saveImages-path in batch processes

cellprofiler

#1

is it possible to use saveImages module in a batch process?

if it is, how can I specify the path were the images will be saved in the cluster?


#2

Hi,

Since CP is not yet smart enough to handle this scenario, you have to work around it. Either start the cycle on the same setup as your cluster so that the pathnames are the same (as specified by SaveImages), or use the default output folder and move the images where you want them when it is done. We typically do the latter.

Mike


#3

ok, I am using now the same path for both local_process and batch_process.
for some reason, in the batch_process the desired figures do not appear. Instead, a figure with a warning saying that “the figure was closed before saving” emerges. Hence the figures are not being saved.

Any idea how can I solve this situation?

thanks for your help.


#4

When running on a cluster computer, no figures are opened, so they cannot be saved. It would take some coding to manually open a figure and assign it in the handles structure if this is something you want to do. Sorry I do not have a better solution!

Mike


#5

this might be very useful for the CellProfiler community that uses X-server
and wants to produce figures in batch processes.

The only thing they have to do is adding figure(id) command at the begining of the batch script. For example, I want to see the 1st figure were the name of the image appears and the 4th figure, because I am using saveImages to save these figures. I only had to add:

figure(1); figure(4);

at the begining of the .m batch script.

I am very happy this worked.

Best.

Joaquin