Mercurial > repos > imgteam > split_image
changeset 2:227e8928af6e draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
| author | imgteam |
|---|---|
| date | Fri, 12 Dec 2025 21:02:25 +0000 |
| parents | 4b7940d0c051 |
| children | |
| files | creators.xml split.py split_image.xml test-data/multiseries.ome.tiff test-data/multiseries_series1.tiff test-data/multiseries_series6.tiff test-data/rgb1.tiff |
| diffstat | 7 files changed, 220 insertions(+), 44 deletions(-) [+] |
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--- a/creators.xml Sat Apr 12 15:05:17 2025 +0000 +++ b/creators.xml Fri Dec 12 21:02:25 2025 +0000 @@ -5,6 +5,11 @@ <yield /> </xml> + <xml name="creators/kostrykin"> + <person givenName="Leonid" familyName="Kostrykin"/> + <yield/> + </xml> + <xml name="creators/rmassei"> <person givenName="Riccardo" familyName="Massei"/> <yield/> @@ -24,5 +29,15 @@ <person givenName="Till" familyName="Korten"/> <yield/> </xml> - + + <xml name="creators/pavanvidem"> + <person givenName="Pavan" familyName="Videm"/> + <yield/> + </xml> + + <xml name="creators/tuncK"> + <person givenName="Tunc" familyName="Kayikcioglu"/> + <yield/> + </xml> + </macros>
--- a/split.py Sat Apr 12 15:05:17 2025 +0000 +++ b/split.py Fri Dec 12 21:02:25 2025 +0000 @@ -1,54 +1,122 @@ import argparse import math +import os +import pathlib +import shutil import giatools -import giatools.util import numpy as np import tifffile -parser = argparse.ArgumentParser() -parser.add_argument('input', type=str) -parser.add_argument('axis', type=str) -parser.add_argument('output', type=str) -parser.add_argument('--squeeze', action='store_true', default=False) -args = parser.parse_args() +class OutputWriter: + + def __init__(self, dir_path: pathlib.Path, num_images: int, squeeze: bool, verbose: bool): + print(f'Writing {num_images} image(s)') + decimals = math.ceil(math.log10(1 + num_images)) + self.output_filepath_pattern = str(dir_path / f'%0{decimals}d.tiff') + self.last_idx = 0 + self.squeeze = squeeze + self.verbose = verbose + + def write(self, img: giatools.Image): + self.last_idx += 1 + if self.squeeze: + img = img.squeeze() + if self.last_idx == 1 or self.verbose: + prefix = f'Output {self.last_idx}' if self.verbose else 'Output' + print(f'{prefix} axes:', img.axes) + print(f'{prefix} shape:', img.data.shape) + img.write(self.output_filepath_pattern % self.last_idx) + -# Validate and normalize input parameters -assert len(args.axis) == 1, 'Axis input must be a single character.' -axis = args.axis.replace('S', 'C') +if __name__ == '__main__': + + parser = argparse.ArgumentParser() + parser.add_argument('input', type=pathlib.Path) + parser.add_argument('axis', type=str, choices=list(giatools.default_normalized_axes) + ['S', '']) + parser.add_argument('output', type=pathlib.Path) + parser.add_argument('--squeeze', action='store_true', default=False) + args = parser.parse_args() -# Read input image with normalized axes -img_in = giatools.Image.read(args.input) + # If splitting a file that contains multiple images... + if args.axis == '': -# Determine the axis to split along -axis_pos = img_in.axes.index(axis) + # Peek the number of series in the input file (if it is a TIFF) + try: + with tifffile.TiffFile(args.input) as tiff: + num_tiff_series = len(tiff.series) + print(f'Found TIFF with {num_tiff_series} series') + except tifffile.TiffFileError: + num_tiff_series = 0 # not a TIFF file + print('Not a TIFF file') -# Perform the splitting -arr = np.moveaxis(img_in.data, axis_pos, 0) -decimals = math.ceil(math.log10(1 + arr.shape[0])) -output_filename_pattern = f'{args.output}/%0{decimals}d.tiff' -for img_idx, img in enumerate(arr): - img = np.moveaxis(img[None], 0, axis_pos) + # If the file is a multi-series TIFF, extract the individual series + # (for consistency, also accept only a single series if squeezing is requested) + if num_tiff_series >= 2 or (num_tiff_series == 1 and args.squeeze): + output = OutputWriter( + dir_path=args.output, + num_images=num_tiff_series, + squeeze=args.squeeze, + verbose=True, + ) + for series in range(num_tiff_series): + img = giatools.Image.read(args.input, series=series) + output.write( + img.squeeze_like(img.original_axes), + ) + + # Otherwise, there is nothing to be split (or squeeze) + # (the input is either a single-series TIFF or not a TIFF at all) + elif num_tiff_series == 1: # input is a single-series TIFF (output = input) + try: + os.symlink(args.input, args.output / '1.tiff') + except OSError: + shutil.copyfile(args.input, args.output / '1.tiff') + else: # input is not a TIFF, conversion needed + img = giatools.Image.read(args.input) + OutputWriter( + dir_path=args.output, + num_images=1, + squeeze=args.squeeze, + verbose=False, + ).write( + img.squeeze_like(img.original_axes), + ) - # 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, - ) + # If splitting along an image axes... + else: + + # Validate and normalize input parameters + axis = args.axis.replace('S', 'C') + + # Read input image with normalized axes + img_in = giatools.Image.read(args.input) + print('Input image axes:', img_in.original_axes) + print('Input image shape:', img_in.squeeze_like(img_in.original_axes).data.shape) + + # Determine the axis to split along + axis_pos = img_in.axes.index(axis) - # Optionally, squeeze the image - if args.squeeze: - 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), + # Perform the splitting + arr = np.moveaxis(img_in.data, axis_pos, 0) + output = OutputWriter( + dir_path=args.output, + num_images=arr.shape[0], + squeeze=args.squeeze, + verbose=False, ) + for img_idx, img in enumerate(arr): + img = np.moveaxis(img[None], 0, axis_pos) - # Save the result - filename = output_filename_pattern % (img_idx + 1) - tifffile.imwrite(filename, img_out.data, metadata=dict(axes=img_out.axes)) + # Construct the output image, remove axes added by normalization + img_out = giatools.Image( + data=img, + axes=img_in.axes, + metadata=img_in.metadata, + ).squeeze_like( + img_in.original_axes, + ) + + # Save the result (write stdout during first iteration) + output.write(img_out)
--- a/split_image.xml Sat Apr 12 15:05:17 2025 +0000 +++ b/split_image.xml Fri Dec 12 21:02:25 2025 +0000 @@ -3,19 +3,23 @@ <macros> <import>creators.xml</import> <import>tests.xml</import> - <token name="@TOOL_VERSION@">2.2.3</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">2.3.5</token> + <token name="@VERSION_SUFFIX@">0</token> </macros> <creator> <expand macro="creators/bmcv"/> + <expand macro="creators/kostrykin"/> </creator> <edam_operations> <edam_operation>operation_3443</edam_operation> </edam_operations> + <xrefs> + <xref type="bio.tools">galaxy_image_analysis</xref> + </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">numpy</requirement> - <requirement type="package" version="0.4.0">giatools</requirement> - <requirement type="package" version="2024.7.24">tifffile</requirement> + <requirement type="package" version="0.5.2">giatools</requirement> + <requirement type="package" version="2025.10.16">tifffile</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ @@ -37,8 +41,10 @@ <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> + <option value="">Split dataset that contains multiple images (e.g., multi-series TIFF)</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." /> + <param name="squeeze" type="boolean" checked="false" truevalue="--squeeze" falsevalue="" label="Squeeze result images" + help="Only non-singleton axes (axes with more than one element) will be retained in the result images. This does not apply for the X and Y axes which always are retained." /> </inputs> <outputs> <collection type="list" name="output" label="Split ${on_string} along ${axis} axis"> @@ -57,6 +63,27 @@ <expand macro="tests/intensity_image_diff/element" name="2.tiff" value="rgb1_g.tiff" ftype="tiff"/> <expand macro="tests/intensity_image_diff/element" name="3.tiff" value="rgb1_b.tiff" ftype="tiff"/> </output_collection> + <assert_stdout> + <has_line line="Input image axes: YXC"/> + <has_line line="Input image shape: (32, 32, 3)"/> + <has_line line="Writing 3 image(s)"/> + <has_line line="Output axes: YXC"/> + <has_line line="Output shape: (32, 32, 1)"/> + </assert_stdout> + </test> + <test> + <param name="input" value="rgb1.png" /> + <param name="axis" value="" /> + <param name="squeeze" value="false" /> + <output_collection name="output" type="list" count="1"> + <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1.tiff" ftype="tiff"/> + </output_collection> + <assert_stdout> + <has_line line="Not a TIFF file"/> + <has_line line="Writing 1 image(s)"/> + <has_line line="Output axes: YXC"/> + <has_line line="Output shape: (32, 32, 3)"/> + </assert_stdout> </test> <!-- TIFF tests --> @@ -68,6 +95,13 @@ <expand macro="tests/intensity_image_diff/element" name="01.tiff" value="zcyx_slice01.tiff" ftype="tiff"/> <expand macro="tests/intensity_image_diff/element" name="25.tiff" value="zcyx_slice25.tiff" ftype="tiff"/> </output_collection> + <assert_stdout> + <has_line line="Input image axes: ZCYX"/> + <has_line line="Input image shape: (25, 2, 50, 50)"/> + <has_line line="Writing 25 image(s)"/> + <has_line line="Output axes: ZCYX"/> + <has_line line="Output shape: (1, 2, 50, 50)"/> + </assert_stdout> </test> <test> <param name="input" value="qyx.tiff" /> @@ -77,6 +111,51 @@ <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> + <assert_stdout> + <has_line line="Input image axes: QYX"/> + <has_line line="Input image shape: (2, 256, 256)"/> + <has_line line="Writing 2 image(s)"/> + <has_line line="Output axes: QYX"/> + <has_line line="Output shape: (1, 256, 256)"/> + </assert_stdout> + </test> + <test> + <param name="input" value="qyx.tiff" /> + <param name="axis" value="" /> + <param name="squeeze" value="false" /> + <output_collection name="output" type="list" count="1"> + <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="qyx.tiff" ftype="tiff"/> + </output_collection> + <assert_stdout> + <has_line line="Found TIFF with 1 series"/> + </assert_stdout> + </test> + + <!-- Test splitting multi-series TIFF --> + <test> + <param name="input" value="multiseries.ome.tiff" /> + <param name="axis" value="" /> + <param name="squeeze" value="false" /> + <output_collection name="output" type="list" count="6"> + <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="multiseries_series1.tiff" ftype="tiff"/> + <expand macro="tests/intensity_image_diff/element" name="6.tiff" value="multiseries_series6.tiff" ftype="tiff"/> + </output_collection> + <assert_stdout> + <has_line line="Found TIFF with 6 series"/> + <has_line line="Writing 6 image(s)"/> + <has_line line="Output 1 axes: CYX"/> + <has_line line="Output 1 shape: (4, 5, 5)"/> + <has_line line="Output 2 axes: CYX"/> + <has_line line="Output 2 shape: (4, 5, 5)"/> + <has_line line="Output 3 axes: CYX"/> + <has_line line="Output 3 shape: (4, 5, 5)"/> + <has_line line="Output 4 axes: CYX"/> + <has_line line="Output 4 shape: (4, 5, 5)"/> + <has_line line="Output 5 axes: CYX"/> + <has_line line="Output 5 shape: (4, 5, 5)"/> + <has_line line="Output 6 axes: CYX"/> + <has_line line="Output 6 shape: (4, 5, 5)"/> + </assert_stdout> </test> <!-- Test squeezing --> @@ -89,6 +168,13 @@ <expand macro="tests/intensity_image_diff/element" name="2.tiff" value="rgb1_squeezed_g.tiff" ftype="tiff"/> <expand macro="tests/intensity_image_diff/element" name="3.tiff" value="rgb1_squeezed_b.tiff" ftype="tiff"/> </output_collection> + <assert_stdout> + <has_line line="Input image axes: YXC"/> + <has_line line="Input image shape: (32, 32, 3)"/> + <has_line line="Writing 3 image(s)"/> + <has_line line="Output axes: YX"/> + <has_line line="Output shape: (32, 32)"/> + </assert_stdout> </test> <!-- Test with missing axes --> @@ -99,6 +185,13 @@ <output_collection name="output" type="list" count="1"> <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1_split_z.tiff" ftype="tiff"/> </output_collection> + <assert_stdout> + <has_line line="Input image axes: YXC"/> + <has_line line="Input image shape: (32, 32, 3)"/> + <has_line line="Writing 1 image(s)"/> + <has_line line="Output axes: YXC"/> + <has_line line="Output shape: (32, 32, 3)"/> + </assert_stdout> </test> </tests>