.png → cnt/00_01.png} +2 -2
- example_imgs/{1977_Well_F-5_Field_1_seg.png → cnt/047cell.png} +2 -2
- example_imgs/cnt/6800-17000_GTEX-XQ3S_Adipose-Subcutaneous.png +3 -0
- 003_img.png → example_imgs/seg/003_img.png +0 -0
- example_imgs/seg/1-23 [Scan I08].png +3 -0
- example_imgs/seg/10X_B2_Tile-15.aligned.png +3 -0
- 1977_Well_F-5_Field_1.png → example_imgs/seg/1977_Well_F-5_Field_1.png +0 -0
- example_imgs/seg/200972823[5179]_RhoGGG_YAP_TAZ [200972823 Well K6 Field #2].png +3 -0
- example_imgs/seg/A172_Phase_C7_1_00d00h00m_1.png +3 -0
- example_imgs/seg/JE2NileRed_oilp22_PMP_101220_011_NR.png +3 -0
- example_imgs/seg/OpenTest_031.png +3 -0
- example_imgs/seg/X_24.png +3 -0
- example_imgs/seg/exp_A01_G002_0001.oir.png +3 -0
- example_imgs/tra/tracking_test_sequence.zip +3 -0
- example_imgs/tra/tracking_test_sequence2.zip +3 -0
.gitattributes
CHANGED
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@@ -37,3 +37,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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1977_Well_F-5_Field_1.png filter=lfs diff=lfs merge=lfs -text
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example_imgs/1977_Well_F-5_Field_1_seg.png filter=lfs diff=lfs merge=lfs -text
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example_imgs/1977_Well_F-5_Field_1.png filter=lfs diff=lfs merge=lfs -text
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1977_Well_F-5_Field_1.png filter=lfs diff=lfs merge=lfs -text
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example_imgs/1977_Well_F-5_Field_1_seg.png filter=lfs diff=lfs merge=lfs -text
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example_imgs/1977_Well_F-5_Field_1.png filter=lfs diff=lfs merge=lfs -text
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+
*.png filter=lfs diff=lfs merge=lfs -text
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app.py
CHANGED
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@@ -27,7 +27,7 @@ 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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except:
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pass
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@@ -203,13 +203,14 @@ def segment_with_choice(use_box_choice, annot_value):
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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("
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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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overlay[binary_mask == 1] = (1 - alpha) * overlay[binary_mask == 1] + alpha * color
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# 绘制轮廓
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@@ -439,6 +440,19 @@ def create_ctc_results_zip(output_dir):
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print(f"✅ ZIP created: {zip_path} ({os.path.getsize(zip_path) / 1024:.1f} KB)")
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return zip_path
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def extract_first_frame(tif_dir):
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"""
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Extract the first frame from a directory of TIF files
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@@ -495,14 +509,14 @@ def create_tracking_visualization(tif_dir, output_dir, valid_tif_files):
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# Create color map for consistent track IDs
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# Use a colormap with many distinct colors
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try:
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except:
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frames = []
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alpha = 0.
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# Process each frame
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num_frames = min(len(valid_tif_files), len(mask_files))
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@@ -570,7 +584,8 @@ def create_tracking_visualization(tif_dir, output_dir, valid_tif_files):
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binary_mask = (mask == track_id)
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# Get consistent color for this track ID
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color = np.array(cmap(int(track_id) % 256)[:3])
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# Blend color onto image
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overlay[binary_mask] = (1 - alpha) * overlay[binary_mask] + alpha * color
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@@ -798,7 +813,10 @@ def track_video_handler(use_box_choice, first_frame_annot, zip_file_obj):
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# ===== 示例图像 =====
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-
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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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# 全局状态
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current_query_id = gr.State(str(uuid.uuid4()))
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user_uploaded_examples = gr.State(
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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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# 示例图片Gallery
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example_gallery = gr.Gallery(
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label="📁 示例图片",
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columns=
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object_fit="cover",
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)
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# 上传示例图片
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image_uploader = gr.Image(
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label="➕ 上传新示例到Gallery",
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type="filepath"
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)
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with gr.Row():
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use_box_radio = gr.Radio(
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run_seg_btn = gr.Button("▶️ 运行分割", variant="primary", size="lg")
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2. (可选) 标注边界框并选择 "Yes"
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3. 点击 "运行分割"
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"""
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)
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with gr.Column(scale=2):
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seg_output = gr.Image(
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type="pil",
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# 下载原始预测结果
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download_mask_btn = gr.File(
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label="📥 下载原始预测 (.tif 格式)",
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visible=True
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)
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# 满意度评分
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# 初始化Gallery显示
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demo.load(
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fn=lambda:
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outputs=example_gallery
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)
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# ===== Tab 2: Counting =====
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with gr.Tab("🔢 计数 (Counting)"):
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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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categories=["cell"]
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)
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# 上传示例图片
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count_image_uploader = gr.Image(
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label="➕ 上传新示例到Gallery",
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type="filepath"
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)
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with gr.Row():
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count_use_box_radio = gr.Radio(
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count_btn = gr.Button("▶️ 运行计数", variant="primary", size="lg")
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with gr.Column(scale=2):
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count_output = gr.Image(
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label="📊 统计信息",
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lines=2
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)
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# 下载原始预测结果
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download_density_btn = gr.File(
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label="📥 下载原始预测 (.npy 格式)",
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visible=True
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)
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#
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fn=count_cells_handler,
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inputs=[count_use_box_radio, count_annotator],
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outputs=[count_output, download_density_btn, count_status]
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)
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# 初始化Gallery显示
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fn=lambda: example_images.copy(),
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outputs=count_example_gallery
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# 绑定事件: 上传示例图片到Counting Gallery
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count_user_examples = gr.State(example_images.copy())
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try:
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fn=add_to_count_gallery,
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inputs=[count_image_uploader, count_user_examples],
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outputs=count_user_examples
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).then(
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fn=lambda imgs: imgs,
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inputs=count_user_examples,
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outputs=count_example_gallery
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)
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#
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def load_from_count_gallery(evt: gr.SelectData, all_imgs):
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if evt.index is not None and evt.index < len(all_imgs):
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-
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return None
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count_example_gallery.select(
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inputs=count_user_examples,
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outputs=count_annotator
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)
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# ===== Tab 3: Tracking =====
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with gr.Tab("🎬 跟踪 (Tracking)"):
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gr.Markdown("## 视频
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with gr.Row():
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with gr.Column(scale=1):
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label="📦 上传视频帧 ZIP 文件",
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file_types=[".zip"]
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)
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-
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# First frame annotation for bounding box
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track_first_frame_annotator = BBoxAnnotator(
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label="🖼️ 首帧边界框标注 (可选)",
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categories=["cell"]
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with gr.Row():
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track_btn = gr.Button("▶️ 运行跟踪", variant="primary", size="lg")
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3. 点击 "运行跟踪"
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4. 下载CTC格式结果
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**注意:**
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- 确保TIFF文件按时间顺序命名 (如: t000.tif, t001.tif...)
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- 边界框将应用于整个视频序列
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- 避免使用macOS的压缩工具
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'''
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)
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with gr.Column(scale=2):
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# Preview of first frame
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track_first_frame_preview = gr.Image(
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label="📸
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type="
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height=
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track_output = gr.Textbox(
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interactive=False
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# Download button for CTC results
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track_download = gr.File(
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label="📥 下载跟踪结果 (CTC格式)",
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visible=False
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)
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| 1140 |
def load_first_frame_for_annotation(zip_file_obj):
|
| 1141 |
'''Load and normalize first frame from ZIP for annotation'''
|
| 1142 |
if zip_file_obj is None:
|
| 1143 |
-
return None
|
| 1144 |
|
| 1145 |
import tifffile
|
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|
| 1146 |
|
| 1147 |
try:
|
| 1148 |
temp_dir = tempfile.mkdtemp()
|
|
@@ -1158,7 +1371,7 @@ with gr.Blocks(title="Microscopy Analysis Suite", theme=gr.themes.Soft()) as dem
|
|
| 1158 |
if tif_dir:
|
| 1159 |
first_frame = extract_first_frame(tif_dir)
|
| 1160 |
if first_frame:
|
| 1161 |
-
#
|
| 1162 |
try:
|
| 1163 |
img_np = tifffile.imread(first_frame)
|
| 1164 |
|
|
@@ -1195,22 +1408,24 @@ with gr.Blocks(title="Microscopy Analysis Suite", theme=gr.themes.Soft()) as dem
|
|
| 1195 |
print(f" Original dtype: {tifffile.imread(first_frame).dtype}")
|
| 1196 |
print(f" Normalized to uint8 RGB for annotation")
|
| 1197 |
|
| 1198 |
-
return temp_img.name
|
| 1199 |
-
# ===== NORMALIZATION ENDS HERE =====
|
| 1200 |
except Exception as e:
|
| 1201 |
print(f"⚠️ Error normalizing first frame: {e}")
|
|
|
|
|
|
|
| 1202 |
# Fallback to original file
|
| 1203 |
-
return first_frame
|
| 1204 |
except Exception as e:
|
| 1205 |
print(f"⚠️ Error loading first frame: {e}")
|
| 1206 |
-
|
| 1207 |
-
|
|
|
|
| 1208 |
|
| 1209 |
-
# Load first frame
|
| 1210 |
track_zip_upload.change(
|
| 1211 |
fn=load_first_frame_for_annotation,
|
| 1212 |
inputs=track_zip_upload,
|
| 1213 |
-
outputs=track_first_frame_annotator
|
| 1214 |
)
|
| 1215 |
|
| 1216 |
# Run tracking
|
|
@@ -1219,6 +1434,29 @@ with gr.Blocks(title="Microscopy Analysis Suite", theme=gr.themes.Soft()) as dem
|
|
| 1219 |
inputs=[track_use_box_radio, track_first_frame_annotator, track_zip_upload],
|
| 1220 |
outputs=[track_download, track_output, track_download, track_first_frame_preview]
|
| 1221 |
)
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|
| 1222 |
|
| 1223 |
gr.Markdown(
|
| 1224 |
"""
|
|
@@ -1232,7 +1470,7 @@ with gr.Blocks(title="Microscopy Analysis Suite", theme=gr.themes.Soft()) as dem
|
|
| 1232 |
if __name__ == "__main__":
|
| 1233 |
demo.queue().launch(
|
| 1234 |
server_name="0.0.0.0",
|
| 1235 |
-
server_port=
|
| 1236 |
share=True,
|
| 1237 |
show_error=True
|
| 1238 |
)
|
|
|
|
| 27 |
if os.path.exists(cache_path):
|
| 28 |
try:
|
| 29 |
shutil.rmtree(cache_path)
|
| 30 |
+
print("✅ Deleted ~/.cache/huggingface/gradio")
|
| 31 |
except:
|
| 32 |
pass
|
| 33 |
|
|
|
|
| 203 |
# ==== Color Overlay (每个实例一个颜色) ====
|
| 204 |
overlay = img_np.copy()
|
| 205 |
alpha = 0.5
|
| 206 |
+
# cmap = cm.get_cmap("hsv", num_instances + 1)
|
| 207 |
|
| 208 |
for inst_id in np.unique(inst_mask):
|
| 209 |
if inst_id == 0:
|
| 210 |
continue
|
| 211 |
binary_mask = (inst_mask == inst_id).astype(np.uint8)
|
| 212 |
+
# color = np.array(cmap(inst_id / (num_instances + 1))[:3]) # RGB only, ignore alpha
|
| 213 |
+
color = get_well_spaced_color(inst_id)
|
| 214 |
overlay[binary_mask == 1] = (1 - alpha) * overlay[binary_mask == 1] + alpha * color
|
| 215 |
|
| 216 |
# 绘制轮廓
|
|
|
|
| 440 |
print(f"✅ ZIP created: {zip_path} ({os.path.getsize(zip_path) / 1024:.1f} KB)")
|
| 441 |
return zip_path
|
| 442 |
|
| 443 |
+
# 使用更智能的颜色分配 - 让相邻的ID颜色差异更大
|
| 444 |
+
def get_well_spaced_color(track_id, num_colors=256):
|
| 445 |
+
"""生成间隔良好的颜色,相邻ID使用对比色"""
|
| 446 |
+
# 使用质数跳跃来分散颜色
|
| 447 |
+
golden_ratio = 0.618033988749895
|
| 448 |
+
hue = (track_id * golden_ratio) % 1.0
|
| 449 |
+
|
| 450 |
+
# 使用高饱和度和明度
|
| 451 |
+
import colorsys
|
| 452 |
+
rgb = colorsys.hsv_to_rgb(hue, 0.9, 0.95)
|
| 453 |
+
return np.array(rgb)
|
| 454 |
+
|
| 455 |
+
|
| 456 |
def extract_first_frame(tif_dir):
|
| 457 |
"""
|
| 458 |
Extract the first frame from a directory of TIF files
|
|
|
|
| 509 |
|
| 510 |
# Create color map for consistent track IDs
|
| 511 |
# Use a colormap with many distinct colors
|
| 512 |
+
# try:
|
| 513 |
+
# cmap = colormaps.get_cmap("hsv")
|
| 514 |
+
# except:
|
| 515 |
+
# from matplotlib import cm
|
| 516 |
+
# cmap = cm.get_cmap("hsv")
|
| 517 |
|
| 518 |
frames = []
|
| 519 |
+
alpha = 0.3 # Transparency for overlay
|
| 520 |
|
| 521 |
# Process each frame
|
| 522 |
num_frames = min(len(valid_tif_files), len(mask_files))
|
|
|
|
| 584 |
binary_mask = (mask == track_id)
|
| 585 |
|
| 586 |
# Get consistent color for this track ID
|
| 587 |
+
# color = np.array(cmap(int(track_id) % 256)[:3])
|
| 588 |
+
color = get_well_spaced_color(int(track_id))
|
| 589 |
|
| 590 |
# Blend color onto image
|
| 591 |
overlay[binary_mask] = (1 - alpha) * overlay[binary_mask] + alpha * color
|
|
|
|
| 813 |
|
| 814 |
|
| 815 |
# ===== 示例图像 =====
|
| 816 |
+
example_images_seg = [f for f in glob("example_imgs/seg/*")]
|
| 817 |
+
# ["example_imgs/seg/003_img.png", "example_imgs/seg/1977_Well_F-5_Field_1.png"]
|
| 818 |
+
example_images_cnt = [f for f in glob("example_imgs/cnt/*")]
|
| 819 |
+
example_tracking_zips = [f for f in glob("example_imgs/tra/*.zip")]
|
| 820 |
|
| 821 |
# ===== Gradio UI =====
|
| 822 |
with gr.Blocks(title="Microscopy Analysis Suite", theme=gr.themes.Soft()) as demo:
|
|
|
|
| 833 |
|
| 834 |
# 全局状态
|
| 835 |
current_query_id = gr.State(str(uuid.uuid4()))
|
| 836 |
+
user_uploaded_examples = gr.State(example_images_seg.copy()) # 初始化时包含原始示例
|
| 837 |
|
| 838 |
with gr.Tabs():
|
| 839 |
# ===== Tab 1: Segmentation =====
|
| 840 |
with gr.Tab("🎨 分割 (Segmentation)"):
|
| 841 |
+
gr.Markdown("## 显微镜物体实例分割")
|
| 842 |
+
gr.Markdown(
|
| 843 |
+
"""
|
| 844 |
+
**使用说明:**
|
| 845 |
+
1. 上传图像或选择示例图片(支持多种格式: .png, .jpg, .tif)
|
| 846 |
+
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"
|
| 847 |
+
3. 点击 "运行分割"
|
| 848 |
+
4. 查看分割结果,下载原始预测mask (.tif格式)
|
| 849 |
+
5. 评分并提交反馈以帮助我们改进模型!
|
| 850 |
+
"""
|
| 851 |
+
)
|
| 852 |
|
| 853 |
with gr.Row():
|
| 854 |
with gr.Column(scale=1):
|
|
|
|
| 860 |
# 示例图片Gallery
|
| 861 |
example_gallery = gr.Gallery(
|
| 862 |
label="📁 示例图片",
|
| 863 |
+
columns=len(example_images_seg),
|
| 864 |
+
rows=1,
|
| 865 |
+
height=120,
|
| 866 |
object_fit="cover",
|
| 867 |
+
show_download_button=False
|
| 868 |
)
|
| 869 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 870 |
|
| 871 |
with gr.Row():
|
| 872 |
use_box_radio = gr.Radio(
|
|
|
|
| 877 |
|
| 878 |
run_seg_btn = gr.Button("▶️ 运行分割", variant="primary", size="lg")
|
| 879 |
|
| 880 |
+
# 上传示例图片
|
| 881 |
+
image_uploader = gr.Image(
|
| 882 |
+
label="➕ 上传新示例到Gallery",
|
| 883 |
+
type="filepath"
|
|
|
|
|
|
|
|
|
|
| 884 |
)
|
| 885 |
|
| 886 |
+
|
| 887 |
with gr.Column(scale=2):
|
| 888 |
seg_output = gr.Image(
|
| 889 |
type="pil",
|
|
|
|
| 894 |
# 下载原始预测结果
|
| 895 |
download_mask_btn = gr.File(
|
| 896 |
label="📥 下载原始预测 (.tif 格式)",
|
| 897 |
+
visible=True,
|
| 898 |
+
height=40,
|
| 899 |
)
|
| 900 |
|
| 901 |
# 满意度评分
|
|
|
|
| 932 |
|
| 933 |
# 初始化Gallery显示
|
| 934 |
demo.load(
|
| 935 |
+
fn=lambda: example_images_seg.copy(),
|
| 936 |
outputs=example_gallery
|
| 937 |
)
|
| 938 |
|
|
|
|
| 994 |
|
| 995 |
# ===== Tab 2: Counting =====
|
| 996 |
with gr.Tab("🔢 计数 (Counting)"):
|
| 997 |
+
gr.Markdown("## 显微镜物体计数分析")
|
| 998 |
+
gr.Markdown(
|
| 999 |
+
"""
|
| 1000 |
+
**使用说明:**
|
| 1001 |
+
1. 上传图像或选择示例图片(支持多种格式: .png, .jpg, .tif)
|
| 1002 |
+
2. (可选) 标注边界框并选择 "Yes",或直接点击 "运行计数"
|
| 1003 |
+
3. 点击 "运行计数"
|
| 1004 |
+
4. 查看密度图,下载原始预测 (.npy格式)
|
| 1005 |
+
5. 评分并提交反馈以帮助我们改进模型!
|
| 1006 |
+
"""
|
| 1007 |
+
)
|
| 1008 |
|
| 1009 |
with gr.Row():
|
| 1010 |
with gr.Column(scale=1):
|
|
|
|
| 1013 |
categories=["cell"]
|
| 1014 |
)
|
| 1015 |
|
| 1016 |
+
# Example gallery with "add" functionality
|
| 1017 |
+
with gr.Row():
|
| 1018 |
+
count_example_gallery = gr.Gallery(
|
| 1019 |
+
label="📁 示例图片",
|
| 1020 |
+
columns=len(example_images_cnt),
|
| 1021 |
+
rows=1,
|
| 1022 |
+
object_fit="cover",
|
| 1023 |
+
height=120,
|
| 1024 |
+
value=example_images_cnt.copy(), # Initialize with examples
|
| 1025 |
+
show_download_button=False
|
| 1026 |
+
)
|
| 1027 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1028 |
|
| 1029 |
with gr.Row():
|
| 1030 |
count_use_box_radio = gr.Radio(
|
|
|
|
| 1035 |
|
| 1036 |
count_btn = gr.Button("▶️ 运行计数", variant="primary", size="lg")
|
| 1037 |
|
| 1038 |
+
# Add button to upload new examples
|
| 1039 |
+
with gr.Row():
|
| 1040 |
+
count_image_uploader = gr.File(
|
| 1041 |
+
label="➕ 添加示例图片",
|
| 1042 |
+
file_types=["image"],
|
| 1043 |
+
type="filepath"
|
| 1044 |
+
)
|
| 1045 |
+
|
| 1046 |
|
| 1047 |
with gr.Column(scale=2):
|
| 1048 |
count_output = gr.Image(
|
|
|
|
| 1054 |
label="📊 统计信息",
|
| 1055 |
lines=2
|
| 1056 |
)
|
|
|
|
|
|
|
| 1057 |
download_density_btn = gr.File(
|
| 1058 |
label="📥 下载原始预测 (.npy 格式)",
|
| 1059 |
visible=True
|
| 1060 |
)
|
| 1061 |
+
|
| 1062 |
+
# 满意度评分
|
| 1063 |
+
score_slider = gr.Slider(
|
| 1064 |
+
minimum=1,
|
| 1065 |
+
maximum=5,
|
| 1066 |
+
step=1,
|
| 1067 |
+
value=5,
|
| 1068 |
+
label="🌟 满意度评分 (1-5)"
|
| 1069 |
+
)
|
| 1070 |
+
|
| 1071 |
+
# 反馈文本框
|
| 1072 |
+
feedback_box = gr.Textbox(
|
| 1073 |
+
placeholder="请输入您的反馈意见...",
|
| 1074 |
+
lines=2,
|
| 1075 |
+
label="💬 反馈意见"
|
| 1076 |
+
)
|
| 1077 |
+
|
| 1078 |
+
# 提交按钮
|
| 1079 |
+
submit_feedback_btn = gr.Button("💾 提交反馈", variant="secondary")
|
| 1080 |
+
|
| 1081 |
+
feedback_status = gr.Textbox(
|
| 1082 |
+
label="✅ 提交状态",
|
| 1083 |
+
lines=1,
|
| 1084 |
+
visible=False
|
| 1085 |
+
)
|
| 1086 |
|
| 1087 |
+
# State for managing gallery images
|
| 1088 |
+
count_user_examples = gr.State(example_images_cnt.copy())
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1089 |
|
| 1090 |
+
# Function to add image to gallery
|
| 1091 |
+
def add_to_count_gallery(new_img_file, current_imgs):
|
| 1092 |
+
"""Add uploaded image to gallery"""
|
| 1093 |
+
if new_img_file is None:
|
| 1094 |
+
return current_imgs, current_imgs
|
| 1095 |
+
|
| 1096 |
try:
|
| 1097 |
+
# Add new image path to list
|
| 1098 |
+
if new_img_file not in current_imgs:
|
| 1099 |
+
current_imgs.append(new_img_file)
|
| 1100 |
+
print(f"✅ Added image to gallery: {new_img_file}")
|
| 1101 |
+
except Exception as e:
|
| 1102 |
+
print(f"⚠️ Failed to add image: {e}")
|
| 1103 |
+
|
| 1104 |
+
return current_imgs, current_imgs
|
| 1105 |
|
| 1106 |
+
# When user uploads a new image file
|
| 1107 |
+
count_image_uploader.upload(
|
| 1108 |
fn=add_to_count_gallery,
|
| 1109 |
inputs=[count_image_uploader, count_user_examples],
|
| 1110 |
+
outputs=[count_user_examples, count_example_gallery]
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1111 |
)
|
| 1112 |
|
| 1113 |
+
# When user selects from gallery, load into annotator
|
| 1114 |
def load_from_count_gallery(evt: gr.SelectData, all_imgs):
|
| 1115 |
+
"""Load selected image from gallery into annotator"""
|
| 1116 |
if evt.index is not None and evt.index < len(all_imgs):
|
| 1117 |
+
selected_img = all_imgs[evt.index]
|
| 1118 |
+
print(f"📸 Loading image from gallery: {selected_img}")
|
| 1119 |
+
return selected_img
|
| 1120 |
return None
|
| 1121 |
|
| 1122 |
count_example_gallery.select(
|
|
|
|
| 1124 |
inputs=count_user_examples,
|
| 1125 |
outputs=count_annotator
|
| 1126 |
)
|
| 1127 |
+
|
| 1128 |
+
# Run counting
|
| 1129 |
+
count_btn.click(
|
| 1130 |
+
fn=count_cells_handler,
|
| 1131 |
+
inputs=[count_use_box_radio, count_annotator],
|
| 1132 |
+
outputs=[count_output, download_density_btn, count_status]
|
| 1133 |
+
)
|
| 1134 |
+
|
| 1135 |
+
# 绑定事件: 提交反馈
|
| 1136 |
+
def submit_user_feedback(query_id, score, comment, annot_val):
|
| 1137 |
+
try:
|
| 1138 |
+
img_path = annot_val[0] if annot_val and len(annot_val) > 0 else None
|
| 1139 |
+
bboxes = annot_val[1] if annot_val and len(annot_val) > 1 else []
|
| 1140 |
+
|
| 1141 |
+
save_feedback(
|
| 1142 |
+
query_id=query_id,
|
| 1143 |
+
feedback_type=f"score_{int(score)}",
|
| 1144 |
+
feedback_text=comment,
|
| 1145 |
+
img_path=img_path,
|
| 1146 |
+
bboxes=bboxes
|
| 1147 |
+
)
|
| 1148 |
+
return "✅ 反馈已提交,感谢您的评价!", gr.update(visible=True)
|
| 1149 |
+
except Exception as e:
|
| 1150 |
+
return f"❌ 提交失败: {str(e)}", gr.update(visible=True)
|
| 1151 |
+
|
| 1152 |
+
submit_feedback_btn.click(
|
| 1153 |
+
fn=submit_user_feedback,
|
| 1154 |
+
inputs=[current_query_id, score_slider, feedback_box, annotator],
|
| 1155 |
+
outputs=[feedback_status, feedback_status]
|
| 1156 |
+
)
|
| 1157 |
|
| 1158 |
# ===== Tab 3: Tracking =====
|
| 1159 |
with gr.Tab("🎬 跟踪 (Tracking)"):
|
| 1160 |
+
gr.Markdown("## 显微镜物体视频跟踪 - 支持 ZIP 压缩包上传")
|
| 1161 |
+
gr.Markdown(
|
| 1162 |
+
"""
|
| 1163 |
+
**使用说明:**
|
| 1164 |
+
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...)
|
| 1165 |
+
2. (可选) 在首帧上标注边界框并选择 "Yes"
|
| 1166 |
+
3. 点击 "运行跟踪"
|
| 1167 |
+
4. 下载CTC格式结果
|
| 1168 |
+
5. 评分并提交反馈以帮助我们改进模型!
|
| 1169 |
+
|
| 1170 |
+
"""
|
| 1171 |
+
)
|
| 1172 |
|
| 1173 |
with gr.Row():
|
| 1174 |
with gr.Column(scale=1):
|
|
|
|
| 1176 |
label="📦 上传视频帧 ZIP 文件",
|
| 1177 |
file_types=[".zip"]
|
| 1178 |
)
|
| 1179 |
+
|
| 1180 |
# First frame annotation for bounding box
|
| 1181 |
track_first_frame_annotator = BBoxAnnotator(
|
| 1182 |
label="🖼️ 首帧边界框标注 (可选)",
|
| 1183 |
+
categories=["cell"],
|
| 1184 |
+
visible=False # Hidden initially
|
| 1185 |
+
)
|
| 1186 |
+
|
| 1187 |
+
# Example ZIP gallery
|
| 1188 |
+
track_example_gallery = gr.Gallery(
|
| 1189 |
+
label="📁 示例视频库 (点击选择)",
|
| 1190 |
+
columns=10,
|
| 1191 |
+
rows=1,
|
| 1192 |
+
height=120,
|
| 1193 |
+
object_fit="contain",
|
| 1194 |
+
show_download_button=False
|
| 1195 |
)
|
| 1196 |
|
| 1197 |
with gr.Row():
|
|
|
|
| 1203 |
|
| 1204 |
track_btn = gr.Button("▶️ 运行跟踪", variant="primary", size="lg")
|
| 1205 |
|
| 1206 |
+
# Add to gallery button
|
| 1207 |
+
track_gallery_upload = gr.File(
|
| 1208 |
+
label="➕ 添加ZIP到示例库",
|
| 1209 |
+
file_types=[".zip"],
|
| 1210 |
+
type="filepath"
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1211 |
)
|
| 1212 |
|
| 1213 |
with gr.Column(scale=2):
|
|
|
|
| 1214 |
track_first_frame_preview = gr.Image(
|
| 1215 |
+
label="📸 跟踪可视化 (动画预览)",
|
| 1216 |
+
type="filepath",
|
| 1217 |
+
height=400,
|
| 1218 |
+
interactive=False
|
| 1219 |
)
|
| 1220 |
|
| 1221 |
track_output = gr.Textbox(
|
|
|
|
| 1224 |
interactive=False
|
| 1225 |
)
|
| 1226 |
|
|
|
|
| 1227 |
track_download = gr.File(
|
| 1228 |
label="📥 下载跟踪结果 (CTC格式)",
|
| 1229 |
visible=False
|
| 1230 |
)
|
| 1231 |
+
|
| 1232 |
+
# 满意度评分
|
| 1233 |
+
score_slider = gr.Slider(
|
| 1234 |
+
minimum=1,
|
| 1235 |
+
maximum=5,
|
| 1236 |
+
step=1,
|
| 1237 |
+
value=5,
|
| 1238 |
+
label="🌟 满意度评分 (1-5)"
|
| 1239 |
+
)
|
| 1240 |
+
|
| 1241 |
+
# 反馈文本框
|
| 1242 |
+
feedback_box = gr.Textbox(
|
| 1243 |
+
placeholder="请输入您的反馈意见...",
|
| 1244 |
+
lines=2,
|
| 1245 |
+
label="💬 反馈意见"
|
| 1246 |
+
)
|
| 1247 |
+
|
| 1248 |
+
# 提交按钮
|
| 1249 |
+
submit_feedback_btn = gr.Button("💾 提交反馈", variant="secondary")
|
| 1250 |
+
|
| 1251 |
+
feedback_status = gr.Textbox(
|
| 1252 |
+
label="✅ 提交状态",
|
| 1253 |
+
lines=1,
|
| 1254 |
+
visible=False
|
| 1255 |
+
)
|
| 1256 |
|
| 1257 |
+
# State for tracking examples
|
| 1258 |
+
track_user_examples = gr.State(example_tracking_zips.copy())
|
| 1259 |
+
|
| 1260 |
+
# Function to get preview image from ZIP
|
| 1261 |
+
def get_zip_preview(zip_path):
|
| 1262 |
+
"""Extract first frame from ZIP for gallery preview"""
|
| 1263 |
+
try:
|
| 1264 |
+
temp_dir = tempfile.mkdtemp()
|
| 1265 |
+
with zipfile.ZipFile(zip_path, 'r') as zip_ref:
|
| 1266 |
+
for member in zip_ref.namelist():
|
| 1267 |
+
basename = os.path.basename(member)
|
| 1268 |
+
if ('__MACOSX' not in member and
|
| 1269 |
+
not basename.startswith('._') and
|
| 1270 |
+
basename.lower().endswith(('.tif', '.tiff', '.png', '.jpg'))):
|
| 1271 |
+
zip_ref.extract(member, temp_dir)
|
| 1272 |
+
extracted_path = os.path.join(temp_dir, member)
|
| 1273 |
+
|
| 1274 |
+
# Load and normalize for preview
|
| 1275 |
+
import tifffile
|
| 1276 |
+
import numpy as np
|
| 1277 |
+
|
| 1278 |
+
img_np = tifffile.imread(extracted_path)
|
| 1279 |
+
if img_np.dtype == np.uint16:
|
| 1280 |
+
img_min, img_max = img_np.min(), img_np.max()
|
| 1281 |
+
if img_max > img_min:
|
| 1282 |
+
img_np = ((img_np.astype(np.float32) - img_min) / (img_max - img_min) * 255).astype(np.uint8)
|
| 1283 |
+
|
| 1284 |
+
if img_np.ndim == 2:
|
| 1285 |
+
img_np = np.stack([img_np]*3, axis=-1)
|
| 1286 |
+
|
| 1287 |
+
# Save preview
|
| 1288 |
+
preview_path = tempfile.NamedTemporaryFile(delete=False, suffix=".png")
|
| 1289 |
+
Image.fromarray(img_np).save(preview_path.name)
|
| 1290 |
+
return preview_path.name
|
| 1291 |
+
except:
|
| 1292 |
+
pass
|
| 1293 |
+
return None
|
| 1294 |
+
|
| 1295 |
+
# Initialize gallery with previews
|
| 1296 |
+
def init_tracking_gallery():
|
| 1297 |
+
"""Create preview images for ZIP examples"""
|
| 1298 |
+
previews = []
|
| 1299 |
+
for zip_path in example_tracking_zips:
|
| 1300 |
+
if os.path.exists(zip_path):
|
| 1301 |
+
preview = get_zip_preview(zip_path)
|
| 1302 |
+
if preview:
|
| 1303 |
+
previews.append(preview)
|
| 1304 |
+
return previews
|
| 1305 |
+
|
| 1306 |
+
# Load gallery on startup
|
| 1307 |
+
demo.load(
|
| 1308 |
+
fn=init_tracking_gallery,
|
| 1309 |
+
outputs=track_example_gallery
|
| 1310 |
+
)
|
| 1311 |
+
|
| 1312 |
+
# Add ZIP to gallery
|
| 1313 |
+
def add_zip_to_gallery(zip_path, current_zips):
|
| 1314 |
+
if not zip_path:
|
| 1315 |
+
return current_zips, track_example_gallery
|
| 1316 |
+
try:
|
| 1317 |
+
if zip_path not in current_zips:
|
| 1318 |
+
current_zips.append(zip_path)
|
| 1319 |
+
print(f"✅ Added ZIP to gallery: {zip_path}")
|
| 1320 |
+
# Regenerate previews
|
| 1321 |
+
previews = []
|
| 1322 |
+
for zp in current_zips:
|
| 1323 |
+
preview = get_zip_preview(zp)
|
| 1324 |
+
if preview:
|
| 1325 |
+
previews.append(preview)
|
| 1326 |
+
return current_zips, previews
|
| 1327 |
+
except Exception as e:
|
| 1328 |
+
print(f"⚠️ Error: {e}")
|
| 1329 |
+
return current_zips, []
|
| 1330 |
+
|
| 1331 |
+
track_gallery_upload.upload(
|
| 1332 |
+
fn=add_zip_to_gallery,
|
| 1333 |
+
inputs=[track_gallery_upload, track_user_examples],
|
| 1334 |
+
outputs=[track_user_examples, track_example_gallery]
|
| 1335 |
+
)
|
| 1336 |
+
|
| 1337 |
+
# Select ZIP from gallery
|
| 1338 |
+
def load_zip_from_gallery(evt: gr.SelectData, all_zips):
|
| 1339 |
+
if evt.index is not None and evt.index < len(all_zips):
|
| 1340 |
+
selected_zip = all_zips[evt.index]
|
| 1341 |
+
print(f"📁 Selected ZIP from gallery: {selected_zip}")
|
| 1342 |
+
return selected_zip
|
| 1343 |
+
return None
|
| 1344 |
+
|
| 1345 |
+
track_example_gallery.select(
|
| 1346 |
+
fn=load_zip_from_gallery,
|
| 1347 |
+
inputs=track_user_examples,
|
| 1348 |
+
outputs=track_zip_upload
|
| 1349 |
+
)
|
| 1350 |
+
|
| 1351 |
+
# Load first frame when ZIP is uploaded
|
| 1352 |
def load_first_frame_for_annotation(zip_file_obj):
|
| 1353 |
'''Load and normalize first frame from ZIP for annotation'''
|
| 1354 |
if zip_file_obj is None:
|
| 1355 |
+
return None, gr.update(visible=False)
|
| 1356 |
|
| 1357 |
import tifffile
|
| 1358 |
+
import numpy as np
|
| 1359 |
|
| 1360 |
try:
|
| 1361 |
temp_dir = tempfile.mkdtemp()
|
|
|
|
| 1371 |
if tif_dir:
|
| 1372 |
first_frame = extract_first_frame(tif_dir)
|
| 1373 |
if first_frame:
|
| 1374 |
+
# Load and normalize the first frame
|
| 1375 |
try:
|
| 1376 |
img_np = tifffile.imread(first_frame)
|
| 1377 |
|
|
|
|
| 1408 |
print(f" Original dtype: {tifffile.imread(first_frame).dtype}")
|
| 1409 |
print(f" Normalized to uint8 RGB for annotation")
|
| 1410 |
|
| 1411 |
+
return temp_img.name, gr.update(visible=True)
|
|
|
|
| 1412 |
except Exception as e:
|
| 1413 |
print(f"⚠️ Error normalizing first frame: {e}")
|
| 1414 |
+
import traceback
|
| 1415 |
+
traceback.print_exc()
|
| 1416 |
# Fallback to original file
|
| 1417 |
+
return first_frame, gr.update(visible=True)
|
| 1418 |
except Exception as e:
|
| 1419 |
print(f"⚠️ Error loading first frame: {e}")
|
| 1420 |
+
import traceback
|
| 1421 |
+
traceback.print_exc()
|
| 1422 |
+
return None, gr.update(visible=False)
|
| 1423 |
|
| 1424 |
+
# Load first frame when ZIP is uploaded
|
| 1425 |
track_zip_upload.change(
|
| 1426 |
fn=load_first_frame_for_annotation,
|
| 1427 |
inputs=track_zip_upload,
|
| 1428 |
+
outputs=[track_first_frame_annotator, track_first_frame_annotator]
|
| 1429 |
)
|
| 1430 |
|
| 1431 |
# Run tracking
|
|
|
|
| 1434 |
inputs=[track_use_box_radio, track_first_frame_annotator, track_zip_upload],
|
| 1435 |
outputs=[track_download, track_output, track_download, track_first_frame_preview]
|
| 1436 |
)
|
| 1437 |
+
|
| 1438 |
+
# 绑定事件: 提交反馈
|
| 1439 |
+
def submit_user_feedback(query_id, score, comment, annot_val):
|
| 1440 |
+
try:
|
| 1441 |
+
img_path = annot_val[0] if annot_val and len(annot_val) > 0 else None
|
| 1442 |
+
bboxes = annot_val[1] if annot_val and len(annot_val) > 1 else []
|
| 1443 |
+
|
| 1444 |
+
save_feedback(
|
| 1445 |
+
query_id=query_id,
|
| 1446 |
+
feedback_type=f"score_{int(score)}",
|
| 1447 |
+
feedback_text=comment,
|
| 1448 |
+
img_path=img_path,
|
| 1449 |
+
bboxes=bboxes
|
| 1450 |
+
)
|
| 1451 |
+
return "✅ 反馈已提交,感谢您的评价!", gr.update(visible=True)
|
| 1452 |
+
except Exception as e:
|
| 1453 |
+
return f"❌ 提交失败: {str(e)}", gr.update(visible=True)
|
| 1454 |
+
|
| 1455 |
+
submit_feedback_btn.click(
|
| 1456 |
+
fn=submit_user_feedback,
|
| 1457 |
+
inputs=[current_query_id, score_slider, feedback_box, annotator],
|
| 1458 |
+
outputs=[feedback_status, feedback_status]
|
| 1459 |
+
)
|
| 1460 |
|
| 1461 |
gr.Markdown(
|
| 1462 |
"""
|
|
|
|
| 1470 |
if __name__ == "__main__":
|
| 1471 |
demo.queue().launch(
|
| 1472 |
server_name="0.0.0.0",
|
| 1473 |
+
server_port=7861,
|
| 1474 |
share=True,
|
| 1475 |
show_error=True
|
| 1476 |
)
|
example_imgs/{1977_Well_F-5_Field_1.png → cnt/00_01.png}
RENAMED
|
File without changes
|
example_imgs/{1977_Well_F-5_Field_1_seg.png → cnt/047cell.png}
RENAMED
|
File without changes
|
example_imgs/cnt/6800-17000_GTEX-XQ3S_Adipose-Subcutaneous.png
ADDED
|
Git LFS Details
|
003_img.png → example_imgs/seg/003_img.png
RENAMED
|
File without changes
|
example_imgs/seg/1-23 [Scan I08].png
ADDED
|
Git LFS Details
|
example_imgs/seg/10X_B2_Tile-15.aligned.png
ADDED
|
Git LFS Details
|
1977_Well_F-5_Field_1.png → example_imgs/seg/1977_Well_F-5_Field_1.png
RENAMED
|
File without changes
|
example_imgs/seg/200972823[5179]_RhoGGG_YAP_TAZ [200972823 Well K6 Field #2].png
ADDED
|
Git LFS Details
|
example_imgs/seg/A172_Phase_C7_1_00d00h00m_1.png
ADDED
|
Git LFS Details
|
example_imgs/seg/JE2NileRed_oilp22_PMP_101220_011_NR.png
ADDED
|
Git LFS Details
|
example_imgs/seg/OpenTest_031.png
ADDED
|
Git LFS Details
|
example_imgs/seg/X_24.png
ADDED
|
Git LFS Details
|
example_imgs/seg/exp_A01_G002_0001.oir.png
ADDED
|
Git LFS Details
|
example_imgs/tra/tracking_test_sequence.zip
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:bda69434e3de8103c98313777640acd35fc7501eec4b1528456304142b18797f
|
| 3 |
+
size 10392163
|
example_imgs/tra/tracking_test_sequence2.zip
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:120cc2a75a4dd571b8f8ee7ea363a9b82a2b4c516376ccf4f287b6864d2dd576
|
| 3 |
+
size 2288296
|