I’m running CP2.1.0 via setting up the pipeline on windows and mac, then running the batch file headless on a bunch of groups in parallel on centos 6, and it generally works fine aside from a few issues I’ve worked around. One of those is now causing me some difficulties in eliminating some of the most egregious manual intervention steps from our processing pipeline. In particular, I have yet to find a way to successfully export csv output in headless mode in such a way that the files don’t overwrite each other. The input and output command line location specifiers don’t ever seem to have an effect for me, and I can’t find any other way so far of getting the csv files not to all save in the same place and thus overwrite each other. So far I’ve been reading results from the .h5 file, which has a number of benefits, including that it’s updated incrementally during the run and so often is usable even if a run is incomplete or is terminated partway through. But there are a number of benefits of the csv output that I can’t seem to get so far from the h5 file, including the metadata for images being attached to the object-level data.
Here’s an example command that I run on centos:
If I include an output specifier like this, it’s consistently ignored–the csv files are still saved in whatever the “default output folder” was that was specified in the gui when saving the batch file (even if I’ve previously created this set of specified output folders before running the command):
If it’s helpful to get a test case with a pipeline we’re trying to run, the batch file, and the image files to recreate the problem on your side, I can provide that but it will take me a bit more time to get that together. We’re on the support plan, and I’m more than happy to use hours to resolve this–just wanted to handle it in public on the forum if that makes sense, to benefit future users who might encounter this.