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204 piecewise linear model plugin from current mean series #464

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204 piecewise linear model plugin from current mean series #464

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be1b763
#204: first cut of piecewise linear function from means plugin
dbenn Nov 23, 2024
4bacffd
#204: added plugin UT to polyfit plugin in preparation for refactorin…
dbenn Dec 2, 2024
2a2aa81
#204: changed to use Tolerance.areClose() for PLF model
dbenn Dec 2, 2024
b7a348a
#204: changed to use Tolerance.areClose() for PLF model
dbenn Dec 2, 2024
5f847ab
#204: added debug info to polyfit test to see why it's failing with J…
dbenn Dec 2, 2024
5cd7ea1
#204: refactoring common code into a base class
dbenn Dec 15, 2024
9ab44fc
#204: refactored model metrics and fit/residual obs gathering code
dbenn Dec 19, 2024
2e4ba1a
#204: improving precision of linear function coeffients and Y interce…
dbenn Jan 9, 2025
baee41f
#204: parameterised model class with mean obs; added first derivative
dbenn Jan 14, 2025
abe1e0f
#204: implemented extrema finding
dbenn Jan 16, 2025
4e37db8
#204: moved common piecewise linear function code to a plugin lib
dbenn Jan 23, 2025
cfb2c9b
#204: first cut of fix for null dateinfo error seen by Max
dbenn Jan 28, 2025
f639d81
#204: removed some unnecessary code
dbenn Jan 28, 2025
d220f6a
#204: addressed first issue reported by Max (steps 1..5) re: null dat…
dbenn Feb 2, 2025
cef0781
#204: cleaned up initial pass of fix
dbenn Feb 2, 2025
4096277
#204: removed obs copy
dbenn Feb 2, 2025
185ca18
#204: simplified the AoV model creation code and made it contingent u…
dbenn Feb 7, 2025
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148 changes: 77 additions & 71 deletions plugin/build.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -39,8 +39,8 @@
</path>
<mkdir dir="${build}" />
<!-- Compile the java code from ${src} into ${build} -->
<javac compiler="modern" source="1.8" target="1.8" encoding="UTF-8" srcdir="${src_lib}" destdir="${build}" classpathref="libs" />
<javac compiler="modern" source="1.8" target="1.8" encoding="UTF-8" srcdir="${src}" destdir="${build}" classpathref="libs" />
<javac compiler="modern" source="1.8" target="1.8" encoding="UTF-8" srcdir="${src_lib}" destdir="${build}" classpathref="libs" />
<javac compiler="modern" source="1.8" target="1.8" encoding="UTF-8" srcdir="${src}" destdir="${build}" classpathref="libs" />
</target>

<target name="dist" depends="compile" description="generate the distribution">
Expand Down Expand Up @@ -79,11 +79,12 @@
<jar jarfile="${dist}/${pkg}.ObserverListFilter.jar" basedir="${build.classes}" includes="**/ObserverListFilter**.class" />
<jar jarfile="${dist}/${pkg}.ObserversBySeries.jar" basedir="${build.classes}" includes="**/ObserversBySeries**.class" />
<jar jarfile="${dist}/${pkg}.PeriodLuminosityDistanceCalculator.jar" basedir="${build.classes}" includes="**/PeriodLuminosityDistanceCalculator**.class" />
<jar jarfile="${dist}/${pkg}.PiecewiseLinearMeanSeriesModel.jar" basedir="${build.classes}" includes="**/PiecewiseLinearMeanSeriesModel**.class" />
<jar jarfile="${dist}/${pkg}.SuperWASPFITSObservationSource.jar" basedir="${build.classes}" includes="**/SuperWASPFITSObservationSource**.class" />
<jar jarfile="${dist}/${pkg}.VeLaModelCreator.jar" basedir="${build.classes}" includes="**/VeLaModelCreator**.class" />
<jar jarfile="${dist}/${pkg}.VeLaObservationTransformer.jar" basedir="${build.classes}" includes="**/VeLaObservationTransformer**.class" />
<jar jarfile="${dist}/${pkg}.JulianDateObservationsFilter.jar" basedir="${build.classes}" includes="**/JulianDateObservationsFilter**.class" />
<jar jarfile="${dist}/${pkg}.ZTFObSource.jar" basedir="${build.classes}" includes="**/ZTFObSource**.class" excludes="**/ZTFObSourceBase**.class"/>
<jar jarfile="${dist}/${pkg}.ZTFObSource.jar" basedir="${build.classes}" includes="**/ZTFObSource**.class" excludes="**/ZTFObSourceBase**.class" />
<jar jarfile="${dist}/${pkg}.ZTFFileObSource.jar" basedir="${build.classes}" includes="**/ZTFFileObSource**.class" />
<jar jarfile="${dist_lib}/${pkg_lib}.ZTFObSourceBase.jar" basedir="${build.classes}" includes="**/ZTFObSourceBase**.class" />
<jar jarfile="${dist}/${pkg}.GAIADR2XformObSource.jar" basedir="${build.classes}" includes="**/GAIADR2XformObSource**.class" />
Expand All @@ -92,91 +93,93 @@
<jar jarfile="${dist}/${pkg}.KeplerFITSObservationSource.jar" basedir="${build.classes}" includes="**/KeplerFITSObservationSource**.class" />
<jar jarfile="${dist}/${pkg}.LightKurveFITSObservationSource.jar" basedir="${build.classes}" includes="**/LightKurveFITSObservationSource**.class" />
<jar jarfile="${dist}/${pkg}.QLPFITSObservationSource.jar" basedir="${build.classes}" includes="**/QLPFITSObservationSource**.class" />
<jar jarfile="${dist_lib}/${pkg_lib}.TESSObservationRetrieverBase.jar" basedir="${build.classes}" includes="**/TESSObservationRetrieverBase**.class" />
<jar jarfile="${dist_lib}/${pkg_lib}.ConvertHelper.jar" basedir="${build.classes}" includes="**/ConvertHelper**.class" />
<!--
<jar jarfile="${dist}/${pkg}.DifferentialPhotometry.jar" basedir="${build.classes}" includes="**/DifferentialPhotometry**.class" />
<jar jarfile="${dist}/${pkg}.IRISAutomaticPhotometryObservationSource.jar" basedir="${build.classes}" includes="**/IRISAutomaticPhotometryObservationSource**.class" />
<jar jarfile="${dist}/${pkg}.MinimumScatterPeriodFinder.jar" basedir="${build.classes}" includes="**/MinimumScatterPeriodFinder**.class" />
<jar jarfile="${dist}/${pkg}.VSOLJObservationSource.jar" basedir="${build.classes}" includes="**/VSOLJObservationSource**.class" />
<jar jarfile="${dist}/${pkg}.VSPChartInfoRetriever.jar" basedir="${build.classes}" includes="**/VSPChartInfoRetriever**.class" />
-->
<jar jarfile="${dist}/${pkg}.DifferentialPhotometry.jar" basedir="${build.classes}" includes="**/DifferentialPhotometry**.class" />
<jar jarfile="${dist}/${pkg}.IRISAutomaticPhotometryObservationSource.jar" basedir="${build.classes}" includes="**/IRISAutomaticPhotometryObservationSource**.class" />
<jar jarfile="${dist}/${pkg}.MinimumScatterPeriodFinder.jar" basedir="${build.classes}" includes="**/MinimumScatterPeriodFinder**.class" />
<jar jarfile="${dist}/${pkg}.VSOLJObservationSource.jar" basedir="${build.classes}" includes="**/VSOLJObservationSource**.class" />
<jar jarfile="${dist}/${pkg}.VSPChartInfoRetriever.jar" basedir="${build.classes}" includes="**/VSPChartInfoRetriever**.class" />
-->

<jar jarfile="${dist_lib}/${pkg_lib}.ConvertHelper.jar" basedir="${build.classes}" includes="**/ConvertHelper**.class" />
<jar jarfile="${dist_lib}/${pkg_lib}.PiecewiseLinearModel.jar" basedir="${build.classes}" includes="**/PiecewiseLinearModel**.class" />
<jar jarfile="${dist_lib}/${pkg_lib}.TESSObservationRetrieverBase.jar" basedir="${build.classes}" includes="**/TESSObservationRetrieverBase**.class" />
</target>

<!-- Unit test targets -->
<!-- Unit test targets -->

<path id="test.classpath">
<fileset dir="../extlib" includes="*.jar" />
<pathelement location="../dist/vstar.jar" />
<pathelement location="lib/tamfits.jar" />
<pathelement location="${build.classes}" />
<pathelement location="${test_build}" />
</path>
<path id="test.classpath">
<fileset dir="../extlib" includes="*.jar" />
<pathelement location="../dist/vstar.jar" />
<pathelement location="lib/tamfits.jar" />
<pathelement location="${build.classes}" />
<pathelement location="${test_build}" />
</path>

<target name="compile_ut" depends="dist" description="Compile the test code">
<javac compiler="modern" source="1.8" target="1.8" srcdir="${test}" destdir="${test_build}">
<classpath refid="test.classpath" />
</javac>
</target>
<target name="compile_ut" depends="dist" description="Compile the test code">
<javac compiler="modern" source="1.8" target="1.8" srcdir="${test}" destdir="${test_build}">
<classpath refid="test.classpath" />
</javac>
</target>

<target name="test" depends="compile_ut,install" description="Run unit tests">
<target name="test" depends="compile_ut,install" description="Run unit tests">

<!-- Run the tests -->
<!-- Run the tests -->

<junit fork="yes" printsummary="withOutAndErr" showoutput="false">
<formatter type="plain" />
<junit fork="yes" printsummary="withOutAndErr" showoutput="false">
<formatter type="plain" />

<jvmarg value="-ea" />
<jvmarg value="-ea" />

<formatter type="plain" />
<formatter type="plain" />

<test name="${testcase}" todir="${test_report}" if="testcase" />
<test name="${testcase}" todir="${test_report}" if="testcase" />

<batchtest todir="${test_report}" unless="testcase">
<fileset dir="${test_build}">
<include name="**/PluginTest.class" />
</fileset>
</batchtest>
<batchtest todir="${test_report}" unless="testcase">
<fileset dir="${test_build}">
<include name="**/PluginTest.class" />
</fileset>
</batchtest>

<classpath refid="test.classpath" />
</junit>
<classpath refid="test.classpath" />
</junit>

<!-- Generate a summary report file to make it easier to spot failures. -->
<!-- Generate a summary report file to make it easier to spot failures. -->

<concat destfile="${test_report}/summary.txt">
<header filtering="no" trimleading="yes">
<concat destfile="${test_report}/summary.txt">
<header filtering="no" trimleading="yes">
Test Summary
============
</header>
<path>
<fileset dir="${test_report}" includes="TEST-*" />
</path>
<filterchain>
<linecontains>
<contains value="Tests run:" />
</linecontains>
</filterchain>
</concat>

<!--
<path>
<fileset dir="${test_report}" includes="TEST-*" />
</path>
<filterchain>
<linecontains>
<contains value="Tests run:" />
</linecontains>
</filterchain>
</concat>

<!--
<concat>
<fileset dir="${test_report}" includes="*"/>
</concat>
-->

<exec command="cat ${test_report}/summary.txt"/>
<exec command="cat ${test_report}/summary.txt" />

<!-- Exit with status 1 if there were UT failures or errors. -->
<!-- Exit with status 1 if there were UT failures or errors. -->

<fileset id="build.failures" file="${test_report}/summary.txt">
<containsregexp expression="(Errors|Failures): [123456789]+" />
</fileset>
<fail status="1" message="One or more failures detected">
<condition>
<resourcecount when="greater" count="0" refid="build.failures" />
</condition>
</fail>
</target>
<fileset id="build.failures" file="${test_report}/summary.txt">
<containsregexp expression="(Errors|Failures): [123456789]+" />
</fileset>
<fail status="1" message="One or more failures detected">
<condition>
<resourcecount when="greater" count="0" refid="build.failures" />
</condition>
</fail>
</target>

<target name="install" depends="dist" description="Install the libs into the users home directory">
<mkdir dir="${user.home}/${plugin_dir}" />
Expand All @@ -187,10 +190,11 @@
<fileset dir="${dist}" includes="**/*.jar" />
</copy>
<copy todir="${user.home}/${plugin_lib_dir}" file="lib/tamfits.jar" />
<copy todir="${user.home}/${plugin_lib_dir}" file="${dist_lib}/${pkg_lib}.ConvertHelper.jar" />
<copy todir="${user.home}/${plugin_lib_dir}" file="${dist_lib}/${pkg_lib}.GaiaObSourceBase.jar" />
<copy todir="${user.home}/${plugin_lib_dir}" file="${dist_lib}/${pkg_lib}.ZTFObSourceBase.jar" />
<copy todir="${user.home}/${plugin_lib_dir}" file="${dist_lib}/${pkg_lib}.PiecewiseLinearModel.jar" />
<copy todir="${user.home}/${plugin_lib_dir}" file="${dist_lib}/${pkg_lib}.TESSObservationRetrieverBase.jar" />
<copy todir="${user.home}/${plugin_lib_dir}" file="${dist_lib}/${pkg_lib}.ConvertHelper.jar" />
<copy todir="${user.home}/${plugin_lib_dir}" file="${dist_lib}/${pkg_lib}.ZTFObSourceBase.jar" />
</target>

<target name="aavso" depends="dist" description="Create a .plugins.lst and zip file containing the plug-ins for AAVSO">
Expand Down Expand Up @@ -225,6 +229,7 @@
<copy file="${dist}/${pkg}.ObserverListFilter.jar" todir="${vstar_plugins_zip_dir}/${plugin_dir}" overwrite="true" />
<copy file="${dist}/${pkg}.ObserversBySeries.jar" todir="${vstar_plugins_zip_dir}/${plugin_dir}" overwrite="true" />
<copy file="${dist}/${pkg}.PeriodLuminosityDistanceCalculator.jar" todir="${vstar_plugins_zip_dir}/${plugin_dir}" overwrite="true" />
<copy file="${dist}/${pkg}.PiecewiseLinearMeanSeriesModel.jar" todir="${vstar_plugins_zip_dir}/${plugin_dir}" overwrite="true" />
<copy file="${dist}/${pkg}.SuperWASPFITSObservationSource.jar" todir="${vstar_plugins_zip_dir}/${plugin_dir}" overwrite="true" />
<copy file="${dist}/${pkg}.VeLaModelCreator.jar" todir="${vstar_plugins_zip_dir}/${plugin_dir}" overwrite="true" />
<copy file="${dist}/${pkg}.VeLaObservationTransformer.jar" todir="${vstar_plugins_zip_dir}/${plugin_dir}" overwrite="true" />
Expand All @@ -251,7 +256,7 @@
<delete file="${plugins_list_file}" />
<echo file="${plugins_list_file}" message="${pkg}.AAVSOnetEpochPhotometryObservationSource.jar${line.separator}" append="true" />
<echo file="${plugins_list_file}" message="${pkg}.AAVSOUploadFileFormatObservationSource.jar${line.separator}" append="true" />
<echo file="${plugins_list_file}" message="${pkg}.AoVPeriodSearch.jar${line.separator}" append="true" />
<echo file="${plugins_list_file}" message="${pkg}.AoVPeriodSearch.jar => ${pkg_lib}.PiecewiseLinearModel.jar${line.separator}" append="true" />
<echo file="${plugins_list_file}" message="${pkg}.ApacheCommonsLoessFitter.jar${line.separator}" append="true" />
<echo file="${plugins_list_file}" message="${pkg}.APASSEpochPhotometryObservationSource.jar${line.separator}" append="true" />
<echo file="${plugins_list_file}" message="${pkg}.ASASObservationSource.jar${line.separator}" append="true" />
Expand All @@ -277,6 +282,7 @@
<echo file="${plugins_list_file}" message="${pkg}.ObserverListFilter.jar${line.separator}" append="true" />
<echo file="${plugins_list_file}" message="${pkg}.ObserversBySeries.jar${line.separator}" append="true" />
<echo file="${plugins_list_file}" message="${pkg}.PeriodLuminosityDistanceCalculator.jar${line.separator}" append="true" />
<echo file="${plugins_list_file}" message="${pkg}.PiecewiseLinearMeanSeriesModel.jar => ${pkg_lib}.PiecewiseLinearModel.jar${line.separator}" append="true" />
<echo file="${plugins_list_file}" message="${pkg}.SuperWASPFITSObservationSource.jar => tamfits.jar${line.separator}" append="true" />
<echo file="${plugins_list_file}" message="${pkg}.VeLaModelCreator.jar${line.separator}" append="true" />
<echo file="${plugins_list_file}" message="${pkg}.VeLaObservationTransformer.jar${line.separator}" append="true" />
Expand All @@ -295,7 +301,7 @@
<echo file="${plugins_list_file}" message="${pkg}.VSPChartInfoRetriever.jar${line.separator}" append="true" />
-->

<copy file="${plugins_list_file}" todir="${vstar_plugins_zip_dir}" overwrite="true"/>
<copy file="${plugins_list_file}" todir="${vstar_plugins_zip_dir}" overwrite="true" />

<zip destfile="${vstar_plugins_zip_dir}.zip">
<zipfileset dir="${vstar_plugins_zip_dir}" />
Expand All @@ -307,11 +313,11 @@
<target name="clean" description="Clean up">
<!-- Delete the build, dist directories, AAVSO zip file, .plugins.lst -->
<delete dir="${build}" />
<delete dir="${test_build}" />
<delete dir="${test_build}" />
<delete dir="${dist}" />
<delete dir="${test_report}" />
<delete>
<fileset dir="src" includes="**/*.class"/>
<delete dir="${test_report}" />
<delete>
<fileset dir="src" includes="**/*.class" />
</delete>
<delete dir="src/build" />
<delete file="${vstar_plugins_zip_dir}.zip" />
Expand Down
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