OpenGATE: Mysterious ROOT File Deletion With `RepeatParametrisedVolume`

Dec 4, 2025 by Admin 72 views

Hey there, OpenGATE community and fellow simulation enthusiasts! Ever faced that gut-wrenching moment when you've run a complex simulation, expecting a treasure trove of data, only to find your crucial output files have vanished into thin air? Well, if you're working with OpenGATE and specifically dabbling with the RepeatParametrisedVolume object, you might have just stumbled upon a rather peculiar and frankly, quite annoying bug. This isn't just a minor glitch, folks; we're talking about a situation where your painstakingly generated ROOT files – the very backbone of your simulation results – are automatically deleted right after your simulation wraps up. And the craziest part? This happens even if you just create the RepeatParametrisedVolume object, without even adding it to your volume manager or configuring it! It's like a phantom process sweeping away your hard-earned data, leaving you scratching your head and wondering what went wrong. Understanding this OpenGATE bug is critical for anyone relying on persistent data output, and we're here to break it down, explore its implications, and hopefully, nudge the community towards a swift resolution. So, buckle up, because we're diving deep into the mysterious case of disappearing ROOT files.

The Mysterious Case of Disappearing ROOT Files in OpenGATE

Alright, let's get straight to the point, guys. Imagine spending hours setting up a detailed simulation in OpenGATE, configuring all your actors, sources, and physics lists. You hit run, the simulation completes, and you eagerly navigate to your output directory, ready to analyze the results contained within your precious ROOT files. But alas! They're gone. Poof! Vanished. All you're left with is perhaps a stat.txt file, which, while useful, certainly doesn't contain the intricate hit data or event information you were expecting. This frustrating scenario is precisely what happens when the RepeatParametrisedVolume object gets involved. It’s an incredibly counter-intuitive issue because the deletion occurs simply by instantiating the object. You don't even need to use it in your geometry; just creating an instance of gate.geometry.volumes.RepeatParametrisedVolume is enough to trigger this automatic data purge of all ROOT files generated by digitizer actors. This means that important information, such as energy deposits, global times, and other critical hit data that you meticulously configured your DigitizerHitsCollectionActor to record, gets deleted. For researchers and developers alike, losing simulation output can be a huge setback, potentially invalidating entire runs or forcing time-consuming re-simulations. It undermines the reliability of your data pipeline and can lead to significant delays in projects. The integrity of your simulation output is paramount, and any mechanism that silently disposes of it is a major concern. We're talking about data persistence, which is a fundamental expectation when running any computational experiment. Without reliable output, the entire simulation effort becomes questionable, hindering scientific discovery and engineering advancements. This bug truly puts a wrench in the works, making it hard to trust the output of an otherwise robust simulation toolkit. It’s a classic example of an unexpected side effect that can have far-reaching consequences for users.

What Exactly is `RepeatParametrisedVolume`?

So, what's this RepeatParametrisedVolume thing, and why is it causing so much trouble? At its core, RepeatParametrisedVolume is a really powerful feature in OpenGATE (and underlying Geant4) designed to simplify the creation of complex geometries involving many similar or identical volumes. Think about it: instead of manually defining hundreds or thousands of individual detector elements, you can define one prototype volume and then use RepeatParametrisedVolume to array it in various configurations. This could be a linear array, a circular arrangement, or even a more complex, parametrised grid where each instance might vary slightly in size, position, or material based on a mathematical function. For instance, in medical imaging, you might have a PET scanner with hundreds or thousands of small crystal detectors arranged in a ring. Manually placing each crystal would be a nightmare! RepeatParametrisedVolume allows you to define one crystal and then tell OpenGATE to repeat it, say, 512 times around a circle. Similarly, in radiation therapy, simulating a phantom with many small, identical dosimeters or a multi-leaf collimator with numerous leaves benefits immensely from this capability. It's meant to be a huge time-saver and a way to keep your geometry definitions clean and manageable, preventing repetitive code and potential errors. When it works as intended, it's a fantastic tool for building highly detailed and realistic simulation environments for tasks like dosimetry, imaging system design, and radiation shielding analysis. The idea is to make complex geometries accessible and efficient to define, compute, and manage. It plays a crucial role in reducing memory footprint and computation time by optimizing how these repeated volumes are handled by the underlying Geant4 kernel. However, when an object designed for such efficiency and utility inadvertently causes critical data loss, it obviously becomes a major point of concern, overshadowing its intended benefits. Normally, you'd define your repeated_volume, set up your positioner, maybe define some parametrisation rules, and then add it to your volume manager. The beauty of it is that OpenGATE handles the intricacies of placing all these instances in the simulated world for you. It's a fundamental building block for advanced geometric setups, which is why its current behavior is so perplexing and impactful.

The Crucial Role of ROOT Files in OpenGATE Simulations

Now, let's talk about why those ROOT files are so darn important and why their disappearance is such a big deal. For those new to the game, ROOT is a powerful object-oriented data analysis framework developed at CERN, widely used in high-energy physics and nuclear physics. It's basically the Swiss Army knife for data storage, processing, and visualization in these fields. OpenGATE, being built on Geant4, naturally leverages ROOT for its output data. When you run an OpenGATE simulation, actors like DigitizerHitsCollectionActor or GateVoxelizedSourceActor or GateDoseActor are designed to generate structured data – hits, events, dose maps, particle tracks, and more – and store them in .root files. These files aren't just plain text; they contain complex data structures like TTrees, which are optimized for efficient storage and fast querying of large datasets. Imagine a TTree as a highly organized database table, where each row is an event or a hit, and columns represent various attributes like energy deposit, global time, position, particle type, etc. This structure allows researchers to perform sophisticated analyses: filtering events, calculating dose distributions, reconstructing images, or studying detector performance with incredible detail and speed. Without these ROOT files, you lose all that granular information. You can't reconstruct particle trajectories, you can't map out precise dose depositions, and you certainly can't perform advanced statistical analysis. They are the primary output for most quantitative studies done with OpenGATE. Losing them means losing the ability to validate your simulation, compare results with experimental data, or draw any meaningful scientific conclusions. It's like baking a cake and then losing the cake itself, only having the recipe card left – the recipe is nice, but you can't eat it! The persistence of these files is absolutely crucial for the entire scientific workflow. Any bug that compromises this persistence directly impacts the scientific rigor and trustworthiness of the simulation results. It's not just an inconvenience; it's a potential blocker for research progress, emphasizing just how critical it is to get this OpenGATE ROOT file deletion bug sorted out promptly.

Unpacking the OpenGATE Bug: A Deep Dive into the Issue

Alright, let's really dig into the nitty-gritty of this particular OpenGATE bug. What we've observed is a very specific and baffling behavior: the mere creation of a RepeatParametrisedVolume object within your Python script causes all subsequently generated ROOT files to be automatically deleted upon simulation completion. This is profoundly problematic because it suggests a side effect linked to object instantiation rather than actual usage or configuration. Normally, when you create an object, especially one representing a geometric component, you'd expect its impact to be limited until it's actually integrated into the simulation environment (e.g., added to the volume_manager). But here, simply having the line rpt = gate.geometry.volumes.RepeatParametrisedVolume(...) in your script is enough to trigger the issue. Let's walk through the minimal script provided to understand the exact sequence of events. First, the script sets up a basic gate.Simulation() instance and defines an output directory. It then creates a minimal world volume and a simple detector box. So far, so good. Then comes the culprit: rpt = gate.geometry.volumes.RepeatParametrisedVolume(name="repeat_detector", repeated_volume=detector). This single line, even though the rpt object is never used, never added to the sim.volume_manager, and never configured with any specific repetition logic, is what causes the bug. The simulation proceeds with defining physics, a source, and two actors: a SimulationStatisticsActor which outputs to stat.txt, and a DigitizerHitsCollectionActor which outputs to test_hits.root. Both actors are configured to write their outputs. When the sim.run() command executes, the simulation runs normally. You'll even see test_hits.root appear in the output directory during the simulation. However, as soon as sim.run() completes and the Python script finishes its execution, test_hits.root is mysteriously gone, while stat.txt remains perfectly intact. This discrepancy, where one type of output persists and another doesn't, strongly points to an issue specifically affecting how ROOT files or certain actor types interacting with ROOT are managed during the simulation's cleanup phase. The bug persists regardless of whether you try to add the repeater to the volume manager or set any of its attributes. It's as if the act of creating the RepeatParametrisedVolume object globally registers a destructor or a cleanup hook that indiscriminately targets ROOT files upon simulation exit. Debugging such an issue can be a nightmare because it involves looking for very subtle interactions, potentially at the C++ level where OpenGATE interfaces with Geant4 and ROOT's file management. It could be a static initializer, a global object being registered, or a memory management issue where destructors are prematurely invoked or incorrectly handled. Understanding this behavior is paramount for resolving the bug and ensuring data integrity for all OpenGATE users.

Reproducing the Bug: Your Step-by-Step Guide

Alright, fellow OpenGATE troubleshooters, if you want to see this OpenGATE bug in action (or confirm it's been fixed!), here's your straightforward guide to reproducing the issue. It's super important for developers to have a minimal, reproducible example, and the script provided earlier does exactly that. So, let's get you set up to witness the disappearing act yourself. First things first, you'll need a working OpenGATE Python environment. Make sure you have OpenGATE installed and configured correctly. Once your environment is ready, grab the following Python script and save it as something like reproduce_root_bug.py:

import opengate as gate
from pathlib import Path
import os

def main():
    sim = gate.Simulation()
    
    # Setup output
    output_dir = Path("output")
    output_dir.mkdir(exist_ok=True)
    sim.output_dir = output_dir
    
    # Minimal world
    sim.world.size = [1 * gate.g4_units.m] * 3
    sim.world.material = "G4_AIR"
    
    # Simple detector volume
    detector = sim.add_volume("Box", "detector")
    detector.mother = "world"
    detector.material = "G4_AIR"
    detector.size = [10 * gate.g4_units.cm] * 3
    
    # THIS LINE CAUSES THE BUG - just creating the object (comment the line below to see the expected behavior)
    rpt = gate.geometry.volumes.RepeatParametrisedVolume(
         name="repeat_detector",
         repeated_volume=detector
    )
    # No need to add it or set any attributes - bug occurs anyway
    
    # Simple physics
    sim.physics_manager.physics_list_name = "G4EmStandardPhysics_option3"
    
    # Simple source
    source = sim.add_source("GenericSource", "test_source")
    source.particle = "gamma"
    source.energy.mono = 511 * gate.g4_units.keV
    source.activity = 100000 * gate.g4_units.Bq
    source.direction.type = "iso"
    
    # Statistics actor (produces stat.txt - this persists)
    stats = sim.add_actor("SimulationStatisticsActor", "Stats")
    stats.output_filename = "stat.txt"
    
    # Actor that produces ROOT file
    hits = sim.add_actor("DigitizerHitsCollectionActor", "Hits")
    hits.attached_to = ["detector"]
    hits.output_filename = "test_hits.root"
    hits.write_to_disk = True
    hits.attributes = ["TotalEnergyDeposit", "GlobalTime"]
    
    # Run
    sim.run_timing_intervals = [[0, 1 * gate.g4_units.s]]
    sim.run()
    
    # Check output
    print("Output files:", os.listdir("output"))
    # BUG: stat.txt persists but test_hits.root will be missing

if __name__ == "__main__":
    main()

Here's how to run it:

Save the script: Save the code above as reproduce_root_bug.py.
Run from your terminal: Open your terminal or command prompt, navigate to the directory where you saved the file, and execute: python reproduce_root_bug.py.

What to expect:

With the bug present (line rpt = ... uncommented): You will see a directory named output created. Inside, you'll find stat.txt, but test_hits.root will be conspicuously absent after the script finishes. The print("Output files:", os.listdir("output")) line will confirm this, likely showing ['stat.txt'].
Without the bug (line rpt = ... commented out): If you comment out the line rpt = gate.geometry.volumes.RepeatParametrisedVolume(...) and run the script again, you should see both stat.txt and test_hits.root in the output directory. This is the expected behavior.

This clear distinction highlights the problem. The OpenGATE bug is reproducibly linked to that single line of code. If you're encountering this in your larger simulations, this minimal script provides a quick way to verify if it's the same issue. Sharing such minimal examples is crucial for developers to pinpoint the exact cause and roll out a fix. So, give it a try, and confirm if you're experiencing the same mysterious file disappearance!

Potential Workarounds and Temporary Solutions

Given the frustration this OpenGATE bug can cause, especially when you're on a tight deadline, let's talk about some potential workarounds and temporary solutions. While we eagerly await an official fix from the OpenGATE developers, sometimes you just need to get your simulation done and your data saved. The most obvious, albeit restrictive, workaround is simply to avoid instantiating RepeatParametrisedVolume altogether if you don't absolutely need it for your current simulation. If your geometry doesn't require repeating volumes, just comment out or delete that line (rpt = gate.geometry.volumes.RepeatParametrisedVolume(...)) from your script. This will revert to the expected behavior where your ROOT files persist. However, this isn't a viable solution if your simulation does indeed rely on repeating volumes. In that case, you might have to explore alternative ways to define your geometry. Perhaps manually creating multiple instances of a volume, though incredibly tedious and memory-intensive for large arrays, might be a temporary measure. Another extremely important temporary solution for all simulation users, regardless of this bug, is robust data backup and verification. This means implementing steps in your workflow to: 1. Copy files immediately: As soon as a simulation step generates a ROOT file, try to programmatically copy it to a separate, temporary directory before the main OpenGATE process fully terminates. You might need to add a small delay or a try-except block to catch the files before they vanish. This could involve using Python's shutil.copy() or os.rename() functions right after your actor writes its output, or even between sim.run() calls if you break your simulation into shorter intervals. 2. Check file existence and integrity: Always verify that your output files exist and are not corrupted immediately after they are supposed to be written. You can use os.path.exists() and check the file size. 3. Version control for scripts: Keep your simulation scripts under version control (like Git). This allows you to easily revert to a working version or experiment with changes without fear of losing your setup. For more advanced users, it might be possible to intercept the file deletion mechanism if it's exposed in the Python bindings, perhaps by overriding a destructor or a cleanup hook, but this would require a deeper understanding of OpenGATE's internal C++ implementation, which is often beyond a typical user's scope. The bug's nature (object instantiation causing a global side effect) suggests a potential issue in the underlying C++ layers of OpenGATE, possibly related to static object registration, global resource management, or incorrect destructor calls. It's a tricky one to diagnose without diving into the source code. However, by being vigilant with data handling and backup, you can mitigate the impact while the core issue is being addressed by the development team. Remember, data integrity is your responsibility, even when software bugs try to challenge it!

The Broader Impact: Data Integrity and Simulation Reliability

Let's zoom out a bit and talk about the bigger picture, guys. This RepeatParametrisedVolume bug, while specific, highlights a much broader and more critical concern: data integrity and simulation reliability. In scientific research and engineering development, simulations like those performed with OpenGATE are often the bedrock upon which significant conclusions are drawn, new technologies are designed, and even medical treatments are planned. The results from these simulations are assumed to be trustworthy and persistent. When a bug causes data to be silently deleted, it erodes that trust. Researchers spend countless hours developing complex models, running simulations that can take days or weeks, and then meticulously analyzing the generated data. If the output data—especially crucial files like ROOT files containing raw event-by-event information or detailed dose maps—is not reliably saved, the entire chain of scientific inquiry breaks down. Imagine a scenario where a medical physicist designs a new radiation therapy plan based on OpenGATE simulations, but due to this bug, critical dose distribution files are deleted, leading to an incomplete or even erroneous understanding of the treatment's impact. Or a detector physicist trying to optimize a new PET scanner, only to find that the hit collection data, essential for evaluating detector efficiency and spatial resolution, vanishes. The implications are severe. It can lead to wasted computational resources, lost research time, flawed conclusions, and ultimately, a lack of confidence in the simulation platform itself. Reliable simulation outputs are not just a convenience; they are a fundamental requirement for reproducible science. Any software that claims to support scientific endeavors must prioritize the integrity and persistence of its generated data. This bug, by its very nature, challenges that fundamental principle. It underscores the importance of rigorous testing, especially for components that might have global side effects or touch file system operations during cleanup. It also emphasizes why open-source projects, with their collaborative debugging potential, are so vital. When unexpected behavior like this arises, the collective vigilance of the community becomes a powerful tool in identifying, understanding, and ultimately fixing issues that could otherwise compromise the integrity of scientific output globally. So, while this particular bug is about disappearing ROOT files, its shadow extends over the entire landscape of simulation reliability.

Engaging with the OpenGATE Community: Reporting and Collaboration

Finally, let's talk about what we, as users and members of the OpenGATE community, can do. This bug report is a fantastic start, but engaging actively is how open-source projects thrive and improve. The core strength of OpenGATE lies not just in its powerful capabilities, but in its vibrant and dedicated user and developer community. When you encounter a bug like this ROOT file deletion issue, your contribution in reporting it is invaluable. First, make sure your bug report is clear, concise, and most importantly, includes a minimal reproducible example, just like the one shared in this discussion. A script that clearly demonstrates the issue with minimal setup allows developers to quickly isolate the problem, rather than sifting through complex, full-scale simulations. This saves them precious time and accelerates the path to a fix. Second, participate in the relevant discussion forums, GitHub issues, or mailing lists associated with OpenGATE. Share your observations, confirm if you're experiencing the same problem, or even suggest potential hypotheses if you have insights into the codebase. Even if you're not a core developer, your testing and feedback are gold. Third, if you have the skills, consider diving into the OpenGATE source code yourself. OpenGATE is, after all, an open-source project. This bug might stem from a subtle interaction in the C++ layers or the Python bindings, perhaps in how global objects are managed or how destructors are called upon program exit. Contributing code, even a small pull request that addresses a specific issue, is the ultimate form of collaboration. Remember, every major software project has its quirks and bugs, but it's the collective effort of its community that transforms these challenges into opportunities for improvement. By working together, sharing knowledge, and providing constructive feedback, we can help make OpenGATE even more robust, reliable, and user-friendly for everyone. Let's get this OpenGATE bug squashed and ensure that no more precious ROOT files vanish into the digital ether!

In summary, the RepeatParametrisedVolume object in OpenGATE is currently causing a mysterious deletion of ROOT output files, even without being actively used. This OpenGATE bug compromises data integrity and simulation reliability, crucial for scientific research. We've explored the problem, its impact, and how to reproduce it. While workarounds exist, the best path forward is active community engagement and a prompt fix from the OpenGATE development team. Let's collaborate to ensure OpenGATE remains a powerful and trustworthy simulation tool for all!