TraitError from s.get_virtual_bse_intensity(roi) for EBSD signal read from Bruker h5ebsd

[hakonanes]

Issue reported by @Fred-Ad in #329:

It's the same with vbse = s.get_virtual_bse_intensity(roi) that gives me this - long - error :

---------------------------------------------------------------------------
TraitError                                Traceback (most recent call last)
<ipython-input-6-a39e5bb3612f> in <module>
----> 1 vbse = s.get_virtual_bse_intensity(roi)
      2 vbse

D:\Python\WPy64-3880\python-3.8.8.amd64\lib\site-packages\kikuchipy\signals\ebsd.py in get_virtual_bse_intensity(self, roi, out_signal_axes)
   1494         """
   1495         vbse = roi(self, axes=self.axes_manager.signal_axes)
-> 1496         vbse_sum = self._get_sum_signal(vbse, out_signal_axes)
   1497         vbse_sum.metadata.General.title = "Virtual backscatter electron image"
   1498         vbse_sum.set_signal_type("VirtualBSEImage")

D:\Python\WPy64-3880\python-3.8.8.amd64\lib\site-packages\kikuchipy\signals\ebsd.py in _get_sum_signal(signal, out_signal_axes)
   1443     @staticmethod
   1444     def _get_sum_signal(signal, out_signal_axes: Optional[List] = None):
-> 1445         out = signal.sum(signal.axes_manager.signal_axes)
   1446         if out_signal_axes is None:
   1447             out_signal_axes = list(

D:\Python\WPy64-3880\python-3.8.8.amd64\lib\site-packages\hyperspy\signal.py in sum(self, axis, out, rechunk)
   3648         if axis is None:
   3649             axis = self.axes_manager.navigation_axes
-> 3650         return self._apply_function_on_data_and_remove_axis(
   3651             np.sum, axis, out=out, rechunk=rechunk)
   3652     sum.__doc__ %= (MANY_AXIS_PARAMETER, OUT_ARG, RECHUNK_ARG)

D:\Python\WPy64-3880\python-3.8.8.amd64\lib\site-packages\hyperspy\signal.py in _apply_function_on_data_and_remove_axis(self, function, axes, out, **kwargs)
   3594             ar_axes = ar_axes[0]
   3595 
-> 3596         s = out or self._deepcopy_with_new_data(None)
   3597 
   3598         if np.ma.is_masked(self.data):

D:\Python\WPy64-3880\python-3.8.8.amd64\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

D:\Python\WPy64-3880\python-3.8.8.amd64\lib\site-packages\hyperspy\signal.py in deepcopy(self)
   4847         :py:meth:`~hyperspy.signal.BaseSignal.copy`
   4848         """
-> 4849         return copy.deepcopy(self)
   4850 
   4851     def change_dtype(self, dtype, rechunk=True):

D:\Python\WPy64-3880\python-3.8.8.amd64\lib\copy.py in deepcopy(x, memo, _nil)
    151             copier = getattr(x, "__deepcopy__", None)
    152             if copier is not None:
--> 153                 y = copier(memo)
    154             else:
    155                 reductor = dispatch_table.get(cls)

D:\Python\WPy64-3880\python-3.8.8.amd64\lib\site-packages\hyperspy\signal.py in __deepcopy__(self, memo)
   4813 
   4814     def __deepcopy__(self, memo):
-> 4815         dc = type(self)(**self._to_dictionary())
   4816         if isinstance(dc.data, np.ndarray):
   4817             dc.data = dc.data.copy()

D:\Python\WPy64-3880\python-3.8.8.amd64\lib\site-packages\kikuchipy\signals\ebsd.py in __init__(self, *args, **kwargs)
     99         optional input parameters.
    100         """
--> 101         Signal2D.__init__(self, *args, **kwargs)
    102 
    103         self._detector = kwargs.pop(

D:\Python\WPy64-3880\python-3.8.8.amd64\lib\site-packages\hyperspy\_signals\signal2d.py in __init__(self, *args, **kw)
    318 
    319     def __init__(self, *args, **kw):
--> 320         super().__init__(*args, **kw)
    321         if self.axes_manager.signal_dimension != 2:
    322             self.axes_manager.set_signal_dimension(2)

D:\Python\WPy64-3880\python-3.8.8.amd64\lib\site-packages\hyperspy\signal.py in __init__(self, data, **kwds)
   2172             self.learning_results = LearningResults()
   2173             kwds['data'] = data
-> 2174             self._load_dictionary(kwds)
   2175             self._plot = None
   2176             self.inav = SpecialSlicersSignal(self, True)

D:\Python\WPy64-3880\python-3.8.8.amd64\lib\site-packages\hyperspy\signal.py in _load_dictionary(self, file_data_dict)
   2438         if 'axes' not in file_data_dict:
   2439             file_data_dict['axes'] = self._get_undefined_axes_list()
-> 2440         self.axes_manager = AxesManager(
   2441             file_data_dict['axes'])
   2442         if 'metadata' not in file_data_dict:

D:\Python\WPy64-3880\python-3.8.8.amd64\lib\site-packages\hyperspy\axes.py in __init__(self, axes_list)
    782             obj : The AxesManager that the event belongs to.
    783             """, arguments=['obj'])
--> 784         self.create_axes(axes_list)
    785         # set_signal_dimension is called only if there is no current
    786         # view. It defaults to spectrum

D:\Python\WPy64-3880\python-3.8.8.amd64\lib\site-packages\hyperspy\axes.py in create_axes(self, axes_list)
    969             axes_list.sort(key=lambda x: x['index_in_array'])
    970         for axis_dict in axes_list:
--> 971             self._append_axis(**axis_dict)
    972 
    973     def _update_max_index(self):

D:\Python\WPy64-3880\python-3.8.8.amd64\lib\site-packages\hyperspy\axes.py in _append_axis(self, *args, **kwargs)
   1032 
   1033     def _append_axis(self, *args, **kwargs):
-> 1034         axis = DataAxis(*args, **kwargs)
   1035         axis.axes_manager = self
   1036         self._axes.append(axis)

D:\Python\WPy64-3880\python-3.8.8.amd64\lib\site-packages\hyperspy\axes.py in __init__(self, size, index_in_array, name, scale, offset, units, navigate)
    262         self.high_index = self.size - 1
    263         self.low_index = 0
--> 264         self.index = 0
    265         self.update_axis()
    266         self.navigate = navigate

D:\Python\WPy64-3880\python-3.8.8.amd64\lib\site-packages\traits\trait_types.py in _validate(self, object, name, value)
   1819                 pass
   1820 
-> 1821         self.error(object, name, value)
   1822 
   1823     def _typed_value(self, value, low, high):

D:\Python\WPy64-3880\python-3.8.8.amd64\lib\site-packages\traits\base_trait_handler.py in error(self, object, name, value)
     72             The proposed new value for the attribute.
     73         """
---> 74         raise TraitError(
     75             object, name, self.full_info(object, name, value), value
     76         )

TraitError: The 'index' trait of a DataAxis instance must be 0 <= a number <= -1, but a value of 0 <class 'int'> was specified.

Originally posted by @Fred-Ad in #329 (comment)

[hakonanes]

Pretty sure this problem is related to #346.

[hakonanes]

The reason for this error was that the RGB ROIs passed to VirtualBSEGenerator.get_rgb_image() (and other methods) weren't scaled to physical coordinates (detector pixel size in microns). Will push a bug fix for this now.