Interactive mask creation

Dynamo contains some really useful interactive tools for creating shape masks. In this mini-tutorial, we will use a legacy version of the dynamo_mapview GUI to create and apply a shaped mask on a reference.

Loading our data into mapview

First, we load our volume my_volume.mrc into the GUI with the following command

dpkdev.legacy.dynamo_mapview('my_volume.mrc');

Getting comfortable with the viewer

Here we go over some of the controls available in this viewer, you might have noticed there are a lot!

You can switch between viewing x-, y- or z-slices with the x, y and z buttons.

xyz switching image

You can switch between viewing either a single projection or a set of slices

singleproj image

Bandpass filters can be applied from the GUI by setting the band parameters then hitting the band button. The filter frequencies are set in Fourier pixels.

bandpass image

Symmetry can be applied from the GUI. Symmetry is applied along the z-axis of the volume.

symmetry image

The volume visualised can be reset to its original state at any time with the reset button.

reset button image

Mask creation

This section covers the basics of mask creation in dpkdev.legacy.dynamo_mapview()

You can create a shaped mask by

  • selecting the check-box next to the word shape in the Mask section

  • selecting either cylinder or ellipsoid

  • setting the x-, y- and z- radii and centers

hit the layer button to bring up a visualisation of the mask on the currently depicted slices. interactive mask creation image

You can save a mask by setting a filename in the Mask section and hitting save save mask image

You can apply a mask onto a volume and save the volume in the File I/O section