installation problem

[zeffiro]

When attempting to install dMRI-AMICO in Ubuntu I get an error:

tz@ALPINE:/mnt/e$ pip install dmri-amico
Defaulting to user installation because normal site-packages is not writeable
Collecting dmri-amico
Using cached dmri_amico-1.5.4-py3-none-any.whl
Collecting dipy>=1.0 (from dmri-amico)
Using cached dipy-1.7.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.7 MB)
Collecting joblib>=1.0.1 (from dmri-amico)
Using cached joblib-1.2.0-py3-none-any.whl (297 kB)
Requirement already satisfied: numpy>=1.12 in /home/tz/.local/lib/python3.10/site-packages (from dmri-amico) (1.24.3)
Collecting packaging (from dmri-amico)
Using cached packaging-23.1-py3-none-any.whl (48 kB)
Requirement already satisfied: scipy>=1.0 in /home/tz/.local/lib/python3.10/site-packages (from dmri-amico) (1.10.1)
Collecting spams>=2.6.5.2 (from dmri-amico)
Using cached spams-2.6.5.4.tar.gz (2.0 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting tqdm>=4.56.0 (from dmri-amico)
Using cached tqdm-4.65.0-py3-none-any.whl (77 kB)
Collecting nibabel>=3.0.0 (from dipy>=1.0->dmri-amico)
Using cached nibabel-5.1.0-py3-none-any.whl (3.3 MB)
Collecting h5py>=2.8.0 (from dipy>=1.0->dmri-amico)
Using cached h5py-3.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB)
Collecting Pillow>=6.0 (from spams>=2.6.5.2->dmri-amico)
Using cached Pillow-9.5.0-cp310-cp310-manylinux_2_28_x86_64.whl (3.4 MB)
Building wheels for collected packages: spams
Building wheel for spams (pyproject.toml) ... error
error: subprocess-exited-with-error

× Building wheel for spams (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [214 lines of output]
running bdist_wheel
running build
running build_py
creating build
.....
Have you seen this before?

[nightwnvol]

Hi @zeffiro,

The problem is related to the installation of the spams package. I would need the full log to catch the error, but usually it fails because the spams package needs a BLAS/LAPACK library installed on your system.

Try running sudo apt install libblas-dev liblapack-dev gfortran, then try reinstalling AMICO.

Let me know if this solve your issue.

[zeffiro]

I started again from a fresh Ubuntu-22.04 install in WSL2. I also installed the Visual C++ package. This time I got no error until I started python and tried to import AMICO.

tz@ALPINE:/mnt/e$ sudo apt install libblas-dev liblapack-dev gfortran
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
gfortran is already the newest version (4:11.2.0-1ubuntu1).
libblas-dev is already the newest version (3.10.0-2ubuntu1).
liblapack-dev is already the newest version (3.10.0-2ubuntu1).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
tz@ALPINE:/mnt/e$ pip install dmri-amico
Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: dmri-amico in /usr/local/lib/python3.10/dist-packages (1.5.4)
Requirement already satisfied: dipy>=1.0 in /home/tz/.local/lib/python3.10/site-packages (from dmri-amico) (1.7.0)
Requirement already satisfied: joblib>=1.0.1 in /home/tz/.local/lib/python3.10/site-packages (from dmri-amico) (1.2.0)
Requirement already satisfied: numpy>=1.12 in /home/tz/.local/lib/python3.10/site-packages (from dmri-amico) (1.24.3)
Requirement already satisfied: packaging in /home/tz/.local/lib/python3.10/site-packages (from dmri-amico) (23.1)
Requirement already satisfied: scipy>=1.0 in /home/tz/.local/lib/python3.10/site-packages (from dmri-amico) (1.10.1)
Requirement already satisfied: spams>=2.6.5.2 in /home/tz/.local/lib/python3.10/site-packages (from dmri-amico) (2.6.5.4)
Requirement already satisfied: tqdm>=4.56.0 in /home/tz/.local/lib/python3.10/site-packages (from dmri-amico) (4.65.0)
Requirement already satisfied: nibabel>=3.0.0 in /home/tz/.local/lib/python3.10/site-packages (from dipy>=1.0->dmri-amico) (5.1.0)
Requirement already satisfied: h5py>=2.8.0 in /home/tz/.local/lib/python3.10/site-packages (from dipy>=1.0->dmri-amico) (3.8.0)
Requirement already satisfied: Pillow>=6.0 in /home/tz/.local/lib/python3.10/site-packages (from spams>=2.6.5.2->dmri-amico) (9.5.0)
tz@ALPINE:/mnt/e$ python3 amico
python3: can't open file '/mnt/e/amico': [Errno 2] No such file or directory
tz@ALPINE:/mnt/e$ python3
Python 3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

import amico
Traceback (most recent call last):
File "", line 1, in
File "/usr/local/lib/python3.10/dist-packages/amico/init.py", line 3, in
from .core import Evaluation, setup
File "/usr/local/lib/python3.10/dist-packages/amico/core.py", line 16, in
import amico.models
File "/usr/local/lib/python3.10/dist-packages/amico/models.py", line 20, in
import spams
File "/home/tz/.local/lib/python3.10/site-packages/spams/init.py", line 6, in
from .spams import *
File "/home/tz/.local/lib/python3.10/site-packages/spams/spams.py", line 6, in
import spams_wrap
File "/home/tz/.local/lib/python3.10/site-packages/spams_wrap/init.py", line 6, in
from .spams_wrap import *
File "/home/tz/.local/lib/python3.10/site-packages/spams_wrap/spams_wrap.py", line 193, in
_spams_wrap.L1COEFFS_swigconstant(_spams_wrap)
AttributeError: module '_spams_wrap' has no attribute 'L1COEFFS_swigconstant'

[nightwnvol]

@zeffiro, this time it seems that the spams package has some problems (although the installation succeeded without errors).

I would suggest you to reinstall AMICO forcing the reinstallation of all its requirements:
pip install dmri-amico --no-cache-dir --force-reinstall

[zeffiro]

I tried that, but got the same problem when I tried to import AMICO. Any other suggestions?

tz@ALPINE:/mnt/e$ pip install dmri-amico --no-cache-dir --force-reinstall
Defaulting to user installation because normal site-packages is not writeable
Collecting dmri-amico
Downloading dmri-amico-1.5.4.tar.gz (3.0 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.0/3.0 MB 19.4 MB/s eta 0:00:00
Preparing metadata (setup.py) ... done
Collecting packaging (from dmri-amico)
Downloading packaging-23.1-py3-none-any.whl (48 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.9/48.9 kB 725.9 MB/s eta 0:00:00
Collecting numpy>=1.12 (from dmri-amico)
Downloading numpy-1.24.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.3/17.3 MB 89.9 MB/s eta 0:00:00
Collecting scipy>=1.0 (from dmri-amico)
Downloading scipy-1.10.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.4 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 34.4/34.4 MB 61.2 MB/s eta 0:00:00
Collecting dipy>=1.0 (from dmri-amico)
Downloading dipy-1.7.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.7 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.7/8.7 MB 63.1 MB/s eta 0:00:00
Collecting spams>=2.6.5.2 (from dmri-amico)
Downloading spams-2.6.5.4.tar.gz (2.0 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 68.0 MB/s eta 0:00:00
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting tqdm>=4.56.0 (from dmri-amico)
Downloading tqdm-4.65.0-py3-none-any.whl (77 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.1/77.1 kB 744.4 MB/s eta 0:00:00
Collecting joblib>=1.0.1 (from dmri-amico)
Downloading joblib-1.2.0-py3-none-any.whl (297 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 298.0/298.0 kB 197.7 MB/s eta 0:00:00
Collecting nibabel>=3.0.0 (from dipy>=1.0->dmri-amico)
Downloading nibabel-5.1.0-py3-none-any.whl (3.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 86.8 MB/s eta 0:00:00
Collecting h5py>=2.8.0 (from dipy>=1.0->dmri-amico)
Downloading h5py-3.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 85.4 MB/s eta 0:00:00
Collecting Pillow>=6.0 (from spams>=2.6.5.2->dmri-amico)
Downloading Pillow-9.5.0-cp310-cp310-manylinux_2_28_x86_64.whl (3.4 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.4/3.4 MB 88.2 MB/s eta 0:00:00
Building wheels for collected packages: dmri-amico, spams
Building wheel for dmri-amico (setup.py) ... done
Created wheel for dmri-amico: filename=dmri_amico-1.5.4-py3-none-any.whl size=3032985 sha256=8e5cf0b5085769a93b03fd0832399a87b8abb0e282869f95e926a650871d9a6b
Stored in directory: /tmp/pip-ephem-wheel-cache-b7428whp/wheels/d8/ba/fb/d28ad0beb0bcfa570169a7e871483a8d70d8c991d29ba35d69
Building wheel for spams (pyproject.toml) ... done
Created wheel for spams: filename=spams-2.6.5.4-cp310-cp310-linux_x86_64.whl size=3931429 sha256=80f90066eb7161d4aedb1b649bc5fe8c6b15b1a09eff279491f244b3de013b21
Stored in directory: /tmp/pip-ephem-wheel-cache-b7428whp/wheels/67/9d/1f/60a6c60785b07ad4f087297f04b723e665a97afcd5112ffb06
Successfully built dmri-amico spams
Installing collected packages: tqdm, Pillow, packaging, numpy, joblib, scipy, nibabel, h5py, spams, dipy, dmri-amico
Attempting uninstall: tqdm
Found existing installation: tqdm 4.65.0
Uninstalling tqdm-4.65.0:
Successfully uninstalled tqdm-4.65.0
Attempting uninstall: Pillow
Found existing installation: Pillow 9.5.0
Uninstalling Pillow-9.5.0:
Successfully uninstalled Pillow-9.5.0
Attempting uninstall: packaging
Found existing installation: packaging 23.1
Uninstalling packaging-23.1:
Successfully uninstalled packaging-23.1
Attempting uninstall: numpy
Found existing installation: numpy 1.24.3
Uninstalling numpy-1.24.3:
Successfully uninstalled numpy-1.24.3
Attempting uninstall: joblib
Found existing installation: joblib 1.2.0
Uninstalling joblib-1.2.0:
Successfully uninstalled joblib-1.2.0
Attempting uninstall: scipy
Found existing installation: scipy 1.10.1
Uninstalling scipy-1.10.1:
Successfully uninstalled scipy-1.10.1
Attempting uninstall: nibabel
Found existing installation: nibabel 5.1.0
Uninstalling nibabel-5.1.0:
Successfully uninstalled nibabel-5.1.0
Attempting uninstall: h5py
Found existing installation: h5py 3.8.0
Uninstalling h5py-3.8.0:
Successfully uninstalled h5py-3.8.0
Attempting uninstall: spams
Found existing installation: spams 2.6.5.4
Uninstalling spams-2.6.5.4:
Successfully uninstalled spams-2.6.5.4
Attempting uninstall: dipy
Found existing installation: dipy 1.7.0
Uninstalling dipy-1.7.0:
Successfully uninstalled dipy-1.7.0
Successfully installed Pillow-9.5.0 dipy-1.7.0 dmri-amico-1.5.4 h5py-3.8.0 joblib-1.2.0 nibabel-5.1.0 numpy-1.24.3 packaging-23.1 scipy-1.10.1 spams-2.6.5.4 tqdm-4.65.0
tz@ALPINE:/mnt/e$ python3
Python 3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

import amico
Traceback (most recent call last):
File "", line 1, in
File "/home/tz/.local/lib/python3.10/site-packages/amico/init.py", line 3, in
from .core import Evaluation, setup
File "/home/tz/.local/lib/python3.10/site-packages/amico/core.py", line 16, in
import amico.models
File "/home/tz/.local/lib/python3.10/site-packages/amico/models.py", line 20, in
import spams
File "/home/tz/.local/lib/python3.10/site-packages/spams/init.py", line 6, in
from .spams import *
File "/home/tz/.local/lib/python3.10/site-packages/spams/spams.py", line 6, in
import spams_wrap
File "/home/tz/.local/lib/python3.10/site-packages/spams_wrap/init.py", line 6, in
from .spams_wrap import *
File "/home/tz/.local/lib/python3.10/site-packages/spams_wrap/spams_wrap.py", line 193, in
_spams_wrap.L1COEFFS_swigconstant(_spams_wrap)
AttributeError: module '_spams_wrap' has no attribute 'L1COEFFS_swigconstant'

For the moment I have the older MATLAB version running smoothly, but I would like to transition to the python version if possible. Thanks for the help..

[nightwnvol]

Have you tried installing it in a virtual environment?

Try the following steps:

• create a clean environment: python -m venv amico-env
• activate the environment: source amico-env/bin/activate
• install AMICO: pip install dmri-amico --no-cache-dir --force-reinstall

[daducci]

I suspect 'pip' and 'python3' do not point to the same Python installation, i.e. 'pip' actually installing all packages in a different Python installation than the one pointed by the 'python3' command.

[nightwnvol]

Hi @zeffiro,

We've just released AMICO v2.0 and have published pre-built wheels on PyPI for both Windows and Linux systems. You should no longer encounter installation problems.

To install the new version, simply run pip install --upgrade dmri-amico.