Patterns load from EDAX .h5 file cannot be plotted directly

[IMBalENce]

Not sure if the title explains the issue accurate enough or not.

The symptom shows up after loading an EDAX .h5 file and plot the data

s = kp.load(datadir + "//" + ebsd, scan_group_names="map20210707165220751")
s

<EBSD, title: TSLmap_0p85nA_8x8 ma..., dimensions: (76, 76|60, 60)>

plt.imshow(s.inav[0, 0].data, cmap="gray")

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_22936/3160823787.py in <module>
----> 1 plt.imshow(s.inav[0, 0].data, cmap="gray")

~\Anaconda3\envs\kp-dev\lib\site-packages\hyperspy\misc\slicing.py in __getitem__(self, slices, out)
    191 
    192     def __getitem__(self, slices, out=None):
--> 193         return self.obj._slicer(slices, self.isNavigation, out=out)
    194 
    195 

~\Anaconda3\envs\kp-dev\lib\site-packages\hyperspy\misc\slicing.py in _slicer(self, slices, isNavigation, out)
    283 
    284         if out is None:
--> 285             _obj = self._deepcopy_with_new_data(new_data,
    286                                                 copy_variance=True)
    287             _to_remove = []

~\Anaconda3\envs\kp-dev\lib\site-packages\hyperspy\signal.py in _deepcopy_with_new_data(self, data, copy_variance, copy_navigator, copy_learning_results)
   2329                 del self.learning_results
   2330             self.models._models = DictionaryTreeBrowser()
-> 2331             ns = self.deepcopy()
   2332             ns.data = data
   2333             return ns

c:\users\zhouxu\01_kikuchipy\kikuchipy master\kikuchipy\signals\ebsd.py in deepcopy(self)
   2003             new._xmap = copy.deepcopy(self.xmap)
   2004         if self.static_background is not None:
-> 2005             new._static_background = self.static_background.copy()
   2006         else:
   2007             new._static_background = copy.deepcopy(self.static_background)

AttributeError: 'int' object has no attribute 'copy'

It seems to have something to do with s.static_background, as I can confirm s.data has been correctly imported. and the value of s.static_background is -1.

I also did a quick comparison by loading a Oxford .ebsp file. The plot function behaves like normal and the value of s.static_background is None in this case.

[IMBalENce]

By the way, I found a way to convert EDAX .up1 and .up2 binaries to .h5 in EDAX OIM, not quite straight forward though. Happy to share them if you find useful.

[hakonanes]

Thanks for reporting this! The cause is a new property EBSD.static_background which replaces EBSD.metadata.Acquisition_instrument.SEM.Detector.EBSD.static_background (for obvious reasons), and the desire to keep the background when deepcopying, which is done with EBSD.inav[]. This only affects develop, so there's no rush to fix this.

The new property was added in anticipation of completing #466, where I try to remove unnecessary metadata and move stuff over to EBSD.xmap and EBSD.detector. But that is a lot of work, so it's done in stages.

Since EDAX HDF5 files store patterns after static background correction, there isn't a static background pattern in the file. The check for whether it's possible to deepcopy EBSD.static_background should be better than just to check whether it's None. Or, perhaps we should use np.copy(self.static_background) instead. If you want, you can make a PR to fix this (to develop), or I'll do it myself next week.

[IMBalENce]

That make sense now, as I've only tested this part on develop very recently.

I'll give it a try to fix it. Otherwise I'll leave it to you.

[hakonanes]

This will be fixed in #537.