Mercurial > repos > imgteam > split_image
changeset 1:73d7a4ffc03d draft default tip
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 15:05:29 +0000 |
| parents | 6b42bec75e69 |
| children | |
| files | split.py split_image.xml test-data/qyx.tiff test-data/qyx_q1.tiff test-data/qyx_q2.tiff test-data/rgb1_b.tiff test-data/rgb1_g.tiff test-data/rgb1_r.tiff test-data/rgb1_split_z.tiff test-data/rgb1_squeezed_b.tiff test-data/rgb1_squeezed_g.tiff test-data/rgb1_squeezed_r.tiff test-data/zcyx_slice01.tiff test-data/zcyx_slice25.tiff |
| diffstat | 14 files changed, 29 insertions(+), 9 deletions(-) [+] |
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--- a/split.py Fri Mar 07 08:08:05 2025 +0000 +++ b/split.py Sat Apr 12 15:05:29 2025 +0000 @@ -18,7 +18,7 @@ assert len(args.axis) == 1, 'Axis input must be a single character.' axis = args.axis.replace('S', 'C') -# Read input image as TZYXC +# Read input image with normalized axes img_in = giatools.Image.read(args.input) # Determine the axis to split along @@ -31,14 +31,24 @@ for img_idx, img in enumerate(arr): img = np.moveaxis(img[None], 0, axis_pos) + # Construct the output image, remove axes added by normalization + img_out = giatools.Image( + data=img, + axes=img_in.axes, + ).squeeze_like( + img_in.original_axes, + ) + # Optionally, squeeze the image if args.squeeze: - 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'] - img = np.squeeze(img, axis=tuple(s)) - img_axes = giatools.util.str_without_positions(img_in.axes, s) - else: - img_axes = img_in.axes + s = [ + axis_pos for axis_pos in range(len(img_out.axes)) + if img_out.data.shape[axis_pos] == 1 and img_out.axes[axis_pos] not in 'YX' + ] + img_out = img_out.squeeze_like( + giatools.util.str_without_positions(img_out.axes, s), + ) # Save the result filename = output_filename_pattern % (img_idx + 1) - tifffile.imwrite(filename, img, metadata=dict(axes=img_axes)) + tifffile.imwrite(filename, img_out.data, metadata=dict(axes=img_out.axes))
--- a/split_image.xml Fri Mar 07 08:08:05 2025 +0000 +++ b/split_image.xml Sat Apr 12 15:05:29 2025 +0000 @@ -4,7 +4,7 @@ <import>creators.xml</import> <import>tests.xml</import> <token name="@TOOL_VERSION@">2.2.3</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <creator> <expand macro="creators/bmcv"/> @@ -14,7 +14,7 @@ </edam_operations> <requirements> <requirement type="package" version="@TOOL_VERSION@">numpy</requirement> - <requirement type="package" version="0.3.2">giatools</requirement> + <requirement type="package" version="0.4.0">giatools</requirement> <requirement type="package" version="2024.7.24">tifffile</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ @@ -36,6 +36,7 @@ <option value="Z">Z-axis (split the slices of a 3-D image or image sequence)</option> <option value="C" selected="true">C-axis (split the channels of an image or image sequence)</option> <option value="S">S-axis (split the samples of an image or image sequence)</option> + <option value="Q">Q-axis (other or unknown axis)</option> </param> <param name="squeeze" type="boolean" checked="false" truevalue="--squeeze" falsevalue="" label="Squeeze result imags" help="Only axes with more than one element will be retained in the result images. Does not apply for X and Y axes." /> </inputs> @@ -68,6 +69,15 @@ <expand macro="tests/intensity_image_diff/element" name="25.tiff" value="zcyx_slice25.tiff" ftype="tiff"/> </output_collection> </test> + <test> + <param name="input" value="qyx.tiff" /> + <param name="axis" value="Q" /> + <param name="squeeze" value="false" /> + <output_collection name="output" type="list" count="2"> + <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="qyx_q1.tiff" ftype="tiff"/> + <expand macro="tests/intensity_image_diff/element" name="2.tiff" value="qyx_q2.tiff" ftype="tiff"/> + </output_collection> + </test> <!-- Test squeezing --> <test>