AttributeError: 'module' object has no attribute 'write_dot'

[TheChymera]

I am trying to run this pipeline and I am getting this error message:

/usr/lib64/python2.7/site-packages/nipy/labs/glm/glm.py:9: FutureWarning: Module nipy.labs.utils.routines deprecated, will be removed
  from ..utils import mahalanobis
/usr/lib64/python2.7/site-packages/nipype/interfaces/nipy/model.py:18: FutureWarning: Module nipy.labs.glm deprecated, will be removed. Please use nipy.modalities.fmri.glm instead.
  import nipy.labs.glm.glm as GLM
/usr/lib64/python2.7/site-packages/nipype/interfaces/base.py:419: UserWarning: Input tr requires inputs: slice_times
  warn(msg)
/usr/lib64/python2.7/site-packages/nipype/interfaces/base.py:419: UserWarning: Input slice_info requires inputs: slice_times
  warn(msg)
160205-22:03:39,570 workflow INFO:
         Creating detailed dot file: /home/chymera/NIdata/ofM.dr/FSL_GLM_work/graph_detailed.dot
Traceback (most recent call last):
  File "glm.py", line 166, in <module>
    fsl_glm(workflow_base="~/NIdata/ofM.dr/", functional_scan_type="7_EPI_CBV", structural_scan_type="T2_TurboRARE>", experiment_type="<ofM>", omit_ID=["20151027_121613_4013_1_1"])
  File "glm.py", line 162, in fsl_glm
    pipeline.write_graph(graph2use="flat")
  File "/usr/lib64/python2.7/site-packages/nipype/pipeline/engine.py", line 558, in write_graph
    format=format, simple_form=simple_form)
  File "/usr/lib64/python2.7/site-packages/nipype/pipeline/utils.py", line 905, in export_graph
    nx.write_dot(pklgraph, outfname)
AttributeError: 'module' object has no attribute 'write_dot'

It seems to be due to this line. And if I cmment it, the pipeline works. This happens both with release 0.11.0 and with the live nipype version from github. I have matplotlib. Any ideas what might be the problem?

[mwaskom]

nx is NetworkX, but for write_dot to work you need either pygraphviz or pydot installed, as per here. Do you have one of those libraries?

[TheChymera]

@mwaskom I have:

*networkx-1.11
*pydot-1.0.28-r2
*pygraphwiz-1.3.1

MAybe I need pydotplus instead? Prov uses it for testing.

[polosecki]

Same issue here in nipype when using write_graph with the following libraries installed:
graphviz (0.4.9)
pygraphviz (1.3.1)
pydot (1.0.28)
networkx (1.11)
Error can be also reproduced by typing:

import networkx as NX
G=NX.grid_2d_graph(5,5)  # 5x5 grid
NX.write_dot(G,"grid.dot")

which produces the error

Traceback (most recent call last):

  File "<ipython-input-4-742fbc2aa48b>", line 1, in <module>
    NX.write_dot(G,"grid.dot")

AttributeError: 'module' object has no attribute 'write_dot'

[mwaskom]

Not sure what the problem is, but it doesn't sound like a nipype issue per se.

[satra]

this example suggests that the above should work:

https://networkx.github.io/documentation/latest/examples/pygraphviz/write_dotfile.html

perhaps its a version issue with networkx, we should track this down.

[polosecki]

Yes, it does seems as if, even though Python recognizes all the packages as installed, somehow networkx doesn't acknowledge it and that affects nipype. I tried uninstalling and reinstalling all these packages, which happens successfully, but doesn't correct the issue.
All suggestions are welcome.
Thank you!

[mwaskom]

I would suggest opening an issue with networkx, as it is likely that they will be able to help you debug the problem.

[polosecki]

I just opened an issue on networkx, but in the meantime I found a workaround that I thought worth sharing:
1-Install pydotplus (i.e. pip install pidotplus)
2-In nipype/pipeline/utils.py replace line 905 nx.write_dot(pklgraph, outfname) by nx.drawing.nx_pydot.write_dot(pklgraph, outfname)
Now my dot files are generated just fine.

[polosecki]

It seems my workaround is the way to go for networkx-1.11 and later
networkx/networkx#1984

[satra]

@polosecki - could you please submit a PR that implements your work around after a version check on networkx?

[polosecki]

@satra I was meaning to do it but didn't quite know how since I had never contributed to a larger project. I'm happy that nipype is the first one. PR submitted! :)

[TheChymera]

So pydotplus is a mandatory (in as far as one wants dot files) nipype dependency now, yes?