openvisuspy
Project description
Instructions
Windows PIP installation
(OPTONAL) Remove old environment:
.venv\Scripts\deactivate
rmdir /s /q .venv
rmdir /s /q "%USERPROFILE%\.jupyter"
Install new version:
- use python
3.10
or3.11
. - DO NOT use
python312
does not have a good match forlibzmq
- use JupyterLab v3 (NOT v4) because bokeh does not work
python -m venv .venv
.venv\Scripts\activate
where python
# OPTIONAL
# python.exe -m pip install --upgrade pip
# removed `itkwidgets`, since pyvista seems to be better maintained/compatible
# see https://github.com/imjoy-team/imjoy-jupyterlab-extension/issues/6#issuecomment-1898703563
# `imjoy` is needed for itkwidgets on jupyterlab
python -m pip install --verbose --no-cache --no-warn-script-location boto3 colorcet fsspec numpy imageio urllib3 pillow xarray xmltodict plotly requests scikit-image scipy seaborn tifffile pandas tqdm matplotlib zarr altair cartopy dash fastparquet folium geodatasets geopandas geoviews lxml numexpr scikit-learn sqlalchemy statsmodels vega_datasets xlrd yfinance pyarrow pydeck h5py hdf5plugin netcdf4 nexpy nexusformat nbgitpuller intake ipysheet ipywidgets bokeh==3.3.4 ipywidgets-bokeh panel==1.3.8 holoviews hvplot datashader vtk pyvista trame trame-vtk trame-vuetify notebook "jupyterlab==3.6.6" jupyter_bokeh jupyter-server-proxy jupyterlab-system-monitor "pyviz_comms>=2.0.0,<3.0.0" "jupyterlab-pygments>=0.2.0,<0.3.0"
# (OPTIONAL) in debug just use local paths
# set PYTHONPATH=C:\projects\OpenVisus\build\RelWithDebInfo;.\src
# or install binaries...
python -m pip install OpenVisusNoGui openvisuspy
# test import
python -c "import OpenVisus"
python -c "import openvisuspy"
# (OPTIONAL) save the output for the future
# pip freeze
Run Dashboards
Change path and script as needed:
.venv\Scripts\activate
# set PYTHONPATH=C:\projects\OpenVisus\build\RelWithDebInfo;.\src
set BOKEH_ALLOW_WS_ORIGIN=*
set BOKEH_LOG_LEVEL=debug
set VISUS_CPP_VERBOSE=1
set VISUS_NETSERVICE_VERBOSE=1
set VISUS_VERBOSE_DISKACCESS=0
set VISUS_CACHE=c:/tmp/visus-cache
python -m panel serve src/openvisuspy/dashboards --dev --args "D:/visus-datasets/david_subsampled/visus.idx"
python -m panel serve src/openvisuspy/dashboards --dev --args "D:/visus-datasets/2kbit1/zip/hzorder/visus.idx"
# not sure why I cannot cache in arco an IDX that is NON arco
python -m panel serve src/openvisuspy/dashboards --dev --args "https://atlantis.sci.utah.edu/mod_visus?dataset=david_subsampled&cached=idx"
python -m panel serve src/openvisuspy/dashboards --dev --args "https://atlantis.sci.utah.edu/mod_visus?dataset=2kbit1&cached=idx"
Chess demos
python -m panel serve src/openvisuspy/dashboards --dev --args "D:/visus-datasets/chess/nsdf-group/dashboards.json"
python -m panel serve src/openvisuspy/dashboards --dev --args "D:\visus-datasets\chess\nsdf-group\datasets\near-field-nexus\visus.idx"
python -m panel serve src/openvisuspy/dashboards --dev --args "https://raw.githubusercontent.com/nsdf-fabric/nsdf-slac/main/dashboards.json"
Signal1d demos
python -m panel serve src/openvisuspy/dashboards --dev --args "D:/visus-datasets/signal1d/visus.idx"
python -m panel serve src/openvisuspy/dashboards --dev --args "D:/visus-datasets/signal1d_slac/visus.idx
python -m panel serve src/openvisuspy/dashboards --dev --args "https://maritime.sealstorage.io/api/v0/s3/utah/visus-datasets/signal1d_slac/visus.idx?cached=arco&access_key=any&secret_key=any&endpoint_url=https://maritime.sealstorage.io/api/v0/s3"
python -m panel serve src/openvisuspy/dashboards --dev --args c:\big\visus-datasets\signal1d_slac_max\visus.idx
python -m panel serve src/openvisuspy/dashboards --dev --args "https://maritime.sealstorage.io/api/v0/s3/utah/visus-datasets/signal1d_slac_max/visus.idx?cached=arco&access_key=any&secret_key=any&endpoint_url=https://maritime.sealstorage.io/api/v0/s3"
# single NUMPY signals (NOTE: it's compunting min-max so it will be slow)
python -m panel serve src/openvisuspy/dashboards --dev --args "https://maritime.sealstorage.io/api/v0/s3/utah/supercdms-data/CDMS/UMN/R68/Raw/07180816_1648/07180816_1648_F0006/events/00135/banks/SCD0/data.npz?profile=sealstorage_ro&endpoint_url=https://maritime.sealstorage.io/api/v0/s3"
Run notebooks
Setup Jupyter Lab
# check jupyter paths
where jupyter
jupyter kernelspec list
# Available kernels:
# python3 C:\projects\openvisuspy\.venv\share\jupyter\kernels\python3
# Check extensions: **all extensions should show `enabled ok...`**
# e.g you will need @bokeh/jupyter_bokeh for bokeh (installed by `jupyter_bokeh``)
# e.g you will need @pyviz/jupyterlab_pyviz for panel (installed by `pyviz_comms``)
# avoid any message `is not compatible with the current JupyterLab` message at the bottom
jupyter labextension list
# if `Build recommended`, or `needs to be included in build:
# @plotly/dash-jupyterlab needs to be included in build
pip install nodejs-bin[cmd]
jupyter lab clean --all
jupyter lab build
# rmdir /s /q C:\Users\scrgi\AppData\Local\Yarn
# Look also for additional extensions loaded from here
# dir .venv\share\jupyter\lab\extensions\*
jupyter labextension list
# empty all output cells
python scripts/run_command.py "jupyter nbconvert --clear-output --inplace {notebook}" "examples/notebooks/*.ipynb"
# trust notebook
python scripts/run_command.py "jupyter trust {notebook}" "examples/notebooks/*.ipynb"
jupyter lab .
# [OK ] test-bokeh.ipynb
# [OK ] test-ipywidgets.ipynb
# [OK ] test-matplotlib.ipynb
# [OK ] test-panel.ipynb
# [OK ] test-pyvista.ipynb
# [OK ] ov-dashboards.ipynb
# [OK ] ov-retina-rabbit-matplot.ipynb
# [OK ] ov-signal.ipynb
# [ERR] ov-vr.ipynb **THIS DOES NOT WORK IN CHROME, problems with VTK?**
(OPTIONAL) Test Volume rendering
# test pyvista
python examples/python/test-pyvista.py
# test vtk volume
python examples/python/test-vtkvolume.py
Developers only
Deploy new binaries
- Update the
PROJECT_VERSION
insidepyproject.toml
# source .venv/bin/activate
./scripts/new_tag.sh
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