Render application is loaded in an iframe. The package allows pointing the iframe at:
- Render deployed to a server
- A Python server running on localhost and serving a production build of render, which has been bundled with this package
The are three ways to load the data:
- Specifying a URL to a server
- Specifying a local path will start a Python server on localhost. The URL to the dataset on localhost will be passed to the application in the iframe
- Dragging-and-dropping the dataset does not use a server, it calls an API from the front end (It should the this under the hood https://developer.mozilla.org/en-US/docs/Web/API/File_API)
Has the ability to work both local and remote versions of Jupyter Notebook.
- Python 3.9+
- polus-server-ext iff running jupyter notebooks remotely.
pip install polus-render
git clone https://github.com/jcaxle/polus-render.git
cd polus-render
[optional] python -m venv venv
[optional] "venv/Scripts/Activate"
pip install -r requirements.txt
Optional steps refer to setting up venv which is recommended.
polus-render
| Build Instructions.md // Instructions on how to update Pypi project
| MANIFEST.in // Packaging entries
| pyproject.toml // Pypi config
| README
| requirements.txt
└───src
| polus.py // Main file, contains render function used by user
| polus-render-wrapper.py // Unused file used for a scrapped project. Can be used as a reference for input sanitization
| zarr_file_server.py // Contains server only used for serving local build of Polus Render
├───apps
│ ├───render-ui // Build files of Polus Render
│ └───updog-render // Server used for serving files.
- Refer to Build Instructions.md
polus-render is bundled with a build of Polus Render which supports additional functionality compared to the web version. Table is accurate as of 10/4/2023.
| Version | Zarr from URL/Path | TIF from URL/Path | Micro-JSON Support | Zarr/TIF Drag & Drop | Micro-JSON Drag & Drop |
|---|---|---|---|---|---|
| Local | ✔️ | ✔️ | ✔️ | ✔️ | ✔️ |
| Online | ✔️ |
TODO
TODO
from polus.polus_render import render, nb_render
# pathlib and urllib are built-ins
from urllib.parse import urlparse
from pathlib import Path
# Embeds an IFrame of a local build of Polus Render into Jupyter Notebooks
render()
# Embeds an IFrame of Polus Render into Jupyter Notebooks
render(use_local_render=False)
# Embeds an IFrame of a local build of Polus Render with an image file hosted at "https://viv-demo.storage.googleapis.com/LuCa-7color_Scan1/"
render(image_location=urlparse("https://viv-demo.storage.googleapis.com/LuCa-7color_Scan1/"))
# Embeds an IFrame of a local build of Polus Render with an image hosted locally at "C:\Users\JeffChen\OneDrive - Axle Informatics\Documents\zarr files\pyramid.zarr"
render(image_location=Path(r"C:\Users\JeffChen\OneDrive - Axle Informatics\Documents\zarr files\pyramid.zarr"))
# Embeds an IFrame of a local build of Polus Render with an image and overlay file that is hosted locally
render(image_location=Path(r"C:\Users\JeffChen\OneDrive - Axle Informatics\Documents\zarr files\pyramid.zarr"), \
microjson_overlay_location=Path(r"C:\Users\JeffChen\OneDrive - Axle Informatics\Documents\overlay files\x00_y01_c1_segmentations.json"))
# Embeds an IFrame of a local build of Polus Render with an image and overlay file that is hosted online
render(image_location=urlparse("https://files.scb-ncats.io/pyramids/segmentations/x00_y01_c1.ome.tif"), \
microjson_overlay_location=urlparse("https://files.scb-ncats.io/pyramids/segmentations/x00_y03_c1_segmentations.json"))
# Embeds an IFrame with a height of 1080 of a local build of Polus Render.
render(height=1080)
# Embeds an IFrame into remote jupyter notebooks. Use this function with argument nbhub_url to specify your notebooks url which must have lab in its url
nb_render(nbhub_url=urlparse("https://jh.scb-ncats.io/user/jeff.chen@axleinfo.com/user-namespaces/lab?"), image_location=Path("work/pyramid.zarr"))def render(image_location:Union[ParseResult, PurePath] = "", microjson_overlay_location:Union[ParseResult, PurePath] = "", width:int=960, height:int=500, image_port:int=0, \
microjson_overlay_port:int=0, use_local_render:bool=True, render_url:str = "https://render.ci.ncats.io/")->str:
"""
Displays Polus Render with args to specify display dimensions, port to serve,
image files to use, and overlay to use.
Param:
image_location(ParseResult|Purepath): Acquired from urllib.parse.ParseResult or Path, renders url in render.
If not specified, renders default render url.
microjson_overlay_location(ParseResult|Purepath): Acquired from urllib.parse.ParseResult or Path, renders url in render.
If not specified, renders default render url
width (int): width of render to be displayed, default is 960
height (int): height of render to be displayed, default is 500
image_port (int): Port to run local zarr server on if used (default is 0 which is the 1st available port).
microjson_overlay_port (int): Port to run local json server on if used (default is 0 which is the 1st available port).
use_local_render (bool): True to run local build of render with 1st available port, False to use render_url (default is True)
render_url (str): URL which refers to Polus Render. Used when run_local_render is False. (default is https://render.ci.ncats.io/)
Pre: zarr_port and json_port selected (if used) is not in use IF path given is Purepath
Returns: Render URL
"""
def nb_render(nbhub_url:ParseResult,image_location:Union[ParseResult, PurePath] = "", microjson_overlay_location:Union[ParseResult, PurePath] = "", width:int=960, height:int=500, \
use_local_render:bool=True, render_url:str = "https://render.ci.ncats.io/")->str:
"""
Variant of render() used for remote jupyter notebooks. Read render() for usage information
Param:
nbhub_url: URL used used for jupyterhub. Contains '/lab/' in its uri
image_location(ParseResult|Purepath): Acquired from urllib.parse.ParseResult or Path, renders url in render.
If not specified, renders default render url.
microjson_overlay_location(ParseResult|Purepath): Acquired from urllib.parse.ParseResult or Path, renders url in render.
If not specified, renders default render url
width (int): width of render to be displayed, default is 960
height (int): height of render to be displayed, default is 500
run_local_render (bool): True to run local build of render with 1st available port, False to use render_url (default is True)
render_url (str): URL which refers to Polus Render. Used when run_local_render is False. (default is https://render.ci.ncats.io/)
Returns: Render URL
"""- render() receives sanatized input. Check polus-render-wrapper.py or sample usage for examples on sanitizing input.
- render() builds up URL scheme fragments for render url, image url, and microjson url.
- If the image url and microjson url are file paths, serve the files on file servers pointing to either user specified port or a free port.
- If local render is used, build a server for it as well.
- At the end, combine render url fragments into a single url, insert it into an IFrame, and display it.
- Complete url string is returned not printed.
- For nb_render(), no servers are launched. Files are served from endpoints generated from the remote Jupyter Notebook's URL. The local build of render is served from the polus-server-ext instead of the bundled build files. Essentially, nb_render() runs serverless with the exception of the server that serves the remote Jupyter Notebooks itself.
- Two type of servers are used.
- Python HTTPServer with CORS and OPTIONS functionality to serve RenderUI
- Modified UpDog Flask server to serve local files to RenderUI