Fixing `saveAs` Failure In `happi.multiPlot` With Scalars

Have you ever encountered the frustrating issue where the saveAs function fails within happi.multiPlot, especially when dealing with Scalar diagnostics? You're not alone! This article dives deep into this problem, offering insights and potential solutions to ensure your data visualizations are saved correctly. Let's explore the reasons behind this failure and how to overcome them.

Understanding the Issue

The problem arises specifically when using happi.multiPlot to plot Scalar diagnostics and attempting to save the plot using the saveAs function. Scalar diagnostics, in this context, refer to single-value data outputs, such as energy or particle counts, which are often crucial in simulations. When you try to save a plot generated from these diagnostics, the saveAs command might not work as expected, leaving you without a saved image file. Let's break down a scenario to illustrate this better.

Consider a simulation run using SmileiPIC, a particle-in-cell code, for studying two-stream instability. You might execute the simulation using a command like:

$ ./smilei.sh benchmarks/tst1d_02_two_str_instability.py

After the simulation, you launch an IPython session to analyze the data:

$ ipython3 --pylab

Within IPython, you import the happi module and open the simulation results:

In [1]: import happi

In [2]: S=happi.Open("benchmarks/tst1d_02_two_str_instability/")
Loaded simulation 'benchmarks/tst1d_02_two_str_instability/'
Scanning for Scalar diagnostics
Scanning for Field diagnostics
Scanning for Probe diagnostics
Scanning for ParticleBinning diagnostics
Scanning for RadiationSpectrum diagnostics
Scanning for Performance diagnostics
Scanning for Screen diagnostics
Scanning for Tracked particle diagnostics
Scanning for new particle diagnostics

Now, you attempt to plot and save Scalar diagnostics, such as Ubal (energy balance) and Ukin (kinetic energy):

In [3]: happi.multiPlot(S.Scalar("Ubal"),S.Scalar("Ukin"),saveAs="tmp.png")

Ideally, this command should save the plot as tmp.png. However, in some cases, no file is saved, indicating a failure in the saveAs function. This issue can be perplexing, especially when you need to document or share your simulation results.

Reproducing the Problem

To further understand the issue, let’s outline the steps to reproduce it. This will help in identifying the root cause and formulating effective solutions.

1. Run a SmileiPIC Simulation: Start by executing a simulation that generates Scalar diagnostics. The example provided uses the tst1d_02_two_str_instability.py benchmark, but any simulation producing Scalar outputs can be used.

2. Open IPython: Launch an IPython session with the pylab environment enabled. This provides the necessary tools for data analysis and plotting.

3. Import happi: Import the happi module within the IPython session. This module is essential for interacting with SmileiPIC simulation data.

4. Open Simulation Data: Use happi.Open() to load the simulation results. This step scans the simulation directory for various diagnostics, including Scalars.

5. Attempt to Plot and Save: Use happi.multiPlot() to plot Scalar diagnostics and include the saveAs argument to save the plot to a file. For instance:

   happi.multiPlot(S.Scalar("Ubal"), S.Scalar("Ukin"), saveAs="tmp.png")
   

6. Check for Saved File: After executing the command, check the directory to see if the file tmp.png has been created. If the file is missing, the issue is successfully reproduced.

By following these steps, you can confirm the saveAs failure and proceed to investigate potential causes and solutions.

Potential Causes and Solutions

Several factors might contribute to the failure of saveAs in happi.multiPlot when dealing with Scalar diagnostics. Let's explore some potential causes and their corresponding solutions.

1. Backend Issues with Matplotlib

happi relies on Matplotlib for plotting, and the choice of Matplotlib backend can sometimes cause issues with saving figures. Certain backends might not be compatible with the saveAs function or the file format you're trying to save in.

Solution: Try changing the Matplotlib backend. You can do this by adding the following line at the beginning of your IPython session, before importing happi:

import matplotlib
matplotlib.use('Agg') # Or try 'TkAgg', 'Qt5Agg', etc.

The 'Agg' backend is a non-interactive backend that is often more reliable for saving figures in various formats. Other backends like 'TkAgg' or 'Qt5Agg' might work better depending on your system and installed libraries. Experimenting with different backends can help resolve this issue.

2. File Permissions

Another common reason for file saving failures is insufficient file permissions. If the script doesn't have the necessary permissions to write to the directory where you're trying to save the file, the saveAs function will fail silently.

Solution: Ensure that the script has write permissions to the directory. You can check and modify permissions using command-line tools. For example, in Linux or macOS, you can use chmod to grant write permissions:

chmod +w /path/to/your/directory

Replace /path/to/your/directory with the actual path where you're trying to save the file. Alternatively, try saving the file in a directory where you know you have write permissions, such as your home directory or a temporary directory.

3. Missing Dependencies

happi and Matplotlib depend on several other libraries for various functionalities. If some of these dependencies are missing or outdated, it can lead to unexpected issues, including failures in the saveAs function.

Solution: Ensure that all necessary dependencies are installed and up to date. You can use pip, the Python package installer, to manage your dependencies. First, check which version of happi is installed:

pip show happi

Then, try reinstalling happi along with its dependencies:

pip install --upgrade happi

This command will update happi and its dependencies to the latest versions, which might resolve compatibility issues. You should also ensure that Matplotlib and other related packages are up to date.

4. Bugs in happi or Matplotlib

Although less common, the issue might stem from a bug within happi or Matplotlib. Software bugs can manifest in various ways, and a failure in the saveAs function could be a symptom of an underlying problem.

Solution: Check for updates and report the bug. First, ensure you are using the latest version of happi. If the issue persists, search the happi GitHub repository for similar issues. If none exist, consider reporting the bug with a detailed description of the problem and steps to reproduce it. The developers might already be aware of the issue or can provide a fix in a future release. Similarly, check for updates and known issues in Matplotlib.

5. Incorrect File Path or Name

A simple yet often overlooked cause is an incorrect file path or name. If the specified path is invalid or the filename contains characters that are not allowed by the operating system, the saveAs function might fail.

Solution: Double-check the file path and name. Ensure that the path is correct and that you have included the file extension (e.g., .png, .pdf). Avoid using special characters or spaces in the filename, as these can sometimes cause issues. Try using a simple filename and saving the file in a known location to rule out this possibility.

Practical Examples and Code Snippets

To further illustrate the solutions, let's look at some practical examples and code snippets.

Changing Matplotlib Backend

As mentioned earlier, setting the Matplotlib backend can be crucial. Here's how you can do it:

import matplotlib
matplotlib.use('Agg') # Use the Agg backend
import happi

S = happi.Open("benchmarks/tst1d_02_two_str_instability/")
happi.multiPlot(S.Scalar("Ubal"), S.Scalar("Ukin"), saveAs="tmp.png")

This snippet sets the backend to 'Agg' before importing happi and attempting to save the plot. If 'Agg' doesn't work, you can try other backends like 'TkAgg' or 'Qt5Agg'.

Ensuring File Permissions

While the Python script itself cannot directly change file permissions, you can ensure that the script saves the file in a directory where you have write access. For example:

import happi
import os

S = happi.Open("benchmarks/tst1d_02_two_str_instability/")

# Save the file in the user's home directory
home_dir = os.path.expanduser("~")
save_path = os.path.join(home_dir, "tmp.png")
happi.multiPlot(S.Scalar("Ubal"), S.Scalar("Ukin"), saveAs=save_path)

This code snippet uses the os module to construct a file path in the user's home directory, which typically has write permissions.

Updating Dependencies

To ensure that happi and its dependencies are up to date, use pip:

pip install --upgrade happi matplotlib

This command will update both happi and Matplotlib to their latest versions, resolving any potential compatibility issues.

Conclusion

The failure of saveAs in happi.multiPlot when plotting Scalar diagnostics can be a significant hurdle in your data analysis workflow. However, by understanding the potential causes—such as backend issues, file permissions, missing dependencies, software bugs, or incorrect file paths—you can systematically troubleshoot and resolve the problem. By trying the solutions outlined in this article, from changing Matplotlib backends to ensuring correct file permissions and updating dependencies, you can get back to visualizing and saving your important simulation results. Remember to double-check your file paths and names, and don't hesitate to report bugs if you encounter persistent issues.

For more information on happi and SmileiPIC, you can visit the official **[SmileiPIC Documentation](https://smilei-pic.github.io/