FLIMJ installing problem

[Michał Majkowski]

Dear ImageJ fans,

 I want to install FLIMJ plugin through ImageJ updater. However for some reasons system can not do it. I received a message:

[ERROR] java.io.FileNotFoundException: C:\Users\MICHAL~1\Fiji.app\update\jars\flimj-ops-2.1.1.jar (System nie może odnaleźć określonej ścieżki)

In brackets is polish language statement indicating that system can not find the path specified or directory path.

Colud you please help me. Thank in advance.


Michal Majkowski
Imaging Specialist

University of Wroclaw
Biotechnology Faculty
Joliot-Curie 14a
50-383 Wroclaw POLAND


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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Mark Hiner-3]

Hi Michal,

> I want to install FLIMJ plugin through ImageJ updater. However for some reasons system can not do it. I received a message:
>
>[ERROR] java.io.FileNotFoundException: C:\Users\MICHAL~1\Fiji.app\update\jars\flimj-ops-2.1.1.jar (System nie może odnaleźć określonej ścieżki)

Did you receive this message during the update process?

You can do the following to check the files from the FLIMJ update site:

1. Run Help > Update...
2. Click the button for "Advanced mode"
3. Under "View options", select "View the files of the 'FLIMJ' site"

You should see the following entries:
jars/flimj-ops.jar
jars/flimj-ui.jar
jars/json-simple.jar
jars/controlsfx.jar
jars/flimlib.jar
jars/win64/flimlib-native-windows_64.jar (this may differ depending on your platform)
 
The "flimj-ops.jar" should show as "Up-to-date" in the Status/Action column. If it is not, you can click the status and tell the updater to install or update the jar, and then "Apply changes" to complete the process.

Side note: FLIMJ requires using a Java with JavaFX (which is NOT included in the Java bundled with Fiji distributions). If needed, you can get a JDK FX bundle from:
https://www.azul.com/downloads/zulu-community/?version=java-8-lts&package=jdk-fx

and change the Java version:
https://imagej.net/Frequently_Asked_Questions.html#How_do_I_launch_ImageJ_with_a_different_version_of_Java.3F

Best,
Mark

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michał Majkowski]

Thank you Mark. It still does not work. I have changed Java and did all what you suggested but with no effect.
Answering your question: yes, this message appears during update process:
[ERROR] java.io.FileNotFoundException: C:\Users\MICHAL~1\Fiji.app\update\jars\flimj-ops-2.1.1.jar (System nie może odnaleźć określonej ścieżki)

Bolded sentence is in polish and means that the system can not find the specified path or directory path

I am totally not advanced in "informatics". Maybe the problem regards the fact that I do not have "update" folder in my Fiji.app folder. But as I said ... this is only a guess.
Thank you
Michal
________________________________
Od: ImageJ Interest Group <[hidden email]> w imieniu użytkownika Mark Hiner <[hidden email]>
Wysłane: poniedziałek, 11 stycznia 2021 14:44
Do: [hidden email] <[hidden email]>
Temat: Re: FLIMJ installing problem

Hi Michal,

> I want to install FLIMJ plugin through ImageJ updater. However for some reasons system can not do it. I received a message:
>
>[ERROR] java.io.FileNotFoundException: C:\Users\MICHAL~1\Fiji.app\update\jars\flimj-ops-2.1.1.jar (System nie może odnaleźć określonej ścieżki)

Did you receive this message during the update process?

You can do the following to check the files from the FLIMJ update site:

1. Run Help > Update...
2. Click the button for "Advanced mode"
3. Under "View options", select "View the files of the 'FLIMJ' site"

You should see the following entries:
jars/flimj-ops.jar
jars/flimj-ui.jar
jars/json-simple.jar
jars/controlsfx.jar
jars/flimlib.jar
jars/win64/flimlib-native-windows_64.jar (this may differ depending on your platform)

The "flimj-ops.jar" should show as "Up-to-date" in the Status/Action column. If it is not, you can click the status and tell the updater to install or update the jar, and then "Apply changes" to complete the process.

Side note: FLIMJ requires using a Java with JavaFX (which is NOT included in the Java bundled with Fiji distributions). If needed, you can get a JDK FX bundle from:
https://www.azul.com/downloads/zulu-community/?version=java-8-lts&package=jdk-fx

and change the Java version:
https://imagej.net/Frequently_Asked_Questions.html#How_do_I_launch_ImageJ_with_a_different_version_of_Java.3F

Best,
Mark

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Mark Hiner-3]

Hi Michal,

> Maybe the problem regards the fact that I do not have "update" folder in my Fiji.app folder.

The "Update" folder exists only intermittently: after initiating an update in Fiji but before restarting Fiji. The act of restarting Fiji is what finalizes the update (by moving the contents of the "Update" folder to their destination).

Can you try the following:

    1. Turn off the FLIMJ update site
    2. Restart Fiji
    3. Turn the FLIMJ update site back on
    4. Restart Fiji

and let me know what happens?

If you still get the error, I have a few questions:

    1. Does the error appear when you turn the FLIMJ update site on, or after Fiji restarts?
    2. Can you open the Help > Update... menu, go to advanced mode, and tell me what files you have listed for the FLIMJ update site and what their status is?
    3. Can you give me the full list of update sites you have enabled? (from the Help > Update... > Manage Update Sites menu)

> I have changed Java

It is still good that you updated the Java version. It won't fix problems with the updater, but it is still necessary to have a JFX-enabled Java to run FLIMJ.

Best,
Mark

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michał Majkowski]

Hi Mark,

I would like to send you some printscreens illustrating my actions and Fiji responses. What do you think about corresponding outside the list?
my e-mail: [hidden email]


Michal Majkowski
Imaging Specialist

University of Wroclaw
Biotechnology Faculty
Joliot-Curie 14a
50-383 Wroclaw POLAND
________________________________
Od: ImageJ Interest Group <[hidden email]> w imieniu użytkownika Mark Hiner <[hidden email]>
Wysłane: wtorek, 12 stycznia 2021 16:45
Do: [hidden email] <[hidden email]>
Temat: Re: ODP: FLIMJ installing problem

Hi Michal,

> Maybe the problem regards the fact that I do not have "update" folder in my Fiji.app folder.

The "Update" folder exists only intermittently: after initiating an update in Fiji but before restarting Fiji. The act of restarting Fiji is what finalizes the update (by moving the contents of the "Update" folder to their destination).

Can you try the following:

    1. Turn off the FLIMJ update site
    2. Restart Fiji
    3. Turn the FLIMJ update site back on
    4. Restart Fiji

and let me know what happens?

If you still get the error, I have a few questions:

    1. Does the error appear when you turn the FLIMJ update site on, or after Fiji restarts?
    2. Can you open the Help > Update... menu, go to advanced mode, and tell me what files you have listed for the FLIMJ update site and what their status is?
    3. Can you give me the full list of update sites you have enabled? (from the Help > Update... > Manage Update Sites menu)

> I have changed Java

It is still good that you updated the Java version. It won't fix problems with the updater, but it is still necessary to have a JFX-enabled Java to run FLIMJ.

Best,
Mark

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Mark Hiner-3]

Michal,

>I would like to send you some printscreens illustrating my actions and Fiji responses. What do you think about corresponding outside the list?

That is fine with me, but instead of e-mail please use the ImageJ community forum: https://forum.image.sc

You can tag me with @hinerm

Best,
Mark

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michał Majkowski]

Thank you.
m
________________________________
Od: ImageJ Interest Group <[hidden email]> w imieniu użytkownika Mark Hiner <[hidden email]>
Wysłane: środa, 13 stycznia 2021 15:03
Do: [hidden email] <[hidden email]>
Temat: Re: ODP: ODP: FLIMJ installing problem

Michal,

>I would like to send you some printscreens illustrating my actions and Fiji responses. What do you think about corresponding outside the list?

That is fine with me, but instead of e-mail please use the ImageJ community forum: https://forum.image.sc

You can tag me with @hinerm

Best,
Mark

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html