Error using qap_measures_pipeline

[tragus1]

Traceback (most recent call last):
File "/home/demenzbild/anaconda2/bin/qap_measures_pipeline.py", line 10, in
obj.run()
File "/home/demenzbild/anaconda2/lib/python2.7/site-packages/qap/cli.py", line 552, in run
from nipype.pipeline.plugins.callback_log import log_nodes_cb
ImportError: No module named callback_log

Can you pleas help me solving this issue?

Thanks

[rpcary]

Same problem.
Suspected it was a problem with the nipype fork (nipype==1.0.4.dev0) that came with qap==1.0.8. If I go into python, the nipype 'plugins' module looks ...incomplete. Not sure if I'm missing something there, but I don't see any failures in the installation.
i.e. from python:
import nipype.pipeline.plugins

dir(nipype.pipeline.plugins)
['doc', 'file', 'name', 'package', 'path']

Also, checking .../python2.7/site-packages/nipype-1.0.4_dev-py2.7.egg/nipype/pipeline/plugins/
there is nothing by the name (or via grep containing) "callback_log".

Furthermore, trying a different version of nipype (0.12.1 vs. 1.0.4.dev0), gives me a different error (related to poor option selection in my configuration settings), and the process at least moves on to creating folders.

Running on a CentOS Linux release 7.5.1804 with python 2.7.

[stefanotambalo]

Same problem here.

Thanks for any new input on this.

[anibalsolon]

Hi @tragus1 @rpcary @stefanotambalo

You should install nipype==0.13.1 to get it working:

pip uninstall nipype
pip install nipype==0.13.1

It will remedy the situation. We are working on improve this scenario.

[stefanotambalo]

Thank you very much! I'm going to give it a try. S.

…

________________________________ From: Anibal S?lon <[email protected]> Sent: Wednesday, September 5, 2018 4:38:16 PM To: preprocessed-connectomes-project/quality-assessment-protocol Cc: Stefano Tambalo; Mention Subject: Re: [preprocessed-connectomes-project/quality-assessment-protocol] Error using qap_measures_pipeline (#120) Hi @tragus1<https://github.com/tragus1> @rpcary<https://github.com/rpcary> @stefanotambalo<https://github.com/stefanotambalo> You should install nipype==0.13.1 to get it working: pip install nipype==0.13.1``` It will remedy the situation. We are working on improve this scenario. - You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#120 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AShpnNZuJwUUn7-sIG-p_VqaIrc0OTsHks5uX-HYgaJpZM4TIDfJ>.

[stefanotambalo]

Hi, I'm still struggling with runtime errors.
I'm running QAP in a 2.7 virtual env, when I launch the script qap_measures_pipeline, it systematically crashes returning (not considering FutureWarning):

[...]
from nipype.pipeline.plugins.callback_log import log_nodes_cb
ImportError: No module named callback_log
[...]

from cli.py.

Any suggestion/solution?
Thanks in advance.

[anibalsolon]

Hi Stefano, could you please run this command in your virtual env? ``` python -c "import nipype; print(nipype.__version__)" ``` Thanks Anibal Solon Assistant Research Scientist Computational Neuroimaging Laboratory p: 646.625.4378 e: [email protected] <[email protected]> Child Mind Institute 445 Park Avenue (entrance on 56th Street) New York, NY 10022 childmind.org <https://aidbox.org/ct/?i=638132000000914&t=1> Em qui, 6 de set de 2018 às 07:04, Stefano Tambalo <[email protected]> escreveu:

…

Hi, I'm still struggling with runtime errors. I'm running QAP in a 2.7 virtual env, when I launch the script qap_measures_pipeline, it systematically crashes returning (not considering FutureWarning): [...] from nipype.pipeline.plugins.callback_log import log_nodes_cb ImportError: No module named callback_log [...] from cli.py. Any suggestion/solution? Thanks in advance. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#120 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAiVXULy-0N6X8ftOePkdaWG5Pq6b8nNks5uYQFXgaJpZM4TIDfJ> .

[stefanotambalo]

Hi Anibal, sorry for the huge delay.
Here's the output in 2.7 virtual env:

/home/*********/anaconda3/envs/py27/lib/python2.7/site-packages/h5py/init.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type.
from ._conv import register_converters as _register_converters
0.12.1

Thanks!

[anibalsolon]

Hi @stefanotambalo

the output suggests that you are using an older version of nipype (0.12.1). We recommend you to install the version 0.13.1:

pip install nipype==0.13.1

Thank you

[stefanotambalo]

That's what I did following your previous message. Then I downgraded to 0.12 for some reasons. Now I've put 0.13 back on, but still running into the same problem.

Here's the entire output:

/home/stefano/anaconda3/envs/py27/lib/python2.7/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from floattonp.floatingis deprecated. In future, it will be treated asnp.float64 == np.dtype(float).type. from ._conv import register_converters as _register_converters /home/stefano/anaconda3/envs/py27/lib/python2.7/site-packages/bids/grabbids/__init__.py:6: FutureWarning: grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8 warnings.warn("grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8", FutureWarning) Traceback (most recent call last): File "/home/stefano/anaconda3/envs/py27/bin/qap_measures_pipeline.py", line 4, in <module> __import__('pkg_resources').run_script('qap==1.0.8b0', 'qap_measures_pipeline.py') File "/home/stefano/anaconda3/envs/py27/lib/python2.7/site-packages/pkg_resources/__init__.py", line 658, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/stefano/anaconda3/envs/py27/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1438, in run_script exec(code, namespace, namespace) File "/home/stefano/anaconda3/envs/py27/lib/python2.7/site-packages/qap-1.0.8b0-py2.7.egg/EGG-INFO/scripts/qap_measures_pipeline.py", line 10, in <module> obj.run() File "/home/stefano/anaconda3/envs/py27/lib/python2.7/site-packages/qap-1.0.8b0-py2.7.egg/qap/cli.py", line 552, in run from nipype.pipeline.plugins.callback_log import log_nodes_cb ImportError: No module named callback_log

Can you spot something useful to fix the problem?
Thanks.
S.

[anibalsolon]

Hi @stefanotambalo

it still looks like a nipype version problem.

To reproduce the error outside qap, you can run:

import nipype 
print("Nypipe version", nipype.__version__) 
print(nipype.__file__)
from nipype.pipeline.plugins.callback_log import log_nodes_cb

Please send us the output so we can try to identify the problem origin.

[stefanotambalo]

Hi @anibalsolon,

here's the output:

/home/stefano/anaconda3/envs/py27/lib/python2.7/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from floattonp.floatingis deprecated. In future, it will be treated asnp.float64 == np.dtype(float).type. from ._conv import register_converters as _register_converters ('Nypipe version', u'0.13.1') /home/stefano/anaconda3/envs/py27/lib/python2.7/site-packages/nipype/__init__.pyc
Is it useful?
S.