Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

plugions -> bdv menu -> export SPIM as remote xml/n5 #11

Open
xulman opened this issue Apr 29, 2022 · 1 comment
Open

plugions -> bdv menu -> export SPIM as remote xml/n5 #11

xulman opened this issue Apr 29, 2022 · 1 comment

Comments

@xulman
Copy link
Member

xulman commented Apr 29, 2022

(Fiji Is Just) ImageJ 2.3.0/1.53q; Java 1.8.0_172 [64-bit]; Linux 5.3.18-lp152.106-default; 108MB of 11042MB (<1%)
 
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:307)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:166)
	at ij.IJ.runPlugIn(IJ.java)
	at ij.Executer.runCommand(Executer.java:152)
	at ij.Executer.run(Executer.java:70)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:303)
	... 5 more
Caused by: java.lang.RuntimeException: Module threw exception
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	... 1 more
Caused by: java.lang.RuntimeException: java.net.ConnectException: Connection refused (Connection refused)
	at bdv.img.remote.XmlIoRemoteImageLoader.fromXml(XmlIoRemoteImageLoader.java:66)
	at bdv.img.remote.XmlIoRemoteImageLoader.fromXml(XmlIoRemoteImageLoader.java:43)
	at mpicbg.spim.data.generic.sequence.XmlIoAbstractSequenceDescription.fromXml(XmlIoAbstractSequenceDescription.java:111)
	at mpicbg.spim.data.generic.XmlIoAbstractSpimData.fromXml(XmlIoAbstractSpimData.java:153)
	at mpicbg.spim.data.generic.XmlIoAbstractSpimData.load(XmlIoAbstractSpimData.java:95)
	at cz.it4i.fiji.datastore.ij.ExportSPIMAsN5PlugIn$ParameterConstructor.tryLoadSPIMData(ExportSPIMAsN5PlugIn.java:570)
	at cz.it4i.fiji.datastore.ij.ExportSPIMAsN5PlugIn$ParameterConstructor.getParameters(ExportSPIMAsN5PlugIn.java:347)
	at cz.it4i.fiji.datastore.ij.ExportSPIMAsN5PlugIn.run(ExportSPIMAsN5PlugIn.java:100)
	at org.scijava.command.CommandModule.run(CommandModule.java:196)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
	... 6 more
Caused by: java.net.ConnectException: Connection refused (Connection refused)
	at java.net.PlainSocketImpl.socketConnect(Native Method)
	at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
	at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
	at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
	at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
	at java.net.Socket.connect(Socket.java:589)
	at java.net.Socket.connect(Socket.java:538)
	at sun.net.NetworkClient.doConnect(NetworkClient.java:180)
	at sun.net.www.http.HttpClient.openServer(HttpClient.java:463)
	at sun.net.www.http.HttpClient.openServer(HttpClient.java:558)
	at sun.net.www.http.HttpClient.<init>(HttpClient.java:242)
	at sun.net.www.http.HttpClient.New(HttpClient.java:339)
	at sun.net.www.http.HttpClient.New(HttpClient.java:357)
	at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1220)
	at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1156)
	at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1050)
	at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:984)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1564)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at java.net.URL.openStream(URL.java:1045)
	at bdv.img.remote.RemoteImageLoader.open(RemoteImageLoader.java:112)
	at bdv.img.remote.RemoteImageLoader.<init>(RemoteImageLoader.java:86)
	at bdv.img.remote.RemoteImageLoader.<init>(RemoteImageLoader.java:78)
	at bdv.img.remote.XmlIoRemoteImageLoader.fromXml(XmlIoRemoteImageLoader.java:62)
	... 16 more
@xulman
Copy link
Member Author

xulman commented Apr 29, 2022

strangely, plugins -> HPC Datastore -> Create -> create new from xml/hdf5 works well
(while it is effectively the same code as above...)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant