osiris-utils 1.1.10a0__tar.gz → 1.2.0__tar.gz

osiris_utils-1.2.0/.pre-commit-config.yaml

@@ -0,0 +1,7 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.8       # pin the latest stable
+    hooks:
+      - id: ruff
+        args: ["--fix", "--select", "F,E,I,W,B,C90"]         # auto‑apply safe fixes (TCH rules disabled here)
+      - id: ruff-format

{osiris_utils-1.1.10a0 → osiris_utils-1.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: osiris_utils
-Version: 1.1.10a0
+Version: 1.2.0
 Summary: Utilities to manipulate and visualise OSIRIS plasma PIC output data
 Author-email: João Pedro Ferreira Biu <joaopedrofbiu@tecnico.ulisboa.pt>
 License: MIT
@@ -12,8 +12,6 @@ Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Natural Language :: English
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
@@ -32,7 +30,6 @@ Requires-Dist: pytest>=8.1; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
 Requires-Dist: pre-commit>=3.7; extra == "dev"
 Requires-Dist: ruff>=0.4; extra == "dev"
-Requires-Dist: isort>=5.13; extra == "dev"
 Requires-Dist: types-tqdm; extra == "dev"
 Requires-Dist: types-Pillow; extra == "dev"
 Provides-Extra: docs
@@ -51,11 +48,13 @@ OSIRIS_UTILS
 .. image:: https://github.com/joaopedrobiu6/osiris_utils/actions/workflows/ci.yml/badge.svg
    :target: https://github.com/joaopedrobiu6/osiris_utils/actions
    :alt: CI status
+
 .. image:: https://codecov.io/gh/joaopedrobiu6/osiris_utils/branch/main/graph/badge.svg
    :target: https://codecov.io/gh/joaopedrobiu6/osiris_utils
    :alt: Coverage
 
-
+.. image:: https://zenodo.org/badge/889119723.svg
+  :target: https://doi.org/10.5281/zenodo.17382244
 
 This package contains a set of utilities to open and analyze OSIRIS output files, using Python. All the methods implemented are fully integrated with `NumPy`, and use `np.ndarray` as the main data structure.
 High-level functions are provided to manipulate data from OSIRIS, from reading the data of the diagnostics, to making post-processing calculations.
@@ -95,6 +94,48 @@ Quick-start
    cd osiris_utils
    python examples/quick_start.py examples/example_data/thermal.1d
 
+Command-Line Interface
+----------------------
+
+osiris_utils includes a command-line interface for common operations. After installation, the ``osiris`` command becomes available::
+
+   osiris --version                     # Check version
+   osiris --help                        # Show available commands
+
+**Available Commands:**
+
+- ``osiris info`` - Display metadata about OSIRIS files and simulations
+- ``osiris export`` - Convert data to CSV, JSON, or NumPy formats
+- ``osiris plot`` - Create quick visualizations
+- ``osiris validate`` - Check file integrity
+
+**Examples:**
+
+Show simulation information::
+
+   osiris info path/to/simulation
+   osiris info path/to/file.h5 --brief
+
+Export data to different formats::
+
+   osiris export file.h5 --format csv --output data.csv
+   osiris export diagnostic/dir --format npy --output data.npy
+
+Generate quick plots::
+
+   osiris plot file.h5 --save plot.png
+   osiris plot file.h5 --save plot.png --title "Ez Field" --cmap viridis
+
+Validate simulation data::
+
+   osiris validate path/to/simulation
+   osiris validate path/to/simulation --check-missing
+
+For detailed help on any command::
+
+   osiris <command> --help
+
+
 Documentation
 -------------
 
@@ -106,7 +147,14 @@ The documentation is available at https://osiris-utils.readthedocs.io or via thi
 
 .. _authors:
 
-Authors and Contributors
-------------------------
+Author
+------
 
 - João Biu
+
+Contributors
+------------
+
+- Diogo Carvalho
+- João Cândido
+- Margarida Pereira

{osiris_utils-1.1.10a0 → osiris_utils-1.2.0}/README.rst

@@ -5,11 +5,13 @@ OSIRIS_UTILS
 .. image:: https://github.com/joaopedrobiu6/osiris_utils/actions/workflows/ci.yml/badge.svg
    :target: https://github.com/joaopedrobiu6/osiris_utils/actions
    :alt: CI status
+
 .. image:: https://codecov.io/gh/joaopedrobiu6/osiris_utils/branch/main/graph/badge.svg
    :target: https://codecov.io/gh/joaopedrobiu6/osiris_utils
    :alt: Coverage
 
-
+.. image:: https://zenodo.org/badge/889119723.svg
+  :target: https://doi.org/10.5281/zenodo.17382244
 
 This package contains a set of utilities to open and analyze OSIRIS output files, using Python. All the methods implemented are fully integrated with `NumPy`, and use `np.ndarray` as the main data structure.
 High-level functions are provided to manipulate data from OSIRIS, from reading the data of the diagnostics, to making post-processing calculations.
@@ -49,6 +51,48 @@ Quick-start
    cd osiris_utils
    python examples/quick_start.py examples/example_data/thermal.1d
 
+Command-Line Interface
+----------------------
+
+osiris_utils includes a command-line interface for common operations. After installation, the ``osiris`` command becomes available::
+
+   osiris --version                     # Check version
+   osiris --help                        # Show available commands
+
+**Available Commands:**
+
+- ``osiris info`` - Display metadata about OSIRIS files and simulations
+- ``osiris export`` - Convert data to CSV, JSON, or NumPy formats
+- ``osiris plot`` - Create quick visualizations
+- ``osiris validate`` - Check file integrity
+
+**Examples:**
+
+Show simulation information::
+
+   osiris info path/to/simulation
+   osiris info path/to/file.h5 --brief
+
+Export data to different formats::
+
+   osiris export file.h5 --format csv --output data.csv
+   osiris export diagnostic/dir --format npy --output data.npy
+
+Generate quick plots::
+
+   osiris plot file.h5 --save plot.png
+   osiris plot file.h5 --save plot.png --title "Ez Field" --cmap viridis
+
+Validate simulation data::
+
+   osiris validate path/to/simulation
+   osiris validate path/to/simulation --check-missing
+
+For detailed help on any command::
+
+   osiris <command> --help
+
+
 Documentation
 -------------
 
@@ -60,7 +104,14 @@ The documentation is available at https://osiris-utils.readthedocs.io or via thi
 
 .. _authors:
 
-Authors and Contributors
-------------------------
+Author
+------
+
+- João Biu
+
+Contributors
+------------
 
-- João Biu
+- Diogo Carvalho
+- João Cândido
+- Margarida Pereira

osiris_utils-1.2.0/benchmarks/benchmark_hdf5_io.py

@@ -0,0 +1,46 @@
+import time
+
+import osiris_utils as ou
+
+
+def benchmark_hdf5_io():
+    """Benchmark HDF5 file opening and reading."""
+    print("=" * 60)
+    print("Benchmarking HDF5 I/O Performance")
+    print("=" * 60)
+
+    filepath = "examples/example_data/MS/FLD/e3/e3-000100.h5"
+
+    # Warm-up (file may be cached by OS)
+    _ = ou.OsirisGridFile(filepath)
+
+    # Benchmark multiple loads
+    n_iterations = 100
+    times = []
+
+    print(f"\nLoading file {n_iterations} times...")
+    for _ in range(n_iterations):
+        start = time.time()
+        data = ou.OsirisGridFile(filepath)
+        times.append(time.time() - start)
+
+    avg_time = sum(times) / len(times)
+    min_time = min(times)
+    max_time = max(times)
+
+    print("\nResults:")
+    print(f"  Average load time: {avg_time * 1000:.2f}ms")
+    print(f"  Min load time: {min_time * 1000:.2f}ms")
+    print(f"  Max load time: {max_time * 1000:.2f}ms")
+    print(f"  Data shape: {data.data.shape}")
+    print(f"  Data size: {data.data.nbytes / 1024:.1f} KB")
+
+    # Calculate throughput
+    throughput = (data.data.nbytes / 1024 / 1024) / avg_time
+    print(f"  Throughput: {throughput:.1f} MB/s")
+
+    print("\n" + "=" * 60)
+
+
+if __name__ == "__main__":
+    benchmark_hdf5_io()

osiris_utils-1.2.0/benchmarks/benchmark_load_all.py

@@ -0,0 +1,54 @@
+import sys
+import time
+
+import osiris_utils as ou
+
+# Use example data if available
+data_path = "examples/example_data"
+
+
+def benchmark_loading():
+    """Benchmark parallel vs sequential loading."""
+    _ = f"{data_path}/MS/FLD/e3"
+
+    print("=" * 60)
+    print("Benchmarking Diagnostic.load_all() performance")
+    print("=" * 60)
+
+    # Test with sequential loading
+    print("\n1. Testing SEQUENTIAL loading...")
+    d = ou.Diagnostic(simulation_folder=data_path)
+    d.get_quantity("e3")
+
+    start = time.time()
+    data_seq = d.load_all(use_parallel=False)
+    seq_time = time.time() - start
+    print(f"   Sequential time: {seq_time:.3f}s for {len(d)} timesteps")
+    print(f"   Data shape: {data_seq.shape}")
+
+    # Unload to test parallel
+    d.unload()
+
+    # Test with parallel loading
+    print("\n2. Testing PARALLEL loading...")
+    start = time.time()
+    data_par = d.load_all(use_parallel=True)
+    par_time = time.time() - start
+    print(f"   Parallel time: {par_time:.3f}s for {len(d)} timesteps")
+    print(f"   Data shape: {data_par.shape}")
+
+    # Calculate speedup
+    speedup = seq_time / par_time if par_time > 0 else 0
+    print(f"\n✓ Speedup: {speedup:.2f}x faster with parallel loading")
+    print(f"  Time saved: {seq_time - par_time:.3f}s ({100 * (seq_time - par_time) / seq_time:.1f}%)")
+
+    print("\n" + "=" * 60)
+
+
+if __name__ == "__main__":
+    try:
+        benchmark_loading()
+    except Exception as e:
+        print(f"Error running benchmark: {e}")
+        print("Make sure example_data is available in the examples directory")
+        sys.exit(1)

osiris_utils-1.2.0/docs/source/api/decks.rst

@@ -0,0 +1,48 @@
+Deck Handling
+=============
+
+This section documents the utilities for handling OSIRIS input decks.
+
+InputDeckIO
+-----------
+
+.. autoclass:: osiris_utils.decks.decks.InputDeckIO
+   :members:
+   :special-members: __init__, __getitem__
+   :undoc-members:
+   :noindex:
+
+   Class to handle parsing and modifying OSIRIS input decks.
+
+   **Key Features:**
+
+   * Parse input decks into python objects
+   * Modify parameters programmatically
+   * Save modified decks to new files
+   * Automatic handling of OSIRIS syntax idiosyncrasies
+
+   **Usage Example:**
+
+   .. code-block:: python
+
+       from osiris_utils.decks import InputDeckIO
+
+       # Load an input deck
+       deck = InputDeckIO("osiris.inp")
+
+       # Get simulation dimension
+       print(f"Simulation dimension: {deck.dim}")
+
+       # Modify a parameter
+       # (Assuming there is a 'time_step' section with 'dt' parameter)
+       deck.set_param("time_step", "dt", "0.05")
+
+       # Save to a new file
+       deck.print_to_file("osiris_modified.inp")
+
+Coordinate Conversion
+---------------------
+
+.. function:: osiris_utils.decks.decks.deval
+
+   .. autofunction:: osiris_utils.decks.decks.deval

{osiris_utils-1.1.10a0 → osiris_utils-1.2.0}/docs/source/api/postprocess.rst

@@ -602,8 +602,72 @@ For large datasets, consider these performance optimizations:
    * Only call `load_all()` when analyzing the full time evolution
    * Use `delete()` and `delete_all()` to free memory when finished with results
 
-2. **Computation Efficiency**:
+   2. **Computation Efficiency**:
 
    * Averaging is computationally inexpensive compared to other operations
    * For 2D/3D data, consider which axis to average along based on your physics
-   * For iterative analysis, calculate fluctuations only when needed
+   * For iterative analysis, calculate fluctuations only when needed
+
+Field Centering
+===============
+
+.. _field-centering-api:
+
+The `FieldCentering` module provides tools to center fields on the grid cells, converting from the Yee mesh positions to cell centers.
+
+FieldCentering_Simulation Class
+-------------------------------
+
+.. autoclass:: osiris_utils.postprocessing.field_centering.FieldCentering_Simulation
+   :members:
+   :special-members: __init__, __getitem__
+   :show-inheritance:
+   :noindex:
+
+   Post-processor for centering electromagnetic fields.
+
+   The FieldCentering_Simulation class provides a convenient interface for centering fields from the Yee mesh to cell centers.
+
+   **Key Features:**
+
+   * Centers fields from Yee mesh to cell centers
+   * Handles periodic boundaries
+   * Supports 1D, 2D, and 3D simulations
+   * Lazy evaluation
+
+   **Usage Examples:**
+
+   .. code-block:: python
+
+       from osiris_utils.data import Simulation
+       from osiris_utils.postprocessing import FieldCentering_Simulation
+
+       # Create a simulation interface
+       sim = Simulation('/path/to/input/deck')
+
+       # Create a field centering processor
+       centered_sim = FieldCentering_Simulation(sim)
+
+       # Get centered E1 field
+       e1_centered = centered_sim['e1']
+
+       # Access specific timestep (interpolated on-demand)
+       timestep_10 = e1_centered[10]
+
+FieldCentering_Diagnostic Class
+-------------------------------
+
+.. autoclass:: osiris_utils.postprocessing.field_centering.FieldCentering_Diagnostic
+   :members:
+   :special-members: __init__, __getitem__
+   :show-inheritance:
+   :noindex:
+
+   Specialized diagnostic that represents the centered field.
+
+   This class handles the actual interpolation while maintaining the Diagnostic interface.
+
+   **Key Methods:**
+
+   * ``load_all()`` - Compute and store the complete centered field
+   * ``__getitem__(index)`` - Compute centered field for a specific timestep on-demand

{osiris_utils-1.1.10a0 → osiris_utils-1.2.0}/docs/source/api/sim_diag.rst

@@ -110,7 +110,7 @@ Diagnostic Base Class
    
    **Key Attributes:**
    
-   * ``species`` - The plasma species being analyzed (Specie object)
+   * ``species`` - The plasma species being analyzed (Species object)
    * ``dx`` - Grid spacing in each direction
    * ``nx`` - Number of grid points in each direction
    * ``x`` - Grid coordinates

{osiris_utils-1.1.10a0 → osiris_utils-1.2.0}/docs/source/api/utilities.rst

@@ -1,7 +1,7 @@
 Utilities API
 =============
 
-This document provides a reference to the osiris_utils utilities API.
+This document provides a reference to the `osiris_utils` utilities API, which includes tools for reading various OSIRIS data formats (Grid, Raw Particles, Tracks, HIST) and helper functions for common physics calculations and data operations.
 
 Data Readers Structures
 -----------------------

{osiris_utils-1.1.10a0 → osiris_utils-1.2.0}/docs/source/conf.py

@@ -26,7 +26,7 @@ sys.path.append(os.path.abspath("../.."))
 project = "osiris_utils"
 copyright = "2025, João Biu"
 author = "João Biu"
-version = "v1.1.10a"
+version = "v1.2.0"
 release = version
 
 
@@ -46,6 +46,7 @@ extensions = [
     "sphinx.ext.napoleon",
     "sphinx_copybutton",
     "sphinx_github_style",
+    "myst_parser",
 ]
 
 nb_execution_mode = "off"  # use stored output; avoids long CI builds

osiris_utils-1.2.0/docs/source/examples/example_Derivatives.md

@@ -0,0 +1,78 @@
+```python
+%load_ext autoreload
+%autoreload 2
+```
+
+
+```python
+import matplotlib.pyplot as plt
+import numpy as np
+
+import osiris_utils as ou
+```
+
+# Derivatives using `Derivative_Simulation` object
+
+In this notebook we will show how to use the `Derivative_Simulation` object to compute derivatives of a function with respect to the time and space coordinates. 
+
+As an example, we will compute the residual of the continuity equation of a thermal plasma, in the x-direction, this is, the LHS of:
+
+$$
+\frac{\partial n}{\partial t} + \frac{\partial}{\partial x}(n v_1) = 0
+$$
+
+For this, we need the derivatives of the density `n` and the velocity `v1` with respect to the time and space coordinates. The `Derivative_Simulation` object will compute these derivatives using finite differences.
+
+Initialize the simulation object:
+
+
+```python
+sim = ou.Simulation(input_deck_path="example_data/thermal.1d")
+```
+
+Initialize the `Derivative_Simulation` objects with respect to the time and $x_1$ coordinate, since these are the derivatives that we want to compute.
+
+
+```python
+d_dt = ou.Derivative_Simulation(sim, "t")
+d_dx1 = ou.Derivative_Simulation(sim, "x1")
+```
+
+Note that the derivative with respect to $x_1$ is applied not to one diagnostic, but to the product of two diagnostics. We can take advantage of the operations between diagnostics to compute this "new" diagnostic, the product of the density and the fluid velocity.
+
+
+```python
+# Create a new diagnostic n * vfl1
+nVfl1 = sim["electrons"]["n"] * sim["electrons"]["vfl1"]
+# Add this to the simulation (electrons)
+sim["electrons"].add_diagnostic(nVfl1, "nVfl1")
+```
+
+Now that we have the diagnostics needed in our `Simulation` object, we can directly reconstruct the equation desired:
+
+
+```python
+continuity = d_dt["electrons"]["n"] + d_dx1["electrons"]["nVfl1"]
+```
+
+This is a new diagnostic, and we can now access to its iterations using indexing
+
+
+```python
+plt.figure(figsize=(8, 6))
+plt.title("Continuity equation residuals")
+plt.xlabel(continuity.axis[0]["plot_label"])
+
+plt.plot(continuity.x, continuity[10], label="Continuity equation")
+plt.legend()
+plt.xlim(continuity.x[0], continuity.x[-1])
+plt.show()
+```
+
+
+```python
+plt.plot(continuity.x, ou.integrate(continuity[10], continuity.dx), label=r"$\int \partial_t n + \partial_x( n v_{fl1}) dx$")
+plt.legend()
+plt.xlim(continuity.x[0], continuity.x[-1])
+plt.show()
+```

osiris_utils-1.2.0/docs/source/examples/example_FFT.md

@@ -0,0 +1,152 @@
+# FFT Analysis
+
+```python
+%load_ext autoreload
+%autoreload 2
+```
+
+
+```python
+import matplotlib.pyplot as plt
+import numpy as np
+from matplotlib.colors import LogNorm
+
+import osiris_utils as ou
+```
+
+## Initialize an object of the Simulation class
+- The Simulation class takes the `simulation_folder`, this is, the file where the input deck is located.
+- It can also take the `species` when we want to use quantities related to a specific species, such as velocities, charge, temperature, etc.
+
+
+```python
+# In this case, since we only want to study the electric field, no species is needed
+sim = ou.Simulation(input_deck_path="example_data/thermal.1d")
+```
+
+The `Simulation` object acts as a container for the simulation diagnostics, that can be easily accessed from the `Simulation` object using a dictionary-like syntax
+In this case, to access the component of the electric field in the z direction, we can use `sim['e3']`. This is a `Diagnostic` object, that loads the data as requested using a data generator, using indices to choose the time step - a lazy loading approach.
+
+
+```python
+# This is a Diagnostic object
+sim["e3"]
+
+# This is also a Diagnostic object but initialized directly and not through the Simulation object
+e3 = ou.Diagnostic(simulation_folder="example_data")
+e3.get_quantity("e3")
+
+print("sim['e3'] class:", sim["e3"].__class__)
+print("e3 class:", e3.__class__)
+```
+
+The data of the diagnostic at a given index can be accessed by indexing the iteration number, e.g. `sim['e3'][0]` will return the electric field in the z direction at the first time step. The data is not stored in memory, but loaded from the file when requested, using a data generator (lazy loading). For example, to plot the electric field in the z direction at the 100th time step, we can use `sim['e3'][100]`, and use the other attributes of the `Diagnostic` object to get the time step, the grid, labels, etc.
+
+
+```python
+plt.figure(figsize=(8, 3))
+plt.plot(sim["e3"].x, sim["e3"][100])
+plt.xlabel(sim["e3"].axis[0]["plot_label"])
+plt.title(rf"${sim['e3'].label}$ @ $t = {sim['e3'].time(100)[0]:.2f}$ $[{sim['e3'].tunits}]$")
+plt.show()
+```
+
+If we want to load the data of the diagnostic at all time steps, we can use the `load_all()` method of the `Diagnostic` object, e.g. `sim['e3'].load_all()` will load the electric field in the z direction at all time steps and store it in memory. This is useful when we want to do the FFT of the data in the time domain, for example. Using the method `unload()` we can clear the data from memory.
+
+
+```python
+sim["e3"].load_all()
+print(sim["e3"].data.shape)
+
+e3.load_all()
+print(e3.data.shape)
+
+np.isclose(sim["e3"].data, e3.data).all()
+
+sim["e3"].unload()
+e3.unload()
+```
+
+Now we are going to use a post process on the simulation data and on the diagnostic. We can think of a `PostProcess` as an operator over the `Diagnostic`'s of the `Simulation`. We define it on the simulation, and to access a post-processed quantity of the simulation, we use the same dictionary-like syntax, e.g. `sim_fft["e3]` to access the FFT of the electric field in the z direction. 
+
+The data is loaded in memory when requested, using a data generator, and can be accessed using the same indexing syntax, e.g. `sim_fft["e3"][0]` to access the FFT of the electric field in the z direction at the first time step. The data can be loaded using the `load_all()` method, and cleared from memory using the `unload()` method.
+
+The post-processing classes inherit from the `PostProcess` class and the `Diagnostic` class, and can be used as a `Diagnostic` object, with the same attributes and methods, ensuring that operations between diagnostics and post-processes are consistent.
+
+Each diagnostic has a version to be applied to `Simulation` objects and another to be applied to `Diagnostic` objects. The first has the name `<name of post-process>`_Simulation, and the second has the name `<name of post-process>_Diagnostic`. For example, the post-process routines for Fast Fourier Transforms are called `FastFourierTransform_Diagnostic` and `FFT_Diagnostic`.
+
+
+```python
+sim_fft = ou.FFT_Simulation(sim, (0, 1))  # "operator" FFT applied to Simulation object, axis 0 and 1
+
+e3_fft = ou.FFT_Diagnostic(e3, (0, 1))  # "operator" FFT applied to Diagnostic object, axis 0 and 1
+```
+
+
+```python
+sim_fft["e3"][100]  # this will only return the kx axis, since we are only requesting the 100th time step of the FFT of e3
+
+e3_fft[100]  # this will return the kx and ky axis, since we are only requesting the 100th time step of the FFT of e3
+
+np.isclose(sim_fft["e3"][100], e3_fft[100]).all()  # They are the same!
+```
+
+Since my goal is to plot the dispersion relation, I will need to use `.load_all()` to load all the time steps, and have access to the data in the frequency domain.
+
+
+```python
+sim_fft["e3"].load_all()
+e3_fft.load_all()
+
+np.isclose(sim_fft["e3"].data, e3_fft.data).all()  # They are the same!
+```
+
+We can now plot!
+
+
+```python
+plt.imshow(
+    sim_fft["e3"].data,
+    origin='lower',
+    norm=LogNorm(vmin=1e-7, vmax=0.01),
+    extent=(-sim_fft["e3"].kmax, sim_fft["e3"].kmax, -sim_fft["e3"].omega_max, sim_fft["e3"].omega_max),
+    aspect='auto',
+    cmap='gray',
+)
+
+# Plotting the dispersion relation
+k = np.linspace(-e3_fft.kmax, e3_fft.kmax, num=512)
+w = np.sqrt(1 + k**2)
+plt.plot(k, w, label=r"$\omega^2 = \omega_p^2 + k^2c^2$", color='r', ls='-.')
+plt.xlim(0, e3_fft.kmax)
+plt.ylim(0, e3_fft.omega_max)
+
+plt.xlabel(r"$k$ $[\omega_e/c]$")
+plt.ylabel(r"$\omega$ $[\omega_e]$")
+plt.legend()
+plt.show()
+```
+
+
+```python
+plt.imshow(
+    e3_fft.data,
+    origin='lower',
+    norm=LogNorm(vmin=1e-7, vmax=0.01),
+    extent=(-e3_fft.kmax, e3_fft.kmax, -e3_fft.omega_max, e3_fft.omega_max),
+    aspect='auto',
+    cmap='gray',
+)
+
+# Plotting the dispersion relation
+k = np.linspace(-e3_fft.kmax, e3_fft.kmax, num=512)
+w = np.sqrt(1 + k**2)
+plt.plot(k, w, label=r"$\omega^2 = \omega_p^2 + k^2c^2$", color='r', ls='-.')
+plt.xlim(0, e3_fft.kmax)
+plt.ylim(0, e3_fft.omega_max)
+
+plt.xlabel(r"$k$ $[\omega_e/c]$")
+plt.ylabel(r"$\omega$ $[\omega_e]$")
+plt.legend()
+plt.show()
+```