Add custom metadata to .xml file

[lucas-diedrich]

Some users requested that the XML file be able to store custom metadata, especially mappings between cell types and wells (wells are stored in the CapID feature).

Quickfix

Note that pyLMD currently provides metadata support via its geopandas integration. For example one can store cell shapes together with custom metadata in a geopandas dataframe.

import geopandas as gpd 
from shapely import Polygon
import lmd.lib as pylmd

gdf = gpd.GeoDataFrame(
     data={"well": ["A1"], "my_annotation": ["T cell"]}, 
     geometry=[Polygon([[0, 0], [1, 0], [0, 1], [0, 0]])
)

gdf.write("/path/to/file-with-metadata.geojson")

A collection can then be created via the collection.load_geopandas function. This drops all unknown metadata.

collection = pylmd.Collection()
collection.load_geopandas(gdf)
collection.save("/path/to/xml-without-metadata.xml")

This creates the issue that there might exist two files with different content.