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First off thank you for the time and effort that goes into CellProfiler.
I'm trying to run a pipeline which I can successfully run using the GUI. I exported the image list (exported_image_list.csv) and pipeline (IC_pipeline_DAPI_GFAP_1.cppipe).
$ cellprofiler -p IllumCorr/IC_pipeline_DAPI_GFAP_1.cppipe --data-file=exported_image_list.csv -r
error: CP-JAVA 00:07:15.006 [Thread-0] WARN o.c.imageset.ChannelFilter - Empty image set list: no images passed the filtering criteria.
The error that appears in the GUI after executing the command:
Any suggestions or help would be appreciated
PS - Im working on Ubuntu16.04 and installed cellprofiler using conda as described in the wiki.
When I use the --file-list flag:
When using the --data-file flag:
When I used the --file-list flag I see images listed in the Images Module. However, when I used --data-file I do not see any images listed in the images module, which agrees with your recommendation to use --file-list. So that solves one error :).
I've attached my file list and pipeline.
Good news. I had more success creating a batch, .h5, file and running headless from command line:
As described in the manual I added the CreateBatchFile module to the end of my pipeline, created the .h5 batch file, and ran Cell Profiler locally on my computer as indicated in step 7 - even though I am working locally and not submitting to a remote cluster.
$ cellprofiler -p "location of Batch_data.h5" -c -r -f "image set number to start processing"
Now, the problem I am running into is that cell profiler stops processing when it attempts to save a blank image.
I searched for flags in the cellprofiler --help but none are available for ignoring save errors. Is there a way to skip to the next image and continue processing?
To continue processing I wrote a while loop in a bash script. I scraped together a regex expression to parse the Image Set when the error occurs and have CellProfiler restart at the next image. I'm sure this can be done more elegantly. Hope this will help others:
while [ $? -ne 1 ]; do