Loading plugins into FIJI
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I just downloaded FIJI. When I try to install macros that I have previously used in ImageJ I get the following error: WARNING: The PluginClassLoader cannot be reset. The macros do not appear in under the plugins menu even after restarting FIJI. The macros are located in the plugins folder, but they do not show up in the list. The macros are text files that I created for image analysis using the basic version of ImageJ (i.e. not FIJI). Any suggestions on how to solve this problem?
-- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Dear Jill,
As far as I remember the macros should have as extension *.ijm and not *.txt to be found in the plugins menu in Fiji. Kees -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jill Kreiling Sent: 09 January 2015 20:25 To: [hidden email] Subject: Loading plugins into FIJI I just downloaded FIJI. When I try to install macros that I have previously used in ImageJ I get the following error: WARNING: The PluginClassLoader cannot be reset. The macros do not appear in under the plugins menu even after restarting FIJI. The macros are located in the plugins folder, but they do not show up in the list. The macros are text files that I created for image analysis using the basic version of ImageJ (i.e. not FIJI). Any suggestions on how to solve this problem? -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Thanks Kees. I tried changing the extension but it still gives me the
warning that the plugin class loader can't be reset, and the file doesn't show up under the plugins menu. Thanks for your help. Jill On Mon, Jan 12, 2015 at 4:09 AM, Straatman, Kees (Dr.) <[hidden email] > wrote: > Dear Jill, > > As far as I remember the macros should have as extension *.ijm and not > *.txt to be found in the plugins menu in Fiji. > > Kees > > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of > Jill Kreiling > Sent: 09 January 2015 20:25 > To: [hidden email] > Subject: Loading plugins into FIJI > > I just downloaded FIJI. When I try to install macros that I have > previously used in ImageJ I get the following error: WARNING: The > PluginClassLoader cannot be reset. The macros do not appear in under the > plugins menu even after restarting FIJI. The macros are located in the > plugins folder, but they do not show up in the list. The macros are text > files that I created for image analysis using the basic version of ImageJ > (i.e. not FIJI). Any suggestions on how to solve this problem? > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- Jill Kreiling, Ph.D. Assistant Professor, Research Department of Molecular Biology, Cell Biology and Biochemistry Brown University Providence, RI 02903 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Jill,
>the plugin class loader can't be reset You get this message because ImageJ 1.x allows new plugins to be discovered dynamically, while Fiji does not. Technical details are available here[1]. Basically it means that you always have to restart Fiji for new plugins to show up in the menu. I am assuming you used the Plugins > Install... or Plugins > Install Plugin... command to install your macro. Per the user guide[2], the requirements to get a Macro into the Plugins menu is 1) to have a .ijm extension, and 2) be located in Imagej/plugins (or Fiji/plugins). The two Install commands copy your plugin to your Fiji/plugins directory, but if your macro is a .txt it still wouldn't be recognized by Fiji for addition to the menus. >I tried changing the extension If you used Plugins > Install... and changed the extension in the "Save Plugin, Macro or Script..." dialog, I ran into a bug where your extension may not actually have changed. Check your Fiji/plugins directory and see if your macros are there already as .txts. If not, just copy them there manually. Then change them to .ijms, restart Fiji and your macros should show up in the menus again. One other thing - [2] also mentions the past requirement of an underscore ( _ ) in the plugin name. This is still a requirement in Fiji, so ensure your macro file names have an underscore. Finally, I opened a new ticket to try and provide future users better feedback when running these commands in Fiji[3]. Best, Mark [1] https://github.com/imagej/ij1-patcher/issues/31 [2] http://imagej.net/docs/guide/146-14.html#sub:Macros-ExtendingIJ [3] https://github.com/imagej/imagej-legacy/issues/98 On Mon, Jan 12, 2015 at 9:56 AM, Kreiling, Jill <[hidden email]> wrote: > Thanks Kees. I tried changing the extension but it still gives me the > warning that the plugin class loader can't be reset, and the file doesn't > show up under the plugins menu. > > Thanks for your help. > Jill > > On Mon, Jan 12, 2015 at 4:09 AM, Straatman, Kees (Dr.) < > [hidden email] > > wrote: > > > Dear Jill, > > > > As far as I remember the macros should have as extension *.ijm and not > > *.txt to be found in the plugins menu in Fiji. > > > > Kees > > > > -----Original Message----- > > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of > > Jill Kreiling > > Sent: 09 January 2015 20:25 > > To: [hidden email] > > Subject: Loading plugins into FIJI > > > > I just downloaded FIJI. When I try to install macros that I have > > previously used in ImageJ I get the following error: WARNING: The > > PluginClassLoader cannot be reset. The macros do not appear in under the > > plugins menu even after restarting FIJI. The macros are located in the > > plugins folder, but they do not show up in the list. The macros are text > > files that I created for image analysis using the basic version of ImageJ > > (i.e. not FIJI). Any suggestions on how to solve this problem? > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > -- > Jill Kreiling, Ph.D. > Assistant Professor, Research > Department of Molecular Biology, Cell Biology and Biochemistry > Brown University > Providence, RI 02903 > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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> On 13. Jan 2015, at 17:37, Mark Hiner <[hidden email]> wrote:
> > Finally, I opened a new ticket to try and provide future users better > feedback when running these commands in Fiji[3]. > > Best, > Mark > > [1] https://github.com/imagej/ij1-patcher/issues/31 > [2] http://imagej.net/docs/guide/146-14.html#sub:Macros-ExtendingIJ > [3] https://github.com/imagej/imagej-legacy/issues/98 A handy feature in ImageJ1 is that you can drag a plugin xxx_.jar onto the ImageJ main window (or the ImageJ icon), then you are asked to store it in the plugins folder. The user doesn't need not to know where this folder is (and in case of Fiji, how to open a package), he just can click OK. This feature still works in Fiji, but the user gets the mentioned error > WARNING: The PluginClassLoader cannot be reset. and he does not know how to continue. Would it be possible to translate this warning into a understandable suggestion, such as showing a dialog which explains that it is enough to restart Fiji? Norbert Vischer -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Norbert,
> Would it be possible to translate this warning into a understandable > suggestion, such as showing a dialog which explains that it is enough > to restart Fiji? Yes, that is precisely what the issue Mark recently filed is all about; see: https://github.com/imagej/imagej-legacy/issues/98 Regards, Curtis On Wed, Jan 14, 2015 at 3:11 PM, Norbert Vischer <[hidden email]> wrote: > > On 13. Jan 2015, at 17:37, Mark Hiner <[hidden email]> wrote: > > > > Finally, I opened a new ticket to try and provide future users better > > feedback when running these commands in Fiji[3]. > > > > Best, > > Mark > > > > [1] https://github.com/imagej/ij1-patcher/issues/31 > > [2] http://imagej.net/docs/guide/146-14.html#sub:Macros-ExtendingIJ > > [3] https://github.com/imagej/imagej-legacy/issues/98 > > > A handy feature in ImageJ1 is that you can drag a plugin xxx_.jar onto the > ImageJ main window (or the ImageJ icon), > then you are asked to store it in the plugins folder. The user doesn't > need not to know where this folder > is (and in case of Fiji, how to open a package), he just can click OK. > > This feature still works in Fiji, but the user gets the mentioned error > > WARNING: The PluginClassLoader cannot be reset. > and he does not know how to continue. > > Would it be possible to translate this warning into a understandable > suggestion, > such as showing a dialog which explains that it is enough to restart Fiji? > > > > Norbert Vischer > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Mark Hiner
Hi Mark,
Sorry for the delayed response, I got side tracked writing a grant. Thank you for the information on how to install ImageJ macros in FIJI. The problem was indeed that the extension didn't change after I manually changed it. It actually had 2 extensions - .ijm.txt. Strangely I couldn't see that unless I opened it in Notepad++. I solved the problem by opening the macro using the edit command: Pluggins-> macro->edit. I can open the text file there and save it with the .ijm extension, then it shows up fine. I've been able to import all of my macros created in ImageJ using this process. Thank you for your help! Jill On Tue, Jan 13, 2015 at 11:37 AM, Mark Hiner <[hidden email]> wrote: > Hi Jill, > > >the plugin class loader can't be reset > > You get this message because ImageJ 1.x allows new plugins to be discovered > dynamically, while Fiji does not. Technical details are available here[1]. > Basically it means that you always have to restart Fiji for new plugins to > show up in the menu. > > I am assuming you used the Plugins > Install... or Plugins > Install > Plugin... command to install your macro. Per the user guide[2], the > requirements to get a Macro into the Plugins menu is 1) to have a .ijm > extension, and 2) be located in Imagej/plugins (or Fiji/plugins). The two > Install commands copy your plugin to your Fiji/plugins directory, but if > your macro is a .txt it still wouldn't be recognized by Fiji for addition > to the menus. > > >I tried changing the extension > > If you used Plugins > Install... and changed the extension in the "Save > Plugin, Macro or Script..." dialog, I ran into a bug where your extension > may not actually have changed. Check your Fiji/plugins directory and see if > your macros are there already as .txts. If not, just copy them there > manually. Then change them to .ijms, restart Fiji and your macros should > show up in the menus again. > > One other thing - [2] also mentions the past requirement of an underscore ( > _ ) in the plugin name. This is still a requirement in Fiji, so ensure your > macro file names have an underscore. > > Finally, I opened a new ticket to try and provide future users better > feedback when running these commands in Fiji[3]. > > Best, > Mark > > [1] https://github.com/imagej/ij1-patcher/issues/31 > [2] http://imagej.net/docs/guide/146-14.html#sub:Macros-ExtendingIJ > [3] https://github.com/imagej/imagej-legacy/issues/98 > > On Mon, Jan 12, 2015 at 9:56 AM, Kreiling, Jill <[hidden email]> > wrote: > > > Thanks Kees. I tried changing the extension but it still gives me the > > warning that the plugin class loader can't be reset, and the file doesn't > > show up under the plugins menu. > > > > Thanks for your help. > > Jill > > > > On Mon, Jan 12, 2015 at 4:09 AM, Straatman, Kees (Dr.) < > > [hidden email] > > > wrote: > > > > > Dear Jill, > > > > > > As far as I remember the macros should have as extension *.ijm and not > > > *.txt to be found in the plugins menu in Fiji. > > > > > > Kees > > > > > > -----Original Message----- > > > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of > > > Jill Kreiling > > > Sent: 09 January 2015 20:25 > > > To: [hidden email] > > > Subject: Loading plugins into FIJI > > > > > > I just downloaded FIJI. When I try to install macros that I have > > > previously used in ImageJ I get the following error: WARNING: The > > > PluginClassLoader cannot be reset. The macros do not appear in under > the > > > plugins menu even after restarting FIJI. The macros are located in the > > > plugins folder, but they do not show up in the list. The macros are > text > > > files that I created for image analysis using the basic version of > ImageJ > > > (i.e. not FIJI). Any suggestions on how to solve this problem? > > > > > > -- > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > -- > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > > > > > > -- > > Jill Kreiling, Ph.D. > > Assistant Professor, Research > > Department of Molecular Biology, Cell Biology and Biochemistry > > Brown University > > Providence, RI 02903 > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- Jill Kreiling, Ph.D. Assistant Professor, Research Department of Molecular Biology, Cell Biology and Biochemistry Brown University Providence, RI 02903 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Jill,
> It actually had 2 extensions - .ijm.txt. Strangely I couldn't see > that unless I opened it in Notepad++. This is a problem with Windows. You have to manually configure Windows not to hide file extensions: http://windows.microsoft.com/en-us/windows/show-hide-file-name-extensions This setting is the first thing I change on every Windows system I use, since keeping file extensions hidden causes serious undesirable side effects. Regards, Curtis On Mon, Feb 23, 2015 at 4:12 PM, Kreiling, Jill <[hidden email]> wrote: > Hi Mark, > > Sorry for the delayed response, I got side tracked writing a grant. Thank > you for the information on how to install ImageJ macros in FIJI. The > problem was indeed that the extension didn't change after I manually > changed it. It actually had 2 extensions - .ijm.txt. Strangely I couldn't > see that unless I opened it in Notepad++. I solved the problem by opening > the macro using the edit command: Pluggins-> macro->edit. I can open the > text file there and save it with the .ijm extension, then it shows up > fine. I've been able to import all of my macros created in ImageJ using > this process. > > Thank you for your help! > Jill > > On Tue, Jan 13, 2015 at 11:37 AM, Mark Hiner <[hidden email]> wrote: > > > Hi Jill, > > > > >the plugin class loader can't be reset > > > > You get this message because ImageJ 1.x allows new plugins to be > discovered > > dynamically, while Fiji does not. Technical details are available > here[1]. > > Basically it means that you always have to restart Fiji for new plugins > to > > show up in the menu. > > > > I am assuming you used the Plugins > Install... or Plugins > Install > > Plugin... command to install your macro. Per the user guide[2], the > > requirements to get a Macro into the Plugins menu is 1) to have a .ijm > > extension, and 2) be located in Imagej/plugins (or Fiji/plugins). The two > > Install commands copy your plugin to your Fiji/plugins directory, but if > > your macro is a .txt it still wouldn't be recognized by Fiji for addition > > to the menus. > > > > >I tried changing the extension > > > > If you used Plugins > Install... and changed the extension in the "Save > > Plugin, Macro or Script..." dialog, I ran into a bug where your extension > > may not actually have changed. Check your Fiji/plugins directory and see > if > > your macros are there already as .txts. If not, just copy them there > > manually. Then change them to .ijms, restart Fiji and your macros should > > show up in the menus again. > > > > One other thing - [2] also mentions the past requirement of an > underscore ( > > _ ) in the plugin name. This is still a requirement in Fiji, so ensure > your > > macro file names have an underscore. > > > > Finally, I opened a new ticket to try and provide future users better > > feedback when running these commands in Fiji[3]. > > > > Best, > > Mark > > > > [1] https://github.com/imagej/ij1-patcher/issues/31 > > [2] http://imagej.net/docs/guide/146-14.html#sub:Macros-ExtendingIJ > > [3] https://github.com/imagej/imagej-legacy/issues/98 > > > > On Mon, Jan 12, 2015 at 9:56 AM, Kreiling, Jill <[hidden email] > > > > wrote: > > > > > Thanks Kees. I tried changing the extension but it still gives me the > > > warning that the plugin class loader can't be reset, and the file > doesn't > > > show up under the plugins menu. > > > > > > Thanks for your help. > > > Jill > > > > > > On Mon, Jan 12, 2015 at 4:09 AM, Straatman, Kees (Dr.) < > > > [hidden email] > > > > wrote: > > > > > > > Dear Jill, > > > > > > > > As far as I remember the macros should have as extension *.ijm and > not > > > > *.txt to be found in the plugins menu in Fiji. > > > > > > > > Kees > > > > > > > > -----Original Message----- > > > > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf > Of > > > > Jill Kreiling > > > > Sent: 09 January 2015 20:25 > > > > To: [hidden email] > > > > Subject: Loading plugins into FIJI > > > > > > > > I just downloaded FIJI. When I try to install macros that I have > > > > previously used in ImageJ I get the following error: WARNING: The > > > > PluginClassLoader cannot be reset. The macros do not appear in under > > the > > > > plugins menu even after restarting FIJI. The macros are located in > the > > > > plugins folder, but they do not show up in the list. The macros are > > text > > > > files that I created for image analysis using the basic version of > > ImageJ > > > > (i.e. not FIJI). Any suggestions on how to solve this problem? > > > > > > > > -- > > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > > > -- > > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > > > > > > > > > > > -- > > > Jill Kreiling, Ph.D. > > > Assistant Professor, Research > > > Department of Molecular Biology, Cell Biology and Biochemistry > > > Brown University > > > Providence, RI 02903 > > > > > > -- > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > -- > Jill Kreiling, Ph.D. > Assistant Professor, Research > Department of Molecular Biology, Cell Biology and Biochemistry > Brown University > Providence, RI 02903 > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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