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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit bb2d58ed37d8eb09583b86e3cdd9f5d1b56c42a0
author imgteam
date Sun, 04 Jan 2026 20:56:17 +0000
parents a4bc9dfde846
children 8e3a52b74876
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4:a4bc9dfde846 5:5530132d500e
1 <tool id="ip_2d_feature_extraction" name="Extract image features" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> 1 <tool id="ip_2d_feature_extraction" name="Extract image features" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>with scikit-image</description> 2 <description>with scikit-image</description>
3 <macros> 3 <macros>
4 <import>creators.xml</import> 4 <import>creators.xml</import>
5 <token name="@TOOL_VERSION@">0.18.1</token> 5 <import>validators.xml</import>
6 <token name="@TOOL_VERSION@">0.25.2</token>
6 <token name="@VERSION_SUFFIX@">0</token> 7 <token name="@VERSION_SUFFIX@">0</token>
8 <xml name="features">
9 <param name="features" type="select" label="Available features" multiple="true" display="checkboxes"
10 help="*) Features marked with an asterisk are only available for 2-D images (not for 3-D images).">
11 <option value="label" selected="true">Label from the label map</option>
12 <yield/>
13 <option value="area">Area</option>
14 <option value="area_convex">Convex area</option>
15 <option value="area_filled">Filled area</option>
16 <option value="axis_major_length">Major axis length</option>
17 <option value="axis_minor_length">Minor axis length</option>
18 <option value="bbox">Bounding box</option>
19 <option value="centroid">Centroid</option>
20 <option value="eccentricity">Eccentricity*</option>
21 <option value="equivalent_diameter_area">Equivalent diameter</option>
22 <option value="euler_number">Euler number</option>
23 <option value="extent">Extent</option>
24 <option value="inertia_tensor_eigvals">Inertia tensor eigenvalues</option>
25 <option value="moments">Moments</option>
26 <option value="moments_hu">Moments Hu*</option>
27 <option value="orientation">Orientation*</option>
28 <option value="perimeter">Perimeter</option>
29 <option value="solidity">Solidity</option>
30 </param>
31 </xml>
32 <xml name="zarr-isolated-feature-test" tokens="feature">
33 <test>
34 <param name="labels" value="input/input13.zarr"/>
35 <conditional name="setup">
36 <param name="mode" value="with-intensities"/>
37 <param name="intensities" value="input/input1_uint8.tiff"/>
38 <param name="features" value="@FEATURE@"/>
39 </conditional>
40 <output name="output" ftype="tabular" value="output/input13-@FEATURE@.tsv"/>
41 </test>
42 </xml>
7 </macros> 43 </macros>
8 <creator> 44 <creator>
9 <expand macro="creators/bmcv"/> 45 <expand macro="creators/bmcv"/>
46 <expand macro="creators/kostrykin"/>
10 </creator> 47 </creator>
11 <edam_operations> 48 <edam_operations>
12 <edam_operation>operation_3443</edam_operation> 49 <edam_operation>operation_3443</edam_operation>
13 </edam_operations> 50 </edam_operations>
14 <xrefs> 51 <xrefs>
15 <xref type="bio.tools">scikit-image</xref> 52 <xref type="bio.tools">scikit-image</xref>
53 <xref type="bio.tools">giatools</xref>
54 <xref type="bio.tools">galaxy_image_analysis</xref>
16 <xref type="biii">scikit-image</xref> 55 <xref type="biii">scikit-image</xref>
17 </xrefs> 56 </xrefs>
18 <requirements> 57 <requirements>
19 <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement> 58 <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
20 <requirement type="package" version="2.2.2">pandas</requirement> 59 <requirement type="package" version="2.2.2">pandas</requirement>
21 <requirement type="package" version="1.23.3">numpy</requirement> 60 <requirement type="package" version="0.7.3">giatools</requirement>
22 <requirement type="package" version="2020.10.1">tifffile</requirement> 61 <requirement type="package" version="0.12.2">ome-zarr</requirement>
23 <requirement type="package" version="0.1">giatools</requirement>
24 </requirements> 62 </requirements>
25 <command detect_errors="aggressive"> 63 <required_files>
26 <![CDATA[ 64 <include type="literal" path="2d_feature_extraction.py"/>
27 python '$__tool_directory__/2d_feature_extraction.py' 65 </required_files>
28 #if $feature_options['features'] == 'all' 66 <command detect_errors="aggressive"><![CDATA[
29 --all 67
30 #else if $feature_options['features'] == 'select' 68 python '$__tool_directory__/2d_feature_extraction.py'
31 ${' '.join(str( $feature_options['selected_features'] ).split(','))} 69
32 #end if 70 #if $labels.extension == "zarr"
33 #if $use_raw_option['use_raw'] == 'raw_image' 71 --labels '$labels.extra_files_path/$labels.metadata.store_root'
34 --raw '$input_raw' 72 #else
35 #end if 73 --labels '$labels'
36 '$input_label' '$output' 74 #end if
37 ]]> 75
38 </command> 76 #if $setup.mode == "with-intensities"
77 #if $setup.intensities.extension == "zarr"
78 --intensities '$setup.intensities.extra_files_path/$setup.intensities.metadata.store_root'
79 #else
80 --intensities '$setup.intensities'
81 #end if
82 #end if
83
84 --output '$output'
85 --params '$params'
86 --verbose
87
88 ]]></command>
89 <configfiles>
90 <configfile name="params"><![CDATA[
91 {
92 "features": [
93 ${ ', '.join('"%s"' % t.strip() for t in str( $setup['features'] ).split(',')) }
94 ]
95 }
96 ]]></configfile>
97 </configfiles>
39 <inputs> 98 <inputs>
40 <param name="input_label" type="data" format="tiff,png" label="Label map"/> 99 <param name="labels" type="data" format="tiff,zarr,png" label="Label map">
41 <conditional name="use_raw_option"> 100 <expand macro="validators/is_single_channel"/>
42 <param label="Use the intensity image to compute additional features" name="use_raw" type="select"> 101 <expand macro="validators/is_single_frame"/>
43 <option selected="True" value="no_original">No intensity image</option> 102 </param>
44 <option value="raw_image">Use intensity image</option> 103 <conditional name="setup">
104 <param label="Features to compute" name="mode" type="select">
105 <option value="without-intensities" selected="true">Only use the label map for feature extraction (no intensity-based features)</option>
106 <option value="with-intensities">Use the intensity image to compute additional features</option>
45 </param> 107 </param>
46 <when value="no_original"/> 108 <when value="without-intensities">
47 <when value="raw_image"> 109 <expand macro="features"/>
48 <param name="input_raw" type="data" format="tiff,png" label="Intensity image"/>
49 </when> 110 </when>
50 </conditional> 111 <when value="with-intensities">
51 <conditional name="feature_options"> 112 <param name="intensities" type="data" format="tiff,zarr,png,jpg" label="Intensity image">
52 <param label="Select features to compute" name="features" type="select"> 113 <expand macro="validators/is_single_channel"/>
53 <option selected="True" value="all">All features</option> 114 <expand macro="validators/is_single_frame"/>
54 <option value="select">Select features</option>
55 </param>
56 <when value="all"> </when>
57 <when value="select">
58 <param name="selected_features" type="select" label="Available features" multiple="true" display="checkboxes">
59 <option value="--label">Label from the label map</option>
60 <option value="--patches">Patches (requires original image)</option>
61 <option value="--max_intensity">Max Intensity (requires original image)</option>
62 <option value="--mean_intensity">Mean Intensity (requires original image)</option>
63 <option value="--min_intensity">Minimum Intensity (requires original image)</option>
64 <option value="--moments_hu">Moments Hu</option>
65 <option value="--centroid">Centroid</option>
66 <option value="--bbox">Bounding box</option>
67 <option value="--area">Area</option>
68 <option value="--filled_area">Filled area</option>
69 <option value="--convex_area">Convex area</option>
70 <option value="--perimeter">Perimeter</option>
71 <option value="--extent">Extent</option>
72 <option value="--eccentricity">Eccentricity</option>
73 <option value="--equivalent_diameter">Equivalent diameter</option>
74 <option value="--euler_number">Euler number</option>
75 <option value="--inertia_tensor_eigvals">Inertia tensor eigenvalues</option>
76 <option value="--major_axis_length">Major axis length</option>
77 <option value="--minor_axis_length">Minor axis length</option>
78 <option value="--orientation">Orientation</option>
79 <option value="--solidity">Solidity</option>
80 <option value="--moments">Moments</option>
81 <option value="--convexity">Convexity</option>
82 </param> 115 </param>
116 <expand macro="features">
117 <option value="max_intensity">Maximum intensity</option>
118 <option value="mean_intensity">Mean intensity</option>
119 <option value="min_intensity">Minimum intensity</option>
120 </expand>
83 </when> 121 </when>
84 </conditional> 122 </conditional>
85 </inputs> 123 </inputs>
86 <outputs> 124 <outputs>
87 <data format="tabular" name="output"/> 125 <data format="tabular" name="output"/>
88 </outputs> 126 </outputs>
89 <tests> 127 <tests>
128 <!-- Single-channel 2-D -->
90 <test> 129 <test>
91 <param name="input_label" value="input.tiff" ftype="tiff"/> 130 <param name="labels" value="input/input12.png"/>
92 <conditional name="feature_options"> 131 <conditional name="setup">
93 <param name="features" value="select"/> 132 <param name="mode" value="without-intensities"/>
94 <param name="selected_features" value="--label,--area"/> 133 <param name="features" value="label,area,area_convex,solidity"/>
95 </conditional> 134 </conditional>
96 <output name="output" ftype="tabular" value="out.tsv"/> 135 <output name="output" ftype="tabular" value="output/input12.tsv"/>
136 </test>
137 <test>
138 <param name="labels" value="input/input11.tiff"/>
139 <conditional name="setup">
140 <param name="mode" value="with-intensities"/>
141 <param name="intensities" value="input/input1_uint8.tiff"/>
142 <param name="features" value="area,mean_intensity,perimeter"/>
143 </conditional>
144 <output name="output" ftype="tabular" value="output/input11.tsv"/>
145 </test>
146 <!-- Single-channel 2-D Zarr (isolated features, verify that Dask arrays are converted to NumPy arrays whenever necessary) -->
147 <expand macro="zarr-isolated-feature-test" feature="area"/>
148 <expand macro="zarr-isolated-feature-test" feature="area_convex"/>
149 <expand macro="zarr-isolated-feature-test" feature="area_filled"/>
150 <expand macro="zarr-isolated-feature-test" feature="axis_major_length"/>
151 <expand macro="zarr-isolated-feature-test" feature="axis_minor_length"/>
152 <expand macro="zarr-isolated-feature-test" feature="bbox"/>
153 <expand macro="zarr-isolated-feature-test" feature="centroid"/>
154 <expand macro="zarr-isolated-feature-test" feature="eccentricity"/>
155 <expand macro="zarr-isolated-feature-test" feature="equivalent_diameter_area"/>
156 <expand macro="zarr-isolated-feature-test" feature="euler_number"/>
157 <expand macro="zarr-isolated-feature-test" feature="extent"/>
158 <expand macro="zarr-isolated-feature-test" feature="inertia_tensor_eigvals"/>
159 <expand macro="zarr-isolated-feature-test" feature="moments"/>
160 <expand macro="zarr-isolated-feature-test" feature="moments_hu"/>
161 <expand macro="zarr-isolated-feature-test" feature="orientation"/>
162 <expand macro="zarr-isolated-feature-test" feature="perimeter"/>
163 <expand macro="zarr-isolated-feature-test" feature="solidity"/>
164 <expand macro="zarr-isolated-feature-test" feature="max_intensity"/>
165 <expand macro="zarr-isolated-feature-test" feature="mean_intensity"/>
166 <expand macro="zarr-isolated-feature-test" feature="min_intensity"/>
167 <!-- Single-channel 3-D, test all features are supported in 3-D -->
168 <test>
169 <param name="labels" value="input/input9.zarr"/>
170 <conditional name="setup">
171 <param name="mode" value="with-intensities"/>
172 <param name="intensities" value="input/input8_zyx.zarr"/>
173 <param name="features" value="area,area_convex,area_filled,axis_major_length,axis_minor_length,bbox,centroid,eccentricity,equivalent_diameter_area,euler_number,extent,inertia_tensor_eigvals,moments,moments_hu,orientation,perimeter,solidity,max_intensity,mean_intensity,min_intensity"/>
174 </conditional>
175 <output name="output" ftype="tabular" value="output/input9.tsv"/>
176 <assert_stdout>
177 <has_line line='Skip feature that is not available for 3-D images: "eccentricity"'/>
178 <has_line line='Skip feature that is not available for 3-D images: "moments_hu"'/>
179 <has_line line='Skip feature that is not available for 3-D images: "orientation"'/>
180 </assert_stdout>
181 </test>
182 <!-- Multi-channel (forbidden) -->
183 <test expect_failure="true">
184 <param name="labels" value="input/input12.png"/>
185 <conditional name="setup">
186 <param name="mode" value="with-intensities"/>
187 <param name="intensities" value="input/input3_uint16.tiff"/>
188 <param name="features" value="label"/>
189 </conditional>
190 <assert_stderr>
191 <!-- Rejected by validator -->
192 <has_n_lines n="0"/>
193 </assert_stderr>
194 <assert_stdout>
195 <!-- Rejected by validator -->
196 <has_n_lines n="0"/>
197 </assert_stdout>
198 </test>
199 <test expect_failure="true">
200 <param name="labels" value="input/input10.zarr"/>
201 <conditional name="setup">
202 <param name="mode" value="without-intensities"/>
203 <param name="features" value="label"/>
204 </conditional>
205 <assert_stderr>
206 <!-- Rejected by py-script -->
207 <has_text text="This tool is not applicable to images with CYX axes."/>
208 </assert_stderr>
97 </test> 209 </test>
98 </tests> 210 </tests>
99 <help> 211 <help>
100 212
101 **Computes features of a label map.** 213 **Computes features of a label map.**
102 214
103 The computed features are computed based solely on the properties of the labels in the label map, 215 The computed features are computed based solely on the properties of the objects in the label map, or, optionally, by also taking the intensities from a corresponding intensity image into account. Labels with value 0 are ignored.
104 or, optionally, by also taking the intensities from a corresponding intensity image into account. 216
105 217 Both images must be 2-D or 3-D single-channel images.
106 The label map must be a 2-D or 3-D single-channel image. 218
219 Supported Features
220 ==================
221
222 **Area:** Area of the region i.e. number of pixels of the region scaled by pixel-area.
223
224 **Convex area:** Area of the convex hull image, which is the smallest convex polygon that encloses the region.
225
226 **Filled area:** Area of the region with all the holes filled in.
227
228 **Major axis length:** The length of the major axis of the ellipse that has the same normalized second central moments as the region.
229
230 **Minor axis length:** The length of the minor axis of the ellipse that has the same normalized second central moments as the region.
231
232 **Bounding box:** Bounding box `(min_row, min_col, max_row, max_col)`. Pixels belonging to the bounding box are in the half-open interval `[min_row; max_row)` and `[min_col; max_col)`.
233
234 **Centroid:** Centroid coordinate tuple `(row, col)`.
235
236 **Eccentricity:** Eccentricity of the ellipse that has the same second-moments as the region. The eccentricity is the ratio of the focal distance (distance between focal points) over the major axis length. The value is in the interval [0, 1). When it is 0, the ellipse becomes a circle.
237
238 **Equivalent diameter:** The diameter of a circle with the same area as the region.
239
240 **Euler number:** Euler characteristic of the set of non-zero pixels. Computed as number of connected components subtracted by number of holes (input.ndim connectivity). In 3-D, number of connected components plus number of holes subtracted by number of tunnels.
241
242 **Extent:** Ratio of pixels in the region to pixels in the total bounding box. Computed as `area / (rows * cols)`.
243
244 **Inertia tensor eigenvalues:** The eigenvalues of the inertia tensor in decreasing order.
245
246 **Moments:** Spatial moments up to 3rd order: `m_ij = sum{ array(row, col) * row^i * col^j }` where the sum is over the row, col coordinates of the region.
247
248 **Moments Hu:** Hu moments (translation, scale and rotation invariant).
249
250 **Orientation:** Angle between the vertical axis (rows) and the major axis of the ellipse that has the same second moments as the region, ranging from `-pi/2` to `pi/2` counter-clockwise.
251
252 **Perimeter:** Perimeter of object which approximates the contour as a line through the centers of border pixels using a 4-connectivity. Generalizes to the surface of an object in 3-D, which uses a different approximation.
253
254 **Solidity:** Ratio of pixels in the region to pixels of the convex hull image.
107 255
108 </help> 256 </help>
109 <citations> 257 <citations>
110 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 258 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
111 </citations> 259 </citations>