mochada_kit

Python code for generating MODA (MOdelling DAta) and CHADA (CHAracterisation DAta) workflow diagrams and tables using plantuml, with machine-readable, enhanced design based on bespoke themes.

Main uses

1. Generate MODA and/or CHADA workflow diagrams with bespoke themes, making them machine readable.

The plantuml code below produces a CHADA workflow diagram for EBSD in the SEM. After a command signalling the start of the code, we load one of the bespoke themes available in mochada_kit. This allows us to apply a "stereotype" to each element, giving it a colour according to its type. Each theme has different colours for the various elements (various colour schemes are available and you can define your own).

• The text to be displayed in an element is defined between a colon and a semicolon e.g. :User Case;
• The type of the element is specified by applying a stereotype between two sets of angled brackets *e.g.* <<user_case>>
• This allows the code to be machine readable: the text of each element can be easily associated with the type of element and connected to the antecedent and descendant elements.
• Note that the definition of an element can be split over multiple lines.

@startuml
!theme MOCHADA-plasma from ../../themes
:Bulk sample or thin film; <<user_case>>
:Set up experimental geometry:
sample tilt (<U+00B0>), working distance (mm),
detector distance (mm); <<experiment>>
:Acquire electron image (SE, BSE, FSE); <<experiment>>
:Electron image(s); <<raw_data>>
:Define rectangular ROI, step size,
detector and indexing parameters; <<experiment>>
:Acquire EBSD patterns at all points in ROI; <<experiment>>
:EBSD pattern for each point; <<raw_data>>
:Hough indexing (automatic); <<data_processing>>
:Euler angles and phase ID
for each point in map; <<final_data>>
:Analysis of orientations (user controlled); <<data_processing>>
:Orientation maps, Pole figures
Quantitative measures //e.g.// grain size; <<final_data>>
@enduml

2. Generate CHADA tables from a single json file, with bespoke themes, and optionally hyperlinking different tables

3. Extract and display metadata from an HDF5 file as an easy-to-read diagram with optional bespoke highlighting

4. Define your own colour schemes and stereotypes

Getting started

• to get an idea of what the workflow diagrams, tables and json diagrams look like, please have a look at the .svg images in `mochada_kit/gallery`. You can open .svg files in any browser. The plantuml (puml) code on which they are based is available in `mochada_kit/gallery/puml_code`.
• detailed examples are provided as jupyter notebooks in `mochada_kit/examples` and as Python scripts in `mochada_kit/examples/python_scripts`. Here is a short description of each example:

Reference

This package is being developed as part of the EU project: MaMMoS