Load other library, such as netCDF4

[SiqiLiOcean]

Hi,

I am writing a python code named 'test_visit.py'. I will run it via 'visit -cli -nowin -s test_visit.py'. In the code, I can load the visit via 'import visit' or 'import visit_utils' successfully.

The test_visit.py is as:
import visit
import netCDF4
fin = "./cbb_0001.nc"
exit()

But when I load the other libraries, such as netCDF4, the error shows:
No module named 'netCDF4'.

I installed it via 'conda install' and it can be loaded in my other python codes and run smoothly via 'python *.py'. Any suggestion would be helpful. Thanks.

Regards,
Siqi

[JustinPrivitera]

The issue is likely with which python you're using. VisIt's python doesn't have access to libraries outside of the following:

alabaster
babel
calver
certifi
charset_normalizer
cython.py
distutils-precedence.pth
docutils
easy-install.pth
editables
flit_core
hatchling
idna
imagesize
importlib_metadata
jinja2
markupsafe
numpy
packaging
pathspec
pip
pkg_resources
pluggy
pygments
pyximport
requests
setuptools
snowballstemmer
sphinx
sphinx_rtd_theme
sphinx_tabs
sphinxcontrib
sphinxcontrib_devhelp-1.0.2-py3.9-nspkg.pth
sphinxcontrib_jsmath-1.0.1-py3.9-nspkg.pth
sphinxcontrib_qthelp-1.0.3-py3.9-nspkg.pth
sphinxcontrib_serializinghtml-1.1.5-py3.9-nspkg.pth
toml
tomli
trove_classifiers
urllib3
wheel
zipp

If you're running a script with VisIt's python, you can't use matplotlib, for example. There is a way to use VisIt with the system python, but it can be somewhat cumbersome. My suggestion would be to try that and let us know what issues you run into.

[SiqiLiOcean]

Thank you so much for your answer.

The reason I want to load netCDF4 is that I want to read the dimension length from the input dataset (in netCDF4 format). For example, my dataset file contains the dimensions like node, nele, siglay, siglev. Is there any way to get their value in VisIt?

Thanks.

[JustinPrivitera]

We can ask for the number of nodes and number of elements using the query interface (if we have an active, non-hidden plot).

Query("NumNodes", use_actual_data=1)
nnodes = GetQueryOutputValue()
Query("NumZones", use_actual_data=1)
nzones = GetQueryOutputValue()

I'm not familiar with netCDF and I don't know what siglay and siglev are. I see that there is a SigmaLayer_Mesh and SigmaLevel_Mesh included with data read from the FVCOMReader in the netCDF plugin. We can ask for the spatial extents of one of these meshes with a Spatial Extents query:

Query("SpatialExtents", use_actual_data=1)
spatialExtents = GetQueryOutputValue()

Does that answer your questions? How can I assist you further?

[SiqiLiOcean]

Thank you so much for your answer.

When I use the command:
Query("NumNodes", use_actual_data=1)
nnodes = GetQueryOutputValue()
Query("NumZones", use_actual_data=1)
nzones = GetQueryOutputValue()

I got nnodes = 56200.0 and nzones = 100377.0 which are different from their real values. If I open the netCDF via python or matlab, the values should be 5620 and 11153.

The siglay and siglev are two dimension lengths for the vertical coordinate of the FVCOM model. I draw a figure and hope it would help. 'siglev' is short for sigma level, and 'siglay' is short for sigma layer. The siglev number is always larger than the siglay number. In the picture below, there are totally 4 siglev and 3 siglay. Each siglay is at the middle of the two siglev.

Thanks.