A sample plugin for girder/slicer_cli_web with examples of slicer CLIs written in python and c++.
Running docker run <image-name> --list_cli will output the list of all CLIs (their relative path and type/language) exposed.
$ docker run cdeepakroy/slicer_cli_web_plugin --list_cli
{
"sample_python_cli": {
"type" : "python"
},
"sample_cpp_cli": {
"type" : "cxx"
}
}
Running docker run <image-name> <cli-rel-path> --xml will output the Slicer XML spec of the CLI.
$ docker run cdeepakroy/slicer_cli_web_plugin sample_python_cli --xml
<?xml version="1.0" encoding="utf-8"?>
<executable>
<category>Developer Tools</category>
<title>sample_python_cli</title>
<description><![CDATA[Sample slicer CLI in Python that shows one of each type of parameter.]]></description>
<version>0.1.0.$Revision$(alpha)</version>
<documentation-url>http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/ExecutionModelTour</documentation-url>
<license/>
<contributor>Deepak Roy Chittajallu (Kitware)</contributor>
<acknowledgements><![CDATA[This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.]]></acknowledgements>
<parameters>
<label>Scalar Parameters</label>
<description><![CDATA[Variations on scalar parameters]]></description>
<integer>
<name>integerVariable</name>
<flag>-i</flag>
<longflag>--integer</longflag>
<description><![CDATA[An integer without constraints]]></description>
<label>Integer Parameter</label>
<default>30</default>
</integer>
<double>
<name>doubleVariable</name>
<flag>-d</flag>
<longflag>--double</longflag>
<description><![CDATA[A double with constraints]]></description>
<label>Double Parameter</label>
<default>30</default>
<constraints>
<minimum>0</minimum>
<maximum>1.e3</maximum>
<step>10</step>
</constraints>
</double>
</parameters>
<parameters>
<label>Vector Parameters</label>
<description><![CDATA[Variations on vector parameters]]></description>
<float-vector>
<name>floatVector</name>
<flag>f</flag>
<description><![CDATA[A vector of floats]]></description>
<label>Float Vector Parameter</label>
<default>1.3,2,-14</default>
</float-vector>
<string-vector>
<name>stringVector</name>
<longflag>string_vector</longflag>
<description><![CDATA[A vector of strings]]></description>
<label>String Vector Parameter</label>
<default>foo,bar,foobar</default>
</string-vector>
</parameters>
<parameters>
<label>Enumeration Parameters</label>
<description><![CDATA[Variations on enumeration parameters]]></description>
<string-enumeration>
<name>stringChoice</name>
<flag>e</flag>
<longflag>enumeration</longflag>
<description><![CDATA[An enumeration of strings]]></description>
<label>String Enumeration Parameter</label>
<default>Bill</default>
<element>Ron</element>
<element>Eric</element>
<element>Bill</element>
<element>Ross</element>
<element>Steve</element>
<element>Will</element>
</string-enumeration>
</parameters>
<parameters>
<label>Boolean Parameters</label>
<description><![CDATA[Variations on boolean parameters]]></description>
<boolean>
<name>boolean1</name>
<longflag>boolean1</longflag>
<description><![CDATA[A boolean default true]]></description>
<label>Boolean Default true</label>
<default>true</default>
</boolean>
<boolean>
<name>boolean2</name>
<longflag>boolean2</longflag>
<description><![CDATA[A boolean default false]]></description>
<label>Boolean Default false</label>
<default>false</default>
</boolean>
<boolean>
<name>boolean3</name>
<longflag>boolean3</longflag>
<description><![CDATA[A boolean with no default, should be defaulting to false]]></description>
<label>Boolean No Default</label>
</boolean>
</parameters>
<parameters>
<label>File, Directory and Image Parameters</label>
<description><![CDATA[Parameters that describe files and direcories.]]></description>
<file fileExtensions=".png,.jpg,.jpeg,.bmp,.tif,.tiff,.gipl,.dcm,.dicom,.nhdr,.nrrd,.mhd,.mha,.mask,.hdr,.nii,.nii.gz,.hdr.gz,.pic,.lsm,.spr,.vtk,.vtkp,.vtki,.stl,.csv,.txt,.xml,.html">
<longflag>file1</longflag>
<description><![CDATA[An input file]]></description>
<label>Input file</label>
<channel>input</channel>
</file>
<file fileExtensions=".png,.jpg,.jpeg,.bmp,.tif,.tiff,.gipl,.dcm,.dicom,.nhdr,.nrrd,.mhd,.mha,.mask,.hdr,.nii,.nii.gz,.hdr.gz,.pic,.lsm,.spr,.vtk,.vtkp,.vtki,.stl,.csv,.txt,.xml,.html" multiple="true">
<longflag>files</longflag>
<description><![CDATA[Multiple input files]]></description>
<label>Input Files</label>
<channel>input</channel>
</file>
<directory>
<longflag>directory1</longflag>
<description><![CDATA[An input directory. If no default is specified, the current directory is used,]]></description>
<label>Input directory</label>
<channel>input</channel>
</directory>
<image>
<longflag>image1</longflag>
<description><![CDATA[An input image]]></description>
<label>Input image</label>
<channel>input</channel>
</image>
<image>
<longflag>image2</longflag>
<description><![CDATA[An output image]]></description>
<label>Output image</label>
<channel>output</channel>
</image>
</parameters>
<parameters>
<label>Index Parameters</label>
<description><![CDATA[Variations on parameters that use index rather than flags.]]></description>
<image>
<name>arg0</name>
<channel>input</channel>
<index>0</index>
<description><![CDATA[First index argument is an image]]></description>
<label>First index argument</label>
</image>
<image>
<name>arg1</name>
<channel>output</channel>
<index>1</index>
<description><![CDATA[Second index argument is an image]]></description>
<label>Second index argument</label>
</image>
</parameters>
<parameters>
<label>Simple return types</label>
<integer>
<name>anintegerreturn</name>
<label>An integer return value</label>
<channel>output</channel>
<default>5</default>
<description><![CDATA[An example of an integer return type]]></description>
</integer>
<boolean>
<name>abooleanreturn</name>
<label>A boolean return value</label>
<channel>output</channel>
<default>false</default>
<description><![CDATA[An example of a boolean return type]]></description>
</boolean>
<float>
<name>afloatreturn</name>
<label>A floating point return value</label>
<channel>output</channel>
<default>7.0</default>
<description><![CDATA[An example of a float return type]]></description>
</float>
<double>
<name>adoublereturn</name>
<label>A double point return value</label>
<channel>output</channel>
<default>14.0</default>
<description><![CDATA[An example of a double return type]]></description>
</double>
<string>
<name>astringreturn</name>
<label>A string point return value</label>
<channel>output</channel>
<default>Hello</default>
<description><![CDATA[An example of a string return type]]></description>
</string>
<integer-vector>
<name>anintegervectorreturn</name>
<label>An integer vector return value</label>
<channel>output</channel>
<default>1,2,3</default>
<description><![CDATA[An example of an integer vector return type]]></description>
</integer-vector>
<string-enumeration>
<name>astringchoicereturn</name>
<channel>output</channel>
<description><![CDATA[An enumeration of strings as a return type]]></description>
<label>A string enumeration return value</label>
<default>Bill</default>
<element>Ron</element>
<element>Eric</element>
<element>Bill</element>
<element>Ross</element>
<element>Steve</element>
<element>Will</element>
</string-enumeration>
</parameters>
</executable>
Running docker run <image-name> <cli-rel-path> --help will output the command-line usage help generated by ctk_cli.CLIArgumentParser for Python CLIs and GenerateCLP's PARSE_ARGS for C++ CLIs.
$ docker run cdeepakroy/slicer_cli_web_plugin sample_python_cli --help
usage: sample_python_cli.py [-h] [-V] [--xml] [--returnparameterfile <file>]
[--boolean1 <boolean>] [--boolean2 <boolean>]
[--boolean3 <boolean>] [-d <double>]
[--directory1 <directory>]
[-e {Ron,Eric,Bill,Ross,Steve,Will}]
[-f <float-vector>] [--file1 <file>]
[--files <file>] [-i <integer>] [--image1 <image>]
[--image2 <image>]
[--string_vector <string-vector>]
arg0 arg1
positional arguments:
arg0 First index argument is an image (type: image)
arg1 Second index argument is an image (type: image)
optional arguments:
-h, --help show this help message and exit
-V, --version show program's version number and exit
--xml Produce xml description of command line arguments
--returnparameterfile <file>
Filename in which to write simple return parameters
(integer, float, integer-vector, etc.) as opposed to
bulk return parameters (image, file, directory,
geometry, transform, measurement, table).
--boolean1 <boolean> A boolean default true (default: True)
--boolean2 <boolean> A boolean default false (default: False)
--boolean3 <boolean> A boolean with no default, should be defaulting to
false
-d <double>, --double <double>
A double with constraints (default: 30.0)
--directory1 <directory>
An input directory. If no default is specified, the
current directory is used,
-e {Ron,Eric,Bill,Ross,Steve,Will}, --enumeration {Ron,Eric,Bill,Ross,Steve,Will}
An enumeration of strings (default: Bill)
-f <float-vector> A vector of floats (default: [1.3, 2.0, -14.0])
--file1 <file> An input file (file-extensions: ['.png', '.jpg',
'.jpeg', '.bmp', '.tif', '.tiff', '.gipl', '.dcm',
'.dicom', '.nhdr', '.nrrd', '.mhd', '.mha', '.mask',
'.hdr', '.nii', '.nii.gz', '.hdr.gz', '.pic', '.lsm',
'.spr', '.vtk', '.vtkp', '.vtki', '.stl', '.csv',
'.txt', '.xml', '.html'])
--files <file> Multiple input files (accepted multiple times) (file-
extensions: ['.png', '.jpg', '.jpeg', '.bmp', '.tif',
'.tiff', '.gipl', '.dcm', '.dicom', '.nhdr', '.nrrd',
'.mhd', '.mha', '.mask', '.hdr', '.nii', '.nii.gz',
'.hdr.gz', '.pic', '.lsm', '.spr', '.vtk', '.vtkp',
'.vtki', '.stl', '.csv', '.txt', '.xml', '.html'])
-i <integer>, --integer <integer>
An integer without constraints (default: 30)
--image1 <image> An input image
--image2 <image> An output image
--string_vector <string-vector>
A vector of strings (default: ['foo', 'bar',
'foobar'])
Title: sample_python_cli
Description: Sample slicer CLI in Python that shows one of each type of
parameter.
Author(s): Deepak Roy Chittajallu (Kitware)
Slicer-cli-web runs docker run <image-name> --list_cli to find the CLI's exposed, runs docker run <image-name> <cli-rel-path> --xml for each CLI to get its XML spec, automatically converts the XML spec into girder-worker task-spec to generate REST end-points and web UI.