Images¶
libsbgnpy does not draw maps itself. render_sbgn sends a document to the rendering web service of Frank Bergmann at https://sbml.bioquant.uni-heidelberg.de/layout, which lays it out and returns the image:
from pathlib import Path
from libsbgnpy import read_sbgn_from_file, render_sbgn
sbgn = read_sbgn_from_file(Path("examples/sbgn/adh.sbgn"))
render_sbgn(sbgn, Path("adh.png"))
The request is equivalent to
Requirements and errors¶
Rendering needs an internet connection. The service is queried with a timeout of 60 seconds, requests raises a RequestException if it cannot be reached or answers with an error. If it answers with something else than an image, e.g., the html page of a proxy, or with an image larger than 50 MB, render_sbgn raises a RenderError, a subclass of RequestException. The image file is written atomically, so a failed rendering never leaves a partial file and an existing image stays as it is.
Only PNG is supported, and the image file has to end in .png (in any case); anything else raises a ValueError before the request is made.
The service currently returns JPEG images
The web service declares its answer as image/png, but currently sends a JPEG. render_sbgn writes the image as it is and logs a warning; most image viewers and browsers detect the actual format.
The layout comes from the document¶
The service draws the map at the coordinates the document carries, i.e., the Bbox of every glyph and the start, end and next points of every arc. It does not compute a layout, so a document without coordinates renders as an empty or a collapsed image. See SBGN maps for how the coordinates are set.
Examples¶
| example | what it shows |
|---|---|
ethanol.py |
build a map step by step and render it after every step |