I need to open SVS images in Python 3.7 and it seems that Openslide is the only module capable of opening images of that size (30k*30k pixels). I have used pip install openslide-python as well as python -m pip install openslide-python and pip 3 install... etc.
I know the module has been successfully installed because if I run any of those commands again the command line returns requirement already satisfied however when I run Python and try to import openslide it gives the error at the bottom.
My guess was that the .whl or .tar.gz files were in the wrong path so I made a bunch of copies and put them in the openslide folders within the Anaconda3 folder. The error persists. I have included the full error code below for clarity.
Extra: If I run help("modules") openslide shows up along with numpy, math, sklearn etc. I can import and run all other modules without issue.
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Users\brimk\Anaconda3\lib\site-packages\openslide\__init__.py", line 29, in <module>
from openslide import lowlevel
File "C:\Users\brimk\Anaconda3\lib\site-packages\openslide\lowlevel.py", line 41, in <module>
_lib = cdll.LoadLibrary('libopenslide-0.dll')
File "C:\Users\brimk\Anaconda3\lib\ctypes\__init__.py", line 434, in LoadLibrary
return self._dlltype(name)
File "C:\Users\brimk\Anaconda3\lib\ctypes\__init__.py", line 356, in __init__
self._handle = _dlopen(self._name, mode)
OSError: [WinError 126] The specified module could not be found
My issue was resolved by the answer from my hero!
It seems that, at least for Openslide, running Python from the Path to the Bin is the easiest solution. It can be done this way.
Download the Windows Binary here.
Extract the download to whatever path you want.
Open command window
pip3 install openslide-python (pip2 if Python 2)
cd C:\Users\Path\to\Openslide-Win64-20171122\bin
python
import openslide
In the future you will have to run python from the path to the Openslide bin (Step 4). This can be done more rigorously by adding that file path to the PATH as described in detail here as well as in the answer above.
Related
I've tried to install jupyter extensions following the instruction here.
The first step named 'Install the python package' in the instruction was succeeded.
But the second one named 'Install javascript and css files' was failed.
I executed jupyter contrib nbextension install --user as instructed, but an error occured.
The error says: pkg_resources.DistributionNotFound: The 'terminado>=0.8.1' distribution was not found and is required by notebook. (All traceback shown is as below.)
But I confirmed that I've already installed 'terminado' v0.8.2 package, which was installed via pip.
How can I handle this problem? Is the problem solely that jupyter command does not know where the 'terminado' is installed? Or is the problem more serious?
All the error message is as below:
Traceback (most recent call last):
File "/usr/local/bin/jupyter-contrib", line 5, in <module>
from pkg_resources import load_entry_point
File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 3241, in <module>
#_call_aside
File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 3225, in _call_aside
f(*args, **kwargs)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 3254, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 583, in _build_master
ws.require(__requires__)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 900, in require
needed = self.resolve(parse_requirements(requirements))
File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 786, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'terminado>=0.8.1' distribution was not found and is required by notebook
I'm using macOS Catalina (but same problem appeared on Mojave.
Summary
The problem is, as it may be turned out with seeing the error message, that the jupyter contrib command uses python2, not python3 which is my preference.
Problem
The usage of python2 by the command was caused by the shebang of /usr/local/bin/jupyter-contrib file.
The shebang was #!/usr/bin/python, which means that it specified jupyter-contrib used python interpreter which located on /usr/bin/python which is python2 on my machine (and many other Mac machine, maybe).
Hence you should specify python3 with the shebang rather than python2.
Solution
First, get your python3 installation path like this:
$ which python3
Copy the returned path.
Open the /usr/local/bin/jupyter-contrib file. Note that this file is read-only but you have to rewrite it, so you should open it with sudo:
$ sudo vim /usr/local/bin/jupyter-contrib
Rewrite the shebang on the 1st line. Shebang may now be like this:
#!/usr/bin/python
where it specifies python2 as its interpreter. You should rewrite the path to python3's path which you copied at step 1:
#!{{Paste your python3's path}}
Save the file.
That's it.
Now jupyter-contrib uses python3.
So jupyter contrib nbextension install --user command should succeeds.
I am trying to just convert my pygame python py to a .exe file using cx_Freeze. The setup file executes correctly and without error, but the issue is that when I run my .exe file the console window (the black cmd-like window)will open quickly and close. My .py which I want to convert is called Salary.py, and it includes a .input('str') codes in it so that the
user can decide which csv file they want to use.
Description of my Salary.py: if the user input an interger, Salary.py help them to parse through one existed csv file and run the
script and output to another csv file.
Chinese is included inside the code.
Once again, there is no error running when I run Salary.py in python3.6, and no error when building the exe file for now.
The setup.py I am using:
from cx_Freeze import setup, Executable
import os
os.environ['TCL_LIBRARY'] = r'D:\Anaconda3\tcl\tcl8.6'
os.environ['TK_LIBRARY'] = r'D:\Anaconda3\tcl\tcl8.6'
setup(name='Salary',
version='0.1',
description='Salarycount',
executables= [Executable("Salary.py")])
I try to execute the Salary.exe in cmd. And it gave this to me:
Traceback (most recent call last):
File "D:\Anaconda3\lib\site-packages\cx_Freeze\initscripts\__startup__.py", line 14, in run
module.run()
File "D:\Anaconda3\lib\site-packages\cx_Freeze\initscripts\Console.py", line 26, in run
exec(code, m.__dict__)
File "Salary.py", line 8, in <module>
File "D:\Anaconda3\lib\site-packages\pandas\__init__.py", line 19, in <module>
"Missing required dependencies {0}".format(missing_dependencies))
ImportError: Missing required dependencies ['numpy']
Apperently, numpy has already installed to my python packages, I don't even know what does it mean.
my environment:
Anaconda 3
python 3.6
cx-Freeze 6.0b1
It looks like your Salary.py script uses the pandas package, is this correct? The pandas package requires the numpy package to work, and one needs to tell cx_Freeze explicitly to include the numpy package. Try to add the following options to setup:
from cx_Freeze import setup, Executable
import os
os.environ['TCL_LIBRARY'] = r'D:\Anaconda3\tcl\tcl8.6'
os.environ['TK_LIBRARY'] = r'D:\Anaconda3\tcl\tcl8.6'
setup(name='Salary',
version='0.1',
description='Salarycount',
options={'build_exe': {'packages': ['numpy']}},
executables= [Executable("Salary.py")])
I am just a beginner to a tensorflow and trying to install TensorFlow with CPU support only.
Initially, I downloaded and installed Python 3.5.2 version from https://www.python.org/downloads/release/python-352/
After successful installation, I ran the command pip3 install --upgrade tensorflow which installed tensorflow-1.8.0.
To test installation i just ran following commands:
> python
> import tensorflow as tf
But this gave me an error:
ImportError: Could not find 'msvcp140.dll'. TensorFlow requires that
this DLL be installed in a directory that is named in your %PATH%
environment variable. You may install this DLL by downloading Visual
C++ 2015 Redistributable Update 3 from this URL:
https://www.microsoft.com/en-us/download/details.aspx?id=53587
I searched for this issue and found link to an issue https://github.com/tensorflow/tensorflow/issues/17393.
According to above i tried running command
pip install tensorflow==1.5
But, this didn't solved my problem.
I even tried downloading msvcp140.dll and manually coping it under C:\Windows\SysWOW64 folder and reinstalling python and tensorflow.
How do I fix this problem.
Thanks in advance.
I copied msvcp140.dll to path C:\Users\PCName\AppData\Local\Programs\Python\Python35
and it worked for me.
I also switched back to tensorflow 1.8 from 1.5.
download msvcp140.dll or click https://www.dll-files.com/msvcp140.dll.html
find your python path
path will find easy from your error
error will show like this
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Users\sky network\AppData\Local\Programs\Python\Python36\lib\site-
packages\tensorflow\__init__.py", line 24, in <module>
from tensorflow.python import *
File "C:\Users\sky network\AppData\Local\Programs\Python\Python36\lib\site-
packages\tensorflow\python\__init__.py", line 49, in <module>
from tensorflow.python import pywrap_tensorflow
File "C:\Users\sky network\AppData\Local\Programs\Python\Python36\lib\site-
packages\tensorflow\python\pywrap_tensorflow.py", line 30, in <module>
self_check.preload_check()
File "C:\Users\sky network\AppData\Local\Programs\Python\Python36\lib\site-
packages\tensorflow\python\platform\self_check.py", line 55, in preload_check
% build_info.msvcp_dll_name)
from my error the python path is
"File "C:\Users\sky network\AppData\Local\Programs\Python\Python36"
if u cant find the AppData folder
click folder view option and enable hidden files
paste the file "msvcp140.dll" into
C:\Users\sky network\AppData\Local\Programs\Python\Python36
You can download the package from the url https://www.microsoft.com/en-us/download/details.aspx?id=53587 and install it. This will solve the issue.
I'm trying to install xlutils package to access xls sheets in Python but unfortunately I'm unable to install it.
Python version 3.5.1
using spyder editor, have got this error.
runfile('E:/python_practice/task2/gen1.py', wdir='E:/python_practice/task2')
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Anaconda3\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py", line 699, in runfile
execfile(filename, namespace)
File "C:\Anaconda3\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py", line 88, in execfile
exec(compile(open(filename, 'rb').read(), filename, 'exec'), namespace)
File "E:/python_practice/task2/gen1.py", line 10, in <module>
from xlutils.copy import copy
ImportError: No module named 'xlutils'
so, downloaded xlutils from https://pypi.python.org/pypi/xlutils and unzipped, copied and pasted in sitepackages folder of python35 folder and as well as anaconda3 folder.But still i'm getting above mentioned error.
Have you read the docs of this module? It clearly explains everythinf you should do. There is a way to install it using pip. Type this in your command-line: pip install xlutils. That should install it. For any further problems, read the documentation.
EDIT: Never mind, this package is unavailable for Python 3.5
This package is support on Python 2.5, 2.6 and 2.7 on Linux, Mac OS X and Windows.
I am attempting to create a .exe on Windows 7 from a python3 script using cx_freeze. the Script involves using pywin32 to manipulate Excel files. I can build the .exe successfully from my setup.py file; however, when I run the .exe, the following error is thrown:
Traceback (most recent call last):
File
"C:\Python33\lib\site-packages\cx_Freeze\initscripts\Console3.py",
line 27, in exec(code,m_dict_)
File "MyScript.py", line
12, in < module >
File
"C:\Python\64-bit\3.3\lib\importlib_bootstrap.py", line 1558, in
_find_and_load
File "C:\Python\64-bit\3.3\lib\importlib_bootstrap.py", line 1505, in
_find_and_load_unlocked
File "C:\Python\64-bit\3.3\lib\importlib_bootstrap.py", line 313, in
_call_with_frames_removed
File "C:\Python\64-bit\3.3\lib\importlib_bootstrap.py", line 1558, in
_find_and_load
File "C:\Python\64-bit\3.3\lib\importlib_bootstrap.py", line 1525, in
_find_and_load_unlocked
File "C:\Python33\lib\site-packages\win32com__init__.py", line 6, in
< module>
import pythoncom
File
"C:\Python\64-bit\3.3\lib\importlib_bootstrap.py", line 1558, in
_find_and_load
File "C:\Python\64-bit\3.3\lib\importlib_bootstrap.py", line 1525, in
_find_and_load_unlocked
File "C:\Python33\lib\site-packages\pythoncom.py", line 3, in
pywintypes._import_pywin32_system_module_("pythoncom", globals())
File "C:\Python33\lib\site-packages\win32\lib\pywintypes.py", line 61,
in _import_pywin32_system_module_
raise ImportError("Module '%s'
isn't in frozen sys.path %s" % (modname, sys.path))
ImportError: Module 'pythoncom' isn't in frozen sys.path
['C:\Python33\build\exe.win-amd64\3.3\MyScript.exe',
'C:\Python33\build\exe.win-amd64\3.3',
'C:\Python33\build\exe.win-amd64\3.3\MyScript.zip',
'C:\Python33\build\exe.win-amd64\3.3\library.zip']
Here is what my setup.py file currently looks like:
import sys
from cx_Freeze import setup, Executable
base = None
if sys.platform == 'win32':
base = 'Win32GUI'
includes = []
packages = []
executables = [Executable('MyScript.py', base=base)]
include_files = ['MyFolder1/','MyFolder2/Spreadsheet.xls']
setup(name='My Script',
version='0.1',
description='My Script',
executables=executables,
options = {'build_exe': {'includes':includes,
'packages':packages,
'include_msvcr':True,
'include_files':include_files}})
So far, I have tried listing both 'pythoncom' and 'win32com' in both the includes and the packages lists. Any help is greatly appreciated!
I had exactly the same issue when using pyinstaller to pack py into executable. Tried everything, but find out the issue is hidden in pyinstaller version. I was using pyinstaller 4.7 but when downgrade into 3.6, the exe works flawlessly.
Looking at the code, it looks like you need to ensure that a file called something like pythoncom33.dll is copied into the build directory.
So the whole problem actually stemmed from having the 32-bit version of pywin32 installed while running 64-bit versions of Python-3.3.2 and Windows 7. After adding pythoncom33.dll to the include_files of my setup.py as Thomas K had suggested, I got another error:
ImportError: DLL load failed: %1 is not a valid Win32 application
After some research, I found that this error is typical when mixing 32-bit and 64-bit. So I uninstalled pywin32 32-bit and installed pywin32 64-bit but my script threw yet another error:
import win32api, sys, os
ImportError: DLL load failed: The specified module could not be found.
As suggested in this post, I copied the 28 win32*.pyd files from the Lib/site-packages/win32 folder to the Python33 folder right next to python.exe , and everything worked.
Add this to the top of your main.py:
import pywintypes
import win32api
seeļ¼
PyWin32 and Python 3.8.0
So I ran into a similar problem where cx_Freeze was failing to pull in the pywintypes DLL, but frustratingly enough it was only on some machines which compelled me to explore the issue a bit further (I have a bad habit of chasing rabbits down holes). It seems that pywin32 tries to install its DLLs into a Windows system directory, but if that fails due to a lack of privileges it will fallback to placing them in your Python directory instead. The behavior I was seeing was a result of the fact that cx_Freeze applies a blacklist of well-known system folder paths against the collection of dependencies it has discovered in order to avoid pulling in operating system DLLs.
Copying these DLLs as needed by adding a path to them to the "include_files" parameter will indeed address the issue (just remember that you can't guarantee that they will be placed in the system folder). An alternative solution is to override the blacklist with a whitelist which you can configure using the "bin_includes" / "bin_path_includes" parameters. Here is a quick example that shows how to configure this parameter using a setup.py file (for Python 2.7, but the only difference should be the pywintypes DLL filename):
from cx_Freeze import setup, Executable
# This can also be an absolute path to the file if you wish to be very specific
bin_includes = ["pywintypes27.dll"]
options = {
"build_exe": {
"bin_includes": bin_includes
}
}
executable = Executable(script='main.py')
setup(version='x.x.x',
options=options,
executables=[executable])
Update pyinstaller related vision.
python -m pip install pyinstaller==3.6