AttributeError: type object 'spmatrix' has no attribute '__div__'

[gaonkimusc]

Hello, I am running a script that calls on the dipy_slr, dipy_recobundles, and dipy_labelsbundles functions and am not sure why the error below is happening. Do you have any ideas/suggestions? Thank you!

Traceback (most recent call last):
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/bin/dipy_slr", line 8, in
sys.exit(run())
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/workflows/cli.py", line 60, in run
mod, _, _ = optional_package(mod_name)
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/utils/optpkg.py", line 77, in optional_package
pkg = importlib.import_module(name)
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1030, in _gcd_import
File "", line 1007, in _find_and_load
File "", line 986, in _find_and_load_unlocked
File "", line 680, in _load_unlocked
File "", line 850, in exec_module
File "", line 228, in _call_with_frames_removed
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/workflows/align.py", line 7, in
from dipy.align.imaffine import AffineMap
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/align/init.py", line 26, in
from dipy.align._public import (syn_registration, register_dwi_to_template, # noqa
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/align/_public.py", line 19, in
from dipy.align.imaffine import (transform_centers_of_mass,
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/align/imaffine.py", line 51, in
from dipy.core.optimize import Optimizer
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/core/optimize.py", line 11, in
cvxpy, have_cvxpy, _ = optional_package("cvxpy", min_version="1.4.1")
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/utils/optpkg.py", line 77, in optional_package
pkg = importlib.import_module(name)
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/cvxpy/init.py", line 25, in
import cvxpy.interface.scipy_wrapper
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/cvxpy/interface/scipy_wrapper.py", line 36, in
method = getattr(spmatrix, method_name)
AttributeError: type object 'spmatrix' has no attribute 'div'
Traceback (most recent call last):
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/bin/dipy_recobundles", line 8, in
sys.exit(run())
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/workflows/cli.py", line 60, in run
mod, _, _ = optional_package(mod_name)
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/utils/optpkg.py", line 77, in optional_package
pkg = importlib.import_module(name)
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1030, in _gcd_import
File "", line 1007, in _find_and_load
File "", line 986, in _find_and_load_unlocked
File "", line 680, in _load_unlocked
File "", line 850, in exec_module
File "", line 228, in _call_with_frames_removed
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/workflows/segment.py", line 11, in
from dipy.segment.bundles import RecoBundles
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/segment/bundles.py", line 11, in
from dipy.align.streamlinear import (StreamlineLinearRegistration,
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/align/init.py", line 26, in
from dipy.align._public import (syn_registration, register_dwi_to_template, # noqa
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/align/_public.py", line 19, in
from dipy.align.imaffine import (transform_centers_of_mass,
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/align/imaffine.py", line 51, in
from dipy.core.optimize import Optimizer
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/core/optimize.py", line 11, in
cvxpy, have_cvxpy, _ = optional_package("cvxpy", min_version="1.4.1")
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/utils/optpkg.py", line 77, in optional_package
pkg = importlib.import_module(name)
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/cvxpy/init.py", line 25, in
import cvxpy.interface.scipy_wrapper
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/cvxpy/interface/scipy_wrapper.py", line 36, in
method = getattr(spmatrix, method_name)
AttributeError: type object 'spmatrix' has no attribute 'div'
Traceback (most recent call last):
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/bin/dipy_labelsbundles", line 8, in
sys.exit(run())
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/workflows/cli.py", line 60, in run
mod, _, _ = optional_package(mod_name)
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/utils/optpkg.py", line 77, in optional_package
pkg = importlib.import_module(name)
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1030, in _gcd_import
File "", line 1007, in _find_and_load
File "", line 986, in _find_and_load_unlocked
File "", line 680, in _load_unlocked
File "", line 850, in exec_module
File "", line 228, in _call_with_frames_removed
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/workflows/segment.py", line 11, in
from dipy.segment.bundles import RecoBundles
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/segment/bundles.py", line 11, in
from dipy.align.streamlinear import (StreamlineLinearRegistration,
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/align/init.py", line 26, in
from dipy.align._public import (syn_registration, register_dwi_to_template, # noqa
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/align/_public.py", line 19, in
from dipy.align.imaffine import (transform_centers_of_mass,
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/align/imaffine.py", line 51, in
from dipy.core.optimize import Optimizer
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/core/optimize.py", line 11, in
cvxpy, have_cvxpy, _ = optional_package("cvxpy", min_version="1.4.1")
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/dipy/utils/optpkg.py", line 77, in optional_package
pkg = importlib.import_module(name)
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/cvxpy/init.py", line 25, in
import cvxpy.interface.scipy_wrapper
File "/ifs/loni/faculty/thompson/four_d/gaonkim/anaconda3/envs/buan/lib/python3.9/site-packages/cvxpy/interface/scipy_wrapper.py", line 36, in
method = getattr(spmatrix, method_name)
AttributeError: type object 'spmatrix' has no attribute 'div'
mv: cannot stat '/ifs/loni/faculty/thompson/four_d/klawrence/enigma_asd/buan/ABIDEII-BNI_1/subjects/control/29011/rec_bundles/*.npy': No such file or directory

[pjsjongsung]

Hi! Can you try pip install -U scipy ? It seems to be an error between scipy and cvxpy version compatibility that might have been fixed last year. Below is the link I referenced from.
OpenBB-finance/OpenBBTerminal#5208

Also if it does not work, can you tell us your numpy scipy cvxpy dipy versions? (Through pip show package_name)It could help us pinpoint the issue.

[gaonkimusc]

Hello! Thank you for getting back to me. I've tried what you suggested and it leads to the same error message. Is there something else that I can try? I've run this script before in dipy 1.7 and it worked and I'm wondering if my recent update to 1.9 might have caused this error? Best, Gaon *Gaon Kim* (She/Her) Neuroscience Graduate Program Imaging Genetics Center *University of Southern California* gao ***@***.***>***@***.*** ***@***.***> ** While I may have sent this email outside of regular office hours, there is no need to respond outside of your normal working hours. **

…

On Mon, Apr 1, 2024 at 6:04 PM Jong Sung Park ***@***.***> wrote: Hi! Can you try pip install -U scipy ? It seems to be an error in an old scipy version that was fixed last year. Below is the link I referenced from. OpenBB-finance/OpenBBTerminal#5208 <https://urldefense.com/v3/__https://github.com/OpenBB-finance/OpenBBTerminal/issues/5208__;!!LIr3w8kk_Xxm!qfCI7ckRBXF3rLMPAWS7wxYOTJA5r5SszfTsGsFD44JF84pMI1qGKt9ZKJUZBlv8Tpb538sQlvz0dxrq5ncv4-Y$> — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/dipy/dipy/discussions/3166*discussioncomment-8977998__;Iw!!LIr3w8kk_Xxm!qfCI7ckRBXF3rLMPAWS7wxYOTJA5r5SszfTsGsFD44JF84pMI1qGKt9ZKJUZBlv8Tpb538sQlvz0dxrqoj5YJQs$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/BHQNYDIXSMHGWW37YFQUJ3TY3H72HAVCNFSM6AAAAABFSK7FW2VHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4DSNZXHE4TQ__;!!LIr3w8kk_Xxm!qfCI7ckRBXF3rLMPAWS7wxYOTJA5r5SszfTsGsFD44JF84pMI1qGKt9ZKJUZBlv8Tpb538sQlvz0dxrqMJYQ9mg$> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[skoudoro]

Hi @gaonkimusc,

Your recent update to DIPY 1.9 means that you need to update your dependencies also.

I believe updating numpy, scipy, and cvxpy will fix your issue.

pip install -U numpy scipy cvxpy

[gaonkimusc]

Hello Serge, Thank you so much, it worked :) Bramsh said that you would know and you do indeed! Thank you! Best, Gaon

…

On Mon, Apr 1, 2024 at 8:58 PM Serge Koudoro ***@***.***> wrote: Hi @gaonkimusc <https://urldefense.com/v3/__https://github.com/gaonkimusc__;!!LIr3w8kk_Xxm!q1lIsbatp5cbECwk1js1wKjzPrk-ZvvrRefHLTheiTKrWLIKqkDBjUjxw7oTQL_qe_o4G4ASD5Z6-DgT7C-cgxQ$> , Your recent update to DIPY 1.9 means that you need to update your dependencies also. I believe updating numpy, scipy, and cvxpy will fix your issue. pip install -U numpy scipy cvxpy — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/dipy/dipy/discussions/3166*discussioncomment-8978875__;Iw!!LIr3w8kk_Xxm!q1lIsbatp5cbECwk1js1wKjzPrk-ZvvrRefHLTheiTKrWLIKqkDBjUjxw7oTQL_qe_o4G4ASD5Z6-DgTZ0yHFw0$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/BHQNYDNLO53TCJJXKHWHXIDY3IUFDAVCNFSM6AAAAABFSK7FW2VHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4DSNZYHA3TK__;!!LIr3w8kk_Xxm!q1lIsbatp5cbECwk1js1wKjzPrk-ZvvrRefHLTheiTKrWLIKqkDBjUjxw7oTQL_qe_o4G4ASD5Z6-DgT1gkbU2g$> . You are receiving this because you were mentioned.Message ID: ***@***.***>