Re: IMAGEJ Digest - 19 Apr 2018 to 20 Apr 2018 (#2018-113)

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Re: IMAGEJ Digest - 19 Apr 2018 to 20 Apr 2018 (#2018-113)

Jim Quinn-3
Wayne and company -

Many of you are also likely on the MSA uscopy listserver.
Nestor posted a message about a new law, which will impact
that listserver.  I am curious how it will impact this listserver.
See below.

thanks and regards,
- Jim



> All Microscopy Listserver Subscribers:
> ----------------------------------------------------------
> ****    This will be your LAST message from the   ****
> **** Microscopy Listserver unless you resubscribe ****
> ----------------------------------------------------------
> A new set of legal rules - namely the General Data Protection Regulation
> or GDPR
> (https://www.eugdpr.org) is propagating around the world concerning
> internet privacy.  These rules
> are  being applied universally to any entity that communicates with groups
> of people using the
> Internet. At the moment it technically  only applies to individuals in the
> European Union but will
> likely will be extended in some form to all countries worldwide in the not
> to distant future.
> Since  information about you (i.e. Name, Affiliation, Email address) is
> being stored in the
> Microscopy Listserver Database,  the GDPR regulations can be  interpreted
> to also apply to the
> Microscopy Listserver. These rules are detailed and non-compliance can
> result in penalties of up to
> $25M if not followed.
> Thus, in order to comply with the GDPR which takes effect on May 25, and
> also to error on the side
> of safety (I don't have $25M, but wish I did),  it will be easiest (for
> me)  to have all individuals
> reconfirm their  desire to be a Microscopy Listserver subscriber.
> So for the first time in  25  years, I must ask each and every active
> subscriber to revisit the
> Microscopy.Com WWW site and renew their subscription.
> All active subscriptions  will be nullified in the existing DBase later
> today (May 20, 2018). My
> apologies to those of you that have either been a long term subscriber, as
> well as those of you who
> have recently subscribed. Because of the number of users on the Listserver,
> this is the simplest
> way to proceed.
> Below is the URL  to the subscription page.  Just copy and past the URL
> into your WWW browser
> and reenter your contact information. This (re)subscription has to be done
> as if you are a "new"
> subscriber.
>         http://microscopy.com/SbscrbeMicroscopy.html
> Your (re)subscription will serve to indicate your consent to continue
> sending you email from the
> Microscopy Listserver as required by the GDPR.  This email also
> reconfirms to you that  Microscopy
> Listserver DataBase information, as has been the policy for the past 25
> years, will not be shared
> with any entity and will only be used to send you correspondence from
> and/or related to the
> Microscopy Listserver, its subscribers or its operations.
> You may, as previously,  unsubscribe at any time using the on-line forms
> on the Microscopy.com WWW
> site (http://microscopy.com), by providing your active subscription email
> address.
> The FAQ page remains  available for questions, or you may also send a
> direct email to me
> ([hidden email]).
>
> Sorry for the hassle and bureaucracy.
> Nestor
> Your Friendly Neighborhood SysOp
>



On Sat, Apr 21, 2018 at 12:00 AM, IMAGEJ automatic digest system <
[hidden email]> wrote:

> There are 11 messages totaling 1400 lines in this issue.
>
> Topics of the day:
>
>   1. Unwanted feature for KeyEvent.VK_DELETE (2)
>   2. Recover pixels imageJ (4)
>   3. Incorporating a plugin into the ij.jar file (4)
>   4. Imagej.cfg file missing, not created
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ----------------------------------------------------------------------
>
> Date:    Fri, 20 Apr 2018 10:28:51 +0200
> From:    Philippe CARL <[hidden email]>
> Subject: Re: Unwanted feature for KeyEvent.VK_DELETE
>
> Hi Philippe,
>
> > yes, I admit, I'm the culprit.
>
> No problem about this!!!
> And since I answer you, I would like to use this opportunity to
> congratulate and thank you for the gorgeous (you did it again!) last big
> update you made on ImageJ (i.e. the one on the tables).
>
> > Philippe: Would it be acceptable to have some modifier key (SHIFT, ALT,
> > CTRL) for the special 'delete' function of your plugin?
>
> I would have no problems with having to use a key modifier together with
> the delete key within my plugin.
> Actually I had already tried this option before sending my first E-mail,
> but the "clear" feature of the delete key is still working even if an
> InputEvent value has been set for my code (unless I'm missing something in
> my code).
>
> My best regards,
>
> Philippe
>
> -----Message d'origine-----
> De : ImageJ Interest Group [mailto:[hidden email]] De la part de
> Michael Schmid
> Envoyé : jeudi 19 avril 2018 21:13
> À : [hidden email]
> Objet : Re: Unwanted feature for KeyEvent.VK_DELETE
>
> Hi Philippe,
>
> yes, I admit, I'm the culprit. The reason was that many other programs I
> am used to require the "delete forward" key to delete things (except on
> Macintosh), e.g. deleting items from a list. ImageJ was kind of an
> exception, so I often ended up using the wrong key, and I was wondering
> why it did not delete.
>
> But maybe I am the only one? What do the others think?
>
>
> Philippe: Would it be acceptable to have some modifier key (SHIFT, ALT,
> CTRL) for the special 'delete' function of your plugin?
> I think it would not be a problem to restrict the ImageJ keyboard
> shortcut to the delete key being pressed without such modifier.
> (currently it does not check for modifiers).
>
>
> Michael
> ________________________________________________________________
> On 19/04/2018 17:02, Philippe CARL wrote:
> > Dear all (probably Michael),
> >
> > I have (i.e. had) a plugin displaying several overlays drawn on top of a
> > stack of pictures and within which the user could draw a ROI and erase
> the
> > overlays found inside the drawn ROI by simply pressing the delete key.
> >
> > Very unfortunately since the update "1.51u 13 February 2018" with the
> > feature:
> >
> > "Thanks to Michael Schmid, the delete key on Windows keyboards can be
> used
> > as a substitute for backspace as a shortcut for the Image>Clear command,
> for
> > deleting ROIs from overlays and for deleting lines in Results Tables and
> in
> > the Log window. In addition, the ',' key on european numeric keypads is
> > mapped to the '.' key."
> >
> > [also I guess it is rather reproducing the "Edit>Clear command" not the
> > "Image>Clear command" one]
> >
> > The use of the delete key within this plugin will as well apply a clear
> > command to the displayed slice of the stack which in this particular
> case of
> > this plugin is quite unwanted.
> >
> > Thus would there a way for me to deactivate the clear command associated
> to
> > the delete key when it is launched from this "old" plugin?
> >
> > Or what alternate options could I have to solve this issue?
> >
> > I thank you very much in advance for your ideas and lightings.
> >
> > My best regards,
> >
> > Philippe
> >
> >
> >
> > Philippe CARL
> >
> > Laboratoire de Bioimagerie et Pathologies
> >
> > UMR 7021 CNRS - Université de Strasbourg
> >
> > Faculté de Pharmacie
> >
> > 74 route du Rhin
> >
> > 67401 ILLKIRCH
> >
> > Tel : +33(0)3 68 85 41 84
> >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Fri, 20 Apr 2018 10:07:34 +0000
> From:    Ndeye Birima Mbaye <[hidden email]>
> Subject: Recover pixels imageJ
>
> Hello,
>
> I'm contacting you because I have a problem with the ImageJ software.
> I have an image which I want to recover the value of each pixel except
> that I do not know how to do it.
> Could you help me please ?
> Thank you in advance.
>
>
> Regards,
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Fri, 20 Apr 2018 12:19:31 +0200
> From:    Herbie <[hidden email]>
> Subject: Re: Recover pixels imageJ
>
> Good day,
>
> not sure, but did you save your image as text-image?
>
> Regards
>
> Herbie
>
> ::::::::::::::::::::::::::::::::::::::::::::::::
> Am 20.04.18 um 12:07 schrieb Ndeye Birima Mbaye:
> > Hello,
> >
> > I'm contacting you because I have a problem with the ImageJ software.
> > I have an image which I want to recover the value of each pixel except
> that I do not know how to do it.
> > Could you help me please ?
> > Thank you in advance.
> >
> >
> > Regards,
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Fri, 20 Apr 2018 10:29:37 +0000
> From:    Ndeye Birima Mbaye <[hidden email]>
> Subject: Re: Recover pixels imageJ
>
> Thank you for your reply.
> Yes I did it but it does not work.
> Is there another way?
>
>
> Regards,
>
>
> ________________________________
> De : ImageJ Interest Group <[hidden email]> de la part de Herbie <
> [hidden email]>
> Envoyé : vendredi 20 avril 2018 10:19
> À : [hidden email]
> Objet : Re: Recover pixels imageJ
>
> Good day,
>
> not sure, but did you save your image as text-image?
>
> Regards
>
> Herbie
>
> ::::::::::::::::::::::::::::::::::::::::::::::::
> Am 20.04.18 um 12:07 schrieb Ndeye Birima Mbaye:
> > Hello,
> >
> > I'm contacting you because I have a problem with the ImageJ software.
> > I have an image which I want to recover the value of each pixel except
> that I do not know how to do it.
> > Could you help me please ?
> > Thank you in advance.
> >
> >
> > Regards,
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> ImageJ List<http://imagej.nih.gov/ij/list.html>
> imagej.nih.gov
> home | news | docs | download | plugins | resources | list | links. ImageJ
> Mailing List The ImageJ mailing list is a discussion group for ImageJ users
> and developers. Subscribing To subscribe, go to the Subscribe or
> Unsubscribe page, enter your name and email address, and click "Subscribe
> (IMAGEJ)".
>
>
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Fri, 20 Apr 2018 13:53:27 +0200
> From:    CARL Philippe (LBP) <[hidden email]>
> Subject: Re: Recover pixels imageJ
>
> Dear Ndeye,
> Are you looking for the macro command "getPixel(x, y)" from:
> https://imagej.nih.gov/ij/developer/macro/functions.html#G=getpixel
> Have a nice weekend,
> Philippe
>
> On Friday, April 20, 2018 12:29 CEST, Ndeye Birima Mbaye <
> [hidden email]> wrote:
>
> > Thank you for your reply.
> > Yes I did it but it does not work.
> > Is there another way?
> >
> >
> > Regards,
> >
> >
> > ________________________________
> > De : ImageJ Interest Group <[hidden email]> de la part de Herbie <
> [hidden email]>
> > Envoyé : vendredi 20 avril 2018 10:19
> > À : [hidden email]
> > Objet : Re: Recover pixels imageJ
> >
> > Good day,
> >
> > not sure, but did you save your image as text-image?
> >
> > Regards
> >
> > Herbie
> >
> > ::::::::::::::::::::::::::::::::::::::::::::::::
> > Am 20.04.18 um 12:07 schrieb Ndeye Birima Mbaye:
> > > Hello,
> > >
> > > I'm contacting you because I have a problem with the ImageJ software.
> > > I have an image which I want to recover the value of each pixel except
> that I do not know how to do it.
> > > Could you help me please ?
> > > Thank you in advance.
> > >
> > >
> > > Regards,
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > ImageJ List<http://imagej.nih.gov/ij/list.html>
> > imagej.nih.gov
> > home | news | docs | download | plugins | resources | list | links.
> ImageJ Mailing List The ImageJ mailing list is a discussion group for
> ImageJ users and developers. Subscribing To subscribe, go to the Subscribe
> or Unsubscribe page, enter your name and email address, and click
> "Subscribe (IMAGEJ)".
> >
> >
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Fri, 20 Apr 2018 14:57:24 +0200
> From:    Michael Schmid <[hidden email]>
> Subject: Re: Unwanted feature for KeyEvent.VK_DELETE
>
> Hi Philippe,
>
> ok, I have sent a suggestion to Wayne, to make the 'delete' and
> 'backspace' shortcuts work only without modifier keys. I hope that this
> does not break something in another place.
>
> Concerning the new table macro functions:
> The kudos should go to Wayne!
> (My only contribution was to provide the initial code for the 'apply
> macro', and writing several emails discussing the macro integration.)
>
> Best,
>
> Michael
> ________________________________________________________________
> On 20/04/2018 10:28, Philippe CARL wrote:
> > Hi Philippe,
> >
> >> yes, I admit, I'm the culprit.
> >
> > No problem about this!!!
> > And since I answer you, I would like to use this opportunity to
> congratulate and thank you for the gorgeous (you did it again!) last big
> update you made on ImageJ (i.e. the one on the tables).
> >
> >> Philippe: Would it be acceptable to have some modifier key (SHIFT, ALT,
> >> CTRL) for the special 'delete' function of your plugin?
> >
> > I would have no problems with having to use a key modifier together with
> the delete key within my plugin.
> > Actually I had already tried this option before sending my first E-mail,
> but the "clear" feature of the delete key is still working even if an
> InputEvent value has been set for my code (unless I'm missing something in
> my code).
> >
> > My best regards,
> >
> > Philippe
> >
> > -----Message d'origine-----
> > De : ImageJ Interest Group [mailto:[hidden email]] De la part de
> Michael Schmid
> > Envoyé : jeudi 19 avril 2018 21:13
> > À : [hidden email]
> > Objet : Re: Unwanted feature for KeyEvent.VK_DELETE
> >
> > Hi Philippe,
> >
> > yes, I admit, I'm the culprit. The reason was that many other programs I
> > am used to require the "delete forward" key to delete things (except on
> > Macintosh), e.g. deleting items from a list. ImageJ was kind of an
> > exception, so I often ended up using the wrong key, and I was wondering
> > why it did not delete.
> >
> > But maybe I am the only one? What do the others think?
> >
> >
> > Philippe: Would it be acceptable to have some modifier key (SHIFT, ALT,
> > CTRL) for the special 'delete' function of your plugin?
> > I think it would not be a problem to restrict the ImageJ keyboard
> > shortcut to the delete key being pressed without such modifier.
> > (currently it does not check for modifiers).
> >
> >
> > Michael
> > ________________________________________________________________
> > On 19/04/2018 17:02, Philippe CARL wrote:
> >> Dear all (probably Michael),
> >>
> >> I have (i.e. had) a plugin displaying several overlays drawn on top of a
> >> stack of pictures and within which the user could draw a ROI and erase
> the
> >> overlays found inside the drawn ROI by simply pressing the delete key.
> >>
> >> Very unfortunately since the update "1.51u 13 February 2018" with the
> >> feature:
> >>
> >> "Thanks to Michael Schmid, the delete key on Windows keyboards can be
> used
> >> as a substitute for backspace as a shortcut for the Image>Clear
> command, for
> >> deleting ROIs from overlays and for deleting lines in Results Tables
> and in
> >> the Log window. In addition, the ',' key on european numeric keypads is
> >> mapped to the '.' key."
> >>
> >> [also I guess it is rather reproducing the "Edit>Clear command" not the
> >> "Image>Clear command" one]
> >>
> >> The use of the delete key within this plugin will as well apply a clear
> >> command to the displayed slice of the stack which in this particular
> case of
> >> this plugin is quite unwanted.
> >>
> >> Thus would there a way for me to deactivate the clear command
> associated to
> >> the delete key when it is launched from this "old" plugin?
> >>
> >> Or what alternate options could I have to solve this issue?
> >>
> >> I thank you very much in advance for your ideas and lightings.
> >>
> >> My best regards,
> >>
> >> Philippe
> >>
> >>
> >>
> >> Philippe CARL
> >>
> >> Laboratoire de Bioimagerie et Pathologies
> >>
> >> UMR 7021 CNRS - Université de Strasbourg
> >>
> >> Faculté de Pharmacie
> >>
> >> 74 route du Rhin
> >>
> >> 67401 ILLKIRCH
> >>
> >> Tel : +33(0)3 68 85 41 84
> >>
> >>
> >> --
> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Fri, 20 Apr 2018 15:16:05 -0400
> From:    Dan McDonald <[hidden email]>
> Subject: Incorporating a plugin into the ij.jar file
>
> Dear List,
>
>
>
> I would like to incorporate the Skeletonize (2D/3D) plugin into the ij.jar
> file.  I have been unsuccessful in finding a way to do so.
>
>
>
> I have the Skeletonize (2D/3D) executable jar file located in my plugin
> folder.  I successfully run the plugin on a daily basis when I use ImageJ.
> I cannot figure out how to add a plugin that is in my plugin folder to the
> ij.jar.
>
>
>
> I have "uncompressed" the ij.jar and placed the Skeletonize3D.class file in
> the jar's plugin folder.  I then went into the IJ Properties.txt file and
> modified it to add Skeletonize (2D/3D) as a user plugin. As shown below:
>
>
>
> # Install user plugins located in ij.jar to Plugins>User Plugins submenu
>
>
>
> user_plugins01="Skeletonize (2D/3D)",ij.plugin.Skeletonize3D_
>
>
>
> (I am not sure what the arguments above are supposed to be.  I could not
> find documentation on adding user plugins via the IJProperties.txt route.
> What I did looked the closest to want other lines had in them.)
>
>
>
> I then rezipped everything.
>
>
>
> When next I startup ImageJ the plugin shows up on the user plugin menu as
> expected.
>
>
>
> Unfortunately I get the following error messages when I select the
> skeletonize function.
>
>
>
> ImageJ 1.51p; Java 1.8.0_141 [64-bit]; Linux 3.13.0-37-generic; 16MB of
> 22020MB (<1%)
>
> java.lang.NoClassDefFoundError: ij/plugin/Skeletonize3D_ (wrong name:
> Skeletonize3D_/Skeletonize3D_)
>
>                at java.lang.ClassLoader.defineClass1(Native Method)
>
>                at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
>
>                at
> java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
>
>                at
> java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
>
>                at java.net.URLClassLoader.access$100(URLClassLoader.
> java:73)
>
>                at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
>
>                at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
>
>                at java.security.AccessController.doPrivileged(Native
> Method)
>
>                at java.net.URLClassLoader.findClass(URLClassLoader.java:
> 361)
>
>                at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>
>                at
> sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
>
>                at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>
>                at java.lang.Class.forName0(Native Method)
>
>                at java.lang.Class.forName(Class.java:264)
>
>                at ij.IJ.runPlugIn(IJ.java:184)
>
>                at ij.Executer.runCommand(Executer.java:137)
>
>                at ij.Executer.run(Executer.java:66)
>
>                at java.lang.Thread.run(Thread.java:748)
>
>
>
> I am not sure if my syntax is incorrect in IJProperties.txt or if I need to
> do more than just drop a class file in the ij.jar plugin folder or both.
>
>
>
> I am not a java person.  Any assistance or pointers to documentation would
> be much appreciated.
>
>
>
> Thank you,
>
>
>
> Dan
>
>
>
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Fri, 20 Apr 2018 14:08:39 -0500
> From:    Curtis Rueden <[hidden email]>
> Subject: Re: Imagej.cfg file missing, not created
>
> Hi Mel,
>
> > Allow me to possibly blow your mind:
> >
> > Do the same procedure you just described (with no cfg file in your
> > folder), change only one thing: Launch Memory & Threads by searching
> > for it in the search box and then starting it from there. No cfg file
> > created. Then try launching it from Edit > Options, it creates a cfg
> > file.
>
> Wow, that does blow my mind! O_O
>
> I did some digging. The cause is that Fiji overrides the Memory & Threads
> command to behave differently.
>
> I filed an issue detailing all the consequences here:
>
>     https://github.com/fiji/fiji/issues/185
>
> I would like to fix it, so that other users do not stumble into this issue.
> But unfortunately, I am not sure of the best approach. Developers with
> ideas are welcome to chime in on the GitHub thread.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Tue, Apr 17, 2018 at 2:21 PM, Menelaos Symeonides <[hidden email]>
> wrote:
>
> > Hi Curtis,
> >
> > This is really strange, but I can't reproduce the problem anymore (after
> > redownloading Fiji). Allow me to possibly blow your mind:
> >
> > Do the same procedure you just described (with no cfg file in your
> > folder), change only one thing: Launch Memory & Threads by searching for
> it
> > in the search box and then starting it from there. No cfg file created.
> > Then try launching it from Edit > Options, it creates a cfg file.
> >
> > What is going on?!
> >
> > Mel
> >
> > On 4/17/2018 2:54 PM, Curtis Rueden wrote:
> >
> > Hi Mel,
> >
> > > Have you been able to replicate this issue?
> >
> > I tried just now, but could not reproduce.
> >
> > * Downloaded a fresh Fiji from https://fiji.sc/#download
> > * Unpacked it to C:\Users\Curtis\Programs\Fiji.app.
> > * Launched ImageJ-win64.exe.
> > * Responded Yes to the Updater prompt; updated the application.
> > * Restarted Fiji when it told me to do so.
> > * Ran Edit > Options > Memory & Threads...
> > * Set the Maximum Memory to 2000 (my default in the VM was ~3300).
> > * Restarted Fiji.
> > * The ImageJ.cfg was created, and Fiji reported 2000MB when I clicked the
> > status bar.
> >
> > Is your Fiji.app directory on your local file system? You are certain you
> > have write access? What happens if you create an ImageJ.cfg yourself with
> > the following contents:
> >
> >   .
> >   jre\bin\javaw.exe
> >   -Xmx2000m -cp ij.jar ij.ImageJ
> >
> > Did you try launching from the command line?
> > http://imagej.net/Troubleshooting#Launching_ImageJ_from_the_console
> >
> > You can pass e.g. "-mx1g" to tell ImageJ to use 1 GB of memory.
> >
> > Regards,
> > Curtis
> >
> > --
> > Curtis Rueden
> > LOCI software architect - https://loci.wisc.edu/software
> > ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> > Did you know ImageJ has a forum? http://forum.imagej.net/
> >
> >
> > On Mon, Apr 16, 2018 at 10:55 AM, Menelaos Symeonides <[hidden email]>
> > wrote:
> >
> >> Hi again Curtis,
> >>
> >> Have you been able to replicate this issue?
> >>
> >> Mel
> >>
> >>
> >> On 4/12/2018 4:08 PM, Menelaos Symeonides wrote:
> >>
> >>> Hi Curtis,
> >>>
> >>> No, that doesn't fix it (thank you for alerting me to the recommended
> >>> installation location, though). I also tried placing it under
> >>> C:\Users\<MyUserName>\Documents\Fiji.app, but it behaves the same,
> with
> >>> or without admin rights.
> >>>
> >>> I was able to replicate this issue on 3 different Windows 10 64-bit
> >>> systems and one Windows 7 32-bit computer.
> >>>
> >>> Thanks,
> >>> Mel
> >>>
> >>>
> >>> On 4/12/2018 1:30 PM, Curtis Rueden wrote:
> >>>
> >>>> Hi Mel,
> >>>>
> >>>> Have you tried putting your Fiji installation into
> >>>> C:\Users\<YourUserName>\Fiji.app, as recommended by the installation
> >>>> instructions [1]?
> >>>>
> >>>> There are often permissions issues placing the Fiji.app installation
> >>>> outside of folders the current user controls.
> >>>>
> >>>> If that also does not work for you, let us know, and I can try to
> >>>> reproduce
> >>>> the issue on my Windows 10 system.
> >>>>
> >>>> Regards,
> >>>> Curtis
> >>>>
> >>>> [1] http://imagej.net/Fiji/Downloads#Installation
> >>>>
> >>>> --
> >>>> Curtis Rueden
> >>>> LOCI software architect - https://loci.wisc.edu/software
> >>>> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> >>>> Did you know ImageJ has a forum? http://forum.imagej.net/
> >>>>
> >>>>
> >>>> On Wed, Apr 11, 2018 at 10:45 PM, Menelaos Symeonides <
> [hidden email]
> >>>> >
> >>>> wrote:
> >>>>
> >>>> Hello,
> >>>>>
> >>>>> I am trying to increase the available memory in Fiji (ImageJ
> >>>>> 2.0.0-rc-65/1.51w, on Windows 10 64-bit) and am getting an error
> saying
> >>>>> that imagej.cfg could not be edited. There is no imagej.cfg file in
> the
> >>>>> Fiji root folder, and none is ever created. The Fiji location is
> >>>>> C:\Fiji.app\.
> >>>>>
> >>>>> I have tried running ImageJ-win64.exe as administrator, and have also
> >>>>> tried deleting the java folder and setting my environment variables
> so
> >>>>> that
> >>>>> it can use my own java version. I also tried creating a dummy
> >>>>> imagej.cfg
> >>>>> file. I even tried deleting my Fiji installation entirely and
> >>>>> re-downloading a fresh one, same thing happens. This is also
> happening
> >>>>> on
> >>>>> two different Windows 10 machines. Otherwise, ImageJ is working
> fine, I
> >>>>> just can't change my memory availability.
> >>>>>
> >>>>> Help would be appreciated!
> >>>>>
> >>>>> Mel
> >>>>>
> >>>>>
> >>>>> --
> >>>>> Menelaos Symeonides
> >>>>> Post-Doctoral Associate, Thali Lab
> >>>>> Department of Microbiology and Molecular Genetics
> >>>>> University of Vermont
> >>>>> 318 Stafford Hall
> >>>>> 95 Carrigan Dr
> >>>>> <https://maps.google.com/?q=95+Carrigan+Dr+%0D%0A+++++++++
> +++++++++++++Burlington,+VT+05405&entry=gmail&source=g>
> >>>>> Burlington, VT 05405
> >>>>> [hidden email]
> >>>>> Phone: 802-656-1161
> >>>>>
> >>>>> --
> >>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>>>>
> >>>>> --
> >>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>>>
> >>>
> >>
> >
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Fri, 20 Apr 2018 15:19:11 -0500
> From:    Curtis Rueden <[hidden email]>
> Subject: Re: Incorporating a plugin into the ij.jar file
>
> Hi Dan,
>
> Before we dive into technical details: could you describe why you want to
> do this? What is your use case? Are you trying to make an "uber-JAR" [1]?
> If so, why?
>
> Regards,
> Curtis
>
> [1] https://imagej.net/Uber-JAR
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Fri, Apr 20, 2018 at 2:16 PM, Dan McDonald <mcdonalddw@
> phenotypescreening.com> wrote:
>
> > Dear List,
> >
> >
> >
> > I would like to incorporate the Skeletonize (2D/3D) plugin into the
> ij.jar
> > file.  I have been unsuccessful in finding a way to do so.
> >
> >
> >
> > I have the Skeletonize (2D/3D) executable jar file located in my plugin
> > folder.  I successfully run the plugin on a daily basis when I use
> ImageJ.
> > I cannot figure out how to add a plugin that is in my plugin folder to
> the
> > ij.jar.
> >
> >
> >
> > I have "uncompressed" the ij.jar and placed the Skeletonize3D.class file
> in
> > the jar's plugin folder.  I then went into the IJ Properties.txt file and
> > modified it to add Skeletonize (2D/3D) as a user plugin. As shown below:
> >
> >
> >
> > # Install user plugins located in ij.jar to Plugins>User Plugins submenu
> >
> >
> >
> > user_plugins01="Skeletonize (2D/3D)",ij.plugin.Skeletonize3D_
> >
> >
> >
> > (I am not sure what the arguments above are supposed to be.  I could not
> > find documentation on adding user plugins via the IJProperties.txt route.
> > What I did looked the closest to want other lines had in them.)
> >
> >
> >
> > I then rezipped everything.
> >
> >
> >
> > When next I startup ImageJ the plugin shows up on the user plugin menu as
> > expected.
> >
> >
> >
> > Unfortunately I get the following error messages when I select the
> > skeletonize function.
> >
> >
> >
> > ImageJ 1.51p; Java 1.8.0_141 [64-bit]; Linux 3.13.0-37-generic; 16MB of
> > 22020MB (<1%)
> >
> > java.lang.NoClassDefFoundError: ij/plugin/Skeletonize3D_ (wrong name:
> > Skeletonize3D_/Skeletonize3D_)
> >
> >                at java.lang.ClassLoader.defineClass1(Native Method)
> >
> >                at java.lang.ClassLoader.defineClass(ClassLoader.java:
> 763)
> >
> >                at
> > java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
> >
> >                at
> > java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
> >
> >                at java.net.URLClassLoader.access
> > $100(URLClassLoader.java:73)
> >
> >                at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
> >
> >                at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
> >
> >                at java.security.AccessController.doPrivileged(Native
> > Method)
> >
> >                at java.net.URLClassLoader.findCl
> > ass(URLClassLoader.java:361)
> >
> >                at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
> >
> >                at
> > sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
> >
> >                at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
> >
> >                at java.lang.Class.forName0(Native Method)
> >
> >                at java.lang.Class.forName(Class.java:264)
> >
> >                at ij.IJ.runPlugIn(IJ.java:184)
> >
> >                at ij.Executer.runCommand(Executer.java:137)
> >
> >                at ij.Executer.run(Executer.java:66)
> >
> >                at java.lang.Thread.run(Thread.java:748)
> >
> >
> >
> > I am not sure if my syntax is incorrect in IJProperties.txt or if I need
> to
> > do more than just drop a class file in the ij.jar plugin folder or both.
> >
> >
> >
> > I am not a java person.  Any assistance or pointers to documentation
> would
> > be much appreciated.
> >
> >
> >
> > Thank you,
> >
> >
> >
> > Dan
> >
> >
> >
> >
> >
> >
> >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Fri, 20 Apr 2018 17:16:27 -0400
> From:    Dan McDonald <[hidden email]>
> Subject: Re: Incorporating a plugin into the ij.jar file
>
> Hi Curtis,
>
> I have a java application which runs ImageJ in a headless mode.  I wrote
> all of the ImageJ macro code but not the java application itself.  ImageJ
> was bundled with an older version of skeletonize.  This ran just fine in my
> application.  I get improved performance with Ignacio's new version.
>
> I have used NetBeans to make simple changes to the Java application. I
> thought adding the Skeletonize3D plugin to the ImageJ internal plugins
> would be simple.  But I just don't know enough to make it work.
>
> Dan
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Curtis Rueden
> Sent: Friday, April 20, 2018 4:19 PM
> To: [hidden email]
> Subject: Re: Incorporating a plugin into the ij.jar file
>
> Hi Dan,
>
> Before we dive into technical details: could you describe why you want to
> do this? What is your use case? Are you trying to make an "uber-JAR" [1]?
> If so, why?
>
> Regards,
> Curtis
>
> [1] https://imagej.net/Uber-JAR
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Fri, Apr 20, 2018 at 2:16 PM, Dan McDonald <mcdonalddw@
> phenotypescreening.com> wrote:
>
> > Dear List,
> >
> >
> >
> > I would like to incorporate the Skeletonize (2D/3D) plugin into the
> ij.jar
> > file.  I have been unsuccessful in finding a way to do so.
> >
> >
> >
> > I have the Skeletonize (2D/3D) executable jar file located in my plugin
> > folder.  I successfully run the plugin on a daily basis when I use
> ImageJ.
> > I cannot figure out how to add a plugin that is in my plugin folder to
> the
> > ij.jar.
> >
> >
> >
> > I have "uncompressed" the ij.jar and placed the Skeletonize3D.class file
> in
> > the jar's plugin folder.  I then went into the IJ Properties.txt file and
> > modified it to add Skeletonize (2D/3D) as a user plugin. As shown below:
> >
> >
> >
> > # Install user plugins located in ij.jar to Plugins>User Plugins submenu
> >
> >
> >
> > user_plugins01="Skeletonize (2D/3D)",ij.plugin.Skeletonize3D_
> >
> >
> >
> > (I am not sure what the arguments above are supposed to be.  I could not
> > find documentation on adding user plugins via the IJProperties.txt route.
> > What I did looked the closest to want other lines had in them.)
> >
> >
> >
> > I then rezipped everything.
> >
> >
> >
> > When next I startup ImageJ the plugin shows up on the user plugin menu as
> > expected.
> >
> >
> >
> > Unfortunately I get the following error messages when I select the
> > skeletonize function.
> >
> >
> >
> > ImageJ 1.51p; Java 1.8.0_141 [64-bit]; Linux 3.13.0-37-generic; 16MB of
> > 22020MB (<1%)
> >
> > java.lang.NoClassDefFoundError: ij/plugin/Skeletonize3D_ (wrong name:
> > Skeletonize3D_/Skeletonize3D_)
> >
> >                at java.lang.ClassLoader.defineClass1(Native Method)
> >
> >                at java.lang.ClassLoader.defineClass(ClassLoader.java:
> 763)
> >
> >                at
> > java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
> >
> >                at
> > java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
> >
> >                at java.net.URLClassLoader.access
> > $100(URLClassLoader.java:73)
> >
> >                at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
> >
> >                at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
> >
> >                at java.security.AccessController.doPrivileged(Native
> > Method)
> >
> >                at java.net.URLClassLoader.findCl
> > ass(URLClassLoader.java:361)
> >
> >                at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
> >
> >                at
> > sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
> >
> >                at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
> >
> >                at java.lang.Class.forName0(Native Method)
> >
> >                at java.lang.Class.forName(Class.java:264)
> >
> >                at ij.IJ.runPlugIn(IJ.java:184)
> >
> >                at ij.Executer.runCommand(Executer.java:137)
> >
> >                at ij.Executer.run(Executer.java:66)
> >
> >                at java.lang.Thread.run(Thread.java:748)
> >
> >
> >
> > I am not sure if my syntax is incorrect in IJProperties.txt or if I need
> to
> > do more than just drop a class file in the ij.jar plugin folder or both.
> >
> >
> >
> > I am not a java person.  Any assistance or pointers to documentation
> would
> > be much appreciated.
> >
> >
> >
> > Thank you,
> >
> >
> >
> > Dan
> >
> >
> >
> >
> >
> >
> >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> Date:    Fri, 20 Apr 2018 16:33:13 -0500
> From:    Curtis Rueden <[hidden email]>
> Subject: Re: Incorporating a plugin into the ij.jar file
>
> Hi Dan,
>
> Thanks for the additional details.
>
> If I understand correctly, you are talking about using this project:
>
>   Plugins>Skeleton, "Skeletonize (2D/3D)"
>   sc.fiji.skeletonize3D.Skeletonize3D_
>   https://github.com/fiji/Skeletonize3D
>
> In lieu of ImageJ1's built-in:
>
>   Process>Binary>Skeletonize
>   ij.plugin.filter.Binary("skel")
>
> If so, why not simply depend on the Skeletonize3D_.jar library in addition
> to ij.jar? Why do you need to create a modified ij.jar?
>
> Is your application code published anywhere?
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Fri, Apr 20, 2018 at 4:16 PM, Dan McDonald <
> [hidden email]> wrote:
>
> > Hi Curtis,
> >
> > I have a java application which runs ImageJ in a headless mode.  I wrote
> > all of the ImageJ macro code but not the java application itself.  ImageJ
> > was bundled with an older version of skeletonize.  This ran just fine in
> my
> > application.  I get improved performance with Ignacio's new version.
> >
> > I have used NetBeans to make simple changes to the Java application. I
> > thought adding the Skeletonize3D plugin to the ImageJ internal plugins
> > would be simple.  But I just don't know enough to make it work.
> >
> > Dan
> >
> > -----Original Message-----
> > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> > Curtis Rueden
> > Sent: Friday, April 20, 2018 4:19 PM
> > To: [hidden email]
> > Subject: Re: Incorporating a plugin into the ij.jar file
> >
> > Hi Dan,
> >
> > Before we dive into technical details: could you describe why you want to
> > do this? What is your use case? Are you trying to make an "uber-JAR" [1]?
> > If so, why?
> >
> > Regards,
> > Curtis
> >
> > [1] https://imagej.net/Uber-JAR
> >
> > --
> > Curtis Rueden
> > LOCI software architect - https://loci.wisc.edu/software
> > ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> > Did you know ImageJ has a forum? http://forum.imagej.net/
> >
> >
> > On Fri, Apr 20, 2018 at 2:16 PM, Dan McDonald <mcdonalddw@
> > phenotypescreening.com> wrote:
> >
> > > Dear List,
> > >
> > >
> > >
> > > I would like to incorporate the Skeletonize (2D/3D) plugin into the
> > ij.jar
> > > file.  I have been unsuccessful in finding a way to do so.
> > >
> > >
> > >
> > > I have the Skeletonize (2D/3D) executable jar file located in my plugin
> > > folder.  I successfully run the plugin on a daily basis when I use
> > ImageJ.
> > > I cannot figure out how to add a plugin that is in my plugin folder to
> > the
> > > ij.jar.
> > >
> > >
> > >
> > > I have "uncompressed" the ij.jar and placed the Skeletonize3D.class
> file
> > in
> > > the jar's plugin folder.  I then went into the IJ Properties.txt file
> and
> > > modified it to add Skeletonize (2D/3D) as a user plugin. As shown
> below:
> > >
> > >
> > >
> > > # Install user plugins located in ij.jar to Plugins>User Plugins
> submenu
> > >
> > >
> > >
> > > user_plugins01="Skeletonize (2D/3D)",ij.plugin.Skeletonize3D_
> > >
> > >
> > >
> > > (I am not sure what the arguments above are supposed to be.  I could
> not
> > > find documentation on adding user plugins via the IJProperties.txt
> route.
> > > What I did looked the closest to want other lines had in them.)
> > >
> > >
> > >
> > > I then rezipped everything.
> > >
> > >
> > >
> > > When next I startup ImageJ the plugin shows up on the user plugin menu
> as
> > > expected.
> > >
> > >
> > >
> > > Unfortunately I get the following error messages when I select the
> > > skeletonize function.
> > >
> > >
> > >
> > > ImageJ 1.51p; Java 1.8.0_141 [64-bit]; Linux 3.13.0-37-generic; 16MB of
> > > 22020MB (<1%)
> > >
> > > java.lang.NoClassDefFoundError: ij/plugin/Skeletonize3D_ (wrong name:
> > > Skeletonize3D_/Skeletonize3D_)
> > >
> > >                at java.lang.ClassLoader.defineClass1(Native Method)
> > >
> > >                at java.lang.ClassLoader.defineClass(ClassLoader.java:
> > 763)
> > >
> > >                at
> > > java.security.SecureClassLoader.defineClass(
> SecureClassLoader.java:142)
> > >
> > >                at
> > > java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
> > >
> > >                at java.net.URLClassLoader.access
> > > $100(URLClassLoader.java:73)
> > >
> > >                at java.net.URLClassLoader$1.run(
> URLClassLoader.java:368)
> > >
> > >                at java.net.URLClassLoader$1.run(
> URLClassLoader.java:362)
> > >
> > >                at java.security.AccessController.doPrivileged(Native
> > > Method)
> > >
> > >                at java.net.URLClassLoader.findCl
> > > ass(URLClassLoader.java:361)
> > >
> > >                at java.lang.ClassLoader.loadClass(ClassLoader.java:
> 424)
> > >
> > >                at
> > > sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
> > >
> > >                at java.lang.ClassLoader.loadClass(ClassLoader.java:
> 357)
> > >
> > >                at java.lang.Class.forName0(Native Method)
> > >
> > >                at java.lang.Class.forName(Class.java:264)
> > >
> > >                at ij.IJ.runPlugIn(IJ.java:184)
> > >
> > >                at ij.Executer.runCommand(Executer.java:137)
> > >
> > >                at ij.Executer.run(Executer.java:66)
> > >
> > >                at java.lang.Thread.run(Thread.java:748)
> > >
> > >
> > >
> > > I am not sure if my syntax is incorrect in IJProperties.txt or if I
> need
> > to
> > > do more than just drop a class file in the ij.jar plugin folder or
> both.
> > >
> > >
> > >
> > > I am not a java person.  Any assistance or pointers to documentation
> > would
> > > be much appreciated.
> > >
> > >
> > >
> > > Thank you,
> > >
> > >
> > >
> > > Dan
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------
>
> End of IMAGEJ Digest - 19 Apr 2018 to 20 Apr 2018 (#2018-113)
> *************************************************************
>

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