Merge pull request #700 from hakonanes/690-oxford-ebsp-aztec-6.1

Fix reading of Oxford Instrument's *.ebsp files with format version 6

CHANGELOG.rst

@@ -13,6 +13,14 @@ its best to adhere to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>
 List entries are sorted in descending chronological order. Contributors to each release
 were listed in alphabetical order by first name until version 0.7.0.
 
+0.11.1 (2024-11-24)
+===================
+
+Fixed
+-----
+- Reading of Oxford binary `*.ebsp` files with version 6.
+ (`#700 <https://github.com/pyxem/kikuchipy/pull/700>`_)
+
 0.11.0 (2024-11-10)
 ===================
 

conftest.py

@@ -51,6 +51,7 @@
 
 
 DATA_PATH = Path(__file__).parent / "src/kikuchipy/data"
+DATA_PATH = DATA_PATH.resolve()
 
 # ------------------------------ Setup ------------------------------ #
 
@@ -511,6 +512,9 @@ def oxford_binary_file(tmpdir, request) -> Generator[TextIOWrapper, None, None]:
 
     for i in new_order:
         r, c = np.unravel_index(i, (nr, nc))
+        if ver > 4:
+            extra_pattern_header = np.array([c, r], dtype=np.int32)
+            extra_pattern_header.tofile(f)
         pattern_header.tofile(f)
         data[r, c].tofile(f)
         if ver > 1:

doc/tutorials/load_save_data.ipynb

@@ -943,7 +943,13 @@
     "Here, the Oxford Instruments binary [file_reader()](../reference/generated/kikuchipy.io.plugins.oxford_binary.file_reader.rst) is called.\n",
     "\n",
     "Every pattern's flattened index into the 2D navigation map, as well as their entry in the file (map order isn't always the same as file order) can be retrieved from `s_oxford.original_metadata.map1d_id` and `s_oxford.original_metadata.file_order`, respectively.\n",
-    "If available in the file, every pattern's row and column beam position in microns can be retrieved from `s_oxford.original_metadata.beam_y` and `s_oxford.original_metadata.beam_x`, respectively.\n",
+    "The following data may be read as well, depending on their presence in the file:\n",
+    "\n",
+    "* `s_oxford.original_metadata.beam_x`: Every pattern's column in microns\n",
+    "* `s_oxford.original_metadata.beam_y`: Every pattern's row in microns\n",
+    "* `s_oxford.original_metadata.map_x`: Every pattern's column\n",
+    "* `s_oxford.original_metadata.map_y`: Every pattern's row\n",
+    "\n",
     "All these are 1D arrays."
    ]
   },
@@ -1100,10 +1106,11 @@
     "## Load and save virtual BSE images\n",
     "\n",
     "One or more virtual backscatter electron (BSE) images in a [VirtualBSEImage](../reference/generated/kikuchipy.signals.VirtualBSEImage.rst) signal can be read and written to file using one of HyperSpy's many readers and writers.\n",
-    "If they are only to be used internally in HyperSpy, they can be written to and read back from HyperSpy's HDF5/zarr specification [as explained above for EBSD master patterns](#Save-patterns).\n",
     "\n",
+    "If they are only to be used internally in HyperSpy, they can be written to and read back from HyperSpy's HDF5/zarr specification [as explained above for EBSD master patterns](#Save-patterns).\n",
     "If we want to write the images to image files, HyperSpy also provides a series of image readers/writers, as explained in their [IO user guide](https://hyperspy.org/hyperspy-doc/v1.7/user_guide/io.html#images).\n",
-    "If we wanted to write them as a stack of TIFF images"
+    "\n",
+    "Writing as a stack of TIFF images"
    ]
   },
   {
@@ -1146,7 +1153,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We can also write them to e.g. `png` or `bmp` files with `Matplotlib`"
+    "Read the TIFF stack back into a `VirtualBSEImage` signal"
    ]
   },
   {
@@ -1155,16 +1162,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "nav_size = vbse.axes_manager.navigation_size\n",
-    "for i in range(nav_size):\n",
-    "    plt.imsave(temp_dir / f\"vbse{i}.png\", vbse.inav[i].data)"
+    "vbse2 = hs.load(temp_dir / vbse_fname, signal_type=\"VirtualBSEImage\")\n",
+    "vbse2"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Read the TIFF stack back into a `VirtualBSEImage` signal"
+    "We can also write them to e.g. `png` or `bmp` files with `Matplotlib`"
    ]
   },
   {
@@ -1173,8 +1179,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vbse2 = hs.load(temp_dir / vbse_fname, signal_type=\"VirtualBSEImage\")\n",
-    "vbse2"
+    "nav_size = vbse.axes_manager.navigation_size\n",
+    "for i in range(nav_size):\n",
+    "    plt.imsave(temp_dir / f\"vbse{i}.png\", vbse.inav[i].data)"
    ]
   },
   {
@@ -1211,7 +1218,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.6"
+   "version": "3.12.7"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

src/kikuchipy/__init__.py

@@ -30,7 +30,7 @@
     "Carter Francis",
     "Magnus Nord",
 ]
-__version__ = "0.11.0"
+__version__ = "0.11.1"
 
 __getattr__, __dir__, __all__ = lazy_loader.attach_stub(__name__, __file__)
 

src/kikuchipy/data/_data.py

@@ -629,7 +629,9 @@ def fetch_file_path(
     ) -> str:
         if show_progressbar is None:
             show_progressbar = hs.preferences.General.show_progressbar
-        downloader = pooch.HTTPDownloader(progressbar=show_progressbar)
+        downloader = pooch.HTTPDownloader(
+            progressbar=show_progressbar, headers={"User-Agent": "agent"}
+        )
 
         if self.is_in_package:
             if self.has_correct_hash: