Batch rename DICOM files with header info

[Michael Doube-2]

Hi All

I was hoping this would be a quick job but I am stuck.  I have a
directory full of DICOM images and matching bitmap thumbnails, both
named with a timestamp by the capture software.  I'd like to rename all
the DICOM files and matching BMP's with the string contained in header
0010,0010.  I can get the string, but don't seem to be able to rename
the files with it.  Any help appreciated,

Mike

macro:
------------------------------------
setBatchMode(true);
open();
path = File.directory();
tag = "0010,0010";
close();

function getTag(tag) {
      info = getImageInfo();
      index1 = indexOf(info, tag);
      if (index1==-1) return "";
      index1 = indexOf(info, ":", index1);
      if (index1==-1) return "";
      index2 = indexOf(info, "\n", index1);
      value = substring(info, index1+1, index2);
      return value;
  }

list = getFileList(path);
showStatus("Getting File List...");
for (i=0; i<list.length; i++){
    if(endsWith(list[i], '.dcm')){
        open(list[i]);
        newtitle = replace(getTag(tag),'^','_');
        newtitle = replace(newtitle, ' ', '_');
        newtitle = substring(newtitle, 1, lengthOf(newtitle)-1);
        print(newtitle);
        close();
        File.rename(list[i], path+newtitle+".dcm");
        thumbnail = replace(list[i], ".dcm", ".bmp");
        File.rename(thumbnail, path+newtitle+".bmp");
    }
}
----------------------------------

[Justin McGrath]

According to the reference
"The file or directory must be in the user's home directory, the
ImageJ directory or the temp directory."

You can just put the files under any directory named ImageJ and it
will work.  There is also now an exec() macro function that will
execute system commands.  I haven't tried it, but you may be able to
use that instead.

Justin

On 9/26/07, Michael Doube <[hidden email]> wrote:

> Hi All
>
> I was hoping this would be a quick job but I am stuck.  I have a
> directory full of DICOM images and matching bitmap thumbnails, both
> named with a timestamp by the capture software.  I'd like to rename all
> the DICOM files and matching BMP's with the string contained in header
> 0010,0010.  I can get the string, but don't seem to be able to rename
> the files with it.  Any help appreciated,
>
> Mike
>
> macro:
> ------------------------------------
> setBatchMode(true);
> open();
> path = File.directory();
> tag = "0010,0010";
> close();
>
> function getTag(tag) {
>       info = getImageInfo();
>       index1 = indexOf(info, tag);
>       if (index1==-1) return "";
>       index1 = indexOf(info, ":", index1);
>       if (index1==-1) return "";
>       index2 = indexOf(info, "\n", index1);
>       value = substring(info, index1+1, index2);
>       return value;
>   }
>
> list = getFileList(path);
> showStatus("Getting File List...");
> for (i=0; i<list.length; i++){
>     if(endsWith(list[i], '.dcm')){
>         open(list[i]);
>         newtitle = replace(getTag(tag),'^','_');
>         newtitle = replace(newtitle, ' ', '_');
>         newtitle = substring(newtitle, 1, lengthOf(newtitle)-1);
>         print(newtitle);
>         close();
>         File.rename(list[i], path+newtitle+".dcm");
>         thumbnail = replace(list[i], ".dcm", ".bmp");
>         File.rename(thumbnail, path+newtitle+".bmp");
>     }
> }
> ----------------------------------
>

[O'Brien.Joseph]

Hi
irfanview has a batch rename feature andcan handle dicom
http://www.irfanview.com/
..might do the trick

Joe O'Brien, City Hospital, Bham



-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Justin McGrath
Sent: 26 September 2007 15.19
To: [hidden email]
Subject: Re: Batch rename DICOM files with header info


According to the reference
"The file or directory must be in the user's home directory, the ImageJ
directory or the temp directory."

You can just put the files under any directory named ImageJ and it will
work.  There is also now an exec() macro function that will execute
system commands.  I haven't tried it, but you may be able to use that
instead.

Justin

On 9/26/07, Michael Doube <[hidden email]> wrote:

> Hi All
>
> I was hoping this would be a quick job but I am stuck.  I have a
> directory full of DICOM images and matching bitmap thumbnails, both
> named with a timestamp by the capture software.  I'd like to rename
> all the DICOM files and matching BMP's with the string contained in
> header 0010,0010.  I can get the string, but don't seem to be able to
> rename the files with it.  Any help appreciated,
>
> Mike
>
> macro:
> ------------------------------------
> setBatchMode(true);
> open();
> path = File.directory();
> tag = "0010,0010";
> close();
>
> function getTag(tag) {
>       info = getImageInfo();
>       index1 = indexOf(info, tag);
>       if (index1==-1) return "";
>       index1 = indexOf(info, ":", index1);
>       if (index1==-1) return "";
>       index2 = indexOf(info, "\n", index1);
>       value = substring(info, index1+1, index2);
>       return value;
>   }
>
> list = getFileList(path);
> showStatus("Getting File List...");
> for (i=0; i<list.length; i++){
>     if(endsWith(list[i], '.dcm')){
>         open(list[i]);
>         newtitle = replace(getTag(tag),'^','_');
>         newtitle = replace(newtitle, ' ', '_');
>         newtitle = substring(newtitle, 1, lengthOf(newtitle)-1);
>         print(newtitle);
>         close();
>         File.rename(list[i], path+newtitle+".dcm");
>         thumbnail = replace(list[i], ".dcm", ".bmp");
>         File.rename(thumbnail, path+newtitle+".bmp");
>     }
> }
> ----------------------------------
>

[Michael Doube-2]

Thanks for your help everyone,

I sorted the problem, which was me not specifying the full path of the
file to rename.  Wooops.  It works pretty well, and handles repeated
tags in successive files so files don't get over-written.  If anyone's
interested, it's here:

http://doube.org/macros.html#dcmrenamer

Mike

O'Brien.Joseph wrote:

> Hi
> irfanview has a batch rename feature andcan handle dicom
> http://www.irfanview.com/
> ..might do the trick
>
> Joe O'Brien, City Hospital, Bham
>
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Justin McGrath
> Sent: 26 September 2007 15.19
> To: [hidden email]
> Subject: Re: Batch rename DICOM files with header info
>
>
> According to the reference
> "The file or directory must be in the user's home directory, the ImageJ
> directory or the temp directory."
>
> You can just put the files under any directory named ImageJ and it will
> work.  There is also now an exec() macro function that will execute
> system commands.  I haven't tried it, but you may be able to use that
> instead.
>
> Justin
>
> On 9/26/07, Michael Doube <[hidden email]> wrote:
>  
>> Hi All
>>
>> I was hoping this would be a quick job but I am stuck.  I have a
>> directory full of DICOM images and matching bitmap thumbnails, both
>> named with a timestamp by the capture software.  I'd like to rename
>> all the DICOM files and matching BMP's with the string contained in
>> header 0010,0010.  I can get the string, but don't seem to be able to
>> rename the files with it.  Any help appreciated,
>>
>> Mike
>>
>> macro:
>> ------------------------------------
>> setBatchMode(true);
>> open();
>> path = File.directory();
>> tag = "0010,0010";
>> close();
>>
>> function getTag(tag) {
>>       info = getImageInfo();
>>       index1 = indexOf(info, tag);
>>       if (index1==-1) return "";
>>       index1 = indexOf(info, ":", index1);
>>       if (index1==-1) return "";
>>       index2 = indexOf(info, "\n", index1);
>>       value = substring(info, index1+1, index2);
>>       return value;
>>   }
>>
>> list = getFileList(path);
>> showStatus("Getting File List...");
>> for (i=0; i<list.length; i++){
>>     if(endsWith(list[i], '.dcm')){
>>         open(list[i]);
>>         newtitle = replace(getTag(tag),'^','_');
>>         newtitle = replace(newtitle, ' ', '_');
>>         newtitle = substring(newtitle, 1, lengthOf(newtitle)-1);
>>         print(newtitle);
>>         close();
>>         File.rename(list[i], path+newtitle+".dcm");
>>         thumbnail = replace(list[i], ".dcm", ".bmp");
>>         File.rename(thumbnail, path+newtitle+".bmp");
>>     }
>> }
>> ----------------------------------
>>
>>    

--
Michael Doube  BPhil BVSc MRCVS
PhD Student
Dental Institute
Queen Mary, University of London
New Rd
London  E1 1BB
United Kingdom

Phone [phone] ext 2681