Merge pull request #18 from sci-visus/cornell2024-demo

Cornell2024 demo

.github/workflows/build-openvisuspy.yml

@@ -0,0 +1,50 @@
+name: build-openvisus
+on: [push] 
+
+env:
+  PYPI_USERNAME: ${{ secrets.PYPI_USERNAME }}
+  PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
+
+
+jobs:
+
+  build-ubuntu:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false  
+      matrix:
+        python-version: [ '3.9', '3.10'] 
+    steps:
+
+      # git clone
+      - uses: actions/checkout@v2
+
+      # login in Docker
+      - uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_TOKEN }}
+
+      # build
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: x64
+      - run: |
+          set -ex
+          export PYTHON_VERSION=${{ matrix.python-version }}
+          source scripts/ubuntu.sh
+
+
+
+
+
+
+
+
+
+
+
+
+
+

.gitignore

@@ -11,5 +11,10 @@ build
 .vscode
 **/*.npz
 **/*.npy
+deploy/.env
+deploy/inventory.ini
+
+
+
 
 

Dockerfile

@@ -0,0 +1,17 @@
+FROM python:3.10
+
+RUN python3 -m pip install --upgrade pip
+
+COPY requirements.txt ./
+RUN python3 -m pip install -r requirements.txt
+
+RUN python3 -m pip install --upgrade OpenVisusNoGui
+
+ARG GIT_TAG
+RUN python3 -m pip install openvisuspy==$GIT_TAG
+
+CMD ["jupyter", "lab", "--allow-root", "--notebook-dir='/usr/local/lib/python3.10/site-packages/openvisuspy/notebooks'", "--port 8888", "--NotebookApp.token=''", "--NotebookApp.allow_origin='*'", "--ip", "0.0.0.0""]
+
+
+
+

README.md

@@ -1,170 +1,125 @@
 # Instructions
 
+Important:
 
-## Windows PIP installation
+- use python `3.10` or `3.11`.  **DO NOT** use `python312` does not have a good match for `libzmq`
+- use  JupyterLab v3 (**NOT v4**) because bokeh does not work (see https://github.com/bokeh/jupyter_bokeh/issues/197)
 
-(OPTONAL) Remove old environment:
+## Installation
 
-```bat
-.venv\Scripts\deactivate
-rmdir /s /q  .venv
-rmdir /s /q  "%USERPROFILE%\.jupyter"
-```
-
-Install new version:
-- use python `3.10` or `3.11`. 
-- **DO NOT** use `python312` does not have a good match for `libzmq`
-- use  JupyterLab v3 (**NOT v4**) because bokeh does not work
-  - https://github.com/bokeh/jupyter_bokeh/issues/197
+In Windows:
 
 ```bash
-python -m venv .venv
-.venv\Scripts\activate
+set PATH=c:\Python310;%PATH%
 where python
 
-# OPTIONAL
-# python.exe -m pip install --upgrade pip
+python.exe -m venv .venv
+.venv\Scripts\activate
 
-# 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" 
+python.exe -m pip install --upgrade pip
+python.exe -m pip install -r requirements.txt
 
+# install the latest version of OpenVisus
+python.exe -m pip install --upgrade OpenVisusNoGui openvisuspy
+```
 
-# (OPTIONAL) in debug just use local paths
-# set PYTHONPATH=C:\projects\OpenVisus\build\RelWithDebInfo;.\src
+In MacOs/Linux:
 
-# or install binaries...
-python -m pip install OpenVisusNoGui openvisuspy
+```bash
 
-# test import 
-python -c "import OpenVisus"
-python -c "import openvisuspy"
+python3 -m venv .venv
+source .venv/Scripts/activate
+python3 -m pip install --upgrade pip
+python3 -m pip install -r requirements.txt
 
-# (OPTIONAL) save the output for the future
-# pip freeze 
+# install the latest version of OpenVisus
+python3 -m pip install --upgrade OpenVisusNoGui openvisuspy
 ```
 
-## Run Dashboards 
-
+## Dashboards 
 
-Change path and script as needed:
+In Windows:
 
 ```bash
 .venv\Scripts\activate
+python.exe -m panel serve ./app --dev --args ./json/dashboards.json
+```
 
-# set PYTHONPATH=C:\projects\OpenVisus\build\RelWithDebInfo;.\src
+In MacOs/Linux:
 
-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
+```bash
+source .venv/bin/activate
+python.exe -m panel serve ./app --dev --args ./json/dashboards.json
+```
+
+## Notebooks
 
-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"
+In Windows:
 
-# 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"
+```bash
+.venv\Scripts\activate
+jupyter lab ./notebooks
 ```
 
-## Chess demos
+In MacOs/Linux:
 
 ```bash
-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"
+source .venv/bin/activate
+jupyter lab ./notebooks
 ```
 
-## Signal1d demos
+Important: if Panel is not working you may have to do:
 
 ```bash
+pskill python
+jupyter nbconvert --clear-output --inplace notebooks/test-panel.ipynb  
+jupyter trust notebooks/test-panel.ipynb  
+```
+
 
-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"
+## Volume Rendering
 
-# 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"
+```bash
+python test/test-pyvista.py
+python test/test-vtkvolume.py 
 ```
 
-## Run notebooks
+## Debug openvisuspy
 
-### Setup Jupyter Lab
+Debug mode in Windows
 
 ```bash
+.venv\Scripts\activate
 
-# 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
-```
-
-```bash
+set PATH=c:\Python310;%PATH%
 
-# empty all output cells
-python scripts/run_command.py "jupyter nbconvert --clear-output --inplace {notebook}" "examples/notebooks/*.ipynb"
+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
 
-# trust notebook
-python scripts/run_command.py "jupyter trust {notebook}" "examples/notebooks/*.ipynb"
+set PYTHONPATH=C:\projects\OpenVisus\build\RelWithDebInfo;.\src
 
-jupyter lab .
+# dashboards
+python.exe -m panel serve ./app --dev --args ./json/dashboards.debug.json
 
-# [OK ] test-bokeh.ipynb
-# [OK ] test-ipywidgets.ipynb
-# [OK ] test-matplotlib.ipynb
-# [OK ] test-panel.ipynb
-# [OK ] test-pyvista.ipynb 
+# jupyter lab
+python.exe -m jupyter lab notebooks/ov-dashboards.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?**
+python.exe -m panel serve ./app --dev --args "https://atlantis.sci.utah.edu/mod_visus?action=readdataset&dataset=chess-intro&cached=arco" --probe
 ```
 
-## (OPTIONAL) Test Volume rendering
+Deploy binaries
 
 ```bash
-# test pyvista
-python examples/python/test-pyvista.py
+./scripts/new_tag.sh
 
-# test vtk volume
-python examples/python/test-vtkvolume.py 
+# you may want to change the tag in docker-compose.yml too
 ```
 
-## Developers only
-
-Deploy new binaries
 
-- **Update the `PROJECT_VERSION` inside `pyproject.toml`**
-
-```bash
-# source .venv/bin/activate
-./scripts/new_tag.sh
-```
 

app/main.py

@@ -0,0 +1,43 @@
+import os
+import sys
+import logging
+import base64
+import json
+import panel as pn
+
+from openvisuspy import SetupLogger, Slice, ProbeTool,cbool
+
+
+# ////////////////////////////////////////////////////////////////////////////
+if __name__.startswith('bokeh'):
+
+    pn.extension(
+        "ipywidgets",
+        "floatpanel",
+        "codeeditor",
+        log_level="DEBUG",
+        notifications=True,
+        sizing_mode="stretch_width"
+    )
+
+    query_params = {k: v for k,v in pn.state.location.query_params.items()}
+
+    log_filename = os.environ.get("OPENVISUSPY_DASHBOARDS_LOG_FILENAME", "/tmp/openvisuspy-dashboards.log")
+    logger = SetupLogger(log_filename=log_filename, logging_level=logging.DEBUG)
+
+    slice = Slice()
+    slice.load(sys.argv[1])
+
+    # load a whole scene
+    if "load" in query_params:
+        body = json.loads(base64.b64decode(query_params['load']).decode("utf-8"))
+        slice.setBody(body)
+
+    # select from list of choices
+    elif "dataset" in query_params:
+        scene_name = query_params["dataset"]
+        slice.scene.value = scene_name
+
+    main_layout = slice.getMainLayout()
+    main_layout.servable()
+