[Bug 590] New: TIA Reader not installing
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bugz...@fiji.sc
Apr 19, 2013, 1:54:06 PM4/19/13
to fiji-...@googlegroups.com
| Bug ID | 590 |
|---|---|
| Summary | TIA Reader not installing |
| Classification | Unclassified |
| Product | Fiji |
| Version | unspecified |
| Hardware | PC |
| OS | Windows |
| Status | NEW |
| Severity | normal |
| Priority | P4 |
| Component | Plugins |
| Assignee | fiji-...@googlegroups.com |
| Reporter | hans...@niaid.nih.gov |
| CC | hans...@niaid.nih.gov |
Hi, I downloaded the TIA_Reader.jar and put it in the plugins folder, but when I restart fiji it doesn't install. Not sure if the file is corrupted, but it simply won't work. Information about your version of Java: os.arch => amd64 os.name => Windows 7 os.version => 6.1 java.version => 1.6.0_24 java.vendor => Sun Microsystems Inc. java.runtime.name => Java(TM) SE Runtime Environment java.runtime.version => 1.6.0_24-b07 java.vm.name => Java HotSpot(TM) 64-Bit Server VM java.vm.version => 19.1-b02 java.vm.vendor => Sun Microsystems Inc. java.vm.info => mixed mode java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment java.specification.name => Java Platform API Specification java.specification.version => 1.6 sun.cpu.endian => little sun.desktop => windows file.separator => \ The up-to-date check says: UP_TO_DATE Information relevant to JAVA_HOME related problems: JAVA_HOME is set to: C:\Users\HANSEN~1\Desktop\Fiji.app/java/win64/jdk1.6.0_24/jre/ ij.dir => C:\Users\HANSEN~1\Desktop\Fiji.app Information about the version of each plugin: 018c76c3fbfc41a7dd3f7c2ac5cd7cbbde8dc21b:018c76c3fbfc41a7dd3f7c2ac5cd7cbbde8dc21b:018c76c3fbfc41a7dd3f7c2ac5cd7cbbde8dc21b 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20130419104615 plugins/Scripts/Plugins/Utilities/Create_Desktop_Icon.bsh b5ee58a22e88116fafb82539fef2281176fe187c 20130419104614 plugins/Scripts/Plugins/Utilities/Find_Jar_For_Class.bsh fc46bd40e7ab175c534bc5bbe71658e3bc3ccd1d 20130419104616 plugins/Scripts/Plugins/Utilities/Record_Desktop.py 9d4d012ab3325fb24ab3ae0957c2aea663c6dd12 20130419104616 plugins/Scripts/Plugins/Utilities/Record_Window.py 36b6b0d091c585ef40aca53c3bf82b6f58b78c76 20130419104736 plugins/Series_Labeler-2.0.0-SNAPSHOT.jar 50ee8cf26b2e4bf1b9774a83d227fae873158ef8 20110307142230 plugins/SheppLogan_.jar 069ebf344bc6f7c431a32d453f3fe136a025e606 20130419104607 plugins/Sholl_Analysis-3.0.0-SNAPSHOT.jar a60f59bea650ca8011ea97363941533256250151 20130419104736 plugins/Simple_Neurite_Tracer-2.0.2-SNAPSHOT.jar 265850b38137898969ca510b0cb1e5e2536f4226 20110307142230 plugins/Siox_Segmentation.jar 34dfe8f4b5518cc3b348ef10ca4f1acae07e1e72 20130419104737 plugins/Skeletonize3D_.jar e71b5942e5343cbc3d591f249cc9f3dfc73c7e29 20110307142230 plugins/Snakuscule_.jar 41d82921719c38520d5472a3608b79394db1b7b0 20110307142230 plugins/SplineDeformationGenerator_.jar b5a0eabcb770437c30575d4ea6f5dbd346b8bd89 20110307142230 plugins/StackReg_.jar 202a7fb92385bce3da4af58179d1459409eb96d7 20130419104504 plugins/Stack_Manipulation.jar 23cae80cce99d71dc4669da51c6909c3a7ca68ca 20110307142230 plugins/Statistical_Region_Merging.jar 16bbe0c22303ff75a1aac4694c2c00177b888318 20130419104546 plugins/Stitching_-2.0.0-SNAPSHOT.jar 6f562f44abb24c381f7b353b427b024dd465a2c7 20130419104303 plugins/Sync_Win.jar b60eef5d020c0e881b4bb97d1579339e1cb2a60e 20110307142230 plugins/Thread_Killer.jar e984a5e3af7b87b718ae82f5c5ba8b36e1665f3b 20130419104303 plugins/Threshold_Colour.jar d822b12368e1df7de1aed0039f285daa7c507723 20130419104627 plugins/Time_Stamper-2.0.0-SNAPSHOT.jar 22fd045b2a57d7ed84b5dcb7b6146484143e36fc 20110307142230 plugins/ToAST_.jar 85cde3427627d577408abbd947525da4d37bc1bd 20130419104629 plugins/TopoJ_.jar e9748aea2548f743a7695a43398cd1ea8de8e6e3 20130419104359 plugins/TrackMate_-2.0.3-SNAPSHOT.jar 0f0b618069dade1115bf3b245586ced7c9219616 20130419104533 plugins/Trainable_Segmentation-2.0.0-SNAPSHOT.jar 48b8264d7be97d82ac4837ce4a19bf154d08cf54 20130419104731 plugins/TrakEM2_.jar 39d4aaafb0c6bea4ef6cdf95bcaf2c4665d9bdc2 20110307142230 plugins/TransformJ_.jar 09868b512410628e06c7dc25a6999c7dda8cf078 20110307142230 plugins/TurboReg_.jar 9558400db089262849c33428a77645c323390145 20110307142230 plugins/UnwarpJ_.jar a32dfe463fa2c8814cb0caf9079478ff4e1c44bf 20110307142230 plugins/Utilities/Close_All_Without_Saving.txt bc18d5f8511074d742235e9396097e264ef1b71c 20130419104643 plugins/VIB_-2.0.0-SNAPSHOT.jar dbea7327d27dac86777079759676492a6c20d509 20130419104259 plugins/Vaa3d_Reader-2.0.0-SNAPSHOT.jar d6cf9638dc212f49fc3d2d4e99ca7aedc78956a2 20110307142230 plugins/Video_Editing.jar f658bff40fb04112a21da67873fbc1e73953f7c5 20130419104550 plugins/View5D_.jar 1f4f9e54835e861f235f58ff6c85479fe8095103 20130419104838 plugins/Volume_Calculator-1.0.1-SNAPSHOT.jar ab3a993a57663edd797891e395f2fca49e4f19a3 20130419104619 plugins/Volume_Viewer-2.01.jar df64e95348d93d638a66bcbcd8de782d1d0956a9 20130419104626 plugins/bUnwarpJ_.jar e7c1c98c51a7a6cc24bdc2591b67b1cf20a6db1b 20130419104535 plugins/blockmatching_.jar 659ad6a335b4947eef8758b1b0cf050779430b78 20110307142230 plugins/ij-ImageIO_.jar 1398b098bf9d094f2dbabe8e7c6ce6fdca8c05ae 20130419104646 plugins/level_sets.jar 8b83ec999bb5ec5ee224a043093b6192f765d98f 20130419104604 plugins/loci_plugins-4.5-SNAPSHOT.jar 5a50a9eb8531ebf052814bb0a0026b662edd4072 20130419104402 plugins/mpicbg_-0.6.0-SNAPSHOT.jar 5e32d936ba53c22ba6b70e5eee3992a361bc2ff8 20110307142230 plugins/panorama_.jar 044f3fef66023d33fc2238491669a0eae280156f 20130419104755 plugins/register_virtual_stack_slices-2.0.0-SNAPSHOT.jar 4d7eaf239c033d305a464a06c3e64c68d096c7e1 20110307142230 plugins/registration_3d.jar e6e0879f5d50afa8d0dd213b4b66e396a39a47b7 20110307142240 retro/backport-util-concurrent-3.1.jar 8759ba201e6dfa1dfc40f34eb5b332a6a73c3516 20130419104252 retro/retrotranslator-runtime-1.2.9.jar a6d5a3b297b4ba3ba2f2d1baa0c5da631fdf86c0 20130419104258 retro/retrotranslator-transformer-1.2.9.jar d7160d38a0b805381cb0c0dcedd60e197e247897 20130419104801 scripts/InstallJava3D.m 05a92a3c3f518ec50976326bf16a8a8858af2183 20130419104802 scripts/IsJava3DInstalled.m ff34d026692414ecd743ba34e828780c8614ea8d 20130419104755 scripts/Matlab3DViewerDemo_1.m 25be149fecd1f6551b9b0ad53946642db65d5a4e 20130419104758 scripts/Matlab3DViewerDemo_2.m cb529b6c4fb0505e6e58f8d18fa8f81fc86ebe82 20130419104801 scripts/Matlab3DViewerDemo_3.m 53d2da73a4a560c41f3c4493d1377c56fe84106c 20130419104756 scripts/Matlab3DViewerIntroduction.m 4bb342fa00a9d96bda9fd36c8e7df515bbfa8b60 20130419104755 scripts/Miji.m 868cd43462fefc57c310656d4b35a028f0bda4f4 20130419104756 scripts/Miji_Test.m d326018044a582f5106efc6fc90ad09f98a6a822 20110307142230 scripts/Record_Desktop.py 0ea7f8fc6683e74065ae7fd82c1b92676e069526 20110307142230 scripts/Record_Window.py dc94c3a32b5edb3106ad7f2c7c68a852d064089a 20130419104755 scripts/bfopen.m
You are receiving this mail because:
- You are the assignee for the bug.
bugz...@fiji.sc
Apr 23, 2013, 1:21:13 PM4/23/13
to fiji-...@googlegroups.com
Johannes Schindelin
changed
bug 590
| What | Removed | Added |
|---|---|---|
| CC | johannes....@gmx.de |
Comment # 1
on bug 590
from Johannes Schindelin
Sorry, I need substantially more details here. For one, please attach the exact TIA_Reader.jar you tried to install to this ticket. Next, please clarify what you mean "it does not install": Do you mean that it throws an exception, that the menu item is missing, that File>Open does not use it? In other words, please specify exactly what you were expecting to see but did not.
![Hansen, Bryan (NIH/NIAID) [F]'s profile photo](http://lh3.googleusercontent.com/a-/ALV-UjWz7Y0F7UCmOV0zCj2Zxc_7zg60dWbHU0jzVksHOiaZ07yHkQ=s40-c)
Hansen, Bryan (NIH/NIAID) [F]
Apr 23, 2013, 3:06:41 PM4/23/13
to bugz...@fiji.sc
Hi,
I have attached the TIA_Reader file that I tried to use. I downloaded it from http://rsbweb.nih.gov/ij/plugins/tia-reader.html . When I say it didn’t install I mean that I moved the .jar file into the plugins folder as described, but when I start fiji TIA_Reader doesn’t show in the plugins list nor does fiji open the files that it should if TIA_Reader was working. I also tried using the install plugin option from the plugins drop down. When I do this I get a message saying TIA_Reader.jar installed successfully, but in the log it says: “C:\Users\HANSEN~1\Desktop\Fiji.app\plugins\TIA_Reader.jar: java.util.zip.ZipException: error in opening zip file” twice. So I can’t open the file type that I should be able to with this plugin because the plugin doesn’t seem to be working. Thank you for your help. Let me know if you need any other information.
Bryan
- You are on the CC list for the bug.
- You reported the bug.
bugz...@fiji.sc
Apr 23, 2013, 3:22:07 PM4/23/13
to fiji-...@googlegroups.com
Curtis Rueden
changed
bug 590
| What | Removed | Added |
|---|---|---|
| CC | ctru...@wisc.edu |
Comment # 2
on bug 590
from Curtis Rueden
Bryan Hansen wrote (to fiji-devel):
> I downloaded TIA_Reader from
> http://rsbweb.nih.gov/ij/plugins/tia-reader.html . When I say it
> didn’t install I mean that I moved the .jar file into the plugins
> folder as described, but when I start fiji TIA_Reader doesn’t show in
> the plugins list nor does fiji open the files that it should if
> TIA_Reader was working. I also tried using the install plugin option
> from the plugins drop down. When I do this I get a message saying
> TIA_Reader.jar installed successfully, but in the log it says:
> “C:\Users\HANSEN~1\Desktop\Fiji.app\plugins\TIA_Reader.jar:
> java.util.zip.ZipException: error in opening zip file” twice. So I
> can’t open the file type that I should be able to with this plugin
> because the plugin doesn’t seem to be working. Thank you for your
> help. Let me know if you need any other information.
I tried to reproduce, but all works as expected on my system. Bryan, it sounds
like your file was corrupted during download. Is your copy of TIA_Reader.jar
71,837 bytes in size?
Hansen, Bryan (NIH/NIAID) [F]
Apr 23, 2013, 3:26:31 PM4/23/13
to bugz...@fiji.sc
Interesting. Did you use the .jar that I had attached or did you download another copy from the website? I attached the exact .jar file that is in my plugins folder. That one does appear to be 71 MB in size though. If the plugin isn't the problem what other things might give the error from the log?
Bryan
________________________________
From: bugz...@fiji.sc [bugz...@fiji.sc]
Sent: Tuesday, April 23, 2013 1:22 PM
Comment # 2<http://fiji.sc/bugzilla/show_bug.cgi?id=590#c2> on bug 590<http://fiji.sc/bugzilla/show_bug.cgi?id=590> from Curtis Rueden<mailto:ctru...@wisc.edu>
Bryan Hansen wrote (to fiji-devel):
> I downloaded TIA_Reader from
> http://rsbweb.nih.gov/ij/plugins/tia-reader.html . When I say it
> didn’t install I mean that I moved the .jar file into the plugins
> folder as described, but when I start fiji TIA_Reader doesn’t show in
> the plugins list nor does fiji open the files that it should if
> TIA_Reader was working. I also tried using the install plugin option
> from the plugins drop down. When I do this I get a message saying
> TIA_Reader.jar installed successfully, but in the log it says:
> “C:\Users\HANSEN~1\Desktop\Fiji.app\plugins\TIA_Reader.jar:
> java.util.zip.ZipException: error in opening zip file” twice. So I
> can’t open the file type that I should be able to with this plugin
> because the plugin doesn’t seem to be working. Thank you for your
> help. Let me know if you need any other information.
I tried to reproduce, but all works as expected on my system. Bryan, it sounds
like your file was corrupted during download. Is your copy of TIA_Reader.jar
71,837 bytes in size?
________________________________
You are receiving this mail because:
* You are on the CC list for the bug.
* You reported the bug.
Bryan
________________________________
From: bugz...@fiji.sc [bugz...@fiji.sc]
Sent: Tuesday, April 23, 2013 1:22 PM
To: Hansen, Bryan (NIH/NIAID) [F]
Subject: [Bug 590] TIA Reader not installing
Curtis Rueden<mailto:ctru...@wisc.edu> changed bug 590<http://fiji.sc/bugzilla/show_bug.cgi?id=590>
Subject: [Bug 590] TIA Reader not installing
Comment # 2<http://fiji.sc/bugzilla/show_bug.cgi?id=590#c2> on bug 590<http://fiji.sc/bugzilla/show_bug.cgi?id=590> from Curtis Rueden<mailto:ctru...@wisc.edu>
Bryan Hansen wrote (to fiji-devel):
> I downloaded TIA_Reader from
> http://rsbweb.nih.gov/ij/plugins/tia-reader.html . When I say it
> didn’t install I mean that I moved the .jar file into the plugins
> folder as described, but when I start fiji TIA_Reader doesn’t show in
> the plugins list nor does fiji open the files that it should if
> TIA_Reader was working. I also tried using the install plugin option
> from the plugins drop down. When I do this I get a message saying
> TIA_Reader.jar installed successfully, but in the log it says:
> “C:\Users\HANSEN~1\Desktop\Fiji.app\plugins\TIA_Reader.jar:
> java.util.zip.ZipException: error in opening zip file” twice. So I
> can’t open the file type that I should be able to with this plugin
> because the plugin doesn’t seem to be working. Thank you for your
> help. Let me know if you need any other information.
I tried to reproduce, but all works as expected on my system. Bryan, it sounds
like your file was corrupted during download. Is your copy of TIA_Reader.jar
71,837 bytes in size?
________________________________
You are receiving this mail because:
* You reported the bug.
Johannes Schindelin
Apr 23, 2013, 4:46:51 PM4/23/13
to Hansen, Bryan (NIH/NIAID) [F], bugz...@fiji.sc
Hi Bryan,
On Tue, 23 Apr 2013, Hansen, Bryan (NIH/NIAID) [F] wrote:
> Interesting. Did you use the .jar that I had attached or did you
> download another copy from the website? I attached the exact .jar file
> that is in my plugins folder. That one does appear to be 71 MB in size
> though. If the plugin isn't the problem what other things might give
> the error from the log?
Please understand that all your mail replies are stuck on the mailing
list. The ticket looks as if you did not care to respond:
http://fiji.sc/bugzilla/show_bug.cgi?id=590
;-)
Ciao,
Johannes
On Tue, 23 Apr 2013, Hansen, Bryan (NIH/NIAID) [F] wrote:
> Interesting. Did you use the .jar that I had attached or did you
> download another copy from the website? I attached the exact .jar file
> that is in my plugins folder. That one does appear to be 71 MB in size
> though. If the plugin isn't the problem what other things might give
> the error from the log?
list. The ticket looks as if you did not care to respond:
http://fiji.sc/bugzilla/show_bug.cgi?id=590
;-)
Ciao,
Johannes
Hansen, Bryan (NIH/NIAID) [F]
Apr 23, 2013, 5:15:52 PM4/23/13
to Johannes Schindelin, bugz...@fiji.sc
Ok....good to know. How/what do I need to put in the ticket? I just tried to upload my TIA_Reader.jar file, but even though when I downloaded it there was a size now that I've opened Fiji and closed it the file has no size. So if my .jar file is corrupted how can I get a non-corrupt one or how do I need to download so it doesn't get corrupted?
Bryan
-----Original Message-----
From: Johannes Schindelin [mailto:Johannes....@gmx.de]
Sent: Tuesday, April 23, 2013 2:47 PM
To: Hansen, Bryan (NIH/NIAID) [F]
Bryan
-----Original Message-----
From: Johannes Schindelin [mailto:Johannes....@gmx.de]
Sent: Tuesday, April 23, 2013 2:47 PM
To: Hansen, Bryan (NIH/NIAID) [F]
Hansen, Bryan (NIH/NIAID) [F]
Apr 23, 2013, 5:23:36 PM4/23/13
to Johannes Schindelin, bugz...@fiji.sc
So....I went to the site below clicked add new comment to try and update the thread, and it just took me to the top of the page. I was going to put in my comment in the additional comment section, but I didn't want to save the comment as fixed. Any suggestion?
Sent: Tuesday, April 23, 2013 2:47 PM
To: Hansen, Bryan (NIH/NIAID) [F]
To: Hansen, Bryan (NIH/NIAID) [F]
Curtis Rueden
Apr 23, 2013, 5:40:41 PM4/23/13
to Hansen, Bryan (NIH/NIAID) [F], Johannes Schindelin, bugz...@fiji.sc
Hi Bryan,
> I was going to put in my comment in the additional comment section,
> but I didn't want to save the comment as fixed.
Don't worry, it will not save it as FIXED unless you also change the status to RESOLVED.
Regarding your problem with TIA_Reader, one other thing you could try: rename the file from TIA_Reader.jar to TIA_Reader.zip (they are the same thing) and see if you can browse into the ZIP file by double clicking it. If you get an error from Windows, the file is corrupt. If it works, I am rather stumped as to why ImageJ is having problems with it.
Regards,
Curtis
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Hansen, Bryan (NIH/NIAID) [F]
Apr 23, 2013, 5:47:07 PM4/23/13
to Curtis Rueden, Johannes Schindelin, bugz...@fiji.sc
Hi Curtis,
I changed the extension to .zip and was able to open it in windows just fine. So what I did was take the contents of the folder and put it into the plugins folder and now it works just fine. Crazy! Thanks so much for your help.
Bryan
bugz...@fiji.sc
Jul 7, 2013, 11:21:57 AM7/7/13
to fiji-...@googlegroups.com
Johannes Schindelin
changed
bug 590
| What | Removed | Added |
|---|---|---|
| Status | NEW | RESOLVED |
| Resolution | --- | WORKSFORME |
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