The Shell tab is a functional Python command line embedded within the program. The pipeline can be accessed directly
from the shell, and behaves like a dictionary keyed by variable names. Pylab is imported in the shell making a number of
MATLAB-style plotting and basic numeric commands accessible (see the matplotlib webpage for more docs).
One can, for example, plot a histogram of point amplitudes by executing
Pipeline data sources can be accessed by entering
pipeline.dataSources[datasource_key]. For a list of datasource keys, type
PYMEVisualize can be used directly from a Jupyter notebook. At the top of the notebook, enter
from PYME.LMVis import VisGUI,
%gui wx, and then
pymevis = VisGUI.ipython_pymevisualize(). This makes it possible to
access a PYMEVisualize instance from a notebook through the
pymevis variable. Setting
gives the user access to the PYMEVisualize pipeline in exactly the same way as described in Shell section.
An example of generating a point cloud, passing it to a tabular data source, and visualizing
the data source is shown in Fig. 16.
Please note that both PYME and the Jupyter kernel must be set up in the Framework build on a Mac
(see https://python-microscopy.org/doc/Installation/InstallationFromSource.html) for this to work.
To install the Jupyter kernel in the Framework build, activate
your_pyme_environment and then type
PATH/TO/CONDA/ENVIRONMENT/python.app/Contents/MacOS/python -m ipykernel install --user --name your_pyme_environment.