Mercurial > repos > imgteam > morphological_operations
changeset 0:f10112b317a1 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
| author | imgteam |
|---|---|
| date | Fri, 08 Mar 2024 11:00:41 +0000 |
| parents | |
| children | ad795d260ba8 |
| files | morphological_operations.py morphological_operations.xml test-data/input1.tiff test-data/input2.png test-data/input3.png test-data/output1_closing.tiff test-data/output1_dilation.tiff test-data/output1_erosion.tiff test-data/output1_opening.tiff test-data/output2_fill_holes.tiff test-data/output3_closing.tiff test-data/output3_dilation.tiff test-data/output3_erosion.tiff test-data/output3_opening.tiff |
| diffstat | 14 files changed, 226 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/morphological_operations.py Fri Mar 08 11:00:41 2024 +0000 @@ -0,0 +1,93 @@ +import argparse + +import numpy as np +import scipy.ndimage as ndi +import skimage.io +import skimage.morphology as morph + + +def create_selem(args): + """ + Creates structuring element based on commandline arguments. + """ + assert args.selem_shape in ( + 'square', + 'disk', + ) + + if args.selem_shape == 'square': + return np.ones((args.selem_size, args.selem_size)) + + elif args.selem_shape == 'disk': + return morph.disk(args.selem_size) + + +def apply_operation(args, im): + """ + Applies morphological operation to a 2-D single-channel image. + """ + assert im.ndim == 2 + selem = create_selem(args) + values_count = len(np.unique(im)) + if values_count <= 2: + im_proxy = np.zeros(im.shape, bool) + im_proxy[im == im.max()] = True + result_proxy = apply_binary_operation(args, im_proxy, selem) + result = np.full(im.shape, im.min(), im.dtype) + result[result_proxy] = im.max() + return result + else: + return apply_intensity_based_operation(args, im, selem) + + +def apply_intensity_based_operation(args, im, selem): + operations = { + 'erosion': ndi.grey_erosion, + 'dilation': ndi.grey_dilation, + 'opening': ndi.grey_opening, + 'closing': ndi.grey_closing, + } + if args.operation in operations: + operation = operations[args.operation] + return operation(input=im, structure=selem) + else: + raise ValueError(f'Operation "{args.operation}" not supported for this image type ({im.dtype}).') + + +def apply_binary_operation(args, im, selem): + operations = { + 'erosion': ndi.binary_erosion, + 'dilation': ndi.binary_dilation, + 'opening': ndi.binary_opening, + 'closing': ndi.binary_closing, + 'fill_holes': ndi.binary_fill_holes, + } + operation = operations[args.operation] + return operation(input=im, structure=selem) + + +if __name__ == '__main__': + + parser = argparse.ArgumentParser() + parser.add_argument('--operation', type=str) + parser.add_argument('--selem-shape', type=str) + parser.add_argument('--selem-size', type=int) + parser.add_argument('input', type=str) + parser.add_argument('output', type=str) + args = parser.parse_args() + + im = skimage.io.imread(args.input) + assert im.ndim in (2, 3), 'Input image must be two-dimensional and either single-channel or multi-channel.' + + if im.ndim == 2: + im_result = apply_operation(args, im) + + else: + ch_result_list = [] + for ch_idx in range(im.shape[2]): + ch = im[:, :, ch_idx] + ch_result = apply_operation(args, ch) + ch_result_list.append(ch_result) + im_result = np.dstack(ch_result_list) + + skimage.io.imsave(args.output, im_result)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/morphological_operations.xml Fri Mar 08 11:00:41 2024 +0000 @@ -0,0 +1,133 @@ +<tool id="morphological_operations" name="Apply a morphological operation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> + <description>with SciPy</description> + <macros> + <token name="@TOOL_VERSION@">1.12.0</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <edam_operations> + <edam_operation>operation_3443</edam_operation> + </edam_operations> + <xrefs> + <xref type="biii">scipy</xref> + </xrefs> + <requirements> + <requirement type="package" version="1.12.0">scipy</requirement> + <requirement type="package" version="0.22.0">scikit-image</requirement> + </requirements> + <command><![CDATA[ + + ## Inputs + + python '$__tool_directory__/morphological_operations.py' '$image' + --operation $operation + --selem-shape $selem_shape + --selem-size $selem_size + + ## Outputs + + ./result.tiff + + ]]> + </command> + <inputs> + <param name="image" type="data" format="png,tiff" label="Input image" /> + <param label="Morphological operation" argument="--operation" type="select"> + <option value="erosion" selected="True">Erosion</option> + <option value="dilation">Dilation</option> + <option value="opening">Opening</option> + <option value="closing">Closing</option> + <option value="fill_holes">Fill holes</option> + </param> + <param label="Structuring element" argument="--selem-shape" type="select"> + <option value="disk" selected="True">Disk</option> + <option value="square">Square</option> + </param> + <param label="Structuring element size" argument="--selem-size" type="integer" min="1" max="256" value="1" help="The radius of the disk, or the width of the square, in pixels." /> + </inputs> + <outputs> + <data format="tiff" name="result" from_work_dir="result.tiff" /> + </outputs> + <tests> + <!-- Test binary operations (input images with two distinct values) --> + <test> + <param name="image" value="input1.tiff" /> + <param name="operation" value="erosion" /> + <param name="selem_shape" value="disk" /> + <param name="selem_size" value="1" /> + <output name="result" value="output1_erosion.tiff" ftype="tiff" compare="sim_size" delta="10" /> + </test> + <test> + <param name="image" value="input1.tiff" /> + <param name="operation" value="dilation" /> + <param name="selem_shape" value="disk" /> + <param name="selem_size" value="2" /> + <output name="result" value="output1_dilation.tiff" ftype="tiff" compare="sim_size" delta="10" /> + </test> + <test> + <param name="image" value="input1.tiff" /> + <param name="operation" value="opening" /> + <param name="selem_shape" value="square" /> + <param name="selem_size" value="1" /> + <output name="result" value="output1_opening.tiff" ftype="tiff" compare="sim_size" delta="10" /> + </test> + <test> + <param name="image" value="input1.tiff" /> + <param name="operation" value="closing" /> + <param name="selem_shape" value="square" /> + <param name="selem_size" value="2" /> + <output name="result" value="output1_closing.tiff" ftype="tiff" compare="sim_size" delta="10" /> + </test> + <!-- Test intensity-based operations (more than two distinct values) --> + <test> + <param name="image" value="input3.png" /> + <param name="operation" value="erosion" /> + <param name="selem_shape" value="disk" /> + <param name="selem_size" value="1" /> + <output name="result" value="output3_erosion.tiff" ftype="tiff" compare="sim_size" delta="10" /> + </test> + <test> + <param name="image" value="input3.png" /> + <param name="operation" value="dilation" /> + <param name="selem_shape" value="disk" /> + <param name="selem_size" value="2" /> + <output name="result" value="output3_dilation.tiff" ftype="tiff" compare="sim_size" delta="10" /> + </test> + <test> + <param name="image" value="input3.png" /> + <param name="operation" value="opening" /> + <param name="selem_shape" value="square" /> + <param name="selem_size" value="1" /> + <output name="result" value="output3_opening.tiff" ftype="tiff" compare="sim_size" delta="10" /> + </test> + <test> + <param name="image" value="input3.png" /> + <param name="operation" value="closing" /> + <param name="selem_shape" value="square" /> + <param name="selem_size" value="2" /> + <output name="result" value="output3_closing.tiff" ftype="tiff" compare="sim_size" delta="10" /> + </test> + <!-- Test multi-channel image (with two distinct values per channel) --> + <test> + <param name="image" value="input2.png" /> + <param name="operation" value="fill_holes" /> + <param name="selem_shape" value="disk" /> + <param name="selem_size" value="1" /> + <output name="result" value="output2_fill_holes.tiff" ftype="tiff" compare="sim_size" delta="10" /> + </test> + </tests> + <help> + Applies a morphological operation to a 2-D image. + For multi-channel images, the operation is applied to each channel separately. + + The following operations are supported: + + - **Erosion:** Shrink bright areas. + - **Dilation:** Grow bright areas. + - **Opening:** Erosion followed by Dilation. Erases tiny bright spots. + - **Closing:** Dilation followed by Erosion. Erases tiny dark holes. + - **Fill holes:** Fills the holes (dark areas) in binary images. + </help> + <citations> + <citation type="doi">10.1038/s41592-019-0686-2</citation> + </citations> +</tool> \ No newline at end of file