05 GaAs Strain measurements

[CMHell]

Hi,

After finally switching to calibrated units ^^ The subpixelrefinementGenerator worked... The center of mass method however does not. Suggestions where I made a mistake?

x_peak = [-0.08,0.27]
y_peak = [-0.45,0.0027]
spg = SubpixelrefinementGenerator(dp, np.asarray([x_peak,y_peak]))
Vs = spg.center_of_mass_method(4)


Output:
0%
0/3000 [00:00<?, ?it/s]
---------------------------------------------------------------------------
UFuncTypeError                            Traceback (most recent call last)
<ipython-input-39-2ca1685e808f> in <module>
      4 y_peak = [-0.45,0.0027]
      5 spg = SubpixelrefinementGenerator(dp, np.asarray([x_peak,y_peak]))
----> 6 Vs = spg.center_of_mass_method(4)

~\.conda\envs\pyxem\lib\site-packages\pyxem\generators\subpixelrefinement_generator.py in center_of_mass_method(self, square_size)
    366             return ((vectors + shifts) - center) * calibration
    367 
--> 368         self.vectors_out = self.dp.map(
    369             _center_of_mass_map,
    370             vectors=self.vector_pixels,

~\.conda\envs\pyxem\lib\site-packages\hyperspy\signal.py in map(self, function, show_progressbar, parallel, max_workers, inplace, ragged, output_signal_size, output_dtype, **kwargs)
   4591                 kwargs["output_dtype"] = output_dtype
   4592             # Iteration over coordinates.
-> 4593             res = self._map_iterate(function, iterating_kwargs=ndkwargs,
   4594                                     show_progressbar=show_progressbar,
   4595                                     parallel=parallel,

~\.conda\envs\pyxem\lib\site-packages\hyperspy\signal.py in _map_iterate(self, function, iterating_kwargs, show_progressbar, parallel, max_workers, ragged, inplace, **kwargs)
   4733 
   4734             with ThreadPoolExecutor(max_workers=max_workers) as executor:
-> 4735                 for ind, res in zip(
   4736                     range(res_data.size), executor.map(func, zip(*iterators))
   4737                 ):

~\.conda\envs\pyxem\lib\concurrent\futures\_base.py in result_iterator()
    606                     # Careful not to keep a reference to the popped future
    607                     if timeout is None:
--> 608                         yield fs.pop().result()
    609                     else:
    610                         yield fs.pop().result(end_time - time.monotonic())

~\.conda\envs\pyxem\lib\concurrent\futures\_base.py in result(self, timeout)
    436                     raise CancelledError()
    437                 elif self._state == FINISHED:
--> 438                     return self.__get_result()
    439 
    440                 self._condition.wait(timeout)

~\.conda\envs\pyxem\lib\concurrent\futures\_base.py in __get_result(self)
    388         if self._exception:
    389             try:
--> 390                 raise self._exception
    391             finally:
    392                 # Break a reference cycle with the exception in self._exception

~\.conda\envs\pyxem\lib\concurrent\futures\thread.py in run(self)
     50 
     51         try:
---> 52             result = self.fn(*self.args, **self.kwargs)
     53         except BaseException as exc:
     54             self.future.set_exception(exc)

~\.conda\envs\pyxem\lib\site-packages\hyperspy\misc\utils.py in func(*args)
   1167     def func(*args):
   1168         dat, these_kwargs = figure_out_kwargs(*args)
-> 1169         return function(dat, **these_kwargs)
   1170 
   1171     return func, iterators

~\.conda\envs\pyxem\lib\site-packages\pyxem\generators\subpixelrefinement_generator.py in _center_of_mass_map(dp, vectors, square_size, center, calibration)
    363             for i, vector in enumerate(vectors):
    364                 expt_disc = _com_experimental_square(dp, vector, square_size)
--> 365                 shifts[i] = [a - square_size / 2 for a in _center_of_mass_hs(expt_disc)]
    366             return ((vectors + shifts) - center) * calibration
    367 

~\.conda\envs\pyxem\lib\site-packages\pyxem\generators\subpixelrefinement_generator.py in _center_of_mass_hs(z)
    325             s = np.sum(z)
    326             if s != 0:
--> 327                 z *= 1 / s
    328             dx = np.sum(z, axis=0)
    329             dy = np.sum(z, axis=1)

UFuncTypeError: Cannot cast ufunc 'multiply' output from dtype('float64') to dtype('uint8') with casting rule 'same_kind'

[pc494]

This is a type error, check what type your dp is (probably uint8) using dp.data.type or similar, then try converting it to float64 - this avoid problems relating to the fact that the operation of division isn't nicely defined for integers.