deploy: sync from GitHub 618f20bc48b85000312050d45345eefcae49b3c6

.gitattributes

@@ -1,35 +1,5 @@
-*.7z filter=lfs diff=lfs merge=lfs -text
-*.arrow filter=lfs diff=lfs merge=lfs -text
+*.pt filter=lfs diff=lfs merge=lfs -text
+*.pth filter=lfs diff=lfs merge=lfs -text
 *.bin filter=lfs diff=lfs merge=lfs -text
-*.bz2 filter=lfs diff=lfs merge=lfs -text
-*.ckpt filter=lfs diff=lfs merge=lfs -text
-*.ftz filter=lfs diff=lfs merge=lfs -text
-*.gz filter=lfs diff=lfs merge=lfs -text
 *.h5 filter=lfs diff=lfs merge=lfs -text
-*.joblib filter=lfs diff=lfs merge=lfs -text
-*.lfs.* filter=lfs diff=lfs merge=lfs -text
-*.mlmodel filter=lfs diff=lfs merge=lfs -text
-*.model filter=lfs diff=lfs merge=lfs -text
-*.msgpack filter=lfs diff=lfs merge=lfs -text
-*.npy filter=lfs diff=lfs merge=lfs -text
-*.npz filter=lfs diff=lfs merge=lfs -text
 *.onnx filter=lfs diff=lfs merge=lfs -text
-*.ot filter=lfs diff=lfs merge=lfs -text
-*.parquet filter=lfs diff=lfs merge=lfs -text
-*.pb filter=lfs diff=lfs merge=lfs -text
-*.pickle filter=lfs diff=lfs merge=lfs -text
-*.pkl filter=lfs diff=lfs merge=lfs -text
-*.pt filter=lfs diff=lfs merge=lfs -text
-*.pth filter=lfs diff=lfs merge=lfs -text
-*.rar filter=lfs diff=lfs merge=lfs -text
-*.safetensors filter=lfs diff=lfs merge=lfs -text
-saved_model/**/* filter=lfs diff=lfs merge=lfs -text
-*.tar.* filter=lfs diff=lfs merge=lfs -text
-*.tar filter=lfs diff=lfs merge=lfs -text
-*.tflite filter=lfs diff=lfs merge=lfs -text
-*.tgz filter=lfs diff=lfs merge=lfs -text
-*.wasm filter=lfs diff=lfs merge=lfs -text
-*.xz filter=lfs diff=lfs merge=lfs -text
-*.zip filter=lfs diff=lfs merge=lfs -text
-*.zst filter=lfs diff=lfs merge=lfs -text
-*tfevents* filter=lfs diff=lfs merge=lfs -text

Dockerfile

@@ -1,14 +1,10 @@
-# Use an official Python runtime as a parent image
-FROM python:3.12
-# FROM nvidia/cuda:12.2.0-runtime-ubuntu22.04
+# CPU image - use Dockerfile.gpu for GPU support
+FROM python:3.12.13-slim-trixie
+# Cache bust: 2026-03-19
 
 # run updates before switching over to non-root user
 RUN apt-get update && apt-get install -y --no-install-recommends \
-    libgl1 \
     libglib2.0-0 \
-    libsm6 \
-    libxrender1 \
-    libxext6 \
     && rm -rf /var/lib/apt/lists/*
 
 # add new user with ID 1000 to avoid permission issues on HF spaces
@@ -17,7 +13,7 @@ USER user
 
 # Set home to user's home dir and add local bin to PATH
 ENV HOME=/home/user \
-    PATH=/user/user/.local/bin:$PATH
+    PATH=/home/user/.local/bin:$PATH
 
 # Set the working directory in the container
 WORKDIR $HOME/app
@@ -25,7 +21,10 @@ WORKDIR $HOME/app
 # Try and run pip command after setting the user with `USER user` to avoid permission issues with Python
 # NOTE - this is from the HF Spaces docs, not sure if necessary
 COPY --chown=user ./requirements.txt .
-RUN pip install --no-cache-dir --upgrade -r requirements.txt
+RUN pip install --no-cache-dir torch==2.7.1 torchvision --index-url https://download.pytorch.org/whl/cpu
+RUN pip install --no-cache-dir --only-binary :all: -r requirements.txt
+# Force headless opencv after ultralytics (which pulls in full opencv-python as a dependency)
+RUN pip install --no-cache-dir --force-reinstall opencv-python-headless==4.13.0.92
 
 # Copy the current directory contents into the container at $HOME/app setting the owner to the user
 COPY --chown=user . $HOME/app
@@ -40,7 +39,7 @@ COPY --chown=user . $HOME/app
 RUN mkdir -p uploads results annotated .yolo_config
 
 # set the env var for YOLO user config directory
-ENV YOLO_CONFIG_DIR=.yolo_config
+ENV YOLO_CONFIG_DIR=$HOME/app/.yolo_config
 
 # Copy the rest of the application code into the container at /app
 # This includes app.py, nemaquant.py, templates/, static/, etc.

README.md

@@ -4,6 +4,7 @@ emoji: 🔬
 colorFrom: indigo
 colorTo: blue
 sdk: docker
+dockerfile: Dockerfile.gpu
 license: apache-2.0
 short_description: "YOLO-based nematode egg detection with real-time processing"
 tags:
@@ -64,14 +65,14 @@ Process 500 images for:
 
 ## Technical Requirements
 
-- Python 3.9+
+- Python 3.11+
 - Key Dependencies:
-  - Flask >= 2.0.0
-  - PyTorch >= 2.0.0
-  - Ultralytics >= 8.0.0
-  - OpenCV Python >= 4.7.0
-  - Pandas >= 1.5.0
-  - NumPy >= 1.21.0
+  - Flask = 3.1.1
+  - PyTorch = 2.7.1
+  - Ultralytics = 8.3.170
+  - OpenCV Python = 4.12.0.88
+  - Pandas = 2.3.1
+  - NumPy = 2.2.6
 
 ## Setup and Deployment
 
@@ -92,22 +93,62 @@ Process 500 images for:
    - Place your `weights.pt` file in the root directory
    - Ensure it's a compatible YOLO model trained for egg detection
 
-4. **Run the Application**:
+4. **Setup Environment**:
+   ```bash
+   mkdir -p uploads results annotated .yolo_config
+   export YOLO_CONFIG_DIR="$PWD/.yolo_config"
+   ```
+
+5. **Run the Application**:
    ```bash
    python app.py
    ```
    The application will be available at `http://localhost:7860`
 
-### Docker Deployment
+### Container Deployment
 
 1. **Build the Container**:
+
+DEfault image `breedinginsight/nemaquant` is exclusive for **CPU usage**.
+For **GPU usage** replace the image by: `breedinginsight/nemaquant:latest-gpu`
+
+- With Docker
+
+   ```bash
+   docker pull breedinginsight/nemaquant
+   ```
+
+
+- With Apptainer/Singularity + Slurm from a server:
+
    ```bash
-   docker build -t nemaquant-flask .
+   # 1) On the login node: pull the image once (creates a .sif file)
+   apptainer pull nemaquant_latest.sif docker://breedinginsight/nemaquant:latest
+
+   # 2) Request an interactive compute allocation (adjust for your cluster and analysis)
+   salloc -c 4 --mem=16G --time=02:00:00
+
+   # 3) On the compute node shell that opens, run the app on port 7860
+   export PORT=7860
+   apptainer run --cleanenv --env PORT=$PORT nemaquant_latest.sif
    ```
 
+For **GPU usage** replace the image by: `breedinginsight/nemaquant:latest-gpu`
+
 2. **Run the Container**:
+
+- With Docker
+
    ```bash
-   docker run -p 7860:7860 -v $(pwd)/results:/app/results nemaquant-flask
+   docker run -p 7860:7860 -v $(pwd)/results:/app/results breedinginsight/nemaquant
+   ```
+
+- With Apptainer/Singularity + Slurm from our local computer (after running the above commands on server):
+
+   ```bash
+   # Replace user and host with your cluster login node.
+   # If your cluster requires a direct tunnel to the compute node, adapt accordingly.
+   ssh -L 7860:localhost:7860 [userID]@[yourcluster.address]
    ```
 
 ### Hugging Face Spaces Deployment
@@ -184,7 +225,3 @@ Process 500 images for:
 - Time of day (free tier performance varies with overall platform usage)
 
 For most users, the free tier is sufficient for small to medium batches (< 200 images), while the CPU upgrade offers a good balance of cost and performance for larger datasets. GPU options are recommended only for time-sensitive processing of large batches or when processing thousands of images.
-
-## License
-
-[Specify your license here]

app.py

@@ -33,20 +33,26 @@ log = logging.getLogger('werkzeug')
 log.setLevel(logging.ERROR)
 
 APP_ROOT = Path(__file__).parent
-UPLOAD_FOLDER = APP_ROOT / 'uploads'
-RESULTS_FOLDER = APP_ROOT / 'results'
-ANNOT_FOLDER = APP_ROOT / 'annotated'
+# On HF Spaces, the app filesystem overlay makes app-root dirs unreliable across requests.
+# Use /tmp (RAM-backed tmpfs, always writable) when running on HF Spaces.
+# Locally, use app root so files persist across container restarts.
+_ON_HF_SPACES = os.environ.get('SPACE_ID') is not None
+_data_root = Path('/tmp/nemaquant') if _ON_HF_SPACES else APP_ROOT
+UPLOAD_FOLDER = _data_root / 'uploads'
+RESULTS_FOLDER = _data_root / 'results'
+ANNOT_FOLDER = _data_root / 'annotated'
 WEIGHTS_FILE = APP_ROOT / 'weights.pt'
 app.config['UPLOAD_FOLDER'] = str(UPLOAD_FOLDER)
 app.config['RESULTS_FOLDER'] = str(RESULTS_FOLDER)
-app.config['WEIGHTS_FILE'] = str(WEIGHTS_FILE)
 app.config['ANNOT_FOLDER'] = str(ANNOT_FOLDER)
+app.config['WEIGHTS_FILE'] = str(WEIGHTS_FILE)
 app.config['ALLOWED_EXTENSIONS'] = {'png', 'jpg', 'jpeg', 'tif', 'tiff'}
 
-# skip these -- created dirs in dockerfile
-# UPLOAD_FOLDER.mkdir(parents=True, exist_ok=True)
-# RESULTS_FOLDER.mkdir(parents=True, exist_ok=True)
-# ANNOT_FOLDER.mkdir(parents=True, exist_ok=True)
+# Create dirs at startup 
+UPLOAD_FOLDER.mkdir(parents=True, exist_ok=True)
+RESULTS_FOLDER.mkdir(parents=True, exist_ok=True)
+ANNOT_FOLDER.mkdir(parents=True, exist_ok=True)
+print(f"Running on HF Spaces: {_ON_HF_SPACES} | Data root: {_data_root}")
 
 # Load model once at startup, use CUDA if available
 MODEL_DEVICE = 'cuda' if cuda.is_available() else 'cpu'
@@ -235,6 +241,7 @@ def get_progress():
                         with open(pkl_file, 'rb') as pf:
                             all_results[uuid_base] = pickle.load(pf)
                     resp['results'] = all_results
+                    print(f"Job executed successfully! {len(all_results)} results aggregated.")
                     return jsonify(resp)
                 
             # If still processing, update progress
@@ -283,7 +290,6 @@ def annotate_image():
 
         if not img_name:
             return jsonify({'error': 'File not found'}), 404
-
         # Load detections from pickle
         result_path = Path(app.config['RESULTS_FOLDER']) / session_id / f"{uuid}.pkl"
         if not result_path.exists():
@@ -367,17 +373,31 @@ def export_csv():
     try:
         data = request.json
         session_id = session['id']
-        threshold = float(data.get('confidence', 0.5))
         job_state = session.get('job_state')
+        filename_map = session.get('filename_map')
+        threshold = float(data.get('confidence', 0.5))
         if not job_state:
             return jsonify({'error': 'Job not found'}), 404
+        
+        # iterate through the results
+        results_dir = Path(app.config['RESULTS_FOLDER']) / session_id
+        pkl_paths = list(results_dir.glob('*.pkl'))
+        all_results = {}
+        for path in pkl_paths:
+            uuid_base = path.stem
+            with open(path, 'rb') as pf:
+                all_results[uuid_base] = pickle.load(pf)
+
+        # populate rows for CSV conversion
         rows = []
-        for orig_name, detections in job_state['detections'].items():
-            count = sum(1 for d in detections if d['score'] >= threshold)
-            rows.append({'Filename': orig_name, 'EggsDetected': count})
+        for uuid in all_results.keys():
+            count = sum(1 for d in all_results[uuid] if d['score'] >= threshold)
+            rows.append({'Filename': filename_map[uuid], 'EggsDetected': count, 'ConfidenceThreshold': threshold})
+        rows = sorted(rows, key=lambda x: x['Filename'].lower())
+        # write the CSV out
         timestamp = datetime.now().strftime('%Y%m%d_%H%M%S')
         output = io.StringIO()
-        writer = csv.DictWriter(output, fieldnames=['Filename', 'EggsDetected'])
+        writer = csv.DictWriter(output, fieldnames=['Filename', 'EggsDetected', 'ConfidenceThreshold'])
         writer.writeheader()
         writer.writerows(rows)
         output.seek(0)

requirements.txt

@@ -1,10 +1,9 @@
 Flask==3.1.1
 numpy==2.2.6
-opencv_python==4.12.0.88
+opencv_python-headless==4.13.0.92
 pandas==2.3.1
 Pillow==11.3.0
 torch==2.7.1
 ultralytics==8.3.170
 watchdog==6.0.0
-Werkzeug==3.1.3
-gunicorn==21.2.0
+Werkzeug==3.1.3

static/script.js

@@ -118,29 +118,8 @@ document.addEventListener('DOMContentLoaded', () => {
                 showSingleCsvDialog(csvFiles[0]);
                 return;
             } else if (csvFiles.length === 0) {
-                const wantToUpload = window.confirm('No CSV key file was found in the folder. Would you like to supply a CSV key file now?');
-                if (wantToUpload) {
-                    // Create a hidden file input for CSV upload
-                    let csvInput = document.createElement('input');
-                    csvInput.type = 'file';
-                    csvInput.accept = '.csv,.CSV';
-                    csvInput.style.display = 'none';
-                    document.body.appendChild(csvInput);
-                    csvInput.addEventListener('change', function() {
-                        if (csvInput.files && csvInput.files.length === 1) {
-                            window.selectedKeyenceCsv = csvInput.files[0];
-                            logStatus(`CSV key file supplied: ${csvInput.files[0].name}`);
-                        } else {
-                            window.selectedKeyenceCsv = null;
-                            logStatus('No CSV key file supplied.');
-                        }
-                        document.body.removeChild(csvInput);
-                    });
-                    csvInput.click();
-                } else {
-                    window.selectedKeyenceCsv = null;
-                    logStatus('No CSV key file will be used.');
-                }
+                showNoCsvDialog();
+                return;
             } else {
                 // Multiple CSVs found, show a custom dialog for selection
                 showCsvSelectionDialog(csvFiles);
@@ -1310,8 +1289,7 @@ document.addEventListener('DOMContentLoaded', () => {
     }
 
     // Custom dialog for selecting among multiple CSV files
-    function showCsvSelectionDialog(csvFiles) {
-        // Create overlay
+    function createDialogOverlay(titleText, messageContent) {
         const overlay = document.createElement('div');
         overlay.style.position = 'fixed';
         overlay.style.top = 0;
@@ -1324,77 +1302,93 @@ document.addEventListener('DOMContentLoaded', () => {
         overlay.style.alignItems = 'center';
         overlay.style.justifyContent = 'center';
 
-        // Create dialog box
         const dialog = document.createElement('div');
         dialog.style.background = '#fff';
         dialog.style.padding = '24px 32px';
         dialog.style.borderRadius = '8px';
         dialog.style.boxShadow = '0 2px 16px rgba(0,0,0,0.2)';
         dialog.style.minWidth = '320px';
-        dialog.innerHTML = `<h3>Select a CSV key file</h3><p>Multiple CSV files were found. Please select one to use as the key file:</p>`;
+        const title = document.createElement('h3');
+        title.textContent = titleText;
+        const message = document.createElement('p');
+        if (typeof messageContent === 'string') {
+            message.textContent = messageContent;
+        } else if (messageContent) {
+            message.appendChild(messageContent);
+        }
+        dialog.appendChild(title);
+        dialog.appendChild(message);
+
+        return { overlay, dialog };
+    }
+
+    function createDialogButton(label, onClick, margin = '8px 0') {
+        const btn = document.createElement('button');
+        btn.textContent = label;
+        btn.style.display = 'block';
+        btn.style.margin = margin;
+        btn.onclick = onClick;
+        return btn;
+    }
+
+    function openCsvPicker(onComplete) {
+        let csvInput = document.createElement('input');
+        csvInput.type = 'file';
+        csvInput.accept = '.csv,.CSV';
+        csvInput.style.display = 'none';
+        document.body.appendChild(csvInput);
+        csvInput.addEventListener('change', function() {
+            if (csvInput.files && csvInput.files.length === 1) {
+                window.selectedKeyenceCsv = csvInput.files[0];
+                logStatus(`CSV key file supplied: ${csvInput.files[0].name}`);
+            } else {
+                window.selectedKeyenceCsv = null;
+                logStatus('No CSV key file supplied.');
+            }
+            document.body.removeChild(csvInput);
+            if (onComplete) onComplete();
+        });
+        csvInput.click();
+    }
+
+    function showCsvSelectionDialog(csvFiles) {
+        const { overlay, dialog } = createDialogOverlay(
+            'Select a CSV key file',
+            'Multiple CSV files were found. Please select one to use as the key file:'
+        );
 
         // List CSV files as buttons
         csvFiles.forEach((file, idx) => {
-            const btn = document.createElement('button');
-            btn.textContent = file.name;
-            btn.style.display = 'block';
-            btn.style.margin = '8px 0';
-            btn.onclick = () => {
+            const btn = createDialogButton(file.name, () => {
                 window.selectedKeyenceCsv = file;
                 logStatus(`CSV key file selected: ${file.name}`);
                 document.body.removeChild(overlay);
-            };
+            });
             dialog.appendChild(btn);
         });
 
         // Option: Use a different .csv
-        const otherBtn = document.createElement('button');
-        otherBtn.textContent = 'Use a different .csv';
-        otherBtn.style.display = 'block';
-        otherBtn.style.margin = '16px 0 8px 0';
-        otherBtn.onclick = () => {
-            let csvInput = document.createElement('input');
-            csvInput.type = 'file';
-            csvInput.accept = '.csv,.CSV';
-            csvInput.style.display = 'none';
-            document.body.appendChild(csvInput);
-            csvInput.addEventListener('change', function() {
-                if (csvInput.files && csvInput.files.length === 1) {
-                    window.selectedKeyenceCsv = csvInput.files[0];
-                    logStatus(`CSV key file supplied: ${csvInput.files[0].name}`);
-                } else {
-                    window.selectedKeyenceCsv = null;
-                    logStatus('No CSV key file supplied.');
-                }
-                document.body.removeChild(csvInput);
+        const otherBtn = createDialogButton('Use a different .csv', () => {
+            openCsvPicker(() => {
                 document.body.removeChild(overlay);
             });
-            csvInput.click();
-        };
+        }, '16px 0 8px 0');
         dialog.appendChild(otherBtn);
 
         // Option: No key file
-        const noneBtn = document.createElement('button');
-        noneBtn.textContent = 'No key file';
-        noneBtn.style.display = 'block';
-        noneBtn.style.margin = '8px 0';
-        noneBtn.onclick = () => {
+        const noneBtn = createDialogButton('No key file', () => {
             window.selectedKeyenceCsv = null;
             logStatus('No CSV key file will be used.');
             document.body.removeChild(overlay);
-        };
+        });
         dialog.appendChild(noneBtn);
 
         // Cancel button
-        const cancelBtn = document.createElement('button');
-        cancelBtn.textContent = 'Cancel';
-        cancelBtn.style.display = 'block';
-        cancelBtn.style.margin = '8px 0';
-        cancelBtn.onclick = () => {
+        const cancelBtn = createDialogButton('Cancel', () => {
             // Do not change selection, just close dialog
             logStatus('CSV key file selection cancelled.');
             document.body.removeChild(overlay);
-        };
+        });
         dialog.appendChild(cancelBtn);
 
         overlay.appendChild(dialog);
@@ -1403,86 +1397,79 @@ document.addEventListener('DOMContentLoaded', () => {
 
     // Custom dialog for single CSV file found
     function showSingleCsvDialog(csvFile) {
-        const overlay = document.createElement('div');
-        overlay.style.position = 'fixed';
-        overlay.style.top = 0;
-        overlay.style.left = 0;
-        overlay.style.width = '100vw';
-        overlay.style.height = '100vh';
-        overlay.style.background = 'rgba(0,0,0,0.4)';
-        overlay.style.zIndex = 9999;
-        overlay.style.display = 'flex';
-        overlay.style.alignItems = 'center';
-        overlay.style.justifyContent = 'center';
-
-        const dialog = document.createElement('div');
-        dialog.style.background = '#fff';
-        dialog.style.padding = '24px 32px';
-        dialog.style.borderRadius = '8px';
-        dialog.style.boxShadow = '0 2px 16px rgba(0,0,0,0.2)';
-        dialog.style.minWidth = '320px';
-        dialog.innerHTML = `<h3>CSV File Found</h3><p>A CSV file named <strong>${csvFile.name}</strong> was found in the folder. Would you like to use this as the key file for this folder?</p>`;
+        const messageFragment = document.createDocumentFragment();
+        messageFragment.append('A CSV file named ');
+        const fileNameStrong = document.createElement('strong');
+        fileNameStrong.textContent = csvFile.name;
+        messageFragment.appendChild(fileNameStrong);
+        messageFragment.append(' was found in the folder. Would you like to use this as the key file for this folder?');
+
+        const { overlay, dialog } = createDialogOverlay(
+            'CSV File Found',
+            messageFragment
+        );
 
         // Yes button
-        const yesBtn = document.createElement('button');
-        yesBtn.textContent = 'Yes';
-        yesBtn.style.display = 'block';
-        yesBtn.style.margin = '8px 0';
-        yesBtn.onclick = () => {
+        const yesBtn = createDialogButton('Yes', () => {
             window.selectedKeyenceCsv = csvFile;
             logStatus(`CSV key file selected: ${csvFile.name}`);
             document.body.removeChild(overlay);
-        };
+        });
         dialog.appendChild(yesBtn);
 
         // Use a different .csv file
-        const otherBtn = document.createElement('button');
-        otherBtn.textContent = 'Use a different .csv file';
-        otherBtn.style.display = 'block';
-        otherBtn.style.margin = '8px 0';
-        otherBtn.onclick = () => {
-            let csvInput = document.createElement('input');
-            csvInput.type = 'file';
-            csvInput.accept = '.csv,.CSV';
-            csvInput.style.display = 'none';
-            document.body.appendChild(csvInput);
-            csvInput.addEventListener('change', function() {
-                if (csvInput.files && csvInput.files.length === 1) {
-                    window.selectedKeyenceCsv = csvInput.files[0];
-                    logStatus(`CSV key file supplied: ${csvInput.files[0].name}`);
-                } else {
-                    window.selectedKeyenceCsv = null;
-                    logStatus('No CSV key file supplied.');
-                }
-                document.body.removeChild(csvInput);
+        const otherBtn = createDialogButton('Use a different .csv file', () => {
+            openCsvPicker(() => {
                 document.body.removeChild(overlay);
             });
-            csvInput.click();
-        };
+        });
         dialog.appendChild(otherBtn);
 
         // Do not use a key file
-        const noneBtn = document.createElement('button');
-        noneBtn.textContent = 'Do not use a key file';
-        noneBtn.style.display = 'block';
-        noneBtn.style.margin = '8px 0';
-        noneBtn.onclick = () => {
+        const noneBtn = createDialogButton('Do not use a key file', () => {
             window.selectedKeyenceCsv = null;
             logStatus('No CSV key file will be used.');
             document.body.removeChild(overlay);
-        };
+        });
         dialog.appendChild(noneBtn);
 
         // Cancel button
-        const cancelBtn = document.createElement('button');
-        cancelBtn.textContent = 'Cancel';
-        cancelBtn.style.display = 'block';
-        cancelBtn.style.margin = '8px 0';
-        cancelBtn.onclick = () => {
+        const cancelBtn = createDialogButton('Cancel', () => {
             // Do not change selection, just close dialog
             logStatus('CSV key file selection cancelled.');
             document.body.removeChild(overlay);
-        };
+        });
+        dialog.appendChild(cancelBtn);
+
+        overlay.appendChild(dialog);
+        document.body.appendChild(overlay);
+    }
+
+    // Custom dialog for no CSV file found
+    function showNoCsvDialog() {
+        const { overlay, dialog } = createDialogOverlay(
+            'No CSV Key File Found',
+            'No CSV key file was found in the folder. Would you like to supply one now?'
+        );
+
+        const uploadBtn = createDialogButton('Upload a CSV key file', () => {
+            openCsvPicker(() => {
+                document.body.removeChild(overlay);
+            });
+        });
+        dialog.appendChild(uploadBtn);
+
+        const noneBtn = createDialogButton('No key file', () => {
+            window.selectedKeyenceCsv = null;
+            logStatus('No CSV key file will be used.');
+            document.body.removeChild(overlay);
+        });
+        dialog.appendChild(noneBtn);
+
+        const cancelBtn = createDialogButton('Cancel', () => {
+            logStatus('CSV key file selection cancelled.');
+            document.body.removeChild(overlay);
+        });
         dialog.appendChild(cancelBtn);
 
         overlay.appendChild(dialog);
@@ -1501,4 +1488,4 @@ document.addEventListener('DOMContentLoaded', () => {
     confidenceSlider.value = 0.6;
     confidenceSlider.dispatchEvent(new Event('input', { bubbles: true }));
     confidenceSlider.dispatchEvent(new Event('change', { bubbles: true }));
-});
+});