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comparison split.py @ 1:4b7940d0c051 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 6152e9fafda27f76c1e96e533143f86fe605e2da
author imgteam
date Sat, 12 Apr 2025 15:05:17 +0000
parents 5deaa390ca62
children
comparison
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0:5deaa390ca62 1:4b7940d0c051
16 16
17 # Validate and normalize input parameters 17 # Validate and normalize input parameters
18 assert len(args.axis) == 1, 'Axis input must be a single character.' 18 assert len(args.axis) == 1, 'Axis input must be a single character.'
19 axis = args.axis.replace('S', 'C') 19 axis = args.axis.replace('S', 'C')
20 20
21 # Read input image as TZYXC 21 # Read input image with normalized axes
22 img_in = giatools.Image.read(args.input) 22 img_in = giatools.Image.read(args.input)
23 23
24 # Determine the axis to split along 24 # Determine the axis to split along
25 axis_pos = img_in.axes.index(axis) 25 axis_pos = img_in.axes.index(axis)
26 26
29 decimals = math.ceil(math.log10(1 + arr.shape[0])) 29 decimals = math.ceil(math.log10(1 + arr.shape[0]))
30 output_filename_pattern = f'{args.output}/%0{decimals}d.tiff' 30 output_filename_pattern = f'{args.output}/%0{decimals}d.tiff'
31 for img_idx, img in enumerate(arr): 31 for img_idx, img in enumerate(arr):
32 img = np.moveaxis(img[None], 0, axis_pos) 32 img = np.moveaxis(img[None], 0, axis_pos)
33 33
34 # Construct the output image, remove axes added by normalization
35 img_out = giatools.Image(
36 data=img,
37 axes=img_in.axes,
38 ).squeeze_like(
39 img_in.original_axes,
40 )
41
34 # Optionally, squeeze the image 42 # Optionally, squeeze the image
35 if args.squeeze: 43 if args.squeeze:
36 s = [axis_pos for axis_pos in range(len(img_in.axes)) if img.shape[axis_pos] == 1 and img_in.axes[axis_pos] not in 'YX'] 44 s = [
37 img = np.squeeze(img, axis=tuple(s)) 45 axis_pos for axis_pos in range(len(img_out.axes))
38 img_axes = giatools.util.str_without_positions(img_in.axes, s) 46 if img_out.data.shape[axis_pos] == 1 and img_out.axes[axis_pos] not in 'YX'
39 else: 47 ]
40 img_axes = img_in.axes 48 img_out = img_out.squeeze_like(
49 giatools.util.str_without_positions(img_out.axes, s),
50 )
41 51
42 # Save the result 52 # Save the result
43 filename = output_filename_pattern % (img_idx + 1) 53 filename = output_filename_pattern % (img_idx + 1)
44 tifffile.imwrite(filename, img, metadata=dict(axes=img_axes)) 54 tifffile.imwrite(filename, img_out.data, metadata=dict(axes=img_out.axes))