Protocols and Viewers
Writing a protocol
In this tutorial we will see how to create a protocol that performs some useful calculation on volumes. As an illustrative example, in this practice we construct a protocol that performs a low pass filter of a volume using a system call. In particular you will learn to:
Define a protocol from scratch and letting Scipion know that it exists
Define a form with a variety of input parameters (FloatParam, EnumParam, PointerParam) and how to hide some of the form parameters depending on specific choices in the form
How to access basic information of EM objects as their pixel size, box size etc.
How to invoke a command line in the shell from inside Scipion
How to register an output object in Scipion so that it can be used as an input for the next protocol
How to read images and volumes in Python in order to perform calculations inside the Python routines
How to construct support functions that help to prevent errors and document the calculations
You can choose to:
Writing a viewer
In Scipion there are two kinds of viewers: with and without GUI forms.
By default any protocol output will be displayed using Scipion default viewer (without any form). This will depend on the type of Scipion object being displayed (Volume, SetOfParticles etc.) However, you may want to construct specific viewers for your protocol.
In this practice you will learn how to:
Access objects from the invoking protocol
Invoke a Scipion viewer for a Scipion object
Invoke a Scipion viewer for a file (that is not an object)
How to construct your own viewer using standard Python libraries
You can learn how to create viewers: