Exporting to MaMut file fails when there isn't an image.

[odinsbane]

When I create an project from an open imagej window, then I go to export the tracks to a MaMut file I get the following error.

java.io.FileNotFoundException: C:\Users\Username\tools\fiji\Fiji.app\Untitled (The system cannot find the file specified)
        at java.base/java.io.FileInputStream.open0(Native Method)
        at java.base/java.io.FileInputStream.open(FileInputStream.java:213)
        at java.base/java.io.FileInputStream.<init>(FileInputStream.java:152)
        at java.base/java.io.FileInputStream.<init>(FileInputStream.java:106)
        at java.base/sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:84)
        at java.base/sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:180)
        at org.apache.xerces.impl.XMLEntityManager.setupCurrentEntity(Unknown Source)
        at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
        at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
        at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:217)
        at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:329)
        at org.jdom2.input.SAXBuilder.build(SAXBuilder.java:1254)
        at org.mastodon.mamut.io.importer.trackmate.MamutExporter.getSAXParsedDocument(MamutExporter.java:645)

There is a warning when creating the project, about the image not being found on disk. Is there a way to fix my project, so that I can export to a MaMut file, or do I need to start from an image on disk.

Thank you

[stefanhahmann]

or do I need to start from an image on disk.

Without having tried to reproduce the problem, the stack trace reads to me as, if do I need to start from an image on disk could be the solution to your problem. Can you try that?

[odinsbane]

That does not solve the problem.

You are correct in your assessment. When I start a new mastodon project based on a image on disk, then an xml file gets written at the beginning and after I create some tracks I can export the resulting tracks to a MaMut file. Everything works fine.

The problem is, if I start from an open image I can create the tracks, but I cannot export them to a mamut file.

I think this is an issue, because when I try to export there is an error that seems to be from a lack of a settings xml file. The error message doesn't say anything that might help fix the problem. Either start from an image or disk, or do something else that would allow me to export the Mamut file without having to recreate the tracking data.

[odinsbane]

One reason I want to work without saving the image file is related to this issue when I use the multichannel image the preview only shows me the first channel. I want to segment the 4th channel. I can select it, and it will detect spots in the appropriate channel, but the preview shows a different channel. I checked with the BDV and the normal BDV interface lets you select the source(s) for display.

I though I could get around this by duplicating my channel of interest, then start a mastodon project for the channel I want to see. I need to save the channel as a separate image, or I cannot export the resulting tracks.

[tinevez]

Hello @odinsbane
It is true that you will get an error this way: MaMuT and exporting to MaMuT requires the image data to be saved as a XML file.
When you annotate an image that is not saved, there is no path to inspect, hence the crash.
What do you think Mastodon should do in this case?

[odinsbane]

I have two suggestions

• Let the user fix the issue some how. "Warning BDV xml is not found, please save the mastodon project and create a bdv source"
• Let the user export to a trackmate xml compatible file, possibly with the same warning given when saving the mastodon project.

I think both of these solutions let the user know what is going on, and offer them a fix if possible.

Ill include the reasoning below.

For a general fiji user, it is a bit confusing. I think a naive attempt at working from a fiji/imagej plugin overview it is natural to start fiji, open your image, then start a plugin. Which you can do in mastodon, but then trying to export to a MaMut file will cause an exception, and it isn't clear why.

Who wants to create MaMut file? Maybe this puts me in a special category, where people who want a MaMut file should know enough this isn't a big issue. I originally targeted trackmate files, (works great thank you!) then it turns out MaMut files also work as trackmate files (also a big thanks). That's why I wonder if it would be possible to export a handicapped version, since I don't use the xml settings anyways.