Merge pull request #898 from CSSFrancis

Merging smaller changes that where originally in RNM

CHANGELOG.rst

@@ -7,6 +7,7 @@ All notable changes to this project will be documented in this file.
 The format is based on `Keep a Changelog <https://keepachangelog.com/en/1.0.0/>`_,
 and this project adheres to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`_.
 
+
 Unreleased
 ==========
 
@@ -15,10 +16,16 @@ Added
 - Added damp_extrapolate_to_zero to ReducedIntensity1D
 - Added in deprecation wrapper class to wrap deprecated functions in pyxem.
 - Center-of-mass algorithm added to get_direct_beam_position (#845)
+- Added `VectorSignal1D` class to handle 1 dimensional signals
 
 Changed
 -------
 - Sklearn is now required to be on the 1.0 series.
+- Changed `set_signal_dimension` to `Hyperspy.signals.BaseSignal.transpose`
+- Moved code from `VectorSignal` to `VectorSignal2D`.  Change is more inline with stated dimensions
+- Fixed bugs resulting from API change in hyperspy/hyperspy#3045. Markers explicitly initialized
+- DiffractionVectors.get_diffraction_pixels_map returns a ragged signal
+- VirtualDarkFieldImage.get_vdf_segment changed to properly handle setting of axes
 
 Fixed
 -----

pyxem/generators/indexation_generator.py

@@ -122,7 +122,10 @@ def __init__(self, signal, diffraction_library):
         self.library = diffraction_library
 
     def correlate(
-        self, n_largest=5, include_phases=None, **kwargs,
+        self,
+        n_largest=5,
+        include_phases=None,
+        **kwargs,
     ):
         """
         Correlates the library of simulated diffraction patterns with the

pyxem/generators/integration_generator.py

@@ -238,7 +238,7 @@ def extract_intensities(self, radius: int = 1):
         )
 
         intensities = BaseSignal(intensities)
-        intensities.axes_manager.set_signal_dimension(0)
+        intensities = intensities.transpose(0)
 
         return intensities
 

pyxem/hyperspy_extension.yaml

@@ -83,12 +83,18 @@ signals:
     dtype: real
     lazy: False
     module: pyxem.signals.diffraction_vectors
+  DiffractionVectors1D:
+    signal_type: diffraction_vectors
+    signal_dimension: 1
+    dtype: real
+    lazy: False
+    module: pyxem.signals.diffraction_vectors1d
   DiffractionVectors2D:
     signal_type: diffraction_vectors
     signal_dimension: 2
     dtype: real
     lazy: False
-    module: pyxem.signals.diffraction_vectors
+    module: pyxem.signals.diffraction_vectors2d
   VectorMatchingResults:
     signal_type: vector_matching
     signal_dimension: 0

pyxem/signals/__init__.py

@@ -31,7 +31,9 @@
 )
 from .diffraction_variance1d import DiffractionVariance1D
 from .diffraction_variance2d import DiffractionVariance2D, ImageVariance
-from .diffraction_vectors import DiffractionVectors, DiffractionVectors2D
+from .diffraction_vectors import DiffractionVectors
+from .diffraction_vectors2d import DiffractionVectors2D
+from .diffraction_vectors1d import DiffractionVectors1D
 from .diffraction1d import Diffraction1D, LazyDiffraction1D
 from .diffraction2d import Diffraction2D, LazyDiffraction2D
 from .electron_diffraction1d import ElectronDiffraction1D, LazyElectronDiffraction1D
@@ -64,6 +66,7 @@
     "DiffractionVariance2D",
     "ImageVariance",
     "DiffractionVectors",
+    "DiffractionVectors1D",
     "DiffractionVectors2D",
     "Diffraction1D",
     "LazyDiffraction1D",

pyxem/signals/diffraction2d.py

@@ -283,7 +283,6 @@ def flip_diffraction_x(self):
         """
         s_out = self.copy()
         s_out.axes_manager = self.axes_manager.deepcopy()
-        s_out.metadata = self.metadata.deepcopy()
         s_out.data = np.flip(self.data, axis=-1)
         return s_out
 
@@ -314,7 +313,6 @@ def flip_diffraction_y(self):
         """
         s_out = self.copy()
         s_out.axes_manager = self.axes_manager.deepcopy()
-        s_out.metadata = self.metadata.deepcopy()
         s_out.data = np.flip(self.data, axis=-2)
         return s_out
 
@@ -615,10 +613,9 @@ def correct_bad_pixels(
 
     """ Direct beam and peak finding tools """
 
-    def get_direct_beam_position(self, method,
-                                 lazy_output=None,
-                                 signal_slice=None,
-                                 **kwargs):
+    def get_direct_beam_position(
+        self, method, lazy_output=None, signal_slice=None, **kwargs
+    ):
         """Estimate the direct beam position in each experimentally acquired
         electron diffraction pattern.
 
@@ -722,17 +719,18 @@ def get_direct_beam_position(self, method,
                 x = x - signal_slice[0]
                 y = y - signal_slice[1]
                 kwargs["mask"] = (x, y, r)
-            centers = signal.center_of_mass(lazy_result=lazy_output,
-                                            show_progressbar=False,
-                                            **kwargs,
-                                            )
+            centers = signal.center_of_mass(
+                lazy_result=lazy_output,
+                show_progressbar=False,
+                **kwargs,
+            )
             shifts = -centers.T + origin_coordinates
 
         if signal_slice is not None:
             shifted_center = [(low_x + high_x) / 2, (low_y + high_y) / 2]
             unshifted_center = np.array(self.axes_manager.signal_shape) / 2
             shift = np.subtract(unshifted_center, shifted_center)
-            shifts = shifts+shift
+            shifts = shifts + shift
 
         shifts.set_signal_type("beam_shift")
 
@@ -836,9 +834,9 @@ def center_direct_beam(
                 max_y = int(signal_center[1] + half_square_width)
                 sig_slice = (min_x, max_x, min_y, max_y)
                 kwargs["signal_slice"] = sig_slice
-            shifts = self.get_direct_beam_position(method=method,
-                                                   lazy_output=lazy_output,
-                                                   **kwargs)
+            shifts = self.get_direct_beam_position(
+                method=method, lazy_output=lazy_output, **kwargs
+            )
         if "order" not in align_kwargs:
             if subpixel:
                 align_kwargs["order"] = 1
@@ -912,7 +910,9 @@ def threshold_and_mask(self, threshold=None, mask=None, show_progressbar=True):
         )
         return s_out
 
-    @deprecated_argument(since="0.15.0", name="lazy_result", alternative="lazy_output", removal="1.00.0")
+    @deprecated_argument(
+        since="0.15.0", name="lazy_result", alternative="lazy_output", removal="1.00.0"
+    )
     def center_of_mass(
         self,
         threshold=None,
@@ -1597,25 +1597,25 @@ def get_variance(
         if method == "Omega":
             one_d_integration = self.get_azimuthal_integral1d(npt=npt, **kwargs)
             variance = (
-                (one_d_integration ** 2).mean(axis=navigation_axes)
+                (one_d_integration**2).mean(axis=navigation_axes)
                 / one_d_integration.mean(axis=navigation_axes) ** 2
             ) - 1
             if dqe is not None:
                 sum_points = self.get_azimuthal_integral1d(
                     npt=npt, sum=True, **kwargs
                 ).mean(axis=navigation_axes)
-                variance = variance - ((sum_points ** -1) * dqe)
+                variance = variance - ((sum_points**-1) * dqe)
 
         elif method == "r":
             one_d_integration = self.get_azimuthal_integral1d(npt=npt, **kwargs)
-            integration_squared = (self ** 2).get_azimuthal_integral1d(
+            integration_squared = (self**2).get_azimuthal_integral1d(
                 npt=npt, **kwargs
             )
             # Full variance is the same as the unshifted phi=0 term in angular correlation
-            full_variance = (integration_squared / one_d_integration ** 2) - 1
+            full_variance = (integration_squared / one_d_integration**2) - 1
 
             if dqe is not None:
-                full_variance = full_variance - ((one_d_integration ** -1) * dqe)
+                full_variance = full_variance - ((one_d_integration**-1) * dqe)
 
             variance = full_variance.mean(axis=navigation_axes)
 
@@ -1627,19 +1627,19 @@ def get_variance(
                 axis=navigation_axes
             )
             integration_squared = (
-                (self ** 2)
+                (self**2)
                 .get_azimuthal_integral1d(npt=npt, **kwargs)
                 .mean(axis=navigation_axes)
             )
-            variance = (integration_squared / one_d_integration ** 2) - 1
+            variance = (integration_squared / one_d_integration**2) - 1
 
             if dqe is not None:
                 sum_int = self.get_azimuthal_integral1d(npt=npt, **kwargs).mean()
-                variance = variance - (sum_int ** -1) * (1 / dqe)
+                variance = variance - (sum_int**-1) * (1 / dqe)
 
         elif method == "VImage":
             variance_image = (
-                (self ** 2).mean(axis=navigation_axes)
+                (self**2).mean(axis=navigation_axes)
                 / self.mean(axis=navigation_axes) ** 2
             ) - 1
             if dqe is not None: