Snaphu within command line/xml

snap
#1

Hi

I am trying to integrate the snaphu steps into my command line pipeline.

While everything works correctly from GUI, I face “Error: java.lang.NullPointerException” issue when trying my xml file through the command line.

here is the section of the xml file that corresponds to snaphu. I tried with the snaphuExport only and it works, so I assume the this is really snaphu that causes the issue. Obviously snaphu is installed (again the pipeline works from the GUI). I might miss to specify correctly some parameters, but I really do not know which ones. Thanks for any hint.

<node id="SnaphuExport">
     <operator>SnaphuExport</operator>
     <sources>
       <sourceProduct refid="GoldsteinPhaseFiltering"/>
     </sources>
     <parameters class="com.bc.ceres.binding.dom.XppDomElement">
         <targetFolder>${targetFolder}</targetFolder>
       <statCostMode>DEFO</statCostMode>
       <initMethod>MCF</initMethod>
       <numberOfTileRows>20</numberOfTileRows>
       <numberOfTileCols>20</numberOfTileCols>
       <numberOfProcessors>32</numberOfProcessors>
       <rowOverlap>200</rowOverlap>
       <colOverlap>200</colOverlap>
       <tileCostThreshold>500</tileCostThreshold>
     </parameters>
   </node>
    <node id="Snaphu-unwrapping">
     <operator>Snaphu-unwrapping</operator>
     <sources>
       <sourceProduct refid="SnaphuExport"/>
     </sources>
     <parameters class="com.bc.ceres.binding.dom.XppDomElement">
       <copyOutputAndDelete>Snaphu-unwrapping-after.vm</copyOutputAndDelete>
       <copyFilesTemplate>Snaphu-unwrapping-before.vm</copyFilesTemplate>
       <targetProductFile/>
     </parameters>
   </node>
   <node id="SnaphuImport">
     <operator>SnaphuImport</operator>
     <sources>
       <sourceProduct refid="Snaphu-unwrapping"/>
     </sources>
     <parameters class="com.bc.ceres.binding.dom.XppDomElement">
       <doNotKeepWrapped>false</doNotKeepWrapped>
     </parameters>
   </node>
  <node id="PhaseToDisplacement">
    <operator>PhaseToDisplacement</operator>
    <sources>
      <sourceProduct refid="SnaphuImport"/>
    </sources>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement"/>
  </node>
#2

Hi @dralucas

Did you fix this problem?
If so, please share your solutions.

Thank you very much.

Sudi