""" Generic microscopy montage generator used for the PhD image arrays. Default layout -------------- 6 rows x 21 columns 500 x 500 pixels per image 2-pixel white grid 180-degree image rotation Arial 40 red position labels JPEG output at 600 dpi Four folders processed concurrently Filename requirement -------------------- Each source filename must end with its grid position before the extension, for example: sample_A01.jpg sample_A1.jpg allopurinol_PVPVA_F21.jpg The final letter identifies the row and the number identifies the column. Montage files containing "_montage" are ignored. To use a different layout, change ROWS and COLUMNS in the settings section. For example, use ROWS = 5 and COLUMNS = 23 for a 5 x 23 montage, or ROWS = 8 and COLUMNS = 8 for an 8 x 8 montage. """ import ctypes import os import re import string from concurrent.futures import ThreadPoolExecutor, as_completed from pathlib import Path from PIL import Image, ImageDraw, ImageFont # ============================================================================= # USER SETTINGS # ============================================================================= # Add the local synced OneDrive folders that contain the source JPG images. # Keep the leading r before each Windows path. IMAGE_FOLDERS = [ r"C:\path\to\first\image_folder", r"C:\path\to\second\image_folder", ] # Montage layout. ROWS = 6 COLUMNS = 21 # Size of every individual image in the montage. SPOT_WIDTH = 500 SPOT_HEIGHT = 500 # White space between adjacent images. GRID_THICKNESS = 2 # Image preparation. ROTATION_DEGREES = 180 # Use 1.0 to retain the complete image. # Use 0.55 to reproduce the earlier central-crop montage format. CENTRE_CROP_FRACTION = 1.0 # Position labels. DRAW_POSITION_LABELS = True LABEL_FONT_SIZE = 40 LABEL_COLOUR = "red" LABEL_OFFSET_X = 5 LABEL_OFFSET_Y = 5 # Output settings. OUTPUT_SUFFIX = "_montage.jpg" JPEG_QUALITY = 95 OUTPUT_DPI = 600 # Number of folders processed at the same time. MAX_WORKERS = 4 # Return downloaded source JPGs to online-only status after the montage has # been created. This is applied only on Windows and does not affect the output. RETURN_SOURCE_IMAGES_TO_ONLINE_ONLY = True IMAGE_EXTENSIONS = {".jpg", ".jpeg"} # ============================================================================= # WINDOWS PATH AND ONEDRIVE HELPERS # ============================================================================= def windows_long_path(path): """Add the Windows long-path prefix when required.""" absolute_path = os.path.abspath(str(path)) if os.name != "nt" or absolute_path.startswith("\\\\?\\"): return absolute_path if absolute_path.startswith("\\\\"): return "\\\\?\\UNC\\" + absolute_path[2:] return "\\\\?\\" + absolute_path def make_online_only(path): """Mark a processed OneDrive source file as unpinned/online-only.""" if os.name != "nt": return file_attribute_pinned = 0x00080000 file_attribute_unpinned = 0x00100000 invalid_file_attributes = 0xFFFFFFFF long_path = windows_long_path(path) kernel32 = ctypes.windll.kernel32 attributes = kernel32.GetFileAttributesW(long_path) if attributes == invalid_file_attributes: print(f"Warning: could not read OneDrive attributes for {path}") return new_attributes = ( attributes | file_attribute_unpinned ) & ~file_attribute_pinned success = kernel32.SetFileAttributesW(long_path, new_attributes) if not success: print(f"Warning: could not return source image online-only: {path}") # ============================================================================= # IMAGE AND FILENAME HELPERS # ============================================================================= def load_arial_font(font_size): """Load Arial from Windows, with a portable fallback.""" possible_fonts = [ r"C:\Windows\Fonts\arial.ttf", "arial.ttf", ] for font_path in possible_fonts: try: return ImageFont.truetype(font_path, font_size) except OSError: continue print("Warning: Arial was unavailable; the default PIL font was used.") return ImageFont.load_default() def centre_crop(image, crop_fraction): """Return a centred crop while preserving the chosen image fraction.""" if not 0 < crop_fraction <= 1: raise ValueError("CENTRE_CROP_FRACTION must be greater than 0 and at most 1.") if crop_fraction == 1: return image width, height = image.size crop_width = max(1, round(width * crop_fraction)) crop_height = max(1, round(height * crop_fraction)) left = (width - crop_width) // 2 top = (height - crop_height) // 2 return image.crop( ( left, top, left + crop_width, top + crop_height, ) ) def prepare_image(image_path): """Open, optionally crop, resize and rotate one microscopy image.""" with Image.open(windows_long_path(image_path)) as source_image: image = source_image.convert("RGB") image = centre_crop(image, CENTRE_CROP_FRACTION) image = image.resize( (SPOT_WIDTH, SPOT_HEIGHT), Image.Resampling.LANCZOS, ) if ROTATION_DEGREES: image = image.rotate( ROTATION_DEGREES, expand=False, ) return image.copy() def position_from_filename(filename): """Extract a final grid code such as A01, F8 or H21.""" filename_stem = Path(filename).stem match = re.search( r"([A-Z])0*(\d{1,2})$", filename_stem, flags=re.IGNORECASE, ) if match is None: return None row_letter = match.group(1).upper() column_number = int(match.group(2)) valid_rows = string.ascii_uppercase[:ROWS] if row_letter not in valid_rows: return None if not 1 <= column_number <= COLUMNS: return None return row_letter, column_number def find_source_images(folder): """Map each expected grid position to its source JPG.""" image_map = {} unexpected_files = [] duplicate_positions = [] for filename in os.listdir(windows_long_path(folder)): file_path = Path(folder) / filename if "_montage" in filename.casefold(): continue if file_path.suffix.casefold() not in IMAGE_EXTENSIONS: continue position = position_from_filename(filename) if position is None: unexpected_files.append(filename) continue if position in image_map: duplicate_positions.append( (position, image_map[position].name, filename) ) continue image_map[position] = file_path if unexpected_files: print(f"\nFiles without a recognised final grid position in {folder}:") for filename in sorted(unexpected_files): print(f" {filename}") if duplicate_positions: print(f"\nDuplicate positions in {folder}; the first file was retained:") for position, retained, ignored in duplicate_positions: code = f"{position[0]}{position[1]:02d}" print(f" {code}: retained {retained}; ignored {ignored}") return image_map # ============================================================================= # MONTAGE CREATION # ============================================================================= def make_montage(image_folder): """Create one labelled montage from a folder of microscopy JPGs.""" folder = Path(image_folder) long_folder = windows_long_path(folder) if not os.path.isdir(long_folder): raise FileNotFoundError(f"Image folder not found: {folder}") print(f"\nProcessing: {folder}") image_map = find_source_images(folder) row_letters = string.ascii_uppercase[:ROWS] montage_width = ( COLUMNS * SPOT_WIDTH + (COLUMNS - 1) * GRID_THICKNESS ) montage_height = ( ROWS * SPOT_HEIGHT + (ROWS - 1) * GRID_THICKNESS ) montage = Image.new( "RGB", (montage_width, montage_height), color="white", ) drawing = ImageDraw.Draw(montage) font = load_arial_font(LABEL_FONT_SIZE) processed_sources = [] missing_positions = [] for row_index, row_letter in enumerate(row_letters): for column_number in range(1, COLUMNS + 1): position = (row_letter, column_number) position_label = f"{row_letter}{column_number:02d}" x_position = (column_number - 1) * ( SPOT_WIDTH + GRID_THICKNESS ) y_position = row_index * ( SPOT_HEIGHT + GRID_THICKNESS ) source_path = image_map.get(position) if source_path is not None: prepared_image = prepare_image(source_path) montage.paste( prepared_image, (x_position, y_position), ) processed_sources.append(source_path) else: missing_positions.append(position_label) if DRAW_POSITION_LABELS: drawing.text( ( x_position + LABEL_OFFSET_X, y_position + LABEL_OFFSET_Y, ), position_label, fill=LABEL_COLOUR, font=font, ) output_path = folder / f"{folder.name}{OUTPUT_SUFFIX}" montage.save( windows_long_path(output_path), format="JPEG", quality=JPEG_QUALITY, subsampling=0, dpi=(OUTPUT_DPI, OUTPUT_DPI), ) print(f"Created: {output_path}") print(f"Images included: {len(processed_sources)}") if missing_positions: print( f"Missing positions ({len(missing_positions)}): " + ", ".join(missing_positions) ) if RETURN_SOURCE_IMAGES_TO_ONLINE_ONLY: for source_path in processed_sources: make_online_only(source_path) print("Processed source JPGs were returned to online-only status.") return output_path # ============================================================================= # PROCESS THE FOLDERS CONCURRENTLY # ============================================================================= def main(): """Generate the requested montages, processing four folders at a time.""" if not IMAGE_FOLDERS: raise ValueError("Add at least one folder to IMAGE_FOLDERS.") completed_outputs = [] failed_folders = [] with ThreadPoolExecutor(max_workers=MAX_WORKERS) as executor: future_to_folder = { executor.submit(make_montage, folder): folder for folder in IMAGE_FOLDERS } for future in as_completed(future_to_folder): folder = future_to_folder[future] try: completed_outputs.append(future.result()) except Exception as error: failed_folders.append((folder, error)) print(f"\nFailed: {folder}\nReason: {error}") print("\nMontage processing complete.") print(f"Successful montages: {len(completed_outputs)}") print(f"Failed folders: {len(failed_folders)}") if completed_outputs: print("\nCreated montage files:") for output_path in completed_outputs: print(f" {output_path}") if failed_folders: print("\nFolders requiring attention:") for folder, error in failed_folders: print(f" {folder}: {error}") if __name__ == "__main__": main()