Merge pull request #416 from hakonanes/fix-413

Allow reading of EDAX TSL .ang files with ten columns

.github/workflows/build.yml

@@ -1,48 +1,64 @@
 name: build
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - '*'
+  pull_request:
+    branches:
+      - '*'
+  workflow_dispatch:
+    workflow: '*'
+
+env:
+  MPLBACKEND: agg
 
 jobs:
   code:
     name: code style
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+
       - uses: psf/black@stable
-      - uses: actions/setup-python@v2
+
+      - uses: actions/setup-python@v4
         with:
           python-version: 3.9
+
       - uses: isort/isort-action@master
         with:
           configuration: --profile black --filter-files --force-sort-within-sections --check-only --diff
 
       - name: Install Black with Jupyter extension
-        run: pip install black[jupyter]
+        run: |
+          pip install black[jupyter]
 
       - name: Check code style of Jupyter notebooks
-        run: black doc/**/*.ipynb --check
+        run: |
+          black doc/**/*.ipynb --check
 
   # Make sure all necessary files will be included in a release
   manifest:
     name: check manifest
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
 
       - name: Install dependencies
-        run: pip install manifix
+        run: |
+          pip install manifix
 
       - name: Check MANIFEST.in file
-        run: python setup.py manifix
+        run: |
+          python setup.py manifix
 
   build-with-pip:
     name: ${{ matrix.os }}-py${{ matrix.python-version }}${{ matrix.LABEL }}
     runs-on: ${{ matrix.os }}
     timeout-minutes: 15
-    env:
-      MPLBACKEND: agg
     strategy:
       fail-fast: false
       matrix:
@@ -55,26 +71,28 @@ jobs:
             DEPENDENCIES: diffpy.structure==3  matplotlib==3.3
             LABEL: -oldest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Display Python and pip versions
-        run: python -V; pip -V
-
       - name: Install depedencies and package
         shell: bash
-        run: pip install -U -e .'[doc, tests]'
+        run: |
+          pip install -U -e .'[doc, tests]'
 
       - name: Install oldest supported version
         if: ${{ matrix.OLDEST_SUPPORTED_VERSION }}
-        run: pip install ${{ matrix.DEPENDENCIES }}
+        run: |
+          pip install ${{ matrix.DEPENDENCIES }}
 
-      - name: Display package versions
-        run: pip list
+      - name: Display Python, pip and package versions
+        run: |
+          python -V
+          pip -V
+          pip list
 
       - name: Run docstring tests
         if: ${{ matrix.os == 'ubuntu-latest' }}
@@ -83,11 +101,13 @@ jobs:
           pytest --doctest-modules --ignore-glob=orix/tests orix/*.py
 
       - name: Run tests
-        run: pytest --cov=orix --pyargs orix
+        run: |
+          pytest -n 2 --cov=orix --pyargs orix
 
       - name: Generate line coverage
         if: ${{ matrix.os == 'ubuntu-latest' }}
-        run: coverage report --show-missing
+        run: |
+          coverage report --show-missing
 
       - name: Upload coverage to Coveralls
         if: ${{ matrix.os == 'ubuntu-latest' }}

CHANGELOG.rst

@@ -28,6 +28,7 @@ Added
 Changed
 -------
 - Bumped minimal version of ``diffpy.structure >= 3.0.2``.
+- Only ASTAR .ang files return crystal maps with ``"nm"`` as scan unit.
 
 Deprecated
 ----------
@@ -37,6 +38,7 @@ Removed
 
 Fixed
 -----
+- Reading of EDAX TSL .ang files with ten columns should now work.
 
 Security
 --------

orix/io/plugins/ang.py

@@ -35,11 +35,6 @@
 
 __all__ = ["file_reader", "file_writer"]
 
-# MTEX has this format sorted out, check out their readers when fixing
-# issues and adapting to other versions of this file format in the future:
-# https://github.com/mtex-toolbox/mtex/blob/develop/interfaces/loadEBSD_ang.m
-# https://github.com/mtex-toolbox/mtex/blob/develop/interfaces/loadEBSD_ACOM.m
-
 # Plugin description
 format_name = "ang"
 file_extensions = ["ang"]
@@ -117,15 +112,16 @@ def file_reader(filename: str) -> CrystalMap:
     )
 
     # Set which data points are not indexed
-    if vendor in ["orix", "tsl"]:
-        data_dict["phase_id"][np.where(data_dict["prop"]["ci"] == -1)] = -1
     # TODO: Add not-indexed convention for INDEX ASTAR
+    if vendor in ["orix", "tsl"]:
+        not_indexed = data_dict["prop"]["ci"] == -1
+        data_dict["phase_id"][not_indexed] = -1
 
     # Set scan unit
-    if vendor in ["tsl", "emsoft"]:
-        scan_unit = "um"
-    else:  # NanoMegas
+    if vendor == "astar":
         scan_unit = "nm"
+    else:
+        scan_unit = "um"
     data_dict["scan_unit"] = scan_unit
 
     # Create rotations
@@ -173,7 +169,8 @@ def _get_vendor_columns(header: List[str], n_cols_file: int) -> Tuple[str, List[
     Returns
     -------
     vendor
-        Determined vendor (``"tsl"``, ``"astar"``, or ``"emsoft"``).
+        Determined vendor (``"tsl"``, ``"astar"``, ``"emsoft"`` or
+        ``"orix"``).
     column_names
         List of column names.
     """
@@ -194,77 +191,101 @@ def _get_vendor_columns(header: List[str], n_cols_file: int) -> Tuple[str, List[
                 footprint_line = line
                 break
 
-    # Vendor column names
+    # Variants of vendor column names encountered in real data sets
     column_names = {
-        "unknown": [
-            "euler1",
-            "euler2",
-            "euler3",
-            "x",
-            "y",
-            "unknown1",
-            "unknown2",
-            "phase_id",
-        ],
-        "tsl": [
-            "euler1",
-            "euler2",
-            "euler3",
-            "x",
-            "y",
-            "iq",  # Image quality from Hough transform
-            "ci",  # Confidence index
-            "phase_id",
-            "unknown1",
-            "fit",  # Pattern fit
-            "unknown2",
-            "unknown3",
-            "unknown4",
-            "unknown5",
-        ],
-        "emsoft": [
-            "euler1",
-            "euler2",
-            "euler3",
-            "x",
-            "y",
-            "iq",  # Image quality from Krieger Lassen's method
-            "dp",  # Dot product
-            "phase_id",
-        ],
-        "astar": [
-            "euler1",
-            "euler2",
-            "euler3",
-            "x",
-            "y",
-            "ind",  # Correlation index
-            "rel",  # Reliability
-            "phase_id",
-            "relx100",  # Reliability x 100
-        ],
-        "orix": [
-            "euler1",
-            "euler2",
-            "euler3",
-            "x",
-            "y",
-            "iq",
-            "ci",
-            "phase_id",
-            "detector_signal",
-            "fit",
-        ],
+        "tsl": {
+            0: [
+                "euler1",
+                "euler2",
+                "euler3",
+                "x",
+                "y",
+                "iq",  # Image quality from Hough transform
+                "ci",  # Confidence index
+                "phase_id",
+                "detector_signal",
+                "fit",  # Pattern fit
+                "unknown1",
+                "unknown2",
+                "unknown3",
+                "unknown4",
+            ],
+            1: [
+                "euler1",
+                "euler2",
+                "euler3",
+                "x",
+                "y",
+                "iq",
+                "ci",
+                "phase_id",
+                "detector_signal",
+                "fit",
+            ],
+        },
+        "emsoft": {
+            0: [
+                "euler1",
+                "euler2",
+                "euler3",
+                "x",
+                "y",
+                "iq",  # Image quality from Krieger Lassen's method
+                "dp",  # Dot product
+                "phase_id",
+            ]
+        },
+        "astar": {
+            0: [
+                "euler1",
+                "euler2",
+                "euler3",
+                "x",
+                "y",
+                "ind",  # Correlation index
+                "rel",  # Reliability
+                "phase_id",
+                "relx100",  # Reliability x 100
+            ],
+        },
+        "orix": {
+            0: [
+                "euler1",
+                "euler2",
+                "euler3",
+                "x",
+                "y",
+                "iq",
+                "ci",
+                "phase_id",
+                "detector_signal",
+                "fit",
+            ],
+        },
+        "unknown": {
+            0: [
+                "euler1",
+                "euler2",
+                "euler3",
+                "x",
+                "y",
+                "unknown1",
+                "unknown2",
+                "phase_id",
+            ]
+        },
     }
 
-    n_cols_expected = len(column_names[vendor])
+    n_variants = len(column_names[vendor])
+    n_cols_expected = [len(column_names[vendor][k]) for k in range(n_variants)]
     if vendor == "orix" and "Column names" in footprint_line:
         # Append names of extra properties found, if any, in the orix
         # .ang file header
-        n_cols = len(column_names[vendor])
+        vendor_column_names = column_names[vendor][0]
+        n_cols = n_cols_expected[0]
         extra_props = footprint_line.split(":")[1].split(",")[n_cols:]
-        column_names[vendor] += [i.lstrip(" ").replace(" ", "_") for i in extra_props]
-    elif n_cols_file != n_cols_expected:
+        vendor_column_names += [i.lstrip(" ").replace(" ", "_") for i in extra_props]
+    elif n_cols_file not in n_cols_expected:
         warnings.warn(
             f"Number of columns, {n_cols_file}, in the file is not equal to "
             f"the expected number of columns, {n_cols_expected}, for the \n"
@@ -273,13 +294,17 @@ def _get_vendor_columns(header: List[str], n_cols_file: int) -> Tuple[str, List[
             "phase_id, unknown3, unknown4, etc."
         )
         vendor = "unknown"
-        n_cols_unknown = len(column_names["unknown"])
-        if n_cols_file > n_cols_unknown:
-            # Add potential extra columns to properties
-            for i in range(n_cols_file - n_cols_unknown):
-                column_names["unknown"].append("unknown" + str(i + 3))
+        vendor_column_names = column_names[vendor][0]
+        n_cols = len(vendor_column_names)
+        if n_cols_file > n_cols:
+            # Add any extra columns as properties
+            for i in range(n_cols_file - n_cols):
+                vendor_column_names.append("unknown" + str(i + 3))
+    else:
+        idx = np.where(np.equal(n_cols_file, n_cols_expected))[0][0]
+        vendor_column_names = column_names[vendor][idx]
 
-    return vendor, column_names[vendor]
+    return vendor, vendor_column_names
 
 
 def _get_phases_from_header(

orix/quaternion/symmetry.py

@@ -476,7 +476,7 @@ def plot(
             default marker style for reprojected vectors is "+". Values
             used for vector(s) on the visible hemisphere are used unless
             another value is passed here.
-        kwargs
+        **kwargs
             Keyword arguments passed to
             :meth:`~orix.plot.StereographicPlot.scatter`, which passes
             these on to :meth:`matplotlib.axes.Axes.scatter`.