### Example output of pyTEMlib version check

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/introduction/installation

Example output from the version check command, showing the installed pyTEMlib version.

```text
pyTEMlib version 0.2025.12.0

```

--------------------------------

### Metadata output example

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i1-adaptive-fourier-filter

Example metadata output showing filename and experiment details.

```text
{'filename': 'C:\\Users\\gduscher\\Documents\\Github\\pyTEMlib\\example_data\\p1-3-hr3.dm3',  'experiment': {'acceleration_voltage': 199990.28125,   'exposure_time': 1.0,   'microscope': 'Libra 200 MC'}}
```

--------------------------------

### Initialize pyTEMlib environment

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/introduction/usefull-equations

Imports necessary libraries and checks the installed version of pyTEMlib.

```python
%matplotlib widget
import matplotlib.pylab as plt
import numpy  as np
import scipy 

import pyTEMlib
pyTEMlib.__version__
```

--------------------------------

### Import libraries and setup

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i2-image-registration

Imports necessary libraries, enables widget manager for Google Colab, mounts drive if in Colab, and prints pyTEMlib version.

```python
%matplotlib widget
import numpy as np
import matplotlib.pylab as plt 
import sys

if 'google.colab' in sys.modules:
    from google.colab import output
    output.enable_custom_widget_manager()
    from google.colab import drive

import sys
sys.path.insert(0, '../../')
import sidpy

%load_ext autoreload
%autoreload 2
if 'google.colab' in sys.modules:
    drive.mount("/content/drive")

import pyTEMlib
    
# For archiving reasons it is a good idea to print the version numbers out at this point
print('pyTEM version: ', pyTEMlib.__version__)

## Do all of registration

notebook_tags= {'notebook': 'Image_Registration',
                'notebook_version': '2025_03_13',
                'pyTEM version': pyTEMlib.__version__}
```

--------------------------------

### Import pyTEMlib and print version

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/introduction/installation

Import pyTEMlib and print its version to verify the installation. Use this minimal command in every notebook or Python instance after installation.

```python
import pyTEMlib
print('pyTEMlib version', pyTEMlib.__version__)
```

--------------------------------

### Install or upgrade pyTEMlib

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i4-structure-analysis

Checks the installed pyTEMlib version and upgrades it if below 0.2026.1.0. The output 'done' confirms the installation step completed.

```python
import sys
import importlib.metadata
def test_package(package_name):
    """Test if package exists and returns version or -1"""
    try:
        version = importlib.metadata.version(package_name)
    except importlib.metadata.PackageNotFoundError:
        version = '-1'
    return version

if test_package('pyTEMlib') < '0.2026.1.0':
    print('installing pyTEMlib')
    !{sys.executable} -m pip install  --upgrade pyTEMlib -q
print('done')

```

```text
done

```

--------------------------------

### Complete registration start output

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i2-image-registration

Output message from the complete registration indicating the start of rigid registration and the stack dimensions.

```text
Rigid_Registration
Stack contains  10  images, each with 1024  pixels in x-direction and  1024  pixels in y-direction
```

--------------------------------

### Load Example Data and Plot Diffraction Pattern

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/diffraction/d1-diffraction-rings

Loads the example dataset GOLD-NP-DIFF.dm3 if load_your_own_data is False, otherwise uses the selected dataset from the file widget. Plots the main dataset with vmax=20000.

```python
if load_your_own_data:
    datasets = fileWidget.datasets
    main_dataset = fileWidget.selected_dataset
else:  # load example
    datasets = pyTEMlib.file_tools.open_file(os.path.join("../../example_data", "GOLD-NP-DIFF.dm3"))
    main_dataset =  datasets['Channel_000']

view = main_dataset.plot(vmax=20000)
```

--------------------------------

### Check and Install pyTEMlib Package

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/diffraction/d1-diffraction-rings

Tests whether pyTEMlib is installed and meets the minimum version requirement. If not, it installs the latest version from the GitHub repository. The version check uses importlib.metadata and the installation uses pip with the --upgrade flag.

```python
import sys
import importlib.metadata
def test_package(package_name):
    """Test whether package exists and returns version or -1"""
    try:
        version = importlib.metadata.version(package_name)
    except importlib.metadata.PackageNotFoundError:
        version = '-1'
    return version

if test_package('pyTEMlib') < '0.2026.06.0':
    print('installing pyTEMlib')
    !{sys.executable} -m pip install git+https://github.com/pycroscopy/pyTEMlib.git@main -q --upgrade

print('done')
```

--------------------------------

### Install pyTEMlib

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i2-image-registration

Checks if pyTEMlib is installed and upgrades it if the version is below 0.2025.2.0.

```python
import sys
import importlib.metadata
def test_package(package_name):
    """Test if package exists and returns version or -1"""
    try:
        version = importlib.metadata.version(package_name)
    except importlib.metadata.PackageNotFoundError:
        version = '-1'
    return version

if test_package('pyTEMlib') < '0.2025.2.0':
    print('installing pyTEMlib')
    !{sys.executable} -m pip install  --upgrade pyTEMlib -q
print('done')
```

--------------------------------

### Load Diffraction Pattern with Optional Google Drive Mount

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/diffraction/d1-diffraction-rings

Sets up data loading: if load_your_own_data is True, mounts Google Drive and opens a file widget; otherwise, loads the example file GOLD-NP-DIFF.dm3. Requires sys and pyTEMlib imports.

```python
# ------Input -------------
load_your_own_data = False
# -------------------------
if 'google.colab' in sys.modules:
        drive.mount("/content/drive")

if load_your_own_data:
    fileWidget = pyTEMlib.file_tools.FileWidget()
```

--------------------------------

### Load necessary packages and show pyTEMlib version

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/introduction/open-files

Sets up the notebook environment: enables interactive matplotlib widgets, imports numpy and matplotlib, and prints the installed pyTEMlib version.

```python
%matplotlib widget
import matplotlib.pyplot as plt
import numpy as np

import pyTEMlib
print('pyTEMlib version', pyTEMlib.__version__)
```

--------------------------------

### Install and upgrade pyTEMlib with version check

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/introduction/installation

Install or upgrade pyTEMlib if the installed version is older than 0.2026.06.0. Run this cell in every notebook, especially in Google Colab where the environment resets each session. The cell uses the current Python executable to run pip and prints 'done' after installation.

```python
import sys
import importlib.metadata
def test_package(package_name):
    """Test if package exists and returns version or -1"""
    try:
        version = importlib.metadata.version(package_name)
    except importlib.metadata.PackageNotFoundError:
        version = '-1'
    return version

if test_package('pyTEMlib') < '0.2026.06.0':
    print('installing pyTEMlib')
    !{sys.executable} -m pip install  --upgrade pyTEMlib -q

print('done')
```

--------------------------------

### Install and verify pyTEMlib

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i1-adaptive-fourier-filter

Checks for the existence of the pyTEMlib package and upgrades it if the version is older than 0.2025.3.0.

```python
import sys
import importlib.metadata
def test_package(package_name):
    """Test if package exists and returns version or -1"""
    try:
        version = importlib.metadata.version(package_name)
    except importlib.metadata.PackageNotFoundError:
        version = '-1'
    return version

if test_package('pyTEMlib') < '0.2025.3.0':
    print('installing pyTEMlib')
    !{sys.executable} -m pip install  --upgrade pyTEMlib -q
print('done')
```

```text
installing pyTEMlib
done
```

--------------------------------

### Check and install pyTEMlib package

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/diffraction/d2-diffraction-spots

This snippet checks if pyTEMlib is installed and has a version at least 0.2024.1.0. If not, it installs the latest version from GitHub. It also installs numpy 1.24.4 if running in Google Colab.

```python
import sys
import importlib.metadata
def test_package(package_name):
    """Test if package exists and returns version or -1"""
    try:
        version = importlib.metadata.version(package_name)
    except importlib.metadata.PackageNotFoundError:
        version = '-1'
    return version

if test_package('pyTEMlib') < '0.2024.1.0':
    print('installing pyTEMlib')
    !{sys.executable} -m pip install git+https://github.com/pycroscopy/pyTEMlib.git@main -q --upgrade

if 'google.colab' in sys.modules:
    !{sys.executable} -m pip install numpy==1.24.4
print('done')
```

```text
done

```

--------------------------------

### Output of Center Extraction

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/diffraction/d1-diffraction-rings

Example output showing the radius and center coordinates in pixels after selection.

```text
radius = 559 pixels
center = 1059.5, 1099.4 [pixels]
```

--------------------------------

### Joblib parallel execution output

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i2-image-registration

Output from the joblib context manager example: shows backend selection and completion message.

```output
[Parallel(n_jobs=2)]: Using backend LokyBackend with 2 concurrent workers.
[Parallel(n_jobs=2)]: Done 20 out of 20 | elapsed:    0.3s finished
```

--------------------------------

### Output of pyTEMlib version check

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/introduction/open-files

Example output of the pyTEMlib version print statement from the previous cell.

```text
pyTEMlib version 0.2025.12.0
```

--------------------------------

### Output of np.nditer iteration

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i2-image-registration

Output of the np.nditer example: shows the iterated element, the array slice at the multi_index, and the multi_index tuple.

```output
0 [0 1 2] (0, 0)
3 [3 4 5] (0, 1)
6 [6 7 8] (1, 0)
9 [ 9 10 11] (1, 1)
```

--------------------------------

### Get all reflections and g-vectors with pyTEMlib.diffraction_tools

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i4-structure-analysis

Calls pyTEMlib.diffraction_tools.get_all_reflections and get_all_g_vectors to compute reciprocal lattice vectors and Miller indices for a given atom structure. The displayed output shows the first five entries of each result.

```python
hkl2, g2=  pyTEMlib.diffraction_tools.get_all_reflections(atoms, 1)
g, hkl = pyTEMlib.diffraction_tools.get_all_g_vectors(1, atoms)

g[:5], g2[:5], hkl2[:5], hkl[:5]
```

```output
(array([[-0.24520622, -0.24520622, -0.24520622],         [-0.24520622, -0.24520622,  0.        ],         [-0.24520622, -0.24520622,  0.24520622],         [-0.24520622,  0.        , -0.24520622],         [-0.24520622,  0.        ,  0.        ]]),  array([[ 0.        ,  0.        , -0.24520622],         [ 0.        ,  0.24520622,  0.        ],         [-0.24520622,  0.        ,  0.        ],         [ 0.        ,  0.        ,  0.24520622],         [ 0.24520622,  0.        ,  0.        ]]),  array([[ 0.,  0., -1.],         [ 0.,  1.,  0.],         [-1.,  0.,  0.],         [ 0.,  0.,  1.],         [ 1.,  0.,  0.]]),  array([[-1., -1., -1.],         [-1., -1.,  0.],         [-1., -1.,  1.],         [-1.,  0., -1.],         [-1.,  0.,  0.]]))
```

--------------------------------

### Progress Bar Output

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i4-structure-analysis

Progress bar output from the refinement process, showing 0% completion at the start. A Jupyter kernel connection is required to fully display this output.

```text
  0%|          | 0/1183 [00:00
```

--------------------------------

### Get structure factors with pyTEMlib

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i4-structure-analysis

Calls pyTEMlib.diffraction_tools.get_structure_factors with atoms and g_non_rot, then prints the shape, atomic positions, and a list of rounded structure factors with corresponding hkl indices. The output shows the shape (1330,), the atomic positions array, and a list of tuples.

```python
s = pyTEMlib.diffraction_tools.get_structure_factors(atoms, g_non_rot)
s.shape, atoms.positions, list(zip(np.round(s[200:210],3), hkl_all[200:210]))
```

```text
((1330,),  array([[0.     , 0.     , 0.     ],         [1.35772, 1.35772, 1.35772],         [2.71544, 2.71544, 0.     ],         [4.07316, 4.07316, 1.35772],         [2.71544, 0.     , 2.71544],         [4.07316, 1.35772, 4.07316],         [0.     , 2.71544, 2.71544],         [1.35772, 4.07316, 4.07316]]),  [(np.float64(0.0), array([-4.,  2., -3.])),   (np.float64(6.863), array([-4.,  2., -2.])),   (np.float64(0.0), array([-4.,  2., -1.])),   (np.float64(0.0), array([-4.,  2.,  0.])),   (np.float64(0.0), array([-4.,  2.,  1.])),   (np.float64(6.863), array([-4.,  2.,  2.])),   (np.float64(0.0), array([-4.,  2.,  3.])),   (np.float64(0.0), array([-4.,  2.,  4.])),   (np.float64(0.0), array([-4.,  2.,  5.])),   (np.float64(0.0), array([-4.,  3., -5.]))])`
```

--------------------------------

### Rigid registration progress bar output

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i4-structure-analysis

Progress bar output from the rigid registration process, showing the start of the 25-image processing. Requires a Jupyter kernel connection to display fully.

```text
  0%|          | 0/25 [00:00
```

--------------------------------

### Import libraries and set up notebook

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i4-structure-analysis

Sets up the notebook environment: enables interactive matplotlib, imports libraries, mounts Google Drive in Colab, and loads pyTEMlib. The output shows the autoreload extension status and the pyTEMlib version.

```python
# import matplotlib and numpy
#                       use "inline" instead of "notebook" for non-interactive
#                       use widget for jupyterlab needs ipympl to be installed
# import matplotlib and numpy
%matplotlib widget  
import matplotlib.pylab as plt
import numpy as np

import sys
if 'google.colab' in sys.modules:
    from google.colab import output
    output.enable_custom_widget_manager()
    from google.colab import drive


%load_ext autoreload
%autoreload 2    

sys.path.insert(0, '../../')
import pyTEMlib

# For archiving reasons it is a good idea to print the version numbers out at this point
print('pyTEM version: ', pyTEMlib.__version__)
if 'google.colab' in sys.modules:
    drive.mount("/content/drive")
## Do all of registration

notebook_tags= {'notebook': 'Structure Analysis',
                'notebook_version': '2025_03_16',
                'pyTEM version': pyTEMlib.__version__}

```

```text
The autoreload extension is already loaded. To reload it, use:
  %reload_ext autoreload
pyTEM version:  0.2026.1.2

```

--------------------------------

### Load libraries and configure environment

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i1-adaptive-fourier-filter

Imports necessary scientific libraries, configures matplotlib for interactive widgets, and initializes the pyTEMlib environment.

```python
%matplotlib widget
import numpy as np
import matplotlib.pylab as plt 
import sys
import scipy

if 'google.colab' in sys.modules:
    from google.colab import output
    output.enable_custom_widget_manager()
    from google.colab import drive

import sys
sys.path.insert(0, '../../')

%load_ext autoreload
%autoreload 2
import pyTEMlib


if 'google.colab' in sys.modules:
    drive.mount("/content/drive")
    
print('pyTEMlib version: ', pyTEMlib.__version__)
note_book_version = '2025.05.19'
note_book_name='pyTEMib/notebooks/Imaging/Adaptive_Fourier_Filter'
```

```text
pyTEMlib version:  0.2026.5.0
```

--------------------------------

### Check for Newest Versions of pyTEMlib

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i3-probe

Tests if pyTEMlib is installed and upgrades it if the version is older than 0.2024.2.3. Uses importlib.metadata to check the version and pip to install the upgrade.

```python
import sys
import importlib.metadata
def test_package(package_name):
    """Test if package exists and returns version or -1"""
    try:
        version = importlib.metadata.version(package_name)
    except importlib.metadata.PackageNotFoundError:
        version = '-1'
    return version

if test_package('pyTEMlib') < '0.2024.2.3':
    print('installing pyTEMlib')
    !{sys.executable} -m pip install  --upgrade pyTEMlib -q

print('done')
```

--------------------------------

### Simulate new notebook and open file

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i1-adaptive-fourier-filter

Reopens the file using the saved filename and creates a ChooseDataset widget to select a dataset.

```python
new_dataset= pyTEMlib.file_tools.open_file(filename)
choose_image = pyTEMlib.file_tools.ChooseDataset(new_dataset)
```

--------------------------------

### Output of Package Loading

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/diffraction/d1-diffraction-rings

Shows the expected output after loading the packages, displaying the pyTEMlib version and notebook version.

```text
pyTEM version:  0.2026.3.0
notebook version:  2025.12.06
```

--------------------------------

### Open File with FileWidget

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i1-adaptive-fourier-filter

Creates a FileWidget instance to select a file and dataset. Requires a Jupyter kernel connection for full display.

```python
fileWidget = pyTEMlib.file_tools.FileWidget()
```

--------------------------------

### Initialize Crystal Structure

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/diffraction/d2-diffraction-spots

Initializes an aluminum crystal structure using pyTEMlib's crystal_tools and visualizes it with ASE.

```python
#Initialize the dictionary with all the input
atoms = pyTEMlib.crystal_tools.structure_by_name('aluminum')
print(atoms)
import ase.visualize
ase.visualize.view(atoms*[4,4,1], viewer='x3d')
```

--------------------------------

### Calculate and plot diffraction pattern with pyTEMlib

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/diffraction/d2-diffraction-spots

Sets up input parameters for a diffraction simulation (zone axis, hkl_max, Sg_max, mistilt angles, acceleration voltage), builds a tags dictionary, calls pyTEMlib.diffraction_tools.get_bragg_reflections to compute reflections, and plots the pattern with plot_diffraction_pattern. The output includes warnings about division by zero and missing legend labels, and a summary of allowed reflections.

```python
# --------------- INPUT ------------------------
zone_hkl = np.array([1, 0, 0])
hkl_max = 25  #  maximum allowed Miller index
sg_max = 0.01   # 1/Ang  maximum allowed excitation error
mistilt_alpha = 1.5   # degrees
mistilt_beta = 1 # degrees
acceleration_voltage = 200.0 * 1000.0 #V

rotation = np.radians(0)  # rotation of diffraction pattern
# -------------------------------------------

tags = {'zone_hkl': zone_hkl,
        'hkl_max': hkl_max,
        'Sg_max': sg_max,
        'mistilt_alpha': np.radians(mistilt_alpha),
        'mistilt_beta': np.radians(mistilt_beta),
        'acceleration_voltage':  acceleration_voltage}

diff_dict ={}
diff_dict = pyTEMlib.diffraction_tools.get_bragg_reflections(atoms, tags, verbose=True) 
diff_dict.setdefault('output',{})['plot_forbidden']=False
diff_dict['output']['plot_dynamically_allowed']=True

v = pyTEMlib.diffraction_tools.plot_diffraction_pattern(diff_dict, unit='1/nm')

```

```text
C:\Users\gduscher\OneDrive - University of Tennessee\GitHub\pyTEMlib\notebooks\Diffraction\../..\pyTEMlib\diffraction_tools\basic.py:375: RuntimeWarning: divide by zero encountered in scalar divide
  alpha = np.arctan(zone[0] / r)
C:\Users\gduscher\OneDrive - University of Tennessee\GitHub\pyTEMlib\notebooks\Diffraction\../..\pyTEMlib\diffraction_tools\diffraction_plot.py:810: UserWarning: No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
  plt.legend() n
```

```text
mistilt
Of the 334 possible reflection 56 are allowed.
Of those, there are 17 in ZOLZ  and 39 in HOLZ
Of the 130 forbidden reflection in ZOLZ  0 can be dynamically activated.

```

--------------------------------

### Load Necessary Packages for Probe Calculation

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i3-probe

Sets up the environment for probe calculation, including matplotlib widget mode, numpy, and pyTEMlib. Also enables autoreload and handles Google Colab specifics.

```python
%matplotlib widget
import matplotlib.pyplot as plt
import numpy as np
import sys
import os
%load_ext autoreload
%autoreload 2
    
sys.path.insert(0,'..//..//pyTEMlib//')

if 'google.colab' in sys.modules:
    from google.colab import output
    from google.colab import drive
    output.enable_custom_widget_manager()
    
from matplotlib.patches import Circle

import pyTEMlib
import pyTEMlib.probe_tools

print('pyTEM version: ', pyTEMlib.__version__)
```

--------------------------------

### Output of joblib parallel processing

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i2-image-registration

Output of the joblib example: a list of six sublists, each containing the squared value repeated 15 times.

```output
[[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4], [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9], [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16], [25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25], [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36]]
```

--------------------------------

### Calculate and plot Bragg reflections with pyTEMlib

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i4-structure-analysis

Sets up the diffraction calculation with pyTEMlib.diffraction_tools.get_bragg_reflections, configures plotting options, and displays the resulting keys of the HOLZ dictionary. The output shows the number of allowed reflections and the keys of the HOLZ dictionary.

```python
tags = {'acceleration_voltage': acceleration_voltage_V,
        'zone_hkl': [1, 1, -0],
        'hkl_max': 15,
        'mistilt_alpha': np.radians(1),
        'mistilt_beta': np.radians(0),
        'Sg_max': 0.03}
diff_dict = {}
diff_dict = pyTEMlib.diffraction_tools.get_bragg_reflections(atoms, tags, verbose=True) 

diff_dict.setdefault('output',{})['plot_forbidden']=False
diff_dict['output']['plot_dynamically_allowed']=True
diff_dict['output']['plot_Kikuchi']=True
diff_dict['output']['plot_HOLZ']=True
diff_dict['convergence_angle'] = 3
pyTEMlib.diffraction_tools.plot_diffraction_pattern(diff_dict, unit='1/nm')

diff_dict['HOLZ'].keys()
```

```text
mistilt
Of the 457 possible reflection 101 are allowed.
Of those, there are 82 in ZOLZ  and 19 in HOLZ
Of the 137 forbidden reflection in ZOLZ  27 can be dynamically activated.
```

```text
dict_keys(['g_deficient', 'g_excess', 'FOLZ', 'SOLZ', 'HOLZ_plus', 'Laue_zones', 'hkl', 'intensities', 'kg'])
```

--------------------------------

### Calculate Ring Pattern with pyTEMlib

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/diffraction/d1-diffraction-rings

Sets up input parameters for ring pattern calculation, loads the structure by name, stores it in the main dataset, and calls pyTEMlib.diffraction_tools.ring_pattern_calculation. Requires pyTEMlib to be imported beforehand.

```python
# -----Input for ring pattern calculation ----
structure = 'aluminum'
hkl_max = 7
verbose = True
# --------------------------------------------

atoms = pyTEMlib.crystal_tools.structure_by_name(structure)
main_dataset.structures['Structure_000'] = atoms
main_dataset.metadata['experiment']['hkl_max']  = hkl_max

pyTEMlib.diffraction_tools.ring_pattern_calculation(main_dataset, verbose=verbose)
```

--------------------------------

### Select dataset with ft.ChooseDataset

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i2-image-registration

Creates a widget to select a dataset from the current channel. Requires a Jupyter kernel connection to fully display the output.

```python
image_choice = ft.ChooseDataset(current_channel)
```

--------------------------------

### Display FileWidget Output (VBox)

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i1-adaptive-fourier-filter

Shows the widget output as a VBox with a directory dropdown. Requires a Jupyter kernel connection.

```python
VBox(children=(Dropdown(description='directory:', layout=Layout(width='90%'), options=('c:\Users\gduscher\O…
```

--------------------------------

### Inspect get_wavelength function

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/introduction/usefull-equations

Displays the help documentation for the get_wavelength function.

```python
help (get_wavelength)
```

```text
Help on function get_wavelength in module __main__:

get_wavelength(e0: float) -> float
    get deBroglie wavelength of electron accelerated by energy e0 (in eV)

    Parameters
    ----------
    e0 : float
        acceleration voltage in eV
    Returns
    -------
    float
        wavelength in meters


```

--------------------------------

### Parallel processing with joblib.Parallel

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i2-image-registration

Parallelizes a data processing function using joblib.Parallel and delayed. The function process_data squares each element and repeats it 15 times; the example processes 6 data items with 6 jobs. The commented line shows the general pattern.

```python
import joblib 

def process_data(data):
    # Simulate a time-consuming data processing step
    import time
    time.sleep(2)
    return [data ** 2]*15

data = [1, 2, 3, 4, 5, 6]

# Parallel(n_jobs=workjob_num)(delayed(func_be_applied)(aug) for elem in array
results = joblib.Parallel(n_jobs=6)(joblib.delayed(process_data)(data[d]) for d in range(6))
print(results)
```

--------------------------------

### Create FileWidget for file selection

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/introduction/open-files

Creates a file selection widget for choosing a file, even in Google Colab. After navigating to the file, select 'Select Main' to load it.

```python
file_list = pyTEMlib.file_tools.FileWidget()
```

--------------------------------

### Create ChooseDataset widget

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/introduction/open-files

Creates a widget to choose a different dataset from the collection.

```python
dataset_chooser = pyTEMlib.file_tools.ChooseDataset(dataset_collection)
```

--------------------------------

### Configure and plot image stack dataset

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i4-structure-analysis

Sets the dataset data type to IMAGE_STACK and spatial dimensions, then plots the dataset and accesses the slope of the x dimension. Requires the selector widget from the previous step.

```python
dataset = selector.dataset
dataset.data_type = 'IMAGE_STACK'
dataset.x.dimension_type = 'SPATIAL'
dataset.y.dimension_type = 'SPATIAL'

view = dataset.plot()
dataset.x.slope

```

--------------------------------

### Create FileWidget for image selection with pyTEMlib.file_tools

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i4-structure-analysis

Creates a FileWidget from pyTEMlib.file_tools to select an image file. The output is an ipywidgets VBox containing a directory dropdown; a Jupyter kernel connection is required to fully display it.

```python
fileWidget = pyTEMlib.file_tools.FileWidget()
```

```output
VBox(children=(Dropdown(description='directory:', layout=Layout(width='90%'), options=('C:\\Users\\gduscher\\o…
```

--------------------------------

### Output of a[1,0]

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i2-image-registration

Output of a[1,0] showing the resulting array.

```output
array([6, 7, 8])
```

--------------------------------

### Print first five detected spots

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i1-adaptive-fourier-filter

Prints the first five rows of the spots array. The spots are ordered from center to outside, and the third parameter of each spot is its angle.

```python
print(spots[:5])
```

```text
[[-2.62027028  2.21908057 -0.86811058]
 [ 2.62027028 -2.21908057  2.27348207]
 [-3.4226497   0.43880124 -1.44328677]
 [ 3.4226497  -0.43880124  1.69830589]
 [-3.22205484 -1.25371784 -1.94187537]]
```

--------------------------------

### Set center and plot ring pattern with pyTEMlib

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/diffraction/d1-diffraction-rings

Sets the scale from the image dimensions and calls pyTEMlib.diffraction_tools.set_center with a 7% larger scale, then plots the ring pattern using pyTEMlib.diffraction_tools.plot_ring_pattern. This produces the publication-quality figure.

```python
scale  = main_dataset.get_image_dims(return_axis=True)[0].slope

pyTEMlib.diffraction_tools.set_center(main_dataset, center, scale=scale*1.07)
v = pyTEMlib.diffraction_tools.plot_ring_pattern(main_dataset.metadata['diffraction'], main_dataset)
```

--------------------------------

### Simulate atomic-resolution image with ASE and pyTEMlib

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i3-probe

Builds an Al fcc(100) slab with ASE, sets the field of view from the cell, and generates a simulated atomic-resolution image by placing Gaussian peaks at atomic positions and convolving with a probe. The printed value is the field of view in Å, used to scale the image.

```python
from ase import build 
sizeX = 512
slab = build.fcc100('Al', size=(20, 20, 1), orthogonal=True)
ab['FOV'] = slab.cell[0,0]
print(ab['FOV'] len(slab.positions))
scale = sizeX/ab['FOV']
FOV = ab['FOV']
img = np.zeros([sizeX,sizeX])
for pos in slab.positions:    
    img += pyTEMlib.probe_tools.make_gauss(sizeX, sizeX, width=0.05*scale, x0=pos[0]*scale-sizeX/2, y0=pos[1]*scale-sizeX/2, intensity=13**2)

import scipy
img2 = scipy.signal.fftconvolve(img, probe, mode='same')
img2.shape
plt.figure()
plt.imshow(img2)
plt.show()
```

```text
57.27564927611035

```

--------------------------------

### Complete registration with pyTEMlib.image_tools.complete_registration

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i2-image-registration

Performs complete registration (rigid and non-rigid) in one step using pyTEMlib.image_tools.complete_registration. The result is set to an image stack and plotted.

```python
demon_registered, rigid_registered = pyTEMlib.image_tools.complete_registration(dataset)
demon_registered.data_type = 'image_stack'
view2 = demon_registered.plot()
```

--------------------------------

### Compute form factor for silicon with pyTEMlib.diffraction_tools.form_factor

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i4-structure-analysis

Calls pyTEMlib.diffraction_tools.form_factor for silicon with the full g_norm array and with a single g vector, also printing g_norm[0]. The output shows the form factor values for all g vectors, the value at the first g, and the magnitude of that first reciprocal lattice vector.

```python
pyTEMlib.diffraction_tools.form_factor('Si', g_norm), form_factor('Si', g_norm[0]), g_norm[0]
```

--------------------------------

### Create dataset chooser widget with pyTEMlib.file_tools.ChooseDataset

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i1-adaptive-fourier-filter

Creates a chooser widget for selecting a dataset from the datasets dictionary for further processing or visualization.

```python
chooser = pyTEMlib.file_tools.ChooseDataset(datasets)
```

--------------------------------

### Detect spots in power spectrum with diffractogram_spots

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i1-adaptive-fourier-filter

Sets spot_threshold to 0.05 (lower values yield more spots), calls pyTEMlib.image_tools.diffractogram_spots on power_spectrum, filters spots by radial distance (between 0.5 and 7), plots the power spectrum with red spot markers, and prints the number of found spots. The output shows 22 spots.

```python
# ------Input----------
spot_threshold=0.05
# ---------------------

spots, _ = pyTEMlib.image_tools.diffractogram_spots(power_spectrum, spot_threshold=spot_threshold)
spots = spots[np.linalg.norm(spots[:,:2],axis=1)<7,:]
spots = spots[np.linalg.norm(spots[:,:2],axis=1)>0.5,:]
power_spectrum.plot()

plt.gca().scatter(spots[:,0],spots[:,1], color='red', alpha=0.4);
print(f"found {len(spots)}")
```

```text
found 22

```

--------------------------------

### Select and plot dataset

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i2-image-registration

Selects the chosen dataset and plots it. The plot is displayed as a figure.

```python
dataset = fileWidget.selected_dataset
v = dataset.plot()
```

--------------------------------

### Compute FFT and create sidpy.Dataset with reciprocal dimensions

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i2-image-registration

Computes the FFT of the image and creates a sidpy.Dataset with reciprocal-space dimensions. The first block prepares the image and computes the FFT; the second block builds the FFT dataset with proper units and dimension types.

```python
new_image = np.array(image)
new_image = new_image - new_image.min()

fft_transform = (np.fft.fftshift(np.fft.fft2(np.array(new_image))))
dset  = image
```

```python
image_dims = dset.get_image_dims(return_axis=True)

units_x = '1/' + image_dims[0].units
units_y = '1/' + image_dims[1].units

fft_dset = sidpy.Dataset.from_array(fft_transform)
fft_dset.quantity = dset.quantity
fft_dset.units = 'a.u.'
fft_dset.data_type = 'IMAGE'
fft_dset.source = dset.title
fft_dset.modality = 'fft'

fft_dset.set_dimension(0, sidpy.Dimension(np.fft.fftshift(np.fft.fftfreq(new_image.shape[0],
                                                                         d=dset.x[1]-dset.x[0])),
                                          name='u', units=units_x, dimension_type='RECIPROCAL',
                                          quantity='reciprocal_length'))
fft_dset.set_dimension(1, sidpy.Dimension(np.fft.fftshift(np.fft.fftfreq(new_image.shape[1],
                                                                         d=dset.y[1]- dset.y[0])),
                                          name='v', units=units_y, dimension_type='RECIPROCAL',
                                          quantity='reciprocal_length'))
```

--------------------------------

### Rigid registration with pyTEMlib.image_tools

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i4-structure-analysis

Applies rigid registration to the loaded image using pyTEMlib.image_tools.rigid_registration and plots the result. The output is an ipywidgets HBox with a play button and slider; a Jupyter kernel connection is required to fully display it.

```python
rigid_registered = pyTEMlib.image_tools.rigid_registration(image)
v= rigid_registered.plot()
```

```output
HBox(children=(Play(value=0, description='Press play', interval=500, max=20), IntSlider(value=0, continuous_up…
```

--------------------------------

### Open EDS file and create dataset selector

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i4-structure-analysis

Opens a file using pyTEMlib's file_tools with EDS stream enabled and creates a dataset selector with sidpy. The first line retrieves the file name from a file widget.

```python
fileWidget.file_name
datasets = pyTEMlib.file_tools.open_file(fileWidget.file_name, eds_stream=True)
selector = sidpy.ChooseDataset(datasets)
```

--------------------------------

### Heading: Select a different dataset

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/introduction/open-files

Heading for the section on selecting a different dataset.

```markdown
### Select a different dataset
```

--------------------------------

### Select Dataset with sidpy.ChooseDataset

Source: https://pycroscopy.github.io/pyTEMlib/notebooks/imaging/i4-structure-analysis

Creates an interactive dataset selector using sidpy.ChooseDataset. This widget requires a Jupyter kernel connection to fully display its output.

```python
image_choice = sidpy.ChooseDataset(datasets)  
```