Slicer3:Execution Model Documentation - Revision history

Grundlett: Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:34:46Z

Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

JChris.FillionR at 01:39, 22 March 2018

2018-03-22T01:39:51Z

Lasso at 21:25, 16 June 2015

2015-06-16T21:25:34Z

Deepak.chittajallu: /* Parameters and C++ code */

2014-12-12T17:21:11Z

Parameters and C++ code

Millerjv: /* XML Schema */

2014-01-08T16:21:14Z

XML Schema

Pieper at 16:40, 23 January 2012

2012-01-23T16:40:47Z

AnthonyBlumfield: Added section "Module with output text presented in GUI" under "Slicer3 GUI Generation" to demonstrated the process of displaying command line module text output in the GUI

2011-12-29T23:09:05Z

Added section "Module with output text presented in GUI" under "Slicer3 GUI Generation" to demonstrated the process of displaying command line module text output in the GUI

Haehn: /* Parameters and C++ code */

2011-02-03T16:25:00Z

Parameters and C++ code

Nicole: /* XML Schema */

2010-12-20T17:05:09Z

XML Schema

Pieper: /* FAQ */

2010-09-14T18:59:29Z

FAQ

@@ Line 674: / Line 674: @@
 === Short Example ===
-This example uses the XML for the [http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation#Module_with_an_integer-vector.2C_one_input_image_and_one_output_image|Median Image Filter example].
+This example uses the XML for the [[Slicer3:Execution_Model_Documentation#Module_with_an_integer-vector.2C_one_input_image_and_one_output_image|Median|Image Filter example]].
 <br>
 '''Note:''' The program '''MUST NOT''' write anything to stdout before the ''PARSE_ARGS'' statement. If something is written, the plugin discovery mechanism will not recognize the program as a plugin.
@@ Line 907: / Line 907: @@
 * Shell Script Example
 * Matlab Example
-* [http://www.slicer.org/slicerWiki/index.php/Slicer3:FiberTrackingIntegration FiberTracking Integration Example]
+* [[Slicer3:FiberTrackingIntegration|FiberTracking Integration Example]]
 == Showing Progress in an Application ==
@@ Line 1,524: / Line 1,524: @@
 == How do I debug my command line module? ==
-See [http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation:Debugging Debugging]
+See [[Slicer3:Execution_Model_Documentation:Debugging|Debugging]]
 Back to [[Slicer3:Documentation |Slicer3 Documentation]].

← Older revision		Revision as of 01:39, 22 March 2018
Line 1:		Line 1:
−	<span style="color: red">'''This page is for reference only. Up-to-date version of the Slicer Execution Model specification is [[Documentation/Nightly/Developers/SlicerExecutionModel\|available here.]]'''</span>	+
		+	{{documentation/banner
		+	\| text = <span style="color: red">'''This page is for reference only. Up-to-date version of the Slicer Execution Model specification is [[Documentation/Nightly/Developers/SlicerExecutionModel\|available here.]]'''</span>}}

	== Introduction ==		== Introduction ==

← Older revision		Revision as of 21:25, 16 June 2015
Line 1:		Line 1:
		+	<span style="color: red">'''This page is for reference only. Up-to-date version of the Slicer Execution Model specification is [[Documentation/Nightly/Developers/SlicerExecutionModel\|available here.]]'''</span>
		+
	== Introduction ==		== Introduction ==

@@ Line 799: / Line 799: @@
 <boolean><br /> <name>debugSwitch</name><br /> <flag>d</flag> <default>true</default><br /> </boolean>
+|
-bool debugSwitch = false;
+bool debugSwitch = true;
+|
 ''prog'' -d

@@ Line 226: / Line 226: @@
 ;;;; <flag [alias="a,b"] [deprecatedalias="c,d"]> (not required if longflag is present)
-:::: A single character command line flag (e.g. s, W). Can provide "alias"'s (comma separated) if different flags can be used to activate the same parameter.  Can provide "deprecatedalias"'s (comma separated) if different flags can be used to set the same parameter but the user should be notified of which "updated" flag to use.
+:::: A single character command line flag (e.g. s, W). Can provide "alias"'s (comma separated) if different flags can be used to activate the same parameter.  Can provide "deprecatedalias"'s (comma separated) if different flags can be used to set the same parameter but the user should be notified of which "updated" flag to use. Parameters with flags are considered "optional" and do not have be specified or assigned.  Parameters with flags allow one to override a default behavior.
 :::: ''for CLP'', used as the short flag on the command line.
 :::: ''for GUI'', used when running the module.
@@ Line 232: / Line 232: @@
 ;;;; <longflag [alias="foo,bar"] [deprecatedalias="garf"]> (not required if flag is present)
-:::: A command line flag (e.g. spacing, Watcher). Can provide "alias"'s (comma separated) if different long flags can be used to activate the same parameter.  Can provide "deprecatedalias"'s (comma separated) if different long flags can be used to set the same parameter but the user should be notified of which "updated" long flag to use.
+:::: A command line flag (e.g. spacing, Watcher). Can provide "alias"'s (comma separated) if different long flags can be used to activate the same parameter.  Can provide "deprecatedalias"'s (comma separated) if different long flags can be used to set the same parameter but the user should be notified of which "updated" long flag to use. Parameters with flags are considered "optional" and do not have be specified or assigned.  Parameters with flags allow one to override a default behavior.
 :::: Note: apparently you can't use hyphens in the longflag, so things like --my-option are not allows.  -gcs
 :::: ''for CLP'', used as the long flag on the command line.

@@ Line 168: / Line 168: @@
 ;; </contributor>
-;; <acknowledgments>
+;; <acknowledgements>
-:: Acknowledgments for funding agency, employer, colleague, (e.g. 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 for funding agency, employer, colleague, (e.g. 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).
 :: for ''CLP'', appears as part of --help
 :: for ''GUI'', may show up in the Help of About section.
-;; </acknowledgments>
+;; </acknowledgements>
 ;; <parameters [advanced="true|''false''"]> (required for each group of parameters)
@@ Line 738: / Line 738: @@
     Author(s): Bill Lorensen
-    Acknowledgments: This command module was derived from
+    Acknowledgements: This command module was derived from
     Insight/Examples/Filtering/MedianImageFilter (copyright) Insight
     Software Consortium

← Older revision		Revision as of 23:09, 29 December 2011
Line 533:		Line 533:

	</executable>		</executable>
		+
		+
		+	=== Module with output text presented in GUI ===
		+
		+	3DSlicer auto generates GUI to display output from the command line module after execution is complete.
		+	The flag [--returnparameterfile <file name>] is used to provide a name of a file that the module uses to store key=value pairs that are displayed in the 3D Slicer GUI. The keys are described in the command line module xml schema using the output channel.
		+
		+	This example demonstrates a portion of an XML schema containing 1 string-enumeration input and 7 string outputs.
		+
		+	Note: This option is supported in Slicer 3.6 but may not be available in some earlier versions.
		+
		+	<div class="floatright"><span>[[Image:RadnosticsBetaOsteoporosisAnalysisGUI.png\|[[Image:RadnosticsBetaOsteoporosisAnalysisGUI.png]]]]</span></div>
		+
		+	<parameters>
		+	<label>Radnostics Beta Osteoporosis Analysis</label>
		+	<string-enumeration>
		+	<name>Osteoporosis</name>
		+	<longflag>--osteoporosis</longflag>
		+	<label>After Segmentation Perform Osteoporosis Analysis</label>
		+	<description>Osteoporosis Analysis will provide a Radnostics Osteoporosis score for the patient.</description>
		+	<default>yes</default>
		+	<element>yes</element>
		+	<element>no</element>
		+	</string-enumeration>
		+	<string>
		+	<name>PatientGender</name>
		+	<label>Gender</label>
		+	<channel>output</channel>
		+	<description>Patient Gender</description>
		+	<default>na</default>
		+	</string>
		+	<string>
		+	<name>PatientAge</name>
		+	<label>Age</label>
		+	<channel>output</channel>
		+	<description>Patient Age</description>
		+	<default>na</default>
		+	</string>
		+	<string>
		+	<name>RadnosticsOsteoporosisScore</name>
		+	<label>Radnostics Osteoporosis Score</label>
		+	<channel>output</channel>
		+	<description>Radnostics Osteoporosis Score</description>
		+	<default>na</default>
		+	</string>
		+	<string>
		+	<name>OsteoporosisComment1</name>
		+	<channel>output</channel>
		+	<label>*</label>
		+	<description>Comment 1</description>
		+	</string>
		+	<string>
		+	<name>OsteoporosisComment2</name>
		+	<channel>output</channel>
		+	<label>*</label>
		+	<description>Comment 2</description>
		+	</string>
		+	<string>
		+	<name>OsteoporosisComment3</name>
		+	<channel>output</channel>
		+	<label>*</label>
		+	<description>Comment 3</description>
		+	</string>
		+	<string>
		+	<name>OsteoporosisComment4</name>
		+	<channel>output</channel>
		+	<label>*</label>
		+	<description>Comment 4</description>
		+	</string>
		+	</parameters>
		+
		+	The command line module outputs key=value pairs to the file supplied by –-returnparameterfile as shown below:
		+	PatientGender = F
		+	PatientAge = 059Y
		+	RadnosticsOsteoporosisScore = 8 (high)
		+	OsteoporosisComment1 = vertebra label 58 has biconcave fracture
		+	OsteoporosisComment2 = vertebra label 56 has mean density of 120 HU
		+
		+

	== Command Line Parsing ==		== Command Line Parsing ==

@@ Line 708: / Line 708: @@
 std::vector<std::string> sites;
+|
-''prog'' --names BWH,GE,Kitware,UNC,MIT,UTAH,GT
+''prog'' --sites BWH,GE,Kitware,UNC,MIT,UTAH,GT
 |-
+|

@@ Line 192: / Line 192: @@
 ;;; <integer> | <float> | <double> | <boolean> | <string> | <integer-vector> | <float-vector> | <double-vector> | <string-vector> | <integer-enumeration> | <float-enumeration> | <double-enumeration> | <string-enumeration> | <file> | <directory> | <image [type="''scalar''|''label''|''tensor''|''diffusion-weighted''|''vector''|''model''"]> | <geometry [type="''fiberbundle''|''model''"]> | <point [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''|''ijk''"]> | <region [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''|''ijk''"]>
-::: The type of the parameter. The scalar types ('''integer''', '''float''', etc.) correspond to the usual programming language types. The '''-vector''' types are represented by comma separated values of the scalar type. The '''-enumeration''' types use the '''<element>''' tag to enumerate choices of the scalar type. '''<image>''' is a special type that indicates that the parameter is a file name that specifies images. If the attribute ''multiple'' is "true", multiple arguments are allowed for '''scalar''', '''file''', '''directory''', '''image''', '''geometry''', '''point''' and '''region''' parameters. The attribute ''coordinateSystem'' is allowed for the parameters '''point''' and '''region'''. The attribute ''fileExtensions'' is allowed for '''file''', '''image''' and '''geometry'''. fileExtensions can contain a list of comma separated file extensions for optional use by the GUI. If the parameter has a ''flag'' or ''longflag'', then the flag may be specified multiple times on the command line. The resulting C++ variable will be a std::vector of the scalar type. If the multiple parameter does not have a flag, then multiple arguments can appear on the command line. However, a multiple parameter with no flags must be the last parameter specified.
+::: The type of the parameter.
 ;;;; <name> (required if longflag is not specified)

← Older revision		Revision as of 18:59, 14 September 2010
Line 1,449:		Line 1,449:

	''Note: logos are limited in size: if your .h file contains a symbol like 'image_bioimagesuite_logo_www' it will work. But if it has several symbols like 'image_bioimagesuite_logo_www_1' 'image_bioimagesuite_logo_www_2' etc then the logo was too large and needs to be downsampled for use.''		''Note: logos are limited in size: if your .h file contains a symbol like 'image_bioimagesuite_logo_www' it will work. But if it has several symbols like 'image_bioimagesuite_logo_www_1' 'image_bioimagesuite_logo_www_2' etc then the logo was too large and needs to be downsampled for use.''
		+
		+	== What do I do if I want to use the CLI outside of slicer? ==
		+
		+	In general CLI executables will depend on shared libraries provided by Slicer (such as ITKCommon, etc). To be sure your run-time environment resolves to the correct versions, you should always use a form like:
		+	./Slicer3 --launch <CLI>
		+	or, you can start a shell from which you can run multiple CLI modules. Something like:
		+	./Slicer3 --launch xterm &
		+
		+	We do not suggest hard-coding the runtime paths into, for example, your .bashrc since this may interfere with other programs and can make it hard to use multiple versions of slicer on the same account.

	= Laundry List =		= Laundry List =