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Hi,
I am trying to write some simple code to try out imglib2, basically opening an image, process it using one of the algorithms and save it.
When I want to open the image as a CellImg, I then get the following error when I call one of the Gauss or Thresholder for example:
Exception in thread "main" java.lang.IllegalStateException: Tried to create a new SCIFIOCellImg without a Reader to use for opening planes.
Call setReader(Reader) before invoking create()
at io.scif.img.cell.SCIFIOCellImgFactory.create(SCIFIOCellImgFactory.java:159)
at io.scif.img.cell.SCIFIOCellImgFactory.create(SCIFIOCellImgFactory.java:71)
at net.imglib2.img.ImgFactory.create(ImgFactory.java:74)
at net.imglib2.algorithm.gauss.AbstractGauss.<init>(AbstractGauss.java:110)
at net.imglib2.algorithm.gauss.GaussFloat.<init>(GaussFloat.java:110)
at net.imglib2.algorithm.gauss.Gauss.inFloatInPlace(Gauss.java:313)
at net.imglib2.algorithm.gauss.Gauss.inFloatInPlace(Gauss.java:271)
at net.imglib2.algorithm.gauss.Gauss.inFloatInPlace(Gauss.java:256)
Here is the code producing the error:
File file = new File( "/path/to/input/DrosophilaWing.tif" );
String path = file.getAbsolutePath();
File fileO = new File( "/path/to/output/DrosophilaWing.tif" );
SCIFIOConfig config = new SCIFIOConfig();
config.imgOpenerSetImgModes( ImgMode.CELL );
ImgOpener imgOpener = new ImgOpener();
System.out.println("Opening input image");
final Img< T > image = (Img<T>) imgOpener.openImg( path, config );
System.out.println(image.factory().getClass());
System.out.println("Convolve image");
Gauss.inFloatInPlace( 2, image);
System.out.println("Save image");
ImgSaver imgSaver = new ImgSaver();
imgSaver.saveImg(fileO.getAbsolutePath(), image);Am I missing something? If I don't put the SCIFIOConfig when opening the image, it is opened as an ArrayImg and I don't get any error.
Thanks!
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