Error importing Reorient2std

[piyusharma95]

from nipype import Reorient2Std

ImportError Traceback (most recent call last)
in ()
----> 1 from nipype import Reorient2Std

/Users/doxbin/.virtualenvs/SMH/lib/python2.7/site-packages/nipype/init.py in ()
49
50
---> 51 from .pipeline import Node, MapNode, JoinNode, Workflow
52 from .interfaces import (DataGrabber, DataSink, SelectFiles, IdentityInterface,
53 Rename, Function, Select, Merge)

/Users/doxbin/.virtualenvs/SMH/lib/python2.7/site-packages/nipype/pipeline/init.py in ()
9 absolute_import)
10 docformat = 'restructuredtext'
---> 11 from .engine import Node, MapNode, JoinNode, Workflow

/Users/doxbin/.virtualenvs/SMH/lib/python2.7/site-packages/nipype/pipeline/engine/init.py in ()
10 from future import absolute_import
11 docformat = 'restructuredtext'
---> 12 from .workflows import Workflow
13 from .nodes import Node, MapNode, JoinNode
14 from .utils import generate_expanded_graph

/Users/doxbin/.virtualenvs/SMH/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py in ()
34 from ...utils.functions import (getsource, create_function_from_source)
35
---> 36 from ...interfaces.base import (traits, TraitedSpec, TraitDictObject,
37 TraitListObject)
38 from ...utils.filemanip import save_json, makedirs, to_str

/Users/doxbin/.virtualenvs/SMH/lib/python2.7/site-packages/nipype/interfaces/init.py in ()
12
13 from .io import DataGrabber, DataSink, SelectFiles, BIDSDataGrabber
---> 14 from .utility import IdentityInterface, Rename, Function, Select, Merge

/Users/doxbin/.virtualenvs/SMH/lib/python2.7/site-packages/nipype/interfaces/utility/init.py in ()
8 """
9
---> 10 from .base import (IdentityInterface, Rename, Select, Split, Merge,
11 AssertEqual)
12 from .csv import CSVReader

/Users/doxbin/.virtualenvs/SMH/lib/python2.7/site-packages/nipype/interfaces/utility/base.py in ()
17 import re
18 import numpy as np
---> 19 import nibabel as nb
20
21 from ..base import (traits, TraitedSpec, DynamicTraitedSpec, File, Undefined,

/Users/doxbin/.virtualenvs/SMH/lib/python2.7/site-packages/nibabel/init.py in ()
36 """
37 # module imports
---> 38 from . import analyze as ana
39 from . import spm99analyze as spm99
40 from . import spm2analyze as spm2

ImportError: cannot import name analyze
HOW TO INSTALL "analyze", "spm99analyze", "spm2analyze" libraries?
pip install analyze doesn't work.

[effigies]

analyze, spm99analyze and spm2analyze are modules in the nibabel package. It's odd that you're unable to load these, given that it seems to be installed. Can you try pip uninstall nibabel && pip install nibabel, to make sure that it's installed correctly?

[piyusharma95]

_The issue still remains. I found out that the main issue remains in :

import nipype

I'm getting

anaconda2/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

Exception Traceback (most recent call last)
in ()
----> 1 import nipype

/Users/doxbin/.virtualenvs/test2/lib/python2.7/site-packages/nipype/init.py in ()
49
50
---> 51 from .pipeline import Node, MapNode, JoinNode, Workflow
52 from .interfaces import (DataGrabber, DataSink, SelectFiles, IdentityInterface,
53 Rename, Function, Select, Merge)

/Users/doxbin/.virtualenvs/test2/lib/python2.7/site-packages/nipype/pipeline/init.py in ()
9 absolute_import)
10 docformat = 'restructuredtext'
---> 11 from .engine import Node, MapNode, JoinNode, Workflow

/Users/doxbin/.virtualenvs/test2/lib/python2.7/site-packages/nipype/pipeline/engine/init.py in ()
10 from future import absolute_import
11 docformat = 'restructuredtext'
---> 12 from .workflows import Workflow
13 from .nodes import Node, MapNode, JoinNode
14 from .utils import generate_expanded_graph

/Users/doxbin/.virtualenvs/test2/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py in ()
34 from ...utils.functions import (getsource, create_function_from_source)
35
---> 36 from ...interfaces.base import (traits, TraitedSpec, TraitDictObject,
37 TraitListObject)
38 from ...utils.filemanip import save_json, makedirs, to_str

/Users/doxbin/.virtualenvs/test2/lib/python2.7/site-packages/nipype/interfaces/init.py in ()
12
13 from .io import DataGrabber, DataSink, SelectFiles, BIDSDataGrabber
---> 14 from .utility import IdentityInterface, Rename, Function, Select, Merge

/Users/doxbin/.virtualenvs/test2/lib/python2.7/site-packages/nipype/interfaces/utility/init.py in ()
8 """
9
---> 10 from .base import (IdentityInterface, Rename, Select, Split, Merge,
11 AssertEqual)
12 from .csv import CSVReader

/Users/doxbin/.virtualenvs/test2/lib/python2.7/site-packages/nipype/interfaces/utility/base.py in ()
17 import re
18 import numpy as np
---> 19 import nibabel as nb
20
21 from ..base import (traits, TraitedSpec, DynamicTraitedSpec, File, Undefined,

/Users/doxbin/.virtualenvs/test2/lib/python2.7/site-packages/nibabel/init.pyc in ()
72 # Note test requirement for "mock". Requirement for "nose" tested by numpy.
73 try:
---> 74 import mock
75 except ImportError:
76 def test(*args, **kwargs):

/Users/doxbin/.virtualenvs/test2/lib/python2.7/site-packages/mock/init.py in ()
1 from future import absolute_import
----> 2 import mock.mock as _mock
3 from mock.mock import *
4 all = _mock.all
5 #import mock.mock as _mock

/Users/doxbin/.virtualenvs/test2/lib/python2.7/site-packages/mock/mock.py in ()
69 from pbr.version import VersionInfo
70
---> 71 _v = VersionInfo('mock').semantic_version()
72 version = _v.release_string()
73 version_info = _v.version_tuple()

/Users/doxbin/.virtualenvs/test2/lib/python2.7/site-packages/pbr/version.pyc in semantic_version(self)
459 """Return the SemanticVersion object for this version."""
460 if self._semantic is None:
--> 461 self._semantic = self._get_version_from_pkg_resources()
462 return self._semantic
463

/Users/doxbin/.virtualenvs/test2/lib/python2.7/site-packages/pbr/version.pyc in _get_version_from_pkg_resources(self)
446 # installed into anything. Revert to setup-time logic.
447 from pbr import packaging
--> 448 result_string = packaging.get_version(self.package)
449 return SemanticVersion.from_pip_string(result_string)
450

/Users/doxbin/.virtualenvs/test2/lib/python2.7/site-packages/pbr/packaging.pyc in get_version(package_name, pre_version)
753 " to pbr.version.VersionInfo. Project name {name} was"
754 " given, but was not able to be found.".format(
--> 755 name=package_name))
756
757

Exception: Versioning for this project requires either an sdist tarball, or access to an upstream git repository. It's also possible that there is a mismatch between the package name in setup.cfg and the argument given to pbr.version.VersionInfo. Project name mock was given, but was not able to be found.

[effigies]

You may want to do the same thing for mock.

[piyusharma95]

The error persists.
testing-cabal/mock#383

[effigies]

What version of setuptools are you using?

python -c 'import setuptools; print(setuptools.__version__)'

Edit: Just going by that issue, it may be possible to upgrade setuptools to a more recent version (>=17.1) with pip install --upgrade setuptools and then re-install mock.

[piyusharma95]

Ran the following commands:

python -c 'import setuptools; print(setuptools.version)'
39.0.1
pip uninstall mock
pip uninstall setuptools
pip install --upgrade setuptools
pip install mock
ipython
In [1]: import mock

---

Exception Traceback (most recent call last)
in ()
----> 1 import mock

/Users/doxbin/.virtualenvs/SMH/lib/python2.7/site-packages/mock/init.py in ()
1 from future import absolute_import
----> 2 import mock.mock as _mock
3 from mock.mock import *
4 all = _mock.all
5 #import mock.mock as _mock

/Users/doxbin/.virtualenvs/SMH/lib/python2.7/site-packages/mock/mock.py in ()
69 from pbr.version import VersionInfo
70
---> 71 _v = VersionInfo('mock').semantic_version()
72 version = _v.release_string()
73 version_info = _v.version_tuple()

/Users/doxbin/.virtualenvs/SMH/lib/python2.7/site-packages/pbr/version.pyc in semantic_version(self)
459 """Return the SemanticVersion object for this version."""
460 if self._semantic is None:
--> 461 self._semantic = self._get_version_from_pkg_resources()
462 return self._semantic
463

/Users/doxbin/.virtualenvs/SMH/lib/python2.7/site-packages/pbr/version.pyc in _get_version_from_pkg_resources(self)
446 # installed into anything. Revert to setup-time logic.
447 from pbr import packaging
--> 448 result_string = packaging.get_version(self.package)
449 return SemanticVersion.from_pip_string(result_string)
450

/Users/doxbin/.virtualenvs/SMH/lib/python2.7/site-packages/pbr/packaging.pyc in get_version(package_name, pre_version)
753 " to pbr.version.VersionInfo. Project name {name} was"
754 " given, but was not able to be found.".format(
--> 755 name=package_name))
756
757

Exception: Versioning for this project requires either an sdist tarball, or access to an upstream git repository. It's also possible that there is a mismatch between the package name in setup.cfg and the argument given to pbr.version.VersionInfo. Project name mock was given, but was not able to be found.

Still the problems persists

[effigies]

I might suggest opening an issue at the mock page to see what they recommend.