MalformedURLException

[WillGiang]

Hi, I'm trying to use MaMuT 0.28.0 on Windows 7 64bit.

I'm getting the following error (unimportant parts of the file path replaced with foo) after trying to load a mamut XML file.

Problem loading the image data file C:\foo_bdv.xml. java.net.MalformedURLException: unknown protocol: c

A quick search on Stack Overflow yields this solution https://stackoverflow.com/a/8474725 But I admit I'm not comfortable enough to make a pull request.

Thanks, Will

[tinevez]

Hi @WillGiang I cannot reproduce the bug. How do you trigger it?

[WillGiang]

Hi @tinevez

I made a Fiji screen cast and also added the xml/h5 files into this Dropbox folder https://www.dropbox.com/sh/i9n87rhsnd55njn/AAArQzum9WuqKTyuTSie5HSya?dl=0

For future reference, I open Fiji and do the following Plugins -> Load -> MaMuT -> Load MaMuT File -> Navigate to MaMuT xml file

output in console is `Computing spot features. Computation done in 0 ms. Computing edge features:

• Edge target in 5 ms.
• Edge velocity in 5 ms. Computation done in 15 ms. Computing track features:
• Track index in 0 ms.
• Track duration in 5 ms.
• Branching analyzer in 9 ms.
• Cell division rate analyzer in 32 ms. Computation done in 51 ms. Problem loading the image data file C:\Users\Will\Brian-Pedro-ilastik\output\objects\arp3 rescues000_Fiji-MaMuT{slice_index}objects.gif_bdv.xml. java.net.MalformedURLException: unknown protocol: c `

These XML files were made by ilastik v1.3.0, so I hope I'm not bothering the wrong person!

[tinevez]

Please try removing the {index} from both files, and edit the MaMuT file accordingly.

[WillGiang]

Ah, the curly braces were the issue, eh?

Thank you for your assistance.

[tinevez]

Yep. I got blocked after: it gave me an error about a missing reader for Ilastik HDF5. But I guessed you would not have this one. So we must simply avoid using forbidden chars in file names.

[imagejan]

@tinevez wrote:

So we must simply avoid using forbidden chars in file names.

Curly brackets are not at all a forbidden char in filenames on most file systems: https://en.wikipedia.org/wiki/Filename#Comparison_of_filename_limitations