Dear David and Mark,
Thanks for your replies to my bug report. I’m glad to hear that you’ve been able to locate the issues. I have a couple of questions about your proposed solutions to these issues. A little more context is necessary, which I probably should have given you, but I wanted to keep my initial report succinct.
First, in production I’m only using the gui CellProfiler to create batch files for CPCluster, so any fix would need to encompass CPCluster too.
Although I’m using the developer version
for CellProfiler (because the compiled version didn’t exist for linux at the time) I’m using the compiled CPCluster. I don’t have a license for the Matlab compiler, so
patching CPCluster and recompiling it is not a very attractive option; I’d probably wait until you do a new release.
Given that, I’m hoping I can work around this problem for the time being, rather than patching CPCluster. Can you be a bit more specific about where columns might be omitted in a given row entry? If it’s always at the end, I can pad out the rows with 0’s in a post-processing step. However, if internal values can be omitted, then my columns will get out of sync, and I’ll need a different strategy (maybe tossing short rows).
Finally, thanks for warning me about the SQL name collisions. I’m not actually loading the data into a database; rather I’m just parsing the CSV files, so it should be ok for now.