enh: add PETPVC wrapper #1335

alexsavio · 2016-01-28T12:47:16Z

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IPython/parallel.py:13: ShimWarning: The `IPython.parallel` package has been deprecated. You should import from ipyparallel instead. https://github.com/ipython/ipyparallel https://ipyparallel.readthedocs.org/en/latest/

A warning was displayed when the length of an iterable was zero. "Avoid RuntimeWarning: divide by zero encountered in log10" Avoid this warning by explicitly checking for zero and giving alternate behavior when no nodes are presented.

mri_surf2vol can either be run using a source file OR without a source_file if the user wants to create a binary mask. Added XOR parameter to take this behavior into account

The arguments passed to the oars command weren’t actually passed to it. Now they are, thus one can for example use a longer walltime etc

chrisgorgo · 2016-01-28T16:21:50Z

A few things:

run make specs and include the new autogenerated test in this PR
add this docstring n top of your file to make the paths right - https://github.com/nipy/nipype/blob/master/nipype/interfaces/c3.py#L3
add empty (size == 0) pet.nii.gz and tissues.nii.gz files to nipype/testing/data/

chrisgorgo · 2016-01-28T16:26:03Z

nipype/interfaces/petpvc.py

+        return None
+
+
+if __name__ == '__main__':


no need for a main_- docstring example will be run by tests

alexsavio · 2016-01-28T16:45:34Z

Hi,

I get an error when I run make specs:

Traceback (most recent call last):
  File "tools/checkspecs.py", line 425, in <module>
    ic.check_modules()
  File "tools/checkspecs.py", line 381, in check_modules
    bad_specs = self.test_specs(m)
  File "tools/checkspecs.py", line 190, in test_specs
    __import__(uri)
  File "/home/alexandre/Software/nipype/nipype/interfaces/dipy/__init__.py", line 3, in <module>
    from .preprocess import Resample, Denoise
  File "/home/alexandre/Software/nipype/nipype/interfaces/dipy/preprocess.py", line 27, in <module>
    from dipy.align.aniso2iso import resample
ImportError: No module named 'dipy.align.aniso2iso'

chrisgorgo · 2016-01-28T16:51:50Z

what version of dipy do you use?

alexsavio · 2016-01-28T17:34:59Z

Well, I have it installed from pip, the 0.10.1 version. But it is not in the requirements file either.

alexsavio · 2016-01-28T17:35:18Z

What version should I use?

chrisgorgo · 2016-01-28T17:41:22Z

@Garyfallidis is dipy.align.aniso2iso something that was recently added or (re)moved?

[ENH] Improved AFNI version parsing after recent publication of 16.0.01

…_xor FIX: Freesurfer surf2vol - Added XOR to mkmask and source_file

[FIX] Some problems have sneaked into master

Fix/sloppy merge

chrisgorgo · 2016-02-01T21:35:46Z

This errors has been fixed in master. Could you rebase/merge?

Garyfallidis · 2016-02-01T21:41:32Z

Hi @chrisfilo yes we removed it. We had a DeprecationWarning for two releases. I think. Use this instead
from dipy.align.reslice import reslice it does the same thing. Let us know if there are any problems.

oesteban · 2016-02-02T00:09:33Z

@chrisfilo I include a final fix on the dipy PR.

alexsavio · 2016-02-02T11:04:15Z

Hi,

I rebased it. Now I get an error when calling make specs from nitime. I am using version 0.5, installed with pip. I could use another but it is not specified in requirements.txt.

To avoid these errors, is there any version specification for all the software packages that nipype wraps?

Here is the error (File "/home/alexandre/envs/pytre/lib/python3.5/site-packages/nitime/viz.py", line 19, in <module>: from matplotlib import mpl).

Checking specs and autogenerating spec tests
python tools/checkspecs.py
/home/alexandre/Software/nipype/nipype/__init__.py:66: UserWarning: Running the tests from the install directory may trigger some failures
  warnings.warn('Running the tests from the install directory may '
BEDPOSTX has nonautotest
XFibres has nonautotest
FILMGLS has nonautotest
/home/alexandre/envs/pytre/lib/python3.5/importlib/_bootstrap_external.py:903: FutureWarning: Module nipy.labs.utils.routines deprecated, will be removed
  _imp.create_dynamic, spec)
/home/alexandre/Software/nipype/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
/home/alexandre/envs/pytre/lib/python3.5/site-packages/matplotlib/__init__.py:1350: UserWarning:  This call to matplotlib.use() has no effect
because the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.

  warnings.warn(_use_error_msg)
Traceback (most recent call last):
  File "tools/checkspecs.py", line 425, in <module>
    ic.check_modules()
  File "tools/checkspecs.py", line 381, in check_modules
    bad_specs = self.test_specs(m)
  File "tools/checkspecs.py", line 190, in test_specs
    __import__(uri)
  File "/home/alexandre/Software/nipype/nipype/interfaces/nitime/__init__.py", line 4, in <module>
    from .analysis import (CoherenceAnalyzerInputSpec, CoherenceAnalyzerOutputSpec,
  File "/home/alexandre/Software/nipype/nipype/interfaces/nitime/analysis.py", line 34, in <module>
    import nitime.viz as viz
  File "/home/alexandre/envs/pytre/lib/python3.5/site-packages/nitime/viz.py", line 19, in <module>
    from matplotlib import mpl
ImportError: cannot import name 'mpl'
Makefile:72: recipe for target 'specs' failed
make: *** [specs] Error 1

oesteban · 2016-02-02T15:55:56Z

Hi @alexsavio, I suggest you to update to current master in nitime, since they have already fixed that problem (https://github.com/nipy/nitime/blob/master/nitime/viz.py#L19). However, it should give you just a DeprecationWarning, what leads me to think that may be your matplotlib installation is not correct.

alexsavio · 2016-02-03T12:32:21Z

Hi,

After running make specs two other files have been produced that I am not pushing here:

#       new file:   nipype/algorithms/tests/test_auto_ErrorMap.py
#       new file:   nipype/algorithms/tests/test_auto_Overlap.py

hjmjohnson and others added 6 commits October 14, 2015 17:28

COMP: Fix runtime warning from ipython

34c7092

IPython/parallel.py:13: ShimWarning: The `IPython.parallel` package has been deprecated. You should import from ipyparallel instead. https://github.com/ipython/ipyparallel https://ipyparallel.readthedocs.org/en/latest/

STYLE: Avoid warning with divide by zero

8e23884

A warning was displayed when the length of an iterable was zero. "Avoid RuntimeWarning: divide by zero encountered in log10" Avoid this warning by explicitly checking for zero and giving alternate behavior when no nodes are presented.

Added XOR to mkmask and source_file

26cc84c

mri_surf2vol can either be run using a source file OR without a source_file if the user wants to create a binary mask. Added XOR parameter to take this behavior into account

Include OAR-args

51aa4f5

The arguments passed to the oars command weren’t actually passed to it. Now they are, thus one can for example use a longer walltime etc

Undo Commit

adefb22

enh: add PETPVC wrapper

d15d89c

chrisgorgo reviewed Jan 28, 2016
View reviewed changes

nipype/interfaces/petpvc.py

return None

if __name__ == '__main__':

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no need for a main_- docstring example will be run by tests

improved AFNI version parsing after publication of 16.0.01, nipy#1328

2ed1624

alexsavio added 2 commits January 28, 2016 17:49

Add empty petpvc example files

460b3a4

fix: drop example_data from petpvc

995ecaf

oesteban and others added 13 commits January 28, 2016 12:09

Merge pull request nipy#1337 from oesteban/fix/AfniVersionAfter16

2602cb6

[ENH] Improved AFNI version parsing after recent publication of 16.0.01

Merge pull request nipy#1284 from srothmei/freesurfer_vol2surf_mkmask…

b8f8e88

…_xor FIX: Freesurfer surf2vol - Added XOR to mkmask and source_file

Merge branch 'master' into AvoidRuntimeWarningDivideByZero

e92aaa2

Merge branch 'AvoidRuntimeWarningDivideByZero'

de946d2

Fixed bad conflict resolution

74f8b78

fixed several errors

463708c

fixed several errors

6be212e

make check-before-commit

b73ec6d

enhance circle CI error reporting

360584d

merge oscars fixes + fix the sloppy merge

b0e5e29

further fixes

69d6c78

make FSL course download slightly easier to debug

6ee17d4

fixed mkdir

0e195b5

oesteban and others added 2 commits January 31, 2016 22:22

Merge pull request nipy#1338 from oesteban/fix/ProblemsInMaster

1262955

[FIX] Some problems have sneaked into master

Merge pull request nipy#1339 from chrisfilo/fix/sloppy_merge

c1e811e

Fix/sloppy merge

oesteban added a commit to oesteban/nipype that referenced this pull request Feb 2, 2016

added fix for nipy#1335 (comment)

10476d0

alexsavio added 4 commits February 2, 2016 11:54

enh: add PETPVC wrapper

333122e

Add empty petpvc example files

248b38f

fix: drop example_data from petpvc

dbd86a8

Merge branch 'petpvc' of github.com:alexsavio/nipype into petpvc

a45bd50

alexsavio added 2 commits February 2, 2016 17:43

add petpvc specs file

435004c

fix non-ascii chars in petpvc.py

a5a857f

chrisgorgo merged commit a5a857f into nipy:master Feb 4, 2016

alexsavio mentioned this pull request Mar 11, 2016

PETPVC wrapper #1332

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enh: add PETPVC wrapper #1335

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enh: add PETPVC wrapper #1335

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