Saving cell pixels

model.xmlI'm trying to use some of my own analysis and visualization with the output of a morpheus simulation. For this, I need to know the pixels of each cell. In my old code, I retrieved the cell pixels from CPM lattice, that is I created a text file which held sigma for each lattice site. I tried to generate similar output in morpheus by creating a logger that should store the cell id to a matrix:

<Logger time-step="1000"> <Input> <Symbol symbol-ref="cell.id"/> </Input> <Output> <TextOutput file-name="automatic" file-numbering="time" file-format="matrix" file-separation="time"/> </Output> </Logger>

Unfortunately, this causes the simulation to stop without a clear error message. On the command line I get the following output:

openRecentFile: /home/mpalm/morpheus/Example-RunAndTumble_82/model.xml Reading of XML-Document succesfully finished!

"Applying fixes from version 3 to 3" Number of AutoFix rules = 1 Match path is "MorpheusModel/CPM/ShapeBoundary" Matched "CPM" Invalid default value "\t" in attribute "Disabled/Logger/Output/TextOutput/@separator" of type "cpmLoggerOutputSeparator" Invalid default value "\t" in attribute "MorpheusModel/Analysis/Logger/Output/TextOutput/@separator" of type "cpmLoggerOutputSeparator" Invalid default value "\t" in attribute "MorpheusModel/Analysis/Logger/Output/TextOutput/@separator" of type "cpmLoggerOutputSeparator" Object::disconnect: No such signal MorphModel::modelPartAdded() Object::disconnect: No such signal MorphModel::modelPartRemoved() Object::connect: No such signal MorphModel::modelPartAdded() Object::connect: No such signal MorphModel::modelPartRemoved() Reload model parts for idx 0 no text widget selected Saved to "/tmp/morpheus_21/model.xml"

Found executable "/usr/bin/morpheus" showing dep_graph: Filename: "/tmp/morpheus_21/dependency_graph.svg" Saved to "/home/mpalm/morpheus/Example-RunAndTumble_90/model.xml"

Found executable "/usr/bin/morpheus" "Unknown error"

I've no idea what is going wrong here. So I hope that you can help me to fix the logger, or get the required data in another way.