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comparison tomo_setup.xml @ 4:7405057bcb29 draft default tip

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author rv43
date Thu, 24 Mar 2022 17:02:54 +0000
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3:e14621486c18 4:7405057bcb29
1 <tool id="tomo_setup" name="Tomo Setup" version="0.1.0" python_template_version="3.9">
2 <description>Preprocess tomography images</description>
3 <requirements>
4 <requirement type="package" version="1.11.0">tomopy</requirement>
5 <requirement type="package" version="0.2.12">pyinputplus</requirement>
6 <requirement type="package" version="3.6.0">h5py</requirement>
7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[
9 cp '$inputfiles' inputfiles.txt &&
10 $__tool_directory__/tomo_setup.py
11 -i inputfiles.txt
12 -c '$config'
13 --theta_range '$thetas.theta_start $thetas.theta_end $thetas.num_thetas'
14 --dark '$dark'
15 --bright '$bright'
16 --tomo '$tomo'
17 --detectorbounds '$detectorbounds'
18 --output_data '$output_data'
19 --output_config '$output_config'
20 -l '$log'
21 #for $s in $tomo_sets# ${s.offset} ${s.num} #end for
22 ]]></command>
23 <configfiles>
24 <configfile name="inputfiles"><![CDATA[#slurp
25 #for $s in $tomo_sets
26 #for $input in $s.inputs
27 #echo str($input) + '\t' + $input.element_identifier #
28 #end for
29 #end for
30 ]]></configfile>
31 </configfiles>
32 <inputs>
33 <param name="config" type='data' format='yaml' optional='false' label="Input config"/>
34 <section name="thetas" title="Tomography angles">
35 <param name="theta_start" type="float" min="0.0" max="360.0" value="0.0" label="Lower bound"/>
36 <param name="theta_end" type="float" min="0.0" max="360.0" value="0.0" label="Upper bound"/>
37 <param name="num_thetas" type="integer" min="0" label="Number of angles"/>
38 </section>
39 <repeat name='tomo_sets' title="Tomography image sets">
40 <param name="inputs" type="data_collection" label="Image file collection"/>
41 <param name="offset" type="integer" min="0" label="Image index offset"/>
42 <param name="num" type="integer" min="1" label="Number of images"/>
43 </repeat>
44 </inputs>
45 <outputs>
46 <data name="inputfiles" format="txt" label="Input files" from_work_dir="inputfiles.txt" hidden="true"/>
47 <data name="dark" format="png" label="Dark field"/>
48 <data name="bright" format="png" label="Bright field"/>
49 <data name="tomo" format="png" label="First tomography image"/>
50 <data name="detectorbounds" format="png" label="Detector bounds"/>
51 <data name="output_data" format="npz" label="Preprocessed tomography data"/>
52 <data name="output_config" format="txt" label="Output config"/>
53 <data name="log" format="txt" label="Log"/>
54 </outputs>
55 <help><![CDATA[
56 Preprocess tomography images.
57 ]]></help>
58 <citations>
59 <citation type="bibtex">
60 @misc{githubsum_files,
61 author = {Verberg, Rolf},
62 year = {2022},
63 title = {Tomo Setup},
64 publisher = {GitHub},
65 journal = {GitHub repository},
66 url = {somewhere},
67 }</citation>
68 </citations>
69
70 </tool>