Mercurial > repos > imgteam > 2d_simple_filter
changeset 2:b2d9c92bc431 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
| author | imgteam |
|---|---|
| date | Fri, 12 Dec 2025 21:18:04 +0000 |
| parents | e2542d0ac64f |
| children | 53c55776a974 |
| files | creators.xml filter.py filter.xml filter_image.py test-data/input1_gaussian.tiff test-data/input1_median.tiff test-data/input1_prewitt_h.tiff test-data/input1_prewitt_v.tiff test-data/input1_sobel_h.tiff test-data/input1_sobel_v.tiff test-data/input1_uint8.tiff test-data/input2_float.tiff test-data/input2_gaussian.tiff test-data/input2_uniform.tiff test-data/res.tif test-data/retina_gaussian_order0.tiff test-data/retina_gaussian_order2_axis0.tiff test-data/sample.tif test-data/scikit-image/LICENSE.txt test-data/scikit-image/retina.png tests.xml |
| diffstat | 21 files changed, 511 insertions(+), 57 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/creators.xml Fri Dec 12 21:18:04 2025 +0000 @@ -0,0 +1,43 @@ +<macros> + + <xml name="creators/bmcv"> + <organization name="Biomedical Computer Vision Group, Heidelberg Universtiy" alternateName="BMCV" url="http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html" /> + <yield /> + </xml> + + <xml name="creators/kostrykin"> + <person givenName="Leonid" familyName="Kostrykin"/> + <yield/> + </xml> + + <xml name="creators/rmassei"> + <person givenName="Riccardo" familyName="Massei"/> + <yield/> + </xml> + + <xml name="creators/alliecreason"> + <person givenName="Allison" familyName="Creason"/> + <yield/> + </xml> + + <xml name="creators/bugraoezdemir"> + <person givenName="Bugra" familyName="Oezdemir"/> + <yield/> + </xml> + + <xml name="creators/thawn"> + <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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter.py Fri Dec 12 21:18:04 2025 +0000 @@ -0,0 +1,110 @@ +import argparse +import json +from typing import ( + Any, + Callable, +) + +import giatools +import numpy as np +import scipy.ndimage as ndi +from skimage.morphology import disk + + +def image_astype(img: giatools.Image, dtype: np.dtype) -> giatools.Image: + return giatools.Image( + data=img.data.astype(dtype), + axes=img.axes, + original_axes=img.original_axes, + metadata=img.metadata, + ) + + +filters = { + 'gaussian': lambda img, sigma, order=0, axis=None: ( + apply_2d_filter( + ndi.gaussian_filter, + img if order == 0 else image_astype(img, float), + sigma=sigma, + order=order, + axes=axis, + ) + ), + 'uniform': lambda img, size: ( + apply_2d_filter(ndi.uniform_filter, img, size=size) + ), + 'median': lambda img, radius: ( + apply_2d_filter(ndi.median_filter, img, footprint=disk(radius)) + ), + 'prewitt': lambda img, axis: ( + apply_2d_filter(ndi.prewitt, img, axis=axis) + ), + 'sobel': lambda img, axis: ( + apply_2d_filter(ndi.sobel, img, axis=axis) + ), +} + + +def apply_2d_filter( + filter_impl: Callable[[np.ndarray, Any, ...], np.ndarray], + img: giatools.Image, + **kwargs: Any, +) -> giatools.Image: + """ + Apply the 2-D filter to the 2-D/3-D, potentially multi-frame and multi-channel image. + """ + result_data = None + for qtzc in np.ndindex( + img.data.shape[ 0], # Q axis + img.data.shape[ 1], # T axis + img.data.shape[ 2], # Z axis + img.data.shape[-1], # C axis + ): + sl = np.s_[*qtzc[:3], ..., qtzc[3]] # noqa: E999 + arr = img.data[sl] + assert arr.ndim == 2 # sanity check, should always be True + + # Perform 2-D filtering + res = filter_impl(arr, **kwargs) + if result_data is None: + result_data = np.empty(img.data.shape, res.dtype) + result_data[sl] = res + + # Return results + return giatools.Image(result_data, img.axes) + + +def apply_filter( + input_filepath: str, + output_filepath: str, + filter_type: str, + **kwargs: Any, +): + # Read the input image + img = giatools.Image.read(input_filepath) + + # Perform filtering + filter_impl = filters[filter_type] + res = filter_impl(img, **kwargs).normalize_axes_like(img.original_axes) + + # Adopt metadata and write the result + res.metadata = img.metadata + res.write(output_filepath, backend='tifffile') + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument('input', type=str, help='Input image filepath') + parser.add_argument('output', type=str, help='Output image filepath (TIFF)') + parser.add_argument('params', type=str) + args = parser.parse_args() + + # Read the config file + with open(args.params) as cfgf: + cfg = json.load(cfgf) + + apply_filter( + args.input, + args.output, + **cfg, + )
--- a/filter.xml Thu Jul 18 08:51:37 2019 -0400 +++ b/filter.xml Fri Dec 12 21:18:04 2025 +0000 @@ -1,42 +1,249 @@ -<tool id="ip_filter_standard" name="Filter Image" version="0.0.3"> - <description>applies a standard filter to an image</description> +<tool id="ip_filter_standard" name="Apply 2-D image filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> + <description>with scipy</description> + <macros> + <import>creators.xml</import> + <import>tests.xml</import> + <token name="@TOOL_VERSION@">1.16.3</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="select_axis"> + <param name="axis" type="select" label="Direction"> + <option value="1" selected="true">Horizontal</option> + <option value="0">Vertical</option> + </param> + </xml> + </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> + <xref type="biii">scipy</xref> + </xrefs> <requirements> - <requirement type="package" version="0.14.2">scikit-image</requirement> - <requirement type="package" version="1.15.4">numpy</requirement> - <requirement type="package" version="5.3.0">pillow</requirement> - <requirement type="package" version="0.15.1">tifffile</requirement> + <requirement type="package" version="@TOOL_VERSION@">scipy</requirement> + <requirement type="package" version="2.3.5">numpy</requirement> + <requirement type="package" version="0.25.2">scikit-image</requirement> + <requirement type="package" version="2025.10.16">tifffile</requirement> + <requirement type="package" version="0.5.2">giatools</requirement> </requirements> - <command detect_errors="aggressive"> - <![CDATA[ - python '$__tool_directory__/filter_image.py' '$input' '$output' $filter_type $radius - ]]> - </command> + <command detect_errors="aggressive"><![CDATA[ + + python '$__tool_directory__/filter.py' + + '$input' + '$output' + '$params' + + ]]></command> + <configfiles> + <configfile name="params"><![CDATA[ + { + + ## ===================================================================== + #if $filter.filter_type == "gaussian" + "sigma": $filter.sigma, + "order": $filter.derivative.order, + + #if $filter.derivative.order != "0" + "axis": $filter.derivative.axis, + #end if + + ## ===================================================================== + #elif $filter.filter_type == "uniform" + "size": $filter.size, + + ## ===================================================================== + #elif $filter.filter_type == "median" + "radius": $filter.radius, + + ## ===================================================================== + #elif $filter.filter_type == "prewitt" or $filter.filter_type == "sobel" + "axis": $filter.axis, + + ## ===================================================================== + #end if + + "filter_type": "$filter.filter_type" + + } + ]]></configfile> + </configfiles> <inputs> - <param name="filter_type" type="select" label="Image type"> - <option value="median" selected="True">Median</option> - <option value="gaussian">Gaussian Blur</option> - <option value="prewitt">Prewitt</option> - <option value="sobel">Sobel</option> - <option value="scharr">Scharr</option> - </param> - <param name="radius" type="integer" value="3" label="Radius/Sigma" /> - <param name="input" type="data" format="tiff" label="Source file" /> + <param name="input" type="data" format="tiff,png" label="Input image"/> + <conditional name="filter"> + <param name="filter_type" type="select" label="Filter type"> + <option value="gaussian" selected="True">Gaussian</option> + <option value="uniform">Box filter (uniform filter)</option> + <option value="median">Median</option> + <option value="prewitt">Prewitt</option> + <option value="sobel">Sobel</option> + </param> + <when value="gaussian"> + <param name="sigma" type="float" value="3" min="0.1" label="Sigma" + help="The half width of the Gaussian bell (in pixels)."/> + <conditional name="derivative"> + <param name="order" type="select" label="Use a derivative?"> + <option value="0">No derivative (mean filter)</option> + <option value="1">1st-order derivative</option> + <option value="2">2nd-order derivative</option> + </param> + <when value="0"> + </when> + <when value="1"> + <expand macro="select_axis"/> + </when> + <when value="2"> + <expand macro="select_axis"/> + </when> + </conditional> + </when> + <when value="uniform"> + <param name="size" type="integer" min="2" value="3" label="Size" + help="Edge length of the neighborhood (square, in pixels)."/> + </when> + <when value="median"> + <param name="radius" type="integer" min="2" value="3" label="Radius" + help="Radius of the neighborhood (circle, in pixels)." /> + </when> + <when value="prewitt"> + <expand macro="select_axis"/> + </when> + <when value="sobel"> + <expand macro="select_axis"/> + </when> + </conditional> </inputs> <outputs> <data format="tiff" name="output" /> </outputs> <tests> - <test> - <param name="input" value="sample.tif" /> - <output name="output" value="res.tif" ftype="tiff" compare="sim_size"/> - <param name="filter_type" value="prewitt" /> - <param name="radius" value="4" /> - </test> + <!-- Tests with uint8 TIFF input image --> + <test> + <param name="input" value="input1_uint8.tiff"/> + <conditional name="filter"> + <param name="filter_type" value="gaussian"/> + </conditional> + <expand macro="tests/intensity_image_diff" name="output" value="input1_gaussian.tiff" ftype="tiff"> + <!-- + + The input file `input1_uint8.tiff` has values ranging between 23 and 254, with a mean value of 63.67. + + Below, we use an assertion in addition to the `image_diff` comparison, to ensure that the range of + values is preserved. The motiviation behind this is that the expectation images are usually checked + visually, which means that the `image_diff` comparison is likely to ensure that the brightness of + the image is correct, thus it's good to double-check the range of values (hence the comparably large + value for `eps`). This also concerns the median filter. + + --> + <has_image_mean_intensity mean_intensity="63.67" eps="10"/> + </expand> + </test> + <test> + <param name="input" value="input1_uint8.tiff"/> + <conditional name="filter"> + <param name="filter_type" value="median"/> + </conditional> + <expand macro="tests/intensity_image_diff" name="output" value="input1_median.tiff" ftype="tiff"> + <!-- See note for Gaussian filter above. --> + <has_image_mean_intensity mean_intensity="63.67" eps="10"/> + </expand> + </test> + <test> + <param name="input" value="input1_uint8.tiff"/> + <conditional name="filter"> + <param name="filter_type" value="prewitt"/> + <param name="axis" value="1"/> + </conditional> + <expand macro="tests/intensity_image_diff" name="output" value="input1_prewitt_h.tiff" ftype="tiff"/> + </test> + <test> + <param name="input" value="input1_uint8.tiff"/> + <conditional name="filter"> + <param name="filter_type" value="prewitt"/> + <param name="axis" value="0"/> + </conditional> + <expand macro="tests/intensity_image_diff" name="output" value="input1_prewitt_v.tiff" ftype="tiff"/> + </test> + <test> + <param name="input" value="input1_uint8.tiff"/> + <conditional name="filter"> + <param name="filter_type" value="sobel"/> + <param name="axis" value="1"/> + </conditional> + <expand macro="tests/intensity_image_diff" name="output" value="input1_sobel_h.tiff" ftype="tiff"/> + </test> + <test> + <param name="input" value="input1_uint8.tiff"/> + <conditional name="filter"> + <param name="filter_type" value="sobel"/> + <param name="axis" value="0"/> + </conditional> + <expand macro="tests/intensity_image_diff" name="output" value="input1_sobel_v.tiff" ftype="tiff"/> + </test> + <!-- Tests with float TIFF input image --> + <test> + <param name="input" value="input2_float.tiff"/> + <conditional name="filter"> + <param name="filter_type" value="gaussian"/> + </conditional> + <expand macro="tests/intensity_image_diff" name="output" value="input2_gaussian.tiff" ftype="tiff"> + <!-- See note for Gaussian filter above. --> + <has_image_mean_intensity mean_intensity="0.25" eps="0.01"/> + </expand> + </test> + <test> + <param name="input" value="input2_float.tiff"/> + <conditional name="filter"> + <param name="filter_type" value="uniform"/> + <param name="size" value="4"/> + </conditional> + <expand macro="tests/intensity_image_diff" name="output" value="input2_uniform.tiff" ftype="tiff"> + <!-- See note for Gaussian filter above. --> + <has_image_mean_intensity mean_intensity="0.25" eps="0.01"/> + </expand> + </test> + <!-- Tests with multi-channel image (RGB) --> + <test> + <param name="input" value="scikit-image/retina.png"/> + <conditional name="filter"> + <param name="filter_type" value="gaussian"/> + <param name="sigma" value="5"/> + <conditional name="derivative"> + <param name="order" value="0"/> + </conditional> + </conditional> + <expand macro="tests/intensity_image_diff" name="output" value="retina_gaussian_order0.tiff" ftype="tiff"/> + </test> + <test> + <param name="input" value="scikit-image/retina.png"/> + <conditional name="filter"> + <param name="filter_type" value="gaussian"/> + <param name="sigma" value="3"/> + <conditional name="derivative"> + <param name="order" value="2"/> + <param name="axis" value="0"/> + </conditional> + </conditional> + <expand macro="tests/intensity_image_diff" name="output" value="retina_gaussian_order2_axis0.tiff" ftype="tiff"/> + </test> </tests> <help> - **What it does** + + **Applies a standard, general-purpose 2-D filter to an image.** + + Support for different image types: - Applies a standard filter to an image. + - For 3-D images, the filter is applied to all z-slices of the image. + - For multi-channel images, the filter is applied to all channels of the image. + - For time-series images, the filter is also applied for all time steps. + + Mean filters like the Gaussian filter, the box filter, or the median filter preserve both the brightness of the image, and + the range of values. This does not hold for the derivative variants of the Gaussian filter, which may produce negative values. + </help> <citations> <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
--- a/filter_image.py Thu Jul 18 08:51:37 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ -import argparse -import sys -import warnings -import numpy as np -import skimage.io -import skimage.filters -import skimage.util -from skimage.morphology import disk -from skimage import img_as_uint - -filterOptions = { - 'median' : lambda img_raw, radius: skimage.filters.median(img_raw, disk(radius)), - 'gaussian' : lambda img_raw, radius: skimage.filters.gaussian(img_raw, sigma=radius), - 'prewitt' : lambda img_raw, radius: skimage.filters.prewitt(img_raw), - 'sobel' : lambda img_raw, radius: skimage.filters.sobel(img_raw), - 'scharr' : lambda img_raw, radius: skimage.filters.scharr(img_raw), -} - -if __name__ == "__main__": - parser = argparse.ArgumentParser() - parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') - parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') - parser.add_argument('filter_type', choices=filterOptions.keys(), help='conversion type') - parser.add_argument('radius', default=3.0, type=float, help='Radius/Sigma') - args = parser.parse_args() - - img_in = skimage.io.imread(args.input_file.name) - res = img_as_uint(filterOptions[args.filter_type](img_in, args.radius)) - skimage.io.imsave(args.out_file.name, res, plugin='tifffile')
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scikit-image/LICENSE.txt Fri Dec 12 21:18:04 2025 +0000 @@ -0,0 +1,28 @@ +Files: * +Copyright: 2009-2022 the scikit-image team +License: BSD-3-Clause + + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions +are met: +1. Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. +2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. +3. Neither the name of the University nor the names of its contributors + may be used to endorse or promote products derived from this software + without specific prior written permission. +. +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE HOLDERS OR +CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests.xml Fri Dec 12 21:18:04 2025 +0000 @@ -0,0 +1,95 @@ +<macros> + + <!-- Macros for verification of image outputs --> + + <xml + name="tests/binary_image_diff" + tokens="name,value,ftype,metric,eps" + token_metric="mae" + token_eps="0.01"> + + <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="0"> + <assert_contents> + <has_image_n_labels n="2"/> + <yield/> + </assert_contents> + </output> + + </xml> + + <xml + name="tests/label_image_diff" + tokens="name,value,ftype,metric,eps,pin_labels" + token_metric="iou" + token_eps="0.01" + token_pin_labels="0"> + + <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="@PIN_LABELS@"> + <assert_contents> + <yield/> + </assert_contents> + </output> + + </xml> + + <xml + name="tests/intensity_image_diff" + tokens="name,value,ftype,metric,eps" + token_metric="rms" + token_eps="0.01"> + + <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@"> + <assert_contents> + <yield/> + </assert_contents> + </output> + + </xml> + + <!-- Variants of the above for verification of collection elements --> + + <xml + name="tests/binary_image_diff/element" + tokens="name,value,ftype,metric,eps" + token_metric="mae" + token_eps="0.01"> + + <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="0"> + <assert_contents> + <has_image_n_labels n="2"/> + <yield/> + </assert_contents> + </element> + + </xml> + + <xml + name="tests/label_image_diff/element" + tokens="name,value,ftype,metric,eps" + token_metric="iou" + token_eps="0.01" + token_pin_labels="0"> + + <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="@PIN_LABELS@"> + <assert_contents> + <yield/> + </assert_contents> + </element> + + </xml> + + <xml + name="tests/intensity_image_diff/element" + tokens="name,value,ftype,metric,eps" + token_metric="rms" + token_eps="0.01"> + + <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@"> + <assert_contents> + <yield/> + </assert_contents> + </element> + + </xml> + +</macros>