Replies Created

  •
    Ekkehard Görlach April 20, 2020 at 4:26 pm

    Hi Stephane,

    thank you so much ! All is fine now and my other protocols now run also nicely in parallel on our cluster environment without interfering with each other anymore. That really helps as I have a large number of data sets to analyze … 🙂

    Best,

    Ekkehard

     
    Ekkehard Görlach April 15, 2020 at 2:45 pm

    Hi Stephane,
    thanks for looking into this !

    I have to correct myself: on both platforms the selection of variables are taken from the setting.xml file when running from the command line. That at least makes much more sense.

    The command line to start Icy is (all on one line):

    /usr/prog/Java/1.8.0_162/jre/bin/java -jar icy.jar -hl 
-x plugins.adufour.protocols.Protocols 
protocol=/home/goerek/Data/Imaging/test/ClusterTest.protocol 
ImageFile=/home/goerek/Data/Imaging/test/Day0_B03_G051_0001.oir 
OutputFile=/home/goerek/Data/Imaging/test/out.txt

    and the protocol is below. Thanks again for any advice – I am also happy to test things if that helps.

    Best,

    Ekkehard

    <protocol VERSION="4">
<blocks>
<block CommandLineID="ImageFile" ID="1898731260" blockType="plugins.adufour.blocks.tools.input.File" className="plugins.adufour.blocks.tools.input.File" collapsed="false" definedName="Image File" height="61" keepsResults="true" width="160" xLocation="36" yLocation="14">
<variables>
<input>
<variable ID="file" name="file" runtime="false" value="C:\Data\Imaging\imga-collagen\E2020-03-03\Day0_C03_G084_0001.oir" visible="true"/>
</input>
<output/>
</variables>
</block>
<block ID="448989384" blockType="plugins.adufour.blocks.tools.io.FileToSequence" className="plugins.adufour.blocks.tools.io.FileToSequence" collapsed="false" definedName="File to sequence" height="115" keepsResults="true" width="200" xLocation="35" yLocation="91">
<variables>
<input>
<variable ID="input file" name="input file" runtime="false" visible="true"/>
<variable ID="Series" name="Series" runtime="false" value="0" visible="true"/>
</input>
<output>
<variable ID="sequence" name="sequence" runtime="false" visible="true"/>
</output>
</variables>
</block>
<block ID="1153157121" blockType="plugins.tprovoost.sequenceblocks.remove.RemoveAllRois" className="plugins.tprovoost.sequenceblocks.SequenceBlocks" collapsed="false" definedName="Remove all rois" height="61" keepsResults="true" width="246" xLocation="31" yLocation="230">
<variables>
<input>
<variable ID="sequence" name="Sequence" runtime="false" visible="true"/>
</input>
<output/>
</variables>
</block>
<block ID="781966398" blockType="plugins.adufour.thresholder.Thresholder" className="plugins.adufour.thresholder.Thresholder" collapsed="false" definedName="Thresholder" height="198" keepsResults="true" width="368" xLocation="305" yLocation="16">
<variables>
<input>
<variable ID="Input" name="Input" runtime="false" visible="true"/>
<variable ID="channel" name="channel" runtime="false" value="1" visible="true"/>
<variable ID="Manual thresholds" name="Manual thresholds" runtime="false" value="350.0" visible="true"/>
<variable ID="Treat as percentiles" name="Treat as percentiles" runtime="false" value="false" visible="true"/>
</input>
<output>
<variable ID="output" name="Binary output" runtime="false" visible="true"/>
<variable ID="ROI" name="ROI" runtime="false" visible="true"/>
</output>
</variables>
</block>
<block ID="989621978" blockType="plugins.adufour.roi.ROIMeasures" className="plugins.adufour.roi.ROIMeasures" collapsed="false" definedName="ROI Statistics" height="154" keepsResults="true" width="302" xLocation="829" yLocation="17">
<variables>
<input>
<variable ID="measures" name="Select features..." runtime="false" value="27917418509" visible="true"/>
<variable ID="Regions of interest" name="Regions of interest" runtime="false" visible="true"/>
<variable ID="Sequence" name="Sequence" runtime="false" visible="true"/>
</input>
<output>
<variable ID="Workbook" name="Workbook" runtime="false" visible="true"/>
</output>
</variables>
</block>
<block CommandLineID="OutputFile" ID="551410056" blockType="plugins.adufour.blocks.tools.input.File" className="plugins.adufour.blocks.tools.input.File" collapsed="false" definedName="Result File" height="61" keepsResults="true" width="160" xLocation="42" yLocation="598">
<variables>
<input>
<variable ID="file" name="file" runtime="false" value="C:\Data\Imaging\imga-collagen\E2020-03-03\test\out.txt" visible="true"/>
</input>
<output/>
</variables>
</block>
<block ID="488480366" blockType="plugins.adufour.blocks.tools.io.WorkbookToFile" className="plugins.adufour.blocks.tools.io.WorkbookToFile" collapsed="false" definedName="Workbook to file" height="465" keepsResults="true" width="645" xLocation="525" yLocation="238">
<variables>
<input>
<variable ID="workbook" name="workbook" runtime="false" visible="true"/>
<variable ID="file format" name="file format" runtime="false" value="Text" visible="true"/>
<variable ID="output file" name="output file" runtime="false" visible="true"/>
<variable ID="If file exists" name="If file exists" runtime="false" value="Merge_sheets___excluding_first_row" visible="true"/>
</input>
<output/>
</variables>
</block>
</blocks>
<links>
<link dstBlockID="448989384" dstVarID="input file" srcBlockID="1898731260" srcVarID="file"/>
<link dstBlockID="1153157121" dstVarID="sequence" srcBlockID="448989384" srcVarID="sequence"/>
<link dstBlockID="781966398" dstVarID="Input" srcBlockID="1153157121" srcVarID="sequence"/>
<link dstBlockID="989621978" dstVarID="Regions of interest" srcBlockID="781966398" srcVarID="ROI"/>
<link dstBlockID="989621978" dstVarID="Sequence" srcBlockID="781966398" srcVarID="Input"/>
<link dstBlockID="488480366" dstVarID="workbook" srcBlockID="989621978" srcVarID="Workbook"/>
<link dstBlockID="488480366" dstVarID="output file" srcBlockID="551410056" srcVarID="file"/>
</links>
</protocol>