Malfunctioning Macro

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Malfunctioning Macro

Michael Doube-2
Dear List

A macro that used to work just fine has stopped working properly.  I
used to install it, then hit [q], and it worked.  Now I have to
File-Import-Raw before it will work, and the second and subsequent
repeats of the macro require me to click on the results window before it
will go again.  I have tried the new version (1.34s) of ij.jar, to no
avail.  I'm using Java 1.5.0_04 and WinXP Pro SP2.  Something has
changed, but I don't know what!

The text of my macro follows

Thanks

Mike

---------------
macro "Standard Grey Peak Finder [q]" {
setBatchMode(true);

run("Raw...", "open... image=8-bit width=512 height=512 offset=128
number=1 gap=0");

row=nResults;

getRawStatistics(area, mean, min, max, std, histogram);

f=0;
for(n=0;n<128;n++){
    if(histogram[n]>f){
        f=histogram[n];
        peak1=n;
    }  
       
}
setResult("Brominated",row,peak1);

g=0;
for(o=255; o>127; o--) {
    if(histogram[o]>g){
        g=histogram[o];
        peak2=o;
    }
   
}
setResult("Iodinated",row,peak2);

    name = getTitle();
    setResult("Label", row, name);  

updateResults();
}

--
Michael Doube  BPhil BVSc MRCVS
MPhil / PhD Student
Dental Institute
Barts and The London School of Medicine and Dentistry
Queen Mary, University of London
New Rd
London  E1 1BB
United Kingdom

Phone +44 (0)20 7377 7000 ext 2681
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Re: Malfunctioning Macro

Wayne Rasband
> A macro that used to work just fine has stopped working
> properly.  I used to install it, then hit [q], and it
> worked.  Now I have to File-Import-Raw before it will work,
> and the second and subsequent repeats of the macro require
> me to click on the results window before it will go again. 
> I have tried the new version (1.34s) of ij.jar, to no
> avail.  I'm using Java 1.5.0_04 and WinXP Pro SP2. 
> Something has changed, but I don't know what!

It works fine for me using ImageJ 1.35g/Mac OS X 10.3.9/Java 1.4.2, but
the run() call looks a little strange. It should probably be

    run("Raw...", "image=8-bit width=512 height=512 offset=128 number=1
gap=0");

which causes a file open dialog to be shown, but not the Import/Raw
dialog.

-wayne


>
> The text of my macro follows
>
> Thanks
>
> Mike
>
> ---------------
> macro "Standard Grey Peak Finder [q]" {
> setBatchMode(true);
>
> run("Raw...", "open... image=8-bit width=512 height=512 offset=128
> number=1 gap=0");
>
> row=nResults;
>
> getRawStatistics(area, mean, min, max, std, histogram);
>
> f=0;
> for(n=0;n<128;n++){
>     if(histogram[n]>f){
>         f=histogram[n];
>         peak1=n;
>     }  
>       
> }
> setResult("Brominated",row,peak1);
>
> g=0;
> for(o=255; o>127; o--) {
>     if(histogram[o]>g){
>         g=histogram[o];
>         peak2=o;
>     }
>   
> }
> setResult("Iodinated",row,peak2);
>
>     name = getTitle();
>     setResult("Label", row, name);  
>
> updateResults();
> }
>
> --
> Michael Doube  BPhil BVSc MRCVS
> MPhil / PhD Student
> Dental Institute
> Barts and The London School of Medicine and Dentistry
> Queen Mary, University of London
> New Rd
> London  E1 1BB
> United Kingdom
>
> Phone +44 (0)20 7377 7000 ext 2681
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Re: Malfunctioning Macro

Michael Doube-2
Thanks Wayne,

Changing the code as you suggest fixed the first part of the problem;
now I don't have to File-Import-Raw before running the macro.

----------new code---------
run("Raw...", "image=8-bit width=512 height=512 offset=128 number=1 gap=0");
----------end------------

However, the second part of the problem remains - third and subsequent
repeats of the macro require me to click on the Results window, as
though it has to be in the foreground in order for ImageJ to properly
catch the [q] keystroke.

I will test it on Linux and see what happens.

Upgrading to 1.35g didn't help.

Regards

Mike

Wayne Rasband wrote:

>> A macro that used to work just fine has stopped working
>> properly.  I used to install it, then hit [q], and it
>> worked.  Now I have to File-Import-Raw before it will work,
>> and the second and subsequent repeats of the macro require
>> me to click on the results window before it will go again.
>> I have tried the new version (1.34s) of ij.jar, to no
>> avail.  I'm using Java 1.5.0_04 and WinXP Pro SP2.
>> Something has changed, but I don't know what!
>
>
> It works fine for me using ImageJ 1.35g/Mac OS X 10.3.9/Java 1.4.2,
> but the run() call looks a little strange. It should probably be
>
>    run("Raw...", "image=8-bit width=512 height=512 offset=128 number=1
> gap=0");
>
> which causes a file open dialog to be shown, but not the Import/Raw
> dialog.
>
> -wayne
>
>
>>
>> The text of my macro follows
>>
>> Thanks
>>
>> Mike
>>
>> ---------------
>> macro "Standard Grey Peak Finder [q]" {
>> setBatchMode(true);
>>
>> run("Raw...", "open... image=8-bit width=512 height=512 offset=128
>> number=1 gap=0");
>>
>> row=nResults;
>>
>> getRawStatistics(area, mean, min, max, std, histogram);
>>
>> f=0;
>> for(n=0;n<128;n++){
>>     if(histogram[n]>f){
>>         f=histogram[n];
>>         peak1=n;
>>     }  
>>      
>> }
>> setResult("Brominated",row,peak1);
>>
>> g=0;
>> for(o=255; o>127; o--) {
>>     if(histogram[o]>g){
>>         g=histogram[o];
>>         peak2=o;
>>     }
>>  
>> }
>> setResult("Iodinated",row,peak2);
>>
>>     name = getTitle();
>>     setResult("Label", row, name);  
>>
>> updateResults();
>> }
>>
>> --
>> Michael Doube  BPhil BVSc MRCVS
>> MPhil / PhD Student
>> Dental Institute
>> Barts and The London School of Medicine and Dentistry
>> Queen Mary, University of London
>> New Rd
>> London  E1 1BB
>> United Kingdom
>>
>> Phone +44 (0)20 7377 7000 ext 2681
>

--
Michael Doube  BPhil BVSc MRCVS
MPhil / PhD Student
Dental Institute
Barts and The London School of Medicine and Dentistry
Queen Mary, University of London
New Rd
London  E1 1BB
United Kingdom

Phone +44 (0)20 7377 7000 ext 2681
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Re: Malfunctioning Macro

Michael Doube-2
Wayne

I have tested the macro using the latest Linux version of ImageJ (1.34s
with Java 1.5.0_04) from your site on Fedora Core 4, and it works fine.

I still can't get it to work properly on WinXP pro.  Could it be a
Java/WinXP issue?  I tried the newer version of JRE (1.5.0_05) on Linux
and that made ImageJ not work properly - it wouldn't do much at all,
including opening plain .tif files

------------------------
Exception in thread "main" java.lang.NullPointerException
   at .get_state (/usr/lib/lib-gnu-java-awt-peer-gtk.so.6.0.0)
   at .Java_gnu_java_awt_peer_gtk_GtkMenuPeer_addItem
(/usr/lib/lib-gnu-java-awt-peer-gtk.so.6.0.0)
   at
gnu.java.awt.peer.gtk.GtkMenuPeer.addItem(java.awt.peer.MenuItemPeer,
int, boolean) (/usr/lib/lib-gnu-java-awt-peer-gtk.so.6.0.0)
   at gnu.java.awt.peer.gtk.GtkMenuPeer.addItem(java.awt.MenuItem)
(/usr/lib/lib-gnu-java-awt-peer-gtk.so.6.0.0)
   at java.awt.Menu.add(java.awt.MenuItem) (/usr/lib/libgcj.so.6.0.0)
   at ij.plugin.MacroInstaller.install() (Unknown Source)
   at ij.plugin.MacroInstaller.install(java.lang.String) (Unknown Source)
   at ij.plugin.MacroInstaller.run(java.lang.String) (Unknown Source)
   at ij.Menus.installStartupMacroSet() (Unknown Source)
   at ij.ImageJ.ImageJ(java.applet.Applet) (Unknown Source)
   at ij.ImageJ.main(java.lang.String[]) (Unknown Source)
   at gnu.java.lang.MainThread.call_main() (/usr/lib/libgcj.so.6.0.0)
   at gnu.java.lang.MainThread.run() (/usr/lib/libgcj.so.6.0.0)
-----------------------------------------------

Cheers

Mike


Michael Doube wrote:

> Thanks Wayne,
>
> Changing the code as you suggest fixed the first part of the problem;
> now I don't have to File-Import-Raw before running the macro.
>
> ----------new code---------
> run("Raw...", "image=8-bit width=512 height=512 offset=128 number=1
> gap=0");
> ----------end------------
>
> However, the second part of the problem remains - third and subsequent
> repeats of the macro require me to click on the Results window, as
> though it has to be in the foreground in order for ImageJ to properly
> catch the [q] keystroke.
>
> I will test it on Linux and see what happens.
>
> Upgrading to 1.35g didn't help.
>
> Regards
>
> Mike
>
> Wayne Rasband wrote:
>
>>> A macro that used to work just fine has stopped working
>>> properly.  I used to install it, then hit [q], and it
>>> worked.  Now I have to File-Import-Raw before it will work,
>>> and the second and subsequent repeats of the macro require
>>> me to click on the results window before it will go again. I have
>>> tried the new version (1.34s) of ij.jar, to no
>>> avail.  I'm using Java 1.5.0_04 and WinXP Pro SP2. Something has
>>> changed, but I don't know what!
>>
>>
>>
>> It works fine for me using ImageJ 1.35g/Mac OS X 10.3.9/Java 1.4.2,
>> but the run() call looks a little strange. It should probably be
>>
>>    run("Raw...", "image=8-bit width=512 height=512 offset=128
>> number=1 gap=0");
>>
>> which causes a file open dialog to be shown, but not the Import/Raw
>> dialog.
>>
>> -wayne
>>
>>
>>>
>>> The text of my macro follows
>>>
>>> Thanks
>>>
>>> Mike
>>>
>>> ---------------
>>> macro "Standard Grey Peak Finder [q]" {
>>> setBatchMode(true);
>>>
>>> run("Raw...", "open... image=8-bit width=512 height=512 offset=128
>>> number=1 gap=0");
>>>
>>> row=nResults;
>>>
>>> getRawStatistics(area, mean, min, max, std, histogram);
>>>
>>> f=0;
>>> for(n=0;n<128;n++){
>>>     if(histogram[n]>f){
>>>         f=histogram[n];
>>>         peak1=n;
>>>     }        }
>>> setResult("Brominated",row,peak1);
>>>
>>> g=0;
>>> for(o=255; o>127; o--) {
>>>     if(histogram[o]>g){
>>>         g=histogram[o];
>>>         peak2=o;
>>>     }
>>>   }
>>> setResult("Iodinated",row,peak2);
>>>
>>>     name = getTitle();
>>>     setResult("Label", row, name);
>>> updateResults();
>>> }
>>>
>>> --
>>> Michael Doube  BPhil BVSc MRCVS
>>> MPhil / PhD Student
>>> Dental Institute
>>> Barts and The London School of Medicine and Dentistry
>>> Queen Mary, University of London
>>> New Rd
>>> London  E1 1BB
>>> United Kingdom
>>>
>>> Phone +44 (0)20 7377 7000 ext 2681
>>
>>
>

--
Michael Doube  BPhil BVSc MRCVS
MPhil / PhD Student
Dental Institute
Barts and The London School of Medicine and Dentistry
Queen Mary, University of London
New Rd
London  E1 1BB
United Kingdom

Phone +44 (0)20 7377 7000 ext 2681