Python make_resampled_transformation_vector Examples

Example #1

File: test_transformation.py Project: erramuzpe/pybraincompare

def test_unmasked_transformation():
    image1 = nibabel.load(get_pair_images()[0])
    nonzero_voxels = len(image1.get_data().flatten())
    image1_vector = make_resampled_transformation_vector(image1,resample_dim=[2,2,2],standard_mask=False)
    assert_equal(nonzero_voxels,len(image1_vector))

    brain_4mm = get_standard_mask(4)
    nonzero_voxels = len(brain_4mm.get_data().flatten())
    image1_vector = make_resampled_transformation_vector(image1,resample_dim=[4,4,4],standard_mask=False)
    assert_equal(nonzero_voxels,len(image1_vector))

Example #2

File: test_transformation.py Project: erramuzpe/pybraincompare

def test_masked_transformation():
    image1 = nibabel.load(get_pair_images()[0])
    brain_4mm = get_standard_mask(4)
    nonzero_voxels = brain_4mm.get_data()[brain_4mm.get_data()!=0].shape[0]
    image1_vector = make_resampled_transformation_vector(image1,resample_dim=[4,4,4],standard_mask=True)
    assert_equal(nonzero_voxels,len(image1_vector))

    brain_8mm = get_standard_mask(8)
    nonzero_voxels = brain_8mm.get_data()[brain_8mm.get_data()!=0].shape[0]
    image1_vector = make_resampled_transformation_vector(image1,resample_dim=[8,8,8],standard_mask=True)
    assert_equal(nonzero_voxels,len(image1_vector))

Example #3

def test_unmasked_transformation():
    image1 = nibabel.load(get_pair_images()[0])
    nonzero_voxels = len(image1.get_data().flatten())
    image1_vector = make_resampled_transformation_vector(
        image1, resample_dim=[2, 2, 2], standard_mask=False)
    assert_equal(nonzero_voxels, len(image1_vector))

    brain_4mm = get_standard_brain(4)
    nonzero_voxels = len(brain_4mm.get_data().flatten())
    image1_vector = make_resampled_transformation_vector(
        image1, resample_dim=[4, 4, 4], standard_mask=False)
    assert_equal(nonzero_voxels, len(image1_vector))

Example #4

def test_masked_transformation():
    image1 = nibabel.load(get_pair_images()[0])
    brain_4mm = get_standard_brain(4)
    nonzero_voxels = brain_4mm.get_data()[brain_4mm.get_data() != 0].shape[0]
    image1_vector = make_resampled_transformation_vector(
        image1, resample_dim=[4, 4, 4], standard_mask=True)
    assert_equal(nonzero_voxels, len(image1_vector))

    brain_8mm = get_standard_brain(8)
    nonzero_voxels = brain_8mm.get_data()[brain_8mm.get_data() != 0].shape[0]
    image1_vector = make_resampled_transformation_vector(
        image1, resample_dim=[8, 8, 8], standard_mask=True)
    assert_equal(nonzero_voxels, len(image1_vector))

Example #5

File: tasks.py Project: cmaumet/NeuroVault

def save_resampled_transformation_single(pk1, resample_dim=[4, 4, 4]):
    from neurovault.apps.statmaps.models import Image
    from six import BytesIO
    import numpy as np

    img = get_object_or_404(Image, pk=pk1)
    nii_obj = nib.load(img.file.path)   # standard_mask=True is default
    image_vector = make_resampled_transformation_vector(nii_obj,resample_dim)

    f = BytesIO()
    np.save(f, image_vector)
    f.seek(0)
    content_file = ContentFile(f.read())
    img.reduced_representation.save("transform_%smm_%s.npy" %(resample_dim[0],img.pk), content_file)

    return img

Example #6

def save_resampled_transformation_single(pk1, resample_dim=[4, 4, 4]):
    from neurovault.apps.statmaps.models import Image
    from six import BytesIO
    import numpy as np

    img = get_object_or_404(Image, pk=pk1)
    nii_obj = nib.load(img.file.path)   # standard_mask=True is default
    image_vector = make_resampled_transformation_vector(nii_obj,resample_dim)

    f = BytesIO()
    np.save(f, image_vector)
    f.seek(0)
    content_file = ContentFile(f.read())
    img.reduced_representation.save("transform_%smm_%s.npy" %(resample_dim[0],img.pk), content_file)

    return img