Illegal character error

[ewestlundicr]

Hi,

About six months ago I set up a script using Bigstitcher which worked great. Now, I'm trying to use it again but I'm getting an error.

When trying to run the steps manually the first Define Dataset works but when trying to do "Calculate pairwise shift" (or when trying to load a dataset) I get:
Cannot parse 'file:/C:/Users/ewestlund/dataset.xml': java.nio.file.InvalidPathException: Illegal char <:> at index 2: /C:/Users/ewestlund/dataset.xml

From my understanding it's the : character that causes an issue, but any path on the PC will have this included. How can I work around this?

Thank you very much

[ScientistRachel]

This is just a note to say that I am getting the same error. I agree that it seems like any Windows path would not be accepted by this new version, so a fix for this would be helpful.

[ewestlundicr]

I manage to get it working by following the instructions from this discussion https://forum.image.sc/t/bigstitcher-4-3-3-parsing-xml-fails-in-windows/104753/9

I replaced the multiview-reconstruction JAR in my Fiji folder with the
multiview-reconstruction-4.3.5-SNAPSHOT.jar found in the above link.

I restarted my Fiji and made the required installation and it worked.

Then it was just a matter of replacing the old commands to the new ones for defining dataset and image fusion etc.

[ScientistRachel]

Updating to the new multiview-reconstruction-4.3.5-SNAPSHOT.jar that is described in the image.sc post also fixed my issue with loading xml files on a PC.

I still have the error described at the end of the linked post: fusion to a BDV compatible pair of files fails. If I fuse to n5 + xml, the n5 folder structure appear to be made correctly, but the xml file is not updated and generates a lot of errors on the console. If fuse to hdf5 + xml, the process fails after making a ~8 kb h5 file and a very incomplete ~2 kb xml.