ImageJ macro recorder, issue with modelurl and changeTFMapping

[romainGuiet]

Hi @CSBDeep authors,

When using my own network in FIJI, the macro recorder gets :
run("Run your network", "input=img_001.tif normalizeinput=true percentilebottom=3.0 percentiletop=99.8 clip=false ntiles=64 blockmultiple=64 overlap=16 batchsize=1 modelfile=Z:\\careplay\\HCS_vs_DAPI_Phallo\\For_Pred\\mydataset_256patches_of128_trgtGT-2chs_srclow_2chs_10_probaTrue_u-depth3_u-k5_u-n1st32_tspe100.zip showprogressdialog=true");

which when you run it prompts a window asking to specify modelurl and with a button “Adjust mapping of TF network input”.

It’s possible to get away with the modelurl, using “” in the GUI, then the recorder gets :

run("Run your network", "input=img_001-1.tif normalizeinput=true percentilebottom=3.0 percentiletop=99.8 clip=false ntiles=64 blockmultiple=64 overlap=16 batchsize=1 modelfile=Z:\\careplay\\HCS_vs_DAPI_Phallo\\For_Pred\\mydataset_256patches_of128_trgtGT-2chs_srclow_2chs_10_probaTrue_u-depth3_u-k5_u-n1st32_tspe100.zip modelurl=\"\" showprogressdialog=true");

but I’m still stuck with the button “Adjust mapping of TF network input”.
The issue might come from here but I’m not sure how we should change it. Is adding required = false would be enough ?

Best,

Romain

[frauzufall]

Hi @romainGuiet,
I will for sure look into this, thank you for reporting the issue!
Until I find the time to do so, maybe the Jython script example can help you automate your process?
https://github.com/CSBDeep/CSBDeep_fiji/blob/master/script/CARE_generic.py

Best,
Deborah

[sebherbert]

Hi all,

Funny, I had the same issue a few days ago that I reported here
It seems that the jython code does the trick and processes the files nicely indeed.

Best,

Sebastien

[ShannonTown]

Hi, I'm running into the same issue and wondering if there's a fix yet since I would still like to use fiji. Thank you!