I am trying to run the following example code in EPD 7.3-2 (64-bit) on OS X:
import numpy as np
import matplotlib.mlab as mlab
import matplotlib.pyplot as plt
mu, sigma = 100, 15
x = mu + sigma*np.random.randn(10000)
n, bins, patches = plt.hist(x, 50, normed=1, alpha=0.75)
y = mlab.normpdf( bins, mu, sigma)
l = plt.plot(bins, y, 'r--', linewidth=1)
plt.xlabel('Smarts')
plt.ylabel('Probability')
plt.title(r'$\mathrm{Histogram\ of\ IQ:}\ \mu=100,\ \sigma=15$')
plt.axis([40, 160, 0, 0.03])
plt.grid(True)
plt.show()
The last line gives me an error:
RuntimeError: Could not open facefile /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf; Cannot_Open_Resource
There are two things I don't understand. First, that Vera.ttf file IS there in the specified location, so I don't know why Python can't open it.
Second, I don't understand why it's looking there at all. My EPD matplotlib installation is at /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib. Why wouldn't it be looking there for Vera.ttf? It does exist in /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf. And there are no 2.6 directories listed in sys.path, only the expected EPD 2.7 directories are listed there. Finally, my PATH environment variable is /Library/Frameworks/EPD64.framework/Versions/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin.
This sounds like an issue with Matplotlib's font caching. Could you try the suggestions in this related post: https://stackoverflow.com/a/4956933/260303
In short, just delete the font cache in the config directory: rm ~/.matplotlib/fontList.cache.
Related
I'm a beginner at OpenCV, and trying to run an open-source program.
http://asrl.utias.utoronto.ca/code/gpusurf/index.html
I currently have the Computer Vision Toolbox OpenCV Interface 20.1.0 installed and Computer Vision Toolbox 9.2.
I cannot run this simple open-source feature matching algorithm without encountering errors.
import cv2
import matplotlib.pyplot as plt
%matplotlib inline
% read images
img1 = cv2.imread('[INSERT PATH #1]');
img2 = cv2.imread('[INSERT PATH #2]');
img1 = cv2.cvtColor(img1, cv2.COLOR_BGR2GRAY);
img2 = cv2.cvtColor(img2, cv2.COLOR_BGR2GRAY);
%sift
sift = cv2.xfeatures2d.SIFT_create();
keypoints_1, descriptors_1 = sift.detectAndCompute(img1,None);
keypoints_2, descriptors_2 = sift.detectAndCompute(img2,None);
len(keypoints_1), len(keypoints_2)
The following message is returned:
Error: File: Keypoints.m Line: 1 Column: 8
The import statement 'import cv2' cannot be found or cannot be imported. Imported names must end with '.*' or be
fully qualified.
However, when I remove Line 1, I instead get the following error.
Error: File: Keypoints.m Line: 2 Column: 8
The import statement 'import matplotlib.pyplot' cannot be found or cannot be imported. Imported names must end
with '.*' or be fully qualified.
Finally, following the error message only results in a sequence of further errors from the cv2 library. Any ideas?
That's because the code you've used isn't MATLAB code, it's python code.
As per the website you've linked:
From within Matlab
The parallel implementation coded in Matlab can be run by using the surf_find_keypoints() function. The output keypoints can be sorted by strength using surf_best_n_keypoints(), and plotted using surf_plot_keypoints().
Check that you've downloaded the correct files and try again.
Furthermore, the Matlab OpenCV Interface is designed to integrate C++ OpenCV code, not python. Documentations here.
Yes, it is correct that this is Python code. I would recommend checking your dependencies/libraries. The PyCharm IDE is what I personally use since it takes care of all the libraries easily.
If you do end up trying out PyCharm click on the red icon when hovering on CV2. It’ll then give you a prompt to download the library.
Edit:
Using Python some setup can be done. Using pip:
Install opencv-python
pip install opencv-python
Install opencv-contrib-python
pip install opencv-contrib-python
Unfortunately, there is some issue with the sift feature since by default it is excluded from newer free versions of OpenCV.
sift = cv2.xfeatures2d.SIFT_create() not working even though have contrib installed
import cv2
Image_1 = cv2.imread("Image_1.png", cv2.IMREAD_COLOR)
Image_2 = cv2.imread("Image_2.jpg", cv2.IMREAD_COLOR)
Image_1 = cv2.cvtColor(Image_1, cv2.COLOR_BGR2GRAY)
Image_2 = cv2.cvtColor(Image_2, cv2.COLOR_BGR2GRAY)
sift = cv2.SIFT_create()
keypoints_1, descriptors_1 = sift.detectAndCompute(Image_1,None)
keypoints_2, descriptors_2 = sift.detectAndCompute(Image_2,None)
len(keypoints_1), len(keypoints_2)
The error I received:
"/Users/michael/Documents/PYTHON/Test Folder/venv/bin/python" "/Users/michael/Documents/PYTHON/Test Folder/Testing.py"
Traceback (most recent call last):
File "/Users/michael/Documents/PYTHON/Test Folder/Testing.py", line 9, in <module>
sift = cv2.SIFT_create()
AttributeError: module 'cv2.cv2' has no attribute 'SIFT_create'
Process finished with exit code 1
I want to execute a Python script from Matlab (on a Windows 7 machine). The libraries necessary are installed in an Anaconda virtual environment. When running the script from command line, it runs flawlessly.
When calling the script from Matlab as follows:
[status, commandOut] = system('C:/Users/user/AppData/Local/Continuum/anaconda3/envs/tf/python.exe test.py');
or with shell commands, I get an Import Error:
commandOut =
'Traceback (most recent call last):
File "C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\lib\site-packages\numpy\core\__init__.py", line 16, in <module>
from . import multiarray
ImportError: DLL load failed: The specified path is invalid.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "test.py", line 2, in <module>
import numpy as np
File "C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\lib\site-packages\numpy\__init__.py", line 142, in <module>
from . import add_newdocs
File "C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\lib\site-packages\numpy\add_newdocs.py", line 13, in <module>
from numpy.lib import add_newdoc
File "C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\lib\site-packages\numpy\lib\__init__.py", line 8, in <module>
from .type_check import *
File "C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\lib\site-packages\numpy\lib\type_check.py", line 11, in <module>
import numpy.core.numeric as _nx
File "C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\lib\site-packages\numpy\core\__init__.py", line 26, in <module>
raise ImportError(msg)
ImportError:
Importing the multiarray numpy extension module failed. Most
likely you are trying to import a failed build of numpy.
If you're working with a numpy git repo, try `git clean -xdf` (removes all
files not under version control). Otherwise reinstall numpy.
Original error was: DLL load failed: The specified path is invalid.
I already changed the default Matlab Python version to the Anaconda env, but no change:
version: '3.5'
executable: 'C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\python.exe'
library: 'C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\python35.dll'
home: 'C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf'
isloaded: 1
Just running my test script without importing numpy works. Reloading numpy (py.importlib.import_module('numpy');) didn't work but threw the same error as before.
Does anyone have an idea how to fix this?
So after corresponding with Matlab support I found out that Matlab depends on the path environment (paths which are deliberately not set when using a virtual environment) and therefore numpy fails to find the necessary paths when called from within Matlab (even if the call contains the path to the virtual environment).
The solution is either to call Matlab from within the virtual environment (via command line) or add the missing paths manually in the path environment.
Maybe this information can help someone else.
First Method
You can change the python interpreter with:
pyversion("/home/nibalysc/Programs/anaconda3/bin/python");
And check it with:
pyversion();
You could also do this in a
startup.m
file in your project folder and every time you start MATLAB from this folder the python interpreter will be changed automatically.
Now you can try to use:
py.importlib.import_module('numpy');
Read up the documentation on how to use the integrated python in MATLAB:
Call user defined custom module
Call modified python module
Alternative Method
Alternative method would be to create a
matlab_shell.sh
file with following content, this is basically the appended code from .bashrc when anaconda is installed and asks you if the installer should modify the .bashrc file:
#!/bin/bash
__conda_setup="$(CONDA_REPORT_ERRORS=false '$HOME/path/to/anaconda3/bin/conda' shell.bash hook 2> /dev/null)"
if [ $? -eq 0 ]; then
\eval "$__conda_setup"
else
if [ -f "$HOME/path/to/anaconda3/etc/profile.d/conda.sh" ]; then
CONDA_CHANGEPS1=false conda activate base
else
\export PATH="$HOME/path/to/anaconda3/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda init <<<
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('$HOME/path/to/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "$HOME/path/to/anaconda3/etc/profile.d/conda.sh" ]; then
. "$HOME/path/to/anaconda3/etc/profile.d/conda.sh"
else
export PATH="$HOME/path/to/anaconda3/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda initialize <<<
conda activate base
eval $2
Then you need to set the MATLAB_SHELL environment variable either before running MATLAB or in MATLAB itself. The best thing in my opinion would be to do it also in the startup.m file like that:
setenv("MATLAB_SHELL", "/path/to/matlab_shell.sh");
Afterwards you can use the system(...) function to run conda python with all your modules installed like that...
String notation:
system("python -c ""python code goes here"");
Char notation:
system('python -c "python code goes here"');
Hope this helps!
Firstly, if you execute your Python script like a regular system command ([status, commandOut] = system('...python.exe test.py'))
the pyversion (and pyenv, since R2019b) got no effect at all. It only matters if you utilize the py. integration, as in the code below (and, in most cases, this is a way better approach).
Currently (I use R2019b update 5) there's a number of pitfalls, that might cause issues similar to yours. I'd recommend to start from the following:
Create a new clean conda environment:
conda create -n test_py36 python=3.6 numpy
Create the following dummy demo1.py:
def dummy_py_method(x):
return x+1
Create the following run_py_code.m:
function run_py_code()
% explicit module import sometimes show more detailed error messages
py.importlib.import_module('numpy');
% to reloads if there would be any changes:
pymodule = py.importlib.import_module('demo1');
py.importlib.reload(pymodule);
% passing data back and forth
x = rand([3 3]);
x_np = py.numpy.array(x);
y_np=pymodule.dummy_py_method(x_np);
y = double(y_np);
disp(y-x);
Create the following before_first_run.m:
setenv('PYTHONUNBUFFERED','1');
setenv('path',['C:\Users\username\Anaconda3\envs\test_py36\Library\bin;'...
getenv('path')]);
pe=pyenv('Version','C:\users\username\Anaconda3\envs\test_py36\pythonw.exe',...
'ExecutionMode','InProcess'...
);
% add "demo1.py" to path
py_file_path = 'W:\tests\Matlab\python_demos\call_pycode\pycode';
if count(py.sys.path,py_file_path) == 0
insert(py.sys.path,int32(0),py_file_path);
end
Run the before_first_run.m first and run the run_py_code.m next.
Notes:
As already mentioned in this answer, one key point is to add the folder, containing the necessary dll files to the %PATH%, before starting python. This could be achieved with setenv from withing Matlab. Usually, the Library\bin is what should be added.
It might be a good idea to try clean officially-supported CPython distribution (e.g. CPython 3.6.8 ). Only install numpy (python -m pip install numpy). To my experience, the setenv is not necessary in this case.
For me, OutOfProcess mode proved to be buggy. Thus, I'd recommend to explicitly setting InProcess mode (for versions before R2019b, the OutOfProcess option is not present, as well as pyenv).
Do not concatenate the two .m files above into one - the py.importlib statements seem to be pre-executed and thus conflict with pyenv.
I have two problem in ipython juypter
1) I want ipython to print all the output without without typing print. Ipython usually prints only the last result
2) I am using python interface of Madagascar package , ( geophysical software) but when I use it in ipython notebook I don't any output.
import m8r
import urllib
#Retrieve
m8r.Fetch('french','french.asc')
fren='french.asc'
french=m8r.dd(form='native').transp().scale(dscale=2)[fren]
french.grey(color='j',allpos='y',bias=1000,scalebar='n',barlabel='Depth',barunit='m',screenratio=1,title='French model').image()
nx = 161
dx = 51.325
nz = 401
dz = 10.265
nxx= 10*(nx-1)+1
dxx= dx/10
dscal = 10/dx
refl=m8r.window(n1=1,f1=30).remap1(n1=nxx,o1=0,d1=dxx)[french]
rdip=m8r.deriv(none="0").scale(dscale=dscal)[refl]
slice =m8r.window(n1=1,f1=30).remap1(n1=nx,o1=0,d1=dx).unif2(n1=nz,d1=dz,v00='1,2')[french]
slice.grey(color='j',allpos='y',bias=1,title='2-D slice',label1='Depth',unit1='m',screenratio=0.5,screenht=6).image()
this code works in sage notebook. when I run it in sage I get graphs but this does not happed in ipython notebook
OS : Ubuntu 14.04LTS
Language : Python Anaconda 2.7 (keras, theano)
GPU : GTX980Ti
CUDA : CUDA 7.5
I wanna run keras python code on IPython Notebook by using my GPU(GTX980Ti)
But I can't find it.
I want to test below code. When I run it on to Ubuntu terminal,
I command as below (It uses GPU well. It doesn't have any problem)
First I set the path like below
export PATH=/usr/local/cuda/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
Second I run the code as below
THEANO_FLAGS='floatX=float32,device=gpu0,nvcc.fastmath=True' python myscript.py
And it runs well.
But when i run the code on pycharm(python IDE) or
When I run it on Ipython Notebook, It doesn't use gpu.
It only uses CPU
myscript.py code is as below.
from theano import function, config, shared, sandbox
import theano.tensor as T
import numpy
import time
vlen = 10 * 30 * 768 # 10 x #cores x # threads per core
iters = 1000
rng = numpy.random.RandomState(22)
x = shared(numpy.asarray(rng.rand(vlen), config.floatX))
f = function([], T.exp(x))
print(f.maker.fgraph.toposort())
t0 = time.time()
for i in xrange(iters):
r = f()
t1 = time.time()
print("Looping %d times took %f seconds" % (iters, t1 - t0))
print("Result is %s" % (r,))
if numpy.any([isinstance(x.op, T.Elemwise) for x in f.maker.fgraph.toposort()]):
print('Used the cpu')
else:
print('Used the gpu')
To solve it, I force the code use gpu as below
(Insert two lines more on myscript.py)
import theano.sandbox.cuda
theano.sandbox.cuda.use("gpu0")
Then It generate the error like below
ERROR (theano.sandbox.cuda): nvcc compiler not found on $PATH. Check your nvcc installation and try again.
how to do it??? I spent two days..
And I surely did the way of using '.theanorc' file at home directory.
I'm using theano on an ipython notebook making use of my system's GPU. This configuration seems to work fine on my system.(Macbook Pro with GTX 750M)
My ~/.theanorc file :
[global]
cnmem = True
floatX = float32
device = gpu0
Various environment variables (I use a virtual environment(macvnev):
echo $LD_LIBRARY_PATH
/opt/local/lib:
echo $PATH
/Developer/NVIDIA/CUDA-7.5/bin:/opt/local/bin:/opt/local/sbin:/Developer/NVIDIA/CUDA-7.0/bin:/Users/Ramana/projects/macvnev/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
echo $DYLD_LIBRARY_PATH
/Developer/NVIDIA/CUDA-7.5/lib:/Developer/NVIDIA/CUDA-7.0/lib:
How I run ipython notebook (For me, the device is gpu0) :
$THEANO_FLAGS=mode=FAST_RUN,device=gpu0,floatX=float32 ipython notebook
Output of $nvcc -V :
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2015 NVIDIA Corporation
Built on Thu_Sep_24_00:26:39_CDT_2015
Cuda compilation tools, release 7.5, V7.5.19
From your post, probably you've set the $PATH variable wrong.
I am using sphinx to document my software. and I am using a virtualenv for the installation. now some packages are only installed in the virtual environment, and sphinx does not see them.
I have this code in my conf.py:
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
p = os.path.abspath('..')
sys.path.insert(0, p)
if 'VIRTUAL_ENV' in os.environ:
q = os.sep.join([os.environ['VIRTUAL_ENV'],
'lib', 'python2.7', 'site-packages'])
sys.path.insert(0, q)
p = p + ":" + q
os.environ['PYTHONPATH'] = p
yet if I make html, I get this sort of warnings:
/home/mario/Local/github/Bauble/bauble.classic/doc/api.rst:358: WARNING: autodoc: failed to import class u'TagItemGUI' from module u'bauble.plugins.tag'; the following exception was raised:
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/sphinx/ext/autodoc.py", line 385, in import_object
__import__(self.modname)
File "/home/mario/Local/github/Bauble/bauble.classic/bauble/plugins/tag/__init__.py", line 30, in <module>
from sqlalchemy import *
ImportError: No module named sqlalchemy
my $VIRTUAL_ENV/lib/python2.7/site-packages contains SQLAlchemy-1.0.4-py2.7-linux-x86_64.egg.
definitely related to question Sphinx autodoc dies on ImportError of third party package, but the description of the procedure I chose to follow is in a broken link.
The problem is that packages are not directly included in virtualenv's site-packages dir, you would need to specify the full path to be able to import package from there. I use the following hack:
if 'VIRTUAL_ENV' in os.environ:
site_packages_glob = os.sep.join([
os.environ['VIRTUAL_ENV'],
'lib', 'python2.7', 'site-packages', 'projectname-*py2.7.egg'])
site_packages = glob.glob(site_packages_glob)[-1]
sys.path.insert(0, site_packages)
Where projectname is the name of the python module I would like to import.
Note that this is error prone, especially when you have multiple versions
of the module, but so far it works for me.