Jupyter notebooks¶
Chemiscope can be used as a widget in Jupyter notebooks, that should work in both Jupyter classic and JupyterLab. The widget can be created in default mode (showing both a structure and a map panel), or used to display only structures or only properties.
Once created, it is possible to interact with the widget using a traitlet interface, modeled after Jupyter widgets.
Creating a chemiscope widget¶
- chemiscope.show(frames=None, properties=None, meta=None, environments=None, shapes=None, settings=None, mode='default')¶
Show the dataset defined by the given
frames
andproperties
(optionallymeta
,environments
andshapes
as well) using an embedded chemiscope visualizer inside a Jupyter notebook. These parameters have the same meaning as in thechemiscope.create_input()
function.The
mode
keyword also allows overriding the default two-panels visualization to show only a structure panel (mode = "structure"
) or the map panel (mode = "map"
). These modes also make it possible to view a dataset for which properties (or frames) are not available.When inside a jupyter notebook, the returned object will create a new chemiscope visualizer displaying the dataset. The object exposes a settings traitlet, that allows to modify the visualization options (possibly even linking the parameters to another widget). Printing the value of the settings property is also a good way to see a full list of the available options.
The returned object also have a
save
function that can be used to save the dataset to a.json
or.json.gz
file to load it in the main website later. The visualization options will be those used in the active widget, so this is also a good way to tweak the appearence of the visualization before saving it.import chemiscope from sklearn.decomposition import PCA import ase.io pca = PCA(n_components=3) frames = ase.io.read(...) properties = { "PCA": pca.fit_transform(some_data), } widget = chemiscope.show(frames, properties) # display the dataset in a chemiscope visualizer inside the notebook widget # ... # NB: due to how traitlet work, you should always set the value of # the `settings` property. Only the properties that are explicitly # indicated will be modified. widget.settings = {"map": {"palette": "seismic"}} widget.settings["map"]["palette"] = "viridis" # << does nothing! # Save the file for later use widget.save("dataset.json")
- chemiscope.show_input(path, mode='default')¶
Loads and shows the chemiscope widget in
path
. Ifpath
ends with.gz
, the file is loaded as a gzip compressed JSON string.- Parameters:
path (str) – load the chemiscope widget from path.
mode (str) – widget mode, either
default
,structure
ormap
.
import chemiscope widget = chemiscope.show_input("dataset.json")