Fix phase list when initializing CrystalMap with a sparse phase list

CHANGELOG.rst

@@ -6,6 +6,14 @@ All user facing changes to this project are documented in this file. The format
 on `Keep a Changelog <https://keepachangelog.com/en/1.0.0/>`__, and this project tries
 its best to adhere to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`__.
 
+2023-03-14 - version 0.11.1
+===========================
+
+Fixed
+-----
+- Initialization of a crystal map with a phase list with fewer phases than in the phase
+  ID array given returns a map with a new phase list with correct phase IDs.
+
 2023-02-09 - version 0.11.0
 ===========================
 

orix/__init__.py

@@ -1,5 +1,5 @@
 __name__ = "orix"
-__version__ = "0.11.0"
+__version__ = "0.11.1"
 __author__ = "orix developers"
 __author_email__ = "pyxem.team@gmail.com"
 __description__ = "orix is an open-source Python library for handling crystal orientation mapping data."

orix/crystal_map/crystal_map.py

@@ -23,7 +23,7 @@
 import numpy as np
 
 from orix.crystal_map.crystal_map_properties import CrystalMapProperties
-from orix.crystal_map.phase_list import Phase, PhaseList
+from orix.crystal_map.phase_list import ALL_COLORS, Phase, PhaseList
 from orix.quaternion import Orientation, Rotation
 
 
@@ -251,7 +251,7 @@ def __init__(
         if phase_list is None:
             self._phases = PhaseList(ids=unique_phase_ids)
         else:
-            phase_list = copy.deepcopy(phase_list)
+            phase_list = phase_list.deepcopy()
             phase_ids = phase_list.ids
             n_different = len(phase_ids) - len(unique_phase_ids)
             if n_different > 0:
@@ -265,15 +265,20 @@ def __init__(
                         break
             elif n_different < 0:
                 # Create new phase list adding the missing phases with
-                # default initial values
-                phase_list = PhaseList(
-                    names=phase_list.names,
-                    space_groups=phase_list.space_groups,
-                    point_groups=phase_list.point_groups,
-                    colors=phase_list.colors,
-                    structures=phase_list.structures,
-                    ids=unique_phase_ids,
+                # default initial values (but unique colors)
+                phase_dict = {}
+                all_colors = list(ALL_COLORS.keys())
+                all_unique_colors = np.delete(
+                    all_colors, np.isin(all_colors, phase_list.colors)
                 )
+                ci = 0
+                for i in unique_phase_ids:
+                    if i in phase_ids:
+                        phase_dict[i] = phase_list[i]
+                    else:
+                        phase_dict[i] = Phase(color=all_unique_colors[ci])
+                        ci += 1
+                phase_list = PhaseList(phase_dict)
             # Ensure phase list IDs correspond to IDs in phase_id array
             new_ids = list(unique_phase_ids.astype(int))
             phase_list._dict = dict(zip(new_ids, phase_list._dict.values()))

orix/tests/test_crystal_map.py

@@ -166,6 +166,31 @@ def test_init_with_phase_list(self, crystal_map_input, expected_presence):
         unique_phase_ids = list(np.unique(crystal_map_input["phase_id"]).astype(int))
         assert xmap.phases.ids == unique_phase_ids
 
+    def test_init_with_sparse_phase_list(self):
+        """Initialize a map with a sparse phase list only containing one
+        of the phase IDs passed in the phase list.
+        """
+        pl = PhaseList(ids=[1], names=["b"], space_groups=[225])
+        phase_id = np.array([0, 0, 1, 1, 1, 3])
+        xmap = CrystalMap(
+            rotations=Rotation.identity(phase_id.size),
+            is_in_data=phase_id == 1,
+            phase_list=pl,
+            phase_id=phase_id,
+        )
+        for i, name, color, sg_name in zip(
+            [0, 1, 3],
+            ["", "b", ""],
+            ["tab:orange", "tab:blue", "tab:green"],
+            [None, "Fm-3m", None],
+        ):
+            assert xmap.phases[i].name == name
+            assert xmap.phases[i].color == color
+            if sg_name is None:
+                assert xmap.phases[i].space_group is None
+            else:
+                assert xmap.phases[i].space_group.short_name == sg_name
+
     def test_init_with_single_point_group(self, crystal_map_input):
         point_group = O
         phase_list = PhaseList(point_groups=point_group)

setup.py

@@ -20,7 +20,7 @@
         "sphinx-design",
         "sphinx-gallery                 < 0.11",
         "sphinx-last-updated-by-git",
-        "pydata-sphinx-theme",
+        "pydata-sphinx-theme            >= 0.13.1",
         "sphinxcontrib-bibtex           >= 1.0",
         "scikit-image",
         "scikit-learn",