Remove master pattern metadata, add projection, hemisphere and phase …

…attributes (#246) * Set up necessary (empty) tests, add desired changes to changelog Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com> * Remove simulation metadata node, add master pattern properties, update docs/tests Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com> * Specify .hspy extension when saving master pattern in test Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
pyxem · Nov 13, 2020 · 8dc22a1 · 8dc22a1
1 parent 6617120
commit 8dc22a1
Show file tree

Hide file tree

Showing 15 changed files with 161 additions and 747 deletions.
diff --git a/doc/changelog.rst b/doc/changelog.rst
@@ -55,6 +55,8 @@ Added
 
 Changed
 -------
+- The EBSDMasterPattern gets unsettable phase, hemisphere and projection
+  properties. (`#246 <https://github.com/pyxem/kikuchipy/pull/246>`_)
 - EMsoft EBSD master pattern plugin can read a single energy pattern. Parameter
   `energy_range`  changed to `energy`.
   (`240 <https://github.com/pyxem/kikuchipy/pull/240>`_)
@@ -70,6 +72,13 @@ Changed
 - Remove language_version in pre-commit config file.
   (`#195 <https://github.com/pyxem/kikuchipy/pull/195>`_)
 
+Removed
+-------
+- The EBSDMasterPattern and EBSD metadata node Sample.Phases, to be replaced
+  by class attributes. The set_phase_parameters() method is removed from both
+  classes, and the set_simulation_parameters() is removed from the former class.
+  (`#246 <https://github.com/pyxem/kikuchipy/pull/246>`_)
+
 Fixed
 -----
 - NumPy array creation when calculating window pixel's distance to the origin is

diff --git a/doc/load_save_data.ipynb b/doc/load_save_data.ipynb
@@ -226,10 +226,7 @@
     "[set_experimental_parameters()](reference.rst#kikuchipy.signals.EBSD.set_experimental_parameters),\n",
     "[set_phase_parameters()](reference.rst#kikuchipy.signals.EBSD.set_phase_parameters),\n",
     "[set_scan_calibration()](reference.rst#kikuchipy.signals.EBSD.set_scan_calibration) and\n",
-    "[set_detector_calibration()](reference.rst#kikuchipy.signals.EBSD.set_detector_calibration),\n",
-    "or the [EBSDMasterPattern](reference.rst#kikuchipy.signals.EBSDMasterPattern)\n",
-    "class methods [set_simulation_parameters()](reference.rst#kikuchipy.signals.EBSDMasterPattern.set_simulation_parameters) or\n",
-    "[set_phase_parameters()](reference.rst#kikuchipy.signals.EBSDMasterPattern.set_phase_parameters).\n",
+    "[set_detector_calibration()](reference.rst#kikuchipy.signals.EBSD.set_detector_calibration).\n",
     "For example, to set or change the accelerating voltage, horizontal pattern\n",
     "centre coordinate and static background pattern (stored as a `numpy.ndarray`):"
    ]
@@ -768,14 +765,9 @@
     "s_mp = kp.load(filename=datadir + emsoft_master_pattern)\n",
     "\n",
     "print(s_mp)\n",
-    "print(\n",
-    "    s_mp.metadata.get_item(\n",
-    "        \"Simulation.EBSD_master_pattern.Master_pattern.projection\"\n",
-    "    ),\n",
-    "    s_mp.metadata.get_item(\n",
-    "        \"Simulation.EBSD_master_pattern.Master_pattern.hemisphere\"\n",
-    "    )\n",
-    ")"
+    "print(s_mp.projection)\n",
+    "print(s_mp.hemisphere)\n",
+    "print(s_mp.phase)"
    ]
   },
   {
@@ -808,14 +800,8 @@
     ")\n",
     "\n",
     "print(s_mp)\n",
-    "print(\n",
-    "    s_mp.metadata.get_item(\n",
-    "        \"Simulation.EBSD_master_pattern.Master_pattern.projection\"\n",
-    "    ),\n",
-    "    s_mp.metadata.get_item(\n",
-    "        \"Simulation.EBSD_master_pattern.Master_pattern.hemisphere\"\n",
-    "    )\n",
-    ")"
+    "print(s_mp.projection)\n",
+    "print(s_mp.hemisphere)"
    ]
   },
   {

diff --git a/doc/metadata.rst b/doc/metadata.rst
@@ -2,20 +2,16 @@
 Metadata structure
 ==================
 
-The :class:`~kikuchipy.signals.EBSD` and
-:class:`~kikuchipy.signals.EBSDMasterPattern` classes store metadata in the
+The :class:`~kikuchipy.signals.EBSD` class stores metadata in the
 ``metadata`` attribute provided by HyperSpy. While kikuchipy's EBSD
-(:func:`~kikuchipy.signals.util.ebsd_metadata`) and EBSDMasterPattern
-(:func:`~kikuchipy.signals.util.ebsd_master_pattern_metadata`) metadata
-structures are based on `HyperSpy's metadata structure
+(:func:`~kikuchipy.signals.util.ebsd_metadata`) metadata structure is based on
+`HyperSpy's metadata structure
 <http://hyperspy.org/hyperspy-doc/current/user_guide/metadata_structure.html>`_,
-they each include a node ``Acquisition_instrument.Sample.Phases`` to store
-phase information, and ``Acquisition_instrument.SEM.Detector.EBSD`` or
-``Simulation.EBSD_master_pattern``, respectively. The information in these nodes
-are written, along with the patterns, to file when saving an EBSD object in the
-`kikuchipy h5ebsd format <load_save_data.ipynb#h5ebsd>`_ 
-or an EBSDMasterPattern object in `the HyperSpy HDF5 format
-<http://hyperspy.org/hyperspy-doc/current/user_guide/io.html#hspy-hyperspy-s-hdf5-specification>`_.
+it includes the nodes ``Acquisition_instrument.Sample.Phases`` to store
+phase information and ``Acquisition_instrument.SEM.Detector.EBSD`` for
+acquisition information. The information in these nodes are written, along with
+the patterns, to file when saving an EBSD signal in the
+`kikuchipy h5ebsd format <load_save_data.ipynb#h5ebsd>`_.
 
 ::
 
@@ -44,49 +40,28 @@ or an EBSDMasterPattern object in `the HyperSpy HDF5 format
     │       ├── magnification
     │       ├── microscope
     │       └── working_distance [mm]
-    ├── Sample
-    │   └── Phases
-    │       └── 1
-    │           ├── atom_coordinates
-    │           │   └── 1
-    │           │       ├── atom
-    │           │       ├── coordinates (x0, y0, z0)
-    │           │       ├── debye_waller_factor [nm^2]
-    │           │       └── site_occupation
-    │           ├── formula
-    │           ├── info
-    │           ├── lattice_constants (a, b, c and alfa, beta, gamma) [nm and º]
-    │           ├── laue_group
-    │           ├── material_name
-    │           ├── point_group
-    │           ├── setting
-    │           ├── source
-    │           ├── space_group
-    │           └── symmetry
-    └── Simulation
-        └── EBSD_master_pattern
-            ├── BSE_simulation
-            │   ├── depth_step [nm]
-            │   ├── energy_step [keV]
-            │   ├── incident_beam_energy [keV]
-            │   ├── max_depth [nm]
-            │   ├── min_beam_energy [keV]
-            │   ├── mode
-            │   ├── number_of_electrons
-            │   ├── pixels_along_x
-            │   └── sample_tilt [º]
-            └── Master_pattern
-                ├── Bethe_parameters
-                │   ├── complete_cutoff
-                │   ├── strong_beam_cutoff
-                │   └── weak_beam_cutoff
-                ├── projection
-                ├── hemisphere
-                └── smallest_interplanar_spacing [nm]
+    └── Sample
+        └── Phases
+            └── 1
+                ├── atom_coordinates
+                │   └── 1
+                │       ├── atom
+                │       ├── coordinates (x0, y0, z0)
+                │       ├── debye_waller_factor [nm^2]
+                │       └── site_occupation
+                ├── formula
+                ├── info
+                ├── lattice_constants (a, b, c and alfa, beta, gamma) [nm and º]
+                ├── laue_group
+                ├── material_name
+                ├── point_group
+                ├── setting
+                ├── source
+                ├── space_group
+                └── symmetry
 
 The utility function :func:`~kikuchipy.signals.util.metadata_nodes` returns the
-node strings for the ``SEM``, ``EBSD`` and ``EBSD_master_pattern`` nodes for
-convenience.
+node strings for the ``SEM`` and ``EBSD`` nodes for convenience.
 
 .. note::
 
@@ -101,20 +76,10 @@ This node contains information relevant for EBSD data. All parameters can be
 set with the method :meth:`~kikuchipy.signals.EBSD.set_experimental_parameters`.
 An explanation of each parameter is given in the method's docstring.
 
-EBSD master pattern
-===================
-
-This node contains information relevant for simulated EBSD master patterns. All
-parameters can be set with the method
-:meth:`~kikuchipy.signals.EBSDMasterPattern.set_simulation_parameters`. An
-explanation of each parameter is given in the method's docstring.
-
 Phases
 ======
 
 This node contains information relevant for EBSD scans or simulated patterns'
 phases. All parameters can be set with the :class:`~kikuchipy.signals.EBSD`
-method :meth:`~kikuchipy.signals.EBSD.set_phase_parameters` or the
-:class:`~kikuchipy.signals.EBSDMasterPattern` method
-:meth:`~kikuchipy.signals.EBSDMasterPattern.set_phase_parameters`.
-An explanation of each parameter is given in the methods' docstring.
+method :meth:`~kikuchipy.signals.EBSD.set_phase_parameters`. An explanation of
+each parameter is given in the methods' docstring.
diff --git a/doc/reference.rst b/doc/reference.rst
@@ -503,12 +503,9 @@ All methods listed here are also available to
 .. autosummary::
     normalize_intensity
     rescale_intensity
-    set_simulation_parameters
-    set_phase_parameters
 
 .. autoclass:: kikuchipy.signals.EBSDMasterPattern
     :members:
-    :undoc-members:
     :inherited-members: Signal2D
     :show-inheritance:
 
@@ -539,7 +536,6 @@ util
 .. currentmodule:: kikuchipy.signals.util
 
 .. autosummary::
-    ebsd_master_pattern_metadata
     ebsd_metadata
     metadata_nodes
 

diff --git a/kikuchipy/data/tests/test_data.py b/kikuchipy/data/tests/test_data.py
@@ -70,18 +70,8 @@ def test_load_nickel_ebsd_master_pattern_small_kwargs(
         assert isinstance(mp, EBSDMasterPattern)
         assert mp.data.shape == desired_shape
         assert np.issubdtype(mp.data.dtype, np.uint8)
-        assert (
-            mp.metadata.get_item(
-                "Simulation.EBSD_master_pattern.Master_pattern.projection"
-            )
-            == projection
-        )
-        assert (
-            mp.metadata.get_item(
-                "Simulation.EBSD_master_pattern.Master_pattern.hemisphere"
-            )
-            == hemisphere
-        )
+        assert mp.projection == projection
+        assert mp.hemisphere == hemisphere
 
         mp_lazy = data.nickel_ebsd_master_pattern_small(lazy=True)
 

diff --git a/kikuchipy/io/plugins/emsoft_ebsd.py b/kikuchipy/io/plugins/emsoft_ebsd.py
@@ -29,9 +29,6 @@
 from orix.quaternion import Rotation
 
 from kikuchipy.io.plugins.h5ebsd import hdf5group2dict
-from kikuchipy.io.plugins.emsoft_ebsd_master_pattern import (
-    _crystal_data_2_metadata,
-)
 from kikuchipy.signals.util._metadata import (
     ebsd_metadata,
     metadata_nodes,
@@ -104,13 +101,6 @@ def file_reader(
                 "title": f.filename.split("/")[-1].split(".")[0],
                 "original_filename": f.filename.split("/")[-1],
             },
-            "Sample": {
-                "Phases": {
-                    "1": _crystal_data_2_metadata(
-                        hdf5group2dict(f["CrystalData"])
-                    )
-                }
-            },
         }
     )
     scan = {"metadata": md, "original_metadata": omd}