Re: merging and z-projection in batch mode

Posted by Michael Schmid on Jun 10, 2009; 2:53pm
URL: http://imagej.273.s1.nabble.com/merging-and-z-projection-in-batch-mode-tp3692193p3692195.html

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