Fix file sizes

util/.gitignore

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+.*.venv

util/README.md

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+# Utility scripts
+
+## Use case: An input TIFF file is too large
+
+Assuming that the TIFF file is an RGB file:
+
+```bash
+../../util/shrink_tiff.sh test-data/input2_float.tiff --channel_axis 2
+```
+
+The script preserves the brightness and range of values of the image.
+
+## Use case: An output TIFF file is too large
+
+Assuming that the TIFF file is an RGB file:
+
+```bash
+../../util/shrink_tiff.sh test-data/res_preserve_values.tiff --channel_axis 2
+```
+
+This shrinks the file, but the *input files* also need to be shrinked accordingly.
+The output of the above command tells the exact scaling factor that was used.
+Denote this factor, and then run:
+
+```bash
+../../util/scale_image.sh test-data/input2_float.tiff --channel_axis 2 --scale SCALE
+```
+
+where you replace `SCALE` by the denoted factor. This also works for PNG files.
+
+The script preserves the brightness and range of values of the image.

util/scale_image.py

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+import argparse
+
+import numpy as np
+import skimage.transform
+import skimage.io
+
+
+def scale_image(filepath, **kwargs):
+    im = skimage.io.imread(filepath)
+    res = skimage.transform.rescale(im, preserve_range=True, **kwargs)
+
+    # Preserve the `dtype` so that both brightness and range of values is preserved
+    if res.dtype != im.dtype:
+        if np.issubdtype(im.dtype, np.integer):
+            res = res.round()
+        res = res.astype(im.dtype)
+
+    skimage.io.imsave(filepath, res)
+    return res
+
+
+if __name__ == '__main__':
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('filepath', type=str, help='Image filepath')
+    parser.add_argument('--scale', type=float, help='Scaling factor', required=True)
+    parser.add_argument('--anti_aliasing', default=False, action='store_true', help='Use anti-aliasing')
+    parser.add_argument('--order', type=int, default=0, help='Order of interpolation (0: nearest-neighbor, 1: bi-linear)')
+    parser.add_argument('--channel_axis', type=int, default=None, help='Given axis will not be rescaled')
+    args = parser.parse_args()
+
+    res = scale_image(
+        filepath=args.filepath,
+        scale=args.scale,
+        anti_aliasing=args.anti_aliasing,
+        order=args.order,
+        channel_axis=args.channel_axis,
+    )
+
+    print(f'File {args.filepath} has been scaled to a resolution of {str(res.shape)} pixels.')

util/scale_image.sh

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+#!/bin/bash
+
+set -e
+
+script_path=$( cd "$(dirname "${BASH_SOURCE[0]}")" ; pwd -P )
+cwd=$( pwd )
+cd "$script_path"
+
+if [ ! -d ".scale_image.venv" ]
+then
+    python -m venv ".scale_image.venv"
+    source ".scale_image.venv/bin/activate"
+    pip install "scikit-image>=0.19" "tifffile" "pillow"
+else
+    source ".scale_image.venv/bin/activate"
+fi
+
+cd "$cwd"
+python "$script_path/scale_image.py" $*

util/shrink_tiff.py

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+import argparse
+import itertools
+import math
+import os
+import tempfile
+import shutil
+
+import humanize
+import skimage.transform
+import tifffile
+
+
+DEFAULT_MAX_SIZE = 1024 ** 2
+
+
+def shrink_tiff(filepath, anti_aliasing, order, channel_axis, max_size=DEFAULT_MAX_SIZE, dry=True):
+    im_full = tifffile.imread(filepath)
+
+    for step in itertools.count(1):
+        scale = math.sqrt(1 / step)
+        im = skimage.transform.rescale(
+            im_full,
+            scale=scale,
+            anti_aliasing=anti_aliasing,
+            order=order,
+            preserve_range=True,
+            channel_axis=channel_axis,
+        )
+
+        with tempfile.NamedTemporaryFile(suffix='.tiff', mode='wb') as fp:
+            tifffile.imwrite(fp.name, im)
+            byte_size = os.path.getsize(fp.name)
+
+            if byte_size <= max_size:
+                if not dry:
+                    shutil.copy(fp.name, filepath)
+                return im, scale, byte_size
+
+
+if __name__ == '__main__':
+
+    exec_name = 'shrink_tiff.sh'
+    long_help = f"""
+
+    Example for single-channel binary images and label maps:
+
+        {exec_name} filepath.tiff
+
+    Example for multi-channel binary images:
+
+        {exec_name} filepath.tiff --channel_axis 2
+
+    Example for single-channel intensity images:
+
+        {exec_name} filepath.tiff --anti_aliasing --order 1
+
+    """
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('filepath', type=str, help='TIFF filepath')
+    parser.add_argument('--max_size', type=int, default=DEFAULT_MAX_SIZE, help='Maximum size in bytes')
+    parser.add_argument('--anti_aliasing', default=False, action='store_true', help='Use anti-aliasing')
+    parser.add_argument('--order', type=int, default=0, help='Order of interpolation (0: nearest-neighbor, 1: bi-linear)')
+    parser.add_argument('--channel_axis', type=int, default=None, help='Given axis will not be rescaled')
+    parser.add_argument('--run', default=False, action='store_true', help='Update the TIFF file (default is dry run)')
+    args = parser.parse_args()
+
+    if not args.run:
+        print(long_help)
+
+    result, scale, result_size = shrink_tiff(
+        filepath=args.filepath,
+        max_size=args.max_size,
+        anti_aliasing=args.anti_aliasing,
+        order=args.order,
+        channel_axis=args.channel_axis,
+        dry=not args.run,
+    )
+
+    result_size_str = humanize.naturalsize(result_size, binary=True)
+    if args.run:
+        print(f'File {args.filepath} has been shrinked to {result_size_str} and a resolution of {str(result.shape)} pixels by a factor of {scale}.')
+    else:
+        print(f'File {args.filepath} will be shrinked to {result_size_str} and a resolution of {str(result.shape)} pixels by a factor of {scale}.')
+        print('\nUse the switch "--run" to update the file.')

util/shrink_tiff.sh

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+#!/bin/bash
+
+set -e
+
+script_path=$( cd "$(dirname "${BASH_SOURCE[0]}")" ; pwd -P )
+cwd=$( pwd )
+cd "$script_path"
+
+if [ ! -d ".shrink_tiff.venv" ]
+then
+    python -m venv ".shrink_tiff.venv"
+    source ".shrink_tiff.venv/bin/activate"
+    pip install "scikit-image>=0.19" "humanize" "tifffile"
+else
+    source ".shrink_tiff.venv/bin/activate"
+fi
+
+cd "$cwd"
+python "$script_path/shrink_tiff.py" $*