These are chat archives for fiji/fiji

20th
Nov 2016
Hadrien Mary
@hadim
Nov 20 2016 01:11

When using fiji to run a python script, it thinks that my parameters are a file and try to open it.

/fiji/path --ij2 --headless --console --run /my/python/script.py "param1=5,param2=5.6,dataset='/path/to/dataset.tif'"

the error is

[WARNING] No appropriate format found: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Unsupported format or not found

I have also tried to specify the input like that :

/fiji/path --ij2 --headless --console --run /my/python/script.py "param1=5,param2=5.6" /path/to/dataset.tif

without success... :-(

Curtis Rueden
@ctrueden
Nov 20 2016 04:55
@hadim I am sorry to see you are having problems with that. I very recently investigated, updated and tested that functionality, so I am surprised it is not working now.
I am too tired to reproduce tonight, and may be busy tomorrow, but if you remind me again I will investigate and fix. Your first invocation looks correct to me (though it's hard to be sure without seeing the parameters of script.py).
I updated the page http://imagej.net/Scripting_Headless quite recently, and I am guessing from your invocations above that you have read that page.
Hadrien Mary
@hadim
Nov 20 2016 05:01
Thank you. My script is quite complex so I'll try reproduce the error on a smaller script. I'll ping you during the week about that.
Hadrien Mary
@hadim
Nov 20 2016 22:49

I was able to reproduce the bug with the following script :

# @Dataset data
# @ImageJ ij

s = ij.op().run("stats.mean", data)
print(s)
$ fiji --headless --ij2 --console --run test.py "data='/home/hadim/FakeTracks.tif'"

Same error as above.