I am novice in python and Simple_ITK both to process .mha 3D image files. I have two problems:
When ever I install ITK, I always get an error as shown below:
and somehow I install ITK It doesn't work at all having no connectivity with python. And I also tried python-insighttoolkit3 package then it shows and error of
" Can't down load Python 2.8:i386" in Ubuntu software Center. I have tried various methods to install Insight Tool Kit in Ubuntu whatever I found but most of the time I get the same error as shown in picture above.
So can anybody guide me how to install and build ITK so that no error like no module named itk found.
Now another problem is I have a .py file and it has a class in which I have to fed input externally otherwise it will consider as None. SO I tried to call the file as
import /path/to/file/xxx.py
but it gives an Syntax error: invalid syntax
so how to call class from a python file from python Console .
Now, I'm using Ubuntu 15.02. For any missing details please ask.
Thanks.
1- For what I see in the image, I see that you are trying to install ITK instead of SimpleITK. For SimpleITK it is very simple using a linux package installer, like pip or easy-install. in this link you have the instructions to install it correctly. Remember to execute the instructions as super user. Maybe it is the reason of your error ( I can't see the instruction you are writing in the console ).
2- I recommend you to read the Python tutorial for modules The fastest way is to be located first on the directory of your .py file. The sequence would be:
cd /path
import module.py
Related
I'm working on linux ubuntu 20.04. I opened new python project using Pycharm IDE, and I've installed a package called aihwkit, the documentation and the source.
When running the examples given with the source code, which use modules imported from a directory called inference such as example 06_lenet5_hardware_aware.py I'm getting an error:
ModuleNotFoundError: No module named 'aihwkit.inference'
although other folders, in the same directory as inference are imported as well and they work well. I'm trying to import this manually, but not sure how to do it.
This is the hierarchy of the folders: I'm calling inference like this:
from aihwkit.inference import PCMLikeNoiseModel
from the file examples/06_lenet5_hardware_aware.py when the module PCMLikeNoiseModel source code lies in the following path: src/aihwkit/inference/noise/pcm.py
please note that the problem is that the name aihwkit.inference is not found, while other names such as aihwkit.nn do not raise any error, and they reside in similar path to inference.
I'm adding a picture of the hierarchy in case it helps:
how can I import this folder manually?
Thank you
Since you're on Linux, you can try to install your package before importing it with:
sudo apt-get install python-#name_of_your_package
written in your terminal, or you can try to install it with pip
I'm running a code on deep learning, which uses the opencv module, by running python main.py (contains import cv2 statement), but always get the error 'ImportError: dynamic module does not define module export function (PyInit_cv2)'.
I've tried to reinstall my anaconda and create new virtual environments, but all got the same result. This problem really confuses me a lot and I've googled for many related problems, none of them works. I think the problem is something related to the environment and has nothing to do with the code, because I got the same result by simply run import cv2 in python prompt. The more confusing thing is that, even after I remove the opencv module, I also get the same problem, but not a ModuleNotFoundError. Does anyone can give me some advice? Thanks a lot!
I think I found one possible reason of this error.
Recently I was configuring the caffe environment on one server, I downloaded the source code of opencv-2.4.13 and compiled manually, added /usr/local/opencv-2.4.13/build/lib to $PYTHONPATH, and caffe worked well. After that, when I entered one of my virtual environment using conda activate py35, which uses python3.5, tried import cv2 in the python prompt, got the error above.
I'm not sure but I think the cause of the error is opencv-2.4.13 compiles a python2 interface so it can't be imported by python3. Python imports packages by searching the directories listed in sys.path, where $PYTHONPATH is in the second place after the current working directory (This is a great article introduces the mechanism of python finding packages). So when we enter the py35 environment, python will first look for $PYTHONPATH and find the opencv installed on the root directory instead of finding the opencv in the virtual environment using conda install opencv-python.
So there are two solutions of this problem:
Use python2 instead.
Remove /usr/local/opencv-2.4.13/build/lib from $PYTHONPATH.
which all work for me.
Similar post, might help:
ImportError: dynamic module does not define init function (initfizzbuzz)
Could you provide info on how you installed the CV module?
I had the same problem, which was caused by the cv2.so file in /usr/local/lib/python2.7/site-packages/cv2.so. After I deleted the file and use command sudo pip3 install opencv-python, it worked for python3.
I installed meshpy (using python 2.7) following the instructions here on my ubuntu 16.04 LTS and trying to run examples from here after browsing into the directory of meshpy. Part of the example that I'm trying to run is below:
from __future__ import division
from __future__ import absolute_import
import meshpy.triangle as triangle
but I keep getting error No module named meshpy._triangle
Does anyone have a hint of what I might be missing ?
Likely you have created file named meshpy within your python package, which leads to the module shadowing, renaming your file shall fix the problem.
See more by next links:
The name shadowing trap
Python: Problem with local modules shadowing global modules
After an entire day of labor I realized the python packages that I had were not correct and causing conflicts. To begin with here is the link to the installation documentation of meshpy which I followed Here is a pointwise summary of what I realized caused problem
Step 1 says download the file, unzip it using the command given in the doc, and browse to the directory 'MeshPy-XXXXX', where 'XXXXX' refers to the version.
The issue in this step is that a file called CMakeList.txt is missing in this directory and while configuring in step 2 the system complains about the missing file.
The solution is to download the git version instead of the direct download as mentioned in the second part of step1 or manually copy the file CMakeList.txt into the MeshPy-XXXXX directory. I chose the latter solution.
In step 2 asks us to browse to the directory and issue the command ./configure on the terminal. This didn't work for me. The directory contains a script called configure.py . Hence instead I issued python3.5 configure.py
If you issue python configure.py and python calling python2.7 then you should make sure python2.7 has matplotlib, numpy installed as meshpy depends on these packages
The last of step2 where you need to issue command python setup.py install is a tricky part where things went crazy for me. Firstly, I issued python setup.py but what I should have done is issuing python3.5 setup.py (or better creating an alias to python3.5 in bash).
When I pinned down the mistake, I started getting another error both with python2.7 and python3.5, last three lines of which looks like below :
bpl-subset/bpl_subset/boost/python/detail/wrap_python.hpp:50:23: fatal error: pyconfig.h: No such file or directory
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
When I looked up stackoverflow for possible similar errors, I came across this article and used the second solution in the post and installed python2.7-dev/python3.5-dev which solved the problem .
Go to the installation page and click on 'Download MeshPy' link. Click on 'Download Files'. Download the tar file. Unzip it. Then copy the 'meshpy' folder and paste it inside your python lib directory where other packages are stored. Hope it will solve the problem.
I'm currently having a lot of trouble getting Wand, the python binding of Image Magick, to work. I have followed all of the installation instructions given here:
http://docs.wand-py.org/en/0.4.3/guide/install.html#install-imagemagick-on-windows
For the ImageMagick verison: ImageMagick-6.9.6-Q16
I have added to my variable environment the variable MAGICK_HOME with path:
"C:\Program Files\ImageMagick-6.9.6-Q16"
I have done a great deal of reading on related posts in stackoverflow, and the consensus seems to be that Wand only works for versions below 7. Also, the bit size of the Python interpreter should be the same as the ImageMagick file. I have taken both of these into account. Nonetheless, I still get the following error when I type import wand into my python interpreter:
ImportError: No module named 'Wand'
I have just installed OpenCV on my Windows 7 machine. As a result, I get a new directory:
C:\OpenCV2.2\Python2.7\Lib\site-packages
In this directory, I have two files: cv.lib and cv.pyd.
Then I try to use the opencv from Python. I do the following:
import sys
sys.path.append('C:\OpenCV2.2\Python2.7\Lib\site-packages')
import cv
As a result I get the following error message:
File "<stdin>", line 1, in <module>
ImportError: DLL load failed: The specified module could not be found.
What am I doing wrong?
ADDED
As it was recommended here, I have copied content of C:\OpenCV2.0\Python2.6\Lib\site-packages to the C:\Python26\Lib\site-packages. It did not help.
ADDED 2
My environment variables have the following values:
Path=C:\Program Files\MiKTex\miktex\bin;C:\OpenCV2.2\bin;C:\Python26;
PYTHONPATH=C:\OpenCV2.2\Python2.7\Lib\site-packages
Do I need to change something? Do I need to add something?
ADDED 3
I think my question is general: How to use a library? Probably I need to find a *.ddl file somewhere? Then I need to use the name of the directory containing this file as a value to some environment variables? Or maybe I need to use sys.addpath? I also need to know how the way to call the library is related to the name of the file that contains the library.
ADDED 4
It is interesting that when I type import cv, I get:
ImportError: DLL load failed: The specified module could not be found.
But when I type import opencv I get:
ImportError: No module named opencv
ADDED 5
It has been suggested that I usthe e inconsistent version of python. In more details, OpenCV tries to use Python2.7 and I had Python2.6. So, I have installed Python 2.7. It makes difference. Now I do not have the old error message, but I have a new one:
ImportError: numpy.core.multiarray failed to import
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: numpy.core.multiarray failed to import
ADDED 6
I have managed to resolve the problem by installing numpy. It took some time because I did not realized that there are different numpy installer corresponding to different versions of Python. Some details can be found in my answer to my own question (see bellow).
The problem was resolved. The following steps has been done:
A new version of python (version 2.7) has been installed.
After that I still was unable to run OpenCV because I had some problems with the numpy library.
I tired to install numpy but the installer did not see my new version of the Python.
I deleted the old version of Python as well as links to the old version in the Path system vatriable.
After that numpy installer was not able to finish the installation.
I have realized that I need to run another numpy installer that is associated with the Python 2.7. It can be found here.
Finally everything worked. I was able to "import cv".
I suspect you have the same problem I've run into. If you have a 64-bit version of Python, it cannot load 32-bit DLLs. OpenCV currently only ships 32-bit binaries. If you want 64-bit .pyd and .dll files, you have to compile them yourself. There are some instructions on the OpenCV Wiki, but it's not for the faint of heart. Expect to have a substantial time investment.
The easiest solution is to:
Uninstall 64-bit Python
Install a 32-bit distribution.
The PythonXY distribution includes pyopencv -- a good set of OpenCV hooks. The only limitation is that it's 32-bit, so don't make plans to process gigapixel astronomy data with it! ;)
If you must have the 64-bit version, follow these instructions to get it OpenCV to compile with Visual Studio 2010. There's a discussion on stackoverflow that describes building 64-bit apps with VC Express.
EDIT: OpenCV now ships with 64-bit Python binaries. The .dll files need to go somewhere in your path (I put them in the scripts folder), and the .pyd files go in your site-packages directory.
I had trouble interfacing OpenCV with Python, and I was looking all over the place for help. Here's what worked for me. I basically followed this post: http://opencvpython.blogspot.com/2012/05/install-opencv-in-windows-for-python.html. After downloading and extracting OpenCV 2.4.6, you basically get a folder called "opencv" with a bunch of stuff in it. Navigate to build->python->2.7. Inside, there is only one file called "cv2.pyd". I copied this file and pasted it in "python-2.7.5\Lib\site-packages". I'm actually using the Spyder IDE, and it works fine. In the python interpreter, typing in "import cv" worked for me.
Maybe you should edit your environment variable
right click on the "My Computer" or something like this, click on properties.
In the properties window click on the Advanced tab.
Then, the environment variables button.
Change the path.