Examples with ArrayImgFactory net.imglib2.img.array.ArrayImgFactory used on opensource projects

Example 1 with ArrayImgFactory

use of net.imglib2.img.array.ArrayImgFactory in project vcell by virtualcell.

the class VCellResultService method importCsv.

public Dataset importCsv(File directory) throws FileNotFoundException {
    File[] files = directory.listFiles();
    // TODO: Better handling
    if (files == null)
        return null;
    ArrayList<ArrayList<Float>> timeSeries = new ArrayList<>(files.length);
    Scanner scanner;
    int dataSize = 0;
    for (File file : files) {
        scanner = new Scanner(file);
        scanner.useDelimiter("[,\n]");
        while (scanner.hasNext() && !scanner.hasNextDouble()) {
            scanner.next();
        }
        if (!scanner.hasNextDouble()) {
            scanner.close();
            return null;
        }
        ArrayList<Float> data = new ArrayList<>();
        while (scanner.hasNextDouble()) {
            data.add(scanner.nextFloat());
        }
        scanner.close();
        timeSeries.add(data);
        dataSize = data.size();
    }
    int[] dimensions = { dataSize, timeSeries.size() };
    Img<FloatType> img = new ArrayImgFactory<FloatType>().create(dimensions, new FloatType());
    Cursor<FloatType> cursor = img.localizingCursor();
    while (cursor.hasNext()) {
        cursor.next();
        int xPos = cursor.getIntPosition(0);
        int tPos = cursor.getIntPosition(1);
        Float val = timeSeries.get(tPos).get(xPos);
        cursor.get().set(val);
    }
    Dataset dataset = datasetService.create(img);
    // Drop single dimensions
    @SuppressWarnings("unchecked") ImgPlus<FloatType> imgPlus = (ImgPlus<FloatType>) dataset.getImgPlus();
    FinalInterval interval = Intervals.createMinMax(0, 0, imgPlus.dimension(0) - 1, imgPlus.dimension(1) - 1);
    ImgPlus<FloatType> cropped = ops.transform().crop(imgPlus, interval, true);
    dataset.setImgPlus(cropped);
    System.out.println(dataset.numDimensions());
    dataset.setName(directory.getName());
    return dataset;
}

Example 2 with ArrayImgFactory

use of net.imglib2.img.array.ArrayImgFactory in project imagej-ops by imagej.

the class FlatIterableViewTest method defaultFlatIterableTest.

@Test
public void defaultFlatIterableTest() {
    Img<DoubleType> img = new ArrayImgFactory<DoubleType>().create(new int[] { 10, 10 }, new DoubleType());
    Cursor<DoubleType> il2 = Views.flatIterable(img).cursor();
    Cursor<DoubleType> opr = ops.transform().flatIterableView(img).cursor();
    while (il2.hasNext()) {
        il2.next();
        opr.next();
        assertEquals(il2.getDoublePosition(0), opr.getDoublePosition(0), 1e-10);
        assertEquals(il2.getDoublePosition(1), opr.getDoublePosition(1), 1e-10);
    }
}

Example 3 with ArrayImgFactory

use of net.imglib2.img.array.ArrayImgFactory in project imagej-ops by imagej.

the class HyperSliceViewTest method defaultHyperSliceTest.

@Test
public void defaultHyperSliceTest() {
    final Img<DoubleType> img = new ArrayImgFactory<DoubleType>().create(new int[] { 10, 10, 10 }, new DoubleType());
    final MixedTransformView<DoubleType> il2 = Views.hyperSlice((RandomAccessible<DoubleType>) img, 1, 8);
    final MixedTransformView<DoubleType> opr = ops.transform().hyperSliceView(deinterval(img), 1, 8);
    for (int i = 0; i < il2.getTransformToSource().getMatrix().length; i++) {
        for (int j = 0; j < il2.getTransformToSource().getMatrix()[i].length; j++) {
            assertEquals(il2.getTransformToSource().getMatrix()[i][j], opr.getTransformToSource().getMatrix()[i][j], 1e-10);
        }
    }
}

Example 4 with ArrayImgFactory

use of net.imglib2.img.array.ArrayImgFactory in project imagej-ops by imagej.

the class IntervalViewTest method intervalMinMaxTest.

@Test
public void intervalMinMaxTest() {
    Img<DoubleType> img = new ArrayImgFactory<DoubleType>().create(new int[] { 10, 10 }, new DoubleType());
    Random r = new Random();
    for (DoubleType d : img) {
        d.set(r.nextDouble());
    }
    Cursor<DoubleType> il2 = Views.interval(img, new long[] { 1, 1 }, new long[] { 8, 9 }).localizingCursor();
    RandomAccess<DoubleType> opr = ops.transform().intervalView(img, new long[] { 1, 1 }, new long[] { 8, 9 }).randomAccess();
    while (il2.hasNext()) {
        DoubleType e = il2.next();
        opr.setPosition(il2);
        assertEquals(e.get(), opr.get().get(), 1e-10);
    }
}

Example 5 with ArrayImgFactory

use of net.imglib2.img.array.ArrayImgFactory in project imagej-ops by imagej.

the class IntervalViewTest method defaultIntervalTest.

@Test
public void defaultIntervalTest() {
    Img<DoubleType> img = new ArrayImgFactory<DoubleType>().create(new int[] { 10, 10 }, new DoubleType());
    Random r = new Random();
    for (DoubleType d : img) {
        d.set(r.nextDouble());
    }
    Cursor<DoubleType> il2 = Views.interval(img, img).localizingCursor();
    RandomAccess<DoubleType> opr = ops.transform().intervalView(img, img).randomAccess();
    while (il2.hasNext()) {
        DoubleType e = il2.next();
        opr.setPosition(il2);
        assertEquals(e.get(), opr.get().get(), 1e-10);
    }
}