common functions / installing multiple macro files

[Benjamin Gilbert]

I have a collection and macros and functions in a single macro text file. I
would now like to translate these routines into a toolset, which requires
making a single macro file for each operation and saving it in the
ImageJ/plugins folder.

The original approach allowed different macros to use common functions, but
it seems that an individual tool must be completely self-contained. I was
hoping that I could install a macro containing all common functions that
would be accessible to tool macros but this does not work. In general, it
appears that only a single macro file can be installed at a time.

Is there a way to do this? I don't want to have multiple instances of the
same functions in different macro files.

thanks!

[Wayne Rasband]

On Jul 31, 2009, at 10:00 AM, Benjamin Gilbert wrote:

> I have a collection and macros and functions in a single macro text  
> file. I
> would now like to translate these routines into a toolset, which  
> requires
> making a single macro file for each operation and saving it in the
> ImageJ/plugins folder.
>
> The original approach allowed different macros to use common  
> functions, but
> it seems that an individual tool must be completely self-contained.  
> I was
> hoping that I could install a macro containing all common functions  
> that
> would be accessible to tool macros but this does not work. In  
> general, it
> appears that only a single macro file can be installed at a time.
>
> Is there a way to do this? I don't want to have multiple instances  
> of the
> same functions in different macro files.

You can do this by adding the common functions to the macro language  
by calling the Interpreter.setAdditionalFunctions() method. Here is an  
example.

Create a folder in the plugins folder named MyMacros. Add these three  
files (CommonFunctions, Macro1 and Macro2) to it:

   CommonFunctions.txt

      function f1() {
          print("f1");
      }
      function f2() {
          print("f2");
      }

   Macro1.ijm

      print("Macro1");
      f1();
      f2();

   Macro2.ijm

      print("Macro2");
      f1();
      f2();

Then add this code to the StartupMacros file  
(Plugins>Macros>StartupMacros)

    macro "AutoRun" {
       path = getDirectory("plugins")+"MyMacros/CommonFunctions.txt";
       functions = File.openAsString(path);
       call("ij.macro.Interpreter.setAdditionalFunctions", functions);
   }

save it and restart ImageJ. You will now have two commands (Macro1 and  
Macro2) in the Plugins>MyMacros submenu implemented by macros that  
share the functions in CommonFunctions. CommonFunctions has a .txt  
extension and no underscore in the name so it does not appear in the  
Plugins>MyPlugins submenu. Macro1 and Macro2 have .ijm (ImageJ Macro)  
extensions so they do appear even though they do not have an  
underscore in the name.

You may decide that it's easier and better to keep the functions and  
macros in a single file (toolset) located in the ImageJ/macros/
toolsets folder. That way the macros and functions can share global  
variables, you can easily add keyboard shortcuts, the toolset can  
contain tools, toolbar menus and action tools as well as macros, and  
you can have multiple toolsets, selected from the ">>" toolbar menu.

-wayne

[Benjamin Gilbert]

Thanks for the very clear reply. I learnt how to store global
variables from an earlier post to the list using call("ij.Prefs.get",
<key>, <value>) ... but perhaps a single toolset would be a simpler
approach!

Is there likely to be support for multivariate fit functions in the
near future? I would like to fit a 2D polynomial to make an image
background.

many thanks

ben

At 4:18 PM -0400 8/1/09, Wayne Rasband wrote:

>On Jul 31, 2009, at 10:00 AM, Benjamin Gilbert wrote:
>
>>I have a collection and macros and functions in a single macro text file. I
>>would now like to translate these routines into a toolset, which requires
>>making a single macro file for each operation and saving it in the
>>ImageJ/plugins folder.
>>
>>The original approach allowed different macros to use common functions, but
>>it seems that an individual tool must be completely self-contained. I was
>>hoping that I could install a macro containing all common functions that
>>would be accessible to tool macros but this does not work. In general, it
>>appears that only a single macro file can be installed at a time.
>>
>>Is there a way to do this? I don't want to have multiple instances of the
>>same functions in different macro files.
>
>You can do this by adding the common functions to the macro language
>by calling the Interpreter.setAdditionalFunctions() method. Here is
>an example.
>
>Create a folder in the plugins folder named MyMacros. Add these
>three files (CommonFunctions, Macro1 and Macro2) to it:
>
>   CommonFunctions.txt
>
>      function f1() {
>          print("f1");
>      }
>      function f2() {
>          print("f2");
>      }
>
>   Macro1.ijm
>
>      print("Macro1");
>      f1();
>      f2();
>
>   Macro2.ijm
>
>      print("Macro2");
>      f1();
>      f2();
>
>Then add this code to the StartupMacros file (Plugins>Macros>StartupMacros)
>
>    macro "AutoRun" {
>       path = getDirectory("plugins")+"MyMacros/CommonFunctions.txt";
>       functions = File.openAsString(path);
>       call("ij.macro.Interpreter.setAdditionalFunctions", functions);
>   }
>
>save it and restart ImageJ. You will now have two commands (Macro1
>and Macro2) in the Plugins>MyMacros submenu implemented by macros
>that share the functions in CommonFunctions. CommonFunctions has a
>.txt extension and no underscore in the name so it does not appear
>in the Plugins>MyPlugins submenu. Macro1 and Macro2 have .ijm
>(ImageJ Macro) extensions so they do appear even though they do not
>have an underscore in the name.
>
>You may decide that it's easier and better to keep the functions and
>macros in a single file (toolset) located in the
>ImageJ/macros/toolsets folder. That way the macros and functions can
>share global variables, you can easily add keyboard shortcuts, the
>toolset can contain tools, toolbar menus and action tools as well as
>macros, and you can have multiple toolsets, selected from the ">>"
>toolbar menu.
>
>-wayne

--

Benjamin Gilbert
Scientist, Earth Science Division
Lawrence Berkeley National Laboratory
1 Cyclotron Road  MS 90R1116
Berkeley, CA 94720   USA

[hidden email]
http://nanogeoscience.berkeley.edu

Office: 90   1143
Lab: 70   158

Office: 1-510 495 2748
Lab: 1-510 486 4424
Cell: 1-608 358 0194

Fax: [phone]

[Wayne Rasband]

On Aug 2, 2009, at 4:45 PM, Benjamin Gilbert wrote:

> Thanks for the very clear reply. I learnt how to store global  
> variables from an earlier post to the list using  
> call("ij.Prefs.get", <key>, <value>) ... but perhaps a single  
> toolset would be a simpler approach!
>
> Is there likely to be support for multivariate fit functions in the  
> near future? I would like to fit a 2D polynomial to make an image  
> background.

The Nonuniform Background Removal plugin at

    http://www.cs.unc.edu/~cquammen/imagej/nonuniform_background_removal.html

uses the JAMA package (http://math.nist.gov/javanumerics/jama/) to fit  
2D cubic polynomials to images. The installation instructions say to  
copy Jama-1.0.2.jar to ImageJ/jre/lib/ext but it also works if you  
copy it to the plugins folder.

-wayne

[Michael Schmid]

Hi Ben,

you can do this directly with the Fit_Polynomial plugin.
  http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:fit_polynomial:start

The plugin uses the old approach for a linear fit, from the days of
programmable pocket calculators: Creating a matrix, and a very simple
matrix inversion algorithm. For well-behaved problems, with fit parameters
having the same order of magnitude, it is works well up to a few dozen fit
parameters. Otherwise, more elaborate methods such as in the JAMA package
are needed.

Michael
______________________________________________________________________



On Sun, August 2, 2009 22:45, Benjamin Gilbert wrote:

> Is there likely to be support for multivariate fit functions in the
> near future? I would like to fit a 2D polynomial to make an image
> background.
>
> many thanks
>
> ben