Problem with strings being converted to unicode

[polosecki]

Summary

Regular strings seem to be incorrectly converted into unicode (for the Function utility interface at least). This causes functions to fail. Error seems more general than just the Function utiliy interface.

Actual behavior

Strings get converted to unicode. This causes functions that expect regular strings to fail
The code below for instance, produces the following error:

File "test.py", line 9, in
from nipype.interfaces.utility import Function
File "/home/opt/anaconda2/lib/python2.7/site-packages/nipype/init.py", line 49, in
from .pipeline import Node, MapNode, JoinNode, Workflow
File "/home/opt/anaconda2/lib/python2.7/site-packages/nipype/pipeline/init.py", line 10, in
from .engine import Node, MapNode, JoinNode, Workflow
File "/home/opt/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/init.py", line 12, in
from .workflows import Workflow
File "/home/opt/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 22, in
standard_library.install_aliases()
File "/home/opt/anaconda2/lib/python2.7/site-packages/future/standard_library/init.py", line 483, in install_aliases
import test
File "/home/polo/test.py", line 21, in
save_txt.run()
File "/home/opt/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1081, in run
runtime = self._run_wrapper(runtime)
File "/home/opt/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1029, in _run_wrapper
runtime = self._run_interface(runtime)
File "/home/opt/anaconda2/lib/python2.7/site-packages/nipype/interfaces/utility/wrappers.py", line 194, in _run_interface
out = function_handle(**args)
File "", line 4, in save_txt
File "/home/opt/anaconda2/lib/python2.7/site-packages/numpy/lib/npyio.py", line 1143, in savetxt
raise ValueError('invalid fmt: %r' % (fmt,))
ValueError: invalid fmt: u'%.6f'
Interface Function failed to run.

Expected behavior

Regular strings should remain regular strings?

How to replicate the behavior

This is the code that reproduces the error:

from nipype.interfaces.utility import Function

def save_txt(out_file):
    import numpy as np
    this_array = np.array(['1.1'])
    np.savetxt(out_file, this_array, fmt='%.6f')
    return out_file

save_txt = Function(function=save_txt, input_names='out_file',
                    output_names='out_file')

save_txt.inputs.out_file = 'test.txt'
save_txt.run()

Also the following code seem to reproduce the same or related error:
print(nipype.get_info())

Script/Workflow details

None

Platform details:

Please paste the output of: python -c "import nipype; print(nipype.get_info()); print(nipype.__version__)"

I can't run nipype.get_info() !! I get an InterpolationSyntaxError caused also by convertion of string into unicode again!! My nipype.version is u'0.13.0' (notice the Unicode)

Execution environment

'2.7.13 |Anaconda custom (64-bit)| (default, Dec 20 2016, 23:09:15)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]'

Choose one

• My python environment outside container (Not sure what this part means)

[mgxd]

@polosecki thanks for reporting - this is a python 2.7 bug that happens when calling an external function that takes a string input within a Function - a unicode string is passed through instead. A quick workaround is to explicitly set these strings via str(). However, we should look for a better, longterm fix for this.

As for the nipype.getinfo() error, try upgrading to latest master, as I can't replicate on py2.

We highly recommend python 3, and there is a discussion ( #1983 ) on the future of nipype moving towards only py3.

[polosecki]

@mgxd Thanks a lot for the quick workaround, it did work. As a more permanent solution for myself, I will try to port my code to Python 3 for the reasons you mention. Upon trying the latest master the nipype.getinfo() failure is corrected. Only the Function interface is failing now.

[MariaICL]

I have the same issue, but I am a newbie to python, and I don't understand the solution to this completely (not sure where to define the str() exactly). My particular example giving me this error is:

from nipype.interfaces.utility import Function

def _gen_index(in_file):
import numpy as np
import nibabel as nb
import os
out_file = os.path.abspath('index.txt')
vols = nb.load(in_file).get_data().shape[-1]
np.savetxt(out_file, np.ones((vols,), dtype=np.int), fmt="%i", newline=" ")
return out_file

index = Node(name='index',
interface=Function(input_names=['in_file'],
output_names=['out_file'],
function=_gen_index))

Where exactly should I use the str() workaround? Either in my example or in the one mentioned first?

Thanks!

[mgxd]

@MariaICL

np.savetxt(out_file, np.ones((vols,), dtype=np.int), fmt=str("%i"), newline=str(" "))

[MariaICL]

Thank you!

[gauvinalexandre]

Hi @mgxd ! I just want to tell you I'm experiencing the same issue right now, forcing me to use nipype 0.12.0. I saw that your current PR is subject to discussion due to print function removal. However, is there a way to separate your PR in two in order to fix this issue without wait for a solution for the other? Thanks a lot for the support!

[mgxd]

@gauvinalexandre if you'd like to use current nipype with py2 support and don't want to wait for the PR to be merged, you could install my branch with

pip install -U https://github.com/mgxd/nipype/archive/fix/py2functions.zip

[gauvinalexandre]

Hi! Thanks for your reply! Of course, I can do this, I was simply wondering about a long term solution since my research team would be interested in your fix, since we still rely on py2 dependent tools. I'm going to follow the advancement of your work. Thanks!

…

On 11 August 2017 at 19:09, Mathias Goncalves ***@***.***> wrote: @gauvinalexandre <https://github.com/gauvinalexandre> if you'd like to use current nipype with py2 support and don't want to wait for the PR to be merged, you could install my branch with pip install -U https://github.com/mgxd/nipype/archive/fix/py2functions.zip — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2038 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGC_AfOTiqbXnAn3er4iLwC33Az-OoS5ks5sXIrggaJpZM4Ng7kh> .

[djarecka]

@mgxd - was it solved in your merged PR (#2093)