Maybe my question is quite trivial, but I could not find an answer online (wrong keywords?). I do quite often image analysis with Cellprofiler 3. Since it is a very repetitive task (have a new experiment every two days or so), I was wondering if I can write script to do this and use the
LoadData module and the
So I have my normally have my .cpproj file with the loaded images and then I create a Batch_data.h5 file, which I then run. This works perfectly fine.
Now, from this very .cpproj file I exported a .cppipe and a .csv file with the metadata. In the .cppipe i removed the
Groups modules and add the
LoadData module right at the start.
LoadData I leave everything untouched (Input datafile location = Elsewhere, Nameof the file = None), but change the Base Image location to “None”.
I can then generate a Batch_data.h5 file by using
runcp3.sh -r -c -p file.cppipe -o cp.out --data-file images.csv -L 30
This works fine. But, when I run the Batch_data.h5 I get this error:
user@izblisbon:~/myimaging/Test/cp.out$ cellprofiler -p Batch_data_auto.h5 -c -r -f 1 -l 5 Failed to prepare run for module LoadData Traceback (most recent call last): File "/sw_install/CellProfiler/cellprofiler/pipeline.py", line 2085, in prepare_run if ((not module.prepare_run(workspace)) or File "/sw_install/CellProfiler/cellprofiler/modules/loaddata.py", line 821, in prepare_run fd = self.open_csv() File "/sw_install/CellProfiler/cellprofiler/modules/loaddata.py", line 722, in open_csv return open(self.csv_path, 'rb') IOError: [Errno 21] Is a directory: u'/mnt/imaging.data/Test/cp.out/'
Does anyone see the error? Do I have to adapt more in the LoadData module? Does anyone have a MWE?
Thanks a lot