empix 0.0.7__tar.gz → 0.0.8__tar.gz

{empix-0.0.7 → empix-0.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: empix
-Version: 0.0.7
+Version: 0.0.8
 Summary: Contains tools for analyzing electron microscopy data that are not available in ``hyperspy``.
 Author-email: Matthew Fitzpatrick <matthew.rc.fitzpatrick@gmail.com>
 Project-URL: Homepage, https://mrfitzpa.github.io/empix

{empix-0.0.7 → empix-0.0.8}/empix/version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.0.7'
-__version_tuple__ = version_tuple = (0, 0, 7)
+__version__ = version = '0.0.8'
+__version_tuple__ = version_tuple = (0, 0, 8)
 
-__commit_id__ = commit_id = 'ge59d9f196'
+__commit_id__ = commit_id = 'ga30344106'

{empix-0.0.7 → empix-0.0.8}/empix.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: empix
-Version: 0.0.7
+Version: 0.0.8
 Summary: Contains tools for analyzing electron microscopy data that are not available in ``hyperspy``.
 Author-email: Matthew Fitzpatrick <matthew.rc.fitzpatrick@gmail.com>
 Project-URL: Homepage, https://mrfitzpa.github.io/empix

{empix-0.0.7 → empix-0.0.8}/examples/basic_usage.ipynb

@@ -83,21 +83,13 @@
     "# be safely ignored.\n",
     "import empix\n",
     "\n",
-    "# For generating data to be used in this demonstration.\n",
+    "# For generating data to be used in this demonstration. Users need not focus on\n",
+    "# the implementation details of this module in order to follow the logic of each\n",
+    "# cell in the remainder of this notebook. Morevoer, users need not import this\n",
+    "# module for their own applications of ``empix``.\n",
     "import helpers_for_basic_usage as helpers"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "c97d0485-cf65-478b-80c4-d5d294879c26",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%matplotlib ipympl\n",
-    "%matplotlib ipympl"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "e667d633",
@@ -114,20 +106,40 @@
     "In this notebook, we demonstrate how one can use each function and class in the\n",
     "``empix`` library.\n",
     "\n",
-    "You can find the documentation for the ``empix`` library\n",
-    "[here](https://mrfitzpa.github.io/empix/_autosummary/empix.html).  It is\n",
+    "In order to execute the cells in this notebook as intended, a set of Python\n",
+    "libraries need to be installed in the Python environment within which the cells\n",
+    "of the notebook are to be executed. For this particular notebook, users need to\n",
+    "install:\n",
+    "\n",
+    "    empix\n",
+    "    jupyter\n",
+    "    ipympl\n",
+    "\n",
+    "Users can install these libraries either via `pip`:\n",
+    "\n",
+    "    pip install empix[examples]\n",
+    "\n",
+    "or `conda`:\n",
+    "\n",
+    "    conda install -y empix jupyter ipympl -c conda-forge\n",
+    "\n",
+    "You can find the documentation for the emicroml library\n",
+    "[here](https://mrfitzpa.github.io/empix/_autosummary/empix.html). It is\n",
     "recommended that you consult the documentation of this library as you explore\n",
     "the notebook. Moreover, users should execute the cells in the order that they\n",
     "appear, i.e. from top to bottom, as some cells reference variables that are set\n",
-    "in other cells above them.\n",
+    "in other cells above them. **Users should make sure to navigate the documentation\n",
+    "for the version of emicroml that they are currently using.**\n",
     "\n",
-    "The last module that we imported above contains helper functions that are used\n",
-    "throughout the remainder of the notebook, specifically to generate data to be\n",
-    "used in this demonstration. It is not essential that users know the\n",
-    "implementation details of these helper functions in order to follow the logic of\n",
-    "each cell in the remainder of this notebook. That being said, if any users are\n",
-    "interested in the implementation details, they can find them in file\n",
-    "``<root>/examples/helpers_for_basic_usage.py``."
+    "The last module that we imported above (i.e. the module with the alias helpers)\n",
+    "contains helper functions that are used throughout the remainder of the\n",
+    "notebook, specifically to generate data to be used in this demonstration. It is\n",
+    "not essential that users know the implementation details of these helper\n",
+    "functions in order to follow the logic of each cell in the remainder of this\n",
+    "notebook. Moreover, users need not import this module for their own applications\n",
+    "of emicroml. That being said, if any users are interested in the implementation\n",
+    "details, they can find them in the file\n",
+    "`<root>/examples/helpers_for_basic_usage.py`."
    ]
   },
   {
@@ -182,6 +194,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%matplotlib ipympl\n",
+    "\n",
     "kwargs = {\"axes_off\": False, \n",
     "          \"scalebar\": False, \n",
     "          \"colorbar\": False, \n",
@@ -675,6 +689,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%matplotlib inline\n",
+    "\n",
     "plt.close(\"all\")  # Close all previous figures to release memory.\n",
     "\n",
     "kwargs = {\"axes_off\": False, \n",
@@ -836,6 +852,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "%matplotlib ipympl\n",
+    "\n",
     "plt.close(\"all\")  # Close all previous figures to release memory.\n",
     "\n",
     "kwargs = {\"axes_off\": False, \n",
@@ -1115,7 +1133,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.13.9"
+   "version": "3.12.12"
   }
  },
  "nbformat": 4,

{empix-0.0.7 → empix-0.0.8}/examples/helpers_for_basic_usage.py

@@ -1,3 +1,16 @@
+# -*- coding: utf-8 -*-
+# Copyright 2024 Matthew Fitzpatrick.
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, version 3.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <https://www.gnu.org/licenses/gpl-3.0.html>.
 """This module contains helper functions for the Jupyter notebook located at
 ``<root>/examples/basic_usage.ipynb``, where ``<root>`` is the root of the
 ``empix`` repository.
@@ -26,18 +39,8 @@ import hyperspy.axes
 # List of public objects in module.
 __all__ = ["generate_real_2d_input_signal",
            "generate_complex_2d_input_signal",
-           "generate_complex_2d_input_signal_data",
-           "generate_complex_2d_input_signal_data_shape",
-           "generate_complex_2d_input_signal_metadata",
-           "generate_ring_centers_in_pixel_coords",
-           "generate_complex_2d_input_signal_axes",
            "generate_real_1d_input_signal",
-           "generate_complex_1d_input_signal",
-           "generate_complex_1d_input_signal_data",
-           "generate_complex_1d_input_signal_data_shape",
-           "generate_complex_1d_input_signal_metadata",
-           "generate_slopes",
-           "generate_complex_1d_input_signal_axes"]
+           "generate_complex_1d_input_signal"]
 
 
 
@@ -60,11 +63,11 @@ def generate_real_2d_input_signal():
 
 
 def generate_complex_2d_input_signal():
-    kwargs = {"data": generate_complex_2d_input_signal_data(), 
-              "metadata": generate_complex_2d_input_signal_metadata()}
+    kwargs = {"data": _generate_complex_2d_input_signal_data(), 
+              "metadata": _generate_complex_2d_input_signal_metadata()}
     complex_2d_input_signal = hyperspy.signals.ComplexSignal2D(**kwargs)
 
-    axes = generate_complex_2d_input_signal_axes()
+    axes = _generate_complex_2d_input_signal_axes()
 
     for axis_idx, axis in enumerate(axes):
         complex_2d_input_signal.axes_manager[axis_idx].update_from(axis)
@@ -75,11 +78,11 @@ def generate_complex_2d_input_signal():
 
 
 
-def generate_complex_2d_input_signal_data():
-    signal_data_shape = generate_complex_2d_input_signal_data_shape()
+def _generate_complex_2d_input_signal_data():
+    signal_data_shape = _generate_complex_2d_input_signal_data_shape()
     Y_dim, X_dim, v_dim, h_dim = signal_data_shape
 
-    metadata = generate_complex_2d_input_signal_metadata()
+    metadata = _generate_complex_2d_input_signal_metadata()
     ring_centers_in_pixel_coords = metadata["ring_centers_in_pixel_coords"]
     inner_ring_radius_in_pixels = metadata["inner_ring_radius_in_pixels"]
     outer_ring_radius_in_pixels = metadata["outer_ring_radius_in_pixels"]
@@ -123,21 +126,21 @@ def generate_complex_2d_input_signal_data():
 
 
 
-def generate_complex_2d_input_signal_data_shape():
+def _generate_complex_2d_input_signal_data_shape():
     complex_2d_input_signal_data_shape = (3, 2, 181, 200)
     
     return complex_2d_input_signal_data_shape
 
 
 
-def generate_complex_2d_input_signal_metadata():
-    axes = generate_complex_2d_input_signal_axes()
+def _generate_complex_2d_input_signal_metadata():
+    axes = _generate_complex_2d_input_signal_axes()
     h_offset = axes[-2].offset
     h_scale = axes[-2].scale
     v_offset = axes[-1].offset
     v_scale = axes[-1].scale
 
-    ring_centers_in_pixel_coords = generate_ring_centers_in_pixel_coords()
+    ring_centers_in_pixel_coords = _generate_ring_centers_in_pixel_coords()
     
     ring_centers = np.array(ring_centers_in_pixel_coords, dtype="float")
     ring_centers[:, :, 0] = h_offset + ring_centers[:, :, 0]*h_scale
@@ -174,8 +177,8 @@ def generate_complex_2d_input_signal_metadata():
 
 
 
-def generate_ring_centers_in_pixel_coords():
-    signal_data_shape = generate_complex_2d_input_signal_data_shape()
+def _generate_ring_centers_in_pixel_coords():
+    signal_data_shape = _generate_complex_2d_input_signal_data_shape()
     Y_dim, X_dim, v_dim, h_dim = signal_data_shape
     
     ring_centers_in_pixel_coords = np.zeros((Y_dim, X_dim, 2), dtype="int")
@@ -194,8 +197,8 @@ def generate_ring_centers_in_pixel_coords():
 
 
 
-def generate_complex_2d_input_signal_axes():
-    signal_data_shape = generate_complex_2d_input_signal_data_shape()
+def _generate_complex_2d_input_signal_axes():
+    signal_data_shape = _generate_complex_2d_input_signal_data_shape()
     Y_dim, X_dim, v_dim, h_dim = signal_data_shape
 
     d_h = 0.1
@@ -238,11 +241,11 @@ def generate_real_1d_input_signal():
 
 
 def generate_complex_1d_input_signal():
-    kwargs = {"data": generate_complex_1d_input_signal_data(), 
-              "metadata": generate_complex_1d_input_signal_metadata()}
+    kwargs = {"data": _generate_complex_1d_input_signal_data(), 
+              "metadata": _generate_complex_1d_input_signal_metadata()}
     complex_1d_input_signal = hyperspy.signals.ComplexSignal1D(**kwargs)
 
-    axes = generate_complex_1d_input_signal_axes()
+    axes = _generate_complex_1d_input_signal_axes()
 
     for axis_idx, axis in enumerate(axes):
         complex_1d_input_signal.axes_manager[axis_idx].update_from(axis)
@@ -253,11 +256,11 @@ def generate_complex_1d_input_signal():
 
 
 
-def generate_complex_1d_input_signal_data():
-    signal_data_shape = generate_complex_1d_input_signal_data_shape()
+def _generate_complex_1d_input_signal_data():
+    signal_data_shape = _generate_complex_1d_input_signal_data_shape()
     Y_dim, X_dim, u_dim = signal_data_shape
 
-    metadata = generate_complex_1d_input_signal_metadata()
+    metadata = _generate_complex_1d_input_signal_metadata()
     slopes = metadata["slopes"]
     y_intercept_of_real_part = metadata["y_intercept_of_real_part"]
     y_intercept_of_imag_part = metadata["y_intercept_of_imag_part"]
@@ -268,7 +271,7 @@ def generate_complex_1d_input_signal_data():
     navigation_dims = (Y_dim, X_dim)
     num_patterns = Y_dim*X_dim
 
-    axes = generate_complex_1d_input_signal_axes()
+    axes = _generate_complex_1d_input_signal_axes()
     d_u = axes[-1].scale
 
     n_u = np.arange(u_dim)
@@ -292,17 +295,17 @@ def generate_complex_1d_input_signal_data():
 
 
 
-def generate_complex_1d_input_signal_data_shape():
+def _generate_complex_1d_input_signal_data_shape():
     complex_1d_input_signal_data_shape = (3, 2, 200)
     
     return complex_1d_input_signal_data_shape
 
 
 
-def generate_complex_1d_input_signal_metadata():
+def _generate_complex_1d_input_signal_metadata():
     metadata = {"General": {"title": "First Complex 1D Input"}, 
                 "Signal": dict(), 
-                "slopes": generate_slopes(), 
+                "slopes": _generate_slopes(), 
                 "y_intercept_of_real_part": 0,
                 "y_intercept_of_imag_part": 10}
 
@@ -312,8 +315,8 @@ def generate_complex_1d_input_signal_metadata():
 
 
 
-def generate_slopes():
-    signal_data_shape = generate_complex_1d_input_signal_data_shape()
+def _generate_slopes():
+    signal_data_shape = _generate_complex_1d_input_signal_data_shape()
     Y_dim, X_dim, r_dim = signal_data_shape
     
     slopes = np.zeros((Y_dim, X_dim))
@@ -328,8 +331,8 @@ def generate_slopes():
 
 
 
-def generate_complex_1d_input_signal_axes():
-    signal_data_shape = generate_complex_1d_input_signal_data_shape()
+def _generate_complex_1d_input_signal_axes():
+    signal_data_shape = _generate_complex_1d_input_signal_data_shape()
     Y_dim, X_dim, u_dim = signal_data_shape
 
     axes_sizes = (X_dim, Y_dim, u_dim)