Merge pull request #704 from hakonanes/post-0.11.1-release-develop-up…

…dates

Post 0.11.1 release develop updates

CHANGELOG.rst

@@ -25,11 +25,26 @@ Changed
 Removed
 -------
 
+Fixed
+-----
+
 Deprecated
 ----------
 
+0.11.1 (2024-11-30)
+===================
+
+Added
+-----
+- Reading of unprocessed patterns from H5OINA files is now possible.
+  (`#701 <https://github.com/pyxem/kikuchipy/pull/701>`_)
+
 Fixed
 -----
+- Reading of Oxford binary `*.ebsp` files with version 6.
+  (`#700 <https://github.com/pyxem/kikuchipy/pull/700>`_)
+- Unnecessary reading of unprocessed patterns from H5OINA files into the EBSD original
+  metadata. (`#701 <https://github.com/pyxem/kikuchipy/pull/701>`_)
 
 0.11.0 (2024-11-10)
 ===================

doc/conf.py

@@ -6,8 +6,10 @@
 import inspect
 import os
 from os.path import dirname, relpath
+from pathlib import Path
 import re
 import sys
+import warnings
 
 from numpydoc.docscrape_sphinx import SphinxDocString
 import pyvista as pv
@@ -53,7 +55,6 @@
 # Create links to references within kikuchipy's documentation to these
 # packages
 intersphinx_mapping = {
-    # Package
     "black": ("https://black.readthedocs.io/en/stable", None),
     "conda": ("https://docs.conda.io/projects/conda/en/latest", None),
     "coverage": ("https://coverage.readthedocs.io/en/latest", None),
@@ -358,7 +359,15 @@ def _str_examples(self):
 }
 autosummary_generate = True
 
-# Download example datasets prior to building the docs
-print("[kikuchipy] Downloading example datasets (if not found in cache)")
-_ = kp.data.nickel_ebsd_large(allow_download=True)
-_ = kp.data.si_ebsd_moving_screen(0, allow_download=True)
+
+def custom_setup():
+    """Download files used in the documentation."""
+    print("[kikuchipy] Downloading example datasets (if not found in cache)")
+    try:
+        _ = kp.data.nickel_ebsd_large(allow_download=True)
+        _ = kp.data.si_ebsd_moving_screen(0, allow_download=True)
+    except () as e:
+        warnings.warn(f"Download failed. Error: {e}")
+
+
+custom_setup()

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."
    ]
   },
@@ -977,7 +983,10 @@
     "As with the kikuchipy h5ebsd reader, multiple scans can be read at once.\n",
     "\n",
     "The projection center (PC) arrays are read into the `detector` attribute and the static background pattern is read into the `static_background` attribute.\n",
-    "The orientation and phase data are so far not read."
+    "The orientation and phase data are so far not read.\n",
+    "\n",
+    "Oxford Instruments allow writing both processed and unprocessed patterns.\n",
+    "To read the unprocessed patterns, pass `processed=False` when loading."
    ]
   },
   {
@@ -1100,10 +1109,11 @@
     "## 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 +1156,7 @@
    "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 +1165,15 @@
    "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 +1182,9 @@
    "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 +1221,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.6"
+   "version": "3.12.7"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

pyproject.toml

@@ -123,6 +123,10 @@ src = ""
 [tool.hatch.build.targets.wheel]
 include = ["src/kikuchipy"]
 
+[tool.hatch.build.targets.wheel.force-include]
+"tests/" = "kikuchipy/tests"
+"conftest.py" = "kikuchipy/conftest.py"
+
 [tool.coverage.report]
 precision = 2
 

src/kikuchipy/__init__.py

@@ -30,7 +30,7 @@
     "Carter Francis",
     "Magnus Nord",
 ]
-__version__ = "0.12.dev0"
+__version__ = "0.12.dev1"
 
 __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: