Acess number of images series of a file

[Sebastian Rhode]

HI guys,

how can I access the number of series present of a specific image file that is store on my disc? I want to loop over all series inside a script.

Sebi

[Osvaldo Fuica]

Hi Sebastian, 

Here you have an example how I do that in python. I hope it would help you.

from icy.file import FileUtil, Loader

from icy.main import Icy

from java.io import FileFilter

class ExtFilter(FileFilter):

def __init__(self, ext):

self.ext = ext

def accept(self, path):

ext = FileUtil.getFileExtension(path.toString(), True);

return (ext.lower() == self.ext)

filter = ExtFilter(".tif")

folder = "/Users/osvaldo/Desktop/test/"

paths=FileUtil.getFiles(folder, filter, True, True, True)

for path in paths:

sequence = Loader.loadSequence(path, 0, False)

Icy.addSequence(sequence)

[Osvaldo Fuica]

Hi Sebastian, 

I forgot include the number of series iteration in the last message.

So, now you have the complete example. That iterates over all files a folder and creates a sequence for each serie.

from icy.file import FileUtil, Loader
from icy.main import Icy
from java.io import FileFilter

from icy.sequence import MetaDataUtil

# filter implementation.

class ExtFilter(FileFilter):
   def __init__(self, ext):
      self.ext = ext
 
   def accept(self, path):
      ext = FileUtil.getFileExtension(path.toString(), True);
      return (ext.lower() == self.ext)

filter = ExtFilter(".tif")
folder = "/Users/osvaldo/Desktop/test/"

# retrive all images files in a folder.

paths=FileUtil.getFiles(folder, filter, True, True, True)

for path in paths:

    meta = Loader.getMetaData(path)
    # get the number of series of a image.
    nSeries = MetaDataUtil.getNumSerie(meta)

    for i in range(0, nSeries):
       # load a serie i.
       sequence = Loader.loadSequence(path, i, False)
       Icy.addSequence(sequence)
 

[Sebastian Rhode]

Hi Osvaldo,

thanks a lot for your help.

Sebi 

[Andras Nagy]

Hi Osvaldo,

Do you have a Javascript version of the same job?

Many thanks,

Andras

[Osvaldo Fuica]

importClass(Packages.icy.main.Icy)
importClass(Packages.icy.sequence.MetaDataUtil)
importClass(Packages.icy.file.Loader)
importClass(Packages.icy.file.FileUtil)

filterExtension = ".tif"
folder = "/Users/osvaldo/Desktop/test/"

filter = new java.io.FileFilter() {    
   accept: function(path) {
      ext = FileUtil.getFileExtension(path.toString(), true)
      return (ext.toLowerCase().equals(filterExtension))
   }
}

paths = FileUtil.getFiles(folder, filter, true, true, true)

for (i = 0; i < paths.length ; ++i ) {
   path = paths[i]
   meta = Loader.getMetaData(path)
   nSeries = MetaDataUtil.getNumSerie(meta)

   for (s = 0; s < nSeries ; ++s) {
      sequence = Loader.loadSequence(path, s, false)
      Icy.addSequence(sequence)
   }
}