merging and z-projection in batch mode

[Johannes-P. Koch]

Dear Listers,

This might be quite an easy question for you, yet not for me, I sort of miss the logic...

I have some (appr. 6000) files from a live cell imaging experiment indexed with "yyCxxxZyyyTzzz", where the yy stand for arbitrary letters and xxx, yyy, zzz indicate the numbers (001-999). C, Z, T of course are for channel, z-position, time...
as the header indicates I want to merge the channels of a Z-projection and save the files in another directory, maybe not only TIFF but even as AVI.

My starting point was the macro at the ImageJ homepage: http://rsbweb.nih.gov/ij/macros/Batch_RGB_Merge.txt

But the big problem here is, that this macro just accounts for indexes at the end of file names. My filename contains three indices and I want to call them separately, so I tried the "substring" macro function...does not work out though....

maybe somebody has some simple and logic advice for me. I included my modified macro in the end.

Thanks
Johannes

PS: by now I have just implemented the merge function and not the z-projection, but that would be easy when my first problem is solved...


Dialog.create("RGB Batch Convert");
  Dialog.addString("Red Prefix:", "d1");
  Dialog.addString("Green Prefix:", "d2");
 Dialog.show();
  redSuffix = Dialog.getString() + ".";
  greenSuffix = Dialog.getString() + ".";
  batchConvert();
  exit;

function batchConvert() {
      dir1 = getDirectory("Choose Source Directory ");
      dir2 = getDirectory("Choose Destination Directory ");
      list = getFileList(dir1);
      setBatchMode(true);
      n = list.length;
      if ((n%2)!=0)
         exit("The number of files must be a multiple of 2");
      stack = 0;
      first = 0;
      for (i=0; i<n/2; i++) {
          showProgress(i+1, n/2);
          red="?"; green="?";
          for (j=first; j<first+2; j++) {
              if (substring(list[j], redSuffix)!=-1)
                  red = list[j];
              if (substring(list[j], greenSuffix)!=-1)
                  green = list[j];
                 }

          open(dir1 +red);
          open(dir1 +green);

          run("RGB Merge...", "red=["+red+"] green=["+green+"]");
          index = indexOf(red, redSuffix);
          name = substring(red, 0, index);
          saveAs("tiff", dir2+name);
          first += 2;
      }
  }




________________________________________
Johannes-P. KOCH
University of Vienna
Department of Biochemistry and Cell Biology
Dr. Bohrgasse 9/5
A-1030 Vienna
Austria

phone: [phone]
fax: [phone]

mail to: [hidden email]

--
Ich verwende die kostenlose Version von SPAMfighter für private Anwender,
die bei mir bis jetzt 305 Spammails entfernt hat.
Rund 6 Millionen Leute nutzen SPAMfighter schon.
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[Fernando Sales]

Johannes,

to retrieve your header, use the method ij.util.Tools().split(String
filename, String
Delimiter)<http://rsbweb.nih.gov/ij/developer/api/ij/util/Tools.html>.
Once you know the format, you can easily split your name in order to get the
numbers. But, in this case, the output will be an array of Strings. Using
the expression:

-------------------------------------------------------------------------------------
String[] dummy = ij.util.Tools.split(filename,"C");
String yy = dummy[0];

String[] dummy2 = ij.util.Tools.split(dummy[1],"Z");
int xxx = new Integer(dummy2[0]).parseInt();

String[] dummy3 = ij.util.Tools.split(dummy[1],"T");
int ttt = new Integer(dummy3[0]).parseInt();
int zzz = new Integer(dummy3[1]).parseInt();
-------------------------------------------------------------------------------------

you will get the correct int value of your strings.
Unfortunatelly, i don't know how to program with macros but it should be
easy to convert this code to a macro code.
I hope this works.
Best regards,
Fernando


On Wed, Jun 10, 2009 at 11:27 AM, Johannes-P. KOCH <
[hidden email]> wrote:

> Dear Listers,
>
> This might be quite an easy question for you, yet not for me, I sort of
> miss the logic...
>
> I have some (appr. 6000) files from a live cell imaging experiment indexed
> with "yyCxxxZyyyTzzz", where the yy stand for arbitrary letters and xxx,
> yyy, zzz indicate the numbers (001-999). C, Z, T of course are for channel,
> z-position, time...
> as the header indicates I want to merge the channels of a Z-projection and
> save the files in another directory, maybe not only TIFF but even as AVI.
>
> My starting point was the macro at the ImageJ homepage:
> http://rsbweb.nih.gov/ij/macros/Batch_RGB_Merge.txt
>
> But the big problem here is, that this macro just accounts for indexes at
> the end of file names. My filename contains three indices and I want to call
> them separately, so I tried the "substring" macro function...does not work
> out though....
>
> maybe somebody has some simple and logic advice for me. I included my
> modified macro in the end.
>
> Thanks
> Johannes
>
> PS: by now I have just implemented the merge function and not the
> z-projection, but that would be easy when my first problem is solved...
>
>
> Dialog.create("RGB Batch Convert");
>  Dialog.addString("Red Prefix:", "d1");
>  Dialog.addString("Green Prefix:", "d2");
>  Dialog.show();
>  redSuffix = Dialog.getString() + ".";
>  greenSuffix = Dialog.getString() + ".";
>  batchConvert();
>  exit;
>
> function batchConvert() {
>      dir1 = getDirectory("Choose Source Directory ");
>      dir2 = getDirectory("Choose Destination Directory ");
>      list = getFileList(dir1);
>      setBatchMode(true);
>      n = list.length;
>      if ((n%2)!=0)
>         exit("The number of files must be a multiple of 2");
>      stack = 0;
>      first = 0;
>      for (i=0; i<n/2; i++) {
>          showProgress(i+1, n/2);
>          red="?"; green="?";
>          for (j=first; j<first+2; j++) {
>              if (substring(list[j], redSuffix)!=-1)
>                  red = list[j];
>              if (substring(list[j], greenSuffix)!=-1)
>                  green = list[j];
>                 }
>
>          open(dir1 +red);
>          open(dir1 +green);
>
>          run("RGB Merge...", "red=["+red+"] green=["+green+"]");
>          index = indexOf(red, redSuffix);
>          name = substring(red, 0, index);
>          saveAs("tiff", dir2+name);
>          first += 2;
>      }
>  }
>
>
>
>
> ________________________________________
> Johannes-P. KOCH
> University of Vienna
> Department of Biochemistry and Cell Biology
> Dr. Bohrgasse 9/5
> A-1030 Vienna
> Austria
>
> phone: [phone]
> fax: [phone]
>
> mail to: [hidden email]
>
> --
> Ich verwende die kostenlose Version von SPAMfighter für private Anwender,
> die bei mir bis jetzt 305 Spammails entfernt hat.
> Rund 6 Millionen Leute nutzen SPAMfighter schon.
> Laden Sie SPAMfighter kostenlos herunter: http://www.spamfighter.com/lde
>

--
**************************************************
Fernando José Ribeiro Sales
**************************************************
Email: [hidden email]
Tel: [phone]
**************************************************

[Michael Schmid]

Hi Johannes,

one more building block for your macro: this is how to convert a  
number 'n' to a string padded with '0'. Here it is for 3 digits:

   s = toString(n);
   while (lengthOf(s)<3) s = "0"+s;

So, n=1 will give s="001", etc.

Michael
________________________________________________________________

On 10 Jun 2009, at 16:46, Fernando Sales wrote:

> Johannes,
>
> to retrieve your header, use the method ij.util.Tools().split(String
> filename, String
> Delimiter)<http://rsbweb.nih.gov/ij/developer/api/ij/util/Tools.html>.
> Once you know the format, you can easily split your name in order  
> to get the
> numbers. But, in this case, the output will be an array of Strings.  
> Using
> the expression:
>
> ----------------------------------------------------------------------
> ---------------
> String[] dummy = ij.util.Tools.split(filename,"C");
> String yy = dummy[0];
>
> String[] dummy2 = ij.util.Tools.split(dummy[1],"Z");
> int xxx = new Integer(dummy2[0]).parseInt();
>
> String[] dummy3 = ij.util.Tools.split(dummy[1],"T");
> int ttt = new Integer(dummy3[0]).parseInt();
> int zzz = new Integer(dummy3[1]).parseInt();
> ----------------------------------------------------------------------
> ---------------
>
> you will get the correct int value of your strings.
> Unfortunatelly, i don't know how to program with macros but it  
> should be
> easy to convert this code to a macro code.
> I hope this works.
> Best regards,
> Fernando
>
>
> On Wed, Jun 10, 2009 at 11:27 AM, Johannes-P. KOCH <
> [hidden email]> wrote:
>
>> Dear Listers,
>>
>> This might be quite an easy question for you, yet not for me, I  
>> sort of
>> miss the logic...
>>
>> I have some (appr. 6000) files from a live cell imaging experiment  
>> indexed
>> with "yyCxxxZyyyTzzz", where the yy stand for arbitrary letters  
>> and xxx,
>> yyy, zzz indicate the numbers (001-999). C, Z, T of course are for  
>> channel,
>> z-position, time...
>> as the header indicates I want to merge the channels of a Z-
>> projection and
>> save the files in another directory, maybe not only TIFF but even  
>> as AVI.
>>
>> My starting point was the macro at the ImageJ homepage:
>> http://rsbweb.nih.gov/ij/macros/Batch_RGB_Merge.txt
>>
>> But the big problem here is, that this macro just accounts for  
>> indexes at
>> the end of file names. My filename contains three indices and I  
>> want to call
>> them separately, so I tried the "substring" macro function...does  
>> not work
>> out though....
>>
>> maybe somebody has some simple and logic advice for me. I included my
>> modified macro in the end.
>>
>> Thanks
>> Johannes
>>
>> PS: by now I have just implemented the merge function and not the
>> z-projection, but that would be easy when my first problem is  
>> solved...
>>
>>
>> Dialog.create("RGB Batch Convert");
>>  Dialog.addString("Red Prefix:", "d1");
>>  Dialog.addString("Green Prefix:", "d2");
>>  Dialog.show();
>>  redSuffix = Dialog.getString() + ".";
>>  greenSuffix = Dialog.getString() + ".";
>>  batchConvert();
>>  exit;
>>
>> function batchConvert() {
>>      dir1 = getDirectory("Choose Source Directory ");
>>      dir2 = getDirectory("Choose Destination Directory ");
>>      list = getFileList(dir1);
>>      setBatchMode(true);
>>      n = list.length;
>>      if ((n%2)!=0)
>>         exit("The number of files must be a multiple of 2");
>>      stack = 0;
>>      first = 0;
>>      for (i=0; i<n/2; i++) {
>>          showProgress(i+1, n/2);
>>          red="?"; green="?";
>>          for (j=first; j<first+2; j++) {
>>              if (substring(list[j], redSuffix)!=-1)
>>                  red = list[j];
>>              if (substring(list[j], greenSuffix)!=-1)
>>                  green = list[j];
>>                 }
>>
>>          open(dir1 +red);
>>          open(dir1 +green);
>>
>>          run("RGB Merge...", "red=["+red+"] green=["+green+"]");
>>          index = indexOf(red, redSuffix);
>>          name = substring(red, 0, index);
>>          saveAs("tiff", dir2+name);
>>          first += 2;
>>      }
>>  }
>>
>>
>>
>>
>> ________________________________________
>> Johannes-P. KOCH
>> University of Vienna
>> Department of Biochemistry and Cell Biology
>> Dr. Bohrgasse 9/5
>> A-1030 Vienna
>> Austria
>>
>> phone: [phone]
>> fax: [phone]
>>
>> mail to: [hidden email]
>>
>> --
>> Ich verwende die kostenlose Version von SPAMfighter für private  
>> Anwender,
>> die bei mir bis jetzt 305 Spammails entfernt hat.
>> Rund 6 Millionen Leute nutzen SPAMfighter schon.
>> Laden Sie SPAMfighter kostenlos herunter: http://
>> www.spamfighter.com/lde
>>
>
>
>
> --
> **************************************************
> Fernando José Ribeiro Sales
> **************************************************
> Email: [hidden email]
> Tel: [phone]
> **************************************************