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open ROI.zip

OBEID Patricia 154904
Hello,
I would like using a macro to open the ROI.zip (generated previously in a 1st macro) and apply them to images.
I write 2 macros to simplify my script writing.
But I don't know how to write the command line to open ROI.zip.
Could you help me please ?
I thank you in advance.
Patricia
____________________________________________________________
[http://www.cea.fr/var/cea/signatures/cea_logo.jpg]<http://www.cea.fr/>[logo_mail]

Patricia OBEÏD
Ingénieur de Recherche /Animateur Informatique Biomics
Institut de Recherche Interdisciplinaire de Grenoble
CEA/DRF / IRIG / DS /BGE U1038/ Biomics / Bât 4020
17 rue des martyrs 38054 Grenoble Cedex 9
Commissariat à l'énergie atomique et aux énergies alternatives
Email : [hidden email]<mailto:[hidden email]>
Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17

Toute notre actualité sur www.cea.fr et sur http://www.cea.fr/drf/big/bge/biomics<http://www.cea.fr/>

<http://www.cea.fr/>Suivez-nous également sur Twitter : @CEA_Recherche<https://twitter.com/#!/CEA_Recherche> et sur https://twitter.com/BiomicsLab




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Re: open ROI.zip

Peter Haub
Hi

you can use the Plugins>Macros>Record... function to record the command
you are currently using manually.
This gives at least important hints.

Here is the result for your question:

// (optinal) reset RoiManager
roiManager("reset");

// Select a roi.zip file vai File Open dialog
run("Open...");

// .. alternatively use a path string pointing to the zip file

//roiManager("reset");
//roiManager("Open", "C:\\PATH_TO_\\RoiSet.zip");

Peter

On 03.08.2020 11:01, OBEID Patricia 154904 wrote:

> Hello,
> I would like using a macro to open the ROI.zip (generated previously in a 1st macro) and apply them to images.
> I write 2 macros to simplify my script writing.
> But I don't know how to write the command line to open ROI.zip.
> Could you help me please ?
> I thank you in advance.
> Patricia
> ____________________________________________________________
> [http://www.cea.fr/var/cea/signatures/cea_logo.jpg]<http://www.cea.fr/>[logo_mail]
>
> Patricia OBEÏD
> Ingénieur de Recherche /Animateur Informatique Biomics
> Institut de Recherche Interdisciplinaire de Grenoble
> CEA/DRF / IRIG / DS /BGE U1038/ Biomics / Bât 4020
> 17 rue des martyrs 38054 Grenoble Cedex 9
> Commissariat à l'énergie atomique et aux énergies alternatives
> Email : [hidden email]<mailto:[hidden email]>
> Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17
>
> Toute notre actualité sur www.cea.fr et sur http://www.cea.fr/drf/big/bge/biomics<http://www.cea.fr/>
>
> <http://www.cea.fr/>Suivez-nous également sur Twitter : @CEA_Recherche<https://twitter.com/#!/CEA_Recherche> et sur https://twitter.com/BiomicsLab
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: open ROI.zip

OBEID Patricia 154904
Thanks Peter,
The problem is, I have a long list of images and ROIs. I want to open the image and the corresponding ROIManager and therefore make a loop for my treatments but it does not work.
I started my macro like this:

dir = getDirectory("Choose a Directory ");
dir3 = getDirectory("Choose Destination Directory ");

list = getFileList(dir);
setBatchMode(true);
for (i=0; i<list.length; i++) {
        if (endsWith(list[i], "ROI.zip")){ //A ADAPTER AU NOM DU CHANNEL
                         roiManager("open", dir+list[i]);
                       
                        //ouvrir image des noyaux
                        pathNuc = replace(path, "ROI.zip", "d1.C01");
                        fileNuc = replace(list[i], "ROI.zip", "d1.C01");
                        open(pathNuc);

Can you help me find out what is wrong?
Thank you




-----Message d'origine-----
De : ImageJ Interest Group <[hidden email]> De la part de Peter Haub
Envoyé : lundi 3 août 2020 11:20
À : [hidden email]
Objet : Re: open ROI.zip

Hi

you can use the Plugins>Macros>Record... function to record the command you are currently using manually.
This gives at least important hints.

Here is the result for your question:

// (optinal) reset RoiManager
roiManager("reset");

// Select a roi.zip file vai File Open dialog run("Open...");

// .. alternatively use a path string pointing to the zip file

//roiManager("reset");
//roiManager("Open", "C:\\PATH_TO_\\RoiSet.zip");

Peter

On 03.08.2020 11:01, OBEID Patricia 154904 wrote:

> Hello,
> I would like using a macro to open the ROI.zip (generated previously in a 1st macro) and apply them to images.
> I write 2 macros to simplify my script writing.
> But I don't know how to write the command line to open ROI.zip.
> Could you help me please ?
> I thank you in advance.
> Patricia
> ____________________________________________________________
> [http://www.cea.fr/var/cea/signatures/cea_logo.jpg]<http://www.cea.fr/
> >[logo_mail]
>
> Patricia OBEÏD
> Ingénieur de Recherche /Animateur Informatique Biomics Institut de
> Recherche Interdisciplinaire de Grenoble CEA/DRF / IRIG / DS /BGE
> U1038/ Biomics / Bât 4020
> 17 rue des martyrs 38054 Grenoble Cedex 9 Commissariat à l'énergie
> atomique et aux énergies alternatives Email :
> [hidden email]<mailto:[hidden email]>
> Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17
>
> Toute notre actualité sur www.cea.fr et sur
> http://www.cea.fr/drf/big/bge/biomics<http://www.cea.fr/>
>
> <http://www.cea.fr/>Suivez-nous également sur Twitter :
> @CEA_Recherche<https://twitter.com/#!/CEA_Recherche> et sur
> https://twitter.com/BiomicsLab
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
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Re: open ROI.zip

Peter Haub
".. it does not work .."
What happens?

replace(path, "ROI.zip", "d1.C01");
=> There is no variable with the name 'path' in your posted macro!

( I assume you want to open an image after opening the Rois. Therefore
you exchange the "ROI.zip" and "d1.C01".
Is your image file ending with "d1.C01". Is there no extension (e.g.
.tif)? )


On 03.08.2020 11:51, OBEID Patricia 154904 wrote:

> Thanks Peter,
> The problem is, I have a long list of images and ROIs. I want to open the image and the corresponding ROIManager and therefore make a loop for my treatments but it does not work.
> I started my macro like this:
>
> dir = getDirectory("Choose a Directory ");
> dir3 = getDirectory("Choose Destination Directory ");
>
> list = getFileList(dir);
> setBatchMode(true);
> for (i=0; i<list.length; i++) {
> if (endsWith(list[i], "ROI.zip")){ //A ADAPTER AU NOM DU CHANNEL
> roiManager("open", dir+list[i]);
>
> //ouvrir image des noyaux
> pathNuc = replace(path, "ROI.zip", "d1.C01");
> fileNuc = replace(list[i], "ROI.zip", "d1.C01");
> open(pathNuc);
>
> Can you help me find out what is wrong?
> Thank you
>
>
>
>
> -----Message d'origine-----
> De : ImageJ Interest Group <[hidden email]> De la part de Peter Haub
> Envoyé : lundi 3 août 2020 11:20
> À : [hidden email]
> Objet : Re: open ROI.zip
>
> Hi
>
> you can use the Plugins>Macros>Record... function to record the command you are currently using manually.
> This gives at least important hints.
>
> Here is the result for your question:
>
> // (optinal) reset RoiManager
> roiManager("reset");
>
> // Select a roi.zip file vai File Open dialog run("Open...");
>
> // .. alternatively use a path string pointing to the zip file
>
> //roiManager("reset");
> //roiManager("Open", "C:\\PATH_TO_\\RoiSet.zip");
>
> Peter
>
> On 03.08.2020 11:01, OBEID Patricia 154904 wrote:
>> Hello,
>> I would like using a macro to open the ROI.zip (generated previously in a 1st macro) and apply them to images.
>> I write 2 macros to simplify my script writing.
>> But I don't know how to write the command line to open ROI.zip.
>> Could you help me please ?
>> I thank you in advance.
>> Patricia
>> ____________________________________________________________
>> [http://www.cea.fr/var/cea/signatures/cea_logo.jpg]<http://www.cea.fr/
>>> [logo_mail]
>> Patricia OBEÏD
>> Ingénieur de Recherche /Animateur Informatique Biomics Institut de
>> Recherche Interdisciplinaire de Grenoble CEA/DRF / IRIG / DS /BGE
>> U1038/ Biomics / Bât 4020
>> 17 rue des martyrs 38054 Grenoble Cedex 9 Commissariat à l'énergie
>> atomique et aux énergies alternatives Email :
>> [hidden email]<mailto:[hidden email]>
>> Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17
>>
>> Toute notre actualité sur www.cea.fr et sur
>> http://www.cea.fr/drf/big/bge/biomics<http://www.cea.fr/>
>>
>> <http://www.cea.fr/>Suivez-nous également sur Twitter :
>> @CEA_Recherche<https://twitter.com/#!/CEA_Recherche> et sur
>> https://twitter.com/BiomicsLab
>>
>>
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: open ROI.zip

OBEID Patricia 154904
replace(path, "ROI.zip", "d1.C01");
=> There is no variable with the name 'path' in your posted macro!
Yes, it is an error because I tried a lot of things to open the ROI.zip ...
It doesn't work and I cannot continue writing the macro because it all depends on the opening of the ROI ... :-(

( I assume you want to open an image after opening the Rois. Therefore you exchange the "ROI.zip" and "d1.C01".
Is your image file ending with "d1.C01". Is there no extension (e.g.
.tif)? )
That's right. The images were done by a Cellomics machine and the extension is .C01. No problem with that.

I come back to the starting point, how to open the ROI ?...

-----Message d'origine-----
De : ImageJ Interest Group <[hidden email]> De la part de Peter Haub
Envoyé : lundi 3 août 2020 12:09
À : [hidden email]
Objet : Re: open ROI.zip

".. it does not work .."
What happens?

replace(path, "ROI.zip", "d1.C01");
=> There is no variable with the name 'path' in your posted macro!

( I assume you want to open an image after opening the Rois. Therefore you exchange the "ROI.zip" and "d1.C01".
Is your image file ending with "d1.C01". Is there no extension (e.g.
.tif)? )


On 03.08.2020 11:51, OBEID Patricia 154904 wrote:

> Thanks Peter,
> The problem is, I have a long list of images and ROIs. I want to open the image and the corresponding ROIManager and therefore make a loop for my treatments but it does not work.
> I started my macro like this:
>
> dir = getDirectory("Choose a Directory ");
> dir3 = getDirectory("Choose Destination Directory ");
>
> list = getFileList(dir);
> setBatchMode(true);
> for (i=0; i<list.length; i++) {
> if (endsWith(list[i], "ROI.zip")){ //A ADAPTER AU NOM DU CHANNEL
> roiManager("open", dir+list[i]);
>
> //ouvrir image des noyaux
> pathNuc = replace(path, "ROI.zip", "d1.C01");
> fileNuc = replace(list[i], "ROI.zip", "d1.C01");
> open(pathNuc);
>
> Can you help me find out what is wrong?
> Thank you
>
>
>
>
> -----Message d'origine-----
> De : ImageJ Interest Group <[hidden email]> De la part de Peter
> Haub Envoyé : lundi 3 août 2020 11:20 À : [hidden email] Objet :
> Re: open ROI.zip
>
> Hi
>
> you can use the Plugins>Macros>Record... function to record the command you are currently using manually.
> This gives at least important hints.
>
> Here is the result for your question:
>
> // (optinal) reset RoiManager
> roiManager("reset");
>
> // Select a roi.zip file vai File Open dialog run("Open...");
>
> // .. alternatively use a path string pointing to the zip file
>
> //roiManager("reset");
> //roiManager("Open", "C:\\PATH_TO_\\RoiSet.zip");
>
> Peter
>
> On 03.08.2020 11:01, OBEID Patricia 154904 wrote:
>> Hello,
>> I would like using a macro to open the ROI.zip (generated previously in a 1st macro) and apply them to images.
>> I write 2 macros to simplify my script writing.
>> But I don't know how to write the command line to open ROI.zip.
>> Could you help me please ?
>> I thank you in advance.
>> Patricia
>> ____________________________________________________________
>> [http://www.cea.fr/var/cea/signatures/cea_logo.jpg]<http://www.cea.fr
>> /
>>> [logo_mail]
>> Patricia OBEÏD
>> Ingénieur de Recherche /Animateur Informatique Biomics Institut de
>> Recherche Interdisciplinaire de Grenoble CEA/DRF / IRIG / DS /BGE
>> U1038/ Biomics / Bât 4020
>> 17 rue des martyrs 38054 Grenoble Cedex 9 Commissariat à l'énergie
>> atomique et aux énergies alternatives Email :
>> [hidden email]<mailto:[hidden email]>
>> Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17
>>
>> Toute notre actualité sur www.cea.fr et sur
>> http://www.cea.fr/drf/big/bge/biomics<http://www.cea.fr/>
>>
>> <http://www.cea.fr/>Suivez-nous également sur Twitter :
>> @CEA_Recherche<https://twitter.com/#!/CEA_Recherche> et sur
>> https://twitter.com/BiomicsLab
>>
>>
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
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Re: open ROI.zip

Aryeh Weiss
It is possible that you need to add the File.separator (*File.separator*
- Returns the file name separator character ("/" or "\").)

so
  roiManager("open", dir+list[i]);
should be
  roiManager("open", dir+File.separator+list[i]);

Best regards
--aryeh


On 03/08/2020 13:36, OBEID Patricia 154904 wrote:

> replace(path, "ROI.zip", "d1.C01");
> => There is no variable with the name 'path' in your posted macro!
> Yes, it is an error because I tried a lot of things to open the ROI.zip ...
> It doesn't work and I cannot continue writing the macro because it all depends on the opening of the ROI ... :-(
>
> ( I assume you want to open an image after opening the Rois. Therefore you exchange the "ROI.zip" and "d1.C01".
> Is your image file ending with "d1.C01". Is there no extension (e.g.
> .tif)? )
> That's right. The images were done by a Cellomics machine and the extension is .C01. No problem with that.
>
> I come back to the starting point, how to open the ROI ?...
>
> -----Message d'origine-----
> De : ImageJ Interest Group <[hidden email]> De la part de Peter Haub
> Envoyé : lundi 3 août 2020 12:09
> À : [hidden email]
> Objet : Re: open ROI.zip
>
> ".. it does not work .."
> What happens?
>
> replace(path, "ROI.zip", "d1.C01");
> => There is no variable with the name 'path' in your posted macro!
>
> ( I assume you want to open an image after opening the Rois. Therefore you exchange the "ROI.zip" and "d1.C01".
> Is your image file ending with "d1.C01". Is there no extension (e.g.
> .tif)? )
>
>
> On 03.08.2020 11:51, OBEID Patricia 154904 wrote:
>> Thanks Peter,
>> The problem is, I have a long list of images and ROIs. I want to open the image and the corresponding ROIManager and therefore make a loop for my treatments but it does not work.
>> I started my macro like this:
>>
>> dir = getDirectory("Choose a Directory ");
>> dir3 = getDirectory("Choose Destination Directory ");
>>
>> list = getFileList(dir);
>> setBatchMode(true);
>> for (i=0; i<list.length; i++) {
>> if (endsWith(list[i], "ROI.zip")){ //A ADAPTER AU NOM DU CHANNEL
>> roiManager("open", dir+list[i]);
>>
>> //ouvrir image des noyaux
>> pathNuc = replace(path, "ROI.zip", "d1.C01");
>> fileNuc = replace(list[i], "ROI.zip", "d1.C01");
>> open(pathNuc);
>>
>> Can you help me find out what is wrong?
>> Thank you
>>
>>
>>
>>
>> -----Message d'origine-----
>> De : ImageJ Interest Group <[hidden email]> De la part de Peter
>> Haub Envoyé : lundi 3 août 2020 11:20 À : [hidden email] Objet :
>> Re: open ROI.zip
>>
>> Hi
>>
>> you can use the Plugins>Macros>Record... function to record the command you are currently using manually.
>> This gives at least important hints.
>>
>> Here is the result for your question:
>>
>> // (optinal) reset RoiManager
>> roiManager("reset");
>>
>> // Select a roi.zip file vai File Open dialog run("Open...");
>>
>> // .. alternatively use a path string pointing to the zip file
>>
>> //roiManager("reset");
>> //roiManager("Open", "C:\\PATH_TO_\\RoiSet.zip");
>>
>> Peter
>>
>> On 03.08.2020 11:01, OBEID Patricia 154904 wrote:
>>> Hello,
>>> I would like using a macro to open the ROI.zip (generated previously in a 1st macro) and apply them to images.
>>> I write 2 macros to simplify my script writing.
>>> But I don't know how to write the command line to open ROI.zip.
>>> Could you help me please ?
>>> I thank you in advance.
>>> Patricia
>>> ____________________________________________________________
>>> [http://www.cea.fr/var/cea/signatures/cea_logo.jpg]<http://www.cea.fr
>>> /
>>>> [logo_mail]
>>> Patricia OBEÏD
>>> Ingénieur de Recherche /Animateur Informatique Biomics Institut de
>>> Recherche Interdisciplinaire de Grenoble CEA/DRF / IRIG / DS /BGE
>>> U1038/ Biomics / Bât 4020
>>> 17 rue des martyrs 38054 Grenoble Cedex 9 Commissariat à l'énergie
>>> atomique et aux énergies alternatives Email :
>>> [hidden email]<mailto:[hidden email]>
>>> Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17
>>>
>>> Toute notre actualité sur www.cea.fr et sur
>>> http://www.cea.fr/drf/big/bge/biomics<http://www.cea.fr/>
>>>
>>> <http://www.cea.fr/>Suivez-nous également sur Twitter :
>>> @CEA_Recherche<https://twitter.com/#!/CEA_Recherche> et sur
>>> https://twitter.com/BiomicsLab
>>>
>>>
>>>
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051


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Re: open ROI.zip

Peter Haub
In reply to this post by OBEID Patricia 154904
???...
If you already know that there is no variable 'path' how can you expect
that the combination
         pathNuc = replace(path, "ROI.zip", "d1.C01");
         open(pathNuc);
gives a result?

Make sure your path string is correct, e.g. by using the following in
your loop:
     path = dir+list[i];
     print(path);

Switch off batch mode by using
     setBatchMode(false);
to see if this is causing the problem.

On 03.08.2020 12:36, OBEID Patricia 154904 wrote:

> replace(path, "ROI.zip", "d1.C01");
> => There is no variable with the name 'path' in your posted macro!
> Yes, it is an error because I tried a lot of things to open the ROI.zip ...
> It doesn't work and I cannot continue writing the macro because it all depends on the opening of the ROI ... :-(
>
> ( I assume you want to open an image after opening the Rois. Therefore you exchange the "ROI.zip" and "d1.C01".
> Is your image file ending with "d1.C01". Is there no extension (e.g.
> .tif)? )
> That's right. The images were done by a Cellomics machine and the extension is .C01. No problem with that.
>
> I come back to the starting point, how to open the ROI ?...
>
> -----Message d'origine-----
> De : ImageJ Interest Group <[hidden email]> De la part de Peter Haub
> Envoyé : lundi 3 août 2020 12:09
> À : [hidden email]
> Objet : Re: open ROI.zip
>
> ".. it does not work .."
> What happens?
>
> replace(path, "ROI.zip", "d1.C01");
> => There is no variable with the name 'path' in your posted macro!
>
> ( I assume you want to open an image after opening the Rois. Therefore you exchange the "ROI.zip" and "d1.C01".
> Is your image file ending with "d1.C01". Is there no extension (e.g.
> .tif)? )
>
>
> On 03.08.2020 11:51, OBEID Patricia 154904 wrote:
>> Thanks Peter,
>> The problem is, I have a long list of images and ROIs. I want to open the image and the corresponding ROIManager and therefore make a loop for my treatments but it does not work.
>> I started my macro like this:
>>
>> dir = getDirectory("Choose a Directory ");
>> dir3 = getDirectory("Choose Destination Directory ");
>>
>> list = getFileList(dir);
>> setBatchMode(true);
>> for (i=0; i<list.length; i++) {
>> if (endsWith(list[i], "ROI.zip")){ //A ADAPTER AU NOM DU CHANNEL
>> roiManager("open", dir+list[i]);
>>
>> //ouvrir image des noyaux
>> pathNuc = replace(path, "ROI.zip", "d1.C01");
>> fileNuc = replace(list[i], "ROI.zip", "d1.C01");
>> open(pathNuc);
>>
>> Can you help me find out what is wrong?
>> Thank you
>>
>>
>>
>>
>> -----Message d'origine-----
>> De : ImageJ Interest Group <[hidden email]> De la part de Peter
>> Haub Envoyé : lundi 3 août 2020 11:20 À : [hidden email] Objet :
>> Re: open ROI.zip
>>
>> Hi
>>
>> you can use the Plugins>Macros>Record... function to record the command you are currently using manually.
>> This gives at least important hints.
>>
>> Here is the result for your question:
>>
>> // (optinal) reset RoiManager
>> roiManager("reset");
>>
>> // Select a roi.zip file vai File Open dialog run("Open...");
>>
>> // .. alternatively use a path string pointing to the zip file
>>
>> //roiManager("reset");
>> //roiManager("Open", "C:\\PATH_TO_\\RoiSet.zip");
>>
>> Peter
>>
>> On 03.08.2020 11:01, OBEID Patricia 154904 wrote:
>>> Hello,
>>> I would like using a macro to open the ROI.zip (generated previously in a 1st macro) and apply them to images.
>>> I write 2 macros to simplify my script writing.
>>> But I don't know how to write the command line to open ROI.zip.
>>> Could you help me please ?
>>> I thank you in advance.
>>> Patricia
>>> ____________________________________________________________
>>> [http://www.cea.fr/var/cea/signatures/cea_logo.jpg]<http://www.cea.fr
>>> /
>>>> [logo_mail]
>>> Patricia OBEÏD
>>> Ingénieur de Recherche /Animateur Informatique Biomics Institut de
>>> Recherche Interdisciplinaire de Grenoble CEA/DRF / IRIG / DS /BGE
>>> U1038/ Biomics / Bât 4020
>>> 17 rue des martyrs 38054 Grenoble Cedex 9 Commissariat à l'énergie
>>> atomique et aux énergies alternatives Email :
>>> [hidden email]<mailto:[hidden email]>
>>> Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17
>>>
>>> Toute notre actualité sur www.cea.fr et sur
>>> http://www.cea.fr/drf/big/bge/biomics<http://www.cea.fr/>
>>>
>>> <http://www.cea.fr/>Suivez-nous également sur Twitter :
>>> @CEA_Recherche<https://twitter.com/#!/CEA_Recherche> et sur
>>> https://twitter.com/BiomicsLab
>>>
>>>
>>>
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
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Re: open ROI.zip

OBEID Patricia 154904
At the moment I don't  expect open the image.
I try first to open the ROI.zip and after I will can open the image with the replace function.
But at the moment I don't know how to write the first step.
I sorry but writing macro is no easy for me.
Patricia

____________________________________________________________

Patricia OBEÏD
Ingénieur de Recherche /Animateur Informatique Biomics
Institut de Recherche Interdisciplinaire de Grenoble
CEA/DRF / IRIG / DS /BGE U1038/ Biomics / Bât 4020
17 rue des martyrs 38054 Grenoble Cedex 9
Commissariat à l'énergie atomique et aux énergies alternatives
Email : [hidden email]
Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17

Toute notre actualité sur www.cea.fr et sur http://www.cea.fr/drf/big/bge/biomics

Suivez-nous également sur Twitter : @CEA_Recherche et sur https://twitter.com/BiomicsLab



-----Message d'origine-----
De : ImageJ Interest Group <[hidden email]> De la part de Peter Haub
Envoyé : lundi 3 août 2020 13:14
À : [hidden email]
Objet : Re: open ROI.zip

???...
If you already know that there is no variable 'path' how can you expect that the combination
         pathNuc = replace(path, "ROI.zip", "d1.C01");
         open(pathNuc);
gives a result?

Make sure your path string is correct, e.g. by using the following in your loop:
     path = dir+list[i];
     print(path);

Switch off batch mode by using
     setBatchMode(false);
to see if this is causing the problem.

On 03.08.2020 12:36, OBEID Patricia 154904 wrote:

> replace(path, "ROI.zip", "d1.C01");
> => There is no variable with the name 'path' in your posted macro!
> Yes, it is an error because I tried a lot of things to open the ROI.zip ...
> It doesn't work and I cannot continue writing the macro because it all
> depends on the opening of the ROI ... :-(
>
> ( I assume you want to open an image after opening the Rois. Therefore you exchange the "ROI.zip" and "d1.C01".
> Is your image file ending with "d1.C01". Is there no extension (e.g.
> .tif)? )
> That's right. The images were done by a Cellomics machine and the extension is .C01. No problem with that.
>
> I come back to the starting point, how to open the ROI ?...
>
> -----Message d'origine-----
> De : ImageJ Interest Group <[hidden email]> De la part de Peter
> Haub Envoyé : lundi 3 août 2020 12:09 À : [hidden email] Objet :
> Re: open ROI.zip
>
> ".. it does not work .."
> What happens?
>
> replace(path, "ROI.zip", "d1.C01");
> => There is no variable with the name 'path' in your posted macro!
>
> ( I assume you want to open an image after opening the Rois. Therefore you exchange the "ROI.zip" and "d1.C01".
> Is your image file ending with "d1.C01". Is there no extension (e.g.
> .tif)? )
>
>
> On 03.08.2020 11:51, OBEID Patricia 154904 wrote:
>> Thanks Peter,
>> The problem is, I have a long list of images and ROIs. I want to open the image and the corresponding ROIManager and therefore make a loop for my treatments but it does not work.
>> I started my macro like this:
>>
>> dir = getDirectory("Choose a Directory ");
>> dir3 = getDirectory("Choose Destination Directory ");
>>
>> list = getFileList(dir);
>> setBatchMode(true);
>> for (i=0; i<list.length; i++) {
>> if (endsWith(list[i], "ROI.zip")){ //A ADAPTER AU NOM DU CHANNEL
>> roiManager("open", dir+list[i]);
>>
>> //ouvrir image des noyaux
>> pathNuc = replace(path, "ROI.zip", "d1.C01");
>> fileNuc = replace(list[i], "ROI.zip", "d1.C01");
>> open(pathNuc);
>>
>> Can you help me find out what is wrong?
>> Thank you
>>
>>
>>
>>
>> -----Message d'origine-----
>> De : ImageJ Interest Group <[hidden email]> De la part de Peter
>> Haub Envoyé : lundi 3 août 2020 11:20 À : [hidden email] Objet :
>> Re: open ROI.zip
>>
>> Hi
>>
>> you can use the Plugins>Macros>Record... function to record the command you are currently using manually.
>> This gives at least important hints.
>>
>> Here is the result for your question:
>>
>> // (optinal) reset RoiManager
>> roiManager("reset");
>>
>> // Select a roi.zip file vai File Open dialog run("Open...");
>>
>> // .. alternatively use a path string pointing to the zip file
>>
>> //roiManager("reset");
>> //roiManager("Open", "C:\\PATH_TO_\\RoiSet.zip");
>>
>> Peter
>>
>> On 03.08.2020 11:01, OBEID Patricia 154904 wrote:
>>> Hello,
>>> I would like using a macro to open the ROI.zip (generated previously in a 1st macro) and apply them to images.
>>> I write 2 macros to simplify my script writing.
>>> But I don't know how to write the command line to open ROI.zip.
>>> Could you help me please ?
>>> I thank you in advance.
>>> Patricia
>>> ____________________________________________________________
>>> [http://www.cea.fr/var/cea/signatures/cea_logo.jpg]<http://www.cea.f
>>> r
>>> /
>>>> [logo_mail]
>>> Patricia OBEÏD
>>> Ingénieur de Recherche /Animateur Informatique Biomics Institut de
>>> Recherche Interdisciplinaire de Grenoble CEA/DRF / IRIG / DS /BGE
>>> U1038/ Biomics / Bât 4020
>>> 17 rue des martyrs 38054 Grenoble Cedex 9 Commissariat à l'énergie
>>> atomique et aux énergies alternatives Email :
>>> [hidden email]<mailto:[hidden email]>
>>> Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17
>>>
>>> Toute notre actualité sur www.cea.fr et sur
>>> http://www.cea.fr/drf/big/bge/biomics<http://www.cea.fr/>
>>>
>>> <http://www.cea.fr/>Suivez-nous également sur Twitter :
>>> @CEA_Recherche<https://twitter.com/#!/CEA_Recherche> et sur
>>> https://twitter.com/BiomicsLab
>>>
>>>
>>>
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: open ROI.zip

Peter Haub
How are the Roi and image files named?
Can you give some examples.

On 03.08.2020 13:20, OBEID Patricia 154904 wrote:

> At the moment I don't  expect open the image.
> I try first to open the ROI.zip and after I will can open the image with the replace function.
> But at the moment I don't know how to write the first step.
> I sorry but writing macro is no easy for me.
> Patricia
>
> ____________________________________________________________
>
> Patricia OBEÏD
> Ingénieur de Recherche /Animateur Informatique Biomics
> Institut de Recherche Interdisciplinaire de Grenoble
> CEA/DRF / IRIG / DS /BGE U1038/ Biomics / Bât 4020
> 17 rue des martyrs 38054 Grenoble Cedex 9
> Commissariat à l'énergie atomique et aux énergies alternatives
> Email : [hidden email]
> Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17
>
> Toute notre actualité sur www.cea.fr et sur http://www.cea.fr/drf/big/bge/biomics
>
> Suivez-nous également sur Twitter : @CEA_Recherche et sur https://twitter.com/BiomicsLab
>
>
>
> -----Message d'origine-----
> De : ImageJ Interest Group <[hidden email]> De la part de Peter Haub
> Envoyé : lundi 3 août 2020 13:14
> À : [hidden email]
> Objet : Re: open ROI.zip
>
> ???...
> If you already know that there is no variable 'path' how can you expect that the combination
>           pathNuc = replace(path, "ROI.zip", "d1.C01");
>           open(pathNuc);
> gives a result?
>
> Make sure your path string is correct, e.g. by using the following in your loop:
>       path = dir+list[i];
>       print(path);
>
> Switch off batch mode by using
>       setBatchMode(false);
> to see if this is causing the problem.
>
> On 03.08.2020 12:36, OBEID Patricia 154904 wrote:
>> replace(path, "ROI.zip", "d1.C01");
>> => There is no variable with the name 'path' in your posted macro!
>> Yes, it is an error because I tried a lot of things to open the ROI.zip ...
>> It doesn't work and I cannot continue writing the macro because it all
>> depends on the opening of the ROI ... :-(
>>
>> ( I assume you want to open an image after opening the Rois. Therefore you exchange the "ROI.zip" and "d1.C01".
>> Is your image file ending with "d1.C01". Is there no extension (e.g.
>> .tif)? )
>> That's right. The images were done by a Cellomics machine and the extension is .C01. No problem with that.
>>
>> I come back to the starting point, how to open the ROI ?...
>>
>> -----Message d'origine-----
>> De : ImageJ Interest Group <[hidden email]> De la part de Peter
>> Haub Envoyé : lundi 3 août 2020 12:09 À : [hidden email] Objet :
>> Re: open ROI.zip
>>
>> ".. it does not work .."
>> What happens?
>>
>> replace(path, "ROI.zip", "d1.C01");
>> => There is no variable with the name 'path' in your posted macro!
>>
>> ( I assume you want to open an image after opening the Rois. Therefore you exchange the "ROI.zip" and "d1.C01".
>> Is your image file ending with "d1.C01". Is there no extension (e.g.
>> .tif)? )
>>
>>
>> On 03.08.2020 11:51, OBEID Patricia 154904 wrote:
>>> Thanks Peter,
>>> The problem is, I have a long list of images and ROIs. I want to open the image and the corresponding ROIManager and therefore make a loop for my treatments but it does not work.
>>> I started my macro like this:
>>>
>>> dir = getDirectory("Choose a Directory ");
>>> dir3 = getDirectory("Choose Destination Directory ");
>>>
>>> list = getFileList(dir);
>>> setBatchMode(true);
>>> for (i=0; i<list.length; i++) {
>>> if (endsWith(list[i], "ROI.zip")){ //A ADAPTER AU NOM DU CHANNEL
>>> roiManager("open", dir+list[i]);
>>>
>>> //ouvrir image des noyaux
>>> pathNuc = replace(path, "ROI.zip", "d1.C01");
>>> fileNuc = replace(list[i], "ROI.zip", "d1.C01");
>>> open(pathNuc);
>>>
>>> Can you help me find out what is wrong?
>>> Thank you
>>>
>>>
>>>
>>>
>>> -----Message d'origine-----
>>> De : ImageJ Interest Group <[hidden email]> De la part de Peter
>>> Haub Envoyé : lundi 3 août 2020 11:20 À : [hidden email] Objet :
>>> Re: open ROI.zip
>>>
>>> Hi
>>>
>>> you can use the Plugins>Macros>Record... function to record the command you are currently using manually.
>>> This gives at least important hints.
>>>
>>> Here is the result for your question:
>>>
>>> // (optinal) reset RoiManager
>>> roiManager("reset");
>>>
>>> // Select a roi.zip file vai File Open dialog run("Open...");
>>>
>>> // .. alternatively use a path string pointing to the zip file
>>>
>>> //roiManager("reset");
>>> //roiManager("Open", "C:\\PATH_TO_\\RoiSet.zip");
>>>
>>> Peter
>>>
>>> On 03.08.2020 11:01, OBEID Patricia 154904 wrote:
>>>> Hello,
>>>> I would like using a macro to open the ROI.zip (generated previously in a 1st macro) and apply them to images.
>>>> I write 2 macros to simplify my script writing.
>>>> But I don't know how to write the command line to open ROI.zip.
>>>> Could you help me please ?
>>>> I thank you in advance.
>>>> Patricia
>>>> ____________________________________________________________
>>>> [http://www.cea.fr/var/cea/signatures/cea_logo.jpg]<http://www.cea.f
>>>> r
>>>> /
>>>>> [logo_mail]
>>>> Patricia OBEÏD
>>>> Ingénieur de Recherche /Animateur Informatique Biomics Institut de
>>>> Recherche Interdisciplinaire de Grenoble CEA/DRF / IRIG / DS /BGE
>>>> U1038/ Biomics / Bât 4020
>>>> 17 rue des martyrs 38054 Grenoble Cedex 9 Commissariat à l'énergie
>>>> atomique et aux énergies alternatives Email :
>>>> [hidden email]<mailto:[hidden email]>
>>>> Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17
>>>>
>>>> Toute notre actualité sur www.cea.fr et sur
>>>> http://www.cea.fr/drf/big/bge/biomics<http://www.cea.fr/>
>>>>
>>>> <http://www.cea.fr/>Suivez-nous également sur Twitter :
>>>> @CEA_Recherche<https://twitter.com/#!/CEA_Recherche> et sur
>>>> https://twitter.com/BiomicsLab
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
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Re: open ROI.zip

OBEID Patricia 154904
Yes, here is
GRE044662_200731060001_B02f00d0.C01
GRE044662_200731060001_B02f00d1.C01
GRE044662_200731060001_B02f00d2.C01
GRE044662_200731060001_B02f00ROI.zip

GRE044662_200731060001_B02f01d0.C01
GRE044662_200731060001_B02f01d1.C01
GRE044662_200731060001_B02f01d2.C01
GRE044662_200731060001_B02f01ROI.zip

Manually, each file open with imageJ.
I would like to open the image d1.C01 and the corresponding ROI.zip and that, for all the images d1.C01.
Patricia
____________________________________________________________

Patricia OBEÏD
Ingénieur de Recherche /Animateur Informatique Biomics
Institut de Recherche Interdisciplinaire de Grenoble
CEA/DRF / IRIG / DS /BGE U1038/ Biomics / Bât 4020
17 rue des martyrs 38054 Grenoble Cedex 9
Commissariat à l'énergie atomique et aux énergies alternatives
Email : [hidden email]
Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17

Toute notre actualité sur www.cea.fr et sur http://www.cea.fr/drf/big/bge/biomics

Suivez-nous également sur Twitter : @CEA_Recherche et sur https://twitter.com/BiomicsLab



-----Message d'origine-----
De : ImageJ Interest Group <[hidden email]> De la part de Peter Haub
Envoyé : lundi 3 août 2020 13:50
À : [hidden email]
Objet : Re: open ROI.zip

How are the Roi and image files named?
Can you give some examples.

On 03.08.2020 13:20, OBEID Patricia 154904 wrote:

> At the moment I don't  expect open the image.
> I try first to open the ROI.zip and after I will can open the image with the replace function.
> But at the moment I don't know how to write the first step.
> I sorry but writing macro is no easy for me.
> Patricia
>
> ____________________________________________________________
>
> Patricia OBEÏD
> Ingénieur de Recherche /Animateur Informatique Biomics Institut de
> Recherche Interdisciplinaire de Grenoble CEA/DRF / IRIG / DS /BGE
> U1038/ Biomics / Bât 4020
> 17 rue des martyrs 38054 Grenoble Cedex 9 Commissariat à l'énergie
> atomique et aux énergies alternatives Email : [hidden email]
> Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17
>
> Toute notre actualité sur www.cea.fr et sur
> http://www.cea.fr/drf/big/bge/biomics
>
> Suivez-nous également sur Twitter : @CEA_Recherche et sur
> https://twitter.com/BiomicsLab
>
>
>
> -----Message d'origine-----
> De : ImageJ Interest Group <[hidden email]> De la part de Peter
> Haub Envoyé : lundi 3 août 2020 13:14 À : [hidden email] Objet :
> Re: open ROI.zip
>
> ???...
> If you already know that there is no variable 'path' how can you expect that the combination
>           pathNuc = replace(path, "ROI.zip", "d1.C01");
>           open(pathNuc);
> gives a result?
>
> Make sure your path string is correct, e.g. by using the following in your loop:
>       path = dir+list[i];
>       print(path);
>
> Switch off batch mode by using
>       setBatchMode(false);
> to see if this is causing the problem.
>
> On 03.08.2020 12:36, OBEID Patricia 154904 wrote:
>> replace(path, "ROI.zip", "d1.C01");
>> => There is no variable with the name 'path' in your posted macro!
>> Yes, it is an error because I tried a lot of things to open the ROI.zip ...
>> It doesn't work and I cannot continue writing the macro because it
>> all depends on the opening of the ROI ... :-(
>>
>> ( I assume you want to open an image after opening the Rois. Therefore you exchange the "ROI.zip" and "d1.C01".
>> Is your image file ending with "d1.C01". Is there no extension (e.g.
>> .tif)? )
>> That's right. The images were done by a Cellomics machine and the extension is .C01. No problem with that.
>>
>> I come back to the starting point, how to open the ROI ?...
>>
>> -----Message d'origine-----
>> De : ImageJ Interest Group <[hidden email]> De la part de Peter
>> Haub Envoyé : lundi 3 août 2020 12:09 À : [hidden email] Objet :
>> Re: open ROI.zip
>>
>> ".. it does not work .."
>> What happens?
>>
>> replace(path, "ROI.zip", "d1.C01");
>> => There is no variable with the name 'path' in your posted macro!
>>
>> ( I assume you want to open an image after opening the Rois. Therefore you exchange the "ROI.zip" and "d1.C01".
>> Is your image file ending with "d1.C01". Is there no extension (e.g.
>> .tif)? )
>>
>>
>> On 03.08.2020 11:51, OBEID Patricia 154904 wrote:
>>> Thanks Peter,
>>> The problem is, I have a long list of images and ROIs. I want to open the image and the corresponding ROIManager and therefore make a loop for my treatments but it does not work.
>>> I started my macro like this:
>>>
>>> dir = getDirectory("Choose a Directory ");
>>> dir3 = getDirectory("Choose Destination Directory ");
>>>
>>> list = getFileList(dir);
>>> setBatchMode(true);
>>> for (i=0; i<list.length; i++) {
>>> if (endsWith(list[i], "ROI.zip")){ //A ADAPTER AU NOM DU CHANNEL
>>> roiManager("open", dir+list[i]);
>>>
>>> //ouvrir image des noyaux
>>> pathNuc = replace(path, "ROI.zip", "d1.C01");
>>> fileNuc = replace(list[i], "ROI.zip", "d1.C01");
>>> open(pathNuc);
>>>
>>> Can you help me find out what is wrong?
>>> Thank you
>>>
>>>
>>>
>>>
>>> -----Message d'origine-----
>>> De : ImageJ Interest Group <[hidden email]> De la part de Peter
>>> Haub Envoyé : lundi 3 août 2020 11:20 À : [hidden email] Objet :
>>> Re: open ROI.zip
>>>
>>> Hi
>>>
>>> you can use the Plugins>Macros>Record... function to record the command you are currently using manually.
>>> This gives at least important hints.
>>>
>>> Here is the result for your question:
>>>
>>> // (optinal) reset RoiManager
>>> roiManager("reset");
>>>
>>> // Select a roi.zip file vai File Open dialog run("Open...");
>>>
>>> // .. alternatively use a path string pointing to the zip file
>>>
>>> //roiManager("reset");
>>> //roiManager("Open", "C:\\PATH_TO_\\RoiSet.zip");
>>>
>>> Peter
>>>
>>> On 03.08.2020 11:01, OBEID Patricia 154904 wrote:
>>>> Hello,
>>>> I would like using a macro to open the ROI.zip (generated previously in a 1st macro) and apply them to images.
>>>> I write 2 macros to simplify my script writing.
>>>> But I don't know how to write the command line to open ROI.zip.
>>>> Could you help me please ?
>>>> I thank you in advance.
>>>> Patricia
>>>> ____________________________________________________________
>>>> [http://www.cea.fr/var/cea/signatures/cea_logo.jpg]<http://www.cea.
>>>> f
>>>> r
>>>> /
>>>>> [logo_mail]
>>>> Patricia OBEÏD
>>>> Ingénieur de Recherche /Animateur Informatique Biomics Institut de
>>>> Recherche Interdisciplinaire de Grenoble CEA/DRF / IRIG / DS /BGE
>>>> U1038/ Biomics / Bât 4020
>>>> 17 rue des martyrs 38054 Grenoble Cedex 9 Commissariat à l'énergie
>>>> atomique et aux énergies alternatives Email :
>>>> [hidden email]<mailto:[hidden email]>
>>>> Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17
>>>>
>>>> Toute notre actualité sur www.cea.fr et sur
>>>> http://www.cea.fr/drf/big/bge/biomics<http://www.cea.fr/>
>>>>
>>>> <http://www.cea.fr/>Suivez-nous également sur Twitter :
>>>> @CEA_Recherche<https://twitter.com/#!/CEA_Recherche> et sur
>>>> https://twitter.com/BiomicsLab
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: open ROI.zip

Peter Haub
Hi Patricia,

hopefully the following macro gives you a start:
(It loads one zip and all 3 images at a time. Click to load the next set.)
(This macro can NOT run in batch mode because in batch no image and no
RoiManager is displayed.)

// ****************   macro start *******************
dir = getDirectory("Choose a Directory ");
dir3 = getDirectory("Choose Destination Directory ");

list = getFileList(dir);
//setBatchMode(true);

for (i=0; i<list.length; i++) {

      if (endsWith(list[i], "ROI.zip")){

           roiManager("reset");

           path = dir+list[i];
           //print("Load Roi: " + path);
           roiManager("open", dir+list[i]);

           //ouvrir image des noyaux
           path_d0 = replace(path, "ROI.zip", "d0.C01");
           path_d1 = replace(path, "ROI.zip", "d1.C01");
           path_d2 = replace(path, "ROI.zip", "d2.C01");

           open(path_d0);
           roiManager("Show All");

           open(path_d1);
           roiManager("Show All");

           open(path_d2);
           roiManager("Show All");

           // Do something with the images ....

           waitForUser("Click to open next Set");

           run("Close All");

      }
}
// ****************   macro end *******************

regards
Peter

On 03.08.2020 14:11, OBEID Patricia 154904 wrote:

> Yes, here is
> GRE044662_200731060001_B02f00d0.C01
> GRE044662_200731060001_B02f00d1.C01
> GRE044662_200731060001_B02f00d2.C01
> GRE044662_200731060001_B02f00ROI.zip
>
> GRE044662_200731060001_B02f01d0.C01
> GRE044662_200731060001_B02f01d1.C01
> GRE044662_200731060001_B02f01d2.C01
> GRE044662_200731060001_B02f01ROI.zip
>
> Manually, each file open with imageJ.
> I would like to open the image d1.C01 and the corresponding ROI.zip and that, for all the images d1.C01.
> Patricia
> ____________________________________________________________
>
> Patricia OBEÏD
> Ingénieur de Recherche /Animateur Informatique Biomics
> Institut de Recherche Interdisciplinaire de Grenoble
> CEA/DRF / IRIG / DS /BGE U1038/ Biomics / Bât 4020
> 17 rue des martyrs 38054 Grenoble Cedex 9
> Commissariat à l'énergie atomique et aux énergies alternatives
> Email : [hidden email]
> Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17
>
> Toute notre actualité sur www.cea.fr et sur http://www.cea.fr/drf/big/bge/biomics
>
> Suivez-nous également sur Twitter : @CEA_Recherche et sur https://twitter.com/BiomicsLab
>
>
>
> -----Message d'origine-----
> De : ImageJ Interest Group <[hidden email]> De la part de Peter Haub
> Envoyé : lundi 3 août 2020 13:50
> À : [hidden email]
> Objet : Re: open ROI.zip
>
> How are the Roi and image files named?
> Can you give some examples.
>
> On 03.08.2020 13:20, OBEID Patricia 154904 wrote:
>> At the moment I don't  expect open the image.
>> I try first to open the ROI.zip and after I will can open the image with the replace function.
>> But at the moment I don't know how to write the first step.
>> I sorry but writing macro is no easy for me.
>> Patricia
>>
>> ____________________________________________________________
>>
>> Patricia OBEÏD
>> Ingénieur de Recherche /Animateur Informatique Biomics Institut de
>> Recherche Interdisciplinaire de Grenoble CEA/DRF / IRIG / DS /BGE
>> U1038/ Biomics / Bât 4020
>> 17 rue des martyrs 38054 Grenoble Cedex 9 Commissariat à l'énergie
>> atomique et aux énergies alternatives Email : [hidden email]
>> Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17
>>
>> Toute notre actualité sur www.cea.fr et sur
>> http://www.cea.fr/drf/big/bge/biomics
>>
>> Suivez-nous également sur Twitter : @CEA_Recherche et sur
>> https://twitter.com/BiomicsLab
>>
>>
>>
>> -----Message d'origine-----
>> De : ImageJ Interest Group <[hidden email]> De la part de Peter
>> Haub Envoyé : lundi 3 août 2020 13:14 À : [hidden email] Objet :
>> Re: open ROI.zip
>>
>> ???...
>> If you already know that there is no variable 'path' how can you expect that the combination
>>            pathNuc = replace(path, "ROI.zip", "d1.C01");
>>            open(pathNuc);
>> gives a result?
>>
>> Make sure your path string is correct, e.g. by using the following in your loop:
>>        path = dir+list[i];
>>        print(path);
>>
>> Switch off batch mode by using
>>        setBatchMode(false);
>> to see if this is causing the problem.
>>
>> On 03.08.2020 12:36, OBEID Patricia 154904 wrote:
>>> replace(path, "ROI.zip", "d1.C01");
>>> => There is no variable with the name 'path' in your posted macro!
>>> Yes, it is an error because I tried a lot of things to open the ROI.zip ...
>>> It doesn't work and I cannot continue writing the macro because it
>>> all depends on the opening of the ROI ... :-(
>>>
>>> ( I assume you want to open an image after opening the Rois. Therefore you exchange the "ROI.zip" and "d1.C01".
>>> Is your image file ending with "d1.C01". Is there no extension (e.g.
>>> .tif)? )
>>> That's right. The images were done by a Cellomics machine and the extension is .C01. No problem with that.
>>>
>>> I come back to the starting point, how to open the ROI ?...
>>>
>>> -----Message d'origine-----
>>> De : ImageJ Interest Group <[hidden email]> De la part de Peter
>>> Haub Envoyé : lundi 3 août 2020 12:09 À : [hidden email] Objet :
>>> Re: open ROI.zip
>>>
>>> ".. it does not work .."
>>> What happens?
>>>
>>> replace(path, "ROI.zip", "d1.C01");
>>> => There is no variable with the name 'path' in your posted macro!
>>>
>>> ( I assume you want to open an image after opening the Rois. Therefore you exchange the "ROI.zip" and "d1.C01".
>>> Is your image file ending with "d1.C01". Is there no extension (e.g.
>>> .tif)? )
>>>
>>>
>>> On 03.08.2020 11:51, OBEID Patricia 154904 wrote:
>>>> Thanks Peter,
>>>> The problem is, I have a long list of images and ROIs. I want to open the image and the corresponding ROIManager and therefore make a loop for my treatments but it does not work.
>>>> I started my macro like this:
>>>>
>>>> dir = getDirectory("Choose a Directory ");
>>>> dir3 = getDirectory("Choose Destination Directory ");
>>>>
>>>> list = getFileList(dir);
>>>> setBatchMode(true);
>>>> for (i=0; i<list.length; i++) {
>>>> if (endsWith(list[i], "ROI.zip")){ //A ADAPTER AU NOM DU CHANNEL
>>>> roiManager("open", dir+list[i]);
>>>>
>>>> //ouvrir image des noyaux
>>>> pathNuc = replace(path, "ROI.zip", "d1.C01");
>>>> fileNuc = replace(list[i], "ROI.zip", "d1.C01");
>>>> open(pathNuc);
>>>>
>>>> Can you help me find out what is wrong?
>>>> Thank you
>>>>
>>>>
>>>>
>>>>
>>>> -----Message d'origine-----
>>>> De : ImageJ Interest Group <[hidden email]> De la part de Peter
>>>> Haub Envoyé : lundi 3 août 2020 11:20 À : [hidden email] Objet :
>>>> Re: open ROI.zip
>>>>
>>>> Hi
>>>>
>>>> you can use the Plugins>Macros>Record... function to record the command you are currently using manually.
>>>> This gives at least important hints.
>>>>
>>>> Here is the result for your question:
>>>>
>>>> // (optinal) reset RoiManager
>>>> roiManager("reset");
>>>>
>>>> // Select a roi.zip file vai File Open dialog run("Open...");
>>>>
>>>> // .. alternatively use a path string pointing to the zip file
>>>>
>>>> //roiManager("reset");
>>>> //roiManager("Open", "C:\\PATH_TO_\\RoiSet.zip");
>>>>
>>>> Peter
>>>>
>>>> On 03.08.2020 11:01, OBEID Patricia 154904 wrote:
>>>>> Hello,
>>>>> I would like using a macro to open the ROI.zip (generated previously in a 1st macro) and apply them to images.
>>>>> I write 2 macros to simplify my script writing.
>>>>> But I don't know how to write the command line to open ROI.zip.
>>>>> Could you help me please ?
>>>>> I thank you in advance.
>>>>> Patricia
>>>>> ____________________________________________________________
>>>>> [http://www.cea.fr/var/cea/signatures/cea_logo.jpg]<http://www.cea.
>>>>> f
>>>>> r
>>>>> /
>>>>>> [logo_mail]
>>>>> Patricia OBEÏD
>>>>> Ingénieur de Recherche /Animateur Informatique Biomics Institut de
>>>>> Recherche Interdisciplinaire de Grenoble CEA/DRF / IRIG / DS /BGE
>>>>> U1038/ Biomics / Bât 4020
>>>>> 17 rue des martyrs 38054 Grenoble Cedex 9 Commissariat à l'énergie
>>>>> atomique et aux énergies alternatives Email :
>>>>> [hidden email]<mailto:[hidden email]>
>>>>> Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17
>>>>>
>>>>> Toute notre actualité sur www.cea.fr et sur
>>>>> http://www.cea.fr/drf/big/bge/biomics<http://www.cea.fr/>
>>>>>
>>>>> <http://www.cea.fr/>Suivez-nous également sur Twitter :
>>>>> @CEA_Recherche<https://twitter.com/#!/CEA_Recherche> et sur
>>>>> https://twitter.com/BiomicsLab
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: open ROI.zip

OBEID Patricia 154904
Thanks everyone!
by taking small pieces in each of your proposals, I have come up with something that works.

dir = getDirectory("Choose a Directory ");
dir3 = getDirectory("Choose Destination Directory ");

list = getFileList(dir);
setBatchMode(false);
for (i=0; i<list.length; i++) {
        if (endsWith(list[i], "d1.C01")){
                        path = dir+list[i];
                        open(path);
                                               
                        roiManager("open", replace(path, "d1.C01", "ROI.zip"));

Good afternoon
Patricia

-----Message d'origine-----
De : ImageJ Interest Group <[hidden email]> De la part de Peter Haub
Envoyé : lundi 3 août 2020 14:45
À : [hidden email]
Objet : Re: open ROI.zip

Hi Patricia,

hopefully the following macro gives you a start:
(It loads one zip and all 3 images at a time. Click to load the next set.) (This macro can NOT run in batch mode because in batch no image and no RoiManager is displayed.)

// ****************   macro start ******************* dir = getDirectory("Choose a Directory ");
dir3 = getDirectory("Choose Destination Directory ");

list = getFileList(dir);
//setBatchMode(true);

for (i=0; i<list.length; i++) {

      if (endsWith(list[i], "ROI.zip")){

           roiManager("reset");

           path = dir+list[i];
           //print("Load Roi: " + path);
           roiManager("open", dir+list[i]);

           //ouvrir image des noyaux
           path_d0 = replace(path, "ROI.zip", "d0.C01");
           path_d1 = replace(path, "ROI.zip", "d1.C01");
           path_d2 = replace(path, "ROI.zip", "d2.C01");

           open(path_d0);
           roiManager("Show All");

           open(path_d1);
           roiManager("Show All");

           open(path_d2);
           roiManager("Show All");

           // Do something with the images ....

           waitForUser("Click to open next Set");

           run("Close All");

      }
}
// ****************   macro end *******************

regards
Peter

On 03.08.2020 14:11, OBEID Patricia 154904 wrote:

> Yes, here is
> GRE044662_200731060001_B02f00d0.C01
> GRE044662_200731060001_B02f00d1.C01
> GRE044662_200731060001_B02f00d2.C01
> GRE044662_200731060001_B02f00ROI.zip
>
> GRE044662_200731060001_B02f01d0.C01
> GRE044662_200731060001_B02f01d1.C01
> GRE044662_200731060001_B02f01d2.C01
> GRE044662_200731060001_B02f01ROI.zip
>
> Manually, each file open with imageJ.
> I would like to open the image d1.C01 and the corresponding ROI.zip and that, for all the images d1.C01.
> Patricia
> ____________________________________________________________
>
> Patricia OBEÏD
> Ingénieur de Recherche /Animateur Informatique Biomics Institut de
> Recherche Interdisciplinaire de Grenoble CEA/DRF / IRIG / DS /BGE
> U1038/ Biomics / Bât 4020
> 17 rue des martyrs 38054 Grenoble Cedex 9 Commissariat à l'énergie
> atomique et aux énergies alternatives Email : [hidden email]
> Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17
>
> Toute notre actualité sur www.cea.fr et sur
> http://www.cea.fr/drf/big/bge/biomics
>
> Suivez-nous également sur Twitter : @CEA_Recherche et sur
> https://twitter.com/BiomicsLab
>
>
>
> -----Message d'origine-----
> De : ImageJ Interest Group <[hidden email]> De la part de Peter
> Haub Envoyé : lundi 3 août 2020 13:50 À : [hidden email] Objet :
> Re: open ROI.zip
>
> How are the Roi and image files named?
> Can you give some examples.
>
> On 03.08.2020 13:20, OBEID Patricia 154904 wrote:
>> At the moment I don't  expect open the image.
>> I try first to open the ROI.zip and after I will can open the image with the replace function.
>> But at the moment I don't know how to write the first step.
>> I sorry but writing macro is no easy for me.
>> Patricia
>>
>> ____________________________________________________________
>>
>> Patricia OBEÏD
>> Ingénieur de Recherche /Animateur Informatique Biomics Institut de
>> Recherche Interdisciplinaire de Grenoble CEA/DRF / IRIG / DS /BGE
>> U1038/ Biomics / Bât 4020
>> 17 rue des martyrs 38054 Grenoble Cedex 9 Commissariat à l'énergie
>> atomique et aux énergies alternatives Email : [hidden email]
>> Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17
>>
>> Toute notre actualité sur www.cea.fr et sur
>> http://www.cea.fr/drf/big/bge/biomics
>>
>> Suivez-nous également sur Twitter : @CEA_Recherche et sur
>> https://twitter.com/BiomicsLab
>>
>>
>>
>> -----Message d'origine-----
>> De : ImageJ Interest Group <[hidden email]> De la part de Peter
>> Haub Envoyé : lundi 3 août 2020 13:14 À : [hidden email] Objet :
>> Re: open ROI.zip
>>
>> ???...
>> If you already know that there is no variable 'path' how can you expect that the combination
>>            pathNuc = replace(path, "ROI.zip", "d1.C01");
>>            open(pathNuc);
>> gives a result?
>>
>> Make sure your path string is correct, e.g. by using the following in your loop:
>>        path = dir+list[i];
>>        print(path);
>>
>> Switch off batch mode by using
>>        setBatchMode(false);
>> to see if this is causing the problem.
>>
>> On 03.08.2020 12:36, OBEID Patricia 154904 wrote:
>>> replace(path, "ROI.zip", "d1.C01");
>>> => There is no variable with the name 'path' in your posted macro!
>>> Yes, it is an error because I tried a lot of things to open the ROI.zip ...
>>> It doesn't work and I cannot continue writing the macro because it
>>> all depends on the opening of the ROI ... :-(
>>>
>>> ( I assume you want to open an image after opening the Rois. Therefore you exchange the "ROI.zip" and "d1.C01".
>>> Is your image file ending with "d1.C01". Is there no extension (e.g.
>>> .tif)? )
>>> That's right. The images were done by a Cellomics machine and the extension is .C01. No problem with that.
>>>
>>> I come back to the starting point, how to open the ROI ?...
>>>
>>> -----Message d'origine-----
>>> De : ImageJ Interest Group <[hidden email]> De la part de Peter
>>> Haub Envoyé : lundi 3 août 2020 12:09 À : [hidden email] Objet :
>>> Re: open ROI.zip
>>>
>>> ".. it does not work .."
>>> What happens?
>>>
>>> replace(path, "ROI.zip", "d1.C01");
>>> => There is no variable with the name 'path' in your posted macro!
>>>
>>> ( I assume you want to open an image after opening the Rois. Therefore you exchange the "ROI.zip" and "d1.C01".
>>> Is your image file ending with "d1.C01". Is there no extension (e.g.
>>> .tif)? )
>>>
>>>
>>> On 03.08.2020 11:51, OBEID Patricia 154904 wrote:
>>>> Thanks Peter,
>>>> The problem is, I have a long list of images and ROIs. I want to open the image and the corresponding ROIManager and therefore make a loop for my treatments but it does not work.
>>>> I started my macro like this:
>>>>
>>>> dir = getDirectory("Choose a Directory ");
>>>> dir3 = getDirectory("Choose Destination Directory ");
>>>>
>>>> list = getFileList(dir);
>>>> setBatchMode(true);
>>>> for (i=0; i<list.length; i++) {
>>>> if (endsWith(list[i], "ROI.zip")){ //A ADAPTER AU NOM DU CHANNEL
>>>> roiManager("open", dir+list[i]);
>>>>
>>>> //ouvrir image des noyaux
>>>> pathNuc = replace(path, "ROI.zip", "d1.C01");
>>>> fileNuc = replace(list[i], "ROI.zip", "d1.C01");
>>>> open(pathNuc);
>>>>
>>>> Can you help me find out what is wrong?
>>>> Thank you
>>>>
>>>>
>>>>
>>>>
>>>> -----Message d'origine-----
>>>> De : ImageJ Interest Group <[hidden email]> De la part de
>>>> Peter Haub Envoyé : lundi 3 août 2020 11:20 À : [hidden email] Objet :
>>>> Re: open ROI.zip
>>>>
>>>> Hi
>>>>
>>>> you can use the Plugins>Macros>Record... function to record the command you are currently using manually.
>>>> This gives at least important hints.
>>>>
>>>> Here is the result for your question:
>>>>
>>>> // (optinal) reset RoiManager
>>>> roiManager("reset");
>>>>
>>>> // Select a roi.zip file vai File Open dialog run("Open...");
>>>>
>>>> // .. alternatively use a path string pointing to the zip file
>>>>
>>>> //roiManager("reset");
>>>> //roiManager("Open", "C:\\PATH_TO_\\RoiSet.zip");
>>>>
>>>> Peter
>>>>
>>>> On 03.08.2020 11:01, OBEID Patricia 154904 wrote:
>>>>> Hello,
>>>>> I would like using a macro to open the ROI.zip (generated previously in a 1st macro) and apply them to images.
>>>>> I write 2 macros to simplify my script writing.
>>>>> But I don't know how to write the command line to open ROI.zip.
>>>>> Could you help me please ?
>>>>> I thank you in advance.
>>>>> Patricia
>>>>> ____________________________________________________________
>>>>> [http://www.cea.fr/var/cea/signatures/cea_logo.jpg]<http://www.cea.
>>>>> f
>>>>> r
>>>>> /
>>>>>> [logo_mail]
>>>>> Patricia OBEÏD
>>>>> Ingénieur de Recherche /Animateur Informatique Biomics Institut de
>>>>> Recherche Interdisciplinaire de Grenoble CEA/DRF / IRIG / DS /BGE
>>>>> U1038/ Biomics / Bât 4020
>>>>> 17 rue des martyrs 38054 Grenoble Cedex 9 Commissariat à l'énergie
>>>>> atomique et aux énergies alternatives Email :
>>>>> [hidden email]<mailto:[hidden email]>
>>>>> Tél : (+33)4 38 78 47 12         Fax : (+33)4 38 78 59 17
>>>>>
>>>>> Toute notre actualité sur www.cea.fr et sur
>>>>> http://www.cea.fr/drf/big/bge/biomics<http://www.cea.fr/>
>>>>>
>>>>> <http://www.cea.fr/>Suivez-nous également sur Twitter :
>>>>> @CEA_Recherche<https://twitter.com/#!/CEA_Recherche> et sur
>>>>> https://twitter.com/BiomicsLab
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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