Merge pull request #18 from shogas/phase_orientation_0_7_update

Phase orientation 0.7 update

Author: dnjohnstone

Phase & Orientation Mapping.ipynb

@@ -208,7 +208,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Define a StructureLibrary containing specifying two crystal structures and orientations of each to include"
+    "Define a StructureLibrary containing specifying two crystal structures and orientations of each to include. The in-plane orientations can be a list of known options (set `inplane_rotations=[0]` in the call to `correlate` below) or the starting points for the list of rotations given to `correlate` below."
    ]
   },
   {
@@ -221,7 +221,7 @@
     "    [('Si', si, 'cubic'),\n",
     "     ('Ga', ga, 'hexagonal')])\n",
     "structure_library = structure_library_generator.get_orientations_from_stereographic_triangle(\n",
-    "    [(0, 10), (0, 10)],  # Inplane rotations to include\n",
+    "    [(0,), (0,)],  # In-plane rotations\n",
     "    5)  # Angular resolution of the library"
    ]
   },
@@ -250,7 +250,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Correlate with the patterns contained in the library with the test data. At this stage the top 3 (n_largest) matching results are retained."
+    "Correlate with the patterns contained in the library with the test data. At this stage the top 3 (`n_largest`) matching results are retained. Test all in-plane rotations at 5 degree increments from 0 to 360."
    ]
   },
   {
@@ -260,7 +260,7 @@
    "outputs": [],
    "source": [
     "indexer = IndexationGenerator(test_data, template_library)\n",
-    "match_results = indexer.correlate(n_largest=3, keys=phase_names)"
+    "match_results = indexer.correlate(n_largest=3, inplane_rotations=np.arange(0, 360, 5))"
    ]
   },
   {
@@ -276,8 +276,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "match_results.plot_best_matching_results_on_signal(test_data, phase_names, template_library,\n",
-    "                                                   permanent_markers=False, cmap='viridis')"
+    "match_results.plot_best_matching_results_on_signal(test_data, template_library, permanent_markers=False, cmap='viridis')"
    ]
   },
   {
@@ -334,7 +333,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Define a structure library for expected phases, defined in section 1."
+    "Define a structure library for the expected phases from section 1."
    ]
   },
   {
@@ -405,7 +404,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Plot indexed peaks on top of the data"
+    "Plot indexed peaks on top of the data using the template library from above to generate peak positions."
    ]
   },
   {
@@ -414,9 +413,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "indexation.plot_best_matching_results_on_signal(test_data, phase_names,\n",
-    "                                                vector_library, ediff, reciprocal_radius,\n",
-    "                                                permanent_markers=False)"
+    "indexation.plot_best_matching_results_on_signal(test_data, template_library, permanent_markers=False)"
    ]
   },
   {
@@ -441,7 +438,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Plot the match rate as a metric for mapping success"
+    "Plot the match rate as a metric for mapping success."
    ]
   },
   {
@@ -517,7 +514,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.6"
+   "version": "3.7.2"
   }
  },
  "nbformat": 4,