Plotting axis angle pairs as a map

[maclariz]

It would be nice to be able to plot the axis/angle pairs nicely as maps. I have the angles out and plotted, although blacking out the bits where there is no data (e.g. vacuum) would make this nicer still. I am still trying to figure out a way to get the axes in a plottable form on a rational color scale.

[hakonanes]

Can you explain what you mean by "maps" in terms of rotations (axis/angle pairs)? You mean giving the axes [uvw] in the inverse pole figure of a symmetry a color, like for orientations?

Masking of maps are most easily done with boolean arrays and CrystalMap, see examples of this a bit down in the "Crystal map/Plotting" section of the tutorial in the docs.

Rotational color scale would be nice, but I haven't considered this at all myself, and don't have time to unfortunately. I'd be happy to help review a pull request.

[maclariz]

Plot a vector from a AxAngle object with a colour given by an pole figure key. Ci symmetry would sensible, as the vector could point anywhere.

[maclariz]

@hakonanes I managed the blacking out with the data via the following:

• I had the object containing all the orientation data (imported from a .ang file).
• I had a blank column of data of no use in this file ('unknown3')
• I used logic to assign angle values to all relevant pixels where there was useful data (a correlation index above a certain threshold) and wrote these to unknown3
• I used similar logic to assign zeros to all pixels where the correlation index was below this and again wrote these to unknown3 for this different pixel selection
• I plotted unknown3 on a mapping (turbo) where zero gives black. I think the documentation on using logic in preparing mappings of calculated parameters could be improved (especially in cases like this where not all the map area should be mapped I don't know if you can create extra keys on the fly. That could be useful.

[hakonanes]

I don't know if you can create extra keys on the fly

Yes, you can. How to do that is detailed in the above referenced tutorial in its own section, "Map properties".

[maclariz]

Useful to know!

[hakonanes]

Also detailed is how to set some data to "not indexed" in the tutorial, which then will not be included when accessing properties like CrystalMap.rotations etc. or when plotting. What I'm saying is that I think all the tools you want are available in the CrystalMap class.

[maclariz]

xmap.phases.add_not_indexed() seems to do nothing on my data

[hakonanes]

That's strange. The general procedure for marking some data as not indexed I usually use is as follows:

>>> from orix import data
>>> xmap = data.sdss_ferrite_austenite(allow_download=True)
Downloading file 'sdss/sdss_ferrite_austenite.ang' from 'https://github.com/pyxem/orix-data/raw/main/sdss_ferrite_austenite/sdss_ferrite_austenite.ang' to '/home/hakon/.cache/orix/0.9.0.post0'.
100%|████████████████████████████████████████| 192k/192k [00:00<00:00, 183MB/s]

# Inspect data and phase map

>>> xmap
Phase   Orientations       Name  Space group  Point group  Proper point group       Color
    1   5657 (48.4%)  austenite         None          432                 432    tab:blue
    2   6043 (51.6%)    ferrite         None          432                 432  tab:orange
Properties: iq, dp
Scan unit: um
>>> xmap.plot()

EDIT: The following original figure contained not-indexed pixels, that was incorrect. Here's the correct figure:

# Inspect values to remove (low image quality)

>>> xmap.plot("iq", colorbar=True)
>>> xmap[xmap.iq < 20]
Phase  Orientations       Name  Space group  Point group  Proper point group       Color
    1   392 (69.0%)  austenite         None          432                 432    tab:blue
    2   176 (31.0%)    ferrite         None          432                 432  tab:orange
Properties: iq, dp
Scan unit: um

# Add "special" not-indexed phase to data

>>> xmap.phases
Id       Name  Space group  Point group  Proper point group       Color
 1  austenite         None          432                 432    tab:blue
 2    ferrite         None          432                 432  tab:orange
>>> xmap.phases.add_not_indexed()
>>> xmap.phases
Id         Name  Space group  Point group  Proper point group       Color
-1  not_indexed         None         None                None           w
 1    austenite         None          432                 432    tab:blue
 2      ferrite         None          432                 432  tab:orange

# Mark values below threshold as not indexed

>>> xmap[xmap.iq < 20].phase_id = -1
>>> xmap
Phase   Orientations         Name  Space group  Point group  Proper point group       Color
   -1     568 (4.9%)  not_indexed         None         None                None           w
    1   5265 (45.0%)    austenite         None          432                 432    tab:blue
    2   5867 (50.1%)      ferrite         None          432                 432  tab:orange
Properties: iq, dp
Scan unit: um
>>> xmap.plot()

[maclariz]

@hakonanes Yes, strange, but not really any trouble. I just created a new prop called "indexed" and marked 0 or 1 depending on whether below or above the threshold. And then used that to set things. Works pretty nicely.