fakecbed 0.3.6__tar.gz → 0.5.0__tar.gz

{fakecbed-0.3.6 → fakecbed-0.5.0}/.gitignore

@@ -13,6 +13,7 @@ pages/
 .python-version
 fakecbed/version.py
 tests/coverage.json
+run_tests.sh
 
 # Ignore generated output coverage files.
 tests/coverage*

{fakecbed-0.3.6 → fakecbed-0.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fakecbed
-Version: 0.3.6
+Version: 0.5.0
 Summary: A Python library for generating quickly images that imitate convergent beam electron diffraction patterns.
 Author-email: Matthew Fitzpatrick <matthew.rc.fitzpatrick@gmail.com>
 Project-URL: Homepage, https://mrfitzpa.github.io/fakecbed
@@ -21,7 +21,8 @@ Classifier: Natural Language :: English
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: distoptica>=0.3.3
+Requires-Dist: distoptica>=0.4.0
+Requires-Dist: empix
 Requires-Dist: hyperspy
 Provides-Extra: tests
 Requires-Dist: pytest-cov; extra == "tests"

{fakecbed-0.3.6 → fakecbed-0.5.0}/examples/basic_usage.ipynb

@@ -45,12 +45,20 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# For performing deep copies.\n",
+    "import copy\n",
+    "\n",
+    "\n",
+    "\n",
     "# For general array handling.\n",
     "import numpy as np\n",
     "\n",
     "# For creating distortion models.\n",
     "import distoptica\n",
     "\n",
+    "# For creating Hyperspy markers.\n",
+    "import hyperspy.api as hs\n",
+    "\n",
     "\n",
     "\n",
     "# The library that is the subject of this demonstration.\n",
@@ -100,6 +108,14 @@
     "## Using the ``fakecbed`` library ##"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "60a6dd71-881c-4e24-9fc3-15f291729d52",
+   "metadata": {},
+   "source": [
+    "### Creating a fake CBED pattern ###"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "07902c93-c509-48a1-9953-fc4fcb6e925a",
@@ -1275,6 +1291,560 @@
     "          \"cmap\": \"jet\"}\n",
     "cbed_pattern.signal.plot(**kwargs)"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "012e8538-e2e9-420c-bfb9-684c18b3ac54",
+   "metadata": {},
+   "source": [
+    "### Creating a cropped fake CBED pattern ###"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c4863267-bbd9-4950-86a5-15494a987f5a",
+   "metadata": {},
+   "source": [
+    "Let us recover the fake CBED pattern we created prior to overriding the image:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "79dfc4f1-5621-4a75-bed7-8e3b18c871ae",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "kwargs = cbed_pattern.core_attrs\n",
+    "cbed_pattern = fakecbed.discretized.CBEDPattern(**kwargs)\n",
+    "\n",
+    "kwargs = {\"axes_off\": False, \n",
+    "          \"scalebar\": False, \n",
+    "          \"colorbar\": False, \n",
+    "          \"gamma\": 0.3,\n",
+    "          \"cmap\": \"jet\"}\n",
+    "cbed_pattern.signal.plot(**kwargs)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "abe6a2d9-9c85-46a9-a34a-f46fb0c4b28b",
+   "metadata": {},
+   "source": [
+    "With this fake CBED pattern we can create a cropped fake CBED pattern:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5318265c-5934-4285-8a63-76634b059f44",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "kwargs = {\"cbed_pattern\": cbed_pattern, \n",
+    "          \"cropping_window_center\": (0.35, 0.35),\n",
+    "          \"cropping_window_dims_in_pixels\": (300, 300),\n",
+    "          \"principal_disk_idx\": 1,\n",
+    "          \"disk_boundary_sample_size\": 64, \n",
+    "          \"mask_frame\": (10, 50, 30, 5)}\n",
+    "cropped_cbed_pattern = fakecbed.discretized.CroppedCBEDPattern(**kwargs)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5829c2c2-e7d0-4cd0-afd1-88345f6677c3",
+   "metadata": {},
+   "source": [
+    "A subset of the attribute names of the\n",
+    "``fakecbed.discretized.CroppedCBEDPattern`` class is equal to the entire set of\n",
+    "attribute names of the ``fakecbed.discretized.CBEDPattern`` class. For instance,\n",
+    "the attribute ``cropped_cbed_pattern.signal`` stores a hyperspy signal\n",
+    "representation of the cropped fake CBED pattern. See\n",
+    "[here](https://mrfitzpa.github.io/fakecbed/_autosummary/fakecbed.discretized.CroppedCBEDPattern.html#fakecbed.discretized.CroppedCBEDPattern.signal)\n",
+    "for a description of the signal representation of the fake cropped CBED pattern.\n",
+    "Note that the image of the discretized cropped CBED pattern is always\n",
+    "automatically min-max normalized. Also, note that the positions of the pixels in\n",
+    "the signal representation of the cropped fake CBED pattern are expressed in the\n",
+    "fractional coordinates of the uncropped fake CBED pattern."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fd130608-2d5e-4fd2-8832-f013a45223dd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cropped_cbed_pattern_signal = cropped_cbed_pattern.signal\n",
+    "\n",
+    "kwargs = {\"axes_off\": False, \n",
+    "          \"scalebar\": False, \n",
+    "          \"colorbar\": False, \n",
+    "          \"gamma\": 0.3,\n",
+    "          \"cmap\": \"jet\"}\n",
+    "cropped_cbed_pattern_signal.plot(**kwargs)\n",
+    "\n",
+    "cropped_cbed_pattern_signal.metadata"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0aa6554a-0036-4ee6-8138-4eaab5d14789",
+   "metadata": {},
+   "source": [
+    "The ``fakecbed.discretized.CroppedCBEDPattern`` class has additional attributes,\n",
+    "one of which is ``principal_disk_is_clipped``, which indicates whether the\n",
+    "\"principal\" CBED disk is clipped in the image of the cropped fake CBED pattern:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7ea653c5-03bc-4918-82e6-4ff08e5341b8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cropped_cbed_pattern.principal_disk_is_clipped"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "80824fd9-43ca-4500-9709-6979e6c3559c",
+   "metadata": {},
+   "source": [
+    "In our current example, the principal CBED disk is not clipped. If the principal\n",
+    "CBED disk does not exist, i.e. if the construction parameter\n",
+    "``principal_disk_idx`` is set to a nonnegative integer greater than or equal to\n",
+    "the number of CBED disks defined in the uncropped fake CBED pattern, then\n",
+    "``principal_disk_is_clipped`` will return ``True``. To be clear,\n",
+    "``principal_disk_is_clipped`` can return ``True`` even if the principal CBED\n",
+    "disk exists. In such a scenario, the principal CBED disk corresponds to a CBED\n",
+    "disk that has been defined, but is clipped in the image of the uncropped fake\n",
+    "CBED pattern."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "569d50f7-7354-448c-abf0-3124eb8b0ecc",
+   "metadata": {},
+   "source": [
+    "Another attribute is ``principal_disk_is_absent``, which indicates whether the\n",
+    "\"principal\" CBED disk is absent in the image of the cropped fake CBED pattern:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fa747739-8f91-4bb1-bc17-23d79018bcda",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cropped_cbed_pattern.principal_disk_is_absent"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "ec76677f-46d2-4aea-a11f-158173f09ebc",
+   "metadata": {},
+   "source": [
+    "In our current example, the principal CBED disk is not absent. If the principal\n",
+    "CBED disk does not exist, then ``principal_disk_is_absent`` will be set to\n",
+    "``True``. To be clear, ``principal_disk_is_absent`` can be set to ``True`` even\n",
+    "if the principal CBED disk exists. In such a scenario, the principal CBED disk\n",
+    "corresponds to a CBED disk that has been defined, but is absent in the image of\n",
+    "the uncropped fake CBED pattern."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "64410367-6786-4d22-98e0-dc2330fd774b",
+   "metadata": {},
+   "source": [
+    "Another attribute is ``principal_disk_is_overlapping``, which indicates whether\n",
+    "the \"principal\" CBED disk is overlapping with another CBED disk in the image of\n",
+    "the cropped fake CBED pattern:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "76ac4578-e7fc-4f4f-83a8-e03f1ac45e4b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cropped_cbed_pattern.principal_disk_is_overlapping"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "151710c6-6ac8-4f0d-8588-81016d5d4156",
+   "metadata": {},
+   "source": [
+    "In our current example, the principal CBED disk is not overlapping. If the\n",
+    "principal CBED disk does not exist, then ``principal_disk_is_overlapping`` will\n",
+    "be set to ``False``."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "9e091d44-7f20-4256-b148-4205460a13e0",
+   "metadata": {},
+   "source": [
+    "Another attribute is\n",
+    "``principal_disk_bounding_box_in_uncropped_image_fractional_coords``, which\n",
+    "stores the bounding box of the unclipped support of the principal CBED disk,\n",
+    "should it exist, in fractional coordinates of the uncropped fake CBED pattern:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b91e8b37-a136-4c57-b1cb-95ed11934c19",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "attr_name = \\\n",
+    "    \"principal_disk_bounding_box_in_uncropped_image_fractional_coords\"\n",
+    "principal_disk_bounding_box_in_uncropped_image_fractional_coords = \\\n",
+    "    getattr(cropped_cbed_pattern, attr_name)\n",
+    "\n",
+    "principal_disk_bounding_box_in_uncropped_image_fractional_coords"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "f48a054e-8fc1-46a7-b72e-9198d97d7a18",
+   "metadata": {},
+   "source": [
+    "In the order that they appear, the coordinates are those of the left, right,\n",
+    "bottom and top sides of the bounding box respectively. If the principal CBED\n",
+    "disk does not exist, then the attribute is set to ``None``.\n",
+    "\n",
+    "We can add the box to the signal representations of the cropped and uncropped\n",
+    "fake CBED patterns:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "23ffa504-3d7d-4784-9a2f-1fd3849aa687",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "L, R, B, T = principal_disk_bounding_box_in_uncropped_image_fractional_coords\n",
+    "\n",
+    "kwargs = {\"axes_off\": False, \n",
+    "          \"scalebar\": False, \n",
+    "          \"colorbar\": False, \n",
+    "          \"gamma\": 0.3,\n",
+    "          \"cmap\": \"jet\"}\n",
+    "cropped_cbed_pattern_signal.plot(**kwargs)\n",
+    "\n",
+    "try:  # For Hyperspy versions >= 2.\n",
+    "    x_box = (R+L)/2\n",
+    "    y_box = (B+T)/2\n",
+    "    box_center = (x_box, y_box)\n",
+    "    kwargs = {\"edgecolors\": \"green\",\n",
+    "              \"linewidths\": 3, \n",
+    "              \"facecolors\": \"none\",\n",
+    "              \"offsets\": (box_center,), \n",
+    "              \"widths\": (R-L), \n",
+    "              \"heights\": (B-T)}\n",
+    "    marker = hs.plot.markers.Rectangles(**kwargs)\n",
+    "except:  # For Hyperspy versions < 2.\n",
+    "    kwargs = {\"edgecolor\": \"green\",\n",
+    "              \"linewidth\": 3, \n",
+    "              \"x1\": L, \n",
+    "              \"x2\": R, \n",
+    "              \"y1\": T, \n",
+    "              \"y2\": B}\n",
+    "    marker = hs.plot.markers.rectangle(**kwargs)\n",
+    "\n",
+    "cropped_cbed_pattern_signal.add_marker(marker, permanent=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "62f80164-125a-4757-a61a-226768c6323b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cbed_pattern_signal = cbed_pattern.signal\n",
+    "\n",
+    "kwargs = {\"axes_off\": False, \n",
+    "          \"scalebar\": False, \n",
+    "          \"colorbar\": False, \n",
+    "          \"gamma\": 0.3,\n",
+    "          \"cmap\": \"jet\"}\n",
+    "cbed_pattern_signal.plot(**kwargs)\n",
+    "\n",
+    "marker = copy.deepcopy(marker)\n",
+    "cbed_pattern_signal.add_marker(marker, permanent=False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "18fe97c8-1692-4076-bb6f-b1dd90fabe80",
+   "metadata": {},
+   "source": [
+    "Another attribute is\n",
+    "``principal_disk_boundary_pts_in_uncropped_image_fractional_coords``, which\n",
+    "stores a sample of points on the boundary of the unclipped support of the\n",
+    "principal CBED disk, should it exist, in fractional coordinates of the uncropped\n",
+    "fake CBED pattern:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f71e51a6-b251-4e4a-ad73-a273e3b600c1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "attr_name = \\\n",
+    "    \"principal_disk_boundary_pts_in_uncropped_image_fractional_coords\"\n",
+    "principal_disk_boundary_pts_in_uncropped_image_fractional_coords = \\\n",
+    "    getattr(cropped_cbed_pattern, attr_name)\n",
+    "\n",
+    "principal_disk_boundary_pts_in_uncropped_image_fractional_coords"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b57fd54c-341c-425a-8bc5-10df91147ab7",
+   "metadata": {},
+   "source": [
+    "If the principal CBED disk does not exist, then the attribute is set to ``None``.\n",
+    "\n",
+    "We can add the sample of points to the signal representations of the cropped and\n",
+    "uncropped fake CBED patterns:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fd90ebc0-5626-444f-9b59-0e9322dba409",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pts = principal_disk_boundary_pts_in_uncropped_image_fractional_coords.tolist()\n",
+    "\n",
+    "kwargs = {\"axes_off\": False, \n",
+    "          \"scalebar\": False, \n",
+    "          \"colorbar\": False, \n",
+    "          \"gamma\": 0.3,\n",
+    "          \"cmap\": \"jet\"}\n",
+    "cropped_cbed_pattern_signal.plot(**kwargs)\n",
+    "\n",
+    "markers = tuple()\n",
+    "\n",
+    "try:  # For Hyperspy versions >= 2.\n",
+    "    for pt in pts:\n",
+    "        kwargs = {\"color\": \"black\", \n",
+    "                  \"sizes\": 3, \n",
+    "                  \"offsets\": pt}\n",
+    "        marker = hs.plot.markers.Points(**kwargs)\n",
+    "        markers += (marker,)\n",
+    "        cropped_cbed_pattern_signal.add_marker(marker, permanent=False)\n",
+    "except:  # For Hyperspy versions < 2.\n",
+    "    for pt in pts:\n",
+    "        kwargs = {\"color\": \"black\", \n",
+    "                  \"size\": 3, \n",
+    "                  \"x\": pt[0], \n",
+    "                  \"y\": pt[1]}\n",
+    "        marker = hs.plot.markers.point(**kwargs)\n",
+    "        markers += (marker,)\n",
+    "        cropped_cbed_pattern_signal.add_marker(marker, permanent=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ecd4c53e-78a4-40e5-86da-c65da6e17626",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "kwargs = {\"axes_off\": False, \n",
+    "          \"scalebar\": False, \n",
+    "          \"colorbar\": False, \n",
+    "          \"gamma\": 0.3,\n",
+    "          \"cmap\": \"jet\"}\n",
+    "cbed_pattern_signal.plot(**kwargs)\n",
+    "\n",
+    "markers = copy.deepcopy(markers)\n",
+    "\n",
+    "for marker in markers:\n",
+    "    cbed_pattern_signal.add_marker(marker, permanent=False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "84c9c73a-4014-49c4-96ae-76f1697ed644",
+   "metadata": {},
+   "source": [
+    "Another attribute is\n",
+    "``principal_disk_bounding_box_in_cropped_image_fractional_coords``, which stores\n",
+    "the bounding box of the unclipped support of the principal CBED disk, should it\n",
+    "exist, in fractional coordinates of the cropped fake CBED pattern:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3e9bf369-fab6-4f19-a11c-995c2951a42b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "attr_name = \\\n",
+    "    \"principal_disk_bounding_box_in_cropped_image_fractional_coords\"\n",
+    "principal_disk_bounding_box_in_cropped_image_fractional_coords = \\\n",
+    "    getattr(cropped_cbed_pattern, attr_name)\n",
+    "\n",
+    "principal_disk_bounding_box_in_cropped_image_fractional_coords"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "bb3e6eb4-c41f-4bfa-b2c1-038e717aa651",
+   "metadata": {},
+   "source": [
+    "If the principal CBED disk does not exist, then the attribute is set to ``None``.\n",
+    "\n",
+    "In order to add properly the box to the signal representation of the cropped\n",
+    "fake CBED pattern, we need to modify signal axes such that the pixel coordinates\n",
+    "are expressed in fractional units of the cropped fake CBED pattern:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b76124a3-2f4f-48be-afb3-78ef50f97183",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "N_h = cropped_cbed_pattern_signal.axes_manager[1].size\n",
+    "N_v = cropped_cbed_pattern_signal.axes_manager[2].size\n",
+    "\n",
+    "cropped_cbed_pattern_signal.axes_manager[1].scale = 1/N_h\n",
+    "cropped_cbed_pattern_signal.axes_manager[2].scale = -1/N_v\n",
+    "\n",
+    "cropped_cbed_pattern_signal.axes_manager[1].offset = 0.5/N_h\n",
+    "cropped_cbed_pattern_signal.axes_manager[2].offset = 1-(1-0.5)/N_v\n",
+    "\n",
+    "cropped_cbed_pattern_signal.axes_manager[1].name = (\"fractional horizontal \"\n",
+    "                                                    \"coordinate of cropped \"\n",
+    "                                                    \"fake CBED pattern\")\n",
+    "cropped_cbed_pattern_signal.axes_manager[2].name = (\"fractional vertical \"\n",
+    "                                                    \"coordinate of cropped \"\n",
+    "                                                    \"fake CBED pattern\")\n",
+    "\n",
+    "L, R, B, T = principal_disk_bounding_box_in_cropped_image_fractional_coords\n",
+    "\n",
+    "kwargs = {\"axes_off\": False, \n",
+    "          \"scalebar\": False, \n",
+    "          \"colorbar\": False, \n",
+    "          \"gamma\": 0.3,\n",
+    "          \"cmap\": \"jet\"}\n",
+    "cropped_cbed_pattern_signal.plot(**kwargs)\n",
+    "\n",
+    "try:  # For Hyperspy versions >= 2.\n",
+    "    x_box = (R+L)/2\n",
+    "    y_box = (B+T)/2\n",
+    "    box_center = (x_box, y_box)\n",
+    "    kwargs = {\"edgecolors\": \"green\",\n",
+    "              \"linewidths\": 3, \n",
+    "              \"facecolors\": \"none\",\n",
+    "              \"offsets\": (box_center,), \n",
+    "              \"widths\": (R-L), \n",
+    "              \"heights\": (B-T)}\n",
+    "    marker = hs.plot.markers.Rectangles(**kwargs)\n",
+    "except:  # For Hyperspy versions < 2.\n",
+    "    kwargs = {\"edgecolor\": \"green\",\n",
+    "              \"linewidth\": 3, \n",
+    "              \"x1\": L, \n",
+    "              \"x2\": R, \n",
+    "              \"y1\": T, \n",
+    "              \"y2\": B}\n",
+    "    marker = hs.plot.markers.rectangle(**kwargs)\n",
+    "\n",
+    "cropped_cbed_pattern_signal.add_marker(marker, permanent=False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "04be66ce-9e31-4610-941b-e8326c85981a",
+   "metadata": {},
+   "source": [
+    "Lastly, another attribute is\n",
+    "``principal_disk_boundary_pts_in_cropped_image_fractional_coords``, which stores\n",
+    "a sample of points on the boundary of the unclipped support of the principal\n",
+    "CBED disk, should it exist, in fractional coordinates of the cropped fake CBED\n",
+    "pattern:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ad6787ca-c22a-4546-a1d6-8bc89df90bcd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "attr_name = \\\n",
+    "    \"principal_disk_boundary_pts_in_cropped_image_fractional_coords\"\n",
+    "principal_disk_boundary_pts_in_cropped_image_fractional_coords = \\\n",
+    "    getattr(cropped_cbed_pattern, attr_name)\n",
+    "\n",
+    "principal_disk_boundary_pts_in_cropped_image_fractional_coords"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "fdcc74bc-9ec4-469e-923d-610c38cd6c4e",
+   "metadata": {},
+   "source": [
+    "If the principal CBED disk does not exist, then the attribute is set to ``None``.\n",
+    "\n",
+    "We can add the sample of points to the signal representations of the cropped and\n",
+    "uncropped fake CBED patterns:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5280b166-8806-4322-90f3-3deb4e9fd8d2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pts = principal_disk_boundary_pts_in_cropped_image_fractional_coords.tolist()\n",
+    "\n",
+    "kwargs = {\"axes_off\": False, \n",
+    "          \"scalebar\": False, \n",
+    "          \"colorbar\": False, \n",
+    "          \"gamma\": 0.3,\n",
+    "          \"cmap\": \"jet\"}\n",
+    "cropped_cbed_pattern_signal.plot(**kwargs)\n",
+    "\n",
+    "markers = tuple()\n",
+    "\n",
+    "try:  # For Hyperspy versions >= 2.\n",
+    "    for pt in pts:\n",
+    "        kwargs = {\"color\": \"black\", \n",
+    "                  \"sizes\": 3, \n",
+    "                  \"offsets\": pt}\n",
+    "        marker = hs.plot.markers.Points(**kwargs)\n",
+    "        markers += (marker,)\n",
+    "        cropped_cbed_pattern_signal.add_marker(marker, permanent=False)\n",
+    "except:  # For Hyperspy versions < 2.\n",
+    "    for pt in pts:\n",
+    "        kwargs = {\"color\": \"black\", \n",
+    "                  \"size\": 3, \n",
+    "                  \"x\": pt[0], \n",
+    "                  \"y\": pt[1]}\n",
+    "        marker = hs.plot.markers.point(**kwargs)\n",
+    "        markers += (marker,)\n",
+    "        cropped_cbed_pattern_signal.add_marker(marker, permanent=False)"
+   ]
   }
  ],
  "metadata": {
@@ -1293,7 +1863,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.12.11"
   }
  },
  "nbformat": 4,