Help needed with 3D Viewer
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Help needed with 3D Viewer
 
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Dear list
when I use 3D Viewer to view volumes out of an image stack I am not able to shift the view. According to the documentation, you drag with the left mouse button while the hand tool is active. But instead of shifting the object, any movement of the mouse makes the object disappear rapidly to the right, out of the viewer window. You can get it back by 'view>center selected' but it is not shifted. I get the same result, using the bat cochlea sample stack in updated FIJI win 32, lifeline version of 2013 of Fiji win 32 and on lifeline version of 2014 on Fiji win 64 on a more powerful machine. Am I missing any important settings or options that I have to change so that 3D viewer would act as documented? Any useful hints? Thank you so much Christian -- --- Christian Goosmann Mikroskopie Max-Planck-Institut für Infektionsbiologie Campus Charité Mitte Charitéplatz 1 10117 Berlin Tel.: +49 30 28460 388 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Help needed with 3D Viewer
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Found a workaround. Using the arrow keys while holding shift will shift
the view, it is just not possible using the mouse. --- Christian Goosmann Mikroskopie Max-Planck-Institut für Infektionsbiologie Campus Charité Mitte Charitéplatz 1 10117 Berlin Tel.: +49 30 28460 388 Christian Goosmann wrote: > Dear list > when I use 3D Viewer to view volumes out of an image stack I am not > able to shift the view. According to the documentation, you drag with > the left mouse button while the hand tool is active. But instead of > shifting the object, any movement of the mouse makes the object > disappear rapidly to the right, out of the viewer window. You can get > it back by 'view>center selected' but it is not shifted. I get the > same result, using the bat cochlea sample stack in updated FIJI win > 32, lifeline version of 2013 of Fiji win 32 and on lifeline version of > 2014 on Fiji win 64 on a more powerful machine. Am I missing any > important settings or options that I have to change so that 3D viewer > would act as documented? Any useful hints? > Thank you so much > Christian > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Christian,
> instead of shifting the object, any movement of the mouse makes the > object disappear rapidly to the right, out of the viewer window. Until recently, there was a bug in the bug tracker about this: http://fiji.sc/bugzilla/show_bug.cgi?id=432 I just closed it as "works for me", since I couldn't reproduce it. And I still cannot reproduce with an up-to-date Fiji using the Bat Cochlea Volume sample. Maybe it is something about your Java3D installation... Could you have a look at: http://wiki.imagej.net/Debugging_intro#Debugging_Java3D_issues ? Thanks, Curtis On Thu, Jun 19, 2014 at 6:09 AM, Christian Goosmann < [hidden email]> wrote: > Found a workaround. Using the arrow keys while holding shift will shift > the view, it is just not possible using the mouse. > > > --- > Christian Goosmann > Mikroskopie > Max-Planck-Institut für Infektionsbiologie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > Tel.: +49 30 28460 388 > > Christian Goosmann wrote: > >> Dear list >> when I use 3D Viewer to view volumes out of an image stack I am not able >> to shift the view. According to the documentation, you drag with the left >> mouse button while the hand tool is active. But instead of shifting the >> object, any movement of the mouse makes the object disappear rapidly to the >> right, out of the viewer window. You can get it back by 'view>center >> selected' but it is not shifted. I get the same result, using the bat >> cochlea sample stack in updated FIJI win 32, lifeline version of 2013 of >> Fiji win 32 and on lifeline version of 2014 on Fiji win 64 on a more >> powerful machine. Am I missing any important settings or options that I >> have to change so that 3D viewer would act as documented? Any useful hints? >> Thank you so much >> Christian >> >> > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Christian,
> Can you confirm from reading the console output, whether I did the > diagnose mode right? If not, how do I use the command line correctly? Unfortunately, not really. I am not an expert on the 3D Viewer code. That wiki page I linked before covers more than I know personally. > It seems that 3D-Viewer is unable to read the ImageJ_3D_Viewer.props > file. The reason is probably that I work in a network with remote > storage of the personal profile. Can't you use "Map network drive" to assign a drive letter to that share, so that it behaves more like a local filesystem as far as your applications are concerned? This will especially help Java applications like ImageJ! > In this case, the Java function "system.get.property(user.home)" > returns nonsense. Unfortunately, Fiji uses this java function to > determine where to write some user settings. Johannes and Stefan > discussed this in Bug 187 and implemented a clever function that would > allow the user to specify a storage folder for settings through an > environment variable. This function from 2010 has been missing in all > more modern versions of Fiji since a year or so. Actually, the function to which you refer -- setting the IJ_PREFS_DIR to override where settings are stored -- is still supposed to work: https://github.com/imagej/ij1-patcher/blob/ij1-patcher-0.10.0/src/main/java/net/imagej/patcher/LegacyExtensions.java#L215-L222 If you are setting that environment variable and it is not taking effect, please file a bug using Help > Report a Bug. > I would assume that 3D Viewer uses default settings as soon as the > file cannot be read and so I am a bit doubtful whether this issue > would be the reason for the strange behavior of 3DViewer. I agree; I am skeptical of the preferences issue being the cause. More likely is an issue with your graphics card driver. I assume the "Test Java3D" plugin works? (http://fiji.sc/Test_Java3D) Is there a newer graphics card driver you can install? Or if you boot with a Linux live CD such as Ubuntu Desktop, can you use the 3D Viewer successfully in that environment? Regards, Curtis On Thu, Jun 26, 2014 at 8:36 AM, Christian Goosmann < [hidden email]> wrote: > ||Hi Curtis, > thanks for responding. Cool that I was not the only one experiencing this. > Next time I will search the bug tracker too and not just the list. I did > try to get the debugging mode to run and I got some output I don't really > know how to interpret. Here's the content of the console window from the > starting command until opening 3D Viewer from Fijis plugin menu. > > ImageJ-win32.exe -Dj3d.debug=true-- --console > > d:\Fiji Backup\fiji-lifeline02jun14\Fiji.app>[INFO] Found 677 plugins. > log4j:WARN No appenders could be found for logger > (org.bushe.swing.event.EventSe > rvice). > log4j:WARN Please initialize the log4j system properly. > log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for > more in > fo. > [INFO] Found 11 DataType plugins. > [INFO] Found 2 Platform plugins. > [INFO] Configuring platform: org.scijava.plugins.platforms. > windows.WindowsPlatfo > rm > [INFO] Configuring platform: org.scijava.platform.DefaultPlatform > [INFO] Found 0 scripts > [WARNING] Overridden plugin ij.plugin.AboutBox is blacklisted > [WARNING] Overridden plugin ij.plugin.LutLoader("3-3-2 RGB") is blacklisted > [WARNING] Overridden plugin ij.plugin.Commands("quit") is blacklisted > [INFO] Found 668 legacy plugins (plus 147 ignored). > [INFO] Found 22 InputWidget plugins. > version = 1.5 > \\fileserver\profiles$\Desktop\.ImageJ_3D_Viewer.props (Das System kann > die ange > gebene Datei nicht finden) > nFrames = 1 > > Can you confirm from reading the console output, whether I did the > diagnose mode right? If not, how do I use the command line correctly? > It seems that 3D-Viewer is unable to read the ImageJ_3D_Viewer.props > file. The reason is probably that I work in a network with remote storage > of the personal profile. In this case, the Java function > "system.get.property(user.home)" returns nonsense. Unfortunately, Fiji > uses this java function to determine where to write some user settings. > Johannes and Stefan discussed this in Bug 187 and implemented a clever > function that would allow the user to specify a storage folder for settings > through an environment variable. This function from 2010 has been missing > in all more modern versions of Fiji since a year or so. It hasn't created > serious problems, because I haven't run into anything yet that just doesn't > work without the saved settings. > > I would assume that 3D Viewer uses default settings as soon as the file > cannot be read and so I am a bit doubtful whether this issue would be the > reason for the strange behavior of 3DViewer. When I have the time I shall > try to reproduce on a machine in local mode where Fiji is able to save the > settings. If that should do the trick I will let you guys know and send a > new bug report. > Best regards > Christian > > > > Christian Goosmann Mikroskopie Max-Planck-Institut für Infektionsbiologie > Campus Charité Mitte Charitéplatz 1 10117 Berlin Tel.: +49 30 28460 388 > Curtis Rueden wrote: > >> Hi Christian, >> >> > instead of shifting the object, any movement of the mouse makes the >> > object disappear rapidly to the right, out of the viewer window. >> >> Until recently, there was a bug in the bug tracker about this: >> >> http://fiji.sc/bugzilla/show_bug.cgi?id=432 >> >> I just closed it as "works for me", since I couldn't reproduce it. >> >> And I still cannot reproduce with an up-to-date Fiji using the Bat >> Cochlea Volume sample. >> >> Maybe it is something about your Java3D installation... >> >> Could you have a look at: >> http://wiki.imagej.net/Debugging_intro#Debugging_Java3D_issues >> ? >> >> Thanks, >> Curtis >> >> >> On Thu, Jun 19, 2014 at 6:09 AM, Christian Goosmann < >> [hidden email] <mailto:[hidden email]>> >> wrote: >> >> Found a workaround. Using the arrow keys while holding shift will >> shift the view, it is just not possible using the mouse. >> >> >> --- >> Christian Goosmann >> Mikroskopie >> Max-Planck-Institut für Infektionsbiologie >> Campus Charité Mitte >> Charitéplatz 1 >> 10117 Berlin >> Tel.: +49 30 28460 388 <tel:%2B49%2030%2028460%20388> >> >> >> Christian Goosmann wrote: >> >> Dear list >> when I use 3D Viewer to view volumes out of an image stack I >> am not able to shift the view. According to the documentation, >> you drag with the left mouse button while the hand tool is >> active. But instead of shifting the object, any movement of >> the mouse makes the object disappear rapidly to the right, out >> of the viewer window. You can get it back by 'view>center >> selected' but it is not shifted. I get the same result, using >> the bat cochlea sample stack in updated FIJI win 32, lifeline >> version of 2013 of Fiji win 32 and on lifeline version of 2014 >> on Fiji win 64 on a more powerful machine. Am I missing any >> important settings or options that I have to change so that 3D >> viewer would act as documented? Any useful hints? >> Thank you so much >> Christian >> >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> >> > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Christian,
> The fact that I can see the same behaviour on an old 2 core system > with onboard graphics and on the most modern workstation we have, > makes it seem less likely that it would be a graphics driver problem > though. That is fair, although it is definitely machine-specific since we are unable to reproduce the bug on several different machines here. > Second, the save preference problem: Good that you mention the > solution should still be in place. I will file a bug report because it > is not taking effect on my Fiji 1.49b though I did set the environment > variable. Great, that is the best way to make sure the bug is not forgotten. Regards, Curtis On Thu, Jul 17, 2014 at 3:45 AM, Christian Goosmann < [hidden email]> wrote: > Hi Curtis > thanks a lot for getting back once more. > About the 3D Viewer: I am not too worried about it any more, ever since I > found out that it works perfect, when I use the arrow keys for shifting > instead of the mouse. The fact that I can see the same behaviour on an old > 2 core system with onboard graphics and on the most modern workstation we > have, makes it seem less likely that it would be a graphics driver problem > though. > Second, the save preference problem: Good that you mention the solution > should still be in place. I will file a bug report because it is not taking > effect on my Fiji 1.49b though I did set the environment variable. > Thanks so much for all your work. > Best regards > Christian > > > --- > Christian Goosmann > Mikroskopie > Max-Planck-Institut für Infektionsbiologie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > Tel.: +49 30 28460 388 > > Curtis Rueden wrote: > >> Hi Christian, >> >> > Can you confirm from reading the console output, whether I did the >> > diagnose mode right? If not, how do I use the command line correctly? >> >> Unfortunately, not really. I am not an expert on the 3D Viewer code. That >> wiki page I linked before covers more than I know personally. >> >> > It seems that 3D-Viewer is unable to read the ImageJ_3D_Viewer.props >> > file. The reason is probably that I work in a network with remote >> > storage of the personal profile. >> >> Can't you use "Map network drive" to assign a drive letter to that share, >> so that it behaves more like a local filesystem as far as your applications >> are concerned? This will especially help Java applications like ImageJ! >> >> > In this case, the Java function "system.get.property(user.home)" >> > returns nonsense. Unfortunately, Fiji uses this java function to >> > determine where to write some user settings. Johannes and Stefan >> > discussed this in Bug 187 and implemented a clever function that would >> > allow the user to specify a storage folder for settings through an >> > environment variable. This function from 2010 has been missing in all >> > more modern versions of Fiji since a year or so. >> >> Actually, the function to which you refer -- setting the IJ_PREFS_DIR to >> override where settings are stored -- is still supposed to work: >> >> https://github.com/imagej/ij1-patcher/blob/ij1-patcher-0.10. >> 0/src/main/java/net/imagej/patcher/LegacyExtensions.java#L215-L222 >> >> If you are setting that environment variable and it is not taking effect, >> please file a bug using Help > Report a Bug. >> >> > I would assume that 3D Viewer uses default settings as soon as the >> > file cannot be read and so I am a bit doubtful whether this issue >> > would be the reason for the strange behavior of 3DViewer. >> >> I agree; I am skeptical of the preferences issue being the cause. More >> likely is an issue with your graphics card driver. I assume the "Test >> Java3D" plugin works? (http://fiji.sc/Test_Java3D) >> >> Is there a newer graphics card driver you can install? Or if you boot >> with a Linux live CD such as Ubuntu Desktop, can you use the 3D Viewer >> successfully in that environment? >> >> Regards, >> Curtis >> >> >> On Thu, Jun 26, 2014 at 8:36 AM, Christian Goosmann < >> [hidden email] <mailto:[hidden email]>> >> wrote: >> >> ||Hi Curtis, >> thanks for responding. Cool that I was not the only one >> experiencing this. Next time I will search the bug tracker too and >> not just the list. I did try to get the debugging mode to run and >> I got some output I don't really know how to interpret. Here's the >> content of the console window from the starting command until >> opening 3D Viewer from Fijis plugin menu. >> >> ImageJ-win32.exe -Dj3d.debug=true-- --console >> >> d:\Fiji Backup\fiji-lifeline02jun14\Fiji.app>[INFO] Found 677 >> plugins. >> log4j:WARN No appenders could be found for logger >> (org.bushe.swing.event.EventSe >> rvice). >> log4j:WARN Please initialize the log4j system properly. >> log4j:WARN See >> http://logging.apache.org/log4j/1.2/faq.html#noconfig for more in >> fo. >> [INFO] Found 11 DataType plugins. >> [INFO] Found 2 Platform plugins. >> [INFO] Configuring platform: >> org.scijava.plugins.platforms.windows.WindowsPlatfo >> rm >> [INFO] Configuring platform: org.scijava.platform.DefaultPlatform >> [INFO] Found 0 scripts >> [WARNING] Overridden plugin ij.plugin.AboutBox is blacklisted >> [WARNING] Overridden plugin ij.plugin.LutLoader("3-3-2 RGB") is >> blacklisted >> [WARNING] Overridden plugin ij.plugin.Commands("quit") is blacklisted >> [INFO] Found 668 legacy plugins (plus 147 ignored). >> [INFO] Found 22 InputWidget plugins. >> version = 1.5 >> \\fileserver\profiles$\Desktop\.ImageJ_3D_Viewer.props (Das System >> kann die ange >> gebene Datei nicht finden) >> nFrames = 1 >> >> Can you confirm from reading the console output, whether I did the >> diagnose mode right? If not, how do I use the command line correctly? >> It seems that 3D-Viewer is unable to read the >> ImageJ_3D_Viewer.props file. The reason is probably that I work in >> a network with remote storage of the personal profile. In this >> case, the Java function "system.get.property(user.home)" returns >> nonsense. Unfortunately, Fiji uses this java function to determine >> where to write some user settings. Johannes and Stefan discussed >> this in Bug 187 and implemented a clever function that would allow >> the user to specify a storage folder for settings through an >> environment variable. This function from 2010 has been missing in >> all more modern versions of Fiji since a year or so. It hasn't >> created serious problems, because I haven't run into anything yet >> that just doesn't work without the saved settings. >> >> I would assume that 3D Viewer uses default settings as soon as the >> file cannot be read and so I am a bit doubtful whether this issue >> would be the reason for the strange behavior of 3DViewer. When I >> have the time I shall try to reproduce on a machine in local mode >> where Fiji is able to save the settings. If that should do the >> trick I will let you guys know and send a new bug report. >> Best regards >> Christian >> >> >> >> Christian Goosmann Mikroskopie Max-Planck-Institut für >> Infektionsbiologie Campus Charité Mitte Charitéplatz 1 10117 >> Berlin Tel.: +49 30 28460 388 <tel:%2B49%2030%2028460%20388> >> >> Curtis Rueden wrote: >> >> Hi Christian, >> >> > instead of shifting the object, any movement of the mouse >> makes the >> > object disappear rapidly to the right, out of the viewer window. >> >> Until recently, there was a bug in the bug tracker about this: >> >> http://fiji.sc/bugzilla/show_bug.cgi?id=432 >> >> I just closed it as "works for me", since I couldn't reproduce it. >> >> And I still cannot reproduce with an up-to-date Fiji using the >> Bat Cochlea Volume sample. >> >> Maybe it is something about your Java3D installation... >> >> Could you have a look at: >> http://wiki.imagej.net/Debugging_intro#Debugging_Java3D_issues >> ? >> >> Thanks, >> Curtis >> >> >> On Thu, Jun 19, 2014 at 6:09 AM, Christian Goosmann >> <[hidden email] >> <mailto:[hidden email]> >> <mailto:[hidden email] >> >> <mailto:[hidden email]>>> wrote: >> >> Found a workaround. Using the arrow keys while holding >> shift will >> shift the view, it is just not possible using the mouse. >> >> >> --- >> Christian Goosmann >> Mikroskopie >> Max-Planck-Institut für Infektionsbiologie >> Campus Charité Mitte >> Charitéplatz 1 >> 10117 Berlin >> Tel.: +49 30 28460 388 <tel:%2B49%2030%2028460%20388> >> <tel:%2B49%2030%2028460%20388> >> >> >> Christian Goosmann wrote: >> >> Dear list >> when I use 3D Viewer to view volumes out of an image >> stack I >> am not able to shift the view. According to the >> documentation, >> you drag with the left mouse button while the hand tool is >> active. But instead of shifting the object, any >> movement of >> the mouse makes the object disappear rapidly to the >> right, out >> of the viewer window. You can get it back by 'view>center >> selected' but it is not shifted. I get the same >> result, using >> the bat cochlea sample stack in updated FIJI win 32, >> lifeline >> version of 2013 of Fiji win 32 and on lifeline version >> of 2014 >> on Fiji win 64 on a more powerful machine. Am I >> missing any >> important settings or options that I have to change so >> that 3D >> viewer would act as documented? Any useful hints? >> Thank you so much >> Christian >> >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> >> >> >> > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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