ImportError Traceback (most recent call last)
Input In [1], in <cell line: 1>()
----> 1 from dipy.data import fetch_sherbrooke_3shell
2 fetch_sherbrooke_3shell()
File ~\anaconda3\envs\test\lib\site-packages\dipy\data__init__.py:14, in <module>
12 import gzip
13 import numpy as np
---> 14 from dipy.core.gradients import GradientTable, gradient_table
15 from dipy.core.sphere import Sphere, HemiSphere
16 from dipy.data.fetcher import (get_fnames,
17 fetch_scil_b0,
18 read_scil_b0,
(...)
53 fetch_bundle_fa_hcp,
54 fetch_gold_standard_io)
File ~\anaconda3\envs\test\lib\site-packages\dipy\core\gradients.py:7, in <module>
4 import numpy as np
5 from scipy.linalg import inv, polar
----> 7 from dipy.io import gradients as io
8 from dipy.core.onetime import auto_attr
9 from dipy.core.geometry import vector_norm, vec2vec_rotmat
File ~\anaconda3\envs\test\lib\site-packages\dipy\io__init__.py:4, in <module>
1 # init for io routines
3 from .gradients import read_bvals_bvecs
----> 4 from .dpy import Dpy
5 from .bvectxt import (read_bvec_file, ornt_mapping, reorient_vectors,
6 reorient_on_axis, orientation_from_string,
7 orientation_to_string)
8 from .pickles import save_pickle, load_pickle
File ~\anaconda3\envs\test\lib\site-packages\dipy\io\dpy.py:12, in <module>
1 """ A class for handling large tractography datasets.
2
3 It is built using the h5py which in turn implement
(...)
8 .. [1] http://www.hdfgroup.org/HDF5/doc/H5.intro.html
9 """
11 import numpy as np
---> 12 import h5py
14 from nibabel.streamlines import ArraySequence as Streamlines
16 # Make sure not to carry across setup module from * import
File ~\anaconda3\envs\test\lib\site-packages\h5py__init__.py:33, in <module>
30 else:
31 raise
---> 33 from . import version
35 if version.hdf5_version_tuple != version.hdf5_built_version_tuple:
36 _warn(("h5py is running against HDF5 {0} when it was built against {1}, "
37 "this may cause problems").format(
38 '{0}.{1}.{2}'.format(version.hdf5_version_tuple),
39 '{0}.{1}.{2}'.format(version.hdf5_built_version_tuple)
40 ))
File ~\anaconda3\envs\test\lib\site-packages\h5py\version.py:15, in <module>
10 """
11 Versioning module for h5py.
12 """
14 from collections import namedtuple
---> 15 from . import h5 as _h5
16 import sys
17 import numpy
File h5py\h5.pyx:1, in init h5py.h5()
ImportError: DLL load failed while importing defs: The specified procedure could not be found.
Hi, I'm new to DIPY. Using Win11, Python 3.10.3 and trying this command
PS D:> pip install fury -U
Collecting fury
Using cached fury-0.8.0-py3-none-any.whl (349 kB)
Collecting pillow>=5.4.1
Using cached Pillow-9.0.1-cp310-cp310-win_amd64.whl (3.2 MB)
Requirement already satisfied: numpy>=1.7.1 in c:\users\rycki\appdata\local\packages\pythonsoftwarefoundation.python.3.10_qbz5n2kfra8p0\localcache\local-packages\python310\site-packages (from fury) (1.22.3)
Requirement already satisfied: packaging in c:\users\rycki\appdata\local\packages\pythonsoftwarefoundation.python.3.10_qbz5n2kfra8p0\localcache\local-packages\python310\site-packages (from fury) (21.3)
Collecting scipy>=0.9
Using cached scipy-1.8.0-cp310-cp310-win_amd64.whl (37.0 MB)
Collecting fury
Using cached fury-0.7.1-py3-none-any.whl (315 kB)
Using cached fury-0.7.0-py3-none-any.whl (294 kB)
Using cached fury-0.6.1-py3-none-any.whl (282 kB)
Using cached fury-0.6.0-py3-none-any.whl (272 kB)
Using cached fury-0.5.1-py3-none-any.whl (245 kB)
Using cached fury-0.5.0-py3-none-any.whl (177 kB)
Using cached fury-0.4.0-py3-none-any.whl (150 kB)
Using cached fury-0.3.0-py3-none-any.whl (147 kB)
Using cached fury-0.2.0-py3-none-any.whl (140 kB)
Using cached fury-0.1.4-py3-none-any.whl (121 kB)
Using cached fury-0.1.3-py3-none-any.whl (121 kB)
Using cached fury-0.1.2-py3-none-any.whl (121 kB)
Using cached fury-0.1.1-py3-none-any.whl (121 kB)
Using cached fury-0.1.0-py3-none-any.whl (121 kB)
ERROR: Cannot install fury==0.1.0, fury==0.1.1, fury==0.1.2, fury==0.1.3, fury==0.1.4, fury==0.2.0, fury==0.3.0, fury==0.4.0, fury==0.5.0, fury==0.5.1, fury==0.6.0, fury==0.6.1, fury==0.7.0, fury==0.7.1 and fury==0.8.0 because these package versions have conflicting dependencies.
The conflict is caused by:
fury 0.8.0 depends on vtk>=9.1.0
fury 0.7.1 depends on vtk!=9.0.0 and >=8.1.2
fury 0.7.0 depends on vtk!=9.0.0 and >=8.1.2
fury 0.6.1 depends on vtk!=9.0.0 and >=8.1.2
fury 0.6.0 depends on vtk!=9.0.0 and >=8.1.2
fury 0.5.1 depends on vtk>=8.1.0
fury 0.5.0 depends on vtk>=8.1.0
fury 0.4.0 depends on vtk>=8.1.0
fury 0.3.0 depends on vtk>=8.1.0
fury 0.2.0 depends on vtk>=8.1.0
fury 0.1.4 depends on vtk>=8.1.0
fury 0.1.3 depends on vtk>=8.1.0
fury 0.1.2 depends on vtk>=8.1.0
fury 0.1.1 depends on vtk>=8.1.0
fury 0.1.0 depends on vtk>=8.1.0
To fix this you could try to:
ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts
What does this mean, please?
@skoudoro Thanks for adding the RESTORE option for the DTI/DKI CLI. Two questions:
Is --sigma
expecting a singular value or a per volume estimate? In the RESTORE example, this line produces a per-volume estimate: sigma = ne.estimate_sigma(data)
Assuming it's expecting a 1D array rather than a single value, is there a CLI exposed option for estimating sigma in an equivalent way?
--sigma
is expecting a singular floating value ( 1.5267 * std(background_noise) recommended). This value will be apply to all volumes. I can update this option to allow multiple values (1D array). Please create an issue and it will be done before the next release.sigma
to allow auto-estimation
. Please, add it to the same issueHi, I faced some problems when I tried to use dipy recently. I don't know why I cannot run command such as "dipy_info -h". I deleted the old version and reinstalled it many times, but the errors still pop up.
It always shows:
(1) pkg_resources.VersionConflict: (dipy 1.5.0 (/home/adduser/anaconda3/lib/python3.9/site-packages), Requirement.parse('dipy==1.6.0.dev0'))
(2) pkg_resources.DistributionNotFound: The 'dipy==1.6.0.dev0' distribution was not found and is required by the application
Here are the detailed error messages:
/home/adduser/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py:122: PkgResourcesDeprecationWarning: 4.0.0-unsupported is an invalid version and will not be supported in a future release warnings.warn(
Traceback (most recent call last):
File "/home/adduser/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 579, in _build_master
ws.require(requires)
File "/home/adduser/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 897, in require
needed = self.resolve(parse_requirements(requirements))
File "/home/adduser/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 788, in resolve
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.VersionConflict: (dipy 1.5.0 (/home/adduser/anaconda3/lib/python3.9/site-packages), Requirement.parse('dipy==1.6.0.dev0'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/adduser/.local/bin/dipy_info", line 4, in <module>
import('pkg_resources').require('dipy==1.6.0.dev0')
File "/home/adduser/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 3247, in <module>
def _initialize_master_working_set():
File "/home/adduser/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 3221, in _call_aside
f(args, *kwargs)
File "/home/adduser/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 3259, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File "/home/adduser/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 581, in _build_master
return cls._build_from_requirements(requires)
File "/home/adduser/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 594, in _build_from_requirements
dists = ws.resolve(reqs, Environment())
File "/home/adduser/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 783, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'dipy==1.6.0.dev0' distribution was not found and is required by the application
What do these errors mean :(
Hi @Wang-Yu-Sheng, this is clearly an environment issue. You have multiple DIPY installed in different environment and they are conflicting.
please, make sure to remove them all before reinstalling.
which dipy_info
to know where it come from and remove the whole foldera lot of cleaning, and not sure we can help we that