mfantle
commented
6 years ago An addendum: I had an older version of Fiji on my laptop and the plugin worked fine. But after I updated, I get the same error as above.
Closed mfantle closed 6 years ago
mfantle
commented
6 years ago An addendum: I had an older version of Fiji on my laptop and the plugin worked fine. But after I updated, I get the same error as above.
taylorwrt
commented
6 years ago Mfantle,
Fiji was updated to version 2.0.0 recently, and that is what is causing the problem you describe. We noticed this a couple of weeks ago, and getting it to run with the new Fiji was not too difficult.
However, I am having some problems getting OpenMIMS to run correctly with the new Fiji within my development environment, so I have not yet put the fixed version on our update server. Since people seem to be running into this more, I will place an interim version on our update server on Monday so you can get it with the normal Fiji update mechanism. I will let you know when I have put it there.
Walter
On Jan 26, 2018, at 8:53 PM, mfantle notifications@github.com wrote:
An addendum: I had an older version of Fiji on my laptop and the plugin worked fine. But after I updated, I get the same error as above.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/BWHCNI/OpenMIMS/issues/55#issuecomment-360950617, or mute the thread https://github.com/notifications/unsubscribe-auth/AR0m5ESKLdEOldKinzOd0VzSdtVXPD4tks5tOoGygaJpZM4Ruwgb.
mfantle
commented
6 years ago Walter
Thanks very much. I appreciate the response. Can I run a previous version of ImageJ in the meanwhile? Or is this something I can't solve that way? I tried installing previous versions, but no dice.
thanks Matt
taylorwrt
commented
6 years ago Matt,
I have not tried installing older versions of Fiji, but I am surprised that it did not work for you. Any older version of Fiji based on ImageJ 1.51s that has been working should still work.
In any case, give me a few days and I will get you up and running again. If nothing else, I will post a version of Fiji (with OpenMIMS) on our Dropbox server, if I can figure out how to make an area there available to people outside of our organization.
Walter
On Jan 26, 2018, at 10:33 PM, mfantle notifications@github.com wrote:
Walter
Thanks very much. I appreciate the response. Can I run a previous version of ImageJ in the meanwhile? Or is this something I can't solve that way? I tried installing previous versions, but no dice.
thanks Matt
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/BWHCNI/OpenMIMS/issues/55#issuecomment-360956673, or mute the thread https://github.com/notifications/unsubscribe-auth/AR0m5KVu66Tog_sIBWjnmdkog0chLXZ-ks5tOpkZgaJpZM4Ruwgb.
taylorwrt
commented
6 years ago Matt,
I have an OpenMIMS jar file that should fix the problem you were having. I placed it on our Dropbox server, but to make it available to you, I need your email address, and I think the one I am using for this message is probably not what I should use.
Walter
Walter Taylor IS Programmer/Analyst Center for NanoImaging Brigham and Women's Hospital 65 Landsdowne St Cambridge, MA 02139
617-803-5874
wrtaylor@partners.org walter.taylor@icloud.com
On Jan 26, 2018, at 10:33:45 PM, mfantle notifications@github.com wrote:
Walter
Thanks very much. I appreciate the response. Can I run a previous version of ImageJ in the meanwhile? Or is this something I can't solve that way? I tried installing previous versions, but no dice.
thanks Matt
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/BWHCNI/OpenMIMS/issues/55#issuecomment-360956673, or mute the thread https://github.com/notifications/unsubscribe-auth/AR0m5KVu66Tog_sIBWjnmdkog0chLXZ-ks5tOpkZgaJpZM4Ruwgb.
mfantle
commented
6 years ago Walter
which email address do you need then? this is my University address.
thanks Matt
On Jan 28, 2018, at 2:57 PM, Walter Taylor notifications@github.com wrote:
Matt,
I have an OpenMIMS jar file that should fix the problem you were having. I placed it on our Dropbox server, but to make it available to you, I need your email address, and I think the one I am using for this message is probably not what I should use.
Walter
Walter Taylor IS Programmer/Analyst Center for NanoImaging Brigham and Women's Hospital 65 Landsdowne St Cambridge, MA 02139
617-803-5874
wrtaylor@partners.org walter.taylor@icloud.com
On Jan 26, 2018, at 10:33:45 PM, mfantle notifications@github.com wrote:
Walter
Thanks very much. I appreciate the response. Can I run a previous version of ImageJ in the meanwhile? Or is this something I can't solve that way? I tried installing previous versions, but no dice.
thanks Matt
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/BWHCNI/OpenMIMS/issues/55#issuecomment-360956673, or mute the thread https://github.com/notifications/unsubscribe-auth/AR0m5KVu66Tog_sIBWjnmdkog0chLXZ-ks5tOpkZgaJpZM4Ruwgb.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/BWHCNI/OpenMIMS/issues/55#issuecomment-361090890, or mute the thread https://github.com/notifications/unsubscribe-auth/AiMFfs6_3wuXTjkPKOOnCDYt4gEhDqF-ks5tPNEjgaJpZM4Ruwgb.
Matthew S. Fantle Associate Professor Department of Geosciences Penn State University 212 Deike Bldg. University Park, PA 16802
Phone: 814-863-9968 mfantle@psu.edu
Geosciences Department http://www.geosc.psu.edu/
Fantle Research Group http://www.personal.psu.edu/msf17/index.html
The Energy and Environmental Sustainability Laboratories (EESL) http://eesl.iee.psu.edu
Astrobiology Minor at PSU http://www.personal.psu.edu/msf17/astrobiominor/
Biogeochemistry Dual Title Graduate Program http://www.biogeochemistry.psu.edu
taylorwrt
commented
6 years ago Matt,
I am a bit confused about this. The email address your messages have with them is notifications@github.com mailto:notifications@github.com. That sounds more like a relay address than your university address.
Walter
Walter Taylor IS Programmer/Analyst Center for NanoImaging Brigham and Women's Hospital 65 Landsdowne St Cambridge, MA 02139
617-803-5874
wrtaylor@partners.org walter.taylor@icloud.com
On Jan 29, 2018, at 8:43:54 AM, mfantle notifications@github.com wrote:
Walter
which email address do you need then? this is my University address.
thanks Matt
On Jan 28, 2018, at 2:57 PM, Walter Taylor notifications@github.com wrote:
Matt,
I have an OpenMIMS jar file that should fix the problem you were having. I placed it on our Dropbox server, but to make it available to you, I need your email address, and I think the one I am using for this message is probably not what I should use.
Walter
Walter Taylor IS Programmer/Analyst Center for NanoImaging Brigham and Women's Hospital 65 Landsdowne St Cambridge, MA 02139
617-803-5874
wrtaylor@partners.org walter.taylor@icloud.com
On Jan 26, 2018, at 10:33:45 PM, mfantle notifications@github.com wrote:
Walter
Thanks very much. I appreciate the response. Can I run a previous version of ImageJ in the meanwhile? Or is this something I can't solve that way? I tried installing previous versions, but no dice.
thanks Matt
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/BWHCNI/OpenMIMS/issues/55#issuecomment-360956673, or mute the thread https://github.com/notifications/unsubscribe-auth/AR0m5KVu66Tog_sIBWjnmdkog0chLXZ-ks5tOpkZgaJpZM4Ruwgb.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/BWHCNI/OpenMIMS/issues/55#issuecomment-361090890, or mute the thread https://github.com/notifications/unsubscribe-auth/AiMFfs6_3wuXTjkPKOOnCDYt4gEhDqF-ks5tPNEjgaJpZM4Ruwgb.
Matthew S. Fantle Associate Professor Department of Geosciences Penn State University 212 Deike Bldg. University Park, PA 16802
Phone: 814-863-9968 mfantle@psu.edu
Geosciences Department http://www.geosc.psu.edu/
Fantle Research Group http://www.personal.psu.edu/msf17/index.html
The Energy and Environmental Sustainability Laboratories (EESL) http://eesl.iee.psu.edu
Astrobiology Minor at PSU http://www.personal.psu.edu/msf17/astrobiominor/
Biogeochemistry Dual Title Graduate Program http://www.biogeochemistry.psu.edu
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/BWHCNI/OpenMIMS/issues/55#issuecomment-361249003, or mute the thread https://github.com/notifications/unsubscribe-auth/AR0m5Esyo2yEhoOw_nWbifoEQcTf0CBMks5tPcsagaJpZM4Ruwgb.
taylorwrt
commented
6 years ago Matt,
I found another way to share the OpenMIMS jar file with you. Click on this link:
https://www.dropbox.com/s/tu39qhqimnpza7j/Open_MIMS.jar?dl=0 https://www.dropbox.com/s/tu39qhqimnpza7j/Open_MIMS.jar?dl=0
and download the jar file.
Here are the steps for installing it:
Download a fresh copy of Fiji, then run it and go to the Help menu, select “Update”. Let it download all updates. Click on the “Manage update sites” button. Scroll to the bottom of the ensuing window and if the OpenMIMS site is not already there, add it by click on the Add Update site button, then entering OpenMIMS in the Name field and http://nrims.partners.org/OpenMIMS-Fiji/ http://nrims.partners.org/OpenMIMS-Fiji/ in the URL field.
Let me know how it goes.
Walter
Walter Taylor IS Programmer/Analyst Center for NanoImaging Brigham and Women's Hospital 65 Landsdowne St Cambridge, MA 02139
617-803-5874
wrtaylor@partners.org walter.taylor@icloud.com
On Jan 29, 2018, at 11:09:51 AM, Walter Taylor walter.taylor@icloud.com wrote:
Matt,
I am a bit confused about this. The email address your messages have with them is notifications@github.com mailto:notifications@github.com. That sounds more like a relay address than your university address.
Walter
Walter Taylor IS Programmer/Analyst Center for NanoImaging Brigham and Women's Hospital 65 Landsdowne St Cambridge, MA 02139
617-803-5874
wrtaylor@partners.org mailto:wrtaylor@partners.org walter.taylor@icloud.com
On Jan 29, 2018, at 8:43:54 AM, mfantle <notifications@github.com mailto:notifications@github.com> wrote:
Walter
which email address do you need then? this is my University address.
thanks Matt
On Jan 28, 2018, at 2:57 PM, Walter Taylor <notifications@github.com mailto:notifications@github.com> wrote:
Matt,
I have an OpenMIMS jar file that should fix the problem you were having. I placed it on our Dropbox server, but to make it available to you, I need your email address, and I think the one I am using for this message is probably not what I should use.
Walter
Walter Taylor IS Programmer/Analyst Center for NanoImaging Brigham and Women's Hospital 65 Landsdowne St Cambridge, MA 02139
617-803-5874
wrtaylor@partners.org mailto:wrtaylor@partners.org walter.taylor@icloud.com mailto:walter.taylor@icloud.com
https://nano.bwh.harvard.edu/ https://nano.bwh.harvard.edu/
On Jan 26, 2018, at 10:33:45 PM, mfantle <notifications@github.com mailto:notifications@github.com> wrote:
Walter
Thanks very much. I appreciate the response. Can I run a previous version of ImageJ in the meanwhile? Or is this something I can't solve that way? I tried installing previous versions, but no dice.
thanks Matt
— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/BWHCNI/OpenMIMS/issues/55#issuecomment-360956673 https://github.com/BWHCNI/OpenMIMS/issues/55#issuecomment-360956673>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AR0m5KVu66Tog_sIBWjnmdkog0chLXZ-ks5tOpkZgaJpZM4Ruwgb https://github.com/notifications/unsubscribe-auth/AR0m5KVu66Tog_sIBWjnmdkog0chLXZ-ks5tOpkZgaJpZM4Ruwgb>.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/BWHCNI/OpenMIMS/issues/55#issuecomment-361090890 https://github.com/BWHCNI/OpenMIMS/issues/55#issuecomment-361090890>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AiMFfs6_3wuXTjkPKOOnCDYt4gEhDqF-ks5tPNEjgaJpZM4Ruwgb https://github.com/notifications/unsubscribe-auth/AiMFfs6_3wuXTjkPKOOnCDYt4gEhDqF-ks5tPNEjgaJpZM4Ruwgb>.
Matthew S. Fantle Associate Professor Department of Geosciences Penn State University 212 Deike Bldg. University Park, PA 16802
Phone: 814-863-9968 mfantle@psu.edu mailto:mfantle@psu.edu
Geosciences Department http://www.geosc.psu.edu/ http://www.geosc.psu.edu/
Fantle Research Group http://www.personal.psu.edu/msf17/index.html http://www.personal.psu.edu/msf17/index.html
The Energy and Environmental Sustainability Laboratories (EESL) http://eesl.iee.psu.edu http://eesl.iee.psu.edu/
Astrobiology Minor at PSU http://www.personal.psu.edu/msf17/astrobiominor/ http://www.personal.psu.edu/msf17/astrobiominor/
Biogeochemistry Dual Title Graduate Program http://www.biogeochemistry.psu.edu http://www.biogeochemistry.psu.edu/
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/BWHCNI/OpenMIMS/issues/55#issuecomment-361249003, or mute the thread https://github.com/notifications/unsubscribe-auth/AR0m5Esyo2yEhoOw_nWbifoEQcTf0CBMks5tPcsagaJpZM4Ruwgb.
mfantle
commented
6 years ago Walter
thanks! i’ll give that a shot.
On Jan 29, 2018, at 11:39 AM, Walter Taylor notifications@github.com wrote:
Matt,
I found another way to share the OpenMIMS jar file with you. Click on this link:
https://www.dropbox.com/s/tu39qhqimnpza7j/Open_MIMS.jar?dl=0 https://www.dropbox.com/s/tu39qhqimnpza7j/Open_MIMS.jar?dl=0
and download the jar file.
Here are the steps for installing it:
Download a fresh copy of Fiji, then run it and go to the Help menu, select “Update”. Let it download all updates. Click on the “Manage update sites” button. Scroll to the bottom of the ensuing window and if the OpenMIMS site is not already there, add it by click on the Add Update site button, then entering OpenMIMS in the Name field and http://nrims.partners.org/OpenMIMS-Fiji/ http://nrims.partners.org/OpenMIMS-Fiji/ in the URL field.
- Close the Manage update sites window and click on the Apply changes button.
- Quit Fiji. Show the Fiji application’s package contents by right-clicking on the app and selecting “Show Package Contents”.
- Copy the new OpenMIMS jar file into the plugin folder of the package contents.
- Restart Fiji and OpenMIMS should now work.
Let me know how it goes.
Walter
Walter Taylor IS Programmer/Analyst Center for NanoImaging Brigham and Women's Hospital 65 Landsdowne St Cambridge, MA 02139
617-803-5874
wrtaylor@partners.org walter.taylor@icloud.com
On Jan 29, 2018, at 11:09:51 AM, Walter Taylor walter.taylor@icloud.com wrote:
Matt,
I am a bit confused about this. The email address your messages have with them is notifications@github.com mailto:notifications@github.com. That sounds more like a relay address than your university address.
Walter
Walter Taylor IS Programmer/Analyst Center for NanoImaging Brigham and Women's Hospital 65 Landsdowne St Cambridge, MA 02139
617-803-5874
wrtaylor@partners.org mailto:wrtaylor@partners.org walter.taylor@icloud.com
On Jan 29, 2018, at 8:43:54 AM, mfantle <notifications@github.com mailto:notifications@github.com> wrote:
Walter
which email address do you need then? this is my University address.
thanks Matt
On Jan 28, 2018, at 2:57 PM, Walter Taylor <notifications@github.com mailto:notifications@github.com> wrote:
Matt,
I have an OpenMIMS jar file that should fix the problem you were having. I placed it on our Dropbox server, but to make it available to you, I need your email address, and I think the one I am using for this message is probably not what I should use.
Walter
Walter Taylor IS Programmer/Analyst Center for NanoImaging Brigham and Women's Hospital 65 Landsdowne St Cambridge, MA 02139
617-803-5874
wrtaylor@partners.org mailto:wrtaylor@partners.org walter.taylor@icloud.com mailto:walter.taylor@icloud.com
https://nano.bwh.harvard.edu/ https://nano.bwh.harvard.edu/
On Jan 26, 2018, at 10:33:45 PM, mfantle <notifications@github.com mailto:notifications@github.com> wrote:
Walter
Thanks very much. I appreciate the response. Can I run a previous version of ImageJ in the meanwhile? Or is this something I can't solve that way? I tried installing previous versions, but no dice.
thanks Matt
— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/BWHCNI/OpenMIMS/issues/55#issuecomment-360956673 https://github.com/BWHCNI/OpenMIMS/issues/55#issuecomment-360956673>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AR0m5KVu66Tog_sIBWjnmdkog0chLXZ-ks5tOpkZgaJpZM4Ruwgb https://github.com/notifications/unsubscribe-auth/AR0m5KVu66Tog_sIBWjnmdkog0chLXZ-ks5tOpkZgaJpZM4Ruwgb>.
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Matthew S. Fantle Associate Professor Department of Geosciences Penn State University 212 Deike Bldg. University Park, PA 16802
Phone: 814-863-9968 mfantle@psu.edu mailto:mfantle@psu.edu
Geosciences Department http://www.geosc.psu.edu/ http://www.geosc.psu.edu/
Fantle Research Group http://www.personal.psu.edu/msf17/index.html http://www.personal.psu.edu/msf17/index.html
The Energy and Environmental Sustainability Laboratories (EESL) http://eesl.iee.psu.edu http://eesl.iee.psu.edu/
Astrobiology Minor at PSU http://www.personal.psu.edu/msf17/astrobiominor/ http://www.personal.psu.edu/msf17/astrobiominor/
Biogeochemistry Dual Title Graduate Program http://www.biogeochemistry.psu.edu http://www.biogeochemistry.psu.edu/
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/BWHCNI/OpenMIMS/issues/55#issuecomment-361249003, or mute the thread https://github.com/notifications/unsubscribe-auth/AR0m5Esyo2yEhoOw_nWbifoEQcTf0CBMks5tPcsagaJpZM4Ruwgb.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/BWHCNI/OpenMIMS/issues/55#issuecomment-361305556, or mute the thread https://github.com/notifications/unsubscribe-auth/AiMFfgeqnDuaOFhRhC6L1qrN1wh25Vl8ks5tPfRQgaJpZM4Ruwgb.
Matthew S. Fantle Associate Professor Department of Geosciences Penn State University 212 Deike Bldg. University Park, PA 16802
Phone: 814-863-9968 mfantle@psu.edu
Geosciences Department http://www.geosc.psu.edu/
Fantle Research Group http://www.personal.psu.edu/msf17/index.html
The Energy and Environmental Sustainability Laboratories (EESL) http://eesl.iee.psu.edu
Astrobiology Minor at PSU http://www.personal.psu.edu/msf17/astrobiominor/
Biogeochemistry Dual Title Graduate Program http://www.biogeochemistry.psu.edu
mfantle
commented
6 years ago It worked Walter. thanks!!
taylorwrt
commented
6 years ago As the discussion above mentions, this issue was a dependency mismatch between the OpenMIMS project and the new Fiji, which is based on ImageJ 2.0.0 and uses updated jar files. Once I made OpenMIMS dependent on the most recent imagej jar file, this problem was resolved. As of Jan 30, 2018, updating Fiji will retrieve the fixed OpenMIMS, assuming you have OpenMIMS already installed. If you are starting from a fresh download of Fiji, get the new OpenMIMS the conventional way:
Run Fiji and go to the Help menu, select “Update”.
Let it download all updates.
Click on the “Manage update sites” button.
Scroll to the bottom of the ensuing window and if the OpenMIMS site is not already there, add it by click on the Add Update site button, then entering OpenMIMS in the Name field and http://nrims.partners.org/OpenMIMS-Fiji/ in the URL field. For the URL, you can also use http://sites.imagej.net/OpenMIMS2/
Close the Manage update sites window and click on the Apply changes button.
Quit and then restart Fiji, and the OpenMIMS plugin should work normally.
Hi:
I just installed Fiji and the OpenMIMS plugin on a Mac Os 10.10 Yosemite, with Java 8 and 6 both installed. I get the following error message when I attempt to load the OpenMIMS plugin. Does anyone know how I can fix this?
thanks
OpenMIMS: [INFO] : com.nrims.NRIMS_Plugin
OpenMIMS: [INFO] NRIMS constructor: id=928570718 : com.nrims.NRIMS_Plugin
OpenMIMS: [INFO] args: open : com.nrims.NRIMS_Plugin run
OpenMIMS: [INFO] ImageJDir: /Applications/Fiji.app/ : com.nrims.MimsCBControl setupLutComboBox
OpenMIMS: [INFO] ImageJDir: /Applications/Fiji.app/ : com.nrims.MimsCBControl setupLutComboBox
OpenMIMS: [INFO] lut directory: /Applications/Fiji.app/luts : com.nrims.MimsCBControl setupLutComboBox
OpenMIMS: [INFO] lut directory: /Applications/Fiji.app/luts : com.nrims.MimsCBControl setupLutComboBox
There was a problem with the class org.jfree.chart.renderer.xy.XYItemRenderer which can be found here:
/Applications/Fiji.app/jars/jfreechart-1.5.0.jar
java.lang.NoSuchMethodError: org.jfree.chart.renderer.xy.XYItemRenderer.setBaseToolTipGenerator(Lorg/jfree/chart/labels/XYToolTipGenerator;)V
at com.nrims.plot.MimsChartFactory.createMimsHistogram(MimsChartFactory.java:95)
at com.nrims.MimsCBControl.setupHistogram(MimsCBControl.java:163)
at com.nrims.MimsCBControl.(MimsCBControl.java:95)
at com.nrims.UI.(UI.java:181)
at com.nrims.UI.(UI.java:224)
at com.nrims.NRIMS_Plugin.run(NRIMS_Plugin.java:156)
at ij.IJ.runUserPlugIn(IJ.java:221)
at ij.IJ.runPlugIn(IJ.java:185)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)
[ERROR] null java.lang.NoSuchMethodException: Could not find method org.jfree.chart.renderer.xy.XYItemRenderer.setBaseToolTipGenerator(Lorg/jfree/chart/labels/XYToolTipGenerator;)V There was a problem with the class org.jfree.chart.renderer.xy.XYItemRenderer which can be found here: /Applications/Fiji.app/jars/jfreechart-1.5.0.jar java.lang.NoSuchMethodError: org.jfree.chart.renderer.xy.XYItemRenderer.setBaseToolTipGenerator(Lorg/jfree/chart/labels/XYToolTipGenerator;)V at com.nrims.plot.MimsChartFactory.createMimsHistogram(MimsChartFactory.java:95) at com.nrims.MimsCBControl.setupHistogram(MimsCBControl.java:163) at com.nrims.MimsCBControl.(MimsCBControl.java:95)
at com.nrims.UI.(UI.java:181)
at com.nrims.UI.(UI.java:224)
at com.nrims.NRIMS_Plugin.run(NRIMS_Plugin.java:156)
at ij.IJ.runUserPlugIn(IJ.java:221)
at ij.IJ.runPlugIn(IJ.java:185)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)