Update docs build

hyperspy · Aug 20, 2024 · da858aa · da858aa
1 parent b9d5de3
commit da858aa
Show file tree

Hide file tree

Showing 58 changed files with 2,351 additions and 499 deletions.
diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 552ab39ab1b009b10d510c93aff97786
+config: 0b78bfefdad59f2bbfa23ed76013d1d1
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip b/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip
diff --git a/_downloads/24831b32e81d1315cd64203e4e17d1bf/simple_arctan_fit.zip b/_downloads/24831b32e81d1315cd64203e4e17d1bf/simple_arctan_fit.zip
diff --git a/_downloads/3b9b969a6a4343ec82db54cb1db2df83/EELS_curve_fitting.zip b/_downloads/3b9b969a6a4343ec82db54cb1db2df83/EELS_curve_fitting.zip
diff --git a/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip b/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip
diff --git a/_downloads/90f956a0ec1a60c2f96c8c92607d6fea/plot_residual.zip b/_downloads/90f956a0ec1a60c2f96c8c92607d6fea/plot_residual.zip
diff --git a/_images/EDS_preferences_gui.png b/_images/EDS_preferences_gui.png
diff --git a/_images/sphx_glr_EELS_curve_fitting_001.png b/_images/sphx_glr_EELS_curve_fitting_001.png
diff --git a/_images/sphx_glr_plot_residual_001.png b/_images/sphx_glr_plot_residual_001.png
diff --git a/_images/sphx_glr_plot_residual_002.png b/_images/sphx_glr_plot_residual_002.png
diff --git a/_images/sphx_glr_simple_arctan_fit_001.png b/_images/sphx_glr_simple_arctan_fit_001.png
diff --git a/_images/sphx_glr_simple_arctan_fit_thumb.png b/_images/sphx_glr_simple_arctan_fit_thumb.png
diff --git a/_sources/auto_examples/model_fitting/EELS_curve_fitting.rst.txt b/_sources/auto_examples/model_fitting/EELS_curve_fitting.rst.txt
@@ -38,8 +38,8 @@ png file.
 
  .. code-block:: none
 
-      0%|                                              | 0.00/42.3M [00:00<?, ?B/s]      0%|                                     | 11.3k/42.3M [00:00<08:13, 85.6kB/s]      0%|                                      | 54.3k/42.3M [00:00<02:49, 249kB/s]      0%|▏                                      | 136k/42.3M [00:00<01:31, 460kB/s]      1%|▎                                      | 298k/42.3M [00:00<00:50, 838kB/s]      1%|▌                                     | 606k/42.3M [00:00<00:27, 1.52MB/s]      3%|█                                    | 1.24M/42.3M [00:00<00:14, 2.91MB/s]      6%|██▏                                  | 2.50M/42.3M [00:00<00:07, 5.61MB/s]     12%|████▍                                | 5.04M/42.3M [00:00<00:03, 11.0MB/s]     19%|███████▏                             | 8.18M/42.3M [00:01<00:02, 16.3MB/s]     25%|█████████▎                           | 10.6M/42.3M [00:01<00:01, 18.6MB/s]     30%|██████████▉                          | 12.5M/42.3M [00:01<00:01, 18.5MB/s]     36%|█████████████▍                       | 15.3M/42.3M [00:01<00:01, 20.5MB/s]     43%|███████████████▉                     | 18.2M/42.3M [00:01<00:01, 22.1MB/s]     50%|██████████████████▍                  | 21.0M/42.3M [00:01<00:00, 22.9MB/s]     56%|████████████████████▋                | 23.7M/42.3M [00:01<00:00, 23.2MB/s]     62%|███████████████████████              | 26.3M/42.3M [00:01<00:00, 23.3MB/s]     69%|█████████████████████████▍           | 29.0M/42.3M [00:01<00:00, 23.6MB/s]     75%|███████████████████████████▉         | 31.9M/42.3M [00:02<00:00, 24.0MB/s]     82%|██████████████████████████████▎      | 34.6M/42.3M [00:02<00:00, 24.2MB/s]     88%|████████████████████████████████▋    | 37.3M/42.3M [00:02<00:00, 24.2MB/s]     95%|███████████████████████████████████  | 40.1M/42.3M [00:02<00:00, 24.2MB/s]      0%|                                              | 0.00/42.3M [00:00<?, ?B/s]    100%|██████████████████████████████████████| 42.3M/42.3M [00:00<00:00, 274GB/s]
-      0%|                                              | 0.00/66.1M [00:00<?, ?B/s]      0%|                                      | 17.4k/66.1M [00:00<07:16, 151kB/s]      0%|                                      | 51.2k/66.1M [00:00<04:37, 238kB/s]      0%|                                       | 135k/66.1M [00:00<02:20, 468kB/s]      0%|▏                                      | 297k/66.1M [00:00<01:17, 849kB/s]      1%|▎                                     | 606k/66.1M [00:00<00:42, 1.53MB/s]      2%|▋                                    | 1.24M/66.1M [00:00<00:22, 2.93MB/s]      4%|█▍                                   | 2.50M/66.1M [00:00<00:11, 5.62MB/s]      8%|██▊                                  | 5.04M/66.1M [00:00<00:05, 11.0MB/s]     12%|████▌                                | 8.14M/66.1M [00:01<00:03, 16.2MB/s]     16%|█████▉                               | 10.7M/66.1M [00:01<00:03, 18.2MB/s]     20%|███████▍                             | 13.2M/66.1M [00:01<00:02, 19.5MB/s]     24%|████████▉                            | 15.9M/66.1M [00:01<00:02, 20.8MB/s]     28%|██████████▍                          | 18.7M/66.1M [00:01<00:02, 22.0MB/s]     33%|████████████                         | 21.5M/66.1M [00:01<00:01, 22.8MB/s]     37%|█████████████▌                       | 24.2M/66.1M [00:01<00:01, 23.2MB/s]     41%|███████████████                      | 26.9M/66.1M [00:01<00:01, 23.4MB/s]     45%|████████████████▌                    | 29.5M/66.1M [00:01<00:01, 23.4MB/s]     49%|██████████████████                   | 32.3M/66.1M [00:02<00:01, 23.7MB/s]     53%|███████████████████▋                 | 35.1M/66.1M [00:02<00:01, 24.1MB/s]     57%|█████████████████████▏               | 37.8M/66.1M [00:02<00:01, 23.9MB/s]     61%|██████████████████████▌              | 40.4M/66.1M [00:02<00:01, 23.8MB/s]     65%|████████████████████████             | 43.0M/66.1M [00:02<00:00, 23.7MB/s]     69%|█████████████████████████▌           | 45.8M/66.1M [00:02<00:00, 23.8MB/s]     73%|███████████████████████████          | 48.4M/66.1M [00:02<00:00, 23.8MB/s]     77%|████████████████████████████▌        | 51.1M/66.1M [00:02<00:00, 23.7MB/s]     81%|██████████████████████████████       | 53.8M/66.1M [00:02<00:00, 23.8MB/s]     86%|███████████████████████████████▋     | 56.5M/66.1M [00:03<00:00, 23.9MB/s]     90%|█████████████████████████████████▏   | 59.2M/66.1M [00:03<00:00, 23.8MB/s]     94%|██████████████████████████████████▋  | 62.0M/66.1M [00:03<00:00, 24.1MB/s]     98%|████████████████████████████████████▏| 64.6M/66.1M [00:03<00:00, 23.9MB/s]      0%|                                              | 0.00/66.1M [00:00<?, ?B/s]    100%|██████████████████████████████████████| 66.1M/66.1M [00:00<00:00, 399GB/s]
+      0%|                                              | 0.00/42.3M [00:00<?, ?B/s]      0%|                                      | 14.3k/42.3M [00:00<05:58, 118kB/s]      0%|                                      | 56.3k/42.3M [00:00<02:42, 259kB/s]      0%|                                       | 126k/42.3M [00:00<01:41, 414kB/s]      1%|▎                                      | 288k/42.3M [00:00<00:52, 800kB/s]      1%|▌                                     | 602k/42.3M [00:00<00:27, 1.49MB/s]      3%|█                                    | 1.24M/42.3M [00:00<00:14, 2.85MB/s]      6%|██▏                                  | 2.53M/42.3M [00:00<00:07, 5.57MB/s]     12%|████▍                                | 5.08M/42.3M [00:00<00:03, 10.8MB/s]     19%|███████▏                             | 8.19M/42.3M [00:01<00:02, 15.8MB/s]     25%|█████████▎                           | 10.6M/42.3M [00:01<00:01, 17.5MB/s]     31%|███████████▎                         | 13.0M/42.3M [00:01<00:01, 18.4MB/s]     37%|█████████████▊                       | 15.8M/42.3M [00:01<00:01, 20.1MB/s]     44%|████████████████                     | 18.4M/42.3M [00:01<00:01, 20.9MB/s]     49%|██████████████████▎                  | 20.9M/42.3M [00:01<00:01, 21.0MB/s]     56%|████████████████████▌                | 23.5M/42.3M [00:01<00:00, 21.5MB/s]     62%|██████████████████████▉              | 26.2M/42.3M [00:01<00:00, 22.1MB/s]     68%|█████████████████████████▏           | 28.8M/42.3M [00:01<00:00, 22.2MB/s]     74%|███████████████████████████▍         | 31.4M/42.3M [00:02<00:00, 22.3MB/s]     81%|█████████████████████████████▊       | 34.1M/42.3M [00:02<00:00, 22.7MB/s]     87%|████████████████████████████████▏    | 36.8M/42.3M [00:02<00:00, 22.8MB/s]     93%|██████████████████████████████████▌  | 39.4M/42.3M [00:02<00:00, 22.8MB/s]    100%|████████████████████████████████████▊| 42.1M/42.3M [00:02<00:00, 23.0MB/s]      0%|                                              | 0.00/42.3M [00:00<?, ?B/s]    100%|██████████████████████████████████████| 42.3M/42.3M [00:00<00:00, 266GB/s]
+      0%|                                              | 0.00/66.1M [00:00<?, ?B/s]      0%|                                      | 15.4k/66.1M [00:00<08:25, 131kB/s]      0%|                                      | 56.3k/66.1M [00:00<04:12, 262kB/s]      0%|                                       | 137k/66.1M [00:00<02:23, 461kB/s]      0%|▏                                      | 297k/66.1M [00:00<01:19, 824kB/s]      1%|▎                                     | 604k/66.1M [00:00<00:44, 1.49MB/s]      2%|▋                                    | 1.24M/66.1M [00:00<00:22, 2.86MB/s]      4%|█▍                                   | 2.53M/66.1M [00:00<00:11, 5.58MB/s]      8%|██▊                                  | 5.08M/66.1M [00:00<00:05, 10.8MB/s]     12%|████▍                                | 8.03M/66.1M [00:01<00:03, 15.3MB/s]     16%|██████                               | 10.8M/66.1M [00:01<00:03, 17.9MB/s]     20%|███████▍                             | 13.3M/66.1M [00:01<00:02, 19.2MB/s]     24%|████████▉                            | 16.0M/66.1M [00:01<00:02, 20.5MB/s]     28%|██████████▌                          | 18.8M/66.1M [00:01<00:02, 21.6MB/s]     33%|████████████                         | 21.5M/66.1M [00:01<00:02, 22.0MB/s]     37%|█████████████▌                       | 24.1M/66.1M [00:01<00:01, 22.3MB/s]     41%|███████████████                      | 26.8M/66.1M [00:01<00:01, 22.6MB/s]     45%|████████████████▊                    | 29.9M/66.1M [00:01<00:01, 23.9MB/s]     50%|██████████████████▎                  | 32.8M/66.1M [00:02<00:01, 24.2MB/s]     54%|███████████████████▉                 | 35.6M/66.1M [00:02<00:01, 24.1MB/s]     58%|█████████████████████▍               | 38.4M/66.1M [00:02<00:01, 24.0MB/s]     62%|███████████████████████              | 41.3M/66.1M [00:02<00:01, 24.5MB/s]     67%|████████████████████████▋            | 44.2M/66.1M [00:02<00:00, 24.6MB/s]     71%|██████████████████████████▍          | 47.1M/66.1M [00:02<00:00, 24.8MB/s]     75%|███████████████████████████▉         | 49.9M/66.1M [00:02<00:00, 24.5MB/s]     80%|█████████████████████████████▌       | 52.8M/66.1M [00:02<00:00, 24.5MB/s]     84%|███████████████████████████████▏     | 55.8M/66.1M [00:03<00:00, 25.0MB/s]     89%|████████████████████████████████▊    | 58.7M/66.1M [00:03<00:00, 25.0MB/s]     93%|██████████████████████████████████▎  | 61.3M/66.1M [00:03<00:00, 24.1MB/s]     97%|███████████████████████████████████▊ | 64.0M/66.1M [00:03<00:00, 23.7MB/s]      0%|                                              | 0.00/66.1M [00:00<?, ?B/s]    100%|██████████████████████████████████████| 66.1M/66.1M [00:00<00:00, 275GB/s]
 
 
 
@@ -76,7 +76,7 @@ png file.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 17.039 seconds)
+   **Total running time of the script:** (0 minutes 18.543 seconds)
 
 
 .. _sphx_glr_download_auto_examples_model_fitting_EELS_curve_fitting.py:

diff --git a/_sources/auto_examples/model_fitting/plot_residual.rst.txt b/_sources/auto_examples/model_fitting/plot_residual.rst.txt
@@ -110,15 +110,15 @@ Fit for all navigation positions:
 
  .. code-block:: none
 
-    Exception ignored in: <function tqdm.__del__ at 0x7f6d53f6d120>
+    Exception ignored in: <function tqdm.__del__ at 0x7f2ea7802020>
     Traceback (most recent call last):
       File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/tqdm/std.py", line 1148, in __del__
         self.close()
       File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/tqdm/notebook.py", line 279, in close
         self.disp(bar_style='danger', check_delay=False)
         ^^^^^^^^^
     AttributeError: 'tqdm_notebook' object has no attribute 'disp'
-      0%|          | 0/10 [00:00<?, ?it/s]    100%|██████████| 10/10 [00:00<00:00, 1495.56it/s]
+      0%|          | 0/10 [00:00<?, ?it/s]    100%|██████████| 10/10 [00:00<00:00, 1463.67it/s]
 
 
 
@@ -164,7 +164,7 @@ sphinx_gallery_thumbnail_number = 2
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.484 seconds)
+   **Total running time of the script:** (0 minutes 0.497 seconds)
 
 
 .. _sphx_glr_download_auto_examples_model_fitting_plot_residual.py:

diff --git a/_sources/auto_examples/model_fitting/sg_execution_times.rst.txt b/_sources/auto_examples/model_fitting/sg_execution_times.rst.txt
@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:17.851** total execution time for 3 files **from auto_examples/model_fitting**:
+**00:19.376** total execution time for 3 files **from auto_examples/model_fitting**:
 
 .. container::
 
@@ -33,11 +33,11 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_model_fitting_EELS_curve_fitting.py` (``EELS_curve_fitting.py``)
-     - 00:17.039
+     - 00:18.543
      - 0.0
    * - :ref:`sphx_glr_auto_examples_model_fitting_plot_residual.py` (``plot_residual.py``)
-     - 00:00.484
+     - 00:00.497
      - 0.0
    * - :ref:`sphx_glr_auto_examples_model_fitting_simple_arctan_fit.py` (``simple_arctan_fit.py``)
-     - 00:00.328
+     - 00:00.337
      - 0.0
diff --git a/_sources/auto_examples/model_fitting/simple_arctan_fit.rst.txt b/_sources/auto_examples/model_fitting/simple_arctan_fit.rst.txt
@@ -42,9 +42,9 @@ Fit an arctan function.
     Active: True
     Parameter Name |    Free |      Value |        Std |        Min |        Max | Linear
     ============== | ======= | ========== | ========== | ========== | ========== | ======
-                 A |    True | 1.00196314 | 0.00217464 |       None |       None |   True
-                 k |    True | 1.02437544 | 0.08926896 |       None |       None |  False
-                x0 |    True | -0.1288537 | 0.08006192 |       None |       None |  False
+                 A |    True | 1.00231136 | 0.00211621 |       None |       None |   True
+                 k |    True | 0.86050124 | 0.06651910 |       None |       None |  False
+                x0 |    True | 0.06398449 | 0.08489840 |       None |       None |  False
 
 
 
@@ -91,7 +91,7 @@ Fit an arctan function.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.328 seconds)
+   **Total running time of the script:** (0 minutes 0.337 seconds)
 
 
 .. _sphx_glr_download_auto_examples_model_fitting_simple_arctan_fit.py:

diff --git a/_sources/reference/index.rst.txt b/_sources/reference/index.rst.txt
@@ -13,3 +13,5 @@ Reference
    material
    models
    signals
+   utils.eds
+   utils.eels
diff --git a/_sources/reference/material.rst.txt b/_sources/reference/material.rst.txt
@@ -6,10 +6,58 @@
 .. autosummary::
 
     atomic_to_weight
-    weight_to_atomic
     density_of_mixture
+    elements
     mass_absorption_coefficient
     mass_absorption_mixture
+    weight_to_atomic
 
 .. automodule:: exspy.material
-   :members:
+   :members:
+
+.. autoattribute:: exspy.material.elements
+   :annotation:
+
+Database of element properties. The following properties are included:
+
+.. code::
+
+    ├── Atomic_properties
+    │   ├── Binding_energies
+    │   └── Xray_lines
+    ├── General_properties
+    │   ├── Z
+    │   ├── atomic_weight
+    │   └── name
+    └── Physical_properties
+        └── density_gcm3
+
+Examples:
+
+.. code::
+
+    >>> exspy.material.elements.Fe.General_properties
+    ├── Z = 26
+    ├── atomic_weight = 55.845
+    └── name = iron
+    >>> exspy.material.elements.Fe.Physical_properties
+    └── density (g/cm^3) = 7.874
+    >>> exspy.material.elements.Fe.Atomic_properties.Xray_lines
+    ├── Ka
+    │   ├── energy (keV) = 6.404
+    │   └── weight = 1.0
+    ├── Kb
+    │   ├── energy (keV) = 7.0568
+    │   └── weight = 0.1272
+    ├── La
+    │   ├── energy (keV) = 0.705
+    │   └── weight = 1.0
+    ├── Lb3
+    │   ├── energy (keV) = 0.792
+    │   └── weight = 0.02448
+    ├── Ll
+    │   ├── energy (keV) = 0.615
+    │   └── weight = 0.3086
+    └── Ln
+        ├── energy (keV) = 0.62799
+        └── weight = 0.12525
diff --git a/_sources/reference/utils.eds.rst.txt b/_sources/reference/utils.eds.rst.txt
@@ -0,0 +1,17 @@
+:mod:`exspy.utils.eds`
+----------------------
+
+.. currentmodule:: exspy.utils.eds
+
+
+.. autosummary::
+   cross_section_to_zeta
+   electron_range
+   get_xray_lines_near_energy
+   take_off_angle
+   xray_range
+   zeta_to_cross_section
+
+
+.. automodule:: exspy.utils.eds
+   :members:
diff --git a/_sources/reference/utils.eels.rst.txt b/_sources/reference/utils.eels.rst.txt
@@ -0,0 +1,17 @@
+:mod:`exspy.utils.eels`
+-----------------------
+
+.. currentmodule:: exspy.utils.eels
+
+
+.. autosummary::
+   effective_angle
+   get_edges_near_energy
+   get_info_from_edges
+   iMFP_angular_correction
+   iMFP_Iakoubovskii
+   iMFP_TPP2M
+
+
+.. automodule:: exspy.utils.eels
+   :members:
diff --git a/_sources/sg_execution_times.rst.txt b/_sources/sg_execution_times.rst.txt
@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:17.851** total execution time for 3 files **from all galleries**:
+**00:19.376** total execution time for 3 files **from all galleries**:
 
 .. container::
 
@@ -33,11 +33,11 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_model_fitting_EELS_curve_fitting.py` (``../examples/model_fitting/EELS_curve_fitting.py``)
-     - 00:17.039
+     - 00:18.543
      - 0.0
    * - :ref:`sphx_glr_auto_examples_model_fitting_plot_residual.py` (``../examples/model_fitting/plot_residual.py``)
-     - 00:00.484
+     - 00:00.497
      - 0.0
    * - :ref:`sphx_glr_auto_examples_model_fitting_simple_arctan_fit.py` (``../examples/model_fitting/simple_arctan_fit.py``)
-     - 00:00.328
+     - 00:00.337
      - 0.0