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astra-toolbox / astra-toolbox

ASTRA Tomography Toolbox
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Installing Astra-Toolbox using Conda on CentOS 7 and Linking with Tomopy #141

Open cbreite opened 6 years ago

cbreite commented 6 years ago

Dear developers,

To reconstruct synchrotron CT scans I'm planning to use you software package. I'm especially interested in using the FBP algorithm.

I was using the provided commands for conda (python 3.6) to install tomopy and astra-toolbox and also verified with "conda list" that both packages would be installed. Please see the installed packages at teh bottom of this message.

In a next step I wanted to complete the examples given on the tomopy webpage to verify that everything works as expected. I was able to get a "gridrec" reconstruction with the tomopy algorithm and wanted to reconstruct the same example file "tooth.h5" with tomopy.astra and "FBP" algorithm (all the commands correspond to the script provided on the tomopy homepage). The sinogram output still worked, but the reconstructed image just appeared complete black. I was trying to reinstall conda and all the packages, but couldn't fix this issue. Please advice how to make the toolbox work.

Thank you very much!

Christian Breite

Name Version Build Channel

_ipyw_jlab_nb_ext_conf 0.1.0 py36he11e457_0
alabaster 0.7.10 py36h306e16b_0
anaconda 5.1.0 py36_2
anaconda-client 1.6.9 py36_0
anaconda-navigator 1.7.0 py36_0
anaconda-project 0.8.2 py36h44fb852_0
asn1crypto 0.24.0 py36_0
astra-toolbox 1.8.3 py36h7e58f7c_0 astra-toolbox astroid 1.6.1 py36_0
astropy 2.0.3 py36h14c3975_0
attrs 17.4.0 py36_0
babel 2.5.3 py36_0
backports 1.0 py36hfa02d7e_1
backports.shutil_get_terminal_size 1.0.0 py36hfea85ff_2
beautifulsoup4 4.6.0 py36h49b8c8c_1
bitarray 0.8.1 py36h14c3975_1
bkcharts 0.2 py36h735825a_0
blaze 0.11.3 py36h4e06776_0
bleach 2.1.2 py36_0
bokeh 0.12.13 py36h2f9c1c0_0
boto 2.48.0 py36h6e4cd66_1
bottleneck 1.2.1 py36haac1ea0_0
bzip2 1.0.6 h9a117a8_4
ca-certificates 2017.08.26 h1d4fec5_0
cairo 1.14.12 h77bcde2_0
certifi 2018.1.18 py36_0
cffi 1.11.4 py36h9745a5d_0
chardet 3.0.4 py36h0f667ec_1
click 6.7 py36h5253387_0
cloudpickle 0.5.2 py36_1
clyent 1.2.2 py36h7e57e65_1
colorama 0.3.9 py36h489cec4_0
conda 4.4.10 py36_0
conda-build 3.4.1 py36_0
conda-env 2.6.0 h36134e3_1
conda-verify 2.0.0 py36h98955d8_0
contextlib2 0.5.5 py36h6c84a62_0
cryptography 2.1.4 py36hd09be54_0
cudatoolkit 8.0 3
curl 7.58.0 h84994c4_0
cycler 0.10.0 py36h93f1223_0
cython 0.27.3 py36h1860423_0
cytoolz 0.9.0 py36h14c3975_0
dask 0.16.1 py36_0
dask-core 0.16.1 py36_0
datashape 0.5.4 py36h3ad6b5c_0
dbus 1.12.2 hc3f9b76_1
decorator 4.2.1 py36_0
distributed 1.20.2 py36_0
docutils 0.14 py36hb0f60f5_0
dxchange 0.1.5 py36_0 conda-forge dxfile 0.4 py36_0 conda-forge edffile 5.0.0 py36_0 conda-forge entrypoints 0.2.3 py36h1aec115_2
et_xmlfile 1.0.1 py36hd6bccc3_0
expat 2.2.5 he0dffb1_0
fastcache 1.0.2 py36h14c3975_2
filelock 2.0.13 py36h646ffb5_0
flask 0.12.2 py36hb24657c_0
flask-cors 3.0.3 py36h2d857d3_0
fontconfig 2.12.4 h88586e7_1
freetype 2.8 hab7d2ae_1
get_terminal_size 1.0.0 haa9412d_0
gevent 1.2.2 py36h2fe25dc_0
glib 2.53.6 h5d9569c_2
glob2 0.6 py36he249c77_0
gmp 6.1.2 h6c8ec71_1
gmpy2 2.0.8 py36hc8893dd_2
graphite2 1.3.10 hf63cedd_1
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harfbuzz 1.7.4 hc5b324e_0
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html5lib 1.0.1 py36h2f9c1c0_0
icu 58.2 h9c2bf20_1
idna 2.6 py36h82fb2a8_1
imageio 2.2.0 py36he555465_0
imagesize 0.7.1 py36h52d8127_0
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ipywidgets 7.1.1 py36_0
isort 4.2.15 py36had401c0_0
itsdangerous 0.24 py36h93cc618_1
jbig 2.1 hdba287a_0
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jinja2 2.10 py36ha16c418_0
jpeg 9b h024ee3a_2
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libastra 1.8.3 h5d93b39_0 astra-toolbox libcurl 7.58.0 h1ad7b7a_0
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libffi 3.2.1 hd88cf55_4
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libsodium 1.0.15 hf101ebd_0
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libstdcxx-ng 7.2.0 h7a57d05_2
libtiff 4.0.9 h28f6b97_0
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locket 0.2.0 py36h787c0ad_1
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tomopy 1.1.2 py36_0 conda-forge toolz 0.9.0 py36_0
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typing 3.6.2 py36h7da032a_0
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dmpelt commented 6 years ago

Hi! Sorry for the late reply. Can you send the script you used for reconstructing the data? Maybe we can use that to figure out what is going wrong...