Adding Keyence folder handling

app.py

@@ -64,14 +64,45 @@ def process_images():
         saved_files = []
         error_files = []
 
-        for file in files:
-            if file and allowed_file(file.filename):
-                filename = secure_filename(file.filename)
-                save_path = job_output_dir / filename
-                file.save(str(save_path))
-                saved_files.append(save_path)
-            elif file:
-                error_files.append(file.filename)
+        # For keyence mode, validate XY subdirectory structure but flatten files
+        if input_mode == 'keyence':
+            xy_subdirs = set()
+            # First pass: validate XY subdirectory structure
+            for file in files:
+                if file and file.filename:
+                    relative_path = file.filename
+                    if '/' in relative_path:
+                        first_dir = relative_path.split('/')[0]
+                        if re.match(r'^XY[0-9][0-9]$', first_dir):
+                            xy_subdirs.add(first_dir)
+            
+            # Validate that we found XY subdirectories
+            if not xy_subdirs:
+                return jsonify({
+                    "error": "Keyence mode requires folder structure with XY[0-9][0-9] subdirectories (e.g., XY01/, XY02/). No such subdirectories found in uploaded folder."
+                }), 400
+            
+            # Second pass: save files with flattened structure
+            for file in files:
+                if file and allowed_file(file.filename):
+                    # Extract just the filename, ignoring the folder structure
+                    filename = secure_filename(Path(file.filename).name)
+                    save_path = job_output_dir / filename
+                    file.save(str(save_path))
+                    saved_files.append(save_path)
+                elif file:
+                    error_files.append(file.filename)
+                
+        else:
+            # Original file handling for non-keyence modes
+            for file in files:
+                if file and allowed_file(file.filename):
+                    filename = secure_filename(file.filename)
+                    save_path = job_output_dir / filename
+                    file.save(str(save_path))
+                    saved_files.append(save_path)
+                elif file:
+                    error_files.append(file.filename)
 
         if not saved_files:
              return jsonify({"error": f"No valid files uploaded. Invalid files: {error_files}"}), 400
@@ -82,6 +113,9 @@ def process_images():
         elif input_mode == 'single':
             input_target = str(saved_files[0])
             img_mode_arg = 'file'
+        elif input_mode == 'keyence':
+            input_target = str(job_output_dir)
+            img_mode_arg = 'keyence'
         else:
             return jsonify({"error": f"Invalid input mode: {input_mode}"}), 400
 
@@ -91,11 +125,11 @@ def process_images():
         cmd = [
             sys.executable,
             str(APP_ROOT / 'nemaquant.py'),
+            '-m', img_mode_arg,
             '-i', input_target,
             '-w', str(WEIGHTS_FILE),
             '-o', str(output_csv),
-            '-a', str(annotated_dir),
-            '--conf', confidence
+            '-a', str(annotated_dir)
         ]
 
         print(f"[{job_id}] Prepared command: {' '.join(cmd)}")

nemaquant.py

@@ -11,10 +11,11 @@ from pathlib import Path
 from ultralytics import YOLO
 from glob import glob
 import re
-import sys # Import sys module
+import sys
 
 def options():
-    parser = argparse.ArgumentParser(description="Nematode egg image processing with YOLOv8 model.")
+    parser = argparse.ArgumentParser(description="Nematode egg image processing with YOLO11 model.")
+    parser.add_argument("-m", "--img_mode", help="Mode to run", required=True)
     parser.add_argument("-i", "--img", help="Target image directory or image (REQUIRED)", required=True)
     parser.add_argument('-w', '--weights', help='Weights file for use with YOLO11 model')
     parser.add_argument("-o","--output", help="Name of results file. If no file is specified, one will be created from the key file name")
@@ -24,21 +25,25 @@ def options():
     args = parser.parse_args()
     return args
 
-# TODO - maybe rework this from a function to custom argparse.Action() subclasses?
 def check_args():
     args = options()
     # basic checks on target file validity
     args.imgpath = Path(args.img)
     if not args.imgpath.exists():
         raise Exception("Target %s is not a valid path" % args.img)
-    if args.imgpath.is_file():
-        args.img_mode = 'file'
-        if not args.imgpath.suffix.lower() in ['.tif','.tiff','.jpg','.jpeg','.png']:
-            raise Exception('Target image %s must of type .png, .tif, .tiff, .jpeg, or .jpg' % args.img)
-    elif args.imgpath.is_dir():
-        args.img_mode = 'dir'
-    else:
-        raise Exception('Target %s does not appear to be a file or directory.' % args.img)
+    # check if img_mode is specified and valid
+    if args.img_mode:
+        valid_modes = ['dir', 'file', 'keyence']
+        if args.img_mode not in valid_modes:
+            raise Exception(f"img_mode must be one of: {', '.join(valid_modes)}")
+    # check for potential images in the target directory
+    if args.img_mode in ['dir','keyence']:
+        potential_images = [x for x in args.imgpath.iterdir() if x.suffix.lower() in ['.tif','.tiff','.jpg','.jpeg','.png']]
+        if len(potential_images) == 0:
+            raise Exception('No valid images (.png, .tif, .tiff, .jpeg, .jpg) in target folder %s' % args.img)
+        else:
+            print('%s valid images found' % len(potential_images))
+            args.subimage_paths = potential_images
 
     # if no weights file, try using the default weights.pt
     if not args.weights:
@@ -49,55 +54,39 @@ def check_args():
         else:
             raise Exception('No weights file specified and default weights.pt not found in script directory')
 
-    # check if subdirectories of format XY00/ exist or if we're running on just a dir of images
-    if args.img_mode == 'dir':
-        subdirs = sorted(list(args.imgpath.glob('XY[0-9][0-9]/')))
-        if len(subdirs) == 0:
-            print("No subdirectories of format /XY../ found in specified imgdir, checking for images...")
-            potential_images = [x for x in args.imgpath.iterdir() if x.suffix.lower() in ['.tif','.tiff','.jpg','.jpeg','.png']]
-            if len(potential_images) == 0:
-                raise Exception('No valid images (.png, .tif, .tiff, .jpeg, .jpg) in target folder %s' % args.img)
-            else:
-                print('%s valid images found' % len(potential_images))
-                args.xy_mode = False
-                args.subimage_paths = potential_images
+    # for /XY00/ subdirectories, we require a valid key
+    # ensure that either a key is specified, or if a single .csv exists in the target dir, use that
+    if args.img_mode == 'keyence':
+        if args.key:
+            args.keypath = Path(args.key)
+            if not arg.keypath.exists():
+                raise Exception('Specified key file does not exist: %s' % args.keypath)
+            if args.keypath.suffix != '.csv':
+                raise Exception("Specified key file is not a .csv: %s" % args.keypath)
         else:
-            args.xy_mode = True
-            args.subdir_paths = subdirs
-        
-        # for /XY00/ subdirectories, we require a valid key
-        # ensure that either a key is specified, or if a single .csv exists in the target dir, use that
-        if args.xy_mode:
-            if args.key:
-                args.keypath = Path(args.key)
-                if not args.keypath.exists():
-                    raise Exception('Specified key file does not exist: %s' % args.keypath)
-                if args.keypath.suffix != '.csv':
-                    raise Exception("Specified key file is not a .csv: %s" % args.keypath)
+            print('Running on /XY00/ subdirectories but no key specified. Looking for key file...')
+            potential_keys = list(args.imgpath.glob('*.csv'))
+            if len(potential_keys) == 0:
+                raise Exception("No .csv files found in target folder %s, please check directory" % args.img)
+            if len(potential_keys) > 1:
+                raise Exception("Multiple .csv files found in target folder %s, please specify which one to use")
             else:
-                print('Running on /XY00/ subdirectories but no key specified. Looking for key file...')
-                potential_keys = list(args.imgpath.glob('*.csv'))
-                if len(potential_keys) == 0:
-                    raise Exception("No .csv files found in target folder %s, please check directory" % args.img)
-                if len(potential_keys) > 1:
-                    raise Exception("Multiple .csv files found in target folder %s, please specify which one to use")
-                else:
-                    args.keypath = potential_keys[0]
-                    args.key = str(potential_keys[0])
+                args.keypath = potential_keys[0]
+                args.key = str(potential_keys[0])
 
-        # if path to results file is specified, ensure it is .csv
-        if args.output:
-            args.outpath = Path(args.output)
-            if args.outpath.suffix != '.csv':
-                raise Exception("Specified output file is not a .csv: %s" % args.outpath)
+    # if path to results file is specified, ensure it is .csv
+    if args.output:
+        args.outpath = Path(args.output)
+        if args.outpath.suffix != '.csv':
+            raise Exception("Specified output file is not a .csv: %s" % args.outpath)
+    else:
+        # for XY00 subdirs, name it after the required key file
+        # for an image directory, name it after the directory
+        if args.img_mode == 'keyence':
+            args.output = '%s_eggcounts.csv' % args.keypath.stem
         else:
-            # for XY00 subdirs, name it after the required key file
-            # for an image directory, name it after the directory
-            if args.xy_mode:
-                args.output = '%s_eggcounts.csv' % args.keypath.stem
-            else:
-                args.output = '%s_eggcounts.csv' % args.imgpath.stem
-            args.outpath = Path(args.output)
+            args.output = '%s_eggcounts.csv' % args.imgpath.stem
+        args.outpath = Path(args.output)
 
     # finally, check the target dir to save annotated images in
     if args.annotated:
@@ -154,8 +143,9 @@ def main():
     tmp_filenames = []
     # single-image mode
     if args.img_mode == 'file':
+        # imread then apply model, one-step predict() can't handle TIFF
         img = cv2.imread(str(args.imgpath))
-        results = model.predict(img, imgsz = 1440, max_det=1000, verbose=False, conf=args.conf)
+        results = model.predict(img, imgsz = 1440, max_det=1000, verbose=False, conf=0.05)
         result = results[0]
         box_classes = [result.names[int(x)] for x in result.boxes.cls]
         # NOTE - filtering by class is not necessary, but would make this easier to extend to multi-class models
@@ -171,8 +161,9 @@ def main():
             cv2.imwrite(str(annot_path), annot)
             print('Saving annotations to %s...' % str(annot_path))
     # multi-image mode, runs differently depending on whether you have /XY00/ subdirectories
-    elif args.img_mode == 'dir':
-        if args.xy_mode:
+    elif args.img_mode in ['dir', 'keyence']:
+        subdir_paths = []
+        if args.img_mode == 'keyence':
             total_subdirs = len(args.subdir_paths)
             for i, subdir in enumerate(args.subdir_paths):
                 # Report progress
@@ -200,7 +191,7 @@ def main():
                 impath = candidate_img_paths[0]
                 # get the actual output
                 img = cv2.imread(str(impath))
-                results = model.predict(img, imgsz = 1440, verbose=False, conf=args.conf)
+                results = model.predict(img, imgsz = 1440, verbose=False, conf=0.05)
                 result = results[0]
                 box_classes = [result.names[int(x)] for x in result.boxes.cls]
                 egg_xy = [x.cpu().numpy().astype(np.int32) for i,x in enumerate(result.boxes.xyxy) if box_classes[i] == 'egg']
@@ -237,7 +228,7 @@ def main():
                 sys.stdout.flush() # Flush output buffer
                 
                 img = cv2.imread(str(impath))
-                results = model.predict(img, imgsz = 1440, verbose=False, conf= args.conf)
+                results = model.predict(img, imgsz = 1440, verbose=False, conf=0.05)
                 result = results[0]
                 box_classes = [result.names[int(x)] for x in result.boxes.cls]
                 egg_xy = [x.cpu().numpy().astype(np.int32) for i,x in enumerate(result.boxes.xyxy) if box_classes[i] == 'egg']

static/script.js

@@ -59,12 +59,18 @@ document.addEventListener('DOMContentLoaded', () => {
             fileInput.setAttribute('multiple', '');
             inputModeHelp.textContent = 'Choose one or more image files for processing';
             uploadText.textContent = 'Drag and drop images here or click to browse';
-        } else {
+        } else if (mode === 'folder') {
             fileInput.setAttribute('webkitdirectory', '');
             fileInput.setAttribute('directory', '');
             fileInput.removeAttribute('multiple');
             inputModeHelp.textContent = 'Select a folder containing images to process';
             uploadText.textContent = 'Click to select a folder containing images';
+        } else if (mode === 'keyence') {
+            fileInput.setAttribute('webkitdirectory', '');
+            fileInput.setAttribute('directory', '');
+            fileInput.removeAttribute('multiple');
+            inputModeHelp.textContent = 'Select a Keyence output folder. Folder should have subdirectories of format XY01, XY02, etc.';
+            uploadText.textContent = 'Click to select a Keyence output folder';
         }
         // Clear any existing files
         fileInput.value = '';
@@ -75,17 +81,104 @@ document.addEventListener('DOMContentLoaded', () => {
     // File Upload Handling
     function handleFiles(files) {
         const allowedTypes = ['image/png', 'image/jpeg', 'image/jpg', 'image/tiff', 'image/tif'];
-        const validFiles = Array.from(files).filter(file => {
-            if (inputMode.value === 'folder') {
-                return allowedTypes.includes(file.type) && 
-                       file.webkitRelativePath && 
-                       !file.webkitRelativePath.startsWith('.');
+        // --- Keyence folder validation ---
+        if (inputMode.value === 'keyence') {
+            // Collect all unique first-level subdirectory names from webkitRelativePath
+            const subdirs = new Set();
+            Array.from(files).forEach(file => {
+                if (file.webkitRelativePath) {
+                    const parts = file.webkitRelativePath.split('/');
+                    if (parts.length > 2) { // Parent/Subdir/File
+                        subdirs.add(parts[1]);
+                    }
+                }
+            });
+            // Check for at least one subdir matching XY[0-9]{2}
+            const xyPattern = /^XY\d{2}$/;
+            const hasXY = Array.from(subdirs).some(name => xyPattern.test(name));
+            if (!hasXY) {
+                // Print the first 5 values in subdirs for debugging
+                const subdirArr = Array.from(subdirs).slice(0, 5);
+                logStatus('First 5 subdirectories found: ' + (subdirArr.length ? subdirArr.join(', ') : '[none]'));
+                logStatus('Error: The selected folder does not contain any subdirectory named like "XY01", "XY02", etc. Please select a valid Keyence output folder.');
+                fileList.innerHTML = '';
+                startProcessingBtn.disabled = true;
+                return;
             }
-            return allowedTypes.includes(file.type);
-        });
+            // --- Check for .csv file(s) ---
+            const csvFiles = Array.from(files).filter(file => file.name.toLowerCase().endsWith('.csv'));
+            if (csvFiles.length === 1) {
+                // Show a custom dialog with multiple options
+                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.');
+                }
+            } else {
+                // Multiple CSVs found, show a custom dialog for selection
+                showCsvSelectionDialog(csvFiles);
+                return; // Wait for user selection before proceeding
+            }
+        }
+        let validFiles;
+        if (inputMode.value === 'keyence') {
+            // Only analyze the first valid image file (alphabetically) in each subdirectory
+            const allowedTypes = ['image/png', 'image/jpeg', 'image/jpg', 'image/tiff', 'image/tif'];
+            // Map: subdir name -> array of files in that subdir
+            const subdirFiles = {};
+            Array.from(files).forEach(file => {
+                if (file.webkitRelativePath) {
+                    const parts = file.webkitRelativePath.split('/');
+                    if (parts.length > 2) { // Parent/Subdir/File
+                        const subdir = parts[1];
+                        if (!subdirFiles[subdir]) subdirFiles[subdir] = [];
+                        if (allowedTypes.includes(file.type) && !file.webkitRelativePath.startsWith('.')) {
+                            subdirFiles[subdir].push(file);
+                        }
+                    }
+                }
+            });
+            // For each subdir, pick the first file alphabetically
+            validFiles = Object.values(subdirFiles).map(filesArr => {
+                return filesArr.sort((a, b) => a.name.localeCompare(b.name))[0];
+            }).filter(Boolean); // Remove undefined
+        } else {
+            validFiles = Array.from(files).filter(file => {
+                if (inputMode.value === 'folder') {
+                    return allowedTypes.includes(file.type) && 
+                           file.webkitRelativePath && 
+                           !file.webkitRelativePath.startsWith('.');
+                }
+                return allowedTypes.includes(file.type);
+            });
+        }
+        filteredValidFiles = validFiles;
+
         const invalidFiles = Array.from(files).filter(file => !allowedTypes.includes(file.type));
 
-        if (invalidFiles.length > 0) {
+        // Only print invalid file warnings if not in Keyence mode
+        if (invalidFiles.length > 0 && inputMode.value !== 'keyence') {
             logStatus(`Warning: Skipped ${invalidFiles.length} invalid files. Only PNG, JPG, and TIFF are supported.`);
             invalidFiles.forEach(file => {
                 logStatus(`- Skipped: ${file.name} (invalid type: ${file.type || 'unknown'})`);
@@ -169,14 +262,17 @@ document.addEventListener('DOMContentLoaded', () => {
     });
 
     function updateUploadState(validFileCount) {
-        const files = fileInput.files;
-        if (!files || files.length === 0) {
-            uploadText.textContent = inputMode.value === 'folder' 
-                ? 'Click to select a folder containing images' 
-                : 'Drag and drop images here or click to browse';
+        // Use filteredValidFiles for enabling/disabling the button
+        if (!filteredValidFiles || filteredValidFiles.length === 0) {
+            if (inputMode.value === 'folder') {
+                uploadText.textContent = 'Click to select a folder containing images';
+            } else if (inputMode.value === 'keyence') {
+                uploadText.textContent = 'Click to select a Keyence output folder';
+            } else {
+                uploadText.textContent = 'Drag and drop images here or click to browse';
+            }
             startProcessingBtn.disabled = true;
         } else {
-            // Show the count here
             uploadText.textContent = `${validFileCount} image${validFileCount === 1 ? '' : 's'} selected`;
             startProcessingBtn.disabled = validFileCount === 0;
         }
@@ -195,7 +291,8 @@ document.addEventListener('DOMContentLoaded', () => {
 
     // Processing
     startProcessingBtn.addEventListener('click', async () => {
-        const files = fileInput.files;
+        // Use filteredValidFiles for processing
+        const files = filteredValidFiles;
         if (!files || files.length === 0) {
             logStatus('Error: No files selected.');
             return;
@@ -284,7 +381,7 @@ document.addEventListener('DOMContentLoaded', () => {
 
         const totalImages = Array.from(fileInput.files).filter(file => {
             const allowedTypes = ['image/png', 'image/jpeg', 'image/jpg', 'image/tiff', 'image/tif'];
-            if (inputMode.value === 'folder') {
+            if (inputMode.value === 'folder' || inputMode.value === 'keyence') {
                 return allowedTypes.includes(file.type) && 
                        file.webkitRelativePath && 
                        !file.webkitRelativePath.startsWith('.');
@@ -311,7 +408,7 @@ document.addEventListener('DOMContentLoaded', () => {
                 updateProgress(data.progress || 0, data.status);
                 
                 // Update image counter based on progress percentage
-                if (data.status === 'running' || data.status === 'starting') {
+                if (data.status === 'Running' || data.status === 'Starting') {
                     const processedImages = Math.floor((data.progress / 90) * totalImages); // 90 is the max progress before completion
                     imageCounter.textContent = `${processedImages} of ${totalImages} images`;
                 }
@@ -378,7 +475,7 @@ document.addEventListener('DOMContentLoaded', () => {
         progressText.textContent = message;
         
         // Clear the image counter when not processing
-        if (message === 'Ready to process' || message === 'Processing complete' || message.startsWith('Error')) {
+        if (message === 'Please upload an image' || message === 'Processing complete' || message.startsWith('Error')) {
             imageCounter.textContent = '';
         }
     }
@@ -922,7 +1019,187 @@ document.addEventListener('DOMContentLoaded', () => {
         imageInfo.innerHTML = infoText;
     }
 
+    // Custom dialog for selecting among multiple CSV files
+    function showCsvSelectionDialog(csvFiles) {
+        // Create overlay
+        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';
+
+        // 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>`;
+
+        // 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 = () => {
+                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);
+                document.body.removeChild(overlay);
+            });
+            csvInput.click();
+        };
+        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 = () => {
+            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 = () => {
+            // 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 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>`;
+
+        // Yes button
+        const yesBtn = document.createElement('button');
+        yesBtn.textContent = 'Yes';
+        yesBtn.style.display = 'block';
+        yesBtn.style.margin = '8px 0';
+        yesBtn.onclick = () => {
+            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);
+                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 = () => {
+            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 = () => {
+            // 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);
+    }
+
     // Initialize
     updateUploadState();
     logStatus('Application ready');
-}); 
+});

templates/index.html

@@ -12,7 +12,7 @@
         <i class="ri-microscope-line"></i>
         NemaQuant
         <small style="display: block; font-size: 1rem; font-weight: normal; color: var(--text-muted);">
-            Automated Nematode Egg Detection and Counting
+            Automated nematode egg detection and counting
         </small>
     </h1>
 
@@ -26,6 +26,7 @@
                     <select id="input-mode" name="input-mode" class="form-control">
                         <option value="files">Select Image(s)</option>
                         <option value="folder">Select Folder</option>
+                        <option value="keyence">Keyence Output Folder</option>
                     </select>
                     <small class="input-help" style="color: var(--text-muted); margin-top: 0.25rem; display: block;">
                         <span id="input-mode-help">Choose one or more image files for processing</span>
@@ -50,11 +51,11 @@
                 <div class="form-group">
                     <label for="confidence-threshold">
                         Confidence Threshold
-                        <i class="ri-information-line" data-tooltip="Recommended range: 0.5-0.7; higher values reduce false detections but may miss eggs, lower values catch more eggs but may include false positives"></i>
+                        <i class="ri-information-line" data-tooltip="Recommended range: 0.4 - 0.7. Higher values produce fewer false positives but more false negatives, while lower values produce fewer false negatives but more false positives."></i>
                     </label>
                     <div class="range-with-value">
                         <input type="range" id="confidence-threshold" name="confidence-threshold" 
-                               min="0" max="1" step="0.05" value="0.6">
+                               min="0.05" max="0.95" step="0.05" value="0.6">
                         <span id="confidence-value">0.6</span>
                     </div>
                 </div>