Documentation/Nightly/Developers/SlicerExecutionModel - Revision history

Lasso at 14:33, 7 May 2021

2021-05-07T14:33:30Z

Lasso: /* XML Schema */

2020-08-12T18:44:36Z

XML Schema

Lasso: /* XML Schema */

2020-08-12T16:17:35Z

XML Schema

Lasso at 14:47, 3 January 2020

2020-01-03T14:47:29Z

JChris.FillionR: /* FAQ */

2019-12-18T18:29:05Z

FAQ

Show changes

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

2019-11-27T02:36:00Z

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

Pieper at 19:47, 29 March 2019

2019-03-29T19:47:02Z

Pinter: Add parameter references section (and specify compatibility for reference attributes)

2019-03-20T19:44:36Z

Add parameter references section (and specify compatibility for reference attributes)

Pinter: Add forward reference

2019-03-20T16:47:08Z

Add forward reference

Lasso: Removed refernces to "IJK" coordinate system. IJK coordinate system only exists in the context of an image volume, not for markups or models. IJK coordinate system support is not implemented either.

2018-07-06T15:05:11Z

Removed refernces to "IJK" coordinate system. IJK coordinate system only exists in the context of an image volume, not for markups or models. IJK coordinate system support is not implemented either.

@@ Line 185: / Line 185: @@
 ;;;</description>
-;;;<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''"] [reference="..."] > | <geometry [type="''fiberbundle''|''model''"] [reference="..."]> | <point [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''"]> | <pointfile [type="''any''|''point''|''line''|''angle''|''curve''|''closedcurve''"] [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''"]> | <region [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''"]> | &lt;table [type="''color''"] [fileExtensions="''.tsv''|''.csv''|''.txt''|''.ctbl''"]> | <transform [type="''linear''|''nonlinear''|''bspline''"] [reference="..."] fileExtensions=".tfm,.h5,.hdf5,.mat,.txt">
+;;;<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''"] [reference="..."] > | <geometry [type="''fiberbundle''|''model''"] [reference="..."]> | <point [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''"]> | <pointfile [type="''any''|''point''|''line''|''angle''|''curve''|''closedcurve''"] [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''"]> | <region [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''"]> | &lt;table [type="''color''"] [fileExtensions="''.tsv''|''.csv''|''.txt''|''.ctbl''"]> | <transform [type="''linear''|''nonlinear''|''bspline''"] [reference="..."] fileExtensions=".h5,.tfm,.hdf5,.mat,.txt,.mrml">
 :::The type of the parameter.
 ::::The scalar types ('''integer''', '''float''', etc.) correspond to the usual programming language types.
@@ Line 680: / Line 680: @@
   <nowiki>#include "MedianImageFilterCLP.h"
-   int main (int argc, char * argv[])
+    int main (int argc, char * argv[])
-−
+     {
-    PARSE_ARGS;
+     PARSE_ARGS;
-    std::cout << "The size of the neighborhood is: " << neighborhood.size()
+     std::cout << "The size of the neighborhood is: " << neighborhood.size()
-      << " and the first element of the neighborhood is: " << neighborhood[0]
+       << " and the first element of the neighborhood is: " << neighborhood[0]
-      << std::endl;
+       << std::endl;
-    std::cout << "The input volume is: " << inputVolume << std::endl;
+     std::cout << "The input volume is: " << inputVolume << std::endl;
-    std::cout << "The output volume is: " << outputVolume << std::endl;
+     std::cout << "The output volume is: " << outputVolume << std::endl;
-    return EXIT_SUCCESS;
+     return EXIT_SUCCESS;
-−
+     }
-   </nowiki>
+    </nowiki>
 Here is the output --help:
@@ Line 971: / Line 971: @@
   <nowiki>#include "vtkPluginFilterWatcher.h"
-   ...
+    ...
-    vtkMarchingCubes *cubes = vtkMarchingCubes::New();
+     vtkMarchingCubes *cubes = vtkMarchingCubes::New();
-      cubes->SetInput(reader->GetOutput());
+       cubes->SetInput(reader->GetOutput());
-    vtkPluginFilterWatcher watchCubes(cubes, "Generate Isosurface", CLPProcessInformation, .5, 0.0);
+     vtkPluginFilterWatcher watchCubes(cubes, "Generate Isosurface", CLPProcessInformation, .5, 0.0);
-    vtkDecimatePro *decimate = vtkDecimatePro::New();
+     vtkDecimatePro *decimate = vtkDecimatePro::New();
-      decimate->SetInput(cubes->GetOutput());
+       decimate->SetInput(cubes->GetOutput());
-    vtkPluginFilterWatcher watchDecimate(decimate, "Reduce Triangle Count", CLPProcessInformation, .5, 0.5);
+     vtkPluginFilterWatcher watchDecimate(decimate, "Reduce Triangle Count", CLPProcessInformation, .5, 0.5);
-    decimate->Update();
+     decimate->Update();
-   </nowiki>
+    </nowiki>
 The following example produces progress for a simple itk program:
   <nowiki>#include "itkPluginFilterWatcher.h
-   ...
+    ...
-   typedef itk::MedianImageFilter<ImageType,ImageType> FilterType;
+    typedef itk::MedianImageFilter<ImageType,ImageType> FilterType;
-   FilterType::Pointer median  = FilterType::New();
+    FilterType::Pointer median  = FilterType::New();
-   itk::PluginFilterWatcher watchMedian(median, "Denoise Image", CLPProcessInformation);
+    itk::PluginFilterWatcher watchMedian(median, "Denoise Image", CLPProcessInformation);
-   </nowiki>
+    </nowiki>
 ==Adding Module Logos to Slicer==

@@ Line 193: / Line 193: @@
 ::::The <region> parameter can be used to specify rectangular ROIs. The command-line syntax is --region X_center,Y_center,Z_center,X_radius,Y_Radius,Z_Radius.
 ::::If the attribute ''multiple'' is "true", multiple arguments are allowed for '''scalar''', '''file''', '''directory''', '''image''', '''geometry''', '''point''', '''pointfile''' and '''region''' parameters. Limitation: the automatically built GUI will not support selecting multiple volumes for the '''image''' and '''pointfile''' argument, but they can be passed on the command line. 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 attribute ''coordinateSystem'' is allowed for the parameters '''point''', '''pointfile''' and '''region'''. Default value is '''lps'''.
+::::The attribute ''coordinateSystem'' is allowed for the parameters '''point''', '''pointfile''' and '''region'''. Default value is '''lps'''. If coordinate system is specified inside the data file then the coordinate system specified in the xml file is ignored.
 ::::The attribute ''fileExtensions'' is allowed for '''file''', '''pointfile''', '''image''', '''transform''' and '''geometry'''. fileExtensions can contain a list of comma separated file extensions for optional use by the GUI.
 ::::Transform types: If not specified then any transform is accepted (linear, non-linar, composite, ...). By specifying a type, accepted transforms can be limited to 'linear' = any linear transform; 'non-linear' = grid, displacement field; 'bspline' = b-spline transform.
@@ Line 680: / Line 680: @@
   <nowiki>#include "MedianImageFilterCLP.h"
-  int main (int argc, char * argv[])
+   int main (int argc, char * argv[])
-−
+    {
-   PARSE_ARGS;
+    PARSE_ARGS;
-   std::cout << "The size of the neighborhood is: " << neighborhood.size()
+    std::cout << "The size of the neighborhood is: " << neighborhood.size()
-     << " and the first element of the neighborhood is: " << neighborhood[0]
+      << " and the first element of the neighborhood is: " << neighborhood[0]
-     << std::endl;
+      << std::endl;
-   std::cout << "The input volume is: " << inputVolume << std::endl;
+    std::cout << "The input volume is: " << inputVolume << std::endl;
-   std::cout << "The output volume is: " << outputVolume << std::endl;
+    std::cout << "The output volume is: " << outputVolume << std::endl;
-   return EXIT_SUCCESS;
+    return EXIT_SUCCESS;
-−
+    }
-  </nowiki>
+   </nowiki>
 Here is the output --help:
@@ Line 971: / Line 971: @@
   <nowiki>#include "vtkPluginFilterWatcher.h"
-  ...
+   ...
-   vtkMarchingCubes *cubes = vtkMarchingCubes::New();
+    vtkMarchingCubes *cubes = vtkMarchingCubes::New();
-     cubes->SetInput(reader->GetOutput());
+      cubes->SetInput(reader->GetOutput());
-   vtkPluginFilterWatcher watchCubes(cubes, "Generate Isosurface", CLPProcessInformation, .5, 0.0);
+    vtkPluginFilterWatcher watchCubes(cubes, "Generate Isosurface", CLPProcessInformation, .5, 0.0);
-   vtkDecimatePro *decimate = vtkDecimatePro::New();
+    vtkDecimatePro *decimate = vtkDecimatePro::New();
-     decimate->SetInput(cubes->GetOutput());
+      decimate->SetInput(cubes->GetOutput());
-   vtkPluginFilterWatcher watchDecimate(decimate, "Reduce Triangle Count", CLPProcessInformation, .5, 0.5);
+    vtkPluginFilterWatcher watchDecimate(decimate, "Reduce Triangle Count", CLPProcessInformation, .5, 0.5);
-   decimate->Update();
+    decimate->Update();
-  </nowiki>
+   </nowiki>
 The following example produces progress for a simple itk program:
   <nowiki>#include "itkPluginFilterWatcher.h
-  ...
+   ...
-  typedef itk::MedianImageFilter<ImageType,ImageType> FilterType;
+   typedef itk::MedianImageFilter<ImageType,ImageType> FilterType;
-  FilterType::Pointer median  = FilterType::New();
+   FilterType::Pointer median  = FilterType::New();
-  itk::PluginFilterWatcher watchMedian(median, "Denoise Image", CLPProcessInformation);
+   itk::PluginFilterWatcher watchMedian(median, "Denoise Image", CLPProcessInformation);
-  </nowiki>
+   </nowiki>
 ==Adding Module Logos to Slicer==

@@ Line 193: / Line 193: @@
 ::::The <region> parameter can be used to specify rectangular ROIs. The command-line syntax is --region X_center,Y_center,Z_center,X_radius,Y_Radius,Z_Radius.
 ::::If the attribute ''multiple'' is "true", multiple arguments are allowed for '''scalar''', '''file''', '''directory''', '''image''', '''geometry''', '''point''', '''pointfile''' and '''region''' parameters. Limitation: the automatically built GUI will not support selecting multiple volumes for the '''image''' and '''pointfile''' argument, but they can be passed on the command line. 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 attribute ''coordinateSystem'' is allowed for the parameters '''point''', '''pointfile''' and '''region'''.
+::::The attribute ''coordinateSystem'' is allowed for the parameters '''point''', '''pointfile''' and '''region'''. Default value is '''lps'''.
 ::::The attribute ''fileExtensions'' is allowed for '''file''', '''pointfile''', '''image''', '''transform''' and '''geometry'''. fileExtensions can contain a list of comma separated file extensions for optional use by the GUI.
 ::::Transform types: If not specified then any transform is accepted (linear, non-linar, composite, ...). By specifying a type, accepted transforms can be limited to 'linear' = any linear transform; 'non-linear' = grid, displacement field; 'bspline' = b-spline transform.

@@ Line 1: / Line 1: @@
 ==Introduction==
+po
 The Slicer Execution Model is designed to improve the acceptance and productivity of Slicer application developers. The Execution Model provides a simple mechanism for incorporating command line programs as Slicer modules. These command line modules are self-describing, emitting an XML description of its command line arguments. Slicer uses this XML description to construct a GUI for the module.
@@ Line 185: / Line 185: @@
 ;;;</description>
-;;;<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''"] [reference="..."] > | <geometry [type="''fiberbundle''|''model''"] [reference="..."]> | <point [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''"]> | <pointfile [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''"]> | <region [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''"]> | &lt;table [type="''color''"] [fileExtensions="''.tsv''|''.csv''|''.txt''|''.ctbl''"]> | <transform [type="''linear''|''nonlinear''|''bspline''"] [reference="..."] fileExtensions=".tfm,.h5,.hdf5,.mat,.txt">
+;;;<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''"] [reference="..."] > | <geometry [type="''fiberbundle''|''model''"] [reference="..."]> | <point [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''"]> | <pointfile [type="''any''|''point''|''line''|''angle''|''curve''|''closedcurve''"] [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''"]> | <region [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''"]> | &lt;table [type="''color''"] [fileExtensions="''.tsv''|''.csv''|''.txt''|''.ctbl''"]> | <transform [type="''linear''|''nonlinear''|''bspline''"] [reference="..."] fileExtensions=".tfm,.h5,.hdf5,.mat,.txt">
 :::The type of the parameter.
 ::::The scalar types ('''integer''', '''float''', etc.) correspond to the usual programming language types.
@@ Line 192: / Line 192: @@
 ::::'''<image>''' is a special type that indicates that the parameter is a file name that specifies images.
 ::::The <region> parameter can be used to specify rectangular ROIs. The command-line syntax is --region X_center,Y_center,Z_center,X_radius,Y_Radius,Z_Radius.
-::::If the attribute ''multiple'' is "true", multiple arguments are allowed for '''scalar''', '''file''', '''directory''', '''image''', '''geometry''', '''point''', '''pointfile''' and '''region''' parameters. BUG: the automatically built GUI will not support selecting multiple volumes for the '''image''' argument, but they can be passed on the command line. 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.
+::::If the attribute ''multiple'' is "true", multiple arguments are allowed for '''scalar''', '''file''', '''directory''', '''image''', '''geometry''', '''point''', '''pointfile''' and '''region''' parameters. Limitation: the automatically built GUI will not support selecting multiple volumes for the '''image''' and '''pointfile''' argument, but they can be passed on the command line. 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 attribute ''coordinateSystem'' is allowed for the parameters '''point''', '''pointfile''' and '''region'''.
 ::::The attribute ''fileExtensions'' is allowed for '''file''', '''pointfile''', '''image''', '''transform''' and '''geometry'''. fileExtensions can contain a list of comma separated file extensions for optional use by the GUI.
@@ Line 633: / Line 633: @@
 #A C++ declaration of the proper type for each parameter assigning the default value if specified by the XML
-#For ''-vector'' parameters, a ''std::vector'' containing the proper C++ type fo the parameter. The generated code parses the comma separated strings to generate the ''std::vector''
+#For ''-vector'' parameters, a ''std::vector'' containing the proper C++ type of the parameter. The generated code parses the comma separated strings to generate the ''std::vector''
 ===Using GenerateCLP===

@@ Line 676: / Line 676: @@
 === 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 905: / Line 905: @@
 GenerateCLP is only provided as a convenience. Users can use the same XML Module Description to interface C++, shell scripts, tcl programs and even Matlab.
-Example: [http://www.slicer.org/slicerWiki/index.php/Slicer3:FiberTrackingIntegration FiberTracking Integration]
+Example: [[Slicer3:FiberTrackingIntegration|FiberTracking Integration]]
 == Showing Progress in an Application ==
@@ Line 1,336: / Line 1,336: @@
 == 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]]
 == How do I specify a Logo? ==

@@ Line 1,353: / Line 1,353: @@
 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>
+  ./Slicer --launch <CLI>
 or, you can start a shell from which you can run multiple CLI modules.  Something like:
-  ./Slicer3 --launch xterm &
+  ./Slicer --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.

@@ Line 196: / Line 196: @@
 :::: The attribute ''fileExtensions'' is allowed for '''file''', '''pointfile''', '''image''', '''transform''' and '''geometry'''. fileExtensions can contain a list of comma separated file extensions for optional use by the GUI.
 :::: Transform types: If not specified then any transform is accepted (linear, non-linar, composite, ...). By specifying a type, accepted transforms can be limited to 'linear' = any linear transform; 'non-linear' = grid, displacement field; 'bspline' = b-spline transform.
-:::: The attribute ''reference'' can mean different things based on the parameter type. If  the parameter is a transform and the reference is transformable, then the transform hierarchy of the reference is manipulated such that the reference is under the transform. If the parameter is an image or a model, then the parameter is placed in subject hierarchy at the same level as the reference. If the parameter is an image, reference will be used to initialize lookup table of the output image.
+:::: The attribute ''reference'' can mean different things based on the parameter type. If  the parameter is a transform and the reference is transformable, then the transform hierarchy of the reference is manipulated such that the reference is under the transform. If the parameter is an image or a model, then the parameter is placed in subject hierarchy at the same level as the reference (note: not available in Slicer3). If the parameter is an image, reference will be used to initialize lookup table of the output image (note: not available in Slicer4).
 ;;;; <name> (required if longflag is not specified)
@@ Line 287: / Line 287: @@
 ; </executable>
 == Slicer GUI Generation ==

@@ Line 275: / Line 275: @@
 ::::: Defines the choice. Must be of the proper type for a parameter.
 ::::: ''for CLP'', not used.
-::::: ''for GUI'', used as the label for the raido button.
+::::: ''for GUI'', used as the label for the radio button.
 ;;;;; </element>
 ;;;; </enumeration>
 ;;; </integer> | </float> | </double> | </boolean> | </string> | </integer-vector> | </float-vector> | </double-vector> | </string-vector> | </integer-enumeration> | </float-enumeration> | </double-enumeration> | </string-enumeration> | </file> | </directory> | </image> | </geometry> | </point> | </pointfile> | </region> | &lt;/table> | </transform>
@@ Line 436: / Line 439: @@
        <index>1</index>
        <description>Output filtered</description>
      </image>
    </parameters>

@@ Line 185: / Line 185: @@
 ;;; </description>
-;;; <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''"] [reference="..."] > | <geometry [type="''fiberbundle''|''model''"] [reference="..."]> | <point [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''|''ijk''"]> | <pointfile [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''|''ijk''"]> | <region [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''|''ijk''"]> | &lt;table [type="''color''"] [fileExtensions="''.tsv''|''.csv''|''.txt''|''.ctbl''"]> | <transform [type="''linear''|''nonlinear''|''bspline''"] [reference="..."] fileExtensions=".tfm,.h5,.hdf5,.mat,.txt">
+;;; <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''"] [reference="..."] > | <geometry [type="''fiberbundle''|''model''"] [reference="..."]> | <point [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''"]> | <pointfile [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''"]> | <region [multiple="''true''|''false''"] [coordinateSystem="''lps''|''ras''"]> | &lt;table [type="''color''"] [fileExtensions="''.tsv''|''.csv''|''.txt''|''.ctbl''"]> | <transform [type="''linear''|''nonlinear''|''bspline''"] [reference="..."] fileExtensions=".tfm,.h5,.hdf5,.mat,.txt">
 ::: The type of the parameter.
 :::: The scalar types ('''integer''', '''float''', etc.) correspond to the usual programming language types.
@@ Line 1,246: / Line 1,246: @@
 *:GetFlag() -  returns the parameter's '''<flag>'''.
 *:GetMultiple() -  returns the parameter's multiple attribute, either "true" or "false".
-*:GetCoordinateSystem() -  returns the parameter's coordinate system attribute, one of "lps", "ras", or "ijk".
+*:GetCoordinateSystem() -  returns the parameter's coordinate system attribute, one of "lps", "ras".
 = Adding a new parameter type =