I am working in a jupyter notebook, and used pip to install ANTsPy:
pip install antspyx
However, using the function from_numpy throws an error:
import ants
Im2Use=Im[0,:,:,:]
fixed, moving, mytx=reg(Im2Use, t_rz)
fwdtransforms=mytx['fwdtransforms']
fixed_ants= ants.from_numpy(Im2Use.astype(float))
moving_ants= ants.from_numpy(t_rz.astype(float))
mywarpedimage=ants.apply_transforms( fixed=fixed_ants, moving=moving_ants,transformlist=fwdtransforms)
AttributeError: module 'ants' has no attribute 'from_numpy'
How can I solve this? I've also tried importing ants using import ants.from_numpy, but that did not work.
Can you please specify your IDE+ if you took care of activating the virtualenv?
Anyways here are the steps to make sure that the python module is propoerly installed in your virtual environment :
python3 -m venv env_name : this will create a virtual env in your current path
source env/bin/activate : this will activate your virtual env (if on windows just cd into activate within your env name .\env\Scripts\activate
If your using vscode hit ctrl+shift+p then select interpreter then go to your created env
now we have our virtual environment just hit pip install antspyx then check with pip list and see in your terminal if the package is propoerly installed
If you still have the error restart your IDE
have you tried:
from ants import from_numpy
The issue in this case was scipy versioning. I downgraded from version 1.7.3 to version 1.2.0, which then solved the problem. Why? It's because ants library expects a function called "factorial" in scipy.misc, but version 1.7.3 moved the location of factorial.
Related
i'm working on a classifier that uses CNN and i need to use the keras tuner so i can find the best CNN architecture
i executed this command "pip install keras-tuner" and it was installed successfully
but when i import it "import keras_tuner as kt" and run the python script
No module named 'keras_tuner'
i'm working offline with python 3.7.9,tensorflow 2.0,keras 2.7 in VSCode
can someone help me? i really need to use the tuner
thanks
so i used
pip install keras_tuner
in VSCode and the packge was really installed but in the global site-packages folder and not in venv/lib folder
so all i did is that i went to venv/pyvenv.cfg file in VSCode
and set
include-system-site-packages = true
I had the same issue using PyCharm. When I installed the keras-tuner package in the Anaconda 3 prompt, I got the message that everything is already installed. The problem was, that the keras-tuner was installed in my base environment and not in the environment (virtual) which I use in PyCharm. You simply need to do the following.
check out your environments in the anaconda prompt using: conda env list
you will probably see the * on the base environment
now change to your working environment for example conda activate tf_cpu -> tf_cpu needs to be changed by your envs name (see on your list)
install your package such as pip install keras_tuner
I have downloaded anaconda and always used Jupiter Notebook, and Spyder with no problem. Now I need to run some code on my computer's python shell (I don't know if this is the appropriate name, I am quite new to coding) but when trying to import numpy I get:
ModuleNotFoundError: No module named 'numpy'
I have tried everything whit pip but is not resolving the problem, it actually shows a syntax error. Should I try to uninstall and install everything? I don't really know how to move, thanks a lot in advance.
When you start a new terminal instance the base conda environment is not activated, so when you do python, the interpreter that is called is not Anaconda's Python, it is most likely the system-wide Python installation.
So to access Anaconda's Python from the terminal:
conda activate to activate the base conda environment
which python should show the path to the Anaconda interpreter
python
Interactive shell:
import numpy
Anaconda is a virtual environment for python. It does not install packages globaly. I strongly recomend reading about VENV (virtual enviroment).
You can install does packages globally, by pip:
pip install numpy
or for python3:
pip3 install numpy
I have recently tried to make some realtime plots for my Ml models.
I have installed livelossplot through this command:
pip install livelossplot
But, when trying to import the module in Jupyter, it returns error:
ModuleNotFoundError: No module named 'livelossplot'
Please,
can someone help me?
You can try this
pip install livelossplot==0.1.2
Refer the below link
https://pypi.org/project/livelossplot/0.1.2/
If it doesn't work then you can clone the below repository
https://github.com/stared/livelossplot
Well there are a couple of ways to go about this problem one way is to start anaconda-navigator
left click on the play type button there in the (base)root environment and select open in terminal
and then simply type
pip install livelossplot
One another method is if you have added anaconda path to you PATH variable in linux or environment variable in WINDOWS then you can log into the environment
like
albin#computer:~$ source activate
(base) albin#computer:~$ pip install livelossplot
if you havent added to the PATH or environment variable then you can log into the enviroment by specifying the full path like
albin#computer:~$ source anaconda3/bin/activate
(base) albin#computer:~$ pip install livelossplot
I am currently trying to work basic python - jupyter projects.
I am stuck on following error during matplotlib:
screenshot on jupyter-error
ModuleNotFoundError: No module named 'matplotlib'
I tried to update, reinstall matplotlib aswell in conda and in pip but it still not working.
happy over every constructive feedback
In a Notebook's cell type and execute the code:
import sys
!{sys.executable} -m pip install --user matplotlib
and reload the kernel
(src: http://jakevdp.github.io/blog/2017/12/05/installing-python-packages-from-jupyter/ )
open terminal and change the directory to Scripts folder where python installed. Then type the following command and hit enter
pip install matplotlib
Hope this will solve the issue.
I was facing the exact issue. It turns out that it was using the system Python version despite me having activated my virtual environment.
This is what eventually worked.
If you are using a virtual environment which has a name say myvenv, first activate it using command:
source activate myvenv
Then install module ipykernel using the command:
pip install ipykernel
Finally run (change myvenv in code below to the name of your environment):
ipykernel install --user --name myvenv --display-name "Python (myvenv)"
Now restart the notebook and it should pick up the Python version on your virtual environment.
While #Frederic's top-voted solution is based on JakeVDP's blog post from 2017, it completely neglects the %pip magic command mentioned in the blog post. Since 2017, that has landed in mainline IPython and the easiest way to access the correct pip instance connected to your current IPython kernel and environment from within a Jupyter notebook is to do
%pip install matplotlib
Take a look at the list of currently available magic commands at IPython's docs.
generally speaking you should try to work within python virtual environments. and once you do that, you then need to tell JupyterLab about it. for example:
# create a virtual environment
# use the exact python you want to work with in this step
python3.9 -m venv myvenv
# 'activate' (or 'enter') it
source myvenv/bin/activate
# install the exact stuff you want to use in that environment
pip install matplotlib
# now tell JupyterLabs about the environment
python -m ipykernel install --user --name="myenv" --display-name="My project (myenv)"
# start it up
jupyter notebook mynotebook
# if you now look under 'Kernel->Change kernel', your 'myenv' should be there
# select it (restart kernel etc if needed) and you should be good
The issue with me was that jupyter was taking python3 for me, you can always check the version of python jupyter is running on by looking on the top right corner (attached screenshot).
When I was doing pip install it was installing the dependencies for python 2.7 which is installed on mac by default.
It got solved by doing:
> pip3 install matplotlib
Having the same issue, installing matplotlib before to create the virtualenv solved it for me. Then I created the virtual environment and installed matplotlib on it before to start jupyter notebook.
in jupter notebook type
print(sys.executable)
this gave me the following
/Users/myusername/opt/anaconda3/bin/python
open terminal, go into the folder
/Users/myusername/opt/anaconda3/bin/
type the following:
python3 -m pip install matplotlib
restart jupyter notebook (mine is vs code mac ox)
If module installed an you are still getting this error, you might need to run specific jupyter:
python -m jupyter notebook
and this is also works
sudo jupyter notebook --allow-root
I try to install Theano by Anaconda. It works, but when I enter the python -i, import theano shows No module named 'theano'. Do I need to switch another interpreter of Python, how? Also, for the packages installed by conda, if I don't double install them, can I find in Python? How is Python related to Python by Anaconda? Thanks!!!
I had have a similar issue, trying to install folium. If you are using the Anaconda:
When you install using conda install -c conda-forge folium, the package will be placed in:
./anaconda3/envs/[name env]/lib/python3.7/site-packages/folium
When you install using pip (with a anaconda env activated), pip install folium, the package will be placed in:
./anaconda3/lib/python3.7/site-packages/folium
Python use first the sites-packages as the target directory of manually built python packages. When you build and install python packages from source (using distutils, probably by executing python setup.py install ), you will find the installed modules in site-packages by default.
In this case you have two places: /anaconda3/lib/python3.7/site-packages/ and /anaconda3/envs/[name env]/lib/python3.7/site-packages/.
First the modules will be available as default in /anaconda3/lib/python3.7/site-packages/. Sometimes (and I really don't know why) the modules inside sites-packages conda env are not available to import automatically without export the PATH.
So, to solve this issue, you have 2 options:
Installing using pip install folium and import folium (don't need install by conda install), or
After conda install , run conda init, close the terminal and open a new one. So, try to import again.
Here are some tips about use a pip in a conda-environment.
You can refer to a specific version of python by using the following at the first line of your .py file
This is for python 2.7
#!/usr/bin/env python2.7
This is for python 3
#!/usr/bin/env python3
As other users already pointed out you need to check if your module is included in your sys path. Use code:
import sys
print(sys.path)
If not you can include this in your sys.path by using the command:
sys.path.append('/path/to/the/folder/of/your/module/file')
or place it in default PYTHONPATH itself.
Other great answers:
https://stackoverflow.com/a/19305076/5381704
The problem is that in the code editor you are using, you are running the default interpreter. Based on your code editor, change the python interpreter to the conda interpreter and it will work.
In my case that happened because conda screwed up the environment variables. Instead of using env-specific python and pip, it used the globally installed ones.
Solution:
conda deactivate your-env
conda activate your-env
In my workstation, I was able to solve No module named <module name> error using two different ways.
First method, I solved this temporarily by:
(1) Open a Terminal
(2) $ conda activate <Conda environment name>
(3) $ export PYTHONPATH=/home/<user name>/anaconda3/envs/<Conda environment name>/lib/<Python package version>/site-packages:$PYTHONPATH
It is a temporary solution. Whenever you run your virtual environment, you have to do this.
My runtime environment:
OS: Unbuntu 18.04
Conda version: 4.8.2
Conda-build version: 3.18,11
Python version 3.7.6.final.0
Second method, I removed the
alias python=/usr/bin/python3.6 line in bashrc file.
Somehow this line blocks using Python tools installed in Anaconda Virtual Environment if the Python version in the Virtual Environment is different.