Tiff and roi files

[Girault France]

Dear all,

 

I'm having some troubles trying to open tif and roi files...

Basically I have a folder with tiff images and another one with roi
files (the roi file is supposed to be the selected particle of the
corresponding image).

I would like to open all the tiff images and their roi by running a
macro, everytime I try, I get the message that the roi file is not found
although the path is correct.

Does anybody know another way to do so?

 

Here is a part of the macro that I'm trying to use:

(...)

            open(path);

            i=getTitle();

            if(endsWith(i, ".tif")==true)
i=substring(i,0,lengthOf(i)-4);

            t=getDirectory("image");

            t=File.getParent(t);

            open(t+"\\Measured_D\\"+i+".roi");

(...)

 

I've also tried to open the complete folder of roi files, but  even if
the folder has more than 1 hundred files and all of them are selected to
be opened, I cannot open them all together... only just few of them. I
open these files by dragging and dropping the selection on ImageJ. It
works well with tiff images where the complete folder can be open but I
don't know how to do so for roi files.

Any ideas of how to do ?

 

Many thanks,

 

France

[Wayne Rasband]

The path to the ROI file is probably incorrect. Try changing this line
in the macro

     open(t+"\\Measured_D\\"+i+".roi");

to

     roiPath = t+"\\Measured_D\\"+i+".roi";
     print(roiPath);
     open(roiPath);

to see what the path looks like. Then open the ROI using File>Open with
the recorder running and compare it to the path generated by the
recorder.

-wayne


On Nov 29, 2006, at 9:05 AM, Girault France wrote:

> Dear all,
>
>
> I'm having some troubles trying to open tif and roi files...
>
> Basically I have a folder with tiff images and another one with roi
> files (the roi file is supposed to be the selected particle of the
> corresponding image).
>
> I would like to open all the tiff images and their roi by running a
> macro, everytime I try, I get the message that the roi file is not
> found
> although the path is correct.
>
> Does anybody know another way to do so?
>
>
>
> Here is a part of the macro that I'm trying to use:
>
> (...)
>
>             open(path);
>
>             i=getTitle();
>
>             if(endsWith(i, ".tif")==true)
> i=substring(i,0,lengthOf(i)-4);
>
>             t=getDirectory("image");
>
>             t=File.getParent(t);
>
>             open(t+"\\Measured_D\\"+i+".roi");
>
> (...)
>
>
>
> I've also tried to open the complete folder of roi files, but  even if
> the folder has more than 1 hundred files and all of them are selected
> to
> be opened, I cannot open them all together... only just few of them. I
> open these files by dragging and dropping the selection on ImageJ. It
> works well with tiff images where the complete folder can be open but I
> don't know how to do so for roi files.
>
> Any ideas of how to do ?
>
>
>
> Many thanks,
>
>
>
> France
>

... [show rest of quote]

[Nick Mortimer]

Just a quick one,

Is there more than one ROI in the file? if so the ending might be .zip

Nick

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Wayne Rasband
Sent: Thursday, 30 November 2006 12:08 AM
To: [hidden email]
Subject: Re: Tiff and roi files

The path to the ROI file is probably incorrect. Try changing this line
in the macro

     open(t+"\\Measured_D\\"+i+".roi");

to

     roiPath = t+"\\Measured_D\\"+i+".roi";
     print(roiPath);
     open(roiPath);

to see what the path looks like. Then open the ROI using File>Open with
the recorder running and compare it to the path generated by the
recorder.

-wayne


On Nov 29, 2006, at 9:05 AM, Girault France wrote:

> Dear all,
>
>
> I'm having some troubles trying to open tif and roi files...
>
> Basically I have a folder with tiff images and another one with roi
> files (the roi file is supposed to be the selected particle of the
> corresponding image).
>
> I would like to open all the tiff images and their roi by running a
> macro, everytime I try, I get the message that the roi file is not
> found
> although the path is correct.
>
> Does anybody know another way to do so?
>
>
>
> Here is a part of the macro that I'm trying to use:
>
> (...)
>
>             open(path);
>
>             i=getTitle();
>
>             if(endsWith(i, ".tif")==true)
> i=substring(i,0,lengthOf(i)-4);
>
>             t=getDirectory("image");
>
>             t=File.getParent(t);
>
>             open(t+"\\Measured_D\\"+i+".roi");
>
> (...)
>
>
>
> I've also tried to open the complete folder of roi files, but  even if
> the folder has more than 1 hundred files and all of them are selected
> to
> be opened, I cannot open them all together... only just few of them. I
> open these files by dragging and dropping the selection on ImageJ. It
> works well with tiff images where the complete folder can be open but

... [show rest of quote]

I

> don't know how to do so for roi files.
>
> Any ideas of how to do ?
>
>
>
> Many thanks,
>
>
>
> France
>