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nolanlab / vortex

VorteX Clustering Environment - Java graphical tool for single-cell analysis, clustering and visualization. Latest release:
https://github.com/nolanlab/vortex/releases
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"export images" not working from MST or FDL plot windows #22

Closed Andrew-InTheBox closed 5 years ago

Andrew-InTheBox commented 5 years ago

I've noticed and seen on two of my vortex installations recently that export images no longer does anything after making spanning tree for force directed graph layouts. I've re-installed the newest version of vortex, and don't see any other java versions installed, but suspect it could be related to java VMs present from flowjo, since I also have noticed odd flowjo behavior when java 8 x64 is present. But that is just a guess.

Any known issues that could cause this behavior? It worked in the past on both these workstations, but many things change b/c they're used by several individuals for cytometry analysis work unfortunately.

vishal266 commented 5 years ago

Hi @nsamusik , Please help out Andy

Andrew-InTheBox commented 5 years ago

Update - I removed flowjo, used the java uninstall tool, then re-installed java 8 x64 using the link recommended in the wiki here. Does not restore normal operation. Also, testing saving to network vs local with short path name, neither works. Thanks.

nsamusik commented 5 years ago

Thanks Vishal, I saw this. I will address this as a part of the VorteX March Overhaul. On Wed, Feb 27, 2019 at 12:24 PM vishal266 notifications@github.com wrote:

Hi @nsamusik https://github.com/nsamusik , Please help out Andy

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Andrew-InTheBox commented 5 years ago

Thanks. Do others have this issue? If not, I can focus more intensely on something related to our environment that may be at fault. I tried rolling back to the June 2017 version of Xshift, but still have the problem, so it doesn't seem to be a newly introduced bug per se.

Andrew-InTheBox commented 5 years ago

Here's Vortex.log information from attempting to save the images.

java.io.FileNotFoundException: C:\Users\acb\Desktop\NilssonTemp\Nillson_TopS_"CD10"-"CD10".png (The filename, directory name, or volume label syntax is incorrect) at java.io.RandomAccessFile.open0(Native Method) at java.io.RandomAccessFile.open(Unknown Source) at java.io.RandomAccessFile.<init>(Unknown Source) at javax.imageio.stream.FileImageOutputStream.<init>(Unknown Source) at com.sun.imageio.spi.FileImageOutputStreamSpi.createOutputStreamInstance(Unknown Source) at javax.imageio.ImageIO.createImageOutputStream(Unknown Source) at javax.imageio.ImageIO.write(Unknown Source) at vortex.clustergraph.frmGraph.cmdExportActionPerformed(frmGraph.java:1240) at vortex.clustergraph.frmGraph.access$800(frmGraph.java:102) at vortex.clustergraph.frmGraph$8.actionPerformed(frmGraph.java:885) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at javax.imageio.ImageIO.write(Unknown Source) at vortex.clustergraph.frmGraph.cmdExportActionPerformed(frmGraph.java:1240) at vortex.clustergraph.frmGraph.access$800(frmGraph.java:102) at vortex.clustergraph.frmGraph$8.actionPerformed(frmGraph.java:885) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source)

Andrew-InTheBox commented 5 years ago

@nsamusik @vishal266 Please close the issue, it's my data. It turns out all the files I've been working with lately have come from R write.csv() functions, which is putting column names in quotes, and breaking image export because it ends up putting strange characters in the exported file names for the png images (see log file above).

In theory, handling quoted column names differently could be useful, as this is the default behavior of R 'write.csv', but also easy to fix via "quote = FALSE" in R as arg to write.csv.

Sorry for the trouble.

nsamusik commented 5 years ago

Hi Andrew,

I looked at the logs and that was my impression too

I will modify Vortex code to make sure it trims away those quotes during the import

Thank you for catching the bug

Nikolay

On Mon, Mar 4, 2019 at 12:58 PM Andrew Box notifications@github.com wrote:

@nsamusik https://github.com/nsamusik @vishal266 https://github.com/vishal266 Please close the issue, it's my data. It turns out all the files I've been working with lately have come from R write.csv() functions, which is putting column names in quotes, and breaking image export because it ends up putting strange characters in the exported file names for the png images (see log file above).

In theory, handling quoted column names differently could be useful, as this is the default behavior of R 'write.csv', but also easy to fix via "quote = FALSE" in R as arg to write.csv.

Sorry for the trouble.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nolanlab/vortex/issues/22#issuecomment-469418828, or mute the thread https://github.com/notifications/unsubscribe-auth/ADacL0bksclmhmgTqFIXbvDXMiqccKTPks5vTYjSgaJpZM4bVTcm .