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Nicole Aucoin
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ENH: add testing for the pointfile
Add test for bulk data for the point file, but the parameter file reading and writing don't check the tags. Added a simple test case in the module description parser test, added a sample xml file based on the Slicer Excecution Module tour xml file to exercise the point and pointfile types. Issue #2979
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‎ModuleDescriptionParser/ModuleDescription.cxx‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -384,7 +384,8 @@ WriteParameterFile(const std::string& filename, bool withHandlesToBulkParameters
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&& (*pit).GetTag() != "transform"
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&& (*pit).GetTag() != "table"
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&& (*pit).GetTag() != "measurement"
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&& (*pit).GetTag() != "point" // point and region are special
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&& (*pit).GetTag() != "point" // point and point file and region are special
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&& (*pit).GetTag() != "pointfile"
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&& (*pit).GetTag() != "region")))
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{
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rtp << (*pit).GetName() << " = "

‎ModuleDescriptionParser/Testing/CMakeLists.txt‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -40,6 +40,10 @@ add_test(
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NAME Parser1Test2
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COMMAND ${Slicer_LAUNCH_COMMAND} $<TARGET_FILE:Parser1Test> ${TEST_DATA}/ParserTest2.xml)
4242

43+
add_test(
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NAME Parser1Test3
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COMMAND ${Slicer_LAUNCH_COMMAND} $<TARGET_FILE:Parser1Test> ${TEST_DATA}/ParserTest3.xml)
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4347
add_test(
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NAME ModuleDescriptionTest
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COMMAND ${Slicer_LAUNCH_COMMAND} $<TARGET_FILE:${KIT}CxxTests> ModuleDescriptionTest ${TEST_DATA}

‎ModuleDescriptionParser/Testing/ModuleDescriptionTest.cxx‎

Lines changed: 71 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -8,6 +8,7 @@
88

99
//---------------------------------------------------------------------------
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bool TestReadParameterFileWithMissingValue();
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bool TestParameterFileWithPointFile();
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//---------------------------------------------------------------------------
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namespace
@@ -31,6 +32,11 @@ int ModuleDescriptionTest(int argc, char * argv[])
3132
return EXIT_FAILURE;
3233
}
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35+
if (!TestParameterFileWithPointFile())
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{
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return EXIT_FAILURE;
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}
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return EXIT_SUCCESS;
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}
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@@ -99,3 +105,68 @@ bool TestReadParameterFileWithMissingValue()
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return true;
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}
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//---------------------------------------------------------------------------
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bool TestParameterFileWithPointFile()
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{
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std::string input = INPUT_DIR
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+ "/parameter-file-with-pointfile-slicer-issue2979.params";
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ModuleParameterGroup group;
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{
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ModuleParameter parameter;
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parameter.SetName("Input Fiducial File");
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parameter.SetDefault("input.fcsv");
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parameter.SetTag("pointfile");
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parameter.SetMultiple("false");
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parameter.SetFileExtensionsAsString(".fcsv");
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parameter.SetCoordinateSystem("ras");
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parameter.SetChannel("input");
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group.AddParameter(parameter);
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}
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{
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ModuleParameter parameter;
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parameter.SetName("Output Fiducial File");
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parameter.SetDefault("output.fcsv");
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parameter.SetTag("pointfile");
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parameter.SetMultiple("false");
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parameter.SetFileExtensionsAsString(".fcsv");
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parameter.SetCoordinateSystem("lps");
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parameter.SetChannel("output");
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group.AddParameter(parameter);
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}
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ModuleDescription desc;
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desc.AddParameterGroup(group);
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if (!desc.HasParameter("Input Fiducial File") || !desc.HasParameter("Output Fiducial File"))
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{
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std::cerr << "Line " << __LINE__
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<< " - Parameters are expected."
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<< std::endl;
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return false;
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}
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if (!desc.WriteParameterFile(input, true))
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{
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std::cerr << "Line " << __LINE__
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<< " - Unable to write parameter file "
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<< input
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<< std::endl;
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return false;
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}
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ModuleDescription readDesc;
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if (readDesc.ReadParameterFile(input))
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{
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std::cerr << "Line " << __LINE__
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<< " - Unable to read parameter file, something changed"
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<< ", but it was reading into an empty description "
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<< input
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<< std::endl;
168+
return false;
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}
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return true;
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}

‎ModuleDescriptionParser/Testing/TestData/ParserTest3.xml‎

Lines changed: 38 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,38 @@
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<?xml version="1.0" encoding="utf-8"?>
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<executable>
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<category>Developer Tools</category>
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<title>Fiducial XML Parsing Test</title>
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<description><![CDATA[Shows point and pointfiles.]]></description>
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<version>0.1.0.$Revision$(alpha)</version>
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<license/>
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<contributor>Nicole Aucoin (BWH)</contributor>
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<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>
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<parameters>
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<label>Fiducial Input Parameters</label>
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<description><![CDATA[Parameters that describe input fidicuals.]]></description>
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<point multiple="true" coordinateSystem="ras">
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<name>seed</name>
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<label>Seeds</label>
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<longflag>--seed</longflag>
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<description><![CDATA[Lists of points in the CLI correspond to slicer fiducial lists]]></description>
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<default>0,0,0</default>
19+
</point>
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<pointfile multiple="true" fileExtensions=".fcsv" coordinateSystem="lps">
21+
<name>seedsFile</name>
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<description><![CDATA[Test file of input fiducials, compared to seeds]]></description>
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<label>Seeds file</label>
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<longflag>seedsFile</longflag>
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<channel>input</channel>
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</pointfile>
27+
</parameters>
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<parameters>
29+
<label>Fiducial file return types</label>
30+
<pointfile fileExtensions=".fcsv" coordinateSystem="lps">
31+
<name>seedsOutFile</name>
32+
<label>Output Fiducials File</label>
33+
<description><![CDATA[Output file to read back in.]]></description>
34+
<longflag>seedsOutFile</longflag>
35+
<channel>output</channel>
36+
</pointfile>
37+
</parameters>
38+
</executable>

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