Marker bugfix

examples/Markers/from_signal.py

@@ -0,0 +1,65 @@
+"""
+Creating Markers from a signal
+==============================
+
+This example shows how to create markers from a signal. This is useful for creating lazy
+markers from some operation such as peak finding on a signal. Here we show how to create
+markers from a simple map function which finds the maximum value and plots a marker at
+that position.
+"""
+import numpy as np
+import hyperspy.api as hs
+
+
+# Making some artificial data
+def find_maxima(data, scale, offset):
+    ind = np.array(np.unravel_index(np.argmax(data, axis=None), data.shape)).astype(int)
+    d = data[ind]
+    ind = ind * scale + offset  # convert to physical units
+    print(ind)
+    print(d)
+    return np.array(
+        [
+            [ind[0], d[0]],
+        ]
+    )
+
+
+def find_maxima_lines(data, scale, offset):
+    ind = np.array(np.unravel_index(np.argmax(data, axis=None), data.shape)).astype(int)
+    ind = ind * scale + offset  # convert to physical units
+    return ind
+
+
+def gaussian(x, mu, sig):
+    return (
+        1.0 / (np.sqrt(2.0 * np.pi) * sig) * np.exp(-np.power((x - mu) / sig, 2.0) / 2)
+    )
+
+
+data = np.empty((4, 120))
+for i in range(4):
+    x_values = np.linspace(-3 + i * 0.1, 3 + i * 0.1, 120)
+    data[i] = gaussian(x_values, mu=0, sig=10)
+
+s = hs.signals.Signal1D(data)
+s.axes_manager.signal_axes[0].scale = 6 / 120
+s.axes_manager.signal_axes[0].offset = -3
+
+
+scale = s.axes_manager.signal_axes[0].scale
+offset = s.axes_manager.signal_axes[0].offset
+max_values = s.map(find_maxima, scale=scale, offset=offset, inplace=False, ragged=True)
+max_values_lines = s.map(
+    find_maxima_lines, scale=scale, offset=offset, inplace=False, ragged=True
+)
+
+point_markers = hs.plot.markers.Points.from_signal(max_values, signal_axes=None)
+line_markers = hs.plot.markers.VerticalLines.from_signal(
+    max_values_lines, signal_axes=None
+)
+
+
+s.plot()
+s.add_marker(point_markers)
+s.add_marker(line_markers)

hyperspy/drawing/markers.py

@@ -541,10 +541,13 @@ def __repr__(self):
 
         text += ", length: "
         if self._is_iterating:
-            lentgh = getattr(self, "__len__ ", "not plotted")
-            text += "variable (current: %s)" % len(self)
+            try:
+                current = len(self)
+            except RuntimeError:
+                current = "not plotted"
+            text += "variable (current: %s)" % current
         else:
-            text += "%s"% len(self)
+            text += "%s" % len(self)
         text += ">"
 
         return text
@@ -555,7 +558,6 @@ def from_signal(
         signal,
         key=None,
         signal_axes="metadata",
-        collection=None,
         **kwargs,
     ):
         """
@@ -569,22 +571,13 @@ def from_signal(
             The key used to create a key value pair to create the subclass of
             :py:class:`matplotlib.collections.Collection`. If ``None`` (default)
             the key is set to ``"offsets"``.
-        collection: None, str or subclass of :py:class:`matplotlib.collections.Collection`
-            The collection which is initialized. If ``None``, default to
-            :py:class:`~.api.plot.markers.Points` markers.
         signal_axes: str, tuple of :py:class:`~.axes.UniformDataAxis` or None
             If ``"metadata"`` look for signal_axes saved in metadata under
             ``s.metadata.Peaks.signal_axes`` and convert from pixel positions
             to real units before creating the collection. If a ``tuple`` of
             signal axes, those axes will be used otherwise (``None``)
             no transformation will happen.
         """
-        if collection is None:
-            # By default, use `Points` with "display" coordinate system to
-            # avoid dependence on data coordinates
-            from hyperspy.utils.markers import Points
-            cls = Points
-            kwargs.setdefault('sizes', 10)
         if signal_axes is None or (
             signal_axes == "metadata"
             and not signal.metadata.has_item("Peaks.signal_axes")

hyperspy/tests/drawing/test_markers.py

@@ -213,6 +213,16 @@ def test_from_signal(self, signal, data, signal_axes):
         else:
             np.testing.assert_array_equal(col.get_current_kwargs()["offsets"], data[1])
 
+    def test_from_signal_lines(self, signal, data):
+        data = np.empty((3,), dtype=object)
+        for i in np.ndindex(data.shape):
+            data[i] = np.ones((10, 2, 2)) * i
+
+        signal = BaseSignal(data, ragged=True)
+        lines = Lines.from_signal(signal,key="segments", signal_axes=None)
+        s = Signal2D(np.ones((3, 5, 6)))
+        s.add_marker(lines)
+
     def test_from_signal_not_ragged(self):
         s = hs.signals.Signal2D(np.ones((2, 3, 5, 6, 7)))
 
@@ -465,8 +475,7 @@ def test_rep_iterating(self, signal):
         for i in range(3):
             offsets[i] = np.array([[1, 1], [2, 2]])
         m = Points(offsets=offsets)
-        with pytest.raises(RuntimeError):
-            print(m)
+        assert m.__repr__() == "<Points, length: variable (current: not plotted)>"
 
         signal.plot()
         signal.add_marker(m)

upcoming_changes/3270.bugfix.rst

@@ -0,0 +1,4 @@
+Fix bugs in new marker implementation:
+
+- Markers str representation fails if the marker isn't added to a signal
+- make :meth:`~.plot.markers.Markers.from_signal` to work with all markers - it was only working with :class:`~.plot.markers.Markers.Points`