|
4
|
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>
|
