macros/AutoRun/*.ijm
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Dear Fiji users,
Fiji learnt a new trick today: it will run the macros stored in the macros/AutoRun/ directory as .ijm files (if any) when starting, unless you have a locally-modified StartupMacros.fiji.ijm. This is in particular useful if you want to serve macros via an update site that need to be installed (e.g. to be available as keyboard shortcuts). Ciao, Johannes P.S.: If you are interested in the details, or want to make the same available in "vanilla ImageJ": https://github.com/fiji/fiji/commit/371d3786ffcacb2c5f2ebbfb31de7526180e6338 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hey Johannes,
that is a nice thought to make things more elegant here. I'll probably use that some time soon.. Regards, Rainer Am 15.03.2013 22:43, schrieb Johannes Schindelin: > Dear Fiji users, > > Fiji learnt a new trick today: it will run the macros stored in the > macros/AutoRun/ directory as .ijm files (if any) when starting, unless you > have a locally-modified StartupMacros.fiji.ijm. > > This is in particular useful if you want to serve macros via an update > site that need to be installed (e.g. to be available as keyboard > shortcuts). > > Ciao, > Johannes > > P.S.: If you are interested in the details, or want to make the same > available in "vanilla ImageJ": > https://github.com/fiji/fiji/commit/371d3786ffcacb2c5f2ebbfb31de7526180e6338 > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Dear Johannes,
On 18.03.2013 17:13, Rainer M. Engel wrote: > Hey Johannes, > > that is a nice thought to make things more elegant here. I absolutely agree with Rainer, this is a very nice feature! Did I get this right, as soon as you're having a modified "StartupMacros.fiji.ijm" the contents of the AutoRun directory will be ignored? Cheers Niko -- Niko Ehrenfeuchter Imaging Core Facility Kragenbau, Room G1055 Biozentrum, University of Basel Klingelbergstrasse 50/70 CH-4056 Basel (Switzerland) Office: +41 (61) 26 72673 Email: [hidden email] -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Niko,
On Mon, 18 Mar 2013, Niko Ehrenfeuchter wrote: > On 18.03.2013 17:13, Rainer M. Engel wrote: > > > that is a nice thought to make things more elegant here. > > I absolutely agree with Rainer, this is a very nice feature! > > Did I get this right, as soon as you're having a modified > "StartupMacros.fiji.ijm" the contents of the AutoRun directory will be > ignored? What I meant is: if you modified StartupMacros.fiji.ijm, the updater will not mark this file for update and therefore you will not get the new version that looks at macros/AutoRun/. Of course, in such a case you could still copy the relevant part from https://github.com/fiji/fiji/blob/master/macros/StartupMacros.fiji.ijm#L48 and paste it into your locally-modified StartupMacros.fiji.ijm. And I completely forgot that StartupMacros.fiji.ijm would not be executed if there is a StartupMacros.ijm in macros/, either... Ciao, Johannes -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi everyone,
> Of course, in such a case you could still copy the relevant part from > > https://github.com/fiji/fiji/blob/master/macros/StartupMacros.fiji.ijm#L48 > > and paste it into your locally-modified StartupMacros.fiji.ijm. Or, you could take your local modifications and "externalize" them by moving them into the macros/AutoRun/ folder, so that your StartupMacros.fiji.ijm is no longer considered locally modified. You still receive the benefit of your customizations, and Fiji can still keep itself fully up to date in the future too! Regards, Curtis On Mon, Mar 18, 2013 at 11:41 AM, Johannes Schindelin <[hidden email]> wrote: > Hi Niko, > > On Mon, 18 Mar 2013, Niko Ehrenfeuchter wrote: > >> On 18.03.2013 17:13, Rainer M. Engel wrote: >> >> > that is a nice thought to make things more elegant here. >> >> I absolutely agree with Rainer, this is a very nice feature! >> >> Did I get this right, as soon as you're having a modified >> "StartupMacros.fiji.ijm" the contents of the AutoRun directory will be >> ignored? > > What I meant is: if you modified StartupMacros.fiji.ijm, the updater will > not mark this file for update and therefore you will not get the new > version that looks at macros/AutoRun/. > > Of course, in such a case you could still copy the relevant part from > > > > and paste it into your locally-modified StartupMacros.fiji.ijm. > > And I completely forgot that StartupMacros.fiji.ijm would not be executed > if there is a StartupMacros.ijm in macros/, either... > > Ciao, > Johannes > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Dear Curtis,
On 18.03.2013 17:49, Curtis Rueden wrote: > Hi everyone, > >> Of course, in such a case you could still copy the relevant part from >> >> > https://github.com/fiji/fiji/blob/master/macros/StartupMacros.fiji.ijm#L48 >> >> and paste it into your locally-modified StartupMacros.fiji.ijm. > > Or, you could take your local modifications and "externalize" them by > moving them into the macros/AutoRun/ folder, so that your > StartupMacros.fiji.ijm is no longer considered locally modified. You still > receive the benefit of your customizations, and Fiji can still keep itself > fully up to date in the future too! that's exactly why I like the approach of the separate directory so much. I just have to tell my users here how to reach this state with their possibly modified FiJi installations :) Thanks for sharing, Niko -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by dscho
Am 18.03.2013 17:41, schrieb Johannes Schindelin:
> Hi Niko, > > On Mon, 18 Mar 2013, Niko Ehrenfeuchter wrote: > >> On 18.03.2013 17:13, Rainer M. Engel wrote: >> >>> that is a nice thought to make things more elegant here. >> >> I absolutely agree with Rainer, this is a very nice feature! >> >> Did I get this right, as soon as you're having a modified >> "StartupMacros.fiji.ijm" the contents of the AutoRun directory will be >> ignored? > > What I meant is: if you modified StartupMacros.fiji.ijm, the updater will > not mark this file for update and therefore you will not get the new > version that looks at macros/AutoRun/. > > Of course, in such a case you could still copy the relevant part from > > https://github.com/fiji/fiji/blob/master/macros/StartupMacros.fiji.ijm#L48 > > and paste it into your locally-modified StartupMacros.fiji.ijm. > > And I completely forgot that StartupMacros.fiji.ijm would not be executed > if there is a StartupMacros.ijm in macros/, either... My StartupMacros doesn't do what it should, I guess. I've downloaded a fresh Fiji for Windows and updated it. I installed "ActionBar" and created an "AutoRun" folder as sub-directory for "macros", but my ActionBar isn't started, although the macro command for itself works.. I saved a short "Hello world"-macro there (to AutoRun) either, which isn't executed too. If an unaltered "StartupMacros.fiji.ijm" executes all scripts from "AutoRun", I would like to have this folder directly from the installation with maybe a short help-file, explaining what this folder is meant for. Best regards, Rainer -- Rainer M. Engel, Dipl. Digital Artist scientific|Media GbR Pichelsdorfer Str. 143 13595 Berlin -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Rainer,
On Tue, 30 Jul 2013, Rainer M. Engel wrote: > Am 18.03.2013 17:41, schrieb Johannes Schindelin: > > > > On Mon, 18 Mar 2013, Niko Ehrenfeuchter wrote: > > > >> On 18.03.2013 17:13, Rainer M. Engel wrote: > >> > >>> that is a nice thought to make things more elegant here. > >> > >> I absolutely agree with Rainer, this is a very nice feature! > >> > >> Did I get this right, as soon as you're having a modified > >> "StartupMacros.fiji.ijm" the contents of the AutoRun directory will be > >> ignored? > > > > What I meant is: if you modified StartupMacros.fiji.ijm, the updater will > > not mark this file for update and therefore you will not get the new > > version that looks at macros/AutoRun/. > > > > Of course, in such a case you could still copy the relevant part from > > > > https://github.com/fiji/fiji/blob/master/macros/StartupMacros.fiji.ijm#L48 > > > > and paste it into your locally-modified StartupMacros.fiji.ijm. > > > > And I completely forgot that StartupMacros.fiji.ijm would not be executed > > if there is a StartupMacros.ijm in macros/, either... > > > My StartupMacros doesn't do what it should, I guess. I've downloaded a > fresh Fiji for Windows and updated it. I installed "ActionBar" and > created an "AutoRun" folder as sub-directory for "macros", but my > ActionBar isn't started, although the macro command for itself works.. Niko actually reported this project, although he did so in the #fiji-devel chat (which is not quite as visible as the ImageJ mailing list). I'll try very hard to find the time to fix this problem as soon as possible! Ciao, Johannes -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Rainer,
On Tue, 30 Jul 2013, Johannes Schindelin wrote: > On Tue, 30 Jul 2013, Rainer M. Engel wrote: > > > Am 18.03.2013 17:41, schrieb Johannes Schindelin: > > > > > > On Mon, 18 Mar 2013, Niko Ehrenfeuchter wrote: > > > > > >> On 18.03.2013 17:13, Rainer M. Engel wrote: > > >> > > >>> that is a nice thought to make things more elegant here. > > >> > > >> I absolutely agree with Rainer, this is a very nice feature! > > >> > > >> Did I get this right, as soon as you're having a modified > > >> "StartupMacros.fiji.ijm" the contents of the AutoRun directory will > > >> be ignored? > > > > > > What I meant is: if you modified StartupMacros.fiji.ijm, the updater > > > will not mark this file for update and therefore you will not get > > > the new version that looks at macros/AutoRun/. > > > > > > Of course, in such a case you could still copy the relevant part > > > from > > > > > > https://github.com/fiji/fiji/blob/master/macros/StartupMacros.fiji.ijm#L48 > > > > > > and paste it into your locally-modified StartupMacros.fiji.ijm. > > > > > > And I completely forgot that StartupMacros.fiji.ijm would not be > > > executed if there is a StartupMacros.ijm in macros/, either... > > > > > > My StartupMacros doesn't do what it should, I guess. I've downloaded a > > fresh Fiji for Windows and updated it. I installed "ActionBar" and > > created an "AutoRun" folder as sub-directory for "macros", but my > > ActionBar isn't started, although the macro command for itself works.. > > Niko actually reported this project, although he did so in the > #fiji-devel chat (which is not quite as visible as the ImageJ mailing > list). > > I'll try very hard to find the time to fix this problem as soon as > possible! It turns out that I misread a patch in ImageJ 1.x to be nicer to Fiji than it actually is: we still have to patch the code to make sure that StartupMacros.fiji.ijm is run if it exists. This has been fixed now, along with a couple of other issues, and uploaded to the update site. Ciao, Johannes P.S.: You may have noticed that Fiji tries to leave 24 hours between bugging you about updates? So you might have to start it manually by clicking on Help>Update Fiji. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Dear list,
I had some modifications in the StartupMacros.txt which I moved to the macros/AutoRun The difference is that while being part of the StartupMacros.txt, the macro was only installed so that it could be called by the F9 key, but the macro was not executed when starting Fiji. After moving the macro to macros/AutoRun, the macro is not only installed but also executed upon starting Fiji // macro to add the marker lane to fusion western blot images macro "Western marker[f9]" { /* * Macro for adding the marker lane to the blot image * with the files from the fusion machine * ......... } Is there a way of installing without execution upon startup? Thanks, Martin |
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Hi Martin,
On Thu, 1 Aug 2013, Martin Höhne wrote: > I had some modifications in the StartupMacros.txt which I moved to the > macros/AutoRun > > The difference is that while being part of the StartupMacros.txt, the > macro was only installed so that it could be called by the F9 key, but > the macro was not executed when starting Fiji. Right, the intention of AutoRun/*.ijm was to run at start up, not necessarily to install shortcuts. > After moving the macro to macros/AutoRun, the macro is not only > installed but also executed upon starting Fiji > > > // macro to add the marker lane to fusion western blot images > macro "Western marker[f9]" { > /* > * Macro for adding the marker lane to the blot image > * with the files from the fusion machine > * > ......... > } > > Is there a way of installing without execution upon startup? forgotten. The reason is that ImageJ 1.x's concept of "installing macros" is quite limited: if you execute Plugins>Macros>Install... and select a file, that file's macros get installed, but not only that: previously installed macros simply are uninstalled. Completely. Just try it: write, say, macro1.ijm with the contents macro "Blub [f7]" { showStatus("f7"); } and, say, macro2.ijm which does the same for f6. Then install macro1.ijm with Plugins>Macros>Install..., verify that f7 triggers "f7" in the status bar, then install macro2.ijm, and f7 will no longer work! I was so close (imagine me holding my fingers about one micro-meter apart, very close to your face) trying to address that in Fiji, but I have a hunch that Wayne will fix this (and the way these fixes work, they always break the work-arounds in Fiji, and I always find out about that the hard and painful way). So in the meantime I suggest that you put your macros defining shortcuts into a single file, say, Fiji.app/macros/my-shortcuts.ijm, and then add a file install-shortcuts.ijm into your Fiji.app/macros/AutoRun containing just these two lines: run("Install...", "install=[" + getDirectory("imagej") + "/macros/my-shortcuts.ijm]"); Sorry, this is the best I can do for the moment... Johannes -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Johannes,
That works perfectly fine! No need to apologize for all the great work you´re doing! Martin |
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There's also another thing. I have written some startupmacros which have their own AutoRun code that it runs at startup. Macro that are installed via this method don't run that code, so this unfortunately does not work for me. What I used to do is just have a file called "StartupMacros.ijm" in the macros folder. This was ideal because it did not interfere with "StartupMacros.fiji.ijm" updating. It overrides it, like I want it to. And when I went to the menu item "StarupMacros" it opened in the Script editor. So my suggestion is that the AutoRun stuff is great for those who need it, but can't we keep the StartupMacros.ijm override for people who want it? Thanks! -Aaron |
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