Open Microscopy Environment

Hello all,

I am looking at how to integrate LOCI with TIFF File series

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HyperStack_t001_z001_c001.tif
HyperStack_t001_z002_c001.tif
HyperStack_t001_z003_c001.tif
HyperStack_t001_z001_c002.tif
HyperStack_t001_z002_c002.tif
HyperStack_t001_z003_c002.tif
...


So calling a simple reader like

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ImageReader reader = new ImageReader();
      String id = "E:\\Tests\\Test_Open_Series\\HyperStack_t001_z001_c001.tif";
      reader.setId(id);


I've been looking at the API to see how to define a string contaning the position data for the reader to understand it, but I am a bit lost. I know I can use setGroupFiles() but what other options can I specify?

I'm trying to do this so that TIFF series are handled by LOCI as well instead of having to do something customized.

Thanks in advance!

Oli

Hi Oli,

So calling a simple reader like

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    ImageReader reader = new ImageReader();
          String id = "E:\\Tests\\Test_Open_Series\\HyperStack_t001_z001_c001.tif";
          reader.setId(id);


I've been looking at the API to see how to define a string contaning the position data for the reader to understand it, but I am a bit lost. I know I can use setGroupFiles() but what other options can I specify?

I'm trying to do this so that TIFF series are handled by LOCI as well instead of having to do something customized.

The 'FileStitcher' class in loci.formats should do exactly this. So if you just do:

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IFormatReader reader = new FileStitcher();
String id = "/path/to/HyperStack_t001_z001_c001.tif";
reader.setId(id);


...then you should see all of the files grouped together. If that doesn't work, though, please do let us know.

Regards,
-Melissa

Hello and thanks for the reply,

Unfortunately it does not work:

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IFormatReader reader2 = new FileStitcher();
int grpOpt = reader2.fileGroupOption(id);
String format = reader2.getFormat();
int imgCnt = reader2.getImageCount();
String[] usedFiles = reader2.getUsedFiles();
boolean comp = reader2.hasCompanionFiles();
boolean group = reader2.isGroupFiles();

IJ.log("GroupOption:"+grpOpt);
IJ.log("Format:"+format);
IJ.log("Image Count:"+imgCnt);
IJ.log("Companion files:"+comp);
IJ.log("Is grouped file:"+group);
IJ.log("Used files:"+usedFiles.length);


Returns

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GroupOption:2
Format:Tagged Image File Format
Image Count:1
Companion files:false
Is grouped file:true
Used files:1
FileData:1


I've also tried using

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public FileStitcher(boolean patternIds)


as a constructor or

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((FileStitcher) reader).setUsingPatternIds(true);

But using

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String id = "E:\\Tests\\Test_Open_Series\\HyperStack_t<001-024_z<001-015>-_c<001-003>.tif";
reader.setId(id);

gives me the following error in the IJ log:

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E:\Tests\Test_Open_Series\HyperStack_t<001-024_z<001-015>-_c<001-003>.tif (The filename, directory name, or volume label syntax is incorrect)

I tried following the examples here: http://pacific.mpi-cbg.de/javadoc/loci/formats/FilePattern.html

Thanks for your time!
Oli

Hi Oli,

Unfortunately it does not work:

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    IFormatReader reader2 = new FileStitcher();
    int grpOpt = reader2.fileGroupOption(id);
    String format = reader2.getFormat();
    int imgCnt = reader2.getImageCount();
    String[] usedFiles = reader2.getUsedFiles();
    boolean comp = reader2.hasCompanionFiles();
    boolean group = reader2.isGroupFiles();

    IJ.log("GroupOption:"+grpOpt);
    IJ.log("Format:"+format);
    IJ.log("Image Count:"+imgCnt);
    IJ.log("Companion files:"+comp);
    IJ.log("Is grouped file:"+group);
    IJ.log("Used files:"+usedFiles.length);


Returns

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    GroupOption:2
    Format:Tagged Image File Format
    Image Count:1
    Companion files:false
    Is grouped file:true
    Used files:1
    FileData:1


I've also tried using

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    public FileStitcher(boolean patternIds)


as a constructor or

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    ((FileStitcher) reader).setUsingPatternIds(true);


But using

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    String id = "E:\\Tests\\Test_Open_Series\\HyperStack_t<001-024_z<001-015>-_c<001-003>.tif";
    reader.setId(id);


gives me the following error in the IJ log:

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    E:\Tests\Test_Open_Series\HyperStack_t<001-024_z<001-015>-_c<001-003>.tif (The filename, directory name, or volume label syntax is incorrect)


Sorry for the confusion - I've attached a small ImageJ plugin that more fully demonstrates how to accomplish this. If you compile and run it, you should be prompted for one of the files in the dataset. The list of all files in the dataset should be automatically calculated, and you should see the complete list of files in the "Log" window. I've tested this against a directory with the following files:

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HyperStack_t001_z001_c001.tif
HyperStack_t001_z001_c002.tif
HyperStack_t001_z002_c001.tif
HyperStack_t001_z002_c002.tif
HyperStack_t001_z003_c001.tif
HyperStack_t001_z003_c002.tif


Choosing any one of the files produces the following output:

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Z = 3
C = 2
T = 1
# of used files = 6
  /home/melissa/test/HyperStack_t001_z001_c001.tif
  /home/melissa/test/HyperStack_t001_z002_c001.tif
  /home/melissa/test/HyperStack_t001_z003_c001.tif
  /home/melissa/test/HyperStack_t001_z001_c002.tif
  /home/melissa/test/HyperStack_t001_z002_c002.tif
  /home/melissa/test/HyperStack_t001_z003_c002.tif


Hopefully that works for you as well, but if not please let us know.

Regards,
-Melissa

Hello!

Thank you very much, I will try it as soon as possible!

Best

Oli