ROI error if axes_manager[0].offset != 0

[ks00x]

Hyperspy 1.62 crashes if the image has an offset > 0. This code example taken from the documentation gives the error traceback below if I dont force the offset to 0. Have the same issue with older data which used to work with code like this and where the image origin is not (0,0) .

holo = hs.datasets.example_signals.object_hologram()

# enabling this 2 lines prevents the crash
#holo.axes_manager[0].offset = 0 
#holo.axes_manager[1].offset = 0

roi = hs.roi.Line2DROI(x1=465.577, y1=445.15, x2=169.4, y2=387.731, linewidth=0)
holo.plot()
ss = roi.interactive(holo)

error trace:

ValueError                                Traceback (most recent call last)
<ipython-input-23-b859ff1fe3d5> in <module>
      5 roi = hs.roi.Line2DROI(x1=465.577, y1=445.15, x2=169.4, y2=387.731, linewidth=0)
      6 holo.plot()
----> 7 ss = roi.interactive(holo)
      8 ss.plot()

C:\develop\anaconda\envs\hyperspy\lib\site-packages\hyperspy\roi.py in interactive(self, signal, navigation_signal, out, color, snap, **kwargs)
    382         if navigation_signal is not None:
    383             if navigation_signal not in self.signal_map:
--> 384                 self.add_widget(navigation_signal, color=color, snap=snap,
    385                                 axes=kwargs.get("axes", None))
    386         if (self.update not in

C:\develop\anaconda\envs\hyperspy\lib\site-packages\hyperspy\roi.py in add_widget(self, signal, axes, widget, color, snap, **kwargs)
    460             widget.color = color
    461             if hasattr(widget, 'snap_all'):
--> 462                 widget.snap_all = snap
    463             else:
    464                 widget.snap_position = snap

C:\develop\anaconda\envs\hyperspy\lib\site-packages\hyperspy\drawing\widget.py in <lambda>(s, v)
    617 
    618     snap_all = property(lambda s: s.snap_size and s.snap_position,
--> 619                         lambda s, v: s._set_snap_all(v))
    620 
    621     def increase_size(self):

C:\develop\anaconda\envs\hyperspy\lib\site-packages\hyperspy\drawing\widget.py in _set_snap_all(self, value)
    613     def _set_snap_all(self, value):
    614         # Snap position first, as snapped size can depend on position.
--> 615         self.snap_position = value
    616         self.snap_size = value
    617 

C:\develop\anaconda\envs\hyperspy\lib\site-packages\hyperspy\drawing\widget.py in <lambda>(s, v)
    442 
    443     snap_position = property(lambda s: s._snap_position,
--> 444                              lambda s, v: s._set_snap_position(v))
    445 
    446     def connect(self, ax):

C:\develop\anaconda\envs\hyperspy\lib\site-packages\hyperspy\drawing\widget.py in _set_snap_position(self, value)
    436         self._snap_position = value
    437         if value:
--> 438             snap_value = self._do_snap_position(self._pos)
    439             if np.any(self._pos != snap_value):
    440                 self._pos = snap_value

C:\develop\anaconda\envs\hyperspy\lib\site-packages\hyperspy\drawing\_widgets\line2d.py in _do_snap_position(self, value)
    189         value = np.array(value) if value is not None else self._pos
    190 
--> 191         ret1 = super(Line2DWidget, self)._do_snap_position(value[0, :])
    192         ret2 = super(Line2DWidget, self)._do_snap_position(value[1, :])
    193 

C:\develop\anaconda\envs\hyperspy\lib\site-packages\hyperspy\drawing\widget.py in _do_snap_position(self, value)
    430         value = np.array(value) if value is not None else self._pos
    431         for i, ax in enumerate(self.axes):
--> 432             value[i] = ax.index2value(ax.value2index(value[i]))
    433         return value
    434 

C:\develop\anaconda\envs\hyperspy\lib\site-packages\hyperspy\axes.py in value2index(self, value, rounding)
    542                 return index
    543             else:
--> 544                 raise ValueError("The value is out of the axis limits")
    545 
    546     def index2value(self, index):

ValueError: The value is out of the axis limits

[ericpre]

Thanks for the bug report, I can reproduce!

There are a few things which need fixing/improvement here:

• the bug itself!
• the error could be more useful because it doesn't tell which axis and what are the axis bounds
• we should have the example of the user guide tested...

[ericpre]

Fixed in #2721.

In the meantime, you can use disable snapping:

import hyperspy.api as hs

holo = hs.datasets.example_signals.object_hologram()
roi = hs.roi.Line2DROI(x1=465.577, y1=445.15, x2=169.4, y2=387.731, linewidth=0)
holo.plot()
ss = roi.interactive(holo, snap=False)

[ks00x]

thanks, the snap workaround works for me as well!