Tiff Unpacker Utility Script

scripts/tiff_unpacker.py

@@ -0,0 +1,126 @@
+# Copyright (C) 2023 ISIS Rutherford Appleton Laboratory UKRI
+# SPDX - License - Identifier: GPL-3.0-or-later
+"""
+This is a Utility script to unpack tiff files into a directory of images using lossless compression.
+This script is temporary while larger work is undertaken to improve how datasets are stored and accessed within Mantid.
+
+Usage:
+    python tiff_unpacker.py -s <path to tiff file> -d <path to output directory>
+    python tiff_unpacker.py
+        -s <path to tiff file>
+        -d <path to output directory>
+        -r <start> <stop>
+        -n <naming convention>
+"""
+import argparse
+from tqdm import tqdm
+from pathlib import Path
+from tifffile import TiffFile, imwrite
+from logging import getLogger, basicConfig, INFO
+
+basicConfig(format='%(asctime)s %(message)s', datefmt='%m/%d/%Y %I:%M:%S %p', level=INFO)
+logger = getLogger(__name__)
+
+
+def unpack_tiff(source: Path, destination: Path, img_range: tuple[int, int], naming_convention: str) -> None:
+    """
+    Unpack a tiff file into a directory of LZW compressed tif images
+
+    Parameters:
+        source: Path to tiff file
+        destination: Path to output directory
+
+    Returns:
+        None
+    """
+    with TiffFile(source) as tif:
+        for i, img in enumerate(tqdm(tif.pages[img_range[0]:img_range[1]], desc="Unpacking tiff file")):
+            imwrite(destination / f"{naming_convention}{i}.tiff",
+                    img.asarray(),
+                    compression="zlib",
+                    predictor=True,
+                    metadata={
+                        'axes': img.axes,
+                        'unit': 'um'
+                    })
+
+
+def validate_input_range(data_length: int, start: int, stop: int) -> tuple[int, int]:
+    """
+    Validate the input range
+
+    If start is greater than stop then raise ValueError
+    If stop is greater than the number of images in the tiff file then raise ValueError
+    If stop is 0 then set stop to the number of images in the tiff file
+    """
+    if start > stop:
+        raise ValueError(f"Start {start} must be less than stop {stop}")
+    if stop > data_length:
+        raise ValueError(f"Stop {stop} must be less than the number of images in the tiff file {data_length}")
+    if stop == 0:
+        stop = data_length
+    return start, stop
+
+
+def validate_paths(source: Path, destination: Path) -> None:
+    """
+    Validate the source and destination paths
+
+    Parameters:
+        source: Path to tiff file
+        destination: Path to output directory
+
+    Returns:
+        None
+    """
+    if not source.is_file():
+        raise ValueError(f"{source} is not a file")
+    if not destination.is_dir():
+        destination.mkdir(parents=True, exist_ok=True)
+        logger.info("Created directory %s as it previously did not exist", destination)
+
+
+def input_parser():
+    """
+    Input parser for the script
+
+    Expected input:
+        python tiff_unpacker.py <path to tiff file> <path to output directory>
+
+    Returns:
+        Path to tiff file
+        Path to output directory
+        Range of images to unpack
+        Naming convention of output images
+    """
+    parser = argparse.ArgumentParser(description="Unpack tiff file into a directory of images")
+    parser.add_argument("-s", "--source", help="Absolute path to tiff file", type=Path, required=True)
+    parser.add_argument("-d", "--destination", help="Absolute path to output directory", type=Path, required=True)
+    parser.add_argument("-r",
+                        "--range",
+                        help="Range of images to unpack start <start stop>",
+                        type=int,
+                        nargs=2,
+                        required=False,
+                        default=[0, 0])
+    parser.add_argument("-n",
+                        "--name",
+                        help="Naming convention of output images (default is tbin_)",
+                        type=str,
+                        required=False,
+                        default="tbin_")
+    args = parser.parse_args()
+    validate_paths(args.source, args.destination)
+    args.range = validate_input_range(len(TiffFile(args.source).pages), *args.range)
+    return args.source, args.destination, args.range, args.name
+
+
+def main():
+    """
+    Main function to unpack tiff file into a directory of images
+    """
+    unpack_tiff(*input_parser())
+
+
+if __name__ == "__main__":
+    main()