Set iterpath, crop_image->crop_signal, import new markers

Signed-off-by: Håkon Wiik Ånes <[email protected]>

examples/selecting_data/crop_signal_axes.py

@@ -5,7 +5,7 @@
 This example shows various ways to crop the signal axes of an
 :class:`~kikuchipy.signals.EBSD` signal using HyperSpy's ``isig`` slicer and the
 :meth:`~kikuchipy.signals.EBSD.crop` and
-:meth:`~hyperspy._signals.signal2d.Signal2D.crop_image` methods (see
+:meth:`~hyperspy._signals.signal2d.Signal2D.crop_signal` methods (see
 :ref:`hyperspy:signal.indexing` for details).
 """
 
@@ -49,10 +49,10 @@
 print(s3.detector)
 
 # %%
-# Do the same inplace using ``crop_image()``
+# Do the same inplace using :meth:`~hyperspy._signals.signal2d.Signal2D.crop_signal`
 
 s4 = s.deepcopy()
-s4.crop_image(top=10, bottom=50, left=5, right=55)
+s4.crop_signal(top=10, bottom=50, left=5, right=55)
 
 _ = hs.plot.plot_images(s4, **plot_kwds)
 print(s4)

kikuchipy/draw/markers.py

@@ -19,7 +19,7 @@
 
 from typing import Union
 
-from hyperspy.utils.markers import line_segment, point, text
+import hyperspy.api as hs
 import numpy as np
 
 
@@ -50,7 +50,7 @@ def get_line_segment_list(lines: Union[list, np.ndarray], **kwargs) -> list:
             y1 = lines[..., i, 1]
             x2 = lines[..., i, 2]
             y2 = lines[..., i, 3]
-            marker_list.append(line_segment(x1=x1, y1=y1, x2=x2, y2=y2, **kwargs))
+            marker_list.append(hs.plot.markers.Lines([[x1, y1], [x2, y2]], **kwargs))
     return marker_list
 
 
@@ -77,7 +77,7 @@ def get_point_list(points: Union[list, np.ndarray], **kwargs) -> list:
     for i in range(points.shape[-2]):  # Iterate over zone axes
         if not np.allclose(points[..., i, :], np.nan, equal_nan=True):
             marker_list.append(
-                point(x=points[..., i, 0], y=points[..., i, 1], **kwargs)
+                hs.plot.markers.Points([points[..., i, 0], points[..., i, 1]], **kwargs)
             )
     return marker_list
 
@@ -114,6 +114,6 @@ def get_text_list(
             y = coordinates[..., i, 1]
             x[~is_finite[..., i]] = np.nan
             y[~is_finite[..., i]] = np.nan
-            text_marker = text(x=x, y=y, text=texts[i], **kwargs)
+            text_marker = hs.plot.markers.Texts([x, y], s=texts[i], **kwargs)
             marker_list.append(text_marker)
     return marker_list

kikuchipy/draw/tests/test_markers.py

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with kikuchipy. If not, see <http://www.gnu.org/licenses/>.
 
-from hyperspy.utils.markers import line_segment, point, text
+import hyperspy.api as hs
 import numpy as np
 import pytest
 
@@ -35,7 +35,7 @@ def test_get_line_segment_list0d(self, n_lines):
         # Number of markers
         assert isinstance(line_markers, list)
         assert len(line_markers) == n_lines
-        assert isinstance(line_markers[0], line_segment)
+        assert isinstance(line_markers, hs.plot.markers.Lines)
 
         # Coordinates, data shape and marker properties
         for line, marker in zip(lines, line_markers):
@@ -119,7 +119,7 @@ def test_get_point_list0d(self, n_points):
         # Number of markers
         assert isinstance(point_markers, list)
         assert len(point_markers) == n_points
-        assert isinstance(point_markers[0], point)
+        assert isinstance(point_markers, hs.plot.markers.Points)
 
         # Coordinates, data shape and marker properties
         for i, marker in zip(points, point_markers):
@@ -212,7 +212,7 @@ def test_get_text_list0d(self, n_labels):
         # Number of markers
         assert isinstance(text_markers, list)
         assert len(text_markers) == n_labels
-        assert isinstance(text_markers[0], text)
+        assert isinstance(text_markers, hs.plot.markers.Texts)
 
         # Coordinates, data shape and marker properties
         for i, (t, marker) in enumerate(zip(text_coords, text_markers)):

kikuchipy/draw/tests/test_navigators.py

@@ -15,9 +15,8 @@
 # You should have received a copy of the GNU General Public License
 # along with kikuchipy. If not, see <http://www.gnu.org/licenses/>.
 
-from hyperspy.misc.rgb_tools import rgb8, rgb16
-import matplotlib.pyplot as plt
 import numpy as np
+from rsciio.utils.rgb_tools import rgb8, rgb16
 
 import kikuchipy as kp
 
@@ -38,5 +37,3 @@ def test_get_rgb_navigator():
     rgb16_data = s_rgb16.data
     assert rgb16_data.shape == nav_shape
     assert np.issubdtype(rgb16_data.dtype, rgb16)
-
-    plt.close("all")

kikuchipy/imaging/vbse.py

@@ -18,12 +18,8 @@
 from typing import List, Optional, Tuple, Union
 
 from dask.array import Array
-from hyperspy.drawing._markers.horizontal_line import HorizontalLine
-from hyperspy.drawing._markers.vertical_line import VerticalLine
-from hyperspy.drawing._markers.rectangle import Rectangle
-from hyperspy.drawing._markers.text import Text
-from hyperspy.roi import BaseInteractiveROI, RectangularROI
-from hyperspy._signals.signal2d import Signal2D
+import hyperspy.api as hs
+from hyperspy.roi import BaseInteractiveROI
 import numpy as np
 
 from kikuchipy.signals import EBSD, LazyEBSD
@@ -165,7 +161,7 @@ def get_rgb_image(
 
             channels.append(image)
 
-        if alpha is not None and isinstance(alpha, Signal2D):
+        if alpha is not None and isinstance(alpha, hs.signals.Signal2D):
             alpha = alpha.data
 
         dtype_out = np.dtype(dtype_out)
@@ -237,7 +233,7 @@ def get_images_from_grid(
 
         return vbse_images
 
-    def roi_from_grid(self, index: Union[Tuple, List[Tuple]]) -> RectangularROI:
+    def roi_from_grid(self, index: Union[Tuple, List[Tuple]]) -> hs.roi.RectangularROI:
         """Return a rectangular region of interest (ROI) on the EBSD
         detector from one or multiple grid tile indices as row(s) and
         column(s).
@@ -266,7 +262,9 @@ def roi_from_grid(self, index: Union[Tuple, List[Tuple]]) -> RectangularROI:
         min_row = rows[min(index[:, 0])] * dr
         max_row = (rows[max(index[:, 0])] + rows[1]) * dr
 
-        return RectangularROI(left=min_col, top=min_row, right=max_col, bottom=max_row)
+        return hs.roi.RectangularROI(
+            left=min_col, top=min_row, right=max_col, bottom=max_row
+        )
 
     def plot_grid(
         self,
@@ -313,18 +311,21 @@ def plot_grid(
             color = kwargs.pop("color", "r")
             for row, col in np.ndindex(*self.grid_shape):
                 markers.append(
-                    Text(
-                        x=cols[col] * dc,
-                        y=(rows[row] + (0.1 * rows[1])) * dr,
-                        text=f"{row,col}",
+                    hs.plot.markers.Texts(
+                        [cols[col] * dc, (rows[row] + (0.1 * rows[1])) * dr],
+                        texts=f"{row,col}",
                         color=color,
                     )
                 )
 
         # Set lines
         kwargs.setdefault("color", "w")
-        markers += [HorizontalLine((i - 0.5) * dr, **kwargs) for i in rows]
-        markers += [VerticalLine((j - 0.5) * dc, **kwargs) for j in cols]
+        markers += [
+            hs.plot.markers.HorizontalLines((i - 0.5) * dr, **kwargs) for i in rows
+        ]
+        markers += [
+            hs.plot.markers.VerticalLines((j - 0.5) * dc, **kwargs) for j in cols
+        ]
 
         # Color RGB tiles
         if rgb_channels is not None:
@@ -334,12 +335,12 @@ def plot_grid(
                 for row, col in channels:
                     kwargs.update({"color": color, "zorder": 3, "linewidth": 2})
                     roi = self.roi_from_grid((row, col))
+
                     markers += [
-                        Rectangle(
-                            x1=(roi.left - 0.5) * dc,
-                            y1=(roi.top - 0.5) * dc,
-                            x2=(roi.right - 0.5) * dr,
-                            y2=(roi.bottom - 0.5) * dr,
+                        hs.plot.markers.Rectangles(
+                            [(roi.left - 0.5) * dc, (roi.top - 0.5) * dr],
+                            (roi.right - roi.left) * dc,
+                            (roi.bottom - roi.top) * dr,
                             **kwargs,
                         )
                     ]

kikuchipy/io/plugins/nordif/_api.py

@@ -151,7 +151,7 @@ def file_reader(
             "load by zero padding incomplete frames."
         )
         # Data is stored image by image
-        pw = [(0, ny * nx * sy * sx - data.size)]
+        pw = [0, ny * nx * sy * sx - data.size]
         data = np.pad(data, pw)
         data = data.reshape((ny, nx, sy, sx))
     scan["data"] = data
@@ -439,8 +439,8 @@ def file_writer(filename: str, signal: Union["EBSD", "LazyEBSD"]):
     """
     with open(filename, "wb") as f:
         if signal._lazy:
-            for pattern in signal._iterate_signal():
-                np.array(pattern.flatten()).tofile(f)
+            for pattern in signal._iterate_signal("flyback"):
+                np.asanyarray(pattern.ravel()).tofile(f)
         else:
-            for pattern in signal._iterate_signal():
-                pattern.flatten().tofile(f)
+            for pattern in signal._iterate_signal("flyback"):
+                pattern.ravel().tofile(f)