jacobjma / pyqstem Goto Github PK

`C:\Users\yisong\anaconda3\envs\qstem\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(14) : Warning Msg: Using deprecated NumPy API, disable it with #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
pywt_extensions_pywt.c(12552): error C2440: '=': cannot convert from 'PyObject *' to 'double'
pywt_extensions_pywt.c(12555): warning C4244: '=': conversion from 'double' to 'float', possible loss of data
pywt_extensions_pywt.c(12566): error C2440: '=': cannot convert from 'PyObject *' to 'double'
pywt_extensions_pywt.c(12569): warning C4244: '=': conversion from 'double' to 'float', possible loss of data
pywt_extensions_pywt.c(12663): error C2440: '=': cannot convert from 'PyObject *' to 'double'
pywt_extensions_pywt.c(12677): error C2440: '=': cannot convert from 'PyObject *' to 'double'
pywt_extensions_pywt.c(12680): warning C4244: '=': conversion from 'double' to 'float', possible loss of data
pywt_extensions_pywt.c(12691): error C2440: '=': cannot convert from 'PyObject *' to 'double'
pywt_extensions_pywt.c(12694): warning C4244: '=': conversion from 'double' to 'float', possible loss of data

error: Setup script exited with error: command 'C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.33.31629\bin\HostX86\x64\cl.exe' failed with exit code 2`

I got problem with the cl.exe file when running "python setup.exe install". I installed Visual Studio 2022 build tools and in an Anaconda vitual environment with Python 3.6. I can see there is a cl.exe file in the same folder. So it shouldn't be a path problem? Could anyone help? Thanks very much.

Hi,

Trying to Install PyQSTEM on Windows 7.

I'm getting the error message 'no module named Cython.' I've followed the installation instructions and can import cython while using python otherwise.

Any suggestions or advice would be helpful

regards

Dear PyQSTEM developers,

I'm trying pyqstem on Ubuntu 20.04.1 LTS (Focal Fossa) and python3.8.2.
I faced segmentation fault in this condition at the line of qstem.build_potential, although it went well on windows.

Code is shown as below;
from future import print_function
import numpy as np
import matplotlib.pyplot as plt
from pyqstem import PyQSTEM
from pyqstem.util import atoms_plot
import ase
from ase.build import nanotube
from pyqstem.imaging import CTF

atoms = nanotube(13,7,length=2, verbose=True)
atoms.wrap()

#Figure
atoms.center(vacuum=2,axis=2)
fig,(ax1,ax2)=plt.subplots(1,2,figsize=(8,4))
atoms_plot(atoms,direction=2,ax=ax1)
atoms_plot(atoms,direction=1,ax=ax2)

qstem = PyQSTEM('TEM')
qstem.set_atoms(atoms)
v0=80

qstem.build_wave('plane',v0,(100,100))
wave=qstem.get_wave()

#wave.view()
#plt.show()

qstem.build_potential(5) #segmentation fault (core dumped)

potential = qstem.get_potential_or_transfunc()

potential.view(method='real')
plt.show()
qstem.run()

wave = qstem.get_wave()
ctf = CTF(defocus=-60, Cs = 0.005, focal_spread = 30)
image_wave=wave.apply_ctf(ctf)

image_wave.view()
plt.show()

Thanks and regards.

@jacobjma Is this still being developed?

I'm trying to use this a bit and could be interested in making it available via pyxem (https://github.com/pyxem/pyxem), but this would need things like writing docstrings for functions. I might also be able to write those - so just thought I'd check what the status of this project now is?

I used Anaconda to install pyqstem in the following step:

1. create an env named qstem

2. activate the above env, install dependencies:
   conda install numpy matplolib scipy jupyter cython scikit-image
conda install -c conda-forge ase

3. cd to pyqstem folder downloaded, install using
   python setup.py install

After all these steps, I open jupyter notebooks to run the examples provided. failed with error msg

DLL load failed: The specified module could not be found.

I checked the folder where pyqstem is installed, qstem_interface.cp36-win_amd64.pyd has been generated by the compiler, is this file the dll file needed?

Any solution to this?

BTW: I successfully installed on MacOX, but I came across this problem in Windows platform...

Hi Jacob,

PyQSTEM sometimes crashes when you reuse the same object with a different number of slices. Using a new pyqstem object in each iteration instead leads to a memory leak.

The attached script shows the problem. On a Mac, it gives the error

Corrupt value: 0x3f0278d13f0278d1
Python(6133,0x1136c5dc0) malloc: *** set a breakpoint in malloc_error_break to debug
Abort trap: 6

On linux, it just gives a Segmentation fault (core dumped). It is not 100% reproducible, the attached script crashes every second time or so.

Hi, I read in your paper that the model is able to output the heights of the atomic columns, but when I try to load an image and run it through the CNN, the only output is the confidence map. The code for the calculation of the column heights has already been implemented? If so, how can I see the heights ?
Thanks.

Hi,

I was trying to install PyQSTEM on Mac OS X 10.12.6. As per the instructions, everything was installed correctly with few warnings but when trying to import pyqstem, I get the following error -

Python 3.6.0 |Anaconda custom (x86_64)| (default, Dec 23 2016, 13:19:00)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

from pyqstem import PyQSTEM
Traceback (most recent call last):
File "", line 1, in
File "/Users/cphatak/Applications/PyQSTEM/pyqstem/init.py", line 2, in
from pyqstem.qstem_interface import PyQSTEM
ModuleNotFoundError: No module named 'pyqstem.qstem_interface'

Any help appreciated. Thanks,

cheers,
-cd

Dear PyQSTEM developers,
I wonder if there is a more detailed doc for pyqstem, for I don't know what the parameter names and meanings of the functions. For example, I am interested in diffration simulations but the notebooks I found are mainly about STEM or TEM image simulation.
Thanks and regards.

Super tiny thing which I was able to fix immediately, but I thought I'd report it anyway. I tried running your very old exit wave reconstruction example, which uses the CTF radial_plot function. Trying to call this function throws an error because spline is no longer part of scipy.interpolate. Looking below in the code, it doesn't look like spline is used anyway. Removing it makes radial_plot work again.

Hi,
I am having an installation problem, would you be able to provide any advice?

I'm running Python 3.6+ (conda), on MacOS 10.13.4

pyqstem/qstem_interface.cpp:582:10: fatal error: 'unordered_map' file not found
#include <unordered_map>
^~~~~~~~~~~~~~~
1 error generated.
error: command 'gcc' failed with exit status 1

Cheers!

after i excuted “python setup.py install”
LINK : fatal error LNK1181: cannot open input file 'fftw3.lib'
error: command 'C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\x86_amd64\link.exe' failed with exit status 1181

i don't know how to deal with this problem...