openvisuspy 1.0.20

openvisuspy

OpenViSUS Visualization project

The official OpenVisus C++ GitHub repository is here.

Install openvisuspy

Create a virtual environment. This step is optional, but best to avoid conflicts:

• for windows users you can do doskey python3=python $* and .venv/Scripts/activate.bat

python3 -m venv .venv
source .venv/bin/activate
python3 -m pip install --upgrade pip

Install python packages, technically only numpy is stricly needed, but to access cloud storage and show dashboards/notebooks, you need additional packages too.

python3 -m pip install numpy boto3 xmltodict colorcet requests scikit-image matplotlib bokeh panel itkwidgets[all] pyvista vtk jupyter

Next, install Openvisus packages.

If you do not need the OpenVisus viewer (or if you are in Windows WSL):

python3 -m pip install --upgrade OpenVisusNoGui
python3 -m pip install --upgrade openvisuspy 

if you do need the OpenVisus viewer:

python3 -m pip install --upgrade OpenVisus
python3 -m OpenVisus configure 
python3 -m pip install --upgrade openvisuspy 

if you are in debugging mode you may want to reference your local packages:

python3 -m pip uninstall OpenVisusNoGui
python3 -m pip uninstall OpenVisus
python3 -m pip uninstall openvisuspy 
export PYTHONPATH=./src;/projects/OpenVisus/build/RelWithDebInfo

Bokeh Dashboards

python3 -m bokeh serve "examples/dashboards/app"  --dev --address localhost --args --single
python3 -m bokeh serve "examples/dashboards/app"  --dev --address localhost --args --multi
python3 -m bokeh serve "examples/dashboards/nasa" --dev --address localhost --args --single

Other misc examples:

python -m bokeh serve "examples/dashboards/app"  --dev --args --dataset  "https://atlantis.sci.utah.edu/mod_visus?dataset=david_subsampled&cached=1" --palette Greys256    --palette-range "[0, 255]"
python -m bokeh serve "examples/dashboards/app"  --dev --args --dataset  "https://atlantis.sci.utah.edu/mod_visus?dataset=2kbit1&cached=1"           --palette Greys256    --palette-range "[0, 255]"
python -m bokeh serve "examples/dashboards/app"  --dev --args --dataset  "https://atlantis.sci.utah.edu/mod_visus?dataset=chess-zip&cached=1"        --palette Viridis256  --palette-range "[-0.017141795, 0.012004322]" --num-views 3 

Probes

# this is needed for windows
# set PYTHONPATH=.\src;c:\projects\OpenVisus\build\RelWithDebInfo

ssh chpc3

screen -ls


export BOKEH_ALLOW_WS_ORIGIN=*
export BOKEH_LOG_LEVEL=debug

python3 -m pip install --upgrade OpenVisus openvisuspy

Chess

screen -S chess-probes
python3  -m bokeh serve examples/dashboards/app \
    --dev    \
    --address="0.0.0.0"    \
    --port 10933 \
   --args  \
   --dataset "http://atlantis.sci.utah.edu/mod_visus?dataset=block_raw&cached=1"\
   --palette "colorcet.coolwarm" \
   --palette-range "[ 8644., 65530.//4]" \
   --probes \
   --show-options "['palette','field','offset','direction']"

Open http://chpc3.nationalsciencedatafabric.org:10933/run

Foam - Probes

Foam, Multiple timesteps (range can be changed as needed):

screen -S foam-probes 
python3  -m bokeh serve examples/dashboards/app \
    --dev \
    --address="0.0.0.0"    \
    --port 10934 \
    --args  \
    --dataset "http://atlantis.sci.utah.edu/mod_visus?dataset=foam-2022-01&cached=1" \
    --palette "colorcet.coolwarm" \
    --palette-range "[ 8644., 65530.//4]" \
    --probes \
    --show-options "['palette','field','offset','direction','timestep']"

Open http://chpc3.nationalsciencedatafabric.org:10934/run

Demo of multiple data sets on one dashboard

python -m bokeh serve "examples/dashboards/app"  --dev --args --dataset  "chess" --palette Viridis256  --palette-range "[-0.017141795, 0.012004322]" --num-views 3

Panel Dashboards

python -m panel serve "examples/dashboards/app"  --dev --address localhost --args --single
python -m panel serve "examples/dashboards/app"  --dev --address localhost --args --multi
python -m panel serve "examples/dashboards/nasa" --dev --address localhost --args --single

Jupyter Notebooks

python3 -m jupyter notebook ./examples/notebooks 

Developers only

Debug run:

• some command can be dangerous

export BOKEH_ALLOW_WS_ORIGIN=*
export BOKEH_LOG_LEVEL=debug
export VISUS_CPP_VERBOSE=0
export VISUS_NETSERVICE_VERBOSE=0
export PYTHONPATH=${PWD}/src

Deploy new binaries

• Update the PROJECT_VERSION inside pyproject.toml

export PYPI_USERNAME="scrgiorgio"
export PYPI_PASSWORD="..."
rm -f dist/*  
python3 -m build .
python3 -m twine upload --username "${PYPI_USERNAME}"  --password "${PYPI_PASSWORD}" --skip-existing "dist/*.whl" --verbose 

(EXPERIMENTAL) Pure Python Backend

This version may be used for cpython too in case you cannot install C++ OpenVisus (e.g., WebAssembly).

It will not work with S3 cloud-storage blocks.

Bokeh dashboards:

python3 -m bokeh serve "examples/dashboards/app"  --dev --address localhost --port 8888 --args --py  --single
python3 -m bokeh serve "examples/dashboards/app"  --dev --address localhost --port 8888 --args --py  --multi

Panel dashboards:

python -m panel serve "examples/dashboards/app"  --dev --address localhost --port 8888 --args --py --single
python -m panel serve "examples/dashboards/app"  --dev --address localhost --port 8888 --args --py --multi

Jupyter notebooks:

export VISUS_BACKEND=py
python3 -m jupyter notebook ./examples/notebooks

Demos

REMEMBER to resize the browswe window, otherwise it will not work:

• https://scrgiorgio.it/david_subsampled.html
• https://scrgiorgio.it/2kbit1.html
• https://scrgiorgio.it/chess_zip.html

DEVELOPERS notes:

• grep for openvisuspy== and change the version consistently.

PyScript

Serve local directory

export VISUS_BACKEND=py
python3 examples/server.py --directory ./

Open the urls in your Google Chrome browser:

• http://localhost:8000/examples/pyscript/index.html
• http://localhost:8000/examples/pyscript/2kbit1.html
• http://localhost:8000/examples/pyscript/chess_zip.html
• http://localhost:8000/examples/pyscript/david_subsampled.html

JupyterLite

export VISUS_BACKEND=py
ENV=/tmp/openvisuspy-lite-last
python3 -m venv ${ENV}
source ${ENV}/bin/activate

# Right now jupyter lite seems to build the output based on installed packages. 
# There should be other ways (e.g., JSON file or command line) for specifying packages, but for now creating a virtual env is good enough\
# you need to have exactly the same package version inside your jupyter notebook (see `12-jupyterlite.ipynb`)
python3 -m pip install \
    jupyterlite==0.1.0b20 pyviz_comms numpy pandas requests xmltodict xyzservices pyodide-http colorcet \
    https://cdn.holoviz.org/panel/0.14.3/dist/wheels/bokeh-2.4.3-py3-none-any.whl \
    panel==0.14.2 \
    openvisuspy==1.0.100 \
    jupyter_server 

rm -Rf ${ENV}/_output 
jupyter lite build --contents /mnt/c/projects/openvisuspy/examples/notebooks --output-dir ${ENV}/_output

# change port to avoid caching
PORT=14445
python3 -m http.server --directory ${ENV}/_output --bind localhost ${PORT}

# or serve
jupyter lite serve --contents ./examples/notebooks --output-dir ${ENV}/_output --port ${PORT} 

# copy the files somewhere for testing purpouse
rsync -arv ${ENV}/_output/* <username>@<hostname>:jupyterlite-demos/