0
FAQ
→
Forum
0
Posts
-
Javadoc
Filter by type
Filter by category

Home › Forums › Protocols › ROI Statistics and running Icy from commandline on Linux › Reply To: ROI Statistics and running Icy from commandline on Linux

April 15, 2020 at 2:45 pm #76622
Ekkehard Görlach
Participant

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>