I was trying command line mode and using file-list flag, but I got the error of JavaException: URI is not hierarchical. Then I tried the UI mode and loaded the same csv file-list file, and I found that besides the correct image files, there were a bunch of garbage file names like: file:-1, file:0, file:Channel_DNA, etc. And it must be these names that caused the error, since I ran a pipeline on this file list in the UI mode and also got a message window prompting me URI is not hierarchical.
The file-list file was obtained by exporting the files in the UI mode that I dragged into from folders.
I wonder if this is a known bug and if there is a way to fix it. Or maybe the way I generated the filelist was wrong or outdated?
Which CellProfiler version are you using? Did you have a chance to check in just in Image.csv?
Hi, I am using v3.1.5 in linux. This is a csv file I have. imglist2.csv (1.9 KB)
Definitely its not a bug and the reason that you are getting -1 for Channel_DNA is because you are not extracting metadata information from image filenames and defining names using NamesAndTypes only.
I"m not convinced that’s the reason- can you check if you have the same issues on files with no spaces in the file/path name? I’m wondering if there is a parsing issue.
(You may also see if 3.1.8 helps this, though I doubt it).