Tips and tricks

Adding this repository to a project

The easiest way is to use git's submodules feature:

git submodule add git@github.com:marcinofulus/misc_tools.git misc_tools

Logging vs print and jupyter notebooks

Because this module can be imported to some non-jupyter project, it's good practice to use the logging module instead of raw print() calls.

To make log entries visible in jupyter notebooks, copy the following code:

import logging
logging.getLogger().setLevel(logging.DEBUG)

To add timestamps (with milliseconds resolution) to those entries, use:

import logging
formatter = logging.Formatter('[%(asctime)s] [%(levelname)7s] [%(name)s] %(message)s')
for handler in logging.getLogger().handlers:
    handler.setFormatter(formatter)

Resources

• VTK Textbook
  https://vtk.org/vtk-textbook/
  https://gitlab.kitware.com/vtk/textbook
• VTK User's Guide
  https://vtk.org/vtk-users-guide/

Changelog

2019.01.31

Renaming:

• vtk2npy --> sailfish_vti_to_npy
• stlImageActor --> read_vtk
• vtlImageActor --> read_vtk
• unstructuredImage --> read_vtk
• getFileReaderOutput --> read_vtk

Logging / print

• replaced all print() calls with logging module.

Added:

• conversions to and from numpy
• SimpleITK conversions