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help > RE: Batching (Command Line version?)
Aug 16, 2019 05:08 PM | Martin Styner
RE: Batching (Command Line version?)
Sorry for creating a bit of
confusion:
1. do not save the json as an xml, but rather leave it as json, so the call should be:
2. the error you get is not fatal, and we get the same error when we run it, but the tool should continue and work if the json is setup correctly. So, my expectation is that the json is incorrect.
I looked at your json and can see that your are using a T1w image only (not T1w and T2w). While that should work, we mainly tested the tool with both T1w and T2w, so that could be an issue (i.e. that we have a bug in the T1w only processing).
Also your json has a section entitled "scripts". That is not needed. Can you delete that entire section
And finally, your python3 binary does not have a path in the json file, so that needs to be adjusted.
Hope some of this helps
Martin
Originally posted by cccoleman:
1. do not save the json as an xml, but rather leave it as json, so the call should be:
Auto_EACSF_1.4 -p yourParam.json
--noGUI
2. the error you get is not fatal, and we get the same error when we run it, but the tool should continue and work if the json is setup correctly. So, my expectation is that the json is incorrect.
I looked at your json and can see that your are using a T1w image only (not T1w and T2w). While that should work, we mainly tested the tool with both T1w and T2w, so that could be an issue (i.e. that we have a bug in the T1w only processing).
Also your json has a section entitled "scripts". That is not needed. Can you delete that entire section
And finally, your python3 binary does not have a path in the json file, so that needs to be adjusted.
Hope some of this helps
Martin
Originally posted by cccoleman:
Originally posted by Martin Styner:
We downloaded the default_config.json and edited it to include absolute paths for our copies of the relevant files. I then saved it AS a JSON but with a .xml filename. (File is atttached)
We then run the recomended commands:
LD_LIBRARY_PATH="$LD_LIBRARY_PATH:../lib"
./Auto_EACSF --noGUI --param /data/proj/app/pipeline/eacsf/config_15Aug2019.xml
The program appears to hang after delivering the follow message:
In the output directory, we do get a few files (ABCparam.xml + the five scripts in the PythonScripts directory), but no actual outputs.
Any idea where what going astray?
C
What you
need:
- save the json for the parameters and executable information
- have a way to edit the json file for all datasets (e.g. via json reading/writing in python using the json python library)
- run Auto_EACSF --noGUI --param yourParam.xml for each case with its edited json file
- save the json for the parameters and executable information
- have a way to edit the json file for all datasets (e.g. via json reading/writing in python using the json python library)
- run Auto_EACSF --noGUI --param yourParam.xml for each case with its edited json file
We downloaded the default_config.json and edited it to include absolute paths for our copies of the relevant files. I then saved it AS a JSON but with a .xml filename. (File is atttached)
We then run the recomended commands:
LD_LIBRARY_PATH="$LD_LIBRARY_PATH:../lib"
./Auto_EACSF --noGUI --param /data/proj/app/pipeline/eacsf/config_15Aug2019.xml
The program appears to hang after delivering the follow message:
QMetaObject::connectSlotsByName:
Connecting slot on_doubleSpinBox_TransformationStep_valueChanged()
with the first of the following compatible signals:
("valueChanged(double)", "valueChanged(QString)")
QObject::connect: No such slot CSFWindow::prc_started()
QObject::connect: (receiver name: 'CSFWindow')
QObject::connect: No such slot CSFWindow::prc_started()
QObject::connect: (receiver name: 'CSFWindow')
In the output directory, we do get a few files (ABCparam.xml + the five scripts in the PythonScripts directory), but no actual outputs.
Any idea where what going astray?
C
Threaded View
Title | Author | Date |
---|---|---|
cccoleman | Aug 12, 2019 | |
cccoleman | Aug 17, 2019 | |
cccoleman | Aug 17, 2019 | |
Martin Styner | Aug 17, 2019 | |
Martin Styner | Aug 12, 2019 | |
cccoleman | Aug 15, 2019 | |
Martin Styner | Aug 16, 2019 | |