dmici / neutompy-toolbox Goto Github PK

Please delete this issue. Apologies.

I faced with the following error during importing of neutompy:
AttributeError: module 'neutompy' has no attribute 'recon'

Hi, I tried the FBP recon with CPU following the example code. However, the recon slices are not as expected. They are all vertical lines as attached. Can you please advise?

Hi,

I tried to install and run NeuTomPy today and ran into the folowwing error:

ImportError: cannot import name 'compare_ssim' from 'skimage.measure'

Apparently the name changed from skimage.measure.compare_ssim to skimage.metrics.structural_similarity in version number 0.16.
Is there any plan to upgrade the dependency or is it up to the user to import an old version of skimage?

Thank you for the support

Hello,

Thank you for developing NeuTomPy. I've enjoyed working with it!

I am trying to do a set of reconstructions on a AWS server (Ubuntu 20.04 Server). I followed the installation instructions. Note that the following step took nearly two hours to finish:
conda install -c conda-forge ipython numpy numexpr matplotlib astropy tifffile opencv scikit-image read-roi mkl_fft scipy six tqdm pywavelets

I then tried to import NeuTomPy to test the installation:
import numpy as np
import neutompy as ntp

This results in the following error:

Traceback (most recent call last):
File "fbp_gpu_reconstruction.py", line 6, in
import neutompy as ntp
File "/home/othman/miniconda3/envs/neutompy_test/lib/python3.6/site-packages/neutompy/init.py", line 20, in
from .preproc.preproc import *
File "/home/othman/miniconda3/envs/neutompy_test/lib/python3.6/site-packages/neutompy/preproc/preproc.py", line 7, in
from skimage.transform import rotate
File "/home/othman/miniconda3/envs/neutompy_test/lib/python3.6/site-packages/skimage/init.py", line 127, in
from .util.dtype import (img_as_float32,
File "/home/othman/miniconda3/envs/neutompy_test/lib/python3.6/site-packages/skimage/util/init.py", line 6, in
from .apply_parallel import apply_parallel
File "/home/othman/miniconda3/envs/neutompy_test/lib/python3.6/site-packages/skimage/util/apply_parallel.py", line 8, in
import dask.array as da
File "/home/othman/miniconda3/envs/neutompy_test/lib/python3.6/site-packages/dask/array/init.py", line 3, in
from .core import (
File "/home/othman/miniconda3/envs/neutompy_test/lib/python3.6/site-packages/dask/array/core.py", line 22, in
from . import chunk
File "/home/othman/miniconda3/envs/neutompy_test/lib/python3.6/site-packages/dask/array/chunk.py", line 68, in
nancumprod = np.nancumprod
AttributeError: module 'numpy' has no attribute 'nancumprod'

I've managed to reproduce this error on my local machine (Ubuntu 20.04). However, on Google Colab notebooks, it works fine.

My initial guess is that an incompatible version of numpy is installed but I can't find a list of dependency versions in the documentation. I've tried re-installing numpy but that hasn't helped.

I've checked whether this is an issue with numpy itself but it is not. I installed numpy separately on a new conda environment and managed to call nancumprod without any issues.

>>> import numpy as np
>>> np.nancumprod(1)
array([1])

Here is a list of all the packages in this anaconda environment in which I run NeuTomPy:

packages in environment at /home/othman/miniconda3/envs/neutompy_test:
Name Version Build Channel
_libgcc_mutex 0.1 main
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
astra-toolbox 1.8 np111py36_1 astra-toolbox
astropy 3.0.5 py36h14c3975_1001 conda-forge
atomicwrites 1.4.0 pyh9f0ad1d_0 conda-forge
attrs 20.3.0 pyhd3deb0d_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.1 py_0 conda-forge
black 20.8b1 py_0 conda-forge
blas 1.0 mkl
bzip2 1.0.8 h516909a_3 conda-forge
ca-certificates 2020.10.14 0 anaconda
cairo 1.16.0 h18b612c_1001 conda-forge
certifi 2020.6.20 py36_0 anaconda
click 7.1.2 pyh9f0ad1d_0 conda-forge
cloudpickle 1.6.0 py_0 conda-forge
cycler 0.10.0 py_2 conda-forge
cytoolz 0.11.0 py36h1d69622_1 conda-forge
dask-core 2.30.0 py_0 conda-forge
dbus 1.13.6 he372182_0 conda-forge
decorator 4.4.2 py_0 conda-forge
expat 2.2.9 he1b5a44_2 conda-forge
ffmpeg 4.0.2 ha0c5888_2 conda-forge
fontconfig 2.13.1 he4413a7_1000 conda-forge
freeglut 3.0.0 hf484d3e_1005 conda-forge
freetype 2.10.4 h7ca028e_0 conda-forge
glib 2.66.1 h92f7085_0
gmp 6.1.2 hf484d3e_1000 conda-forge
gnutls 3.5.19 h2a4e5f8_1 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
gst-plugins-base 1.14.0 hbbd80ab_1
gstreamer 1.14.0 hb31296c_0
harfbuzz 1.8.8 hffaf4a1_0
hdf5 1.10.2 hc401514_3 conda-forge
hypothesis 5.41.3 pyhd8ed1ab_0 conda-forge
icu 58.2 hf484d3e_1000 conda-forge
imageio 2.9.0 py_0 conda-forge
importlib-metadata 3.1.0 pyhd8ed1ab_0 conda-forge
importlib_metadata 3.1.0 hd8ed1ab_0 conda-forge
intel-openmp 2020.2 254
ipython 7.16.1 py36h95af2a2_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
jasper 2.0.14 h07fcdf6_1
jedi 0.17.2 py36h5fab9bb_1 conda-forge
jpeg 9b h024ee3a_2
kiwisolver 1.3.1 py36h51d7077_0 conda-forge
ld_impl_linux-64 2.33.1 h53a641e_7
libastra 1.8 0 astra-toolbox
libblas 3.8.0 21_mkl conda-forge
libcblas 3.8.0 21_mkl conda-forge
libedit 3.1.20191231 h14c3975_1
libffi 3.3 he6710b0_2
libgcc-ng 9.1.0 hdf63c60_0
libgfortran 3.0.0 1 conda-forge
libgfortran-ng 7.3.0 hdf63c60_0
libglu 9.0.0 he1b5a44_1001 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.8.0 21_mkl conda-forge
libopencv 3.4.2 hb342d67_1
libpng 1.6.37 hbc83047_0
libstdcxx-ng 9.1.0 hdf63c60_0
libtiff 4.1.0 h2733197_1
libuuid 2.32.1 h14c3975_1000 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxml2 2.9.9 h13577e0_2 conda-forge
lz4-c 1.9.2 heb0550a_3
matplotlib 3.1.0 py36_0 conda-forge
matplotlib-base 3.1.0 py36h5f35d83_0 conda-forge
mkl 2020.2 256
mkl-service 2.3.0 py36he904b0f_0
mkl_fft 1.0.10 py36_0 conda-forge
more-itertools 8.6.0 pyhd8ed1ab_0 conda-forge
mypy_extensions 0.4.3 py36h9f0ad1d_2 conda-forge
ncurses 6.2 he6710b0_1
nettle 3.3 0 conda-forge
networkx 2.5 py_0 conda-forge
neutompy 1.0.10 pypi_0 pypi
numexpr 2.6.9 py36h637b7d7_1000 conda-forge
numpy 1.11.3 py36h7e9f1db_12
numpy-base 1.11.3 py36hde5b4d6_12
olefile 0.46 pyh9f0ad1d_1 conda-forge
opencv 3.4.2 py36h6fd60c2_1
openh264 1.8.0 hdbcaa40_1000 conda-forge
openssl 1.1.1h h7b6447c_0 anaconda
parso 0.7.1 pyh9f0ad1d_0 conda-forge
pathspec 0.8.1 pyhd3deb0d_0 conda-forge
pcre 8.44 he1b5a44_0 conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 7.1.2 py36hb39fc2d_0
pip 20.2.4 py36h06a4308_0
pixman 0.38.0 h516909a_1003 conda-forge
pluggy 0.13.1 py36h9880bd3_3 conda-forge
prompt-toolkit 3.0.8 pyha770c72_0 conda-forge
psutil 5.7.3 py36he6145b8_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
py 1.9.0 pyh9f0ad1d_0 conda-forge
py-opencv 3.4.2 py36hb342d67_1
pygments 2.7.2 py_0 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyqt 5.9.2 py36hcca6a23_4 conda-forge
pyqt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.8.1 pypi_0 pypi
pytest 3.10.1 py36_1000 conda-forge
pytest-arraydiff 0.3 py_0 conda-forge
pytest-astropy 0.7.0 py_0 conda-forge
pytest-astropy-header 0.1.2 py_0 conda-forge
pytest-doctestplus 0.6.1 pyh9f0ad1d_0 conda-forge
pytest-openfiles 0.4.0 py_0 conda-forge
pytest-remotedata 0.3.2 pyh9f0ad1d_0 conda-forge
python 3.6.12 hcff3b4d_2
python-dateutil 2.8.1 py_0 conda-forge
python_abi 3.6 1_cp36m conda-forge
pywavelets 1.0.3 py36hd352d35_1 conda-forge
pyyaml 5.3.1 py36he6145b8_1 conda-forge
qt 5.9.7 h5867ecd_1
read-roi 1.6.0 py_0 conda-forge
readline 8.0 h7b6447c_0
regex 2020.11.13 py36h1d69622_0 conda-forge
scikit-image 0.15.0 py36he1b5a44_0 conda-forge
scipy 1.2.1 py36h09a28d5_1 conda-forge
setuptools 50.3.1 py36h06a4308_1
simpleitk 2.0.1 py36hf484d3e_0 simpleitk
sip 4.19.8 py36hf484d3e_1000 conda-forge
six 1.15.0 pyh9f0ad1d_0 conda-forge
sortedcontainers 2.3.0 pyhd8ed1ab_0 conda-forge
sqlite 3.33.0 h62c20be_0
tifffile 0.15.1 py36h3010b51_1001 conda-forge
tk 8.6.10 hbc83047_0
toml 0.10.2 pyhd8ed1ab_0 conda-forge
toolz 0.11.1 py_0 conda-forge
tornado 6.1 py36h1d69622_0 conda-forge
tqdm 4.54.0 pyhd8ed1ab_0 conda-forge
traitlets 4.3.3 py36h9f0ad1d_1 conda-forge
typed-ast 1.4.1 py36h1d69622_1 conda-forge
typing_extensions 3.7.4.3 py_0 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
wheel 0.35.1 pyhd3eb1b0_0
x264 1!152.20180806 h14c3975_0 conda-forge
xorg-fixesproto 5.0 h14c3975_1002 conda-forge
xorg-inputproto 2.3.2 h14c3975_1002 conda-forge
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge
xorg-libice 1.0.10 h516909a_0 conda-forge
xorg-libsm 1.2.3 h84519dc_1000 conda-forge
xorg-libx11 1.6.12 h516909a_0 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xorg-libxext 1.3.4 h516909a_0 conda-forge
xorg-libxfixes 5.0.3 h516909a_1004 conda-forge
xorg-libxi 1.7.10 h516909a_0 conda-forge
xorg-libxrender 0.9.10 h516909a_1002 conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
xorg-xextproto 7.3.0 h14c3975_1002 conda-forge
xorg-xproto 7.0.31 h14c3975_1007 conda-forge
xz 5.2.5 h7b6447c_0
yaml 0.2.5 h516909a_0 conda-forge
zipp 3.4.0 py_0 conda-forge
zlib 1.2.11 h7b6447c_3
zstd 1.4.5 h9ceee32_0

I'd appreciate your thoughts on this.

Also, if you have a working anaconda environment, would you mind sharing your yml file?

Thanks,

Othman