Default scanning region

[mondracek]

I see the defaults for scanMin and scanMax are hard-wired as [0.0, 0.0, 5.0] and [20.0, 20.0, 8.0], respectively. I think it would be better to adjust the default depending on the atomic structure. This would be kind of a natural continuation of (now closed) issue #52.

[NikoOinonen]

I'll mention here that the GUI already does this under the hood when loading a new geometry:

ppafm/ppafm/cli/gui/ppafm_gui.py

Lines 237 to 243 in b70773e

	def scanWindowFromGeom(self):
	"""Infer and set scan window from current geometry"""
	if self.xyzs is None:
	return
	scan_size = self.xyzs[:, :2].max(axis=0) - self.xyzs[:, :2].min(axis=0) + 2 * self.sw_pad
	scan_size = np.minimum(scan_size, [25, 25]) # Let's not make it automatically too large, so that we don't run out of memory
	scan_start = (self.xyzs[:, :2].max(axis=0) + self.xyzs[:, :2].min(axis=0)) / 2 - scan_size / 2