Documentation: Clean up more mapping

CHANGELOG.rst

@@ -17,6 +17,7 @@ Fixed
 - Replace ``matplotlib.cm.get_cmap`` (removed in matplotlib 3.9) with ``matplotlib.colormaps``. (#1023)
 - Documentation fixes and improvement. (#1028)
 - Fixed bug with flattening diffraction Vectors when there are different scales (#1024)
+- Fixed intersphinx links and improved api documentation (#1056)
 
 Added
 -----

pyxem/signals/diffraction1d.py

@@ -29,9 +29,9 @@ class Diffraction1D(CommonDiffraction, Signal1D):
     Parameters
     ----------
     *args
-        See :class:`~hyperspy._signals.signal1d.Signal1D`.
+        See :class:`hyperspy.api.signals.Signal1D`.
     **kwargs
-        See :class:`~hyperspy._signals.signal1d.Signal1D`
+        See :class:`hyperspy.api.signals.Signal1D`
     """
 
     _signal_type = "diffraction"

pyxem/signals/diffraction2d.py

@@ -1006,7 +1006,8 @@ def template_match_disk(self, disk_r=4, inplace=False, **kwargs):
         lazy_output : bool, default True
             If True, will return a LazyDiffraction2D object. If False,
             will compute the result and return a Diffraction2D object.
-        show_progressbar : bool, default True
+        kwargs :
+            Passed to :func:`pyxem.utils.diffraction.normalize_template_match`
 
         Returns
         -------
@@ -1021,8 +1022,9 @@ def template_match_disk(self, disk_r=4, inplace=False, **kwargs):
 
         See Also
         --------
-        template_match_ring
-        template_match
+        :meth:`pyxem.signals.DiffractionSignal2D.template_match_ring`
+        :meth:`pyxem.signals.DiffractionSignal2D.template_match`
+        :func:`pyxem.utils.diffraction.normalize_template_match`
 
         """
         disk = morphology.disk(disk_r, self.data.dtype)
@@ -1043,10 +1045,11 @@ def template_match_ring(self, r_inner=5, r_outer=7, inplace=False, **kwargs):
         ----------
         r_inner, r_outer : scalar, optional
             Inner and outer radius of the rings.
-        lazy_output : bool, default True
-            If True, will return a LazyDiffraction2D object. If False,
-            will compute the result and return a Diffraction2D object.
-        show_progressbar : bool, default True
+        inplace : bool, optional
+            If True, the data is replaced by the filtered data. If False, a
+            new signal is returned. Default False.
+        kwargs :
+            Passed to :func:`pyxem.utils.diffraction.normalize_template_match`
 
         Returns
         -------
@@ -1060,9 +1063,9 @@ def template_match_ring(self, r_inner=5, r_outer=7, inplace=False, **kwargs):
 
         See Also
         --------
-        template_match_disk
-        template_match
-
+        :meth:`pyxem.signals.DiffractionSignal2D.template_match_disk`
+        :meth:`pyxem.signals.DiffractionSignal2D.template_match`
+        :func:`pyxem.utils.diffraction.normalize_template_match`
         """
         if r_outer <= r_inner:
             raise ValueError(
@@ -1130,7 +1133,14 @@ def template_match(self, template, inplace=False, **kwargs):
 
         Parameters
         ----------
-        template : 2-D NumPy array
+        template : numpy.ndarray
+            The 2D template to match with the signal.
+        inplace : bool, optional
+            If True, the data is replaced by the filtered data. If False, a
+            new signal is returned. Default False.
+        **kwargs :
+            Any additional keyword arguments to be passed to
+            :func:`pyxem.utils.diffraction.normalize_template_match`
 
         Returns
         -------
@@ -1147,8 +1157,9 @@ def template_match(self, template, inplace=False, **kwargs):
 
         See Also
         --------
-        template_match_disk
-        template_match_ring
+        :meth:`pyxem.signals.DiffractionSignal2D.template_match_disk`
+        :meth:`pyxem.signals.DiffractionSignal2D.template_match_ring`
+        :func:`pyxem.utils.diffraction.normalize_template_match`
 
         """
 
@@ -1387,7 +1398,7 @@ def add_peak_array_as_markers(self, peak_array, permanent=True, **kwargs):
             Default False, if True the markers will be added to the
             signal permanently.
         **kwargs :
-            Passed to :py:class:`hyperspy.api.plot.markers.Points`
+            Passed to :class:`hyperspy.api.plot.markers.Points`
 
         Examples
         --------
@@ -1462,7 +1473,7 @@ def angular_mask(self, angle0, angle1, centre_x_array=None, centre_y_array=None)
 
         Returns
         -------
-        mask_array : NumPy array
+        mask_array : numpy.ndarray
             The True values will be the region between angle0 and angle1.
             The array will have the same dimensions as the signal.
 

pyxem/signals/diffraction_variance1d.py

@@ -26,9 +26,9 @@ class DiffractionVariance1D(Diffraction1D):
     Parameters
     ----------
     *args
-        See :class:`~hyperspy._signals.signal1d.Signal1D`.
+        See :class:`hyperspy.api.signals.Signal1D`.
     **kwargs
-        See :class:`~hyperspy._signals.signal1d.Signal1D`
+        See :class:`hyperspy.api.signals.Signal1D`
     """
 
     _signal_type = "diffraction_variance"

pyxem/signals/diffraction_variance2d.py

@@ -28,9 +28,9 @@ class DiffractionVariance2D(Diffraction2D):
     Parameters
     ----------
     *args
-        See :class:`~hyperspy._signals.signal2d.Signal2D`.
+        See :class:`hyperspy.api.signals.Signal2D`.
     **kwargs
-        See :class:`~hyperspy._signals.signal2d.Signal2D`
+        See :class:`hyperspy.api.signals.Signal2D`
     """
 
     _signal_type = "diffraction_variance"

pyxem/signals/diffraction_vectors.py

@@ -77,10 +77,10 @@ class is likely to change as the API for diffraction vectors is developed.
 
     Attributes
     ----------
-    cartesian : np.array()
+    cartesian : numpy.array
         Array of 3-vectors describing Cartesian coordinates associated with
         each diffraction vector.
-    hkls : np.array()
+    hkls : numpy.array
         Array of Miller indices associated with each diffraction vector
         following indexation.
     """
@@ -183,7 +183,7 @@ def from_peaks(
 
         Parameters
         ----------
-        peaks : Signal
+        peaks : hyperspy.api.signals.BaseSignal
             Signal containing lists (np.array) of pixel coordinates specifying
             the reflection positions
         center : np.array or None
@@ -193,7 +193,7 @@ def from_peaks(
 
         Returns
         -------
-        vectors : :obj:`pyxem.signals.diffraction_vectors.DiffractionVectors`
+        vectors : :class:`pyxem.signals.diffraction_vectors.DiffractionVectors`
             List of diffraction vectors
         """
         if center is None and peaks.metadata.has_item("Peaks.signal_axes"):
@@ -294,7 +294,7 @@ def subpixel_refine(
 
         Parameters
         ----------
-        signal : Signal
+        signal : hyperspy.api.signals.BaseSignal
             The signal which will be used to refine the diffraction vectors.
         method : str
             The method used to refine the diffraction vectors. Currently

pyxem/signals/diffraction_vectors2d.py

@@ -243,9 +243,10 @@ def to_roi(self, radius=0.1, columns=None, include_labels=False, **kwargs):
         columns: list
             The columns to use for the ROIs. If None, columns 0 and 1 are used to create the ROIs.
         include_labels: bool
-            If True, the labels for each ROI are returned as well using hyperspy's Texts class.
+            If True, the labels for each ROI are returned as well using hyperspy's
+             :class:`hyperspy.api.plot.markers.Texts` class.
         kwargs: dict
-            Keyword arguments to pass to the hyperspy Texts class.
+            Keyword arguments to pass to the :class:`hyperspy.api.plot.markers.Texts` class.
         """
         if self.has_navigation_axis:
             raise NotImplementedError(

pyxem/signals/electron_diffraction1d.py

@@ -27,9 +27,9 @@ class ElectronDiffraction1D(Diffraction1D):
     Parameters
     ----------
     *args
-        See :class:`~hyperspy._signals.signal1d.Signal1D`.
+        See :class:`hyperspy.api.signals.Signal1D`.
     **kwargs
-        See :class:`~hyperspy._signals.signal1d.Signal1D`
+        See :class:`hyperspy.api.signals.Signal1D`
     """
 
     _signal_type = "electron_diffraction"

pyxem/signals/electron_diffraction2d.py

@@ -31,9 +31,9 @@ class ElectronDiffraction2D(Diffraction2D):
     Parameters
     ----------
     *args
-        See :class:`~hyperspy._signals.signal2d.Signal2D`.
+        See :class:`hyperspy.api.signals.Signal2D`.
     **kwargs
-        See :class:`~hyperspy._signals.signal2d.Signal2D`
+        See :class:`hyperspy.api.signals.Signal2D`
     """
 
     _signal_type = "electron_diffraction"

pyxem/signals/indexation_results.py

@@ -36,14 +36,14 @@ def crystal_from_vector_matching(z_matches):
 
     Parameters
     ----------
-    z_matches : numpy.array
+    z_matches : numpy.ndarray
         Template matching results in an array of shape (m,5) sorted by
         total_error (ascending) within each phase, with entries
         [phase, R, match_rate, ehkls, total_error]
 
     Returns
     -------
-    results_array : numpy.array
+    results_array : numpy.ndarray
         Crystallographic mapping results in an array of shape (3) with entries
         [phase, np.array((z, x, z)), dict(metrics)]
 
@@ -79,12 +79,12 @@ def _get_best_match(z):
 
     Parameters
     ----------
-    z : np.array
+    z : numpy.ndarray
         array with shape (5,n_matches), the 5 elements are phase, alpha, beta, gamma, score
 
     Returns
     -------
-    z_best : np.array
+    z_best : numpy.ndarray
         array with shape (5,)
 
     """
@@ -96,7 +96,7 @@ def _get_phase_reliability(z):
 
     Parameters
     ----------
-    z : np.array
+    z : numpy.ndarray
         array with shape (5,n_matches), the 5 elements are phase, alpha, beta, gamma, score
 
     Returns
@@ -125,7 +125,7 @@ def _get_second_best_phase(z):
 
     Parameters
     ----------
-    z : np.array
+    z : numpy.ndarray
         array with shape (5,n_matches), the 5 elements are phase, alpha, beta, gamma, score
 
     Returns
@@ -205,7 +205,7 @@ class VectorMatchingResults(BaseSignal):
 
     Attributes
     ----------
-    vectors : DiffractionVectors
+    vectors : pyxem.signals.DiffractionVectors
         Diffraction vectors indexed.
     hkls : BaseSignal
         Miller indices associated with each diffraction vector.
@@ -253,12 +253,12 @@ def get_indexed_diffraction_vectors(
 
         Parameters
         ----------
-        vectors : DiffractionVectors
+        vectors : pyxem.signals.DiffractionVectors
             A diffraction vectors object to be indexed.
 
         Returns
         -------
-        indexed_vectors : DiffractionVectors
+        indexed_vectors : pyxem.signals.DiffractionVectors
             An indexed diffraction vectors object.
 
         """

pyxem/signals/insitu_diffraction2d.py

@@ -43,9 +43,9 @@ class InSituDiffraction2D(Diffraction2D):
     Parameters
     ----------
     *args:
-        See :class:`~hyperspy._signals.signal2d.Signal2D`.
+        See :class:`hyperspy.api.signals.Signal2D`.
     **kwargs:
-        See :class:`~hyperspy._signals.signal2d.Signal2D`
+        See :class:`hyperspy.api.signals.Signal2D`
     """
 
     _signal_type = "insitu_diffraction"
@@ -92,7 +92,7 @@ def get_drift_vectors(
 
         Parameters
         ----------
-        s: :class:`~hyperspy.api.signals.Signal2D`
+        s: :class:`hyperspy.api.signals.Signal2D`
             Time series of reconstructed images
         reference: 'current', 'cascade', or 'stat'
             reference argument passed to :meth:`~hyperspy.api.signals.Signal2D.estimate_shift2D`

pyxem/signals/pair_distribution_function1d.py

@@ -27,9 +27,9 @@ class PairDistributionFunction1D(Signal1D):
     Parameters
     ----------
     *args
-        See :class:`~hyperspy._signals.signal1d.Signal1D`.
+        See :class:`hyperspy.api.signals.Signal1D`.
     **kwargs
-        See :class:`~hyperspy._signals.signal1d.Signal1D`
+        See :class:`hyperspy.api.signals.Signal1D`
     """
 
     _signal_type = "pair_distribution_function"
@@ -49,9 +49,9 @@ def normalise_signal(self, s_min=0, inplace=False, *args, **kwargs):
             If True (default), this signal is overwritten. Otherwise, returns a
             new signal.
         *args:
-            Arguments to be passed to map().
+            Arguments to be passed to :meth:`hyperspy.api.signals.BaseSignal.map`.
         **kwargs:
-            Keyword arguments to be passed to map().
+            Keyword arguments to be passed to :meth:`hyperspy.api.signals.BaseSignal.map`.
 
         """
         s_scale = self.axes_manager.signal_axes[0].scale

pyxem/signals/polar_diffraction2d.py

@@ -55,9 +55,9 @@ def get_angular_correlation(
         normalize: bool
             Normalize the radial correlation by the average value at some radius.
         kwargs: dict
-            Any additional options for the hyperspy.BaseSignal.map() function
+            Any additional options for the :meth:`hyperspy.api.signals.BaseSignal.map` function
         inplace: bool
-            From hyperspy.signal.map(). inplace=True means the signal is
+            From :meth:`hyperspy.api.signals.BaseSignal.map`. inplace=True means the signal is
             overwritten.
 
         Returns
@@ -100,10 +100,10 @@ def get_angular_power(self, mask=None, normalize=True, inplace=False, **kwargs):
          normalize: bool
              Normalize the radial correlation by the average value at some radius.
         inplace: bool
-            From :meth:`~hyperspy.signal.BaseSignal.map` inplace=True means the signal is
+            From :meth:`hyperspy.api.signals.BaseSignal.map` inplace=True means the signal is
             overwritten.
         kwargs: dict
-            Any additional options for the :meth:`~hyperspy.signal.BaseSignal.map` function
+            Any additional options for the :meth:`hyperspy.api.signals.BaseSignal.map` function
 
         Returns
         -------
@@ -133,7 +133,7 @@ def get_full_pearson_correlation(
 
         Parameters
         ----------
-        mask: Numpy array
+        mask: numpy.ndarray
             A bool mask of values to ignore of shape equal to the signal shape.
             True for elements masked, False for elements unmasked
         krange: tuple of int or float

pyxem/signals/polar_vectors.py

@@ -63,7 +63,7 @@ def get_angles(
             Which means that two vectors even with a small angle between them will be
             considered.
         **kwargs:
-            Keyword arguments to map().
+            Keyword arguments to :meth:`hyperspy.api.signals.BaseSignal.map`.
 
         Returns
         -------

pyxem/signals/power2d.py

@@ -31,9 +31,9 @@ class Power2D(Signal2D):
     Parameters
     ----------
     *args
-        See :class:`~hyperspy._signals.signal2d.Signal2D`.
+        See :class:`hyperspy.api.signals.Signal2D`.
     **kwargs
-        See :class:`~hyperspy._signals.signal2d.Signal2D`
+        See :class:`hyperspy.api.signals.Signal2D`
     """
 
     _signal_type = "power"