Hello,
First, I want to sincerely thank you for developing and maintaining this great utility — it has been extremely helpful, especially when working with large datasets.
Recently, I’ve been running it in headless mode to automatically crop datasets and save them in another image format such as .nrrd. The cropping works correctly in the GUI mode, but when running headlessly, the script fails to handle the value "Infinity". Specifically, the error occurs because Java attempts to execute Long.parseLong("Infinity") which throws a NumberFormatException.
As a temporary workaround, I replaced "Infinity" with a large number (for example, 9999999) that exceeds the z-stack depth, and it works fine. However, since N5-Utils can already read the dataset’s metadata, I wonder if there could be a strategy to automatically resolve "Infinity" to the actual dataset bounds during parsing.
This issue seems to stem from the parseCropParameters() function, where "Infinity" is not handled gracefully in headless mode. I just wanted to share this error message in case it helps improve robustness in future updates.
Lastly, thank you again for your excellent work. The N5/Zarr formats have made large-scale image processing much more manageable. However, since Zarr v3 currently does not support the N5 store, it can sometimes be inconvenient when working across environments that require Zarr v3 for compatibility.
Hello,
First, I want to sincerely thank you for developing and maintaining this great utility — it has been extremely helpful, especially when working with large datasets.
Recently, I’ve been running it in headless mode to automatically crop datasets and save them in another image format such as .nrrd. The cropping works correctly in the GUI mode, but when running headlessly, the script fails to handle the value "Infinity". Specifically, the error occurs because Java attempts to execute
Long.parseLong("Infinity")which throws aNumberFormatException.As a temporary workaround, I replaced "Infinity" with a large number (for example, 9999999) that exceeds the z-stack depth, and it works fine. However, since N5-Utils can already read the dataset’s metadata, I wonder if there could be a strategy to automatically resolve "Infinity" to the actual dataset bounds during parsing.
This issue seems to stem from the
parseCropParameters()function, where "Infinity" is not handled gracefully in headless mode. I just wanted to share this error message in case it helps improve robustness in future updates.Lastly, thank you again for your excellent work. The N5/Zarr formats have made large-scale image processing much more manageable. However, since Zarr v3 currently does not support the N5 store, it can sometimes be inconvenient when working across environments that require Zarr v3 for compatibility.