hyperspy
Line2DROI does not work with stacks
Describe the bug
I have a signal2D stack (filtered_stack) with dimensions 16 x (412, 412) where I cannot apply Line2DROI directly getting the error message below. Instead I have to split up the stack, which is very inefficient for larger data sets and I lose the capability to handle directly the whole stack for example for plotting.
---------------------------------------------------------------------------
Exception Traceback (most recent call last)
Cell In[52], line 6
3 filtered_stack.inav[0].plot(norm='log', cmap = 'inferno', vmin = 0.000002, vmax = 0.005, scalebar_color='red',title ='')
5 line_roi = hs.roi.Line2DROI(280, 730, 330, 220, 5)
----> 6 roi0 = line_roi.interactive(filtered_stack.inav[0])
7 ax2 = hs.plot.plot_spectra([roi0])
File /usr/lib/python3.11/site-packages/hyperspy/roi.py:430, in BaseInteractiveROI.interactive(self, signal, navigation_signal, out, color, snap, **kwargs)
428 if navigation_signal is not None:
429 if navigation_signal not in self.signal_map:
--> 430 self.add_widget(navigation_signal, color=color, snap=snap,
431 axes=kwargs.get("axes", None))
432 if (self.update not in
433 signal.axes_manager.events.any_axis_changed.connected):
434 signal.axes_manager.events.any_axis_changed.connect(
435 self.update,
436 [])
File /usr/lib/python3.11/site-packages/hyperspy/roi.py:513, in BaseInteractiveROI.add_widget(self, signal, axes, widget, color, snap, **kwargs)
511 if widget.ax is None:
512 if signal._plot is None or signal._plot.signal_plot is None:
--> 513 raise Exception(
514 f"{repr(signal)} does not have an active plot. Plot the "
515 "signal before calling this method.")
517 ax = _get_mpl_ax(signal._plot, axes)
518 widget.set_mpl_ax(ax)
Exception: <Signal2D, title: Stack of Time Series at 200, dimensions: (|412, 412)> does not have an active plot. Plot the signal before calling this method.
This is the executed code:
filtered_stack.inav[0].plot()
line_roi = hs.roi.Line2DROI(280, 730, 330, 220, 5)
roi0 = line_roi.interactive(filtered_stack.inav[0])
ax2 = hs.plot.plot_spectra([roi0])
If I use instead this code, it works, I lose however the ability to work with the whole stack, which can be very handy, especially for plotting:
qq = hs.signals.Signal2D(filtered_stack.inav[0])
qq.plot()
line_roi = hs.roi.Line2DROI(170, 280, 210, 280, 30)
roi0 = line_roi.interactive(qq)
ax2 = hs.plot.plot_spectra([roi0])
Expected behavior
Interactive plotting should work with individual sets of a stack as well.
Minimal example which does not work (basically I pick one element of the stack):
import numpy as np
import hyperspy.api as hs
import matplotlib.pyplot as plt
%matplotlib qt
images = [np.random.random((100, 100)) for _ in range(10)]
# Convert each numpy array to a HyperSpy signal
signals = [hs.signals.Signal2D(img) for img in images]
# Stack the signals into a single signal
stacked = hs.stack(signals)
stacked.inav[0].plot()
line_roi = hs.roi.Line2DROI(10, 10, 30, 30, 5)
roi0 = line_roi.interactive(stacked.inav[0])
ax2 = hs.plot.plot_spectra([roi0])
Minimal example which does work (without stack):
iimport numpy as np
import hyperspy.api as hs
import matplotlib.pyplot as plt
%matplotlib qt
images = [np.random.random((100, 100)) for _ in range(10)]
# Convert each numpy array to a HyperSpy signal
signals = [hs.signals.Signal2D(img) for img in images]
# Stack the signals into a single signal
stacked = hs.stack(signals)
qq = stacked.inav[0]
qq.plot()
line_roi = hs.roi.Line2DROI(10, 10, 30, 30, 5)
roi0 = line_roi.interactive(qq)
ax2 = hs.plot.plot_spectra([roi0])
Can you provide a minimum reproducible example? It needs to be self-contained, otherwise it is ambiguous.
Can you provide a minimum reproducible example? It needs to be self-contained, otherwise it is ambiguous.
Thanks, @ericpre I added it to the original post.